AnGenMap

Sample Discussion

Subjects:
- Considerable increase in publishing fees
- Compulsory OAP will cause an even larger increase in publishing
- OA fees and Towards a referee factor index
- Simple numbers
- Publish or Perish

From DeckerJEmissouri.edu  Fri Feb 22 10:24:53 2013
From: "Decker, Jared Egan" <DeckerJEmissouri.edu>
Subject: Re: Considerable increase in publishing fees
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Fri, 22 Feb 2013 10:24:53 -0600

You may be interested in a new journal called PeerJ.  https://peerj.com/

Jared Decker
University of Missouri

----- Reply message -----
.From: "Miguel Perez-Enciso" <miguel.perezuab.cat>
.To: "Multiple Recipients of" <angenmapanimalgenome.org>
.Subject: Considerable increase in publishing fees
.Date: Fri, Feb 22, 2013 9:38 AM

Dear all

I have observed a considerable increase in the publishing fees in many
journals, but I think specifically of BMC journals. Although there is
always a trade between accessibility to published materials and right to
make money of publishers, I really feel this is going too far. In the
case of BMC, editing quality has only worsened, papers that stall
somewehere in the process, very long time of response, or similar. In
addition, we do the refereeing for free, we do the editing for free.

Sometime ago, BMC offered a lower rate if you had edited or refereed
papers but that does not hold any more.  Supposedly, PLOS phylosophy was
this one, but their rates are also quite high. Intriguingly, they say
that use fees to cover in part, among other things, the cost of refereeing.

Any ideas on how to spread the costs and benefits of publishing in a
more fair manner? My proposal is that refereeing and editing should be
rewarded some how, at least discounting fees.

Best

--
===============================================================
Miguel Perez-Enciso
ICREA professor
Centre for Research in Agricultural Genomics (CRAG)
and Facultat de Veterinaria UAB
Campus Universitat Autonoma Barcelona
Bellaterra
E-08193 Spain
Tel: +34 935636600 ext 3346
Fax: +34 935636601
miguel.perezuab.es
http://www.icrea.cat/...cStaff/Miguel-Perez-Enciso-255
http://bioinformatics.cragenomica.es/numgenomics/
================================================================
Sociedad Espanyola de Genetica: http://www.segenetica.es/
================================================================

From igi2cornell.edu  Fri Feb 22 10:46:11 2013
From: Ikhide Imumorin <igi2cornell.edu>
Subject: RE: Considerable increase in publishing fees 
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Fri, 22 Feb 2013 10:46:11 -0600

Dear All,

Miguel is very right about this problem. One of the reasons that Open
Access (OA) publishers gave when they started was that the profit-oriented
publishers used us to do all the work, and then turned around to charge us
and our institutions to access our own research. The profit publishers
argue that they add value to the publishing process through the review,
editing, typesetting, distribution and archiving of research. But many if
not most of them also have shareholders who demand increase in value and so
they have to make a profit. But OA publishers rightly argue that publishing
is not without costs and they have to charge Article Processing Charges
(APC) to cover the cost of publishing and archiving the papers. I agree
with that. But here is the problem, if they are NON-PROFIT, how come their
APCd are so high? The most critical part of scholarly publishing is to
determine that the work is of good quality and contributes to the body of
knowledge, and to do that they use peer-reviewers who work for FREE. Once
that stage is done, most of the remaining tasks are mostly automated now
and do not require dozens or hundreds of paid workers - in fact most of
these OA journals do not even have hard copies as they are exclusively
online journals. Where is the cost for which they need very high APCs?

Perhaps there is a need for a movement among scientists to demand a better
model that does not charge us more than $2,500 (USD) to publish a paper.
Imagine a very productive lab that publishes say 10 papers a year, that
comes to $25,000 just to cover APCs! In the age of tight research budgets
and hard-to-get grants, few people can spare that kind of money to publish
papers. However, if we push back and demand a fairer treatment then BMC and
other journals will reinstate the fee discount or even allow you to publish
one paper for free for every one you review. My new decision is to
routinely decline invitations for review from OA journals unless it is a
journal I have not reviewed for before and it is generally high profile...I
am looking into only publishing my own research in good journals that do
not charge at all. Most Universities have institutional subscriptions if
anyone wants to read the full length article or they can contact me as the
corresponding author for a free PDF copy.

Will be interesting to know what others think.

Cheers, Ikhide

 
Ikhide Imumorin, PhD 
Assistant Professor 
Animal Breeding, Genetics and Genomics Group 
Dept of Animal Science 
267 Morrison Hall 
Cornell University 
Ithaca, NY 14853 
USA 
T 607-255-2850 
F 607-255-9829 
igi2cornell.edu 

http://www.ansci.cornell.edu/faculty/imumorin.html

 
Editorial Board, Journal of Veterinary Science and Medical Diagnosis
 - http://www.scitechnol.com/jvsmdhome.php 
Associate Editor, Genomics and Quantitative Genetics
 - http://www.knoblauchpublishing.com 
Associate Editor, Journal of Applied Animal Research
 - http://www.tandf.co.uk/journals/TAAR 
Review Editor, Frontiers in Genetics
 - http://www.frontiersin.org/genetics 

"So why not go out on a limb, isn't that where the fruit is?" - Frank
Scully

________________________________________ 
.From: Miguel Perez-Enciso [miguel.perezuab.cat] 
.Sent: Friday, February 22, 2013 10:37 AM 
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: Considerable increase in publishing fees 

Dear all

I have observed a considerable increase in the publishing fees in many
journals, but I think specifically of BMC journals. Although there is
always a trade between accessibility to published materials and right to
make money of publishers, I really feel this is going too far. In the case
of BMC, editing quality has only worsened, papers that stall somewehere in
the process, very long time of response, or similar. In addition, we do the
refereeing for free, we do the editing for free.

Sometime ago, BMC offered a lower rate if you had edited or refereed papers
but that does not hold any more. Supposedly, PLOS phylosophy was this one,
but their rates are also quite high. Intriguingly, they say that use fees
to cover in part, among other things, the cost of refereeing.

Any ideas on how to spread the costs and benefits of publishing in a more
fair manner? My proposal is that refereeing and editing should be rewarded
some how, at least discounting fees.

Best

-- 
=============================================================== 
Miguel Perez-Enciso 
ICREA professor 
Centre for Research in Agricultural Genomics (CRAG) 
and Facultat de Veterinaria UAB 
Campus Universitat Autonoma Barcelona 
Bellaterra 
E-08193 Spain 
Tel: +34 935636600 ext 3346 
Fax: +34 935636601 
miguel.perezuab.es 
http://www.icrea.cat/...cStaff/Miguel-Perez-Enciso-255 
http://bioinformatics.cragenomica.es/numgenomics/ 
================================================================ 
Sociedad Espanyola de Genetica: http://www.segenetica.es/ 
================================================================ 

From igi2cornell.edu  Fri Feb 22 11:58:58 2013
From: Ikhide Imumorin <igi2cornell.edu>
Subject: RE: Considerable increase in publishing fees 
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Fri, 22 Feb 2013 11:58:58 -0600

I meant to say there is a need for a movement among scientists to demand a better
model that will not charge us as much as $2,500 (USD) or even more to publish a
paper. Something has to be done about high publishing fees when we know that the
Internet has shrunk down the costs of publishing. I believe OA publishers are
making money publishing OA papers... with very little overhead. Manuscript
submission, review, editing, typesetting and conversion to final PDF version are
done for free by reviewers or automated by software platforms, requiring modest
management of the process by paid staff.


Ikhide Imumorin, PhD
Assistant Professor
Animal Breeding, Genetics and Genomics Group
Dept of Animal Science
267 Morrison Hall
Cornell University
Ithaca, NY 14853
USA
T 607-255-2850
F 607-255-9829
igi2cornell.edu

http://www.ansci.cornell.edu/faculty/imumorin.html

From John.ColeARS.USDA.GOV  Fri Feb 22 12:02:15 2013
From: "Cole, John" <John.ColeARS.USDA.GOV>
Subject: Re: Considerable increase in publishing fees 
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Fri, 22 Feb 2013 12:02:15 -0600

Dear Colleagues-

One alternative could be increased use of preprint servers such as arXiv
(http://arxiv.org/). This is not a substitute for peer-reviewed journals,
but it does address the problem of absurdly long times between submission
and publication. arXiv is commonly used by the mathematics and physics
communities, and citations to preprints common. This is a cultural
difference between the agricultural sciences and the physical/mathematical
sciences, but I note that there is a growing body of quantitative biology
papers being posted to arXiv. Much like with PLoS ONE, the good papers
rise to the top and the poor papers sink to the bottom.

Best wishes,

John

--
Dr. John B. Cole, Research Geneticist (Animal)
Animal Improvement Programs Laboratory, ARS, USDA
Room 306, Bldg 005, BARC-West
10300 Baltimore Avenue
Beltsville, MD 20705-2350

E-mail: john.colears.usda.gov
Phone: 301-504-8665
Cell: 240-603-8426
Fax: 301-504-8092



On 2/22/13 11:46 AM, "Ikhide Imumorin" <igi2cornell.edu> wrote:

>Dear All,
>
>Miguel is very right about this problem. One of the reasons that Open
>Access (OA) publishers gave when they started was that the profit-oriented
>publishers used us to do all the work, and then turned around to charge us
>and our institutions to access our own research. The profit publishers
>argue that they add value to the publishing process through the review,
>editing, typesetting, distribution and archiving of research. But many if
>not most of them also have shareholders who demand increase in value and so
>they have to make a profit. But OA publishers rightly argue that publishing
>is not without costs and they have to charge Article Processing Charges
>(APC) to cover the cost of publishing and archiving the papers. I agree
>with that. But here is the problem, if they are NON-PROFIT, how come their
>APCd are so high? The most critical part of scholarly publishing is to
>determine that the work is of good quality and contributes to the body of
>knowledge, and to do that they use peer-reviewers who work for FREE. Once
>that stage is done, most of the remaining tasks are mostly automated now
>and do not require dozens or hundreds of paid workers - in fact most of
>these OA journals do not even have hard copies as they are exclusively
>online journals. Where is the cost for which they need very high APCs?
>
>Perhaps there is a need for a movement among scientists to demand a better
>model that does not charge us more than $2,500 (USD) to publish a paper.
>Imagine a very productive lab that publishes say 10 papers a year, that
>comes to $25,000 just to cover APCs! In the age of tight research budgets
>and hard-to-get grants, few people can spare that kind of money to publish
>papers. However, if we push back and demand a fairer treatment then BMC and
>other journals will reinstate the fee discount or even allow you to publish
>one paper for free for every one you review. My new decision is to
>routinely decline invitations for review from OA journals unless it is a
>journal I have not reviewed for before and it is generally high profile...
>I am looking into only publishing my own research in good journals that do
>not charge at all. Most Universities have institutional subscriptions if
>anyone wants to read the full length article or they can contact me as the
>corresponding author for a free PDF copy.
>
>Will be interesting to know what others think.
>
>Cheers, Ikhide
>
>
>Ikhide Imumorin, PhD
>Assistant Professor
>Animal Breeding, Genetics and Genomics Group
>Dept of Animal Science
>267 Morrison Hall
>Cornell University
>Ithaca, NY 14853
>USA
>T 607-255-2850
>F 607-255-9829
>igi2cornell.edu
>
>http://www.ansci.cornell.edu/faculty/imumorin.html
>
>
>Editorial Board, Journal of Veterinary Science and Medical Diagnosis -
>http://www.scitechnol.com/jvsmdhome.php
>Associate Editor, Genomics and Quantitative Genetics -
>http://www.knoblauchpublishing.com
>Associate Editor, Journal of Applied Animal Research -
>http://www.tandf.co.uk/journals/TAAR
>Review Editor, Frontiers in Genetics -
>http://www.frontiersin.org/genetics
>
>"So why not go out on a limb, isn't that where the fruit is?" - Frank
>Scully
>
>________________________________________
>.From: Miguel Perez-Enciso [miguel.perezuab.cat]
>.Sent: Friday, February 22, 2013 10:37 AM
>.To: Multiple Recipients of <AnGenMapanimalgenome.org>
>.Subject: Considerable increase in publishing fees
>
>Dear all
>
>I have observed a considerable increase in the publishing fees in many
>journals, but I think specifically of BMC journals. Although there is
>always a trade between accessibility to published materials and right to
>make money of publishers, I really feel this is going too far. In the case
>of BMC, editing quality has only worsened, papers that stall somewehere in
>the process, very long time of response, or similar. In addition, we do
>the refereeing for free, we do the editing for free.
>
>Sometime ago, BMC offered a lower rate if you had edited or refereed papers
>but that does not hold any more. Supposedly, PLOS phylosophy was this one,
>but their rates are also quite high. Intriguingly, they say that use fees
>to cover in part, among other things, the cost of refereeing.
>
>Any ideas on how to spread the costs and benefits of publishing in a more
>fair manner? My proposal is that refereeing and editing should be rewarded
>some how, at least discounting fees.
>
>Best
>
>--
>===============================================================
>Miguel Perez-Enciso
>ICREA professor
>Centre for Research in Agricultural Genomics (CRAG)
>and Facultat de Veterinaria UAB
>Campus Universitat Autonoma Barcelona
>Bellaterra
>E-08193 Spain
>Tel: +34 935636600 ext 3346
>Fax: +34 935636601
>miguel.perezuab.es
>http://www.icrea.cat/...cStaff/Miguel-Perez-Enciso-255
>http://bioinformatics.cragenomica.es/numgenomics/
>================================================================
>Sociedad Espanyola de Genetica: http://www.segenetica.es/
>================================================================
  

From m.fortesuq.edu.au  Mon Feb 25 07:24:40 2013
From: Marina Fortes <m.fortesuq.edu.au>
Subject: RE: Considerable increase in publishing fees
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Mon, 25 Feb 2013 07:24:40 -0600

I like the idea of   https://peerj.com/
What might be a problem is that this journal is not listed on Web of 
Science or PubMed...


Marina R S Fortes
Post Doctoral Research Fellow
University of Queensland - QAAFI
Gatton bld 8114, room 314
Phone 61 7 54601969
Mobile 0431141617


-----Original Message-----
.From: Decker, Jared Egan [mailto:DeckerJEmissouri.edu] 
.Sent: Saturday, 23 February 2013 2:25 AM
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: Re: Considerable increase in publishing fees

http://www.animalgenome.org/community/discuss ] 

You may be interested in a new journal called PeerJ.  https://peerj.com/

Jared Decker
University of Missouri

----- Reply message -----
.From: "Miguel Perez-Enciso" <miguel.perezuab.cat>
.To: "Multiple Recipients of" <angenmapanimalgenome.org>
.Subject: Considerable increase in publishing fees
.Date: Fri, Feb 22, 2013 9:38 AM

Dear all

I have observed a considerable increase in the publishing fees in many 
journals, but I think specifically of BMC journals. Although there is always 
a trade between accessibility to published materials and right to make money 
of publishers, I really feel this is going too far. In the case of BMC, 
editing quality has only worsened, papers that stall somewehere in the 
process, very long time of response, or similar. In addition, we do the 
refereeing for free, we do the editing for free.

Sometime ago, BMC offered a lower rate if you had edited or refereed papers 
but that does not hold any more.  Supposedly, PLOS phylosophy was this one, 
but their rates are also quite high.  Intriguingly, they say that use fees 
to cover in part, among other things, the cost of refereeing.

Any ideas on how to spread the costs and benefits of publishing in a more 
fair manner? My proposal is that refereeing and editing should be rewarded 
some how, at least discounting fees.

Best

--
===============================================================
Miguel Perez-Enciso
ICREA professor
Centre for Research in Agricultural Genomics (CRAG) and Facultat de 
Veterinaria UAB Campus 
Universitat Autonoma Barcelona Bellaterra
E-08193 Spain
Tel: +34 935636600 ext 3346
Fax: +34 935636601
miguel.perezuab.es
http://www.icrea.cat/...cStaff/Miguel-Perez-Enciso-255
http://bioinformatics.cragenomica.es/numgenomics/
================================================================
Sociedad Espanyola de Genetica: http://www.segenetica.es/ 
================================================================
From christopher.moransydney.edu.au  Mon Feb 25 17:46:14 2013
From: Christopher Moran <christopher.moransydney.edu.au>
Subject: RE: Considerable increase in publishing fees 
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Mon, 25 Feb 2013 17:46:14 -0600

Publishing costs money and there are two models for paying these costs i)
Pay to read - the traditional model and ii) Pay to publish - ie so-called
open access.

The objective of open access publishing is to make scientific information
"freely" available to anyone who wants to read it by removing the barrier
of journal subscription costs or other costs for accessing individual
papers. The problem is that the proponents of this model of publishing
ignore the hugely significant barrier to the dissemination of knowledge of
the cost of paying to publish. With open access pay-to-publish costs in
reputable journals of around US$2000 per paper (and I have no idea whether
this is a reasonable cost or a highly profitable charge for the open access
journals), many authors simply cannot afford even to consider publishing in
open access journals. Even though some countries, eg the UK, are about to
make it compulsory for publicly funded research to be published in open
access journals, there is no guarantee that the research funding agencies
in those countries will provide the necessary funds to do so.

I fear that open access publishing is a trend that may come back to bite us
when research funds become even tighter.

Finally I disclose a potential conflict of interest in my contribution to
this discussion as I am the editor in chief of a conventional journal,
Animal Genetics, published by Wiley for the International Society of Animal
Genetics as a for profit pay-to-read journal. Animal Genetics does offer an
open access option to authors who are willing or able to pay the charges
and I expect that we will necessarily see an increase in the use of this
option by UK scientists. For others not obliged to use open access,
publication is free except for the cost of colour reproduction.

CHRISTOPHER MORAN
Professor of Animal Genetics | Faculty of Veterinary Science | Editor in 
Chief Animal Genetics
THE UNIVERSITY OF SYDNEY
Rm 512, RMC Gunn Building B19 | The University of Sydney | NSW | 2006 | Australia
T +61 2 93513553 | F +61 2 93512114 | M +61 431 266 925 
E Christopher.Moransydney.edu.au  | W http://sydney.edu.au/vetfac
CRICOS 00026A

 
-----Original Message----- 
.From: Marina Fortes [mailto:m.fortesuq.edu.au]  
.Sent: Tuesday, 26 February 2013 12:25 AM 
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: RE: Considerable increase in publishing fees 

I like the idea of https://peerj.com/ What might be a problem is that this
journal is not listed on Web of Science or PubMed...

 
Marina R S Fortes 
Post Doctoral Research Fellow 
University of Queensland - QAAFI 
Gatton bld 8114, room 314 
Phone 61 7 54601969 
Mobile 0431141617 

 
-----Original Message----- 
.From: Decker, Jared Egan [mailto:DeckerJEmissouri.edu] 
.Sent: Saturday, 23 February 2013 2:25 AM 
.To: Multiple Recipients of <AnGenMapanimalgenome.org> 
.Subject: Re: Considerable increase in publishing fees 

http://www.animalgenome.org/community/discuss ]

You may be interested in a new journal called PeerJ. https://peerj.com/

Jared Decker University of Missouri

----- Reply message ----- 
.From: "Miguel Perez-Enciso" <miguel.perezuab.cat> 
.To: "Multiple Recipients of" <angenmapanimalgenome.org> 
.Subject: Considerable increase in publishing fees 
.Date: Fri, Feb 22, 2013 9:38 AM 

Dear all

I have observed a considerable increase in the publishing fees in many
journals, but I think specifically of BMC journals. Although there is
always a trade between accessibility to published materials and right to
make money of publishers, I really feel this is going too far. In the case
of BMC, editing quality has only worsened, papers that stall somewehere in
the process, very long time of response, or similar. In addition, we do the
refereeing for free, we do the editing for free.

Sometime ago, BMC offered a lower rate if you had edited or refereed papers
but that does not hold any more. Supposedly, PLOS phylosophy was this one,
but their rates are also quite high. Intriguingly, they say that use fees
to cover in part, among other things, the cost of refereeing.

Any ideas on how to spread the costs and benefits of publishing in a more
fair manner? My proposal is that refereeing and editing should be rewarded
some how, at least discounting fees.

Best

-- 
=============================================================== 
Miguel Perez-Enciso 
ICREA professor 
Centre for Research in Agricultural Genomics (CRAG) and 
 Facultat de Veterinaria UAB Campus Universitat Autonoma Barcelona Bellaterra 
E-08193 Spain 
Tel: +34 935636600 ext 3346 
Fax: +34 935636601 
miguel.perezuab.es 
http://www.icrea.cat/...cStaff/Miguel-Perez-Enciso-255 
http://bioinformatics.cragenomica.es/numgenomics/ 
================================================================ 
Sociedad Espanyola de Genetica: http://www.segenetica.es/ 
================================================================ 

From gianolaansci.wisc.edu  Mon Feb 25 18:25:13 2013 
From: Daniel Gianola <gianolaansci.wisc.edu> 
Subject: RE: Considerable increase in publishing fees  
Postmaster: submission approved 
To: Multiple Recipients of <angenmapanimalgenome.org> 
Date: Mon, 25 Feb 2013 18:25:13 -0600 

We may get help from the US Government. This article was published in the
New York Times on February 22. Regards. Daniel

----------------------------------------------------- 
U.S. Moves to Provide Quicker Access to Publicly Financed Scientific Research 
By KENNETH CHANG 

Published: February 22, 2013

If you paid for it, you should be able to read it. For publicly financed
science research, the Obama administration agrees.

In a memorandum issued on Friday, John P. Holdren, science adviser to
President Obama, called for scientific papers that report the results of
federally financed research to become freely accessible within a year or so
after publication. The findings are typically published in scientific
journals, many of which are open only to paying subscribers.

The new policy would apply to federal agencies, including the National
Science Foundation, the Department of Energy and the Department of
Agriculture, that finance more than $100 million a year of research. The
agencies have six months to submit plans for how they would carry out the
new policy.

The hope is that broad access to scientific results will encourage faster
progress on research and will let anyone apply the knowledge for
technological advances.

"We have seen, over the last 15 years, in the era of the Internet, that the
more widely available a publication is, the more likely it is to be cited
and the more likely it is to be used in patent applications," said Myron
Gutmann, an assistant director at the National Science Foundation.

"We know that the small and medium enterprise, the business community,
doesn't have a lot of access to scientific publications right now," Dr.
Gutmann said, "and the more we can make things available for those
communities, the more innovation there is likely to be." He estimated that
25,000 to 40,000 journal articles based on research financed by the science
foundation are published annually.

At the Agriculture Department, Catherine Woteki, the agency's chief
scientist, said the new policy fit in with efforts to make agriculture data
like plant genomes more widely available. "We can reduce in half the time
that it takes for breeding drought- and pest- and disease-resistant crops,"
she said.

The agencies could model their policies on one established by the National
Institutes of Health in 2008. The N.I.H. requires scientists receiving
grants to ensure that their papers can be made available on PubMed Central,
a publicly available Web site, within one year.

An online petition last May on the White House's Web site called for "free
access over the Internet to scientific journal articles arising from
taxpayer-funded research."

More than 65,000 people signed the petition, easily passing the 25,000-
signature threshold that merited an official White House response. (The
threshold was raised in January to 100,000 after a petition that called for
building a Death Star like that in the movie "Star Wars" garnered 34,435
signatures; administration officials rejected that suggestion.)

In a response posted Friday to the signers of the open-access petitioners,
Dr. Holdren agreed.

"Americans should have easy access to the results of the research they help
support," Dr. Holden wrote, adding, "the logic behind enhanced access is
plain."

A version of this article appeared in print on February 23, 2013, on page
A9 of the New York edition with the headline: U.S. Moves to Provide Quicker
Access to Publicly Financed Scientific Research.


From miguel.perezuab.cat  Tue Feb 26 07:42:09 2013
From: Miguel Perez-Enciso <miguel.perezuab.cat>
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Subject: Compulsory OAP will cause an even larger increase in publishing fees
Date: Tue, 26 Feb 2013 07:42:09 -0600

Dear authors

I agree with paying for publishing. As I see it, the two main questions 
are whether publishing fees are fair and whether reviewers and editors 
should charge for their work to publishers, either in kind or in cash. 
Under a normal economic model, you could choose between the most 
competitive offer but we are limited by the impact factor, on which our 
careers depend in part.

I am afraid that policies making obligatory OAP will cause an 
inflationary process in publishing fees. The idea of making tax payers 
get what they pay for taxes is very reasonable, that of giving profit to 
private companies per se, not so much. So, the state is responsible for 
paying a MAXIMUM for publishing fees, the amount that should cover 
accountable costs excluding profit. This will be reasonable and will 
help control quasi monopolies. It would be great that these same 65,000 
people sign  a letter in these terms.

To summarise, publishing is a big business and we are getting a tiny 
part with much effort. Reviewing and editing should be paid.

PS 1: I disclose also that I am editor of J Anim Breed Genet, a journal 
with policies similar to those of Animal Genetics. At least in this 
case, I am paid a small amount and get a discount on books from the 
publisher.

PS 2: I offer myself to write a letter to Obama and Cameron as well (via 
Nature or Science) warning him of the inflationary dangers of compulsory 
OAP and recommending to pay only for actual costs - not profit part. If 
anyone is willing to help, please email me and we shall write something 
that could be distributed to the rest of communities and submitted to 
any or both of these journals.

Miguel

El 26/02/2013 1:25, Daniel Gianola escribi:
>
> We may get help from the US Government. This article was published in the New
> York Times on February 22. Regards. Daniel
>
> U.S. Moves to Provide Quicker Access to Publicly Financed Scientific Research
> By KENNETH CHANG
>
> Published: February 22, 2013
>
> If you paid for it, you should be able to read it. For publicly financed cience
> research, the Obama administration agrees.
>
> In a memorandum issued on Friday, John P. Holdren, science adviser to President
> Obama, called for scientific papers that report the results of federally financed
> research to become freely accessible within a year or so after publication. The
> findings are typically published in scientific journals, many of which are open
> only to paying subscribers.
>
> The new policy would apply to federal agencies, including the National Science
> Foundation, the Department of Energy and the Department of Agriculture, that
> finance more than $100 million a year of research. The agencies have six months
> to submit plans for how they would carry out the new policy.
>
> The hope is that broad access to scientific results will encourage faster
> progress on research and will let anyone apply the knowledge for technological
> advances.
>
> "We have seen, over the last 15 years, in the era of the Internet, that the more
> widely available a publication is, the more likely it is to be cited and the more
> likely it is to be used in patent applications," said Myron Gutmann, an assistant
> director at the National Science Foundation.
>
> "We know that the small and medium enterprise, the business community, doesn't
> have a lot of access to scientific publications right now," Dr. Gutmann said,
> "and the more we can make things available for those communities, the more
> innovation there is likely to be." He estimated that 25,000 to 40,000 journal
> articles based on research financed by the science foundation are published
annually.
>
> At the Agriculture Department, Catherine Woteki, the agency's chief scientist,
> said the new policy fit in with efforts to make agriculture data like plant
> genomes more widely available. "We can reduce in half the time that it takes for
> breeding drought- and pest- and disease-resistant crops," she said.
>
> The agencies could model their policies on one established by the National
> Institutes of Health in 2008. The N.I.H. requires scientists receiving grants to
> ensure that their papers can be made available on PubMed Central, a publicly
> available Web site, within one year.
>
> An online petition last May on the White House's Web site called for "free access
> over the Internet to scientific journal articles arising from taxpayer-funded
> research."
>
> More than 65,000 people signed the petition, easily passing the 25,000-signature
> threshold that merited an official White House response. (The threshold was
> raised in January to 100,000 after a petition that called for building a Death
> Star like that in the movie "Star Wars" garnered 34,435 signatures;
> administration officials rejected that suggestion.)
>
> In a response posted Friday to the signers of the open-access petitioners, Dr.
> Holdren agreed.
>
> "Americans should have easy access to the results of the research they help
> support," Dr. Holden wrote, adding, "the logic behind enhanced access is plain."
>
> A version of this article appeared in print on February 23, 2013, on page A9 of
> the New York edition with the headline: U.S. Moves to Provide Quicker Access to
> Publicly Financed Scientific Research.

-- 
===============================================================
Miguel Perez-Enciso
ICREA professor
Centre for Research in Agricultural Genomics (CRAG)
and Facultat de Veterinaria UAB
Campus Universitat Autonoma Barcelona
Bellaterra
E-08193 Spain
Tel: +34 935636600 ext 3346
Fax: +34 935636601
miguel.perezuab.es
http://www.icrea.cat/...cStaff/Miguel-Perez-Enciso-255
http://bioinformatics.cragenomica.es/numgenomics/
================================================================
Sociedad Espanyola de Genetica: http://www.segenetica.es/
================================================================



  

From grosawisc.edu  Tue Feb 26 10:44:51 2013
Subject: Re: Compulsory OAP will cause an even larger increase in publishing
From: "Guilherme J. M. Rosa" <grosawisc.edu>
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Tue, 26 Feb 2013 10:44:51 -0600

Miguel, 

I totally agree with your comments regarding publishing costs, potential 
over profit of some publishing houses, and the compensation of editors and 
reviewers for their work.

But on this email you raised another issue, which refers to your comment 
that "we are limited by the impact factor, on which our careers depend 
inpart". This is another big concern and something I believe the scientific 
community should do something about.

In my opinion we should not be looking at the impact factor of the journal 
where a manuscript has been published, but instead at the impact of the 
manuscript itself. Of course it is hard to measure impact (of journals or of 
manuscripts), but if you are okay with the assessment of the impact of a 
journal by, say, counting the number of citations of its papers on the 2 
years following publication (of course this is already another topic for 
discussion), then we could use similar approach and assess impact of 
manuscripts by counting the number of their citations (maybe excluding self-
citation, or by combining it with the number of full downloads, etc.)

The emphasis we give to the impact of the journals, in my opinion, is not 
necessarily good for science. For example, how many times after a submission 
we get a message from an editor-in-chief saying, on the basis of a very 
subject assessment, that "The Board concluded that while interesting, your 
paper lacked the broad appeal necessary for further consideration by the 
journal". And sometimes this assessment is performed by a single individual. 
An also, probably the main concern of the editor-in-chief is with the impact 
index of the journal. Then, in case you manuscript is approved on this first 
triage, it goes to a review process in which two anonymous reviewers will 
assess the paper. So, two or three people decide if your paper should be 
published or not and, despite the best intention and fairness concern of all 
editors and reviewers (hopefully), everybody has his her own views and 
biases, and weird things can happen. There are many examples in the 
literature, one of the most notorious being Fisher's struggle to publish his 
revolutionizing ideas on analysis of variance

So, my opinion is that the scientific community should try different ways to 
evaluate, publish and assess impact of manuscripts. For example, I like very 
much the philosophy of Frontiers in Science 
(http://www.frontiersin.org/news/Science), in which reviewers assess 
manuscripts mostly for clear flaws, and also offer comments and suggestions 
for improvement of the papers. This process is performed in an open and clear 
way, with an iterative on-line discussion between reviewers and authors. 
After acceptance, manuscripts are published on the so-called "first tier". 
Then, it is the whole scientific community that will evaluate each manuscript 
(not a senior editor or two anonymous reviewers). Frontiers keep track of 
public access to abstracts and full texts, citations etc., and "good" papers 
go up on the ladder, to tiers 2, 3 and 4.

Frontiers is a non-profit organization, founded and managed by scientists to 
serve scientists and science. It is open access, authors retain their 
copyrights, it is published on line only, it is indexed in many databases, 
including PubMed, and many other things I guess we like to see in a journal.

Those in this discussion list will be mostly interested on Frontiers in 
Genetics (http://www.frontiersin.org/Genetics), which includes many specialty 
journals including Livestock Genomics 
(http://www.frontiersin.org/Livestock_Genomics).

I also want to disclosure that I am the editor-in-chief of Frontiers in 
Livestock Genomics, a service that I do with no financial compensation. In 
addition, many members of this list are in the editorial board of this 
journal, including Miguel.

In my opinion, Frontiers in Science is the closest in terms of philosophy to 
what Larry Schaeffer suggested on this list a few months ago.

My two cents,

Guilherme.

PS: I understand that for earlier carrier (and not yet tenured) researchers, 
publishing in high impact journals may be viewed as the best way to show the 
relevance of their work before his her papers start being cited in the 
literature. However, I think senior scientists, research grant panel members, 
university and research institutions administrators, etc. should try to use 
other forms of evaluating our own research.

-- 
Guilherme J. M. Rosa
University of Wisconsin - Madison
444 Animal Science Building
1675 Observatory Dr.
Madison, WI 53706 USA
Phone: + 1 (608) 265-8617
Fax: + 1 (608) 263-9412
E-mail: grosawisc.edu
Webpage: https://mywebspace.wisc.edu/grosa/web/


On 2/26/13 7:42 AM, "Miguel Perez-Enciso" <miguel.perezuab.cat> wrote:

> 
> Dear authors
> 
> I agree with paying for publishing. As I see it, the two main questions
> are whether publishing fees are fair and whether reviewers and editors
> should charge for their work to publishers, either in kind or in cash.
> Under a normal economic model, you could choose between the most
> competitive offer but we are limited by the impact factor, on which our
> careers depend in part.
> 
> I am afraid that policies making obligatory OAP will cause an
> inflationary process in publishing fees. The idea of making tax payers
> get what they pay for taxes is very reasonable, that of giving profit to
> private companies per se, not so much. So, the state is responsible for
> paying a MAXIMUM for publishing fees, the amount that should cover
> accountable costs excluding profit. This will be reasonable and will
> help control quasi monopolies. It would be great that these same 65,000
> people sign a letter in these terms.
> 
> To summarise, publishing is a big business and we are getting a tiny
> part with much effort. Reviewing and editing should be paid.
> 
> PS 1: I disclose also that I am editor of J Anim Breed Genet, a journal
> with policies similar to those of Animal Genetics. At least in this
> case, I am paid a small amount and get a discount on books from the
> publisher.
> 
> PS 2: I offer myself to write a letter to Obama and Cameron as well (via
> Nature or Science) warning him of the inflationary dangers of compulsory
> OAP and recommending to pay only for actual costs - not profit part. If
> anyone is willing to help, please email me and we shall write something
> that could be distributed to the rest of communities and submitted to
> any or both of these journals.
> 
> Miguel
From igi2cornell.edu  Tue Feb 26 11:20:37 2013
From: Ikhide Imumorin <igi2cornell.edu>
Subject: RE: Compulsory OAP will cause an even larger increase in publishing fees 
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Tue, 26 Feb 2013 11:20:37 -0600

Dear Colleagues, I totally agree with Miguel on this issue. If journals,
especially OA journals will charge all these exorbitant fees for publishing
papers to be read freely, then editors and reviewers should be paid in
cash, but preferably in kind. For example BMC Ltd can institute a policy
that say you get a discount (say 25% off) your next paper if you review a
paper, and if you review this many papers per year, you get to publish one
paper for free. As it stands now scientists are used to do all the heavy
lifting of judging the science of their peers for free... and the only ones
making money from this whole thing is the companies... whether OA or not.

Will publishers step up to the plate and do the right thing? If the next
time you get a paper from a journal and you decline reviewing it, aren't we
all busy? or you ask for some kind of compensation in the form of discount
in publishing in that journal, a new movement that help us scientists might
be born. The process of scientific publishing depends on peer review, but
that job right now is unpaid and burdensome. After you have reviewed a few
papers for a journal and you can put that in your CV under "Professional
Service", is there any incentive to do any more for that journal?

Compulsory OA publishing will inflate publishing fees to the point where
grant agencies will be forced to devote a significant portion to
publication fees. Soon you may have to include as much as $30,000 to your
application to NIH/NSF/USDA etc for a 4 year project for publication
charges. This is quite possible for large projects that may publish as many
as 10 papers from a project since some OA journals cost as much as $3,000!
Is the cost of publishing a paper on a Web platform really that high? Most
new generation OA journals do not have hard copies and most of the
publishing operations are automated by sophisticated software. I know
establishing such tools cannot be cheap, but that is usually part of the
upfront costs to get things started. Once it is up and running, it mostly
just need only modest management and maintenance.

I am on board with doing a letter with others to sound the alarm on this
problem.

Regards, Ikhide

 
 
Ikhide Imumorin, PhD 
Assistant Professor 
Animal Breeding, Genetics and Genomics Group 
Dept of Animal Science 
267 Morrison Hall 
Cornell University 
Ithaca, NY 14853 
USA 
T 607-255-2850 
F 607-255-9829 
igi2cornell.edu 

http://www.ansci.cornell.edu/faculty/imumorin.html

Editorial Board, Journal of Veterinary Science and Medical Diagnosis
 - http://www.scitechnol.com/jvsmdhome.php
Associate Editor, Genomics and Quantitative Genetics
 - http://www.knoblauchpublishing.com
Associate Editor, Journal of Applied Animal Research
 - http://www.tandf.co.uk/journals/TAAR
Review Editor, Frontiers in Genetics
 - http://www.frontiersin.org/genetics

"So why not go out on a limb, isn't that where the fruit is?" - Frank Scully

 
 
________________________________________ 
.From: Miguel Perez-Enciso [miguel.perezuab.cat] 
.Sent: Tuesday, February 26, 2013 8:42 AM 
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: Compulsory OAP will cause an even larger increase in publishing fees 

Dear authors

I agree with paying for publishing. As I see it, the two main questions are
whether publishing fees are fair and whether reviewers and editors should
charge for their work to publishers, either in kind or in cash. Under a
normal economic model, you could choose between the most competitive offer
but we are limited by the impact factor, on which our careers depend in
part.

I am afraid that policies making obligatory OAP will cause an inflationary
process in publishing fees. The idea of making tax payers get what they pay
for taxes is very reasonable, that of giving profit to private companies
per se, not so much. So, the state is responsible for paying a MAXIMUM for
publishing fees, the amount that should cover accountable costs excluding
profit. This will be reasonable and will help control quasi monopolies. It
would be great that these same 65,000 people sign a letter in these terms.

To summarise, publishing is a big business and we are getting a tiny part
with much effort. Reviewing and editing should be paid.

PS 1: I disclose also that I am editor of J Anim Breed Genet, a journal
with policies similar to those of Animal Genetics. At least in this case, I
am paid a small amount and get a discount on books from the publisher.

PS 2: I offer myself to write a letter to Obama and Cameron as well (via
Nature or Science) warning him of the inflationary dangers of compulsory
OAP and recommending to pay only for actual costs - not profit part. If
anyone is willing to help, please email me and we shall write something
that could be distributed to the rest of communities and submitted to any
or both of these journals.

Miguel

El 26/02/2013 1:25, Daniel Gianola escribi: >
> We may get help from the US Government. This article was published in the New 
> York Times on February 22. Regards. Daniel 
> 
> U.S. Moves to Provide Quicker Access to Publicly Financed Scientific Research 
> By KENNETH CHANG 
> 
> Published: February 22, 2013 
> 
> If you paid for it, you should be able to read it. For publicly financed cience 
> research, the Obama administration agrees. 
> 
> In a memorandum issued on Friday, John P. Holdren, science adviser to President 
> Obama, called for scientific papers that report the results of federally financed 
> research to become freely accessible within a year or so after publication. The 
> findings are typically published in scientific journals, many of which are open 
> only to paying subscribers. 
> 
> The new policy would apply to federal agencies, including the National Science 
> Foundation, the Department of Energy and the Department of Agriculture, that 
> finance more than $100 million a year of research. The agencies have six months 
> to submit plans for how they would carry out the new policy. 
> 
> The hope is that broad access to scientific results will encourage faster 
> progress on research and will let anyone apply the knowledge for technological 
> advances. 
> 
> "We have seen, over the last 15 years, in the era of the Internet, that the more 
> widely available a publication is, the more likely it is to be cited and the more 
> likely it is to be used in patent applications," said Myron Gutmann, an assistant 
> director at the National Science Foundation. 
> 
> "We know that the small and medium enterprise, the business community, doesn't 
> have a lot of access to scientific publications right now," Dr. Gutmann said, 
> "and the more we can make things available for those communities, the more 
> innovation there is likely to be." He estimated that 25,000 to 40,000 journal 
> articles based on research financed by the science foundation are published 
> annually. 
> 
> At the Agriculture Department, Catherine Woteki, the agency's chief scientist, 
> said the new policy fit in with efforts to make agriculture data like plant 
> genomes more widely available. "We can reduce in half the time that it takes for 
> breeding drought- and pest- and disease-resistant crops," she said. 
> 
> The agencies could model their policies on one established by the National 
> Institutes of Health in 2008. The N.I.H. requires scientists receiving grants to 
> ensure that their papers can be made available on PubMed Central, a publicly 
> available Web site, within one year. 
> 
> An online petition last May on the White House's Web site called for "free access 
> over the Internet to scientific journal articles arising from taxpayer-funded 
> research." 
> 
> More than 65,000 people signed the petition, easily passing the 25,000-signature 
> threshold that merited an official White House response. (The threshold was 
> raised in January to 100,000 after a petition that called for building a Death 
> Star like that in the movie "Star Wars" garnered 34,435 signatures; 
> administration officials rejected that suggestion.) 
> 
> In a response posted Friday to the signers of the open-access petitioners, Dr. 
> Holdren agreed. 
> 
> "Americans should have easy access to the results of the research they help 
> support," Dr. Holden wrote, adding, "the logic behind enhanced access is plain." 
> 
> A version of this article appeared in print on February 23, 2013, on page A9 of 
> the New York edition with the headline: U.S. Moves to Provide Quicker Access to 
> Publicly Financed Scientific Research. 

-- 
=============================================================== 
Miguel Perez-Enciso 
ICREA professor 
Centre for Research in Agricultural Genomics (CRAG) 
and Facultat de Veterinaria UAB 
Campus Universitat Autonoma Barcelona 
Bellaterra 
E-08193 Spain 
Tel: +34 935636600 ext 3346 
Fax: +34 935636601 
miguel.perezuab.es 
http://www.icrea.cat/...cStaff/Miguel-Perez-Enciso-255 
http://bioinformatics.cragenomica.es/numgenomics/ 
================================================================ 
Sociedad Espanyola de Genetica: http://www.segenetica.es/ 
================================================================ 
 

From andrea.wilsonroslin.ed.ac.uk  Tue Feb 26 16:36:55 2013
From: WILSON Andrea <andrea.wilsonroslin.ed.ac.uk>
Subject: RE: Compulsory OAP will cause an even larger increase in publishing
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Tue, 26 Feb 2013 16:36:55 -0600

Dear colleagues,

I would support an alarm letter as proposed by Ikhide as the current situation
seems unfair to me. It may strengthen our argument if we knew how much profit (if
any) a journal makes on average per OA article. Does anybody in the community know?

Best wishes
Andrea


-----Original Message-----
.From: Ikhide Imumorin [mailto:igi2cornell.edu] 
.Sent: 26 February 2013 17:21
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: RE: Compulsory OAP will cause an even larger increase in publishing fees 

Dear Colleagues, I totally agree with Miguel on this issue. If journals,
especially OA journals will charge all these exorbitant fees for publishing
papers to be read freely, then editors and reviewers should be paid in
cash, but preferably in kind. For example BMC Ltd can institute a policy
that say you get a discount (say 25% off) your next paper if you review a
paper, and if you review this many papers per year, you get to publish one
paper for free. As it stands now scientists are used to do all the heavy
lifting of judging the science of their peers for free... and the only ones
making money from this whole thing is the companies... whether OA or not.

Will publishers step up to the plate and do the right thing? If the next
time you get a paper from a journal and you decline reviewing it, aren't we
all busy? or you ask for some kind of compensation in the form of discount
in publishing in that journal, a new movement that help us scientists might
be born. The process of scientific publishing depends on peer review, but
that job right now is unpaid and burdensome. After you have reviewed a few
papers for a journal and you can put that in your CV under "Professional
Service", is there any incentive to do any more for that journal?

Compulsory OA publishing will inflate publishing fees to the point where
grant agencies will be forced to devote a significant portion to
publication fees. Soon you may have to include as much as $30,000 to your
application to NIH/NSF/USDA etc for a 4 year project for publication
charges. This is quite possible for large projects that may publish as many
as 10 papers from a project since some OA journals cost as much as $3,000!
Is the cost of publishing a paper on a Web platform really that high? Most
new generation OA journals do not have hard copies and most of the
publishing operations are automated by sophisticated software. I know
establishing such tools cannot be cheap, but that is usually part of the
upfront costs to get things started. Once it is up and running, it mostly
just need only modest management and maintenance.

I am on board with doing a letter with others to sound the alarm on this
problem.

Regards, Ikhide

 
Ikhide Imumorin, PhD 
Assistant Professor 
Animal Breeding, Genetics and Genomics Group 
Dept of Animal Science 
267 Morrison Hall 
Cornell University 
Ithaca, NY 14853 
USA 
T 607-255-2850 
F 607-255-9829 
igi2cornell.edu 

http://www.ansci.cornell.edu/faculty/imumorin.html

Editorial Board, Journal of Veterinary Science and Medical Diagnosis
 - http://www.scitechnol.com/jvsmdhome.php
Associate Editor, Genomics and Quantitative Genetics
 - http://www.knoblauchpublishing.com
Associate Editor, Journal of Applied Animal Research
 - http://www.tandf.co.uk/journals/TAAR
Review Editor, Frontiers in Genetics
 - http://www.frontiersin.org/genetics

"So why not go out on a limb, isn't that where the fruit is?" - Frank Scully

 
________________________________________ 
.From: Miguel Perez-Enciso [miguel.perezuab.cat] 
.Sent: Tuesday, February 26, 2013 8:42 AM 
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: Compulsory OAP will cause an even larger increase in publishing fees 

Dear authors

I agree with paying for publishing. As I see it, the two main questions are
whether publishing fees are fair and whether reviewers and editors should
charge for their work to publishers, either in kind or in cash. Under a
normal economic model, you could choose between the most competitive offer
but we are limited by the impact factor, on which our careers depend in
part.

I am afraid that policies making obligatory OAP will cause an inflationary
process in publishing fees. The idea of making tax payers get what they pay
for taxes is very reasonable, that of giving profit to private companies
per se, not so much. So, the state is responsible for paying a MAXIMUM for
publishing fees, the amount that should cover accountable costs excluding
profit. This will be reasonable and will help control quasi monopolies. It
would be great that these same 65,000 people sign a letter in these terms.

To summarise, publishing is a big business and we are getting a tiny part
with much effort. Reviewing and editing should be paid.

PS 1: I disclose also that I am editor of J Anim Breed Genet, a journal
with policies similar to those of Animal Genetics. At least in this case, I
am paid a small amount and get a discount on books from the publisher.

PS 2: I offer myself to write a letter to Obama and Cameron as well (via
Nature or Science) warning him of the inflationary dangers of compulsory
OAP and recommending to pay only for actual costs - not profit part. If
anyone is willing to help, please email me and we shall write something
that could be distributed to the rest of communities and submitted to any
or both of these journals.

Miguel

El 26/02/2013 1:25, Daniel Gianola escribi: >
> We may get help from the US Government. This article was published in the New 
> York Times on February 22. Regards. Daniel 
> 
> U.S. Moves to Provide Quicker Access to Publicly Financed Scientific Research 
> By KENNETH CHANG 
> 
> Published: February 22, 2013 
> 
> If you paid for it, you should be able to read it. For publicly financed ience 
> research, the Obama administration agrees. 
> 
> In a memorandum issued on Friday, John P. Holdren, science adviser to resident 
> Obama, called for scientific papers that report the results of federally financed 
> research to become freely accessible within a year or so after publication. The 
> findings are typically published in scientific journals, many of which are open 
> only to paying subscribers. 
> 
> The new policy would apply to federal agencies, including the National Science 
> Foundation, the Department of Energy and the Department of Agriculture, that 
> finance more than $100 million a year of research. The agencies have six months 
> to submit plans for how they would carry out the new policy. 
> 
> The hope is that broad access to scientific results will encourage faster 
> progress on research and will let anyone apply the knowledge for technological 
> advances. 
> 
> "We have seen, over the last 15 years, in the era of the Internet, that the more 
> widely available a publication is, the more likely it is to be cited and the more 
> likely it is to be used in patent applications," said Myron Gutmann, an assistant 
> director at the National Science Foundation. 
> 
> "We know that the small and medium enterprise, the business community, doesn't 
> have a lot of access to scientific publications right now," Dr. Gutmann said, 
> "and the more we can make things available for those communities, the more 
> innovation there is likely to be." He estimated that 25,000 to 40,000 journal 
> articles based on research financed by the science foundation are published 
> annually. 
> 
> At the Agriculture Department, Catherine Woteki, the agency's chief scientist, 
> said the new policy fit in with efforts to make agriculture data like plant 
> genomes more widely available. "We can reduce in half the time that it takes for 
> breeding drought- and pest- and disease-resistant crops," she said. 
> 
> The agencies could model their policies on one established by the National 
> Institutes of Health in 2008. The N.I.H. requires scientists receiving grants to 
> ensure that their papers can be made available on PubMed Central, a publicly 
> available Web site, within one year. 
> 
> An online petition last May on the White House's Web site called for "free access 
> over the Internet to scientific journal articles arising from taxpayer-funded 
> research." 
> 
> More than 65,000 people signed the petition, easily passing the 25,000-signature 
> threshold that merited an official White House response. (The threshold was 
> raised in January to 100,000 after a petition that called for building a Death 
> Star like that in the movie "Star Wars" garnered 34,435 signatures; 
> administration officials rejected that suggestion.) 
> 
> In a response posted Friday to the signers of the open-access petitioners, Dr. 
> Holdren agreed. 
> 
> "Americans should have easy access to the results of the research they help 
> support," Dr. Holden wrote, adding, "the logic behind enhanced access is plain." 
> 
> A version of this article appeared in print on February 23, 2013, on page A9 of 
> the New York edition with the headline: U.S. Moves to Provide Quicker Access to 
> Publicly Financed Scientific Research. 

-- 
=============================================================== 
Miguel Perez-Enciso 
ICREA professor 
Centre for Research in Agricultural Genomics (CRAG) 
and Facultat de Veterinaria UAB 
Campus Universitat Autonoma Barcelona 
Bellaterra 
E-08193 Spain 
Tel: +34 935636600 ext 3346 
Fax: +34 935636601 
miguel.perezuab.es 
http://www.icrea.cat/...cStaff/Miguel-Perez-Enciso-255 
http://bioinformatics.cragenomica.es/numgenomics/ 
================================================================ 
Sociedad Espanyola de Genetica: http://www.segenetica.es/ 
================================================================ 

From igi2cornell.edu  Tue Feb 26 16:50:50 2013
From: Ikhide Imumorin <igi2cornell.edu>
Subject: RE: Compulsory OAP will cause an even larger increase in publishing
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Tue, 26 Feb 2013 16:50:50 -0600

That my friend is a trade secret that most OA journals will probably not
divulge... how else can they defend not paying us for reviewing and editing
papers for them?


Ikhide Imumorin, PhD
Assistant Professor
Animal Breeding, Genetics and Genomics Group
Dept of Animal Science
267 Morrison Hall
Cornell University
Ithaca, NY 14853
USA
T 607-255-2850
F 607-255-9829
igi2cornell.edu

http://www.ansci.cornell.edu/faculty/imumorin.html

Editorial Board, Journal of Veterinary Science and Medical Diagnosis -
http://www.scitechnol.com/jvsmdhome.php
Associate Editor, Genomics and Quantitative Genetics -
http://www.knoblauchpublishing.com
Associate Editor, Journal of Applied Animal Research -
http://www.tandf.co.uk/journals/TAAR
Review Editor, Frontiers in Genetics - http://www.frontiersin.org/genetics

"So why not go out on a limb, isn't that where the fruit is?" - Frank Scully


________________________________________
.From: WILSON Andrea [andrea.wilsonroslin.ed.ac.uk]
.Sent: Tuesday, February 26, 2013 5:23 PM
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: RE: Compulsory OAP will cause an even larger increase in publishing fees

Dear colleagues, apologies for accidentally cluttering your mailbox with a
message containing half a sentence.
Meant to say that I would support an alarm letter as proposed by Ikhide as the
current situation seems unfair to me. It may strengthen our argument if we knew
how much profit (if any) a journal makes on average per OA article. Does anybody
in the community know?

Best wishes
Andrea


From schnabelrmissouri.edu  Tue Feb 26 17:09:52 2013
From: "Schnabel, Robert D." <schnabelrmissouri.edu>
Subject: RE: Compulsory OAP will cause an even larger increase in publishing 
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Tue, 26 Feb 2013 17:09:52 -0600

I have to chime in here. I think recent post discussing publisher profits
are misguided. What difference does it make if a publisher makes a dollar
or a billion? Intel, AMD and Apple make large profits but I don't hear any
outcry about the price of your computers which you rely upon to do your
research. Illumina does alright but I don't hear anyone proposing to write
a letter to someone complaining about the price of snp chips or sequencing
reagents citing Illumina's profit margins. If you want to make a case for
the problem of increasing publishing costs don't bring in "fairness" and
publishers profits. You'll get much more traction if you present a coherent
case and more importantly a solution.

Bob

************************************************* 
Robert Schnabel 
Research Associate Professor 
University of Missouri-Columbia 
Animal Sciences Unit, Rm.162 
920 East Campus Drive 
Columbia, MO 65211-5300 
Phone: 573-884-4106 
Fax:   573-882-6827 
http://animalgenomics.missouri.edu 
************************************************* 

 
-----Original Message----- 
.From: WILSON Andrea [mailto:andrea.wilsonroslin.ed.ac.uk]  
.Sent: Tuesday, February 26, 2013 4:37 PM 
.To: Multiple Recipients of <AnGenMapanimalgenome.org> 
.Subject: RE: Compulsory OAP will cause an even larger increase in publishing 

Dear colleagues,

I would support an alarm letter as proposed by Ikhide as the current
situation seems unfair to me. It may strengthen our argument if we knew how
much profit (if any) a journal makes on average per OA article. Does
anybody in the community know?

Best wishes Andrea

 
-----Original Message----- 
.From: Ikhide Imumorin [mailto:igi2cornell.edu] 
.Sent: 26 February 2013 17:21 
.To: Multiple Recipients of <AnGenMapanimalgenome.org> 
.Subject: RE: Compulsory OAP will cause an even larger increase in publishing fees  

Dear Colleagues, I totally agree with Miguel on this issue. If journals,
especially OA journals will charge all these exorbitant fees for publishing
papers to be read freely, then editors and reviewers should be paid in
cash, but preferably in kind. For example BMC Ltd can institute a policy
that say you get a discount (say 25% off) your next paper if you review a
paper, and if you review this many papers per year, you get to publish one
paper for free. As it stands now scientists are used to do all the heavy
lifting of judging the science of their peers for free... and the only ones
making money from this whole thing is the companies... whether OA or not.

Will publishers step up to the plate and do the right thing? If the next
time you get a paper from a journal and you decline reviewing it, aren't we
all busy? or you ask for some kind of compensation in the form of discount
in publishing in that journal, a new movement that help us scientists might
be born. The process of scientific publishing depends on peer review, but
that job right now is unpaid and burdensome. After you have reviewed a few
papers for a journal and you can put that in your CV under "Professional
Service", is there any incentive to do any more for that journal?

Compulsory OA publishing will inflate publishing fees to the point where
grant agencies will be forced to devote a significant portion to
publication fees. Soon you may have to include as much as $30,000 to your
application to NIH/NSF/USDA etc for a 4 year project for publication
charges. This is quite possible for large projects that may publish as many
as 10 papers from a project since some OA journals cost as much as $3,000!
Is the cost of publishing a paper on a Web platform really that high? Most
new generation OA journals do not have hard copies and most of the
publishing operations are automated by sophisticated software. I know
establishing such tools cannot be cheap, but that is usually part of the
upfront costs to get things started. Once it is up and running, it mostly
just need only modest management and maintenance.

I am on board with doing a letter with others to sound the alarm on this
problem.

Regards, Ikhide

  
Ikhide Imumorin, PhD 
Assistant Professor 
Animal Breeding, Genetics and Genomics Group Dept of Animal Science 
267 Morrison Hall 
Cornell University 
Ithaca, NY 14853 
USA 
T 607-255-2850 
F 607-255-9829 
igi2cornell.edu  

http://www.ansci.cornell.edu/faculty/imumorin.html

Editorial Board, Journal of Veterinary Science and Medical Diagnosis -
http://www.scitechnol.com/jvsmdhome.php Associate Editor, Genomics and
Quantitative Genetics - http://www.knoblauchpublishing.com Associate
Editor, Journal of Applied Animal Research -
http://www.tandf.co.uk/journals/TAAR Review Editor, Frontiers in Genetics -
http://www.frontiersin.org/genetics

"So why not go out on a limb, isn't that where the fruit is?" - Frank
Scully

  
________________________________________ 
.From: Miguel Perez-Enciso [miguel.perezuab.cat] 
.Sent: Tuesday, February 26, 2013 8:42 AM 
.To: Multiple Recipients of <AnGenMapanimalgenome.org> 
.Subject: Compulsory OAP will cause an even larger increase in publishing fees  

Dear authors

I agree with paying for publishing. As I see it, the two main questions are
whether publishing fees are fair and whether reviewers and editors should
charge for their work to publishers, either in kind or in cash. Under a
normal economic model, you could choose between the most competitive offer
but we are limited by the impact factor, on which our careers depend in
part.

I am afraid that policies making obligatory OAP will cause an inflationary
process in publishing fees. The idea of making tax payers get what they pay
for taxes is very reasonable, that of giving profit to private companies
per se, not so much. So, the state is responsible for paying a MAXIMUM for
publishing fees, the amount that should cover accountable costs excluding
profit. This will be reasonable and will help control quasi monopolies. It
would be great that these same 65,000 people sign a letter in these terms.

To summarise, publishing is a big business and we are getting a tiny part
with much effort. Reviewing and editing should be paid.

PS 1: I disclose also that I am editor of J Anim Breed Genet, a journal
with policies similar to those of Animal Genetics. At least in this case, I
am paid a small amount and get a discount on books from the publisher.

PS 2: I offer myself to write a letter to Obama and Cameron as well (via
Nature or Science) warning him of the inflationary dangers of compulsory
OAP and recommending to pay only for actual costs - not profit part. If
anyone is willing to help, please email me and we shall write something
that could be distributed to the rest of communities and submitted to any
or both of these journals.

Miguel

El 26/02/2013 1:25, Daniel Gianola escribi: >
> We may get help from the US Government. This article was published in  
> the New York Times on February 22. Regards. Daniel 
>  
> U.S. Moves to Provide Quicker Access to Publicly Financed Scientific  
> Research By KENNETH CHANG 
>  
> Published: February 22, 2013 
>  
> If you paid for it, you should be able to read it. For publicly  
> financed ience research, the Obama administration agrees. 
>  
> In a memorandum issued on Friday, John P. Holdren, science adviser to  
> resident Obama, called for scientific papers that report the results  
> of federally financed research to become freely accessible within a  
> year or so after publication. The findings are typically published in  
> scientific journals, many of which are open only to paying subscribers. 
>  
> The new policy would apply to federal agencies, including the National  
> Science Foundation, the Department of Energy and the Department of  
> Agriculture, that finance more than $100 million a year of research.  
> The agencies have six months to submit plans for how they would carry
> out the new policy. 
>  
> The hope is that broad access to scientific results will encourage  
> faster progress on research and will let anyone apply the knowledge  
> for technological advances. 
>  
> "We have seen, over the last 15 years, in the era of the Internet,  
> that the more widely available a publication is, the more likely it is  
> to be cited and the more likely it is to be used in patent  
> applications," said Myron Gutmann, an assistant director at the National
> Science Foundation. 
>  
> "We know that the small and medium enterprise, the business community,  
> doesn't have a lot of access to scientific publications right now,"  
> Dr. Gutmann said, "and the more we can make things available for those  
> communities, the more innovation there is likely to be." He estimated  
> that 25,000 to 40,000 journal articles based on research financed by  
> the science foundation are published annually. 
>  
> At the Agriculture Department, Catherine Woteki, the agency's chief  
> scientist, said the new policy fit in with efforts to make agriculture  
> data like plant genomes more widely available. "We can reduce in half  
> the time that it takes for breeding drought- and pest- and disease-
> resistant crops," she said. 
>  
> The agencies could model their policies on one established by the  
> National Institutes of Health in 2008. The N.I.H. requires scientists  
> receiving grants to ensure that their papers can be made available on  
> PubMed Central, a publicly available Web site, within one year. 
>  
> An online petition last May on the White House's Web site called for  
> "free access over the Internet to scientific journal articles arising  
> from taxpayer-funded research." 
>  
> More than 65,000 people signed the petition, easily passing the  
> 25,000-signature threshold that merited an official White House  
> response. (The threshold was raised in January to 100,000 after a  
> petition that called for building a Death Star like that in the movie  
> "Star Wars" garnered 34,435 signatures; administration officials  
> rejected that suggestion.) 
>  
> In a response posted Friday to the signers of the open-access petitioners,
> Dr. Holdren agreed.  
>  
> "Americans should have easy access to the results of the research they  
> help support," Dr. Holden wrote, adding, "the logic behind enhanced access
> is plain." 
>  
> A version of this article appeared in print on February 23, 2013, on  
> page A9 of the New York edition with the headline: U.S. Moves to  
> Provide Quicker Access to Publicly Financed Scientific Research. 

-- 
=============================================================== 
Miguel Perez-Enciso 
ICREA professor 
Centre for Research in Agricultural Genomics (CRAG) and Facultat de Veterinaria
UAB Campus Universitat Autonoma Barcelona Bellaterra 
E-08193 Spain 
Tel: +34 935636600 ext 3346 
Fax: +34 935636601 
miguel.perezuab.es 
http://www.icrea.cat/...cStaff/Miguel-Perez-Enciso-255 
http://bioinformatics.cragenomica.es/numgenomics/ 
================================================================ 

From gianolaansci.wisc.edu  Tue Feb 26 17:30:52 2013
From: Daniel Gianola <gianolaansci.wisc.edu>
Subject: RE: Compulsory OAP will cause an even larger increase in publishing 
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Tue, 26 Feb 2013 17:30:52 -0600

Robert,

Do you write apps for free for smart phones, or internal code? Well, we do
contribute significantly to the journals via material (imagine, if the
hypothetical "Columbia, Missouri" post would not pay its columnists), or via
reviews (imagine if the New York Times Review of Books would not pay its
reviewers). This was well articulated by Miguel.

There is room for a more balance approached.

Regards,

Daniel
________________________________________
.From: Schnabel, Robert D. [schnabelrmissouri.edu]
.Sent: Tuesday, February 26, 2013 5:09 PM
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: RE: Compulsory OAP will cause an even larger increase in publishing

I have to chime in here. I think recent post discussing publisher profits
are misguided. What difference does it make if a publisher makes a dollar
or a billion? Intel, AMD and Apple make large profits but I don't hear any
outcry about the price of your computers which you rely upon to do your
research. Illumina does alright but I don't hear anyone proposing to write
a letter to someone complaining about the price of snp chips or sequencing
reagents citing Illumina's profit margins. If you want to make a case for
the problem of increasing publishing costs don't bring in "fairness" and
publishers profits. You'll get much more traction if you present a coherent
case and more importantly a solution.

Bob

*************************************************
Robert Schnabel
Research Associate Professor
University of Missouri-Columbia
Animal Sciences Unit, Rm.162
920 East Campus Drive
Columbia, MO 65211-5300
Phone: 573-884-4106
Fax:   573-882-6827
http://animalgenomics.missouri.edu
*************************************************


-----Original Message-----
.From: WILSON Andrea [mailto:andrea.wilsonroslin.ed.ac.uk]
.Sent: Tuesday, February 26, 2013 4:37 PM
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: RE: Compulsory OAP will cause an even larger increase in publishing

Dear colleagues,

I would support an alarm letter as proposed by Ikhide as the current
situation seems unfair to me. It may strengthen our argument if we knew how
much profit (if any) a journal makes on average per OA article. Does
anybody in the community know?

Best wishes Andrea


-----Original Message-----
.From: Ikhide Imumorin [mailto:igi2cornell.edu]
.Sent: 26 February 2013 17:21
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: RE: Compulsory OAP will cause an even larger increase in publishing fees

Dear Colleagues, I totally agree with Miguel on this issue. If journals,
especially OA journals will charge all these exorbitant fees for publishing
papers to be read freely, then editors and reviewers should be paid in
cash, but preferably in kind. For example BMC Ltd can institute a policy
that say you get a discount (say 25% off) your next paper if you review a
paper, and if you review this many papers per year, you get to publish one
paper for free. As it stands now scientists are used to do all the heavy
lifting of judging the science of their peers for free... and the only ones
making money from this whole thing is the companies... whether OA or not.

Will publishers step up to the plate and do the right thing? If the next
time you get a paper from a journal and you decline reviewing it, aren't we
all busy? or you ask for some kind of compensation in the form of discount
in publishing in that journal, a new movement that help us scientists might
be born. The process of scientific publishing depends on peer review, but
that job right now is unpaid and burdensome. After you have reviewed a few
papers for a journal and you can put that in your CV under "Professional
Service", is there any incentive to do any more for that journal?

Compulsory OA publishing will inflate publishing fees to the point where
grant agencies will be forced to devote a significant portion to
publication fees. Soon you may have to include as much as $30,000 to your
application to NIH/NSF/USDA etc for a 4 year project for publication
charges. This is quite possible for large projects that may publish as many
as 10 papers from a project since some OA journals cost as much as $3,000!
Is the cost of publishing a paper on a Web platform really that high? Most
new generation OA journals do not have hard copies and most of the
publishing operations are automated by sophisticated software. I know
establishing such tools cannot be cheap, but that is usually part of the
upfront costs to get things started. Once it is up and running, it mostly
just need only modest management and maintenance.

I am on board with doing a letter with others to sound the alarm on this
problem.

Regards, Ikhide


Ikhide Imumorin, PhD
Assistant Professor
Animal Breeding, Genetics and Genomics Group Dept of Animal Science
267 Morrison Hall
Cornell University
Ithaca, NY 14853
USA
T 607-255-2850
F 607-255-9829
igi2cornell.edu

http://www.ansci.cornell.edu/faculty/imumorin.html

Editorial Board, Journal of Veterinary Science and Medical Diagnosis -
http://www.scitechnol.com/jvsmdhome.php Associate Editor, Genomics and
Quantitative Genetics - http://www.knoblauchpublishing.com Associate
Editor, Journal of Applied Animal Research -
http://www.tandf.co.uk/journals/TAAR Review Editor, Frontiers in Genetics -
http://www.frontiersin.org/genetics

"So why not go out on a limb, isn't that where the fruit is?" - Frank
Scully


________________________________________
.From: Miguel Perez-Enciso [miguel.perezuab.cat]
.Sent: Tuesday, February 26, 2013 8:42 AM
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: Compulsory OAP will cause an even larger increase in publishing fees

Dear authors

I agree with paying for publishing. As I see it, the two main questions are
whether publishing fees are fair and whether reviewers and editors should
charge for their work to publishers, either in kind or in cash. Under a
normal economic model, you could choose between the most competitive offer
but we are limited by the impact factor, on which our careers depend in
part.

I am afraid that policies making obligatory OAP will cause an inflationary
process in publishing fees. The idea of making tax payers get what they pay
for taxes is very reasonable, that of giving profit to private companies
per se, not so much. So, the state is responsible for paying a MAXIMUM for
publishing fees, the amount that should cover accountable costs excluding
profit. This will be reasonable and will help control quasi monopolies. It
would be great that these same 65,000 people sign a letter in these terms.

To summarise, publishing is a big business and we are getting a tiny part
with much effort. Reviewing and editing should be paid.

PS 1: I disclose also that I am editor of J Anim Breed Genet, a journal
with policies similar to those of Animal Genetics. At least in this case, I
am paid a small amount and get a discount on books from the publisher.

PS 2: I offer myself to write a letter to Obama and Cameron as well (via
Nature or Science) warning him of the inflationary dangers of compulsory
OAP and recommending to pay only for actual costs - not profit part. If
anyone is willing to help, please email me and we shall write something
that could be distributed to the rest of communities and submitted to any
or both of these journals.

Miguel

El 26/02/2013 1:25, Daniel Gianola escribi: >
> We may get help from the US Government. This article was published in
> the New York Times on February 22. Regards. Daniel
>
> U.S. Moves to Provide Quicker Access to Publicly Financed Scientific
> Research By KENNETH CHANG
>
> Published: February 22, 2013
>
> If you paid for it, you should be able to read it. For publicly
> financed ience research, the Obama administration agrees.
>
> In a memorandum issued on Friday, John P. Holdren, science adviser to
> resident Obama, called for scientific papers that report the results
> of federally financed research to become freely accessible within a
> year or so after publication. The findings are typically published in
> scientific journals, many of which are open only to paying subscribers.
>
> The new policy would apply to federal agencies, including the National
> Science Foundation, the Department of Energy and the Department of
> Agriculture, that finance more than $100 million a year of research.
> The agencies have six months to submit plans for how they would carry
> out the new policy.
>
> The hope is that broad access to scientific results will encourage
> faster progress on research and will let anyone apply the knowledge
> for technological advances.
>
> "We have seen, over the last 15 years, in the era of the Internet,
> that the more widely available a publication is, the more likely it is
> to be cited and the more likely it is to be used in patent
> applications," said Myron Gutmann, an assistant director at the National
> Science Foundation.
>
> "We know that the small and medium enterprise, the business community,
> doesn't have a lot of access to scientific publications right now,"
> Dr. Gutmann said, "and the more we can make things available for those
> communities, the more innovation there is likely to be." He estimated
> that 25,000 to 40,000 journal articles based on research financed by
> the science foundation are published annually.
>
> At the Agriculture Department, Catherine Woteki, the agency's chief
> scientist, said the new policy fit in with efforts to make agriculture
> data like plant genomes more widely available. "We can reduce in half
> the time that it takes for breeding drought- and pest- and disease-
> resistant crops," she said.
>
> The agencies could model their policies on one established by the
> National Institutes of Health in 2008. The N.I.H. requires scientists
> receiving grants to ensure that their papers can be made available on
> PubMed Central, a publicly available Web site, within one year.
>
> An online petition last May on the White House's Web site called for
> "free access over the Internet to scientific journal articles arising
> from taxpayer-funded research."
>
> More than 65,000 people signed the petition, easily passing the
> 25,000-signature threshold that merited an official White House
> response. (The threshold was raised in January to 100,000 after a
> petition that called for building a Death Star like that in the movie
> "Star Wars" garnered 34,435 signatures; administration officials
> rejected that suggestion.)
>
> In a response posted Friday to the signers of the open-access petitioners,
> Dr. Holdren agreed.
>
> "Americans should have easy access to the results of the research they
> help support," Dr. Holden wrote, adding, "the logic behind enhanced access
> is plain."
>
> A version of this article appeared in print on February 23, 2013, on
> page A9 of the New York edition with the headline: U.S. Moves to
> Provide Quicker Access to Publicly Financed Scientific Research.

--
===============================================================
Miguel Perez-Enciso
ICREA professor
Centre for Research in Agricultural Genomics (CRAG) and Facultat de Veterinaria
UAB Campus Universitat Autonoma Barcelona Bellaterra
E-08193 Spain
Tel: +34 935636600 ext 3346
Fax: +34 935636601
miguel.perezuab.es
http://www.icrea.cat/...cStaff/Miguel-Perez-Enciso-255
http://bioinformatics.cragenomica.es/numgenomics/
================================================================
  

From andrea.wilsonroslin.ed.ac.uk  Tue Feb 26 18:26:13 2013
From: WILSON Andrea <andrea.wilsonroslin.ed.ac.uk>
Subject: RE: Compulsory OAP will cause an even larger increase in publishing  
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Tue, 26 Feb 2013 18:26:13 -0600

I hear your argument, Bob, and I think you make an interesting point. But
journalists get paid by newspapers for contributing an article, not the other way
round. Is our case so different? Asking the scientists to carry the full cost of
publishing seems grossly unfair assuming that we don't publish for our personal
benefit but for the benefit of the scientific community and end users. Usually
it's the end users that pay for a product, not the producer. 
Asking the authors to pay for publishing also generates a bias towards richer,
but not necessarily better scientists to publish in high impact journals. Doesn't
this bias violate the basic principle of science, which should be judged
according to its scientific merit rather by the impact factor of a journal in
which only a few selected can afford to publish?
In my mind this bias could easily be resolved by splitting the costs between the
end users (the scientists including both authors and readers and the wider
community who in the end will benefit from progress in science (taxpayers)). 

Andrea


-- 

From zhuiastate.edu  Tue Feb 26 18:44:42 2013
From: "Hu, Zhiliang [AN S]" <zhuiastate.edu>
Subject: RE: Compulsory OAP will cause an even larger increase in publishing 
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Tue, 26 Feb 2013 18:44:42 -0600

I am afraid Intel/AMD/Apple may not be a good analog to OA publishers.

First Intel/AMD/Apple makes profit for (1) what they create; (2) quality
production costs.  The OA publishers cannot compare in these 2 fronts.
To me what they do is like hijacking the publishing process for profit.
Remember the OA publishing came into the play by 2 claims: free access
and low costs (we pay once, not twice).  Note the steep price hike is
after they have made their "market" share.

Second, the reviewers are exploited for free intelligent works; the 
authors are exploited for giving up their copy-rights; in addition the 
OA publishing processes/costs obviously don't justify the high charges.
It's a sin to make (extra) profits on research dollars because it hurts 
science.

By the way I like Rosa's comments about Frontiers journals. One more
feature I like Frontiers is that once a paper got accepted, the reviewers'  
names are made known and listed to recognize the values they have helped 
to add by their critical reviews, while they are made responsible for what 
they have granted green lights for.

Why can't there be a non-profit organization to do the publications?

Zhiliang


-----Original Message-----
.From: Schnabel, Robert D. [mailto:schnabelrmissouri.edu] 
.Sent: Tuesday, February 26, 2013 5:10 PM
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: RE: Compulsory OAP will cause an even larger increase in publishing 

I have to chime in here. I think recent post discussing publisher profits are
misguided. What difference does it make if a publisher makes a dollar or a
billion? Intel, AMD and Apple make large profits but I don't hear any outcry
about the price of your computers which you rely upon to do your research.
Illumina does alright but I don't hear anyone proposing to write a letter to
someone complaining about the price of snp chips or sequencing reagents citing
Illumina's profit margins. If you want to make a case for the problem of
increasing publishing costs don't bring in "fairness" and publishers profits.
You'll get much more traction if you present a coherent case and more importantly
a solution.

Bob

*************************************************
Robert Schnabel
Research Associate Professor
University of Missouri-Columbia
Animal Sciences Unit, Rm.162
920 East Campus Drive
Columbia, MO 65211-5300
Phone: 573-884-4106 
Fax:   573-882-6827 
http://animalgenomics.missouri.edu
************************************************* 

 
-----Original Message-----
.From: WILSON Andrea [mailto:andrea.wilsonroslin.ed.ac.uk]
.Sent: Tuesday, February 26, 2013 4:37 PM
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: RE: Compulsory OAP will cause an even larger increase in publishing 

Dear colleagues,

I would support an alarm letter as proposed by Ikhide as the current situation
seems unfair to me. It may strengthen our argument if we knew how much profit (if
any) a journal makes on average per OA article. Does anybody in the community know?

Best wishes Andrea

 
-----Original Message-----
.From: Ikhide Imumorin [mailto:igi2cornell.edu]
.Sent: 26 February 2013 17:21
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: RE: Compulsory OAP will cause an even larger increase in publishing fees  

Dear Colleagues, I totally agree with Miguel on this issue. If journals,
especially OA journals will charge all these exorbitant fees for publishing
papers to be read freely, then editors and reviewers should be paid in cash, but
preferably in kind. For example BMC Ltd can institute a policy that say you get a
discount (say 25% off) your next paper if you review a paper, and if you review
this many papers per year, you get to publish one paper for free. As it stands
now scientists are used to do all the heavy lifting of judging the science of
their peers for free... and the only ones making money from this whole thing is
the companies... whether OA or not.

Will publishers step up to the plate and do the right thing? If the next time you
get a paper from a journal and you decline reviewing it, aren't we all busy? or
you ask for some kind of compensation in the form of discount in publishing in
that journal, a new movement that help us scientists might be born. The process
of scientific publishing depends on peer review, but that job right now is unpaid
and burdensome. After you have reviewed a few papers for a journal and you can
put that in your CV under "Professional Service", is there any incentive to do
any more for that journal?

Compulsory OA publishing will inflate publishing fees to the point where grant
agencies will be forced to devote a significant portion to publication fees. Soon
you may have to include as much as $30,000 to your application to NIH/NSF/USDA
etc for a 4 year project for publication charges. This is quite possible for
large projects that may publish as many as 10 papers from a project since some OA
journals cost as much as $3,000!
Is the cost of publishing a paper on a Web platform really that high? Most new
generation OA journals do not have hard copies and most of the publishing
operations are automated by sophisticated software. I know establishing such
tools cannot be cheap, but that is usually part of the upfront costs to get
things started. Once it is up and running, it mostly just need only modest
management and maintenance.

I am on board with doing a letter with others to sound the alarm on this problem.

Regards, Ikhide

Ikhide Imumorin, PhD
Assistant Professor
Animal Breeding, Genetics and Genomics Group Dept of Animal Science
267 Morrison Hall
Cornell University
Ithaca, NY 14853
USA
T 607-255-2850
F 607-255-9829
igi2cornell.edu  

http://www.ansci.cornell.edu/faculty/imumorin.html

Editorial Board, Journal of Veterinary Science and Medical Diagnosis -
http://www.scitechnol.com/jvsmdhome.php Associate Editor, Genomics and
Quantitative Genetics - http://www.knoblauchpublishing.com Associate Editor,
Journal of Applied Animal Research - http://www.tandf.co.uk/journals/TAAR Review
Editor, Frontiers in Genetics - http://www.frontiersin.org/genetics

"So why not go out on a limb, isn't that where the fruit is?" - Frank Scully

________________________________________
.From: Miguel Perez-Enciso [miguel.perezuab.cat]
.Sent: Tuesday, February 26, 2013 8:42 AM
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: Compulsory OAP will cause an even larger increase in publishing fees  

Dear authors

I agree with paying for publishing. As I see it, the two main questions are
whether publishing fees are fair and whether reviewers and editors should charge
for their work to publishers, either in kind or in cash. Under a normal economic
model, you could choose between the most competitive offer but we are limited by
the impact factor, on which our careers depend in part.

I am afraid that policies making obligatory OAP will cause an inflationary
process in publishing fees. The idea of making tax payers get what they pay for
taxes is very reasonable, that of giving profit to private companies per se, not
so much. So, the state is responsible for paying a MAXIMUM for publishing fees,
the amount that should cover accountable costs excluding profit. This will be
reasonable and will help control quasi monopolies. It would be great that these
same 65,000 people sign a letter in these terms.

To summarise, publishing is a big business and we are getting a tiny part with
much effort. Reviewing and editing should be paid.

PS 1: I disclose also that I am editor of J Anim Breed Genet, a journal with
policies similar to those of Animal Genetics. At least in this case, I am paid a
small amount and get a discount on books from the publisher.

PS 2: I offer myself to write a letter to Obama and Cameron as well (via Nature
or Science) warning him of the inflationary dangers of compulsory OAP and
recommending to pay only for actual costs - not profit part. If anyone is willing
to help, please email me and we shall write something that could be distributed
to the rest of communities and submitted to any or both of these journals.

Miguel

El 26/02/2013 1:25, Daniel Gianola escribi: >
> We may get help from the US Government. This article was published in 
> the New York Times on February 22. Regards. Daniel
> U.S. Moves to Provide Quicker Access to Publicly Financed Scientific 
> Research By KENNETH CHANG
> Published: February 22, 2013
> If you paid for it, you should be able to read it. For publicly 
> financed ience research, the Obama administration agrees.
> In a memorandum issued on Friday, John P. Holdren, science adviser to 
> resident Obama, called for scientific papers that report the results 
> of federally financed research to become freely accessible within a 
> year or so after publication. The findings are typically published in 
> scientific journals, many of which are open only to paying subscribers.
> The new policy would apply to federal agencies, including the National 
> Science Foundation, the Department of Energy and the Department of 
> Agriculture, that finance more than $100 million a year of research.
> The agencies have six months to submit plans for how they would carry 
> out the new policy.
> The hope is that broad access to scientific results will encourage 
> faster progress on research and will let anyone apply the knowledge 
> for technological advances.
> "We have seen, over the last 15 years, in the era of the Internet, 
> that the more widely available a publication is, the more likely it is 
> to be cited and the more likely it is to be used in patent 
> applications," said Myron Gutmann, an assistant director at the 
> National Science Foundation.
> "We know that the small and medium enterprise, the business community, 
> doesn't have a lot of access to scientific publications right now,"
> Dr. Gutmann said, "and the more we can make things available for those 
> communities, the more innovation there is likely to be." He estimated 
> that 25,000 to 40,000 journal articles based on research financed by 
> the science foundation are published annually.
> At the Agriculture Department, Catherine Woteki, the agency's chief 
> scientist, said the new policy fit in with efforts to make agriculture 
> data like plant genomes more widely available. "We can reduce in half 
> the time that it takes for breeding drought- and pest- and disease- 
> resistant crops," she said.
> The agencies could model their policies on one established by the 
> National Institutes of Health in 2008. The N.I.H. requires scientists 
> receiving grants to ensure that their papers can be made available on 
> PubMed Central, a publicly available Web site, within one year.
> An online petition last May on the White House's Web site called for 
> "free access over the Internet to scientific journal articles arising 
> from taxpayer-funded research."
> More than 65,000 people signed the petition, easily passing the 
> 25,000-signature threshold that merited an official White House 
> response. (The threshold was raised in January to 100,000 after a 
> petition that called for building a Death Star like that in the movie 
> "Star Wars" garnered 34,435 signatures; administration officials 
> rejected that suggestion.)
> In a response posted Friday to the signers of the open-access 
> petitioners, Dr. Holdren agreed.
> "Americans should have easy access to the results of the research they 
> help support," Dr. Holden wrote, adding, "the logic behind enhanced 
> access is plain."
> A version of this article appeared in print on February 23, 2013, on 
> page A9 of the New York edition with the headline: U.S. Moves to 
> Provide Quicker Access to Publicly Financed Scientific Research.

--
===============================================================
Miguel Perez-Enciso
ICREA professor
Centre for Research in Agricultural Genomics (CRAG) and Facultat de Veterinaria
UAB Campus Universitat Autonoma Barcelona Bellaterra
E-08193 Spain
Tel: +34 935636600 ext 3346
Fax: +34 935636601
miguel.perezuab.es
http://www.icrea.cat/...cStaff/Miguel-Perez-Enciso-255
http://bioinformatics.cragenomica.es/numgenomics/
================================================================ 

http://www.animalgenome.org Help desk: bioinfo-teamanimalgenome.org -o
Unsubscribe: email "unsubscribe" to: angenmap-requestanimalgenome.org 




From igi2cornell.edu  Tue Feb 26 20:45:28 2013 
From: Ikhide Imumorin <igi2cornell.edu> 
Subject: RE: Compulsory OAP will cause an even larger increase in publishing  
Postmaster: submission approved 
To: Multiple Recipients of <angenmapanimalgenome.org> 
Date: Tue, 26 Feb 2013 20:45:28 -0600 

I am totally with Zhiliang's reasoning. Some journals publish the names of
reviewers on the published paper and that is commendable that Frontiers
does that. But putting my name on a paper does not do much for the
economics of my sustaining my research program. We have come to a time when
the way scientists are rewarded should be revisited and realize that mere
"recognition" is no longer enough, not when others are making money off
your sweat.

Most of these OA publishers call themselves "non profit" but that is not
reflected in the sky high costs of what they euphemistically call "article
publishing charges". Unfortunately, between impact factors, where journals
are indexed, heavy duty names on editorial boards, all of which are highly
invested in the status-quo, I am not very sure that anything major will
happen soon, but I am hopeful. Only senior and established scientists can
make the right moves not untenured assistant professors... but of course it
is mostly untenured assistant professors who have fewer resources to pay
these OA fees!

Disclaimer I am very active with Frontiers where I serve as a Reviewer and
has published a paper there. I still think Frontiers should pioneer a fair
and balanced approach both to incentivize being reviewers and reward the
use of intellectual resources of fellow scientists. For example, let
scientists publish with a sharp discount if they review a paper or set a
threshold that allows you to publish one paper for free after reviewing so
many papers. If Frontiers truly wants to be a game changer they should take
leadership of this issue.

 
 
Ikhide Imumorin, PhD 
Assistant Professor 
Animal Breeding, Genetics and Genomics Group 
Dept of Animal Science 
267 Morrison Hall 
Cornell University 
Ithaca, NY 14853 
USA 
T 607-255-2850 
F 607-255-9829 
igi2cornell.edu 

http://www.ansci.cornell.edu/faculty/imumorin.html

Editorial Board, Journal of Veterinary Science and Medical Diagnosis -
http://www.scitechnol.com/jvsmdhome.php Associate Editor, Genomics and
Quantitative Genetics - http://www.knoblauchpublishing.com Associate
Editor, Journal of Applied Animal Research -
http://www.tandf.co.uk/journals/TAAR Review Editor, Frontiers in Genetics -
http://www.frontiersin.org/genetics

"So why not go out on a limb, isn't that where the fruit is?" - Frank
Scully
 
 
________________________________________ 
.From: Hu, Zhiliang [AN S] [zhuiastate.edu] 
.Sent: Tuesday, February 26, 2013 7:44 PM 
.To: Multiple Recipients of <AnGenMapanimalgenome.org> 
.Subject: RE: Compulsory OAP will cause an even larger increase in publishing 

 
I am afraid Intel/AMD/Apple may not be a good analog to OA publishers. 

First Intel/AMD/Apple makes profit for (1) what they create; (2) quality
production costs. The OA publishers cannot compare in these 2 fronts. To me
what they do is like hijacking the publishing process for profit. Remember
the OA publishing came into the play by 2 claims: free access and low costs
(we pay once, not twice). Note the steep price hike is after they have made
their "market" share.

Second, the reviewers are exploited for free intelligent works; the authors
are exploited for giving up their copy-rights; in addition the OA
publishing processes/costs obviously don't justify the high charges. It's a
sin to make (extra) profits on research dollars because it hurts science.

By the way I like Rosa's comments about Frontiers journals. One more
feature I like Frontiers is that once a paper got accepted, the reviewers'
names are made known and listed to recognize the values they have helped to
add by their critical reviews, while they are made responsible for what
they have granted green lights for.

Why can't there be a non-profit organization to do the publications?

Zhiliang

 
-----Original Message----- 
.From: Schnabel, Robert D. [mailto:schnabelrmissouri.edu] 
.Sent: Tuesday, February 26, 2013 5:10 PM 
.To: Multiple Recipients of <AnGenMapanimalgenome.org> 
.Subject: RE: Compulsory OAP will cause an even larger increase in publishing 

I have to chime in here. I think recent post discussing publisher profits
are misguided. What difference does it make if a publisher makes a dollar
or a billion? Intel, AMD and Apple make large profits but I don't hear any
outcry about the price of your computers which you rely upon to do your
research. Illumina does alright but I don't hear anyone proposing to write
a letter to someone complaining about the price of snp chips or sequencing
reagents citing Illumina's profit margins. If you want to make a case for
the problem of increasing publishing costs don't bring in "fairness" and
publishers profits. You'll get much more traction if you present a coherent
case and more importantly a solution.

Bob

************************************************* 
Robert Schnabel 
Research Associate Professor 
University of Missouri-Columbia 
Animal Sciences Unit, Rm.162 
920 East Campus Drive 
Columbia, MO 65211-5300 
Phone: 573-884-4106 
Fax:   573-882-6827 
http://animalgenomics.missouri.edu 
************************************************* 

 
-----Original Message----- 
.From: WILSON Andrea [mailto:andrea.wilsonroslin.ed.ac.uk] 
.Sent: Tuesday, February 26, 2013 4:37 PM 
.To: Multiple Recipients of <AnGenMapanimalgenome.org> 
.Subject: RE: Compulsory OAP will cause an even larger increase in publishing 

Dear colleagues,

I would support an alarm letter as proposed by Ikhide as the current
situation seems unfair to me. It may strengthen our argument if we knew how
much profit (if any) a journal makes on average per OA article. Does
anybody in the community know?

Best wishes Andrea

 
-----Original Message----- 
.From: Ikhide Imumorin [mailto:igi2cornell.edu] 
.Sent: 26 February 2013 17:21 
.To: Multiple Recipients of <AnGenMapanimalgenome.org> 
.Subject: RE: Compulsory OAP will cause an even larger increase in publishing fees 

Dear Colleagues, I totally agree with Miguel on this issue. If journals,
especially OA journals will charge all these exorbitant fees for publishing
papers to be read freely, then editors and reviewers should be paid in
cash, but preferably in kind. For example BMC Ltd can institute a policy
that say you get a discount (say 25% off) your next paper if you review a
paper, and if you review this many papers per year, you get to publish one
paper for free. As it stands now scientists are used to do all the heavy
lifting of judging the science of their peers for free... and the only ones
making money from this whole thing is the companies... whether OA or not.

Will publishers step up to the plate and do the right thing? If the next
time you get a paper from a journal and you decline reviewing it, aren't we
all busy? or you ask for some kind of compensation in the form of discount
in publishing in that journal, a new movement that help us scientists might
be born. The process of scientific publishing depends on peer review, but
that job right now is unpaid and burdensome. After you have reviewed a few
papers for a journal and you can put that in your CV under "Professional
Service", is there any incentive to do any more for that journal?

Compulsory OA publishing will inflate publishing fees to the point where
grant agencies will be forced to devote a significant portion to
publication fees. Soon you may have to include as much as $30,000 to your
application to NIH/NSF/USDA etc for a 4 year project for publication
charges. This is quite possible for large projects that may publish as many
as 10 papers from a project since some OA journals cost as much as $3,000!
Is the cost of publishing a paper on a Web platform really that high? Most
new generation OA journals do not have hard copies and most of the
publishing operations are automated by sophisticated software. I know
establishing such tools cannot be cheap, but that is usually part of the
upfront costs to get things started. Once it is up and running, it mostly
just need only modest management and maintenance.

I am on board with doing a letter with others to sound the alarm on this
problem.

Regards, Ikhide

Ikhide Imumorin, PhD Assistant Professor Animal Breeding, Genetics and
Genomics Group Dept of Animal Science 267 Morrison Hall Cornell University
Ithaca, NY 14853 USA T 607-255-2850 F 607-255-9829 igi2cornell.edu

http://www.ansci.cornell.edu/faculty/imumorin.html

Editorial Board, Journal of Veterinary Science and Medical Diagnosis -
http://www.scitechnol.com/jvsmdhome.php Associate Editor, Genomics and
Quantitative Genetics - http://www.knoblauchpublishing.com Associate
Editor, Journal of Applied Animal Research -
http://www.tandf.co.uk/journals/TAAR Review Editor, Frontiers in Genetics -
http://www.frontiersin.org/genetics

"So why not go out on a limb, isn't that where the fruit is?" - Frank
Scully

________________________________________ 
.From: Miguel Perez-Enciso [miguel.perezuab.cat] 
.Sent: Tuesday, February 26, 2013 8:42 AM 
.To: Multiple Recipients of <AnGenMapanimalgenome.org> 
.Subject: Compulsory OAP will cause an even larger increase in publishing fees 

Dear authors

I agree with paying for publishing. As I see it, the two main questions are
whether publishing fees are fair and whether reviewers and editors should
charge for their work to publishers, either in kind or in cash. Under a
normal economic model, you could choose between the most competitive offer
but we are limited by the impact factor, on which our careers depend in
part.

I am afraid that policies making obligatory OAP will cause an inflationary
process in publishing fees. The idea of making tax payers get what they pay
for taxes is very reasonable, that of giving profit to private companies
per se, not so much. So, the state is responsible for paying a MAXIMUM for
publishing fees, the amount that should cover accountable costs excluding
profit. This will be reasonable and will help control quasi monopolies. It
would be great that these same 65,000 people sign a letter in these terms.

To summarise, publishing is a big business and we are getting a tiny part
with much effort. Reviewing and editing should be paid.

PS 1: I disclose also that I am editor of J Anim Breed Genet, a journal
with policies similar to those of Animal Genetics. At least in this case, I
am paid a small amount and get a discount on books from the publisher.

PS 2: I offer myself to write a letter to Obama and Cameron as well (via
Nature or Science) warning him of the inflationary dangers of compulsory
OAP and recommending to pay only for actual costs - not profit part. If
anyone is willing to help, please email me and we shall write something
that could be distributed to the rest of communities and submitted to any
or both of these journals.

Miguel

El 26/02/2013 1:25, Daniel Gianola escribi: >
> We may get help from the US Government. This article was published in 
> the New York Times on February 22. Regards. Daniel 
> U.S. Moves to Provide Quicker Access to Publicly Financed Scientific 
> Research By KENNETH CHANG 
> Published: February 22, 2013 
> If you paid for it, you should be able to read it. For publicly 
> financed ience research, the Obama administration agrees. 
> In a memorandum issued on Friday, John P. Holdren, science adviser to 
> resident Obama, called for scientific papers that report the results 
> of federally financed research to become freely accessible within a 
> year or so after publication. The findings are typically published in 
> scientific journals, many of which are open only to paying subscribers. 
> The new policy would apply to federal agencies, including the National 
> Science Foundation, the Department of Energy and the Department of 
> Agriculture, that finance more than $100 million a year of research. 
> The agencies have six months to submit plans for how they would carry 
> out the new policy. 
> The hope is that broad access to scientific results will encourage 
> faster progress on research and will let anyone apply the knowledge 
> for technological advances. 
> "We have seen, over the last 15 years, in the era of the Internet, 
> that the more widely available a publication is, the more likely it is 
> to be cited and the more likely it is to be used in patent 
> applications," said Myron Gutmann, an assistant director at the 
> National Science Foundation. 
> "We know that the small and medium enterprise, the business community, 
> doesn't have a lot of access to scientific publications right now," 
> Dr. Gutmann said, "and the more we can make things available for those 
> communities, the more innovation there is likely to be." He estimated 
> that 25,000 to 40,000 journal articles based on research financed by 
> the science foundation are published annually. 
> At the Agriculture Department, Catherine Woteki, the agency's chief 
> scientist, said the new policy fit in with efforts to make agriculture 
> data like plant genomes more widely available. "We can reduce in half 
> the time that it takes for breeding drought- and pest- and disease- 
> resistant crops," she said. 
> The agencies could model their policies on one established by the 
> National Institutes of Health in 2008. The N.I.H. requires scientists 
> receiving grants to ensure that their papers can be made available on 
> PubMed Central, a publicly available Web site, within one year. 
> An online petition last May on the White House's Web site called for 
> "free access over the Internet to scientific journal articles arising 
> from taxpayer-funded research." 
> More than 65,000 people signed the petition, easily passing the 
> 25,000-signature threshold that merited an official White House 
> response. (The threshold was raised in January to 100,000 after a 
> petition that called for building a Death Star like that in the movie 
> "Star Wars" garnered 34,435 signatures; administration officials 
> rejected that suggestion.) 
> In a response posted Friday to the signers of the open-access 
> petitioners, Dr. Holdren agreed. 
> "Americans should have easy access to the results of the research they 
> help support," Dr. Holden wrote, adding, "the logic behind enhanced 
> access is plain." 
> A version of this article appeared in print on February 23, 2013, on 
> page A9 of the New York edition with the headline: U.S. Moves to 
> Provide Quicker Access to Publicly Financed Scientific Research. 

-- 
============================================================= 
== 
Miguel Perez-Enciso 
ICREA professor 
Centre for Research in Agricultural Genomics (CRAG) and Facultat de Veterinaria 
UAB Campus Universitat Autonoma Barcelona Bellaterra 
E-08193 Spain 
Tel: +34 935636600 ext 3346 
Fax: +34 935636601 
miguel.perezuab.es 
http://www.icrea.cat/...cStaff/Miguel-Perez-Enciso-255 
http://bioinformatics.cragenomica.es/numgenomics/ 
============================================================= 
=== 

From m.fortesuq.edu.au  Tue Feb 26 20:45:47 2013 
From: Marina Fortes <m.fortesuq.edu.au> 
Subject: RE: Compulsory OAP will cause an even larger increase in publishing  
Postmaster: submission approved 
To: Multiple Recipients of <angenmapanimalgenome.org> 
Date: Tue, 26 Feb 2013 20:45:47 -0600 

Only the past 2 weeks I have volunteered my time to Animal Genetics, BMC
genetics and Theriogenology (and I know I don't get recruited as much as
some of you). Therefore, I do agree with Daniel.

 
Marina R S Fortes 
Post Doctoral Research Fellow 
University of Queensland - QAAFI 
Gatton bld 8114, room 314 
Phone 61 7 54601969 
Mobile 0431141617 

 
-----Original Message----- 
.From: Daniel Gianola [mailto:gianolaansci.wisc.edu]  
.Sent: Wednesday, 27 February 2013 9:31 AM 
.To: Multiple Recipients of <AnGenMapanimalgenome.org> 
.Subject: RE: Compulsory OAP will cause an even larger increase in publishing  

http://www.animalgenome.org/community/discuss ]

Robert,

Do you write apps for free for smart phones, or internal code? Well, we do
contribute significantly to the journals via material (imagine, if the
hypothetical "Columbia, Missouri" post would not pay its columnists), or
via reviews (imagine if the New York Times Review of Books would not pay
its reviewers). This was well articulated by Miguel.

There is room for a more balance approached.

Regards,

Daniel
________________________________________ 
.From: Schnabel, Robert D. [schnabelrmissouri.edu] 
.Sent: Tuesday, February 26, 2013 5:09 PM 
.To: Multiple Recipients of <AnGenMapanimalgenome.org> 
.Subject: RE: Compulsory OAP will cause an even larger increase in publishing 

I have to chime in here. I think recent post discussing publisher profits
are misguided. What difference does it make if a publisher makes a dollar
or a billion? Intel, AMD and Apple make large profits but I don't hear any
outcry about the price of your computers which you rely upon to do your
research. Illumina does alright but I don't hear anyone proposing to write
a letter to someone complaining about the price of snp chips or sequencing
reagents citing Illumina's profit margins. If you want to make a case for
the problem of increasing publishing costs don't bring in "fairness" and
publishers profits. You'll get much more traction if you present a coherent
case and more importantly a solution.

Bob

************************************************* 
Robert Schnabel 
Research Associate Professor 
University of Missouri-Columbia 
Animal Sciences Unit, Rm.162 
920 East Campus Drive 
Columbia, MO 65211-5300 
Phone: 573-884-4106 
Fax:   573-882-6827 
http://animalgenomics.missouri.edu 
************************************************* 

From igi2cornell.edu  Tue Feb 26 20:46:38 2013 
From: Ikhide Imumorin <igi2cornell.edu> 
Subject: RE: Compulsory OAP will cause an even larger increase in publishing  
Postmaster: submission approved 
To: Multiple Recipients of <angenmapanimalgenome.org> 
Date: Tue, 26 Feb 2013 20:46:38 -0600 

I think Robert made a point but he is comparing apples and oranges. If
Apple, Intel, AMD, IBM etc contacts you to do something for them such as
develop a new software or consult on a project, they WILL NEVER suggest
that you do stuff for them for free. Why? Because they are for-profit
commercial companies who create value through services and products which
they sell to MAKE MONEY. But when a journal asks you to review and edit a
manuscript, you do not get paid for doing it, but the finished product is
sold by the publisher to make money. How is that not free labor? In fact it
gets worse... the scientists also pay to read the work they helped
produce!!

Even writing book chapters for publishers is the same thing. I think the
publishing system has hijacked our need to "publish or perish" and is using
it against us. A well known scientific publisher recently published a book
that I contributed a chapter to, but I never got any compensation, except
that my peers can read the book chapter and it is listed in my CV and may
help my promotion and reputation. In a balanced and fair world, I should
get a small royalty check in the mail. Do people write books for Random
House, Penguin, Macmillan-Palmgrave, Harper-Collins etc for free? Only in
academia is it glorified to work for free... yet compared to our long
education and skills, we are not even that well paid to begin with!!

If care is not taken, we may see a reverse move back to journals that do
not charge to publish, but charge to read (think Cambridge University
Press, Elsevier, Springer). After all, if you think the research is
important enough to you, pay to read it. Society has already provided
grants to do the research and now also paying for it to be read, all the
while society is subsiding commercial companies or "non profit" publishers
who are actually making money off our sweat. As things stand now, only rich
labs can afford to publish in many of these OA journals and it leads to the
rich getting richer and the poor getting poorer... kind of a self-
fulfilling prophecy.

I want to suggest a model where scientific publishers treat scientists
fairly and evenly, for without our work product (research papers) and our
labor (reviewing and editing), they will not exist. It is not that hard to
compensate us for what we do in kind that is reasonable and fair. For each
paper you review, you get something off publishing your own paper, and
after so many papers, you get to publish a paper free. How many times have
you received what borders on harassing emails from a journal editor about
not responding to a review invitation or sending in your review by the
deadline, and you are thinking, "I am busy man, I don't even get paid for
doing this!" What I propose is not hard and it will not stop them from
making profits.

As an illustration of what I am talking about, a few years I was contacted
by a well known academic publisher to contribute to the Solutions Manual
for a well known general genetics textbook. The work took a month or so to
do and I got a check for $3,000. That is how life is supposed to work.

I rest my case...

 
 
Ikhide Imumorin, PhD 
Assistant Professor 
Animal Breeding, Genetics and Genomics Group 
Dept of Animal Science 
267 Morrison Hall 
Cornell University 
Ithaca, NY 14853 
USA 
T 607-255-2850 
F 607-255-9829 
igi2cornell.edu 

http://www.ansci.cornell.edu/faculty/imumorin.html

Editorial Board, Journal of Veterinary Science and Medical Diagnosis -
http://www.scitechnol.com/jvsmdhome.php Associate Editor, Genomics and
Quantitative Genetics - http://www.knoblauchpublishing.com Associate
Editor, Journal of Applied Animal Research -
http://www.tandf.co.uk/journals/TAAR Review Editor, Frontiers in Genetics -
http://www.frontiersin.org/genetics

"So why not go out on a limb, isn't that where the fruit is?" - Frank
Scully

 
 
 
________________________________________ 
.From: Daniel Gianola [gianolaansci.wisc.edu] 
.Sent: Tuesday, February 26, 2013 6:30 PM 
.To: Multiple Recipients of <AnGenMapanimalgenome.org> 
.Subject: RE: Compulsory OAP will cause an even larger increase in publishing 

 
Robert, 

Do you write apps for free for smart phones, or internal code? Well, we do
contribute significantly to the journals via material (imagine, if the
hypothetical "Columbia, Missouri" post would not pay its columnists), or
via reviews (imagine if the New York Times Review of Books would not pay
its reviewers). This was well articulated by Miguel.

There is room for a more balance approached.

Regards,

Daniel
________________________________________ 
.From: Schnabel, Robert D. [schnabelrmissouri.edu] 
.Sent: Tuesday, February 26, 2013 5:09 PM 
.To: Multiple Recipients of <AnGenMapanimalgenome.org> 
.Subject: RE: Compulsory OAP will cause an even larger increase in publishing 

I have to chime in here. I think recent post discussing publisher profits
are misguided. What difference does it make if a publisher makes a dollar
or a billion? Intel, AMD and Apple make large profits but I don't hear any
outcry about the price of your computers which you rely upon to do your
research. Illumina does alright but I don't hear anyone proposing to write
a letter to someone complaining about the price of snp chips or sequencing
reagents citing Illumina's profit margins. If you want to make a case for
the problem of increasing publishing costs don't bring in "fairness" and
publishers profits. You'll get much more traction if you present a coherent
case and more importantly a solution.

Bob

************************************************* 
Robert Schnabel 
Research Associate Professor 
University of Missouri-Columbia 
Animal Sciences Unit, Rm.162 
920 East Campus Drive 
Columbia, MO 65211-5300 
Phone: 573-884-4106 
Fax:   573-882-6827 
http://animalgenomics.missouri.edu 
************************************************* 

From igi2cornell.edu  Tue Feb 26 21:08:15 2013
From: Ikhide Imumorin <igi2cornell.edu>
Subject: RE: Compulsory OAP will cause an even larger increase in publishing 
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Tue, 26 Feb 2013 21:08:15 -0600

I am passionate about this issue because in the past year, I have been 
invited to review manuscripts by Animal Genetics, Journal of Animal Science, 
Physiological Genomics, Frontiers in Genetics, Tropical Animal Health and 
Production, Livestock Science, PLos Pathogens, Journal of Animal Science and 
Biotechnology, BMC Genomics, Journal of Structural and Functional Genomics, 
Journal of Proteomics and Bioinformatics and African Journal of 
Biotechnology. But I did not agree to every single request, because my time 
is limited and I sure do not get paid to spend valuable time reviewing all 
these papers.


Ikhide Imumorin, PhD
Assistant Professor
Animal Breeding, Genetics and Genomics Group
Dept of Animal Science
267 Morrison Hall
Cornell University
Ithaca, NY 14853
USA
T 607-255-2850
F 607-255-9829
igi2cornell.edu

http://www.ansci.cornell.edu/faculty/imumorin.html

Editorial Board, Journal of Veterinary Science and Medical Diagnosis
 - http://www.scitechnol.com/jvsmdhome.php
Associate Editor, Genomics and Quantitative Genetics
 - http://www.knoblauchpublishing.com
Associate Editor, Journal of Applied Animal Research
 - http://www.tandf.co.uk/journals/TAAR
Review Editor, Frontiers in Genetics - http://www.frontiersin.org/genetics

"So why not go out on a limb, isn't that where the fruit is?" - Frank Scully


________________________________________
.From: Marina Fortes [m.fortesuq.edu.au]
.Sent: Tuesday, February 26, 2013 9:45 PM
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: RE: Compulsory OAP will cause an even larger increase in publishing


Only the past 2 weeks I have volunteered my time to Animal Genetics, BMC 
genetics and Theriogenology (and I know I don't get recruited as much as 
some of you). Therefore, I do agree with Daniel.


Marina R S Fortes
Post Doctoral Research Fellow
University of Queensland - QAAFI
Gatton bld 8114, room 314
Phone 61 7 54601969
Mobile 0431141617


-----Original Message-----
.From: Daniel Gianola [mailto:gianolaansci.wisc.edu]
.Sent: Wednesday, 27 February 2013 9:31 AM
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: RE: Compulsory OAP will cause an even larger increase in publishing

http://www.animalgenome.org/community/discuss ]

Robert,

Do you write apps for free for smart phones, or internal code? Well, we do 
contribute significantly to the journals via material (imagine, if the 
hypothetical "Columbia, Missouri" post would not pay its columnists), or via 
reviews (imagine if the New York Times Review of Books would not pay its 
reviewers). This was well articulated by Miguel.

There is room for a more balance approached.

Regards,

Daniel
________________________________________
.From: Schnabel, Robert D. [schnabelrmissouri.edu]
.Sent: Tuesday, February 26, 2013 5:09 PM
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: RE: Compulsory OAP will cause an even larger increase in publishing

I have to chime in here. I think recent post discussing publisher profits 
are misguided. What difference does it make if a publisher makes a dollar or 
a billion? Intel, AMD and Apple make large profits but I don't hear any 
outcry about the price of your computers which you rely upon to do your 
research. Illumina does alright but I don't hear anyone proposing to write 
a letter to someone complaining about the price of snp chips or sequencing 
reagents citing Illumina's profit margins. If you want to make a case for 
the problem of increasing publishing costs don't bring in "fairness" and 
publishers profits. You'll get much more traction if you present a coherent 
case and more importantly a solution.

Bob

*************************************************
Robert Schnabel
Research Associate Professor
University of Missouri-Columbia
Animal Sciences Unit, Rm.162
920 East Campus Drive
Columbia, MO 65211-5300
Phone: 573-884-4106
Fax:   573-882-6827
http://animalgenomics.missouri.edu
*************************************************




From PSamollowcvm.tamu.edu  Tue Feb 26 21:40:55 2013
From: "Samollow, Paul" <PSamollowcvm.tamu.edu>
Subject: Re: Compulsory OAP will cause an even larger increase in publishing  
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Tue, 26 Feb 2013 21:40:55 -0600

I agree with Bob - publishers must make a profit to stay in business, and
carping about how much someone has to pay to publish in these journals, or
how much profit the journal make, misses the point. But I don't believe his
examples are relevant to question here. We are not tapped by Apple or Intel
or AMD to give them free services. The situation with OA journals is
different.

OA journals are a new phenomenon; but we've always had to pay page charges.
The fundamental difference with OA journals is that in traditional
publications consumers payed something for the product, and that defrayed
part of the cost and yielded more profit), but now it is the manufacturer
(investigator) who pays the whole bill. The issue is that we have the
expertise the publishers need and they get it for free. So, the question is
- should they pay for our expertise or not? Or more bluntly, should
reviewer remuneration be a cost of business for publishers? Traditionally
it has not been; we pitch in for the common good. But maybe those days are
over.

Paul

 
Paul B. Samollow, Ph.D. 
Professor 
------------------------------------------------------------------------------
Postal address: 
Department of Veterinary Integrative Biosciences 
4458 TAMU 
Texas A&M University 
College Station, TX  77843-4458 

Express/Courier address: Department of Veterinary Integrative Biosciences
VMA Building, Room 107 Texas A&M University College Station, TX 77843-4458

Phone: 979 845-7095

FAX: 979 845-9972 Email: psamollowcvm.tamu.edu
------------------------------------------------------------------------------
 
 
On Feb 26, 2013, at 5:09 PM, Schnabel, Robert D. wrote: 

I have to chime in here. I think recent post discussing publisher profits
are misguided. What difference does it make if a publisher makes a dollar
or a billion? Intel, AMD and Apple make large profits but I don't hear any
outcry about the price of your computers which you rely upon to do your
research. Illumina does alright but I don't hear anyone proposing to write
a letter to someone complaining about the price of snp chips or sequencing
reagents citing Illumina's profit margins. If you want to make a case for
the problem of increasing publishing costs don't bring in "fairness" and
publishers profits. You'll get much more traction if you present a coherent
case and more importantly a solution.

Bob

************************************************* 
Robert Schnabel 
Research Associate Professor 
University of Missouri-Columbia 
Animal Sciences Unit, Rm.162 
920 East Campus Drive 
Columbia, MO 65211-5300 
Phone: 573-884-4106 
Fax:   573-882-6827 
http://animalgenomics.missouri.edu 
************************************************* 

 
-----Original Message----- 
.From: WILSON Andrea [mailto:andrea.wilsonroslin.ed.ac.uk] 
.Sent: Tuesday, February 26, 2013 4:37 PM 
.To: Multiple Recipients of <AnGenMapanimalgenome.org> 
.Subject: RE: Compulsory OAP will cause an even larger increase in publishing 

Dear colleagues,

I would support an alarm letter as proposed by Ikhide as the current
situation seems unfair to me. It may strengthen our argument if we knew how
much profit (if any) a journal makes on average per OA article. Does
anybody in the community know?

Best wishes Andrea

 
-----Original Message----- 
.From: Ikhide Imumorin [mailto:igi2cornell.edu] 
.Sent: 26 February 2013 17:21 
.To: Multiple Recipients of <AnGenMapanimalgenome.org> 
.Subject: RE: Compulsory OAP will cause an even larger increase in publishing fees 

Dear Colleagues, I totally agree with Miguel on this issue. If journals,
especially OA journals will charge all these exorbitant fees for publishing
papers to be read freely, then editors and reviewers should be paid in
cash, but preferably in kind. For example BMC Ltd can institute a policy
that say you get a discount (say 25% off) your next paper if you review a
paper, and if you review this many papers per year, you get to publish one
paper for free. As it stands now scientists are used to do all the heavy
lifting of judging the science of their peers for free... and the only ones
making money from this whole thing is the companies... whether OA or not.

Will publishers step up to the plate and do the right thing? If the next
time you get a paper from a journal and you decline reviewing it, aren't we
all busy? or you ask for some kind of compensation in the form of discount
in publishing in that journal, a new movement that help us scientists might
be born. The process of scientific publishing depends on peer review, but
that job right now is unpaid and burdensome. After you have reviewed a few
papers for a journal and you can put that in your CV under "Professional
Service", is there any incentive to do any more for that journal?

Compulsory OA publishing will inflate publishing fees to the point where
grant agencies will be forced to devote a significant portion to
publication fees. Soon you may have to include as much as $30,000 to your
application to NIH/NSF/USDA etc for a 4 year project for publication
charges. This is quite possible for large projects that may publish as many
as 10 papers from a project since some OA journals cost as much as $3,000!
Is the cost of publishing a paper on a Web platform really that high? Most
new generation OA journals do not have hard copies and most of the
publishing operations are automated by sophisticated software. I know
establishing such tools cannot be cheap, but that is usually part of the
upfront costs to get things started. Once it is up and running, it mostly
just need only modest management and maintenance.

I am on board with doing a letter with others to sound the alarm on this
problem.

Regards, Ikhide

 
Ikhide Imumorin, PhD 
Assistant Professor 
Animal Breeding, Genetics and Genomics Group Dept of Animal Science 
267 Morrison Hall 
Cornell University 
Ithaca, NY 14853 
USA 
T 607-255-2850 
F 607-255-9829 
igi2cornell.edu 

http://www.ansci.cornell.edu/faculty/imumorin.html

Editorial Board, Journal of Veterinary Science and Medical Diagnosis -
http://www.scitechnol.com/jvsmdhome.php Associate Editor, Genomics and
Quantitative Genetics - http://www.knoblauchpublishing.com Associate
Editor, Journal of Applied Animal Research -
http://www.tandf.co.uk/journals/TAAR Review Editor, Frontiers in Genetics -
http://www.frontiersin.org/genetics

"So why not go out on a limb, isn't that where the fruit is?" - Frank
Scully

 
________________________________________ 
.From: Miguel Perez-Enciso [miguel.perezuab.cat] 
.Sent: Tuesday, February 26, 2013 8:42 AM 
.To: Multiple Recipients of <AnGenMapanimalgenome.org> 
.Subject: Compulsory OAP will cause an even larger increase in publishing fees 

Dear authors

I agree with paying for publishing. As I see it, the two main questions are
whether publishing fees are fair and whether reviewers and editors should
charge for their work to publishers, either in kind or in cash. Under a
normal economic model, you could choose between the most competitive offer
but we are limited by the impact factor, on which our careers depend in
part.

I am afraid that policies making obligatory OAP will cause an inflationary
process in publishing fees. The idea of making tax payers get what they pay
for taxes is very reasonable, that of giving profit to private companies
per se, not so much. So, the state is responsible for paying a MAXIMUM for
publishing fees, the amount that should cover accountable costs excluding
profit. This will be reasonable and will help control quasi monopolies. It
would be great that these same 65,000 people sign a letter in these terms.

To summarise, publishing is a big business and we are getting a tiny part
with much effort. Reviewing and editing should be paid.

PS 1: I disclose also that I am editor of J Anim Breed Genet, a journal
with policies similar to those of Animal Genetics. At least in this case, I
am paid a small amount and get a discount on books from the publisher.

PS 2: I offer myself to write a letter to Obama and Cameron as well (via
Nature or Science) warning him of the inflationary dangers of compulsory
OAP and recommending to pay only for actual costs - not profit part. If
anyone is willing to help, please email me and we shall write something
that could be distributed to the rest of communities and submitted to any
or both of these journals.

Miguel

El 26/02/2013 1:25, Daniel Gianola escribi: > We may get help from the US
Government. This article was published in the New York Times on February
22. Regards. Daniel

U.S. Moves to Provide Quicker Access to Publicly Financed Scientific
Research By KENNETH CHANG

Published: February 22, 2013

If you paid for it, you should be able to read it. For publicly financed
ience research, the Obama administration agrees.

In a memorandum issued on Friday, John P. Holdren, science adviser to
resident Obama, called for scientific papers that report the results of
federally financed research to become freely accessible within a year or so
after publication. The findings are typically published in scientific
journals, many of which are open only to paying subscribers.

The new policy would apply to federal agencies, including the National
Science Foundation, the Department of Energy and the Department of
Agriculture, that finance more than $100 million a year of research. The
agencies have six months to submit plans for how they would carry out the
new policy.

The hope is that broad access to scientific results will encourage faster
progress on research and will let anyone apply the knowledge for
technological advances.

"We have seen, over the last 15 years, in the era of the Internet, that the
more widely available a publication is, the more likely it is to be cited
and the more likely it is to be used in patent applications," said Myron
Gutmann, an assistant director at the National Science Foundation.

"We know that the small and medium enterprise, the business community,
doesn't have a lot of access to scientific publications right now," Dr.
Gutmann said, "and the more we can make things available for those
communities, the more innovation there is likely to be." He estimated that
25,000 to 40,000 journal articles based on research financed by the science
foundation are published annually.

At the Agriculture Department, Catherine Woteki, the agency's chief
scientist, said the new policy fit in with efforts to make agriculture data
like plant genomes more widely available. "We can reduce in half the time
that it takes for breeding drought- and pest- and disease- resistant
crops," she said.

The agencies could model their policies on one established by the National
Institutes of Health in 2008. The N.I.H. requires scientists receiving
grants to ensure that their papers can be made available on PubMed Central,
a publicly available Web site, within one year.

An online petition last May on the White House's Web site called for "free
access over the Internet to scientific journal articles arising from
taxpayer-funded research."

More than 65,000 people signed the petition, easily passing the 25,000-
signature threshold that merited an official White House response. (The
threshold was raised in January to 100,000 after a petition that called for
building a Death Star like that in the movie "Star Wars" garnered 34,435
signatures; administration officials rejected that suggestion.)

In a response posted Friday to the signers of the open-access petitioners,
Dr. Holdren agreed.

"Americans should have easy access to the results of the research they help
support," Dr. Holden wrote, adding, "the logic behind enhanced access is
plain."

A version of this article appeared in print on February 23, 2013, on page
A9 of the New York edition with the headline: U.S. Moves to Provide Quicker
Access to Publicly Financed Scientific Research.

-- 
=============================================================== 
Miguel Perez-Enciso 
ICREA professor 
Centre for Research in Agricultural Genomics (CRAG) and Facultat de Veterinaria 
UAB Campus Universitat Autonoma Barcelona Bellaterra 
E-08193 Spain 
Tel: +34 935636600 ext 3346 
Fax: +34 935636601 
miguel.perezuab.es 
http://www.icrea.cat/...cStaff/Miguel-Perez-Enciso-255 
http://bioinformatics.cragenomica.es/numgenomics/ 
================================================================ 

From igi2cornell.edu  Tue Feb 26 21:55:42 2013
From: Ikhide Imumorin <igi2cornell.edu>
Subject: RE: Compulsory OAP will cause an even larger increase in publishing
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Tue, 26 Feb 2013 21:55:42 -0600

I totally agree with Paul Samollow. No one says for profit companies should not
make a profit, or "non-profit" ones should not recover the cost of doing business
under the OA model and then some. Even in the old model before OA, it was still
wrong that scientists did all the heavy lifting and the publishers made all the
profit. It is even more wrong now with the flattening of the world brought about
by software and the Internet. They used to incur cost of mailing manuscripts to
reviewers along with a pre-paid envelope to send it back, but now it is all
online and automated... 

The point is, in this new world, it is no longer cool to get something for free
then sell it for profit.  Publishers should do the right thing and pay scientists
for reviewing and editing papers and books. We can have a conversation about how
to calibrate that payment but simply using us to make profit is not right. I have
already proposed a simple and relatively cheap way for the publishers to step up.
Establish a quid-pro-quo for reviewing/editing papers such that it incentivizes
it for scientists and create a more equitable and just environment for all. They
make their profit, scientists feel less used and get at least something for what
is essentially slave labor right now, and everyone is happy... what is wrong with
that? How can anyone have a problem with that?


Ikhide Imumorin, PhD
Assistant Professor
Animal Breeding, Genetics and Genomics Group
Dept of Animal Science
267 Morrison Hall
Cornell University
Ithaca, NY 14853
USA
T 607-255-2850
F 607-255-9829
igi2cornell.edu

http://www.ansci.cornell.edu/faculty/imumorin.html

Editorial Board, Journal of Veterinary Science and Medical Diagnosis -
http://www.scitechnol.com/jvsmdhome.php
Associate Editor, Genomics and Quantitative Genetics -
http://www.knoblauchpublishing.com
Associate Editor, Journal of Applied Animal Research -
http://www.tandf.co.uk/journals/TAAR
Review Editor, Frontiers in Genetics - http://www.frontiersin.org/genetics

"So why not go out on a limb, isn't that where the fruit is?" - Frank Scully


________________________________________
.From: Samollow, Paul [PSamollowcvm.tamu.edu]
.Sent: Tuesday, February 26, 2013 10:40 PM
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: Re: Compulsory OAP will cause an even larger increase in publishing

I agree with Bob - publishers must make a profit to stay in business, and
carping about how much someone has to pay to publish in these journals, or
how much profit the journal make, misses the point. But I don't believe his
examples are relevant to question here. We are not tapped by Apple or Intel
or AMD to give them free services. The situation with OA journals is
different.

OA journals are a new phenomenon; but we've always had to pay page charges.
The fundamental difference with OA journals is that in traditional
publications consumers payed something for the product, and that defrayed
part of the cost and yielded more profit), but now it is the manufacturer
(investigator) who pays the whole bill. The issue is that we have the
expertise the publishers need and they get it for free. So, the question is
- should they pay for our expertise or not? Or more bluntly, should
reviewer remuneration be a cost of business for publishers? Traditionally
it has not been; we pitch in for the common good. But maybe those days are
over.

Paul


Paul B. Samollow, Ph.D.
Professor
---------------------------------------------------------------------------------
Postal address:
Department of Veterinary Integrative Biosciences
4458 TAMU
Texas A&M University
College Station, TX  77843-4458

Express/Courier address: Department of Veterinary Integrative Biosciences
VMA Building, Room 107 Texas A&M University College Station, TX 77843-4458

Phone: 979 845-7095

FAX: 979 845-9972 Email: psamollowcvm.tamu.edu
---------------------------------------------------------------------------------


On Feb 26, 2013, at 5:09 PM, Schnabel, Robert D. wrote:

I have to chime in here. I think recent post discussing publisher profits
are misguided. What difference does it make if a publisher makes a dollar
or a billion? Intel, AMD and Apple make large profits but I don't hear any
outcry about the price of your computers which you rely upon to do your
research. Illumina does alright but I don't hear anyone proposing to write
a letter to someone complaining about the price of snp chips or sequencing
reagents citing Illumina's profit margins. If you want to make a case for
the problem of increasing publishing costs don't bring in "fairness" and
publishers profits. You'll get much more traction if you present a coherent
case and more importantly a solution.

Bob

*************************************************
Robert Schnabel
Research Associate Professor
University of Missouri-Columbia
Animal Sciences Unit, Rm.162
920 East Campus Drive
Columbia, MO 65211-5300
Phone: 573-884-4106
Fax:   573-882-6827
http://animalgenomics.missouri.edu
*************************************************


-----Original Message-----
.From: WILSON Andrea [mailto:andrea.wilsonroslin.ed.ac.uk]
.Sent: Tuesday, February 26, 2013 4:37 PM
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: RE: Compulsory OAP will cause an even larger increase in publishing

Dear colleagues,

I would support an alarm letter as proposed by Ikhide as the current
situation seems unfair to me. It may strengthen our argument if we knew how
much profit (if any) a journal makes on average per OA article. Does
anybody in the community know?

Best wishes Andrea


-----Original Message-----
.From: Ikhide Imumorin [mailto:igi2cornell.edu]
.Sent: 26 February 2013 17:21
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: RE: Compulsory OAP will cause an even larger increase in publishing fees

Dear Colleagues, I totally agree with Miguel on this issue. If journals,
especially OA journals will charge all these exorbitant fees for publishing
papers to be read freely, then editors and reviewers should be paid in
cash, but preferably in kind. For example BMC Ltd can institute a policy
that say you get a discount (say 25% off) your next paper if you review a
paper, and if you review this many papers per year, you get to publish one
paper for free. As it stands now scientists are used to do all the heavy
lifting of judging the science of their peers for free... and the only ones
making money from this whole thing is the companies... whether OA or not.

Will publishers step up to the plate and do the right thing? If the next
time you get a paper from a journal and you decline reviewing it, aren't we
all busy? or you ask for some kind of compensation in the form of discount
in publishing in that journal, a new movement that help us scientists might
be born. The process of scientific publishing depends on peer review, but
that job right now is unpaid and burdensome. After you have reviewed a few
papers for a journal and you can put that in your CV under "Professional
Service", is there any incentive to do any more for that journal?

Compulsory OA publishing will inflate publishing fees to the point where
grant agencies will be forced to devote a significant portion to
publication fees. Soon you may have to include as much as $30,000 to your
application to NIH/NSF/USDA etc for a 4 year project for publication
charges. This is quite possible for large projects that may publish as many
as 10 papers from a project since some OA journals cost as much as $3,000!
Is the cost of publishing a paper on a Web platform really that high? Most
new generation OA journals do not have hard copies and most of the
publishing operations are automated by sophisticated software. I know
establishing such tools cannot be cheap, but that is usually part of the
upfront costs to get things started. Once it is up and running, it mostly
just need only modest management and maintenance.

I am on board with doing a letter with others to sound the alarm on this
problem.

Regards, Ikhide


Ikhide Imumorin, PhD
Assistant Professor
Animal Breeding, Genetics and Genomics Group Dept of Animal Science
267 Morrison Hall
Cornell University
Ithaca, NY 14853
USA
T 607-255-2850
F 607-255-9829
igi2cornell.edu

http://www.ansci.cornell.edu/faculty/imumorin.html

Editorial Board, Journal of Veterinary Science and Medical Diagnosis -
http://www.scitechnol.com/jvsmdhome.php Associate Editor, Genomics and
Quantitative Genetics - http://www.knoblauchpublishing.com Associate
Editor, Journal of Applied Animal Research -
http://www.tandf.co.uk/journals/TAAR Review Editor, Frontiers in Genetics -
http://www.frontiersin.org/genetics

"So why not go out on a limb, isn't that where the fruit is?" - Frank
Scully


________________________________________
.From: Miguel Perez-Enciso [miguel.perezuab.cat]
.Sent: Tuesday, February 26, 2013 8:42 AM
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: Compulsory OAP will cause an even larger increase in publishing fees

Dear authors

I agree with paying for publishing. As I see it, the two main questions are
whether publishing fees are fair and whether reviewers and editors should
charge for their work to publishers, either in kind or in cash. Under a
normal economic model, you could choose between the most competitive offer
but we are limited by the impact factor, on which our careers depend in
part.

I am afraid that policies making obligatory OAP will cause an inflationary
process in publishing fees. The idea of making tax payers get what they pay
for taxes is very reasonable, that of giving profit to private companies
per se, not so much. So, the state is responsible for paying a MAXIMUM for
publishing fees, the amount that should cover accountable costs excluding
profit. This will be reasonable and will help control quasi monopolies. It
would be great that these same 65,000 people sign a letter in these terms.

To summarise, publishing is a big business and we are getting a tiny part
with much effort. Reviewing and editing should be paid.

PS 1: I disclose also that I am editor of J Anim Breed Genet, a journal
with policies similar to those of Animal Genetics. At least in this case, I
am paid a small amount and get a discount on books from the publisher.

PS 2: I offer myself to write a letter to Obama and Cameron as well (via
Nature or Science) warning him of the inflationary dangers of compulsory
OAP and recommending to pay only for actual costs - not profit part. If
anyone is willing to help, please email me and we shall write something
that could be distributed to the rest of communities and submitted to any
or both of these journals.

Miguel

El 26/02/2013 1:25, Daniel Gianola escribi: > We may get help from the US
Government. This article was published in the New York Times on February
22. Regards. Daniel

U.S. Moves to Provide Quicker Access to Publicly Financed Scientific
Research By KENNETH CHANG

Published: February 22, 2013

If you paid for it, you should be able to read it. For publicly financed
ience research, the Obama administration agrees.

In a memorandum issued on Friday, John P. Holdren, science adviser to
resident Obama, called for scientific papers that report the results of
federally financed research to become freely accessible within a year or so
after publication. The findings are typically published in scientific
journals, many of which are open only to paying subscribers.

The new policy would apply to federal agencies, including the National
Science Foundation, the Department of Energy and the Department of
Agriculture, that finance more than $100 million a year of research. The
agencies have six months to submit plans for how they would carry out the
new policy.

The hope is that broad access to scientific results will encourage faster
progress on research and will let anyone apply the knowledge for
technological advances.

"We have seen, over the last 15 years, in the era of the Internet, that the
more widely available a publication is, the more likely it is to be cited
and the more likely it is to be used in patent applications," said Myron
Gutmann, an assistant director at the National Science Foundation.

"We know that the small and medium enterprise, the business community,
doesn't have a lot of access to scientific publications right now," Dr.
Gutmann said, "and the more we can make things available for those
communities, the more innovation there is likely to be." He estimated that
25,000 to 40,000 journal articles based on research financed by the science
foundation are published annually.

At the Agriculture Department, Catherine Woteki, the agency's chief
scientist, said the new policy fit in with efforts to make agriculture data
like plant genomes more widely available. "We can reduce in half the time
that it takes for breeding drought- and pest- and disease- resistant
crops," she said.

The agencies could model their policies on one established by the National
Institutes of Health in 2008. The N.I.H. requires scientists receiving
grants to ensure that their papers can be made available on PubMed Central,
a publicly available Web site, within one year.

An online petition last May on the White House's Web site called for "free
access over the Internet to scientific journal articles arising from
taxpayer-funded research."

More than 65,000 people signed the petition, easily passing the 25,000-
signature threshold that merited an official White House response. (The
threshold was raised in January to 100,000 after a petition that called for
building a Death Star like that in the movie "Star Wars" garnered 34,435
signatures; administration officials rejected that suggestion.)

In a response posted Friday to the signers of the open-access petitioners,
Dr. Holdren agreed.

"Americans should have easy access to the results of the research they help
support," Dr. Holden wrote, adding, "the logic behind enhanced access is
plain."

A version of this article appeared in print on February 23, 2013, on page
A9 of the New York edition with the headline: U.S. Moves to Provide Quicker
Access to Publicly Financed Scientific Research.

--
===============================================================
Miguel Perez-Enciso
ICREA professor
Centre for Research in Agricultural Genomics (CRAG) and Facultat de Veterinaria
UAB Campus Universitat Autonoma Barcelona Bellaterra
E-08193 Spain
Tel: +34 935636600 ext 3346
Fax: +34 935636601
miguel.perezuab.es
http://www.icrea.cat/...cStaff/Miguel-Perez-Enciso-255
http://bioinformatics.cragenomica.es/numgenomics/
================================================================



  

From msargoluoguelph.ca  Tue Feb 26 22:13:51 2013
From: Mehdi Sargolzaei <msargoluoguelph.ca>
Subject: Re: Compulsory OAP will cause an even larger increase in publishing
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Tue, 26 Feb 2013 22:13:51 -0600

Last year Larry Schaeffer proposed "You-Pub" idea, which potentially can
eliminate publishing and access costs. So I forward his email for those
interested.

However, I don't think this is going to change things quickly. The system
should be set up and works for few years to attract enough attention if
successful.

-- 
Mehdi Sargolzaei
Research Genomist
Boviteq Alliance
Adjunct Professor
University of Guelph
Tel: +1 519-824-4120 Ext. 52482
Fax: +1 519-836-9873


-------- Original Message --------
.Subject: 	[AGDG-LIST:1230] You-Pub
.Date: 	Fri, 06 Jul 2012 15:55:29 -0400
.From: 	Larry Schaeffer <lrsuoguelph.ca>
.Reply-To: 	lrsuoguelph.ca
.To: 	Animal Geneticist's Discussion <agdg-listcolostate.edu>

Promotion and Tenure Committees have forced the academic world into a
peer-reviewed journal system in order to decide promotion and tenure on
faculty.  Journals, therefore, feel compelled to have reviewers judge
the adequacy of each submission, based on reviewer biases and prejudices
of which there may be lots or little depending on the reviewer.
Journals find it ever increasingly difficult to find suitable reviewers,
and reviewers have trouble finding time to spend on the review process.
The on-line systems, however, allow the review process to be speedy.

Alas, I propose "You-Pub", a website where you submit .pdf manuscripts
the way you, the authors, want to see them presented. If you submit
garbage, then garbage will appear, but will likely not be read.  The
website allows anyone to view the submissions by date, author, title,
subject matter, species, or latest ratings, latest submisstions.  After
reading a paper, a reader may give a short review and rating of the
paper (useful to useless, interesting to boring, correct to incorrect,
new to old hat).  The reviews are accumulated for a paper as well as the
ratings and an average presented (which can be seen by other visitors to
the website).  If, after a suitable period of time, a paper does not
receive any reviews or ratings, or if the reviews are below certain
norms, then it is removed from the site.  The better papers remain
available, and have a specific citation reference.  Papers with really
high ratings reach the permanent status and remain available
indefinitely.   First Authors can be given ratings based on the ratings
of their submitted papers.

There is no formal review process, there is no cost to submission, an
editor decides if the paper has appropriate subject matter for the
journal.  Length of papers is up to the authors.  Once set-up the site
takes care of itself.  There is no subscription fee or publication fee
or visitor fee.

I propose this for animal breeding and genetics, genomics, quantitative
genetics, theory, practical, computing papers,
any country, any languages.

If interested or not interested in the idea, then send me your
comments.  lrsuoguelph.ca

From m.fortesuq.edu.au  Wed Feb 27 07:40:09 2013
From: Marina Fortes <m.fortesuq.edu.au>
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Subject: RE: Compulsory OAP will cause an even larger increase in publishing
  - simple numbers
Date: Wed, 27 Feb 2013 07:40:09 -0600

BMC genetics charges 2055 dollars per paper published, they publish something
like 110-120 papers per year ~= 226K - 246K
They declare in their FAQ that Article-processing charges pay for:

- Immediate, worldwide open access to the full article text
- Developing and maintaining electronic tools for peer review and publication
- Preparation in various formats for online publication
- Securing inclusion in CrossRef, enabling electronic citation in other journals
  that are available electronically

They fail to mention that they employ 4 people in the Editorial team:
Executive Editor Simon Harold; Journal Development Manager Genevieve Horne;
Senior Managing Editor Diana Marshall; Publisher Jo Appleford-Cook.

I don't think this people work for free...

Jus to add some facts, or a case-study, to the discussion.

Regards,

Marina R S Fortes
Post Doctoral Research Fellow
University of Queensland - QAAFI
Gatton bld 8114, room 314
Phone 61 7 54601969
Mobile 0431141617


-----Original Message-----
.From: Matukumalli, Lakshmi [mailto:lmatukumallinifa.usda.gov] 
.Sent: Wednesday, 27 February 2013 2:13 PM
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: White house (OSTP) guidance on publications

Based on the on-going discussions ... I wanted to bring your attention to a few
recent announcements.

This may be applicable to US Scientists where the guidance on publications was
released this weekend.

http://www.whitehouse.gov/...ults-federally-funded-research
 
Based on the guidance there was an article in Washington post with comments from
USDA REE undersecretary,  Dr.Cathy Woteki. 

http://www.washingtonpost.com/...1a46c2cde3d_story.html?hpid=z2

Based on this guidance from OSTP, USDA is now developing its own policy based on
this guidance for both journal publications and research data.

The G8 Countries are participating as well in the open data initiative and are
meeting this April.

http://www.whitehouse.gov/...onference-open-data-agricultur
 
 
Lakshmi Kumar 

Lakshmi Kumar Matukumalli National Program Leader, Animal Breeding, Genetics and
Genomics National Institute of Food and Agriculture, USDA E-
mail: lmatukumallinifa.usda.gov Office: 202-401-1766 Cell: 202-841-6009
http://www.nifa.usda.gov

INVESTING IN SCIENCE | SECURING OUR FUTURE
  

From dj.dekoningroslin.ed.ac.uk  Wed Feb 27 07:41:05 2013
From: DE KONING DJ <dj.dekoningroslin.ed.ac.uk>
Subject: RE: Compulsory OAP will cause an even larger increase in publishing
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Wed, 27 Feb 2013 07:41:05 -0600

Dear All,

 I think there is another aspect in this whole discussion, which I raised when
Michael Eisen was doing his PLOS Rave at PAGXIX:
Many of the so-called "learned societies" depend on their subscription journals
to make enough money to fulfill their roles. If you think about Genetics, Animal
Genetics and Heredity, they all support great organizations that organize
meetings and support young scientists (GSA, ISAG and Genetics Society UK,
respectively). Only a fraction of the income (5% for Genetics Society UK) from
these societies comes from membership fees, the vast majority is journal income.
 If the subscription model disappears the societies will have to revise their
funding model entirely.

At present we can offer �750 travel scholarships to students who join for as
little as �10. This may well become a thing of the past. I for one feel quite
strongly about the role of learned societies to create communities, which
explains my list of COI: former associate editor of Animal Genetics, senior
editor of G3, Editorial board of Heredity and executive committee member of
Genetics Society UK.

For institutions, the only difference is that they shift from paying for
subscriptions toward paying for publishing. Unfortunately, all too often the bill
for the latter ends up on the researchers' plate, while the former was within the
institutional overheads.

DJ de Koning



________________________________________
.From: Ikhide Imumorin [igi2cornell.edu]
.Sent: 27 February 2013 03:55
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: RE: Compulsory OAP will cause an even larger increase in publishing

I totally agree with Paul Samollow. No one says for profit companies should not
make a profit, or "non-profit" ones should not recover the cost of doing business
under the OA model and then some. Even in the old model before OA, it was still
wrong that scientists did all the heavy lifting and the publishers made all the
profit. It is even more wrong now with the flattening of the world brought about
by software and the Internet. They used to incur cost of mailing manuscripts to
reviewers along with a pre-paid envelope to send it back, but now it is all
online and automated...

The point is, in this new world, it is no longer cool to get something for free
then sell it for profit.  Publishers should do the right thing and pay scientists
for reviewing and editing papers and books. We can have a conversation about how
to calibrate that payment but simply using us to make profit is not right. I have
already proposed a simple and relatively cheap way for the publishers to step up.
Establish a quid-pro-quo for reviewing/editing papers such that it incentivizes
it for scientists and create a more equitable and just environment for all. They
make their profit, scientists feel less used and get at least something for what
is essentially slave labor right now, and everyone is happy... what is wrong with
that? How can anyone have a problem with that?


Ikhide Imumorin, PhD
Assistant Professor
Animal Breeding, Genetics and Genomics Group
Dept of Animal Science
267 Morrison Hall
Cornell University
Ithaca, NY 14853
USA
T 607-255-2850
F 607-255-9829
igi2cornell.edu

http://www.ansci.cornell.edu/faculty/imumorin.html

Editorial Board, Journal of Veterinary Science and Medical Diagnosis -
http://www.scitechnol.com/jvsmdhome.php
Associate Editor, Genomics and Quantitative Genetics -
http://www.knoblauchpublishing.com
Associate Editor, Journal of Applied Animal Research -
http://www.tandf.co.uk/journals/TAAR
Review Editor, Frontiers in Genetics - http://www.frontiersin.org/genetics

"So why not go out on a limb, isn't that where the fruit is?" - Frank Scully


________________________________________
.From: Samollow, Paul [PSamollowcvm.tamu.edu]
.Sent: Tuesday, February 26, 2013 10:40 PM
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: Re: Compulsory OAP will cause an even larger increase in publishing

I agree with Bob - publishers must make a profit to stay in business, and
carping about how much someone has to pay to publish in these journals, or
how much profit the journal make, misses the point. But I don't believe his
examples are relevant to question here. We are not tapped by Apple or Intel
or AMD to give them free services. The situation with OA journals is
different.

OA journals are a new phenomenon; but we've always had to pay page charges.
The fundamental difference with OA journals is that in traditional
publications consumers payed something for the product, and that defrayed
part of the cost and yielded more profit), but now it is the manufacturer
(investigator) who pays the whole bill. The issue is that we have the
expertise the publishers need and they get it for free. So, the question is
- should they pay for our expertise or not? Or more bluntly, should
reviewer remuneration be a cost of business for publishers? Traditionally
it has not been; we pitch in for the common good. But maybe those days are
over.

Paul


Paul B. Samollow, Ph.D.
Professor
---------------------------------------------------------------------------------
Postal address:
Department of Veterinary Integrative Biosciences
4458 TAMU
Texas A&M University
College Station, TX  77843-4458

Express/Courier address: Department of Veterinary Integrative Biosciences
VMA Building, Room 107 Texas A&M University College Station, TX 77843-4458

Phone: 979 845-7095

FAX: 979 845-9972 Email: psamollowcvm.tamu.edu
---------------------------------------------------------------------------------


On Feb 26, 2013, at 5:09 PM, Schnabel, Robert D. wrote:

I have to chime in here. I think recent post discussing publisher profits
are misguided. What difference does it make if a publisher makes a dollar
or a billion? Intel, AMD and Apple make large profits but I don't hear any
outcry about the price of your computers which you rely upon to do your
research. Illumina does alright but I don't hear anyone proposing to write
a letter to someone complaining about the price of snp chips or sequencing
reagents citing Illumina's profit margins. If you want to make a case for
the problem of increasing publishing costs don't bring in "fairness" and
publishers profits. You'll get much more traction if you present a coherent
case and more importantly a solution.

Bob

*************************************************
Robert Schnabel
Research Associate Professor
University of Missouri-Columbia
Animal Sciences Unit, Rm.162
920 East Campus Drive
Columbia, MO 65211-5300
Phone: 573-884-4106
Fax:   573-882-6827
http://animalgenomics.missouri.edu
*************************************************



-- 

From miguel.perezuab.es  Wed Feb 27 07:41:39 2013
From: Miguel Perez-Enciso <miguel.perezuab.es>
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Subject: OA fees and Towards a referee factor index?
Date: Wed, 27 Feb 2013 07:41:39 -0600

Along the lines of Guilherme (by the way, Frontiers' fees are among the 
highest) a partial way to mitigate this publishing distortion would be 
to set a referees factor index which, like number of citations, would 
contain number of papers reviewed, and the number of citations received 
by each paper you recommended rejection and of those for which you 
recommended acceptance. This should be stratified by journal.

Over the years, many rejected papers become published, and can 
potentially be cited. If you are a bad referee, there will be no 
distinction among those rejected and accepted. On the other hand, if you 
are a 'good' referee journals will look for you insistently so you have 
have a right to be paid or get a discount, because journals want their 
papers to be cited or at least accessed.

Finally, if you know how many papers each of us review per year and in 
time, you can decline reviewing for a 'selfish but highly productive 
colleague' and explain that in the rejection letter. I promise to accept 
reviewing the next one by Ikhide!

Of course I am very well aware this or similar is VERY difficult to 
implement, particularly for privacy. I still believe anonymity is a good 
thing for critical unbiased assessements. Finally, it is very well 
possible to know to an extent how much profit a company is doing, so 
this does not preclude paying a fair part only to publishers, at least 
compulsorily.

Best

Miguel

El 27/02/2013 5:13, Mehdi Sargolzaei escribi:
>
> Last year Larry Schaeffer proposed "You-Pub" idea, which potentially can
> eliminate publishing and access costs. So I forward his email for those
> interested.
>
> However, I don't think this is going to change things quickly. The system
> should be set up and works for few years to attract enough attention if
> successful.
>


  

From anubhavgunagmail.com  Wed Feb 27 07:43:09 2013
From: "Anubhav  Jain" <anubhavgunagmail.com>
Subject: RE:Compulsory OAP will cause an even larger increase in publishing
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Wed, 27 Feb 2013 07:43:09 -0600

I do agree with Prof. Imumorin. The OA publishers are using the
Scientific community for editing/reviewing for FREE and charging the same
community for publishing their research work. In this way, researchers
are exploited in both ways.

The reviewers should be either paid or should be exempted from publishing
charge.

________________________________________
>From igi2cornell.edu  Tue Feb 26 21:55:42 2013
.From: Ikhide Imumorin <igi2cornell.edu>
.Subject: RE: Compulsory OAP will cause an even larger increase in publishing
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Date: Tue, 26 Feb 2013 21:55:42 -0600

I totally agree with Paul Samollow. No one says for profit companies should not
make a profit, or "non-profit" ones should not recover the cost of doing business
under the OA model and then some. Even in the old model before OA, it was still
wrong that scientists did all the heavy lifting and the publishers made all the
profit. It is even more wrong now with the flattening of the world brought about
by software and the Internet. They used to incur cost of mailing manuscripts to
reviewers along with a pre-paid envelope to send it back, but now it is all
online and automated...

The point is, in this new world, it is no longer cool to get something for free
then sell it for profit.  Publishers should do the right thing and pay scientists
for reviewing and editing papers and books. We can have a conversation about how
to calibrate that payment but simply using us to make profit is not right. I have
already proposed a simple and relatively cheap way for the publishers to step up.
Establish a quid-pro-quo for reviewing/editing papers such that it incentivizes
it for scientists and create a more equitable and just environment for all. They
make their profit, scientists feel less used and get at least something for what
is essentially slave labor right now, and everyone is happy... what is wrong with
that? How can anyone have a problem with that?


Ikhide Imumorin, PhD
Assistant Professor
Animal Breeding, Genetics and Genomics Group
Dept of Animal Science
267 Morrison Hall
Cornell University
Ithaca, NY 14853
USA
T 607-255-2850
F 607-255-9829
igi2cornell.edu

http://www.ansci.cornell.edu/faculty/imumorin.html

Editorial Board, Journal of Veterinary Science and Medical Diagnosis -
http://www.scitechnol.com/jvsmdhome.php
Associate Editor, Genomics and Quantitative Genetics -
http://www.knoblauchpublishing.com
Associate Editor, Journal of Applied Animal Research -
http://www.tandf.co.uk/journals/TAAR
Review Editor, Frontiers in Genetics -
http://www.frontiersin.org/genetics

"So why not go out on a limb, isn't that where the fruit is?" - Frank
Scully

From Paul.Boettcherfao.org  Wed Feb 27 07:44:39 2013
From: "Boettcher, Paul (AGAG)" <Paul.Boettcherfao.org>
Subject: RE: Compulsory OAP will cause an even larger increase in publishing
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Wed, 27 Feb 2013 07:44:39 -0600

Dear all,

Thanks for the very interesting discussion.

However, it seems like one somewhat relevant point to consider is what our
employers think about this situation. I think it's safe to say that none of us is
working for free, so if our employers are aware that we are spending time
reviewing papers for for-profit journals and are fine with it (or even consider
it part of our job descriptions), then I guess we should be too. They may
actually think it's perfectly fine, assuming it decreases library costs, for
example. If they are simply unaware that this is going on, then we should write
to our respective administrators to alert them to the problem, rather than to the
various publishers.

Kind regards,
Paul Boettcher

-----Original Message-----
.From: Ikhide Imumorin [mailto:igi2cornell.edu]
.Sent: Wednesday, February 27, 2013 4:56 AM
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: RE: Compulsory OAP will cause an even larger increase in publishing

I totally agree with Paul Samollow. No one says for profit companies should not
make a profit, or "non-profit" ones should not recover the cost of doing business
under the OA model and then some. Even in the old model before OA, it was still
wrong that scientists did all the heavy lifting and the publishers made all the
profit. It is even more wrong now with the flattening of the world brought about
by software and the Internet. They used to incur cost of mailing manuscripts to
reviewers along with a pre-paid envelope to send it back, but now it is all
online and automated...

The point is, in this new world, it is no longer cool to get something for free
then sell it for profit.  Publishers should do the right thing and pay scientists
for reviewing and editing papers and books. We can have a conversation about how
to calibrate that payment but simply using us to make profit is not right. I have
already proposed a simple and relatively cheap way for the publishers to step up.

Establish a quid-pro-quo for reviewing/editing papers such that it incentivizes
it for scientists and create a more equitable and just environment for all. They
make their profit, scientists feel less used and get at least something for what
is essentially slave labor right now, and everyone is happy... what is wrong with
that? How can anyone have a problem with that?


Ikhide Imumorin, PhD
Assistant Professor
Animal Breeding, Genetics and Genomics Group Dept of Animal Science
267 Morrison Hall
Cornell University
Ithaca, NY 14853
USA
T 607-255-2850
F 607-255-9829
igi2cornell.edu

http://www.ansci.cornell.edu/faculty/imumorin.html

Editorial Board, Journal of Veterinary Science and Medical Diagnosis -
http://www.scitechnol.com/jvsmdhome.php
Associate Editor, Genomics and Quantitative Genetics -
http://www.knoblauchpublishing.com
Associate Editor, Journal of Applied Animal Research -
http://www.tandf.co.uk/journals/TAAR
Review Editor, Frontiers in Genetics - http://www.frontiersin.org/genetics

"So why not go out on a limb, isn't that where the fruit is?" - Frank Scully


________________________________________
.From: Samollow, Paul [PSamollowcvm.tamu.edu]
.Sent: Tuesday, February 26, 2013 10:40 PM
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: Re: Compulsory OAP will cause an even larger increase in publishing

I agree with Bob - publishers must make a profit to stay in business, and carping
about how much someone has to pay to publish in these journals, or how much
profit the journal make, misses the point. But I don't believe his examples are
relevant to question here. We are not tapped by Apple or Intel or AMD to give
them free services. The situation with OA journals is different.

OA journals are a new phenomenon; but we've always had to pay page charges.
The fundamental difference with OA journals is that in traditional publications
consumers payed something for the product, and that defrayed part of the cost and
yielded more profit), but now it is the manufacturer
(investigator) who pays the whole bill. The issue is that we have the expertise
the publishers need and they get it for free. So, the question is
- should they pay for our expertise or not? Or more bluntly, should reviewer
remuneration be a cost of business for publishers? Traditionally it has not been;
we pitch in for the common good. But maybe those days are over.

Paul


Paul B. Samollow, Ph.D.
Professor
---------------------------------------------------------------------------------
Postal address:
Department of Veterinary Integrative Biosciences
4458 TAMU
Texas A&M University
College Station, TX  77843-4458

Express/Courier address: Department of Veterinary Integrative Biosciences VMA
Building, Room 107 Texas A&M University College Station, TX 77843-4458

Phone: 979 845-7095

FAX: 979 845-9972 Email: psamollowcvm.tamu.edu
---------------------------------------------------------------------------------


On Feb 26, 2013, at 5:09 PM, Schnabel, Robert D. wrote:

I have to chime in here. I think recent post discussing publisher profits are
misguided. What difference does it make if a publisher makes a dollar or a
billion? Intel, AMD and Apple make large profits but I don't hear any outcry
about the price of your computers which you rely upon to do your research.
Illumina does alright but I don't hear anyone proposing to write a letter to
someone complaining about the price of snp chips or sequencing reagents citing
Illumina's profit margins. If you want to make a case for the problem of
increasing publishing costs don't bring in "fairness" and publishers profits.
You'll get much more traction if you present a coherent case and more importantly
a solution.

Bob

*************************************************
Robert Schnabel
Research Associate Professor
University of Missouri-Columbia
Animal Sciences Unit, Rm.162
920 East Campus Drive
Columbia, MO 65211-5300
Phone: 573-884-4106
Fax:   573-882-6827
http://animalgenomics.missouri.edu
*************************************************


-----Original Message-----
.From: WILSON Andrea [mailto:andrea.wilsonroslin.ed.ac.uk]
.Sent: Tuesday, February 26, 2013 4:37 PM
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: RE: Compulsory OAP will cause an even larger increase in publishing

Dear colleagues,

I would support an alarm letter as proposed by Ikhide as the current situation
seems unfair to me. It may strengthen our argument if we knew how much profit (if
any) a journal makes on average per OA article. Does anybody in the community know?

Best wishes Andrea


-----Original Message-----
.From: Ikhide Imumorin [mailto:igi2cornell.edu]
.Sent: 26 February 2013 17:21
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: RE: Compulsory OAP will cause an even larger increase in publishing fees

Dear Colleagues, I totally agree with Miguel on this issue. If journals,
especially OA journals will charge all these exorbitant fees for publishing
papers to be read freely, then editors and reviewers should be paid in cash, but
preferably in kind. For example BMC Ltd can institute a policy that say you get a
discount (say 25% off) your next paper if you review a paper, and if you review
this many papers per year, you get to publish one paper for free. As it stands
now scientists are used to do all the heavy lifting of judging the science of
their peers for free... and the only ones making money from this whole thing is
the companies... whether OA or not.

Will publishers step up to the plate and do the right thing? If the next time you
get a paper from a journal and you decline reviewing it, aren't we all busy? or
you ask for some kind of compensation in the form of discount in publishing in
that journal, a new movement that help us scientists might be born. The process
of scientific publishing depends on peer review, but that job right now is unpaid
and burdensome. After you have reviewed a few papers for a journal and you can
put that in your CV under "Professional Service", is there any incentive to do
any more for that journal?

Compulsory OA publishing will inflate publishing fees to the point where grant
agencies will be forced to devote a significant portion to publication fees. Soon
you may have to include as much as $30,000 to your application to NIH/NSF/USDA
etc for a 4 year project for publication charges. This is quite possible for
large projects that may publish as many as 10 papers from a project since some OA
journals cost as much as $3,000!
Is the cost of publishing a paper on a Web platform really that high? Most new
generation OA journals do not have hard copies and most of the publishing
operations are automated by sophisticated software. I know establishing such
tools cannot be cheap, but that is usually part of the upfront costs to get
things started. Once it is up and running, it mostly just need only modest
management and maintenance.

I am on board with doing a letter with others to sound the alarm on this problem.

Regards, Ikhide


Ikhide Imumorin, PhD
Assistant Professor
Animal Breeding, Genetics and Genomics Group Dept of Animal Science
267 Morrison Hall
Cornell University
Ithaca, NY 14853
USA
T 607-255-2850
F 607-255-9829
igi2cornell.edu

http://www.ansci.cornell.edu/faculty/imumorin.html

Editorial Board, Journal of Veterinary Science and Medical Diagnosis -
http://www.scitechnol.com/jvsmdhome.php Associate Editor, Genomics and
Quantitative Genetics - http://www.knoblauchpublishing.com Associate Editor,
Journal of Applied Animal Research - http://www.tandf.co.uk/journals/TAAR Review
Editor, Frontiers in Genetics - http://www.frontiersin.org/genetics

"So why not go out on a limb, isn't that where the fruit is?" - Frank Scully


________________________________________
.From: Miguel Perez-Enciso [miguel.perezuab.cat]
.Sent: Tuesday, February 26, 2013 8:42 AM
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: Compulsory OAP will cause an even larger increase in publishing fees

Dear authors

I agree with paying for publishing. As I see it, the two main questions are
whether publishing fees are fair and whether reviewers and editors should charge
for their work to publishers, either in kind or in cash. Under a normal economic
model, you could choose between the most competitive offer but we are limited by
the impact factor, on which our careers depend in part.

I am afraid that policies making obligatory OAP will cause an inflationary
process in publishing fees. The idea of making tax payers get what they pay for
taxes is very reasonable, that of giving profit to private companies per se, not
so much. So, the state is responsible for paying a MAXIMUM for publishing fees,
the amount that should cover accountable costs excluding profit. This will be
reasonable and will help control quasi monopolies. It would be great that these
same 65,000 people sign a letter in these terms.

To summarise, publishing is a big business and we are getting a tiny part with
much effort. Reviewing and editing should be paid.

PS 1: I disclose also that I am editor of J Anim Breed Genet, a journal with
policies similar to those of Animal Genetics. At least in this case, I am paid a
small amount and get a discount on books from the publisher.

PS 2: I offer myself to write a letter to Obama and Cameron as well (via Nature
or Science) warning him of the inflationary dangers of compulsory OAP and
recommending to pay only for actual costs - not profit part. If anyone is willing
to help, please email me and we shall write something that could be distributed
to the rest of communities and submitted to any or both of these journals.

Miguel

El 26/02/2013 1:25, Daniel Gianola escribi: > We may get help from the US
Government. This article was published in the New York Times on February 22.
Regards. Daniel

U.S. Moves to Provide Quicker Access to Publicly Financed Scientific Research By
KENNETH CHANG

Published: February 22, 2013

If you paid for it, you should be able to read it. For publicly financed ience
research, the Obama administration agrees.

In a memorandum issued on Friday, John P. Holdren, science adviser to resident
Obama, called for scientific papers that report the results of federally financed
research to become freely accessible within a year or so after publication. The
findings are typically published in scientific journals, many of which are open
only to paying subscribers.

The new policy would apply to federal agencies, including the National Science
Foundation, the Department of Energy and the Department of Agriculture, that
finance more than $100 million a year of research. The agencies have six months
to submit plans for how they would carry out the new policy.

The hope is that broad access to scientific results will encourage faster
progress on research and will let anyone apply the knowledge for technological
advances.

"We have seen, over the last 15 years, in the era of the Internet, that the more
widely available a publication is, the more likely it is to be cited and the more
likely it is to be used in patent applications," said Myron Gutmann, an assistant
director at the National Science Foundation.

"We know that the small and medium enterprise, the business community, doesn't
have a lot of access to scientific publications right now," Dr.
Gutmann said, "and the more we can make things available for those communities,
the more innovation there is likely to be." He estimated that
25,000 to 40,000 journal articles based on research financed by the science
foundation are published annually.

At the Agriculture Department, Catherine Woteki, the agency's chief scientist,
said the new policy fit in with efforts to make agriculture data like plant
genomes more widely available. "We can reduce in half the time that it takes for
breeding drought- and pest- and disease- resistant crops," she said.

The agencies could model their policies on one established by the National
Institutes of Health in 2008. The N.I.H. requires scientists receiving grants to
ensure that their papers can be made available on PubMed Central, a publicly
available Web site, within one year.

An online petition last May on the White House's Web site called for "free access
over the Internet to scientific journal articles arising from taxpayer-funded
research."

More than 65,000 people signed the petition, easily passing the 25,000- signature
threshold that merited an official White House response. (The threshold was
raised in January to 100,000 after a petition that called for building a Death
Star like that in the movie "Star Wars" garnered 34,435 signatures;
administration officials rejected that suggestion.)

In a response posted Friday to the signers of the open-access petitioners, Dr.
Holdren agreed.

"Americans should have easy access to the results of the research they help
support," Dr. Holden wrote, adding, "the logic behind enhanced access is plain."

A version of this article appeared in print on February 23, 2013, on page
A9 of the New York edition with the headline: U.S. Moves to Provide Quicker
Access to Publicly Financed Scientific Research.

--
===============================================================
Miguel Perez-Enciso
ICREA professor
Centre for Research in Agricultural Genomics (CRAG) and Facultat de Veterinaria
UAB Campus Universitat Autonoma Barcelona Bellaterra
E-08193 Spain
Tel: +34 935636600 ext 3346
Fax: +34 935636601
miguel.perezuab.es
http://www.icrea.cat/...cStaff/Miguel-Perez-Enciso-255
http://bioinformatics.cragenomica.es/numgenomics/
================================================================

  

From cktuggleiastate.edu  Wed Feb 27 08:38:04 2013
From: "Tuggle, Chris K [AN S]" <cktuggleiastate.edu>
Subject: Re: simple numbers
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Wed, 27 Feb 2013 08:38:04 -0600

Hi Marina- these folks are not employed to work on BMC Genetics only;
check out the "Editorial Team" for BMC Genomics; only the Executive Editor
is different, and BMC Genomics publishes a much larger number of papers
per year. From other posts, it appears that Jo Appleford-Cook is Publisher
of all BMC series journals.

So while the employment base for each journal is still a bit opaque,
certainly the journal publishing revenue for BMC Genetics is not
supporting these four people only.

As others, I am enjoying the range of opinions and comments by others.

Chris

***************************************************************
Christopher K. Tuggle
Professor, Molecular Genetics
Chair, Interdepartmental Genetics Program
Iowa State University
Department of Animal Science
2255 Kildee Hall
Ames, IA 50011
PHONE 515-294-4252
FAX 515-294-2401
email: cktuggle at iastate.edu replace at with @ symbol
http://www.ans.iastate.edu/faculty/index.php?id=cktuggle
**************************************************************





On 2/27/13 7:40 AM, "Marina Fortes" <m.fortesuq.edu.au> wrote:

>
>BMC genetics charges 2055 dollars per paper published, they publish
>something
>like 110-120 papers per year ~= 226K - 246K
>They declare in their FAQ that Article-processing charges pay for:
>
>Immediate, worldwide open access to the full article text
>Developing and maintaining electronic tools for peer review and
>publication
>Preparation in various formats for online publication
>Securing inclusion in CrossRef, enabling electronic citation in other
>journals
>that are available electronically
>
>They fail to mention that they employ 4 people in the Editorial team:
>Executive Editor Simon Harold; Journal Development Manager Genevieve
>Horne;
>Senior Managing Editor Diana Marshall; Publisher Jo Appleford-Cook.
>
>I don't think this people work for free...
>
>Jus to add some facts, or a case-study, to the discussion.
>
>Regards,
>
>Marina R S Fortes
>Post Doctoral Research Fellow
>University of Queensland - QAAFI
>Gatton bld 8114, room 314
>Phone 61 7 54601969
>Mobile 0431141617
>
>
>-----Original Message-----
>.From: Matukumalli, Lakshmi [mailto:lmatukumallinifa.usda.gov]
>.Sent: Wednesday, 27 February 2013 2:13 PM
>.To: Multiple Recipients of <AnGenMapanimalgenome.org>
>.Subject: White house (OSTP) guidance on publications
>
>Based on the on-going discussions ... I wanted to bring your attention to
>a few
>recent announcements.
>
>This may be applicable to US Scientists where the guidance on
>publications was
>released this weekend.
>
>http://www.whitehouse.gov/...panding-public-access-results-
>federally-funded-research
>Based on the guidance there was an article in Washington post with
>comments from
>USDA REE undersecretary,  Dr.Cathy Woteki.
>
>http://www.washingtonpost.com/...h-science/white-house-moves-to
>-make-federally-funded-research-open-to-the-public/2013/02/22/e2de59fc-7d2
>2-11e2-82e8-61a46c2cde3d_story.html?hpid=z2
>
>Based on this guidance from OSTP, USDA is now developing its own policy
>based on
>this guidance for both journal publications and research data.
>
>The G8 Countries are participating as well in the open data initiative
>and are
>meeting this April.
>
>http://www.whitehouse.gov/...en-call-innovators-apply-prese
>nt-g-8-international-conference-open-data-agricultur
>Lakshmi Kumar 
>
>Lakshmi Kumar Matukumalli National Program Leader, Animal Breeding,
>Genetics and
>Genomics National Institute of Food and Agriculture, USDA E-
>mail: lmatukumallinifa.usda.gov Office: 202-401-1766 Cell: 202-841-6009
>http://www.nifa.usda.gov
>
>INVESTING IN SCIENCE | SECURING OUR FUTURE
>
>
>



From ayreslucasme.com  Wed Feb 27 08:57:52 2013
From: Lucas <ayreslucasme.com>
Subject: Re: Compulsory OAP will cause an even larger increase in publishing
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Wed, 27 Feb 2013 08:57:52 -0600

Below is a link to an article from The Economist which dwells on this topic.

http://www.economist.com/node/21559317

Lucas Ayres
undergraduate student with an interest in animal genetics
Universidade Federal de Minas Gerais

A 27/2/2013, s 10:44, "Boettcher, Paul (AGAG)" <Paul.Boettcherfao.org> escreveu:

> Dear all,
> 
> Thanks for the very interesting discussion.
> 
> However, it seems like one somewhat relevant point to consider is what our
> employers think about this situation. I think it's safe to say that none of us is
> working for free, so if our employers are aware that we are spending time
> reviewing papers for for-profit journals and are fine with it (or even consider
> it part of our job descriptions), then I guess we should be too. They may
> actually think it's perfectly fine, assuming it decreases library costs, for
> example. If they are simply unaware that this is going on, then we should write
> to our respective administrators to alert them to the problem, rather than to the
> various publishers.
> 
> Kind regards,
> Paul Boettcher
> 
> -----Original Message-----
> .From: Ikhide Imumorin [mailto:igi2cornell.edu]
> .Sent: Wednesday, February 27, 2013 4:56 AM
> .To: Multiple Recipients of <AnGenMapanimalgenome.org>
> .Subject: RE: Compulsory OAP will cause an even larger increase in publishing
> 
> I totally agree with Paul Samollow. No one says for profit companies should not
> make a profit, or "non-profit" ones should not recover the cost of doing business
> under the OA model and then some. Even in the old model before OA, it was still
> wrong that scientists did all the heavy lifting and the publishers made all the
> profit. It is even more wrong now with the flattening of the world brought about
> by software and the Internet. They used to incur cost of mailing manuscripts to
> reviewers along with a pre-paid envelope to send it back, but now it is all
> online and automated...
> 
> The point is, in this new world, it is no longer cool to get something for free
> then sell it for profit.  Publishers should do the right thing and pay scientists
> for reviewing and editing papers and books. We can have a conversation about how
> to calibrate that payment but simply using us to make profit is not right. I have
> already proposed a simple and relatively cheap way for the publishers to step up.
> 
> Establish a quid-pro-quo for reviewing/editing papers such that it incentivizes
> it for scientists and create a more equitable and just environment for all. They
> make their profit, scientists feel less used and get at least something for what
> is essentially slave labor right now, and everyone is happy... what is wrong with
> that? How can anyone have a problem with that?
> 
> 
> Ikhide Imumorin, PhD
> Assistant Professor
> Animal Breeding, Genetics and Genomics Group Dept of Animal Science
> 267 Morrison Hall
> Cornell University
> Ithaca, NY 14853
> USA
> T 607-255-2850
> F 607-255-9829
> igi2cornell.edu

From grosawisc.edu  Wed Feb 27 09:17:00 2013
Subject: Re: OA fees and Towards a referee factor index?
From: "Guilherme J. M. Rosa" <grosawisc.edu>
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Wed, 27 Feb 2013 09:17:00 -0600

Hi Miguel:

It is true that Frontiers' fees are high, but their justification is that
they are in an expansion phase so revenues have been used to off set cost
related to that. Also, as far as I know, they waive charges from labs or
research groups that indicate inability to pay such charges. Kind of Robin
Wood (Robyn Hode) philosophy�

But at any rate, I'm not involved in the finances of Frontiers and so I
can not speak more about that. But hopefully they are doing the right
thing and hopefully other scientists are monitoring all this.
Back to the reviewers compensation's topic, something along the lines of
Ikhide suggested has been practiced by, for example, the journal
'Statistical Applications in Genetics and Molecular Biology'
(http://www.degruyter.com/view/j/sagmb), in which you get a free of charge
publication after reviewing 4 manuscripts on time.

Miguel, your idea of a 'reviewer index' is great. It would be interesting
if we could develop an index for reviewers, for example adding the
citations of all manuscripts recommended for publication and subtract from
this total all citations of those manuscripts he or she recommended
rejection. Maybe positive and negative (criticisms) citations could be
also used in the index�

Thanks all for the interesting discussion.

I know other scientific communities (especially math) have already debated
over such issues so it is indeed time for us to do this exercise.

Cheers,
Guilherme.

PS: Regarding the OA discussion, if we should pay to publish or to read,
or split costs, I also tend more towards a Robin Hood's approach, and try
to make scientific finds as available as possible for the whole world. I
guess in this sense the OA helps, in which developed countries and strong
scientific groups (with higher research budgets) make their manuscripts
available to other groups and countries with mooch tighter budgets for
subscriptions, paper downloading, etc.


-- 
Guilherme J. M. Rosa
University of Wisconsin - Madison
444 Animal Science Building
1675 Observatory Dr.
Madison, WI 53706 USA
Phone: + 1 (608) 265-8617
Fax: + 1 (608) 263-9412
E-mail: grosawisc.edu
Webpage: https://mywebspace.wisc.edu/grosa/web/


On 2/27/13 7:41 AM, "Miguel Perez-Enciso" <miguel.perezuab.es> wrote:

>Along the lines of Guilherme (by the way, Frontiers' fees are among the
>highest) a partial way to mitigate this publishing distortion would be
>to set a referees factor index which, like number of citations, would
>contain number of papers reviewed, and the number of citations received
>by each paper you recommended rejection and of those for which you
>recommended acceptance. This should be stratified by journal.
>
>Over the years, many rejected papers become published, and can
>potentially be cited. If you are a bad referee, there will be no
>distinction among those rejected and accepted. On the other hand, if you
>are a 'good' referee journals will look for you insistently so you have
>have a right to be paid or get a discount, because journals want their
>papers to be cited or at least accessed.
>
>Finally, if you know how many papers each of us review per year and in
>time, you can decline reviewing for a 'selfish but highly productive
>colleague' and explain that in the rejection letter. I promise to accept
>reviewing the next one by Ikhide!
>
>Of course I am very well aware this or similar is VERY difficult to
>implement, particularly for privacy. I still believe anonymity is a good
>thing for critical unbiased assessements. Finally, it is very well
>possible to know to an extent how much profit a company is doing, so
>this does not preclude paying a fair part only to publishers, at least
>compulsorily.
>
>Best
>
>Miguel
>
>El 27/02/2013 5:13, Mehdi Sargolzaei escribi:
>>
>> Last year Larry Schaeffer proposed "You-Pub" idea, which potentially can
>> eliminate publishing and access costs. So I forward his email for those
>> interested.
>>
>> However, I don't think this is going to change things quickly. The system
>> should be set up and works for few years to attract enough attention if
>> successful.
 

From reedx054umn.edu  Wed Feb 27 09:17:46 2013
From: Kent Reed PhD <reedx054umn.edu>
Subject: Re: Compulsory OAP will cause an even larger increase in publishing
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Wed, 27 Feb 2013 09:17:46 -0600

I review manuscripts as a obligation to the scientific community. This 
is a responsibility we all have REGARDLESS if someone is making money on 
the other end.

-- 
Kent M Reed, PhD
Professor
College of Veterinary Medicine
Department of Veterinary and Biomedical Sciences
University of Minnesota
295 ASVM 1988 Fitch Ave
St. Paul, MN 55108

(reedx054umn.edu)
Office (612) 624-1287
Lab    (612) 624-5390
FAX   (612) 625-0204

http://www.cvm.umn.edu/vbs/faculty/Reed/home.html
http://www.tc.umn.edu/~reedx054/

From jillian.maddoxalumni.unimelb.edu.au  Wed Feb 27 19:54:37 2013
From: Jill Maddox <jillian.maddoxalumni.unimelb.edu.au>
Subject: Re: simple numbers
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Wed, 27 Feb 2013 19:54:37 -0600

Hi All

To add to Marina's comment.

Using BMC as an example. There are now 64 BMC journals. It appears 
that at least 3 of the staff that Marina mentioned are for all BMC 
journals so their salary costs come from the whole suite of BMC 
journals not just BMC Genetics. There will also be other costs but 
nowhere near as much as for a print journal. I have no idea how many 
papers are published per year for each BMC journal and whether authors 
are charged the same amount for each journal (a quick glance at a 
couple shows the same pricing) but assuming 100 papers per year, 
$2000 per paper, 64 journals we're talking about income from authors 
in excess of $10 million per year - one would assume that necessary 
operating costs for the BMC series would be less than $2 million per 
year. BMC do state that they routinely waive fees for authors from 
low income countries and authors don't have to pay if their 
institutions are members or pay reduced amounts if their institute 
is a supporting member (institutes pay to be a member).

One of my pet gripes as a scientific reviewer is that most journals 
do not appear to have a process by which the English in the paper is 
corrected even if you indicate that there is a problem with the 
English.  I believe that it is important that published papers use 
good English so that the communication of scientific results and 
discussion about them is as clear as possible. I do not believe that 
it is the scientific reviewer's role to correct the English as it is 
very time consuming for a scientific reviewer to correct the English 
on a paper - they should just be able to focus on the science.  
Unfortunately it appears that if the scientific reviewer doesn't 
explicitly advise of every typographical and grammatical error in 
a paper then these errors do not get fixed.  There are some excellent 
English proof reading services costing ~$200 - $500 per paper 
depending on turnaround time and length (e.g. Nature Publishing 
Group Language Editing http://languageediting.nature.com/, enago 
http://www.enago.com/ and many more). I think that journals should 
encourage greater utilisation of these services - they could charge 
submitting authors a reduced rate if such a service had been used or 
pay for it themselves out of submission costs (I'm sure journals 
would get better rates being high volume customers than authors do). 
It would be good if this happened before papers were sent out to 
review but I realise this is probably unrealistic for journals with 
high rejection rates.

Regards

Jill


At 12:40 AM 28/02/2013, Marina Fortes wrote:
>From: Marina Fortes <m.fortesuq.edu.au>
>Subject: simple numbers
>To: Multiple Recipients of <angenmapanimalgenome.org>
>
>BMC genetics charges 2055 dollars per paper published, they publish something
>like 110-120 papers per year ~= 226K - 246K
>They declare in their FAQ that Article-processing charges pay for:
>
>Immediate, worldwide open access to the full article text
>Developing and maintaining electronic tools for peer review and publication
>Preparation in various formats for online publication
>Securing inclusion in CrossRef, enabling electronic citation in other journals
>that are available electronically
>
>They fail to mention that they employ 4 people in the Editorial team:
>Executive Editor Simon Harold; Journal Development Manager Genevieve Horne;
>Senior Managing Editor Diana Marshall; Publisher Jo Appleford-Cook.
>
>I don't think this people work for free...
>
>Jus to add some facts, or a case-study, to the discussion.
>
>Regards,
>
>Marina R S Fortes
>Post Doctoral Research Fellow
>University of Queensland - QAAFI
>Gatton bld 8114, room 314
>Phone 61 7 54601969
>Mobile 0431141617

***************************************************************

Jill Maddox
16 Park Square
Port Melbourne, 3207
Australia
phone: 03 9646 0428
E-mail: jillian.maddoxalumni.unimelb.edu.au

***************************************************************

From christopher.moransydney.edu.au  Wed Feb 27 23:26:57 2013
From: Christopher Moran <christopher.moransydney.edu.au>
Subject: RE: Compulsory OAP will cause an even larger increase in publishing 
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Wed, 27 Feb 2013 23:26:57 -0600

I think DJ makes an extremely important point here. The International
Society of Animal Genetics which owns Animal Genetics derives an important
income stream from the journal which is all turned into support for members
of the society - travel bursaries to students, conference prizes, support
for special issues etc.

Also in relation to the issue of availability of traditional journal
content to researchers in developing countries, publishers have special
arrangements to make such content freely available. I know that Animal
Genetics and other journals are made available in that way by Wiley.

Finally I also agree with DJ that researchers are not better off having
financial responsibility for publishing costs dumped on them under an open
access model when it was formerly an institutional library responsibility
under the pay to read model.

Chris

 
CHRISTOPHER MORAN | Professor of Animal Genetics | Facultyof Veterinary 
Science | Editor in Chief Animal Genetics| THE UNIVERSITY OF SYDNEY 
Rm 512, RMC Gunn Building B19 | The University of Sydney | NSW | 2006 | 
Australia	 
T +61 2 93513553 | F +61 2 93512114 | M +61 431 266 925  
E Christopher.Moransydney.edu.au  | W http://sydney.edu.au/vetfac 
CRICOS 00026A 

-----Original Message----- 
.From: DE KONING DJ [mailto:dj.dekoningroslin.ed.ac.uk]  
.Sent: Thursday, 28 February 2013 12:41 AM 
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: RE: Compulsory OAP will cause an even larger increase in publishing 

Dear All,

 I think there is another aspect in this whole discussion, which I raised 
when Michael Eisen was doing his PLOS Rave at PAGXIX: Many of the so-called 
"learned societies" depend on their subscription journals to make enough 
money to fulfill their roles. If you think about Genetics, Animal Genetics 
and Heredity, they all support great organizations that organize meetings and 
support young scientists (GSA, ISAG and Genetics Society UK, respectively). 
Only a fraction of the income (5% for Genetics Society UK) from these 
societies comes from membership fees, the vast majority is journal income. 

 If the subscription model disappears the societies will have to revise their 
funding model entirely. 

At present we can offer 750 travel scholarships to students who join for as
little as 10. This may well become a thing of the past. I for one feel
quite strongly about the role of learned societies to create communities,
which explains my list of COI: former associate editor of Animal Genetics,
senior editor of G3, Editorial board of Heredity and executive committee
member of Genetics Society UK.

For institutions, the only difference is that they shift from paying for
subscriptions toward paying for publishing. Unfortunately, all too often
the bill for the latter ends up on the researchers' plate, while the former
was within the institutional overheads.

DJ de Koning

 
 
________________________________________ 
.From: Ikhide Imumorin [igi2cornell.edu] 
.Sent: 27 February 2013 03:55 
.To: Multiple Recipients of <AnGenMapanimalgenome.org> 
.Subject: RE: Compulsory OAP will cause an even larger increase in publishing 

I totally agree with Paul Samollow. No one says for profit companies should
not make a profit, or "non-profit" ones should not recover the cost of
doing business under the OA model and then some. Even in the old model
before OA, it was still wrong that scientists did all the heavy lifting and
the publishers made all the profit. It is even more wrong now with the
flattening of the world brought about by software and the Internet. They
used to incur cost of mailing manuscripts to reviewers along with a pre-
paid envelope to send it back, but now it is all online and automated...

The point is, in this new world, it is no longer cool to get something for
free then sell it for profit. Publishers should do the right thing and pay
scientists for reviewing and editing papers and books. We can have a
conversation about how to calibrate that payment but simply using us to
make profit is not right. I have already proposed a simple and relatively
cheap way for the publishers to step up. Establish a quid-pro-quo for
reviewing/editing papers such that it incentivizes it for scientists and
create a more equitable and just environment for all. They make their
profit, scientists feel less used and get at least something for what is
essentially slave labor right now, and everyone is happy... what is wrong
with that? How can anyone have a problem with that?

 
Ikhide Imumorin, PhD 
Assistant Professor 
Animal Breeding, Genetics and Genomics Group Dept of Animal Science 
267 Morrison Hall 
Cornell University 
Ithaca, NY 14853 
USA 
T 607-255-2850 
F 607-255-9829 
igi2cornell.edu 

http://www.ansci.cornell.edu/faculty/imumorin.html

Editorial Board, Journal of Veterinary Science and Medical Diagnosis -
http://www.scitechnol.com/jvsmdhome.php Associate Editor, Genomics and
Quantitative Genetics - http://www.knoblauchpublishing.com Associate
Editor, Journal of Applied Animal Research -
http://www.tandf.co.uk/journals/TAAR Review Editor, Frontiers in Genetics -
http://www.frontiersin.org/genetics

"So why not go out on a limb, isn't that where the fruit is?" - Frank
Scully

 
________________________________________ 
.From: Samollow, Paul [PSamollowcvm.tamu.edu] 
.Sent: Tuesday, February 26, 2013 10:40 PM 
.To: Multiple Recipients of <AnGenMapanimalgenome.org> 
.Subject: Re: Compulsory OAP will cause an even larger increase in publishing 

I agree with Bob - publishers must make a profit to stay in business, and
carping about how much someone has to pay to publish in these journals, or
how much profit the journal make, misses the point. But I don't believe his
examples are relevant to question here. We are not tapped by Apple or Intel
or AMD to give them free services. The situation with OA journals is
different.

OA journals are a new phenomenon; but we've always had to pay page charges.
The fundamental difference with OA journals is that in traditional
publications consumers payed something for the product, and that defrayed
part of the cost and yielded more profit), but now it is the manufacturer
(investigator) who pays the whole bill. The issue is that we have the
expertise the publishers need and they get it for free. So, the question is
- should they pay for our expertise or not? Or more bluntly, should reviewer 
remuneration be a cost of business for publishers? Traditionally it has not 
been; we pitch in for the common good. But maybe those days are over. 

Paul

 
Paul B. Samollow, Ph.D. 
Professor 
---------------------------------------------------------------------------
Postal address: 
Department of Veterinary Integrative Biosciences 
4458 TAMU 
Texas A&M University 
College Station, TX  77843-4458 

Express/Courier address: Department of Veterinary Integrative Biosciences
VMA Building, Room 107 Texas A&M University College Station, TX 77843-4458

Phone: 979 845-7095

FAX: 979 845-9972 Email: psamollowcvm.tamu.edu
--------------------------------------------------------------------------- 

 
On Feb 26, 2013, at 5:09 PM, Schnabel, Robert D. wrote: 

I have to chime in here. I think recent post discussing publisher profits
are misguided. What difference does it make if a publisher makes a dollar
or a billion? Intel, AMD and Apple make large profits but I don't hear any
outcry about the price of your computers which you rely upon to do your
research. Illumina does alright but I don't hear anyone proposing to write
a letter to someone complaining about the price of snp chips or sequencing
reagents citing Illumina's profit margins. If you want to make a case for
the problem of increasing publishing costs don't bring in "fairness" and
publishers profits. You'll get much more traction if you present a coherent
case and more importantly a solution.

Bob

************************************************* 
Robert Schnabel 
Research Associate Professor 
University of Missouri-Columbia 
Animal Sciences Unit, Rm.162 
920 East Campus Drive 
Columbia, MO 65211-5300 
Phone: 573-884-4106 
Fax:   573-882-6827 
http://animalgenomics.missouri.edu 
************************************************* 

From dr.akin.palagmail.com  Thu Feb 28 08:08:42 2013
From: Akin Pala <dr.akin.palagmail.com>
Subject: Re: simple numbers
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Thu, 28 Feb 2013 08:08:42 -0600

Hi all,

I know some journals have that system. Animal Science Journal in Japan has
a second service that does some corrections in addition to the editor and
the reviewer, and they don't charge you for it. I believe Journal of Dairy
Science had somebody else correct more stuff in my paper after it was
accepted and all looked fine for the reviewer and the editor. They charged
me only for the paper.


Assoc. Prof. Dr. Akin Pala
Department Head of Animal Science
CEO, Canakkale Research & Technology Park Inc.



On Thu, Feb 28, 2013 at 3:54 AM, Jill Maddox
 <jillian.maddoxalumni.unimelb.edu.au> wrote:

> Hi All
>
> To add to Marina's comment.
>
> Using BMC as an example. There are now 64 BMC journals. It appears
> that at least 3 of the staff that Marina mentioned are for all BMC
> journals so their salary costs come from the whole suite of BMC
> journals not just BMC Genetics. There will also be other costs but
> nowhere near as much as for a print journal. I have no idea how many
> papers are published per year for each BMC journal and whether authors
> are charged the same amount for each journal (a quick glance at a
> couple shows the same pricing) but assuming 100 papers per year,
> $2000 per paper, 64 journals we're talking about income from authors
> in excess of $10 million per year - one would assume that necessary
> operating costs for the BMC series would be less than $2 million per
> year. BMC do state that they routinely waive fees for authors from
> low income countries and authors don't have to pay if their
> institutions are members or pay reduced amounts if their institute
> is a supporting member (institutes pay to be a member).
>
> One of my pet gripes as a scientific reviewer is that most journals
> do not appear to have a process by which the English in the paper is
> corrected even if you indicate that there is a problem with the
> English.  I believe that it is important that published papers use
> good English so that the communication of scientific results and
> discussion about them is as clear as possible. I do not believe that
> it is the scientific reviewer's role to correct the English as it is
> very time consuming for a scientific reviewer to correct the English
> on a paper - they should just be able to focus on the science.
> Unfortunately it appears that if the scientific reviewer doesn't
> explicitly advise of every typographical and grammatical error in
> a paper then these errors do not get fixed.  There are some excellent
> English proof reading services costing ~$200 - $500 per paper
> depending on turnaround time and length (e.g. Nature Publishing
> Group Language Editing http://languageediting.nature.com/, enago
> http://www.enago.com/ and many more). I think that journals should
> encourage greater utilisation of these services - they could charge
> submitting authors a reduced rate if such a service had been used or
> pay for it themselves out of submission costs (I'm sure journals
> would get better rates being high volume customers than authors do).
> It would be good if this happened before papers were sent out to
> review but I realise this is probably unrealistic for journals with
> high rejection rates.
>
> Regards
>
> Jill
>
>
> At 12:40 AM 28/02/2013, Marina Fortes wrote:
> >From: Marina Fortes <m.fortesuq.edu.au>
> >Subject: simple numbers
> >To: Multiple Recipients of <angenmapanimalgenome.org>
> >
> >BMC genetics charges 2055 dollars per paper published, they publish
> something
> >like 110-120 papers per year ~= 226K - 246K
> >They declare in their FAQ that Article-processing charges pay for:
> >
> >Immediate, worldwide open access to the full article text
> >Developing and maintaining electronic tools for peer review and
> publication
> >Preparation in various formats for online publication
> >Securing inclusion in CrossRef, enabling electronic citation in other
> journals
> >that are available electronically
> >
> >They fail to mention that they employ 4 people in the Editorial team:
> >Executive Editor Simon Harold; Journal Development Manager Genevieve
> Horne;
> >Senior Managing Editor Diana Marshall; Publisher Jo Appleford-Cook.
> >
> >I don't think this people work for free...
> >
> >Jus to add some facts, or a case-study, to the discussion.
> >
> >Regards,
> >
> >Marina R S Fortes
> >Post Doctoral Research Fellow
> >University of Queensland - QAAFI
> >Gatton bld 8114, room 314
> >Phone 61 7 54601969
> >Mobile 0431141617
>
> ***************************************************************
>
> Jill Maddox
> 16 Park Square
> Port Melbourne, 3207
> Australia
> phone: 03 9646 0428
> E-mail: jillian.maddoxalumni.unimelb.edu.au
>
> ***************************************************************

From grosawisc.edu  Thu Feb 28 09:19:54 2013
Subject: Re: OA fees and Towards a referee factor index?
From: "Guilherme J. M. Rosa" <grosawisc.edu>
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Thu, 28 Feb 2013 09:19:54 -0600

If you're interested, I just got some interesting news from Frontiers and
Nature:
http://www.frontiersin.org/...ce_to_further_open_science/266

Cheers,
Guilherme.

-- 

Guilherme J. M. Rosa
University of Wisconsin - Madison
444 Animal Science Building
1675 Observatory Dr.
Madison, WI 53706 USA
Phone: + 1 (608) 265-8617
Fax: + 1 (608) 263-9412
E-mail: grosawisc.edu
Webpage: https://mywebspace.wisc.edu/grosa/web/



On 2/27/13 7:41 AM, "Miguel Perez-Enciso" <miguel.perezuab.es> wrote:

>Along the lines of Guilherme (by the way, Frontiers' fees are among the
>highest) a partial way to mitigate this publishing distortion would be
>to set a referees factor index which, like number of citations, would
>contain number of papers reviewed, and the number of citations received
>by each paper you recommended rejection and of those for which you
>recommended acceptance. This should be stratified by journal.
>
>Over the years, many rejected papers become published, and can
>potentially be cited. If you are a bad referee, there will be no
>distinction among those rejected and accepted. On the other hand, if you
>are a 'good' referee journals will look for you insistently so you have
>have a right to be paid or get a discount, because journals want their
>papers to be cited or at least accessed.
>
>Finally, if you know how many papers each of us review per year and in
>time, you can decline reviewing for a 'selfish but highly productive
>colleague' and explain that in the rejection letter. I promise to accept
>reviewing the next one by Ikhide!
>
>Of course I am very well aware this or similar is VERY difficult to
>implement, particularly for privacy. I still believe anonymity is a good
>thing for critical unbiased assessements. Finally, it is very well
>possible to know to an extent how much profit a company is doing, so
>this does not preclude paying a fair part only to publishers, at least
>compulsorily.
>
>Best
>
>Miguel
>
>El 27/02/2013 5:13, Mehdi Sargolzaei escribi:
>>
>> Last year Larry Schaeffer proposed "You-Pub" idea, which potentially can
>> eliminate publishing and access costs. So I forward his email for those
>> interested.
>>
>> However, I don't think this is going to change things quickly. The
>>system
>> should be set up and works for few years to attract enough attention if
>> successful.
>>

From dab22psu.edu  Thu Feb 28 10:19:26 2013
From: DAVID A BLIZARD <dab22psu.edu>
Subject: Re: Compulsory OAP will cause an even larger increase in publishing 
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Thu, 28 Feb 2013 10:19:26 -0600

 From David A Blizard at Penn State, University Park PA.

I agree with many of the sentiments already expressed.

1. Support your professional societies! They, not for-profit journals, are
concerned with development of the fields in which we work, including
support of training opportunities, promotion of the field in many different
ways, enhancement of enjoyment of the field via conduct of professional
meetings, presentations to governmental and other funding entities (the
list goes on).

2. A not negligible point is that if you publish in a professional journal
your paper is likely to be widely for many years into the future which
means that its archives (including your papers) are likely to be preserved
and made available perhaps not in perpetuity but certainly for a long time.

3. The upsurge in titles during the digital publication revolution raises
the issue of whether there may be a need for professional societies to be
more dynamic in developing new titles of their own (presuming that there is
a need for them.

4. Some journals which are privately owned may give the impression that
they are the house journal of a particular group or annual meetings (that
may not have progressed to the level of a professional society with its own
bye-laws and journal). Researchers should be aware of such issues when
considering suitable places to publish their work.

DAB

----- Original Message ----- 
.From: "Christopher Moran" <christopher.moransydney.edu.au> 
.To: "Multiple Recipients of" <angenmapanimalgenome.org> 
.Sent: Thursday, February 28, 2013 12:26:57 AM 
.Subject: RE: Compulsory OAP will cause an even larger increase in publishing  

I think DJ makes an extremely important point here. The International
Society of Animal Genetics which owns Animal Genetics derives an important
income stream from the journal which is all turned into support for members
of the society - travel bursaries to students, conference prizes, support
for special issues etc.

Also in relation to the issue of availability of traditional journal
content to researchers in developing countries, publishers have special
arrangements to make such content freely available. I know that Animal
Genetics and other journals are made available in that way by Wiley.

Finally I also agree with DJ that researchers are not better off having
financial responsibility for publishing costs dumped on them under an open
access model when it was formerly an institutional library responsibility
under the pay to read model.

Chris

From thamukeshgmail.com  Thu Feb 28 10:40:01 2013
From: "Mukesh Thakur" <thamukeshgmail.com>
Subject: Re: Compulsory OAP will cause an even larger increase in publishing
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Thu, 28 Feb 2013 10:40:01 -0600

I agree with the many points that have been already discussed regarding the 
compulsory OAP charges by the author. To this concern, I would like to 
thank Editor, BMC Research Notes who accepted my request of full waiver for 
a recently submitted MS. Being a research scholar at the moment, I 
expressed my incapability to afford the publication charges. The editor 
asked me to submit a letter from one of the regular employee of my 
institute who was not the coauthor in the MS. I submitted this and my 
request was considered.

 From this mail, I want to raise the point the few journals of BMC (like BMC 
Research Notes) do consider the request of a full/partial waiver depending 
upon the circumstances. However, I don't have experience of other journal of 
BMC.

Thanking you.
Kind regards,
Mukesh   


  

From igi2cornell.edu  Thu Feb 28 10:40:52 2013
From: Ikhide Imumorin <igi2cornell.edu>
Subject: RE: Compulsory OAP will cause an even larger increase in publishing 
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Thu, 28 Feb 2013 10:40:52 -0600

There is a need to rethink the roles and strategies of professional societies
that publish journals. For instance, the average time from submission to press is
longer than a year for most societies' journals even if extensive revisions are
not mandated by peer review. This is where OA journals have capitalized on
dissatisfaction with this process to lure away scientists who can publish a paper
within weeks to a few months instead of a year or more. If money was not an issue
for a scientist, where do you think they will send their papers? And if the time
to publication was comparable, don't you think they will prefer to use their
professional society's journal to communicate their findings? It is good for the
scientist, the society and for science as a whole when professional societies use
their journals to promote their field.

Professional societies have a greater stake in the communication of findings in
their fields than commercial publishing houses. They need to step up to the plate
and do more to balance the field. Perhaps members of the professional societies
should be REQUIRED to review for the journal as part of their professional
membership obligations, and they can be rewarded with steep discounts to publish
(in the case where there is page charges), or the societies should revamp their
publishing models to make things faster. In the digital world, competition is
fierce to attract good quality papers and OA journals have done a much better job
to get many scientists to publish, which in turn increases impact factors. The
more papers you publish, the more likely things are cited which improves IF. If a
paper takes a year or more to be published, your competitors will already have
published in an OA journal which gets cited more!


Ikhide Imumorin, PhD
Assistant Professor
Animal Breeding, Genetics and Genomics Group
Dept of Animal Science
267 Morrison Hall
Cornell University
Ithaca, NY 14853
USA
T 607-255-2850
F 607-255-9829
igi2cornell.edu

http://www.ansci.cornell.edu/faculty/imumorin.html

Editorial Board, Journal of Veterinary Science and Medical Diagnosis -
http://www.scitechnol.com/jvsmdhome.php
Associate Editor, Genomics and Quantitative Genetics -
http://www.knoblauchpublishing.com
Associate Editor, Journal of Applied Animal Research -
http://www.tandf.co.uk/journals/TAAR
Review Editor, Frontiers in Genetics - http://www.frontiersin.org/genetics

"So why not go out on a limb, isn't that where the fruit is?" - Frank Scully




________________________________________
.From: DAVID A BLIZARD [dab22psu.edu]
.Sent: Thursday, February 28, 2013 11:19 AM
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: Re: Compulsory OAP will cause an even larger increase in publishing


 From David A Blizard at Penn State, University Park PA.

I agree with many of the sentiments already expressed.

1. Support your professional societies! They, not for-profit journals, are
concerned with development of the fields in which we work, including
support of training opportunities, promotion of the field in many different
ways, enhancement of enjoyment of the field via conduct of professional
meetings, presentations to governmental and other funding entities (the
list goes on).

2. A not negligible point is that if you publish in a professional journal
your paper is likely to be widely for many years into the future which
means that its archives (including your papers) are likely to be preserved
and made available perhaps not in perpetuity but certainly for a long time.

3. The upsurge in titles during the digital publication revolution raises
the issue of whether there may be a need for professional societies to be
more dynamic in developing new titles of their own (presuming that there is
a need for them.

4. Some journals which are privately owned may give the impression that
they are the house journal of a particular group or annual meetings (that
may not have progressed to the level of a professional society with its own
bye-laws and journal). Researchers should be aware of such issues when
considering suitable places to publish their work.

DAB

From christopher.moransydney.edu.au  Thu Feb 28 15:59:36 2013
From: Christopher Moran <christopher.moransydney.edu.au>
Subject: Re: Compulsory OAP will cause an even larger increase in publishing  
Content-Language: en-US 
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Thu, 28 Feb 2013 15:59:36 -0600

I challenge Ikhide to provide the data to support his assertion that
traditional journals take over a year to publication compared with much
faster publication times in open access journals. For open access journals
which don't have proper peer review processes, this may be true, but I
wouldn't want to publish in them. If there is proper peer review, the open
access journals are at the mercy if the reviewers just as traditional
journals (surely that has been an important point of much if the discussion
so far). I can assure you that difficulty in finding reviewers and getting
them to deliver their reports is largely responsible for the delays in
publication, open access or not.

Finally traditional journals which still publish in hard copy (and they are
a rapidly disappearing species), make papers available electronically via
online early or similar mechanisms as soon as the proofing process has been
completed and this may occur several months before the hard copy appears.

Chris Moran
 

On 01/03/2013, at 3:44 AM, "Ikhide Imumorin" <igi2cornell.edu> wrote:

> There is a need to rethink the roles and strategies of professional societies 
> that publish journals. For instance, the average time from submission to press is 
> longer than a year for most societies' journals even if extensive revisions are 
> not mandated by peer review. This is where OA journals have capitalized on 
> dissatisfaction with this process to lure away scientists who can publish a paper 
> within weeks to a few months instead of a year or more. If money was not an issue 
> for a scientist, where do you think they will send their papers? And if the time 
> to publication was comparable, don't you think they will prefer to use their 
> professional society's journal to communicate their findings? It is good for the 
> scientist, the society and for science as a whole when professional societies use 
> their journals to promote their field. 
>  
> Professional societies have a greater stake in the communication of findings in 
> their fields than commercial publishing houses. They need to step up to the plate 
> and do more to balance the field. Perhaps members of the professional societies 
> should be REQUIRED to review for the journal as part of their professional 
> membership obligations, and they can be rewarded with steep discounts to publish 
> (in the case where there is page charges), or the societies should revamp their 
> publishing models to make things faster. In the digital world, competition is 
> fierce to attract good quality papers and OA journals have done a much better job 
> to get many scientists to publish, which in turn increases impact factors. The 
> more papers you publish, the more likely things are cited which improves IF. If a 
> paper takes a year or more to be published, your competitors will already have 
> published in an OA journal which gets cited more! 
>  
>  
> Ikhide Imumorin, PhD 
> Assistant Professor 
> Animal Breeding, Genetics and Genomics Group 
> Dept of Animal Science 
> 267 Morrison Hall 
> Cornell University 
> Ithaca, NY 14853 
> USA 
> T 607-255-2850 
> F 607-255-9829 
> igi2cornell.edu 
>  
> http://www.ansci.cornell.edu/faculty/imumorin.html 
>  
> Editorial Board, Journal of Veterinary Science and Medical Diagnosis - 
> http://www.scitechnol.com/jvsmdhome.php 
> Associate Editor, Genomics and Quantitative Genetics - 
> http://www.knoblauchpublishing.com 
> Associate Editor, Journal of Applied Animal Research - 
> http://www.tandf.co.uk/journals/TAAR 
> Review Editor, Frontiers in Genetics - http://www.frontiersin.org/genetics 
>  
> "So why not go out on a limb, isn't that where the fruit is?" - Frank Scully 
  

From Eduardo.CasasARS.USDA.GOV  Fri Mar  1 14:56:25 2013
From: "Casas, Eduardo" <Eduardo.CasasARS.USDA.GOV>
Subject: RE: Compulsory OAP will cause an even larger increase in publishing
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Fri, 01 Mar 2013 14:56:25 -0600

Dear all,

This message is an offshoot of the main topic, but Chris Moran just touched on an
issue in publishing scientific literature (and maybe one of my pet peeves):
finding reviewers that can deliver their reports on time. I have had the "joy" of
being an Associate Editor for a couple of journals. In this position, one
difficulty is to reply to authors who complain their manuscript has taken too
long to review. The problem resides mostly with the reviewers. Most of you have
or will be tagged to review a manuscript. Therefore, I would like to plea to all
of you the following:

1.      IF YOU DO NOT WANT TO REVIEW A MANUSCRIPT, DON'T ACCEPT THE INVITATION.
If you receive a message inviting you to review a manuscript, accept or decline
it soon after reading the message. This will allow the manuscript to move
forward. If you don't have time for a review, decline it immediately. There is no
harm in declining the review of a manuscript. Your action will allow the editor
to look for another reviewer who can do it in a timely fashion. Sometimes I have
had the "privilege" to wait anywhere from 2 to 4 weeks to hear back from a
potential reviewer (and at the end they would decline). Why would it take you so
long?

2.      IF YOU ACCEPT THE INVITATION TO REVIEW A MANUSCRIPT, DO IT WITHIN THE
TIME INDICATED BY THE JOURNAL. Remember that journals will give you anywhere
between 2 and 4 weeks to review the manuscript. If you don't plan to review the
document in the allotted time, please decline the invitation. I understand there
are unforeseen circumstances that will not allow for you to complete the review
on time once you have accepted the invitation. If this is the case, let the
editor know. In some occasions I had the "honor" to wait up to 6 months before
the reviewer would contact me to say "I'm sorry, I forgot the manuscript". In
another occasion, one reviewer never returned the review. After waiting for 4
months, I had to look for another reviewer. Can you imagine how upset the authors
were? Please review manuscripts on time.

3.      PLEASE WRITE COHERENT REVIEWS. Reviewers often complain about language in
the manuscripts. Let me tell you that you, as reviewer, are not that great
either. Some reviewers go on and on about something (like I am doing here), and
at the end neither the editor nor the authors know what the reviewer meant or
wants. Please be concise and make your point.

We all complain about the time it takes to review a manuscript, but we, as
reviewers, are part of the problem. There are conscious reviewers that provide
their reviews on time; however, most of us take longer than we should. If you do
your part, the process can be shortened considerably. Remember you are not God's
gift to the reviewing world. The editor can always look for somebody else with
similar expertise than you if you don't get in the way (by not responding or
taking too long to do something you agreed to do).

Eduardo Casas, Ph.D.
NADC
Ames, IA 50010
Eduardo.casasars.usda.gov


-----Original Message-----
.From: Christopher Moran [mailto:christopher.moransydney.edu.au]
.Sent: Thursday, February 28, 2013 4:00 PM
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: Re: Compulsory OAP will cause an even larger increase in publishing

I challenge Ikhide to provide the data to support his assertion that traditional
journals take over a year to publication compared with much faster publication
times in open access journals. For open access journals which don't have proper
peer review processes, this may be true, but I wouldn't want to publish in them.
If there is proper peer review, the open access journals are at the mercy if the
reviewers just as traditional journals (surely that has been an important point
of much if the discussion so far). I can assure you that difficulty in finding
reviewers and getting them to deliver their reports is largely responsible for
the delays in publication, open access or not.

Finally traditional journals which still publish in hard copy (and they are a
rapidly disappearing species), make papers available electronically via online
early or similar mechanisms as soon as the proofing process has been completed
and this may occur several months before the hard copy appears.

Chris Moran

From igi2cornell.edu  Fri Mar  1 16:10:36 2013
From: Ikhide Imumorin <igi2cornell.edu>
Subject: RE: Compulsory OAP will cause an even larger increase in publishing
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Fri, 01 Mar 2013 16:10:36 -0600

As associate editor of a couple of journals and a regular reviewer of journals I
totally understand Eduardo's concerns. However this comes back to the original
root problem I raised. Reviewers do this as a service with no compensation of any
kind. Under such a system, all of us are the mercy of kind reviewers who chose to
do this a service to the scientific community. I know how many times I have to
"beg and plead" with reviewers to return reviews that they accepted to do. I have
a case of a paper under review for a year until I had to review it myself. But if
reviewers do not do it, what do you do? You either be patient or find another
reviewer, but how easy is it to find reviewers? Ask any editor/associate editor
of a scientific journal and they will tell you the worst headache of being an
editor is (1) finding qualified reviewers and (2) then getting them to review on
time! There are folks on this listserve that I invited to review papers who
simply did not even bother respond to the invitation!

There was a time there were just a few journals in every scientific discipline
but with the explosion of journals, now will be the time to incentivize peer
review to help with this situation... think about it. 


Ikhide Imumorin, PhD
Assistant Professor
Animal Breeding, Genetics and Genomics Group
Dept of Animal Science
267 Morrison Hall
Cornell University
Ithaca, NY 14853
USA
T 607-255-2850
F 607-255-9829
igi2cornell.edu

http://www.ansci.cornell.edu/faculty/imumorin.html

Editorial Board, Journal of Veterinary Science and Medical Diagnosis -
http://www.scitechnol.com/jvsmdhome.php
Associate Editor, Genomics and Quantitative Genetics -
http://www.knoblauchpublishing.com
Associate Editor, Journal of Applied Animal Research -
http://www.tandf.co.uk/journals/TAAR
Review Editor, Frontiers in Genetics - http://www.frontiersin.org/genetics

"So why not go out on a limb, isn't that where the fruit is?" - Frank Scully


________________________________________
.From: Casas, Eduardo [Eduardo.CasasARS.USDA.GOV]
.Sent: Friday, March 01, 2013 3:56 PM
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: RE: Compulsory OAP will cause an even larger increase in publishing

Dear all,

This message is an offshoot of the main topic, but Chris Moran just touched on an
issue in publishing scientific literature (and maybe one of my pet peeves):
finding reviewers that can deliver their reports on time. I have had the "joy" of
being an Associate Editor for a couple of journals. In this position, one
difficulty is to reply to authors who complain their manuscript has taken too
long to review. The problem resides mostly with the reviewers. Most of you have
or will be tagged to review a manuscript. Therefore, I would like to plea to all
of you the following:

1.      IF YOU DO NOT WANT TO REVIEW A MANUSCRIPT, DON'T ACCEPT THE INVITATION.
If you receive a message inviting you to review a manuscript, accept or decline
it soon after reading the message. This will allow the manuscript to move
forward. If you don't have time for a review, decline it immediately. There is no
harm in declining the review of a manuscript. Your action will allow the editor
to look for another reviewer who can do it in a timely fashion. Sometimes I have
had the "privilege" to wait anywhere from 2 to 4 weeks to hear back from a
potential reviewer (and at the end they would decline). Why would it take you so
long?

2.      IF YOU ACCEPT THE INVITATION TO REVIEW A MANUSCRIPT, DO IT WITHIN THE
TIME INDICATED BY THE JOURNAL. Remember that journals will give you anywhere
between 2 and 4 weeks to review the manuscript. If you don't plan to review the
document in the allotted time, please decline the invitation. I understand there
are unforeseen circumstances that will not allow for you to complete the review
on time once you have accepted the invitation. If this is the case, let the
editor know. In some occasions I had the "honor" to wait up to 6 months before
the reviewer would contact me to say "I'm sorry, I forgot the manuscript". In
another occasion, one reviewer never returned the review. After waiting for 4
months, I had to look for another reviewer. Can you imagine how upset the authors
were? Please review manuscripts on time.

3.      PLEASE WRITE COHERENT REVIEWS. Reviewers often complain about language in
the manuscripts. Let me tell you that you, as reviewer, are not that great
either. Some reviewers go on and on about something (like I am doing here), and
at the end neither the editor nor the authors know what the reviewer meant or
wants. Please be concise and make your point.

We all complain about the time it takes to review a manuscript, but we, as
reviewers, are part of the problem. There are conscious reviewers that provide
their reviews on time; however, most of us take longer than we should. If you do
your part, the process can be shortened considerably. Remember you are not God's
gift to the reviewing world. The editor can always look for somebody else with
similar expertise than you if you don't get in the way (by not responding or
taking too long to do something you agreed to do).

Eduardo Casas, Ph.D.
NADC
Ames, IA 50010
Eduardo.casasars.usda.gov

From igi2cornell.edu  Fri Mar  1 16:11:24 2013
From: Ikhide Imumorin <igi2cornell.edu>
Subject: RE: Compulsory OAP will cause an even larger increase in publishing 
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Fri, 01 Mar 2013 16:11:24 -0600

To Chris Moran: I was not referring to any one specific journal, just making
general comments that comes from my experience and experience of others with
societies' journals overall. Making early online views possible after acceptance
is a recent phenomenon, perhaps to compete with OA journals, which pioneered it
and that is a good thing. Anything that creates competition in the market place
results in better service to society. Good OA journals undergo rigorous peer
review ... no one will seriously argue that most BMC, Frontiers and PLOS journals
are not rigorously peer-reviewed, but most have higher IF and publish far more
papers than traditional/society journals even though they are expensive to
publish in. I think many traditional/societies are issued monthly or quarterly
while many OA journals are published online more frequently regardless of the
number of articles they get for a volume/issue. 

To Everyone:
So lets use specific journals like BMC Genomics (since 2000) versus Genomics
(since 1987) which are essentially competitors, yet the former has IF of 4 after
12 years while the latter has IF of 3 after 26 years. In addition BMC Genomics
charges an arm and a leg to publish while Genomics is free to authors. Obviously
BMC Genomics did something right to be only 12 years old and have a higher IF
than Genomics that is twice as old and indeed was born at the beginning of the
discipline of Genomics with a foreword written by the great Victor McKusick in
Volume 1, No 1. Clearly, there may be many reasons, but OA and fast publication
are two of the reasons. Does anyone have other explanations? They both draw
reviewers from essentially the same pool of scientists... someone said (Miguel I
think) at the beginning BMC had a publication discount to reward reviewers... if
true they used it to shorten turn around time from reviewers and build a rapid
reputation for fast publication that has served them well..

If there is an incentive to review for a journal, and I get a paper from that
journal versus another journal that has no such incentive, guess which paper I
will likely review first? My time is limited and as a rational human being, I
will make the choice that benefits me most. If folks think this is not a big
deal, that is fine. Everyone will decide how best to use their time.
Unfortunately publications is the currency of our career and life work, so we can
leave the system broken as it is now or try to improve things. If we are all
forced to the high priced OA model (looking more and more likely), it is only
going to be bad for science overall... because only those who have big grants
(not necessarily the best ideas) can publish in "good" journals. In some
disciplines such as high throughput genomics, only the well funded can do
meaningful work anymore... can you imagine trying to genotype say 3,000 animals
for GWAS with a high density SNP chip or do RNA-Seq of dozens of tissues without
a major grant of hundreds of thousands of dollars? So it looks like very soon,
you may not be able to publish your work unless you can come up with $2,000 -
$3,000 to pay "article processing charges". Traditional non-paying journals have
already launched the OA option that cost $3,000 - $3,500!


Ikhide Imumorin, PhD
Assistant Professor
Animal Breeding, Genetics and Genomics Group
Dept of Animal Science
267 Morrison Hall
Cornell University
Ithaca, NY 14853
USA
T 607-255-2850
F 607-255-9829
igi2cornell.edu

http://www.ansci.cornell.edu/faculty/imumorin.html

Editorial Board, Journal of Veterinary Science and Medical Diagnosis -
http://www.scitechnol.com/jvsmdhome.php
Associate Editor, Genomics and Quantitative Genetics -
http://www.knoblauchpublishing.com
Associate Editor, Journal of Applied Animal Research -
http://www.tandf.co.uk/journals/TAAR
Review Editor, Frontiers in Genetics - http://www.frontiersin.org/genetics

"So why not go out on a limb, isn't that where the fruit is?" - Frank Scully


________________________________________
.From: Christopher Moran [christopher.moransydney.edu.au]
.Sent: Thursday, February 28, 2013 4:36 PM
.To: Ikhide Imumorin
.Cc: Multiple Recipients of
.Subject: Re: Compulsory OAP will cause an even larger increase in publishing

I challenge Ikhide to provide the data to support his assertion that traditional
journals take over a year to publication compared with much faster publication
times in open access journals. For open access journals which don't have proper
peer review processes, this may be true, but I wouldn't want to publish in them.
If there is proper peer review, the open access journals are at the mercy if the
reviewers just as traditional journals (surely that has been an important point
of much if the discussion so far). I can assure you that difficulty in finding
reviewers and getting them to deliver their reports is largely responsible for
the delays in publication, open access or not.

Finally traditional journals which still publish in hard copy (and they are a
rapidly disappearing species), make papers available electronically via online
early or similar mechanisms as soon as the proofing process has been completed
and this may occur several months before the hard copy appears.
Chris Moran

From jillian.maddoxalumni.unimelb.edu.au  Sun Mar  3 23:02:28 2013
From: Jill Maddox <jillian.maddoxalumni.unimelb.edu.au>
Subject: RE: Compulsory OAP will cause an even larger increase in
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Sun, 03 Mar 2013 23:02:28 -0600

Hi Journal Editors

One big problem I have as a reviewer with doing timely reviews is 
when there is a problem with the quality of the English in a paper. 
The bigger the problem then the longer it takes me to do a review. 
This wastes a lot of time and I really resent receiving papers to 
review that are poorly written. I think the journal editors should 
not waste reviewers' time by sending out such papers. If journal 
editors insist on sending out such papers to reviewers then maybe 
there should be a category where a reviewer doesn't do a 
comprehensive review but simply states that the paper is within the 
scope of the journal and recommends that the English gets fixed 
before the paper is properly reviewed. I understand that many of 
these papers come from non-native English speakers (but some also 
come from native English speakers) and that some of them come from 
laboratories that do not have much funding but I think it is unfair 
to place the burden of suggesting corrections for English problems on 
to scientific reviewers (especially given there are excellent English 
proofreading services that are reasonably priced and offer rapid 
turnaround). On occasion when I have not made detailed suggestions as 
to how to remove typos, correct the grammar and improve the style, 
and have simply said that the English needs to be improved before 
publication, I have been horrified to see that papers have then been 
published without this happening. Publishing poorly written papers 
makes it much harder for readers to understand what the authors are 
trying to convey (particularly in the discussion section), and also 
sets bad examples for other authors to copy styles from. It probably 
also reduces the potential citation rate of the paper and the journal.

For those of you who haven't read it, Calcagno et al (2012 Science 
338: 1065-1069) demonstrate the value of reviewers in the citation 
rate for published papers https://www.sciencemag.org/content/338/6110/1065.

Regards


Jill


At 07:56 AM 2/03/2013, Casas, Eduardo wrote:
> From: "Casas, Eduardo" <Eduardo.CasasARS.USDA.GOV>
> Subject: RE: Compulsory OAP will cause an even larger increase in publishing
> To: Multiple Recipients of <angenmapanimalgenome.org>
>
> Dear all,
>
> This message is an offshoot of the main topic, but Chris Moran just touched 
> on an issue in publishing scientific literature (and maybe one of my pet 
> peeves): finding reviewers that can deliver their reports on time. I have
> had the "joy" of being an Associate Editor for a couple of journals. In this
> position, one difficulty is to reply to authors who complain their manuscript
> has taken too long to review. The problem resides mostly with the reviewers. 
> Most of you have or will be tagged to review a manuscript. Therefore, I would 
> like to plea to all of you the following:
>
> 1.  IF YOU DO NOT WANT TO REVIEW A MANUSCRIPT, DON'T ACCEPT THE INVITATION.
> If you receive a message inviting you to review a manuscript, accept or
> decline it soon after reading the message. This will allow the manuscript
> to move forward. If you don't have time for a review, decline it immediately. 
> There is no harm in declining the review of a manuscript. Your action will 
> allow the editor to look for another reviewer who can do it in a timely 
> fashion. Sometimes I have had the "privilege" to wait anywhere from 2 to 4 
> weeks to hear back from a potential reviewer (and at the end they would 
> decline). Why would it take you so long?
>
> 2.  IF YOU ACCEPT THE INVITATION TO REVIEW A MANUSCRIPT, DO IT WITHIN THE
> TIME INDICATED BY THE JOURNAL. Remember that journals will give you anywhere
> between 2 and 4 weeks to review the manuscript. If you don't plan to 
> review the document in the allotted time, please decline the invitation. I 
> understand there are unforeseen circumstances that will not allow for you to 
> complete the review on time once you have accepted the invitation. If this is
> the case, let the editor know. In some occasions I had the "honor" to wait up 
> to 6 months before the reviewer would contact me to say "I'm sorry, I forgot
> the manuscript". In another occasion, one reviewer never returned the review.
> After waiting for 4 months, I had to look for another reviewer. Can you 
> imagine how upset the authors were? Please review manuscripts on time.
>
> 3.  PLEASE WRITE COHERENT REVIEWS. Reviewers often complain about language in
> the manuscripts. Let me tell you that you, as reviewer, are not that great
> either. Some reviewers go on and on about something (like I am doing here),
> and at the end neither the editor nor the authors know what the reviewer meant 
> or wants. Please be concise and make your point.
>
> We all complain about the time it takes to review a manuscript, but we, as
> reviewers, are part of the problem. There are conscious reviewers that provide
> their reviews on time; however, most of us take longer than we should. If you >
do your part, the process can be shortened considerably. Remember you are not >
God's gift to the reviewing world. The editor can always look for somebody 
> else with similar expertise than you if you don't get in the way (by not 
> responding or taking too long to do something you agreed to do).
>
> Eduardo Casas, Ph.D.
> NADC
> Ames, IA 50010
> Eduardo.casasars.usda.gov

***************************************************************

Jill Maddox
16 Park Square
Port Melbourne, 3207
Australia
phone: 03 9646 0428
E-mail: jillian.maddoxalumni.unimelb.edu.au

***************************************************************
 

From joseluciohotmail.com Mon Mar  4 16:13:43 2013 
Date: Mon, 4 Mar 2013 16:13:41 +0000 
From: jose guerra <joseluciohotmail.com> 
To: angenmapanimalgenome.org
Subject: RE: Compulsory OAP will cause an even larger increase in 

Hi 

Have always not understood the business model behind the scientific
journals, maybe I am too simple minded for it. So here it is in my opinion
(how it is to me only) it is a business that someone comes up with the idea
and does the research, writes it up, and sends it to a publisher, who then
uses volunteers to review it for free, and then charges then inventor to
publish his work. The margin of profit on this must be nice for those in
the receiving end. It seems to me like another business that goes like
this: charge people to collect their money, to give to them their money,
and for the consequences of investing poorly their money: e.g. BANKS? it
seems that just like societies cannot do without the banks we the scientists 
cannot do without the scientific publishing system? (anologically only I 
am not fin or fiscal anarchy) Maybe if there was a group, like a labor 
union of science the situation could be improved? but it is a difficult 
situation for sure, nice topic to discuss.

Jose L. L. Guerra, Ph.D

Quantitative Genetics/Breeding StrategiesKeygene N.V.
    Agro Business Park 90  
    6708 PW Wageningen  
    The   Netherlands 


> From: jillian.maddoxalumni.unimelb.edu.au 
> Subject: RE: Compulsory OAP will cause an even larger increase in 
> To: angenmapanimalgenome.org 
> Date: Sun, 3 Mar 2013 23:02:28 -0600 
>  
> Hi Journal Editors 
>  
> One big problem I have as a reviewer with doing timely reviews is  
> when there is a problem with the quality of the English in a paper.  
> The bigger the problem then the longer it takes me to do a review.  
> This wastes a lot of time and I really resent receiving papers to  
> review that are poorly written. I think the journal editors should  
> not waste reviewers' time by sending out such papers. If journal  
> editors insist on sending out such papers to reviewers then maybe  
> there should be a category where a reviewer doesn't do a  
> comprehensive review but simply states that the paper is within the  
> scope of the journal and recommends that the English gets fixed  
> before the paper is properly reviewed. I understand that many of  
> these papers come from non-native English speakers (but some also  
> come from native English speakers) and that some of them come from  
> laboratories that do not have much funding but I think it is unfair  
> to place the burden of suggesting corrections for English problems on  
> to scientific reviewers (especially given there are excellent English  
> proofreading services that are reasonably priced and offer rapid  
> turnaround). On occasion when I have not made detailed suggestions as  
> to how to remove typos, correct the grammar and improve the style,  
> and have simply said that the English needs to be improved before  
> publication, I have been horrified to see that papers have then been  
> published without this happening. Publishing poorly written papers  
> makes it much harder for readers to understand what the authors are  
> trying to convey (particularly in the discussion section), and also  
> sets bad examples for other authors to copy styles from. It probably  
> also reduces the potential citation rate of the paper and the journal. 
>  
> For those of you who haven't read it, Calcagno et al (2012 Science  
> 338: 1065-1069) demonstrate the value of reviewers in the citation  
> rate for published papers https://www.sciencemag.org/content/338/6110/1065. 
>  
> Regards 
>  
>  
> Jill 
>  
>  
> At 07:56 AM 2/03/2013, Casas, Eduardo wrote: 
> > From: "Casas, Eduardo" <Eduardo.CasasARS.USDA.GOV> 
> > Subject: RE: Compulsory OAP will cause an even larger increase in publishing 
> > To: Multiple Recipients of <angenmapanimalgenome.org> 
> > 
> > Dear all, 
> > 
> > This message is an offshoot of the main topic, but Chris Moran just touched  
> > on an issue in publishing scientific literature (and maybe one of my pet  
> > peeves): finding reviewers that can deliver their reports on time. I have 
> > had the "joy" of being an Associate Editor for a couple of journals. In this 
> > position, one difficulty is to reply to authors who complain their manuscript 
> > has taken too long to review. The problem resides mostly with the reviewers.  
> > Most of you have or will be tagged to review a manuscript. Therefore, I would  
> > like to plea to all of you the following: 
> > 
> > 1.  IF YOU DO NOT WANT TO REVIEW A MANUSCRIPT, DON'T ACCEPT THE INVITATION. 
> > If you receive a message inviting you to review a manuscript, accept or 
> > decline it soon after reading the message. This will allow the manuscript 
> > to move forward. If you don't have time for a review, decline it immediately.  
> > There is no harm in declining the review of a manuscript. Your action will  
> > allow the editor to look for another reviewer who can do it in a timely  
> > fashion. Sometimes I have had the "privilege" to wait anywhere from 2 to 4  
> > weeks to hear back from a potential reviewer (and at the end they would  
> > decline). Why would it take you so long? 
> > 
> > 2.  IF YOU ACCEPT THE INVITATION TO REVIEW A MANUSCRIPT, DO IT WITHIN THE 
> > TIME INDICATED BY THE JOURNAL. Remember that journals will give you anywhere 
> > between 2 and 4 weeks to review the manuscript. If you don't plan to  
> > review the document in the allotted time, please decline the invitation. I  
> > understand there are unforeseen circumstances that will not allow for you to  
> > complete the review on time once you have accepted the invitation. If this is 
> > the case, let the editor know. In some occasions I had the "honor" to wait up  
> > to 6 months before the reviewer would contact me to say "I'm sorry, I forgot 
> > the manuscript". In another occasion, one reviewer never returned the review. 
> > After waiting for 4 months, I had to look for another reviewer. Can you  
> > imagine how upset the authors were? Please review manuscripts on time. 
> > 
> > 3.  PLEASE WRITE COHERENT REVIEWS. Reviewers often complain about language in 
> > the manuscripts. Let me tell you that you, as reviewer, are not that great 
> > either. Some reviewers go on and on about something (like I am doing here), 
> > and at the end neither the editor nor the authors know what the reviewer meant  
> > or wants. Please be concise and make your point. 
> > 
> > We all complain about the time it takes to review a manuscript, but we, as 
> > reviewers, are part of the problem. There are conscious reviewers that provide 
> > their reviews on time; however, most of us take longer than we should. If you
> > do your part, the process can be shortened considerably. Remember you are not 
> > God's gift to the reviewing world. The editor can always look for somebody  
> > else with similar expertise than you if you don't get in the way (by not  
> > responding or taking too long to do something you agreed to do). 
> > 
> > Eduardo Casas, Ph.D. 
> > NADC 
> > Ames, IA 50010 
> > Eduardo.casasars.usda.gov 
>  
> *************************************************************** 
>  
> Jill Maddox 
> 16 Park Square 
> Port Melbourne, 3207 
> Australia 
> phone: 03 9646 0428 
> E-mail: jillian.maddoxalumni.unimelb.edu.au 
>  
> *************************************************************** 

From zhuiastate.edu  Mon Mar 25 10:33:26 2013
From: "Hu, Zhiliang [AN S]" <zhuiastate.edu>
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Subject: FW: Publish or Perish
Date: Mon, 25 Mar 2013 10:33:26 -0500

-----Original Message-----
.From: Larry Schaeffer [lrsuoguelph.ca]
.Sent: Monday, March 25, 2013 10:15 AM
.To: Animal Geneticist's Discussion
.Subject: Publish or Perish

WELCOME TO THE FUTURE OF SCIENTIFIC PUBLISHING

ELARES is a new website for the collection and dissemination of scientific
research in Breeding and Genetics.

     No publication costs - free
     No subscription costs - free access, (must register as a user)
     No membership costs - free
     Immediate publication - no pre-review process
	
	Authors are responsible for content, quality, and appearance of papers
	No format specifications - authors are encouraged to be creative, use
colours and good taste
	
	Review Process is replaced by member ratings
	Average Ratings help viewers pick papers for reading
	
	Number of unique hits indicates popularity and/or usefulness of a paper,
can be used for promotion and tenure purposes
	Submitted papers are accessible to the world
	
	Members can choose to be notified of new submissions
	Enablers can submit and rate papers
	
	The first five papers in system are examples
	Papers may be updated after submission, if desired, by the person who 
submitted the paper

Go to

http://lirpa.aps.uoguelph.ca/elares/

ELARES will be subject to modification and improvements over the first year 
as comments are forthcoming.

Any questions, send to lrsuoguelph.ca

Larry Schaeffer

From igi2cornell.edu  Mon Mar 25 10:48:10 2013
From: Ikhide Godwin Imumorin <igi2cornell.edu>
Subject: RE: Publish or Perish
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Mon, 25 Mar 2013 10:48:10 -0500

This is great! I think we needed something like this for a long time. It would
serve to get attention to one's work from peers before peer-review for
publication in a scientific journal. Is this correct?


Ikhide Imumorin, PhD
Assistant Professor
Animal Breeding, Genetics and Genomics Group
Dept of Animal Science
267 Morrison Hall
Cornell University
Ithaca, NY 14853
USA
T 607-255-2850
F 607-255-9829
igi2cornell.edu

http://www.ansci.cornell.edu/faculty/imumorin.html

Editorial Board, Journal of Veterinary Science and Medical Diagnosis -
http://www.scitechnol.com/jvsmdhome.php
Associate Editor, Genomics and Quantitative Genetics -
http://www.knoblauchpublishing.com
Associate Editor, Journal of Applied Animal Research -
http://www.tandf.co.uk/journals/TAAR
Review Editor, Frontiers in Genetics - http://www.frontiersin.org/genetics

"So why not go out on a limb, isn't that where the fruit is?" - Frank Scully


-----Original Message-----
.From: Larry Schaeffer [lrsuoguelph.ca]
.Sent: Monday, March 25, 2013 10:15 AM
.To: Animal Geneticist's Discussion
.Subject: Publish or Perish

WELCOME TO THE FUTURE OF SCIENTIFIC PUBLISHING

ELARES is a new website for the collection and dissemination of scientific
research in Breeding and Genetics.

     No publication costs - free
     No subscription costs - free access, (must register as a user)
     No membership costs - free
     Immediate publication - no pre-review process

        Authors are responsible for content, quality, and appearance of papers
        No format specifications - authors are encouraged to be creative, use
   colours and good taste

        Review Process is replaced by member ratings
        Average Ratings help viewers pick papers for reading

        Number of unique hits indicates popularity and/or usefulness of a paper,
can be
used for promotion and tenure purposes
        Submitted papers are accessible to the world

        Members can choose to be notified of new submissions
        Enablers can submit and rate papers

        The first five papers in system are examples
        Papers may be updated after submission, if desired, by the person who
submitted
the paper

Go to

http://lirpa.aps.uoguelph.ca/elares/

ELARES will be subject to modification and improvements over the first year as
comments are forthcoming.

Any questions, send to lrsuoguelph.ca

Larry Schaeffer

From dj.dekoningroslin.ed.ac.uk  Mon Mar 25 15:28:48 2013
From: DE KONING DJ <dj.dekoningroslin.ed.ac.uk>
Subject: RE: Publish or Perish
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Mon, 25 Mar 2013 15:28:48 -0500

Dear Larry et al,
 
This may be one future of Scientific Publishing but I will nail my colours 
the mast and whole heartedly disagree.

Without a proper peer review your online paper is nothing more than a 
glorified Blog Post and the 'post-publishing review' is no substitute for 
proper editorial and peer review procedures.  Even WIKIPEDIA entries are 
subject to more scrutiny than proposed for this journal.
 
With all of us complaining about the refereeing loads that we have, how do 
you expect that researchers with the right expertise to assess a manuscript (!) 
will voluntarily take time to do a proper review of a manuscript that is 
posted online?  Would you trust a publication in ELARES enough to cite it 
in your own work? 

I will look with great suspicion upon a job applicant with glowing repertoire 
of ELARES publications rather than regular journals.

I agree the current system of publishing is not perfect but some of the 
alternatives, including the one outlined here, reduce scientific publishing 
to game of 'likes' and 'dislikes' that I really do not want to be part of.


DJ de Koning

________________________________________
.From: Hu, Zhiliang [AN S] [zhuiastate.edu]
.Sent: 25 March 2013 15:33
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: FW: Publish or Perish

-----Original Message-----
.From: Larry Schaeffer [lrsuoguelph.ca]
.Sent: Monday, March 25, 2013 10:15 AM
.To: Animal Geneticist's Discussion
.Subject: Publish or Perish

WELCOME TO THE FUTURE OF SCIENTIFIC PUBLISHING

ELARES is a new website for the collection and dissemination of scientific
research in Breeding and Genetics.

     No publication costs - free
     No subscription costs - free access, (must register as a user)
     No membership costs - free
     Immediate publication - no pre-review process
    
    Authors are responsible for content, quality, and appearance of papers
    No format specifications - authors are encouraged to be creative, use
colours and good taste
    
    Review Process is replaced by member ratings
    Average Ratings help viewers pick papers for reading
    
    Number of unique hits indicates popularity and/or usefulness of a paper,
can be used for promotion and tenure purposes
    Submitted papers are accessible to the world
    
    Members can choose to be notified of new submissions
    Enablers can submit and rate papers
    
    The first five papers in system are examples
    Papers may be updated after submission, if desired, by the person who 
submitted the paper

Go to

http://lirpa.aps.uoguelph.ca/elares/

ELARES will be subject to modification and improvements over the first year 
as comments are forthcoming.

Any questions, send to lrsuoguelph.ca

Larry Schaeffer

From steibeljmsu.edu  Mon Mar 25 16:04:21 2013
From: Juan Pedro Steibel <steibeljmsu.edu>
Subject: Re: Publish or Perish
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Mon, 25 Mar 2013 16:04:21 -0500

Hello Everyone,
This discussion may turn VERY interesting.

Given posts by Larry Schaeffer and DJ DeKoning I have a couple question 
(to the managers of ELARES and to editors of peer-reviewed journals) on 
the practical aspects of submitting to ELARES and to peer-review journals.

1) Does uploading a manuscript to ELARES precludes (later) submission of 
a "revised version" to a journal? If the answer is yes, my follow up 
question is 'why?'
2) If a "revised version" is published in a peer review journal would 
there be a way to indicate (maybe link) that in ELARES?
3) If a revised version is submitted to a journal, should the author be 
able to include 'preliminary review and evidence of potential impact' 
from ELARES record in the letter to the editors? Should such reviews be 
taken into account by the editors and referees?
4) If a manuscript is submitted and reviewed in ELARES and 
(substantially) improved, then submitted somewhere else, would it be 
desirable (morally right?) to invite (public) ELARES reviewers as 
co-authors?
5) If two versions get out (in ELARES and peer-review journal), and both 
versions of the paper start to be cited... How would we 
measure/summarize/compare impact of the creation represented by two papers?

I might have more as I "ruminate" all this.

Cheers and thanks in advance!!!
Juan P.

On 3/25/2013 4:28 PM, DE KONING DJ wrote:

> Dear Larry et al,
>   
> This may be one future of Scientific Publishing but I will nail my colours 
> the mast and whole heartedly disagree.
>
> Without a proper peer review your online paper is nothing more than a 
> glorified Blog Post and the 'post-publishing review' is no substitute for 
> proper editorial and peer review procedures.
> Even WIKIPEDIA entries are subject to more scrutiny than proposed for this 
> journal.
>   
> With all of us complaining about the refereeing loads that we have, how do you 
> expect that researchers with the right expertise to assess a manuscript (!) 
> will voluntarily take time to do a
> proper review of a manuscript that is posted online?  Would you trust 
> publication in ELARES enough to cite it in your own work?
>
> I will look with great suspicion upon a job applicant with glowing repertoire 
> of ELARES publications rather than regular journals.
>
> I agree the current system of publishing is not perfect but some of the 
> alternatives, including the one outlined here, reduce scientific publishing to 
> game of 'likes' and 'dislikes' that I really do not want to be part of.
>
>
> DJ de Koning

-- 
=============================
Juan Pedro Steibel

Assistant Professor
Statistical Genetics and Genomics

Department of Animal Science &
Department of Fisheries and Wildlife

Michigan State University
1205-I Anthony Hall
East Lansing, MI
48824 USA

Phone: 1-517-353-5102
E-mail: steibeljmsu.edu
=============================
  

From gianolaansci.wisc.edu  Mon Mar 25 16:33:34 2013
From: Daniel Gianola <gianolaansci.wisc.edu>
Subject: RE: Publish or Perish
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Mon, 25 Mar 2013 16:33:34 -0500

I just wish to note that a strong tradition in mathematics and statistics is
that of publishing technical reports, prior to publication in refereed
papers. The reason for this is that the review times are much longer; some
of my colleagues in mathematics say that sometime it may take one to two
tears before obtaining a review. People cite Technical Reports all over the
place and I see little indication of serious damage there.

ELARES may provide a means for interaction (and implicit scoring) as well as
for a wider and faster dissemination of scientific results. I am less
skeptical than DJ concerning "negative" effects or "quality control"
matters. A good counter-example is that of R: it is free, rich, flexible,
and you use it at your own risk. How much damage does R produce? I often see
that scientist publishing in high profile journals use R to make splendid,
spectacular graphs. Should this cause us to doubt the content of those
papers because R is not peer reviewed? Is there a chance that these
spectacular graphs are wrong even if published in Nature or Science?

Are there any randomized studies in favor of the current system showing,
beyond reasonable doubt, that the present system is the best possible one in
terms of advancing knowledge?

I do not have an answer, but ELARES is an experiment, and the hypothesis of
whether it is good or bad can be refuted experimentally.

Larry, thanks for the initiative.

Daniel


-----Original Message-----
.From: Juan Pedro Steibel [mailto:steibeljmsu.edu] 
.Sent: Monday, March 25, 2013 4:04 PM
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: Re: Publish or Perish

Hello Everyone,
This discussion may turn VERY interesting.

Given posts by Larry Schaeffer and DJ DeKoning I have a couple question (to
the managers of ELARES and to editors of peer-reviewed journals) on the
practical aspects of submitting to ELARES and to peer-review journals.

1) Does uploading a manuscript to ELARES precludes (later) submission of a
"revised version" to a journal? If the answer is yes, my follow up question
is 'why?'
2) If a "revised version" is published in a peer review journal would there
be a way to indicate (maybe link) that in ELARES?
3) If a revised version is submitted to a journal, should the author be able
to include 'preliminary review and evidence of potential impact' 
from ELARES record in the letter to the editors? Should such reviews be
taken into account by the editors and referees?
4) If a manuscript is submitted and reviewed in ELARES and
(substantially) improved, then submitted somewhere else, would it be
desirable (morally right?) to invite (public) ELARES reviewers as
co-authors?
5) If two versions get out (in ELARES and peer-review journal), and both
versions of the paper start to be cited... How would we
measure/summarize/compare impact of the creation represented by two papers?

I might have more as I "ruminate" all this.

Cheers and thanks in advance!!!
Juan P.

On 3/25/2013 4:28 PM, DE KONING DJ wrote:

> Dear Larry et al,
>   
> This may be one future of Scientific Publishing but I will nail my 
> colours the mast and whole heartedly disagree.
>
> Without a proper peer review your online paper is nothing more than a 
> glorified Blog Post and the 'post-publishing review' is no substitute 
> for proper editorial and peer review procedures.
> Even WIKIPEDIA entries are subject to more scrutiny than proposed for 
> this journal.
>   
> With all of us complaining about the refereeing loads that we have, 
> how do you expect that researchers with the right expertise to assess 
> a manuscript (!) will voluntarily take time to do a proper review of a 
> manuscript that is posted online?  Would you trust publication in 
> ELARES enough to cite it in your own work?
>
> I will look with great suspicion upon a job applicant with glowing 
> repertoire of ELARES publications rather than regular journals.
>
> I agree the current system of publishing is not perfect but some of 
> the alternatives, including the one outlined here, reduce scientific 
> publishing to game of 'likes' and 'dislikes' that I really do not want to
be part of.
>
>
> DJ de Koning

--
=============================
Juan Pedro Steibel

Assistant Professor
Statistical Genetics and Genomics

Department of Animal Science &
Department of Fisheries and Wildlife

Michigan State University
1205-I Anthony Hall
East Lansing, MI
48824 USA

Phone: 1-517-353-5102
E-mail: steibeljmsu.edu
=============================
  

From david.machughucd.ie  Mon Mar 25 17:04:53 2013
From: "David MacHugh" <david.machughucd.ie>
Subject: RE: Publish or Perish
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Mon, 25 Mar 2013 17:04:53 -0500

Does arXiv not already represent a solution to the problem being discussed
here?

http://arxiv.org/archive/q-bio

http://en.wikipedia.org/wiki/ArXiv

Best regards,

David.

-----Original Message-----
.From: Daniel Gianola [mailto:gianolaansci.wisc.edu] 
.Sent: 25 March 2013 21:34
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: RE: Publish or Perish

I just wish to note that a strong tradition in mathematics and statistics is
that of publishing technical reports, prior to publication in refereed
papers. The reason for this is that the review times are much longer; some
of my colleagues in mathematics say that sometime it may take one to two
tears before obtaining a review. People cite Technical Reports all over the
place and I see little indication of serious damage there.

ELARES may provide a means for interaction (and implicit scoring) as well as
for a wider and faster dissemination of scientific results. I am less
skeptical than DJ concerning "negative" effects or "quality control"
matters. A good counter-example is that of R: it is free, rich, flexible,
and you use it at your own risk. How much damage does R produce? I often see
that scientist publishing in high profile journals use R to make splendid,
spectacular graphs. Should this cause us to doubt the content of those
papers because R is not peer reviewed? Is there a chance that these
spectacular graphs are wrong even if published in Nature or Science?

Are there any randomized studies in favor of the current system showing,
beyond reasonable doubt, that the present system is the best possible one in
terms of advancing knowledge?

I do not have an answer, but ELARES is an experiment, and the hypothesis of
whether it is good or bad can be refuted experimentally.

Larry, thanks for the initiative.

Daniel


-----Original Message-----
.From: Juan Pedro Steibel [mailto:steibeljmsu.edu]
.Sent: Monday, March 25, 2013 4:04 PM
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: Re: Publish or Perish

Hello Everyone,
This discussion may turn VERY interesting.

Given posts by Larry Schaeffer and DJ DeKoning I have a couple question (to
the managers of ELARES and to editors of peer-reviewed journals) on the
practical aspects of submitting to ELARES and to peer-review journals.

1) Does uploading a manuscript to ELARES precludes (later) submission of a
"revised version" to a journal? If the answer is yes, my follow up question
is 'why?'
2) If a "revised version" is published in a peer review journal would there
be a way to indicate (maybe link) that in ELARES?
3) If a revised version is submitted to a journal, should the author be able
to include 'preliminary review and evidence of potential impact' 
from ELARES record in the letter to the editors? Should such reviews be
taken into account by the editors and referees?
4) If a manuscript is submitted and reviewed in ELARES and
(substantially) improved, then submitted somewhere else, would it be
desirable (morally right?) to invite (public) ELARES reviewers as
co-authors?
5) If two versions get out (in ELARES and peer-review journal), and both
versions of the paper start to be cited... How would we
measure/summarize/compare impact of the creation represented by two papers?

I might have more as I "ruminate" all this.

Cheers and thanks in advance!!!
Juan P.

On 3/25/2013 4:28 PM, DE KONING DJ wrote:

> Dear Larry et al,
> This may be one future of Scientific Publishing but I will nail my 
> colours the mast and whole heartedly disagree.
>
> Without a proper peer review your online paper is nothing more than a 
> glorified Blog Post and the 'post-publishing review' is no substitute 
> for proper editorial and peer review procedures.
> Even WIKIPEDIA entries are subject to more scrutiny than proposed for 
> this journal.
> With all of us complaining about the refereeing loads that we have, 
> how do you expect that researchers with the right expertise to assess 
> a manuscript (!) will voluntarily take time to do a proper review of a 
> manuscript that is posted online?  Would you trust publication in 
> ELARES enough to cite it in your own work?
>
> I will look with great suspicion upon a job applicant with glowing 
> repertoire of ELARES publications rather than regular journals.
>
> I agree the current system of publishing is not perfect but some of 
> the alternatives, including the one outlined here, reduce scientific 
> publishing to game of 'likes' and 'dislikes' that I really do not want 
> to
be part of.
>
>
> DJ de Koning

--
=============================
Juan Pedro Steibel

Assistant Professor
Statistical Genetics and Genomics

Department of Animal Science &
Department of Fisheries and Wildlife

Michigan State University
1205-I Anthony Hall
East Lansing, MI
48824 USA

Phone: 1-517-353-5102
E-mail: steibeljmsu.edu
=============================



From dj.dekoningroslin.ed.ac.uk  Tue Mar 26 07:40:48 2013
From: DE KONING DJ <dj.dekoningroslin.ed.ac.uk>
Subject: RE: Publish or Perish
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Tue, 26 Mar 2013 07:40:48 -0500

Dear Juan-Pedro,

If a paper is published online in full many (all?) of the current peer-reviewed
journals will consider the manuscript published and they will not consider it for
publication.

The reason of 'why' is very simple:

Journals want to attract readers and citations and so if the exciting results are
already in the public domain who needs to read the journal article anyway?
Journals, and faculties, like to write press releases when they have some really
interesting results in order to deal with the promotion of the science (and the
journal!).

You can check the IFA of journals but most state that the cover letter must
include a statement that the work is not considered for publication elsewhere. Or
they ha a similar tick box in the online submission.

This would include publication through ELARES I think.

DJ 

________________________________________
.From: Juan Pedro Steibel [steibeljmsu.edu]
.Sent: 25 March 2013 20:54
.To: DE KONING DJ
.Cc: Multiple Recipients of
.Subject: Re: Publish or Perish

Hello Everyone,
This discussion may turn VERY interesting.

Given posts by Larry Schaeffer and DJ DeKoning I have a couple question
(to the managers of ELARES and to editors of peer-reviewed journals) on
the practical aspects of submitting to ELARES and to peer-review journals.

1) Does uploading a manuscript to ELARES precludes (later) submission of
a "revised version" to a journal? If the answer is yes, my follow up
question is 'why?'
2) If a "revised version" is published in a peer review journal would
there be a way to indicate (maybe link) that in ELARES?
3) If a revised version is submitted to a journal, should the author be
able to include 'preliminary review and evidence of potential impact'
from ELARES record in the letter to the editors? Should such reviews be
taken into account by the editors and referees?
4) If a manuscript is submitted and reviewed in ELARES and
(substantially) improved, then submitted somewhere else, would it be
desirable (morally right?) to invite (public) ELARES reviewers as
co-authors?
5) If two versions get out (in ELARES and peer-review journal), and both
versions of the paper start to be cited... How would we
measure/summarize/compare impact of the creation represented by two papers?

I might have more as I "ruminate" all this.

Cheers and thanks in advance!!!
Juan P.

From ctbmsu.edu  Tue Mar 26 07:41:41 2013
From: "C. Titus Brown" <ctbmsu.edu>
Subject: Re: Publish or Perish
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Tue, 26 Mar 2013 07:41:41 -0500

On Mon, Mar 25, 2013 at 05:04:53PM -0500, David MacHugh wrote:

> Does arXiv not already represent a solution to the problem being discussed
> here?
> 
> http://arxiv.org/archive/q-bio
> 
> http://en.wikipedia.org/wiki/ArXiv
> 
> Best regards,
> 
> David.

Please see

http://haldanessieve.org/faq/

for some good commonly-asked questions about preprints and biology and
arXiv.

best,

--titus

From John.ColeARS.USDA.GOV  Tue Mar 26 07:42:44 2013
From: "Cole, John" <John.ColeARS.USDA.GOV>
Subject: Re: Publish or Perish
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Tue, 26 Mar 2013 07:42:44 -0500

David-

My understanding is that arXiv could be a solution if there is a group of
people willing to pay to have a new section added to the site. That is,
while it's free to submit to arXiv, they do not add new
discipline-specific sections without 1) a careful consideration as to the
demand/size of community interested in that topic, and 2) some payment for
the work required to make the necessary changes to their system to support
that. I believe that is an integral part of their sustainability plan.

That said, I think that ELARES can look to arXiv as a model. There's a lot
of nonsense posted there -- physics does appear to attract more than its
fair share of cranks -- which is promptly ignored by the scientific
community. That is, the wheat is separated from the chaff fairly
effectively. I do note, though, that there isn't a nice DOI-type
identifier that can be used to refer to ELARES articles (yet?).

Personally, I see the value of ELARES at two-fold: 1) it can be used to
establish the priority of discovery or formulation of an idea, and 2) it
is MUCH faster than going through the traditional peer review process,
particularly when the length of time required for technical editing and
typesetting for journal such as JDS is considered.

I don't get the impression that Larry or anyone else is suggesting that
this is a replacement for the current model of scientific publishing which
includes peer review. In most cases, I find that review dramatically
improves the quality of my papers, and I hope I'm not alone in that. I do
think that it could be a good place to share incremental or highly
speculative work, software announcements, and that kind of thing. As the
number of submissions reaches a critical mass the quality will increase.

Best wishes,

John
--
Dr. John B. Cole, Research Geneticist (Animal)
Animal Improvement Programs Laboratory, ARS, USDA
Room 306, Bldg 005, BARC-West
10300 Baltimore Avenue
Beltsville, MD 20705-2350

E-mail: john.colears.usda.gov
Phone: 301-504-8665
Cell: 240-603-8426
Fax: 301-504-8092


On 3/25/13 6:04 PM, "David MacHugh" <david.machughucd.ie> wrote:

>Does arXiv not already represent a solution to the problem being discussed
>here?
>
>http://arxiv.org/archive/q-bio
>
>http://en.wikipedia.org/wiki/ArXiv
>
>Best regards,
>
>David.

From dj.dekoningroslin.ed.ac.uk  Tue Mar 26 08:05:43 2013
From: DE KONING DJ <dj.dekoningroslin.ed.ac.uk>
Subject: RE: Publish or Perish
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Tue, 26 Mar 2013 08:05:43 -0500

A very good overview of journal policies regarding pre-print services is on:
http://www.sherpa.ac.uk/romeo/search.php

Most journals allow a pre-submission copy to be deposited. Whether you are
allowed to post a copy post peer-review varies per journal.
 Most journal do not allow depositing of a type-set copy of the manuscript.
If in doubt, check with the editor.

DJ

________________________________________
.From: Juan Pedro Steibel [steibeljmsu.edu]
.Sent: 25 March 2013 20:54
.To: DE KONING DJ
.Cc: Multiple Recipients of
.Subject: Re: Publish or Perish

Hello Everyone,
This discussion may turn VERY interesting.

Given posts by Larry Schaeffer and DJ DeKoning I have a couple question
(to the managers of ELARES and to editors of peer-reviewed journals) on
the practical aspects of submitting to ELARES and to peer-review journals.

1) Does uploading a manuscript to ELARES precludes (later) submission of
a "revised version" to a journal? If the answer is yes, my follow up
question is 'why?'
2) If a "revised version" is published in a peer review journal would
there be a way to indicate (maybe link) that in ELARES?
3) If a revised version is submitted to a journal, should the author be
able to include 'preliminary review and evidence of potential impact'
from ELARES record in the letter to the editors? Should such reviews be
taken into account by the editors and referees?
4) If a manuscript is submitted and reviewed in ELARES and
(substantially) improved, then submitted somewhere else, would it be
desirable (morally right?) to invite (public) ELARES reviewers as
co-authors?
5) If two versions get out (in ELARES and peer-review journal), and both
versions of the paper start to be cited... How would we
measure/summarize/compare impact of the creation represented by two papers?

I might have more as I "ruminate" all this.

Cheers and thanks in advance!!!
Juan P.

From Frank.Siewerdtcobb-vantress.com  Tue Mar 26 08:40:29 2013
From: "Siewerdt, Frank" <Frank.Siewerdtcobb-vantress.com>
Subject: RE: Publish or Perish
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Tue, 26 Mar 2013 08:40:29 -0500

Larry,

One has to applaud your initiative. Naturally there will be a lot of pushback
because, as humans, we are all afraid of getting out of our comfort zones. The
existence of this current system of peer-reviewed publication is no indication
that it is the ideal one. Good things have come out of it, but also out of 
manual typewriters, Ford T cars, MSX computers (remember those?), the postal 
service, and many other things that we consider "obsolete" today.

Moving forward is never easy. The argument that publishers want to attract
readers is legitimate but to attract citations is a travesty that needs to be 
put down as soon as possible. This notion that metrics can be put into judging 
a paper is ludicrous. Remember the scene from "Dead Poets Society" where the
English teacher was patronizing the author of the textbook that claimed that
poetry had two dimensions and that the quality and relevance of a poem could 
be plotted on a Cartesian coordinate system? But it is the easy way that some
academic administrators found to cut down the hard work of thoroughly 
evaluating effort and relevance. It also gives room for big egos to flourish 
and for grant money to be hoarded in a way that is convenient to some groups. 
We all know that.  It's the 600 pound octopus in the room that is conveniently 
ignored.

ELARES will be a success. Many concerns raised by Juan Pedro, Daniel, DJ are
valid and very relevant but on the long run some of the current practices and
barriers that were created are somewhat artificial (like Juan Pedro's first 
point).

Happy publishing!

Frank.

Frank Siewerdt, Ph.D.
Geneticist, Cobb-Vantress, Inc.
370 Cobb Rd., Deer Lodge, TN 37726 USA
Phone: +1 (423) 965 5030 ext. 222
Mobile: +1 (423) 215 1146
Email: frank.siewerdtcobb-vantress.com


-----Original Message-----
.From: Cole, John [mailto:John.ColeARS.USDA.GOV] 
.Sent: Tuesday, March 26, 2013 8:43 AM
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: Re: Publish or Perish

David-

My understanding is that arXiv could be a solution if there is a group of people
willing to pay to have a new section added to the site. That is, while it's free
to submit to arXiv, they do not add new discipline-specific sections without 1) 
a careful consideration as to the demand/size of community interested in that
topic, and 2) some payment for the work required to make the necessary changes 
to their system to support that. I believe that is an integral part of their 
sustainability plan.

That said, I think that ELARES can look to arXiv as a model. There's a lot 
of nonsense posted there -- physics does appear to attract more than its fair 
share of cranks -- which is promptly ignored by the scientific community. That 
is, the wheat is separated from the chaff fairly effectively. I do note, 
though, that there isn't a nice DOI-type identifier that can be used to refer 
to ELARES articles (yet?).

Personally, I see the value of ELARES at two-fold: 1) it can be used to 
establish the priority of discovery or formulation of an idea, and 2) it is 
MUCH faster than going through the traditional peer review process, 
particularly when the length of time required for technical editing and 
typesetting for journal such as JDS is considered.

I don't get the impression that Larry or anyone else is suggesting that this 
is a replacement for the current model of scientific publishing which includes 
peer review. In most cases, I find that review dramatically improves the 
quality of my papers, and I hope I'm not alone in that. I do think that it 
could be a good place to share incremental or highly speculative work, software 
announcements, and that kind of thing. As the number of submissions reaches a 
critical mass the quality will increase.

Best wishes,

John
--
Dr. John B. Cole, Research Geneticist (Animal) Animal Improvement Programs
Laboratory, ARS, USDA Room 306, Bldg 005, BARC-West
10300 Baltimore Avenue
Beltsville, MD 20705-2350

E-mail: john.colears.usda.gov
Phone: 301-504-8665
Cell: 240-603-8426
Fax: 301-504-8092


On 3/25/13 6:04 PM, "David MacHugh" <david.machughucd.ie> wrote:

>Does arXiv not already represent a solution to the problem being 
>discussed here?
>
>http://arxiv.org/archive/q-bio
>
>http://en.wikipedia.org/wiki/ArXiv
>
>Best regards,
>
>David.

From mick.watsonroslin.ed.ac.uk  Tue Mar 26 09:36:50 2013
From: WATSON Mick <mick.watsonroslin.ed.ac.uk>
Subject: Re: Publish or Perish
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Tue, 26 Mar 2013 09:36:50 -0500

But why couldn't genetics papers go into the existing qbio section of arXiv?  I
imagine most genetics papers have a significant quantitative biology influence...

WATSON Mick


-------- Original message --------
.From: "Cole, John" <John.ColeARS.USDA.GOV>
.Date:
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: Re: Publish or Perish

David-

My understanding is that arXiv could be a solution if there is a group of
people willing to pay to have a new section added to the site. That is,
while it's free to submit to arXiv, they do not add new
discipline-specific sections without 1) a careful consideration as to the
demand/size of community interested in that topic, and 2) some payment for
the work required to make the necessary changes to their system to support
that. I believe that is an integral part of their sustainability plan.

That said, I think that ELARES can look to arXiv as a model. There's a lot
of nonsense posted there -- physics does appear to attract more than its
fair share of cranks -- which is promptly ignored by the scientific
community. That is, the wheat is separated from the chaff fairly
effectively. I do note, though, that there isn't a nice DOI-type
identifier that can be used to refer to ELARES articles (yet?).

Personally, I see the value of ELARES at two-fold: 1) it can be used to
establish the priority of discovery or formulation of an idea, and 2) it
is MUCH faster than going through the traditional peer review process,
particularly when the length of time required for technical editing and
typesetting for journal such as JDS is considered.

I don't get the impression that Larry or anyone else is suggesting that
this is a replacement for the current model of scientific publishing which
includes peer review. In most cases, I find that review dramatically
improves the quality of my papers, and I hope I'm not alone in that. I do
think that it could be a good place to share incremental or highly
speculative work, software announcements, and that kind of thing. As the
number of submissions reaches a critical mass the quality will increase.

Best wishes,

John
--
Dr. John B. Cole, Research Geneticist (Animal)
Animal Improvement Programs Laboratory, ARS, USDA
Room 306, Bldg 005, BARC-West
10300 Baltimore Avenue
Beltsville, MD 20705-2350

E-mail: john.colears.usda.gov
Phone: 301-504-8665
Cell: 240-603-8426
Fax: 301-504-8092


On 3/25/13 6:04 PM, "David MacHugh" <david.machughucd.ie> wrote:

>Does arXiv not already represent a solution to the problem being discussed
>here?
>
>http://arxiv.org/archive/q-bio
>
>http://en.wikipedia.org/wiki/ArXiv
>
>Best regards,
>
>David.

From takele_tayeyahoo.com  Tue Mar 26 09:43:53 2013
From: takele taye <takele_tayeyahoo.com>
Subject: Re: Publish or Perish
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Tue, 26 Mar 2013 09:43:53 -0500

Dear All
 
I thought that, it might be more appealing to perform the peer review process 
at the institution (s) of the authors by colleagues and staffs instead of 
submitting non-reviewed manuscripts directly to ELARES. However, the reviewing 
staffs need to be motivated for example through rank promotion or if possible 
through financial incentives.  Posting non-reviewed manuscripts might have 
less importance for the advancement of science.

Kindest regards

Takele Taye Desta

Centre for Genetics and Genomics,
School of Biology,
University of Nottingham,
University Park, Nottingham, UK


--- On Tue, 3/26/13, Cole, John <John.ColeARS.USDA.GOV> wrote:

.From: Cole, John <John.ColeARS.USDA.GOV>
.Subject: Re: Publish or Perish
.To: "Multiple Recipients of" <angenmapanimalgenome.org>
.Date: Tuesday, March 26, 2013, 5:42 AM

David-

My understanding is that arXiv could be a solution if there is a group of
people willing to pay to have a new section added to the site. That is,
while it's free to submit to arXiv, they do not add new
discipline-specific sections without 1) a careful consideration as to the
demand/size of community interested in that topic, and 2) some payment for
the work required to make the necessary changes to their system to support
that. I believe that is an integral part of their sustainability plan.

That said, I think that ELARES can look to arXiv as a model. There's a lot
of nonsense posted there -- physics does appear to attract more than its
fair share of cranks -- which is promptly ignored by the scientific
community. That is, the wheat is separated from the chaff fairly
effectively. I do note, though, that there isn't a nice DOI-type
identifier that can be used to refer to ELARES articles (yet?).

Personally, I see the value of ELARES at two-fold: 1) it can be used to
establish the priority of discovery or formulation of an idea, and 2) it
is MUCH faster than going through the traditional peer review process,
particularly when the length of time required for technical editing and
typesetting for journal such as JDS is considered.

I don't get the impression that Larry or anyone else is suggesting that
this is a replacement for the current model of scientific publishing which
includes peer review. In most cases, I find that review dramatically
improves the quality of my papers, and I hope I'm not alone in that. I do
think that it could be a good place to share incremental or highly
speculative work, software announcements, and that kind of thing. As the
number of submissions reaches a critical mass the quality will increase.

Best wishes,

John
--
Dr. John B. Cole, Research Geneticist (Animal)
Animal Improvement Programs Laboratory, ARS, USDA
Room 306, Bldg 005, BARC-West
10300 Baltimore Avenue
Beltsville, MD 20705-2350

E-mail: john.colears.usda.gov
Phone: 301-504-8665
Cell: 240-603-8426
Fax: 301-504-8092


On 3/25/13 6:04 PM, "David MacHugh" <david.machughucd.ie> wrote:

>Does arXiv not already represent a solution to the problem being discussed
>here?
>
>http://arxiv.org/archive/q-bio
>
>http://en.wikipedia.org/wiki/ArXiv
>
>Best regards,
>
>David.

From zhuiastate.edu  Tue Mar 26 17:35:41 2013
From: "Hu, Zhiliang [AN S]" <zhuiastate.edu>
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Subject: FW: Publish or Perish
Date: Tue, 26 Mar 2013 17:35:41 -0500

This is again a forward, with permission, of Larry Schaeffer's follow up 
email on the subject originally posted on AGDG list. Note that Larry is
currently not on ANGENMAP list. Please write directly to him if so wished.

Zhiliang


-----Original Message-----
.From: Larry Schaeffer [lrsuoguelph.ca]
.Sent: Tuesday, March 26, 2013 11:08 AM
.To: Animal Geneticist's Discussion
.Subject: RE: Publish or Perish

Since my message yesterday there have been over 260 new registered 
users.  Photos of the users are optional, but I was surprised by the 
number who actually put in a photo of themselves.

So far, no submitted papers.  But that first paper will be viewed by 260 
users as soon as it is posted.  Imagine the pressure on the authors to 
submit something of quality.

ELARES is an experiment.  I don't have any answers on where it might 
lead, but we'll see.  All I know is that it is possible to publish 
papers for nothing, and to not charge anyone for looking at them. And 
release is as soon as the authors submit it.  I don't see any other 
journals coming close to this kind of operation.  I wanted to give 
people an alternative to the status quo.  Any issues you might have are 
your own prejudices and biases.  I didn't expect this to agree with 
everyone's taste.  You can ignore it, or you can use it, your choice, 
but let everyone make up their own mind.

My son is in computer science/mathematics doing a Masters.  He has 6 
papers in arXiv, of which 1 has been cited 3 times by other authors.  
Those papers are not likely to be published anywhere else.  Math is 
different from genetics.  In Math you have proofs for everything, and 
the proof is either correct or not.  If not, it doesn't get submitted.  
In genetics, we have models and we know that all models are incorrect.  
Always a non-zero probability that it is wrong.  My point is that my son 
has had his papers exposed to the world and that has got him attention, 
all during the course of his MSc program of 2 years.  He hasn't had to 
wait a year to get his papers published formally.  Those papers got him 
offers for PhD work at MIT and Stanford.  If arXiv didn't exist, who knows?

I hope when people are evaluating someone (job applicant for example) 
that they not just count the number of referreed papers versus not 
refereed, but look more at the content of those papers, from either 
source.  Not all referreed papers are equal.  Nor will be all 
non-referreed papers.  Suppose one applicant has 2 referreed papers, and 
another has 20 non-referreed papers.  The second applicant is at least 
doing more work, I'd say.  But then I would look carefully at those 
papers too, for both applicants.  People that need number counts to 
determine quality are not doing justice to society.

A lot of people making comments about ELARES have not even registered 
and looked around the site.  How open minded is that?

Larry Schaeffer


  

From mfrothsciastate.edu  Wed Mar 27 09:39:00 2013
From: "Rothschild, Max F [AN S]" <mfrothsciastate.edu>
Subject: RE: Publish or Perish
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Wed, 27 Mar 2013 09:39:00 -0500

Dear Colleagues,

I am sure I will regret this but.....

I have read most of the notes recently posted on Angenmap and on AGDG.  Many of
the comments focus on complaints about the present system and the need to find
alternatives that are free, easy and open.  I agree with many of the complaints
but the solutions proposed seem full of potholes.

While some insist quality will follow I have my doubts.  As someone who has
published a number of papers in many journals let me state the obvious:

Reviews are often slow and on occasion poor.
Journals are expensive to own and many time publication costs seem excessive.
Formatting is a pain in the...
it would be nice to write the work up and publish in a few days.

But let me remind you of the old saying "things are usually worth their cost"

The new publishing model proposed has many flaws.
If there is no peer review and there is no cost how will these journals be any
different than the usual stuff on the web that no one really can verify?

Frankly, I am really disappointed in my colleagues who are such rigorous
scientists and conduct outstanding research and then at the finish line don't
want to publish in the usual way - as I said sure we all have complaints BUT we
can improve the system


 1) volunteer to do more reviews
 2) do you reviews without bias
 3) do your reviews in a more speedy manner
 4) offer to be on editorial boards
 5) if you don't like the cost find a different journal with lower costs

Let's try to fix the system instead of trying to build a new one.


Max Rothschild
Iowa State University
  

From robertonzimagmail.com  Wed Mar 27 09:53:43 2013
From: Robert Onzima <robertonzimagmail.com>
Subject: Re: Publish or Perish
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Wed, 27 Mar 2013 09:53:43 -0500

Dear all,

I will concur with the view. Indeed the journals may be expensive and slow,
BUT probably at the end the cost and time is worth, needless to say that
there needs to be strategies to minimize the 'abnormal' disparities. We can
surely improve and plan better.

Robert


On Wed, Mar 27, 2013 at 5:39 PM, Rothschild, Max F [AN S] <mfrothsciastate.edu> 
wrote:

> Dear Colleagues,
>
> I am sure I will regret this but.....
>
> I have read most of the notes recently posted on Angenmap and on AGDG. Many of
> the comments focus on complaints about the present system and the need to find
> alternatives that are free, easy and open.  I agree with many of the complaints
> but the solutions proposed seem full of potholes.
>
> While some insist quality will follow I have my doubts.  As someone who has
> published a number of papers in many journals let me state the obvious:
>
> Reviews are often slow and on occasion poor.
> Journals are expensive to own and many time publication costs seem excessive.
> Formatting is a pain in the...
> it would be nice to write the work up and publish in a few days.
>
> But let me remind you of the old saying "things are usually worth their cost"
>
> The new publishing model proposed has many flaws.
> If there is no peer review and there is no cost how will these journals be any
> different than the usual stuff on the web that no one really can verify?
>
> Frankly, I am really disappointed in my colleagues who are such rigorous
> scientists and conduct outstanding research and then at the finish line don't
> want to publish in the usual way - as I said sure we all have complaints BUT we
> can improve the system
>
>  1) volunteer to do more reviews
>  2) do you reviews without bias
>  3) do your reviews in a more speedy manner
>  4) offer to be on editorial boards
>  5) if you don't like the cost find a different journal with lower costs
>
> Let's try to fix the system instead of trying to build a new one.
>
>
> Max Rothschild
> Iowa State University

-- 
Ir. Robert B. Onzima,
Research Officer - Animal Production Science
National Agricultural Research Organization (NARO)/
Kachwekano ZARDI
P.O.Box 421, Kabale,
Tel. +256 426 492 (Office)/ +256782/714/701 701 185 (Cell)
Email: robertonzimagmail.com/ robertonzimayahoo.co.uk.

From ctbmsu.edu  Wed Mar 27 10:10:49 2013
From: "C. Titus Brown" <ctbmsu.edu>
Subject: Re: Publish or Perish
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Wed, 27 Mar 2013 10:10:49 -0500

On Wed, Mar 27, 2013 at 09:39:00AM -0500, Rothschild, Max F [AN S] wrote:

> Dear Colleagues,
> 
> I am sure I will regret this but.....
> 
> I have read most of the notes recently posted on Angenmap and on AGDG.  Many of
> the comments focus on complaints about the present system and the need to find
> alternatives that are free, easy and open.  I agree with many of the complaints
> but the solutions proposed seem full of potholes.
> 
> While some insist quality will follow I have my doubts.  As someone who has
> published a number of papers in many journals let me state the obvious:
> 
> Reviews are often slow and on occasion poor.
> Journals are expensive to own and many time publication costs seem excessive.
> Formatting is a pain in the...
> it would be nice to write the work up and publish in a few days.
> 
> But let me remind you of the old saying "things are usually worth their cost"
> 
> The new publishing model proposed has many flaws.
> If there is no peer review and there is no cost how will these journals be any
> different than the usual stuff on the web that no one really can verify?
> 
> Frankly, I am really disappointed in my colleagues who are such rigorous
> scientists and conduct outstanding research and then at the finish line don't
> want to publish in the usual way - as I said sure we all have complaints BUT we
> can improve the system
> 
>  1) volunteer to do more reviews
>  2) do you reviews without bias
>  3) do your reviews in a more speedy manner
>  4) offer to be on editorial boards
>  5) if you don't like the cost find a different journal with lower costs
> 
> Let's try to fix the system instead of trying to build a new one.

Max et al.,

is is clear that we are stuck with the current system for a while, and I share
your concern about moving too fast.  However, there are substantial and real
concerns about the current model, which evolved over many decades and has
little data to support its optimality.

For an excellent review of the problems, I refer you to

Classical peer review: an empty gun, by Richard Smith
http://breast-cancer-research.com/content/12/S4/S13

Joe Pickrell has a nice summary of the paper in this excellent blog post,
http://www.genomesunzipped.org/...in-peer-reviewed-journals.php:

"""
To summarize, peer review is costly (in terms of time and money), random (the
correlation in perceived "publishability" of a paper between two groups
of reviewers is little better than zero), ineffective at detecting errors,
biased towards established groups and against originality, and sometimes abused
(in that reviewers can steal ideas from papers they review or block the
publication of competitors).
"""

Given the demonstrated success of approaches like arXiv in other fields of
science:

http://www.nature.com/...l/v476/n7359/full/476145a.html

I think it behooves us biologists to explore these other successful models
and see if we can use them or, if not, adapt them to our needs.

best,
--titus
-- 
C. Titus Brown, ctbmsu.edu
  

From Roger.VallejoARS.USDA.GOV  Wed Mar 27 10:23:23 2013
From: "Vallejo, Roger" <Roger.VallejoARS.USDA.GOV>
Subject: RE: Publish or Perish
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Wed, 27 Mar 2013 10:23:23 -0500

Hi Max,

No. This time, you will not regret about this because there is not a perfect
system of peer reviewed publications. Of course we should improve the current
one, the problem is in the how? I will simply say that I pretty much agree with
your 1-5 cents.

Roger


Roger L. Vallejo, Ph.D.
U.S. Department of Agriculture, ARS, NCCCWA
Voice:  (304) 724-8340 Ext. 2141
Email:  roger.vallejoars.usda.gov
http://www.ars.usda.gov/...people/people.htm?personid7662


-----Original Message-----
.From: Rothschild, Max F [AN S] [mailto:mfrothsciastate.edu]
.Sent: Wednesday, March 27, 2013 10:39 AM
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: RE: Publish or Perish

Dear Colleagues,

I am sure I will regret this but.....

I have read most of the notes recently posted on Angenmap and on AGDG.  Many of
the comments focus on complaints about the present system and the need to find
alternatives that are free, easy and open.  I agree with many of the complaints
but the solutions proposed seem full of potholes.

While some insist quality will follow I have my doubts.  As someone who has
published a number of papers in many journals let me state the obvious:

Reviews are often slow and on occasion poor.
Journals are expensive to own and many time publication costs seem excessive.
Formatting is a pain in the...
it would be nice to write the work up and publish in a few days.

But let me remind you of the old saying "things are usually worth their cost"

The new publishing model proposed has many flaws.
If there is no peer review and there is no cost how will these journals be any
different than the usual stuff on the web that no one really can verify?

Frankly, I am really disappointed in my colleagues who are such rigorous
scientists and conduct outstanding research and then at the finish line don't
want to publish in the usual way - as I said sure we all have complaints BUT we
can improve the system

 1) volunteer to do more reviews
 2) do you reviews without bias
 3) do your reviews in a more speedy manner
 4) offer to be on editorial boards
 5) if you don't like the cost find a different journal with lower costs

Let's try to fix the system instead of trying to build a new one.


Max Rothschild
Iowa State University  

From gianolaansci.wisc.edu  Wed Mar 27 10:35:22 2013
From: Daniel Gianola <gianolaansci.wisc.edu>
Subject: RE: Publish or Perish
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Wed, 27 Mar 2013 10:35:22 -0500

Titus:

Good points. Concerning your comment:

<<Joe Pickrell has a nice summary of the paper in this excellent blog post,
http://www.genomesunzipped.org/...lish-science-in-peer-reviewed-
journals.php:

"""
To summarize, peer review is costly (in terms of time and money), random
(the correlation in perceived "publishability" of a paper between two groups
of reviewers is little better than zero), ineffective at detecting errors,
biased towards established groups and against originality, and sometimes
abused (in that reviewers can steal ideas from papers they review or block
the publication of competitors).
"""
>>

The same applies to research proposals, a theme we discussed some time ago
in this forum. I will share an example: a few years ago, I submitted a
proposal to NSF (interface between mathematics and biology). The grant was
rejected 3 times, but the interesting thing was that, in each subsequent
iteration, the reviewer's scores were decreasing monotonically, as opposed
to increasing, contrary to expectation (one would assume that if one
complies with reviewers' requirements, the proposal should get better and
better). In other words, the peer review instead of increasing the perceived
value of the project, deteriorated it.

The whole process took 4 years. Finally, the project did not get funded.

A serious problem is that, like human beings they are, scientists are biased
and conservative and, quite often, they tend to stick with the null
hypothesis even if shown wrong, sometimes arguing that the alternative is
not much more "useful"...I thought that, contrary to technology, any valid
scientific result is useful, irrespective of whether the results refute or
corroborate some standing paradigm.

Daniel


  

From craig.primmerutu.fi  Wed Mar 27 10:57:51 2013
From: Craig Primmer <craig.primmerutu.fi>
Subject: RE: Publish or Perish
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Wed, 27 Mar 2013 10:57:51 -0500

Dear all,

now that the discussion has moved in a slightly different direction, I would like
to draw your attention to a new concept that is designed to help improve some
aspects of the current system as highlighted by Max. It is called Peerage of
Science (http://www.peerageofscience.org/) , and has been set up by several
Finnish scientists who are aiming to change the way the peer review process is
conducted in order to benefit particularly authors, but also those offering their
services for free: reviewers and associate editors.

The idea is that instead of sending a manuscript from journal to journal and a
separate review process being conducted each time, articles are submitted to PoS
and reviewed by volunteer reviewers only once. All that review the manuscript
rate the reviews of the other reviewers (a reviewer quality score) and the
authors then revise the manuscript and finally, any journal using the system
could make an offer to publish. If authors got multiple offers, they could then
choose the journal they wish to publish in. A (smallish) number of papers have
been accepted via the system now (mostly ecology journals).

The benefits for authors is that the time to acceptance should be shorter, and
more predictable, for reviewers, if you're a good reviewer and get a good score,
you can add it to your CV, for associate editors- you never have to find another
reviewer, but rather just scan reviewed manuscripts and make offers on the ones
that suit your journal.

I will not go into this further, but feel free to check out the website and
decide if you would like to be involved. The system is slowly gaining momentum in
ecology and evolution circles, but they are aiming to work across fields, so any
field where the main journals join the service could benefit.

I have joined the community there and reviewed an article, but I have not yet
submitted any papers. I have no conflicts of interest to declare other than
living in the same country as the founders and discussing the system with them
over a few beers ;)

Best

Craig Primmer

PS- I am just a messenger, so please direct questions to the founders via the
website. They are very keen to discuss this!

-------------------------------------------------
Craig Primmer


Academy Professor
Division of Genetics and Physiology
Department of Biology (Vesilinnantie 5)
20014 University of Turku
FINLAND


Office +358 2 333 5571
Mobile +358 40 1560 365
Fax. +358 2 333 6680
craig.primmerutu.fi
http://users.utu.fi/primmer
-------------------------------------------------

________________________________________
.From: C. Titus Brown [ctbmsu.edu]
.Sent: 27 March 2013 17:10
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: Re: Publish or Perish

On Wed, Mar 27, 2013 at 09:39:00AM -0500, Rothschild, Max F [AN S] wrote:

> Dear Colleagues,
>
> I am sure I will regret this but.....
>
> I have read most of the notes recently posted on Angenmap and on AGDG.  Many of
> the comments focus on complaints about the present system and the need to find
> alternatives that are free, easy and open.  I agree with many of the complaints
> but the solutions proposed seem full of potholes.
>
> While some insist quality will follow I have my doubts.  As someone who has
> published a number of papers in many journals let me state the obvious:
>
> Reviews are often slow and on occasion poor.
> Journals are expensive to own and many time publication costs seem excessive.
> Formatting is a pain in the...
> it would be nice to write the work up and publish in a few days.
>
> But let me remind you of the old saying "things are usually worth their cost"
>
> The new publishing model proposed has many flaws.
> If there is no peer review and there is no cost how will these journals be any
> different than the usual stuff on the web that no one really can verify?
>
> Frankly, I am really disappointed in my colleagues who are such rigorous
> scientists and conduct outstanding research and then at the finish line don't
> want to publish in the usual way - as I said sure we all have complaints BUT we
> can improve the system
>
>  1) volunteer to do more reviews
>  2) do you reviews without bias
>  3) do your reviews in a more speedy manner
>  4) offer to be on editorial boards
>  5) if you don't like the cost find a different journal with lower costs
>
> Let's try to fix the system instead of trying to build a new one.

Max et al.,

is is clear that we are stuck with the current system for a while, and I share
your concern about moving too fast.  However, there are substantial and real
concerns about the current model, which evolved over many decades and has
little data to support its optimality.

For an excellent review of the problems, I refer you to

Classical peer review: an empty gun, by Richard Smith
http://breast-cancer-research.com/content/12/S4/S13

Joe Pickrell has a nice summary of the paper in this excellent blog post,
http://www.genomesunzipped.org/...in-peer-reviewed-journals.php:

"""
To summarize, peer review is costly (in terms of time and money), random (the
correlation in perceived "publishability" of a paper between two groups
of reviewers is little better than zero), ineffective at detecting errors,
biased towards established groups and against originality, and sometimes abused
(in that reviewers can steal ideas from papers they review or block the
publication of competitors).
"""

Given the demonstrated success of approaches like arXiv in other fields of
science:

http://www.nature.com/...l/v476/n7359/full/476145a.html

I think it behooves us biologists to explore these other successful models
and see if we can use them or, if not, adapt them to our needs.

best,
--titus
--
C. Titus Brown, ctbmsu.edu
  

From mheydarpuoguelph.ca  Wed Mar 27 10:58:23 2013
From: Mahyar Heydarpour <mheydarpuoguelph.ca>
Subject: Re: Publish or Perish
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Wed, 27 Mar 2013 10:58:23 -0500

When Mark Zuckerberg (2004) invented Facebook website for himself and 3 of his
classmates at Harvard University, nobody could imagine the number of members
exceeded over 1 billion users just after 8 years.

I think "ELARES" is a great idea particularly for the young scientists who have
not enough money like "MAX" to publish their research works. In fact ELARES is a
good place that people can share their knowledge and their scientific research
findings with each others. I don't think at the moment ELARES give any credit to
anybody who submit his/her articles. Let see the half of the full glass of water,
because anybody can see the empty part! 

I would like to congratulate Larry for his creativity and invented this useful
tool. Of course nothing is perfect in our world however we can try to make it
better and better. I don't think is fair enough to judge about ELARES after 3
days of announcement. We can have a fair evaluation after one year at least!

Have a great day!

Mahyar 

----------------------------
Mahyar Heydarpour (PhD)
Research Scientist
CABG genomics group
Harvard Medical School
Boston, MA, 02115



----- Original Message -----
.From: "Max F Rothschild [AN S]" <mfrothsciastate.edu>
.To: "Multiple Recipients of" <angenmapanimalgenome.org>
.Sent: Wednesday, March 27, 2013 10:39:00 AM
.Subject: RE: Publish or Perish

Dear Colleagues,

I am sure I will regret this but.....

I have read most of the notes recently posted on Angenmap and on AGDG.  Many of
the comments focus on complaints about the present system and the need to find
alternatives that are free, easy and open.  I agree with many of the complaints
but the solutions proposed seem full of potholes.

While some insist quality will follow I have my doubts.  As someone who has
published a number of papers in many journals let me state the obvious:

Reviews are often slow and on occasion poor.
Journals are expensive to own and many time publication costs seem excessive.
Formatting is a pain in the...
it would be nice to write the work up and publish in a few days.

But let me remind you of the old saying "things are usually worth their cost"

The new publishing model proposed has many flaws.
If there is no peer review and there is no cost how will these journals be any
different than the usual stuff on the web that no one really can verify?

Frankly, I am really disappointed in my colleagues who are such rigorous
scientists and conduct outstanding research and then at the finish line don't
want to publish in the usual way - as I said sure we all have complaints BUT we
can improve the system

 1) volunteer to do more reviews
 2) do you reviews without bias
 3) do your reviews in a more speedy manner
 4) offer to be on editorial boards
 5) if you don't like the cost find a different journal with lower costs

Let's try to fix the system instead of trying to build a new one.

Max Rothschild
Iowa State University

From danyel.jennenmaastrichtuniversity.nl  Wed Mar 27 11:45:58 2013
From: "Jennen Danyel (TGX)" <danyel.jennenmaastrichtuniversity.nl>
Subject: RE: Publish or Perish 
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Wed, 27 Mar 2013 11:45:58 -0500

Dear all,

In the past I've used Nature Precedings to submit some work presented at a
conference. An ideal way to present unpublished data for free and to be
able to cite it in a peer-reviewed paper. Unfortunately, since April 2012
(after 5 years) Nature Precedings stopped accepting any new contributions,
but past contributions remain accessible. One of the latest contributions
fits the discussion on Angenmap:
http://precedings.nature.com/documents/7151/version/1 In this brief report
5 qualities an open data-sharing platform should have are proposed and 10
benefits are mentioned.

Qualities 
1. Quality control 
2. User-friendly 
3. Low costs 
4. Permanent and citable 
5. Social and search engine optimized 
 
Benefits: 
1. Negative data can be reported and shared 
2. Preliminary data reporting can foster collaborations 
3. Demonstration of feasability and preliminary data for grant applications 
   with shrinking page limits 
4. Students can publish their findings on small projects that enable them 
   to establish themselves in scientific research 
5. Novel findings can be established in a permanent and citable digital record 
6. Findings from unfunded pilot projects can be reported 
7. Free general public access to scientific findings 
8. Copyright is retained by the creator of the work, the researcher, not the 
   publisher 
9. Fast (days) compared to the established peer review model (months) 
10. Venue for early crowd-funding of small project 

Also in the report several other QDSPs have been mentioned, including Arxiv: 
http://www.f1000research.com/ 
http://figshare.com/ 
http://www.neuro-cloud.net/ 
http://arxiv.org/

ELARES should be added to this list.

Best regards, Danyel

 
	Danyel Jennen  
	Assistant Professor 
	Department of Toxicogenomics 
	danyel.jennenmaastrichtuniversity.nl  
	www.toxicogenomics-um.nl  

	Room 5.578A, Universiteitssingel 40, 6229 ER Maastricht  
	P.O. Box 616, 6200 MD Maastricht, The Netherlands  
	T +31 (0)43-3883983 F +31 (0)43-3884146  

	website: www.toxicogenomics.nl  
    Please consider your environmental responsibility before printing this e-mail.  


From gabor.meszarosboku.ac.at  Wed Mar 27 15:04:18 2013
From: "Gabor Meszaros" <gabor.meszarosboku.ac.at>
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Subject: Antw: RE: Publish or Perish
Date: Wed, 27 Mar 2013 15:04:18 -0500

Dear all,

I have been following the email discussions over ELARES, but I don't
feel my publication record allows me to judge the "classical" system vs
the new one. I tend to agree with the people who say: Let's wait and see. 
Clearly there can be no harm done. If a big-enough group will adopt the
idea, then it is great, if not, and ELARES should fade away... well...
at least there was a honest try. The time will tell.

What I would like to really ask, if the site could be used for slightly
other purposes as well, in addition to the  "conventional" research
papers. Some possibilities were outlined in the previous emails, but I
have something specific in mind, which I would call keynote papers.
I imagine these as short, 1-2 page documents about any topic in which
the animal breeding community is interested in. Some examples of the
research proposal, review and publication systems were discussed on this
forum, but it is hard to find them once the hype is over. ELARES could
serve a a safe place visited by many, providig the basis and and the
medium of the discussion. I can imagine "response papers" from those who
strongly disagree or the papers can be referred to in the discussions
such as this one.

I would love to read about the thoughts of experienced people who have
something to say, or which could not be otherwise published in the
mainstream journals.


Kind regards,
Gabor


Dr. G�bor M�sz�ros
University of Natural Resources and Life Sciences
Division of Livestock Sciences
(Universit�t f�r Bodenkultur
Institut f�r Nutztierwissenschaften) 
Gregor-Mendel-Stra�e 33
A-1180 Vienna, Austria

Tel. (office): +43 1 47654 3259
mail: gabor.meszarosboku.ac.at

>>> Craig Primmer  27.03.13 16.59 Uhr >>>


Dear all,

now that the discussion has moved in a slightly different direction, I would like
to draw your attention to a new concept that is designed to help improve some
aspects of the current system as highlighted by Max. It is called Peerage of
Science (http://www.peerageofscience.org/) , and has been set up by several
Finnish scientists who are aiming to change the way the peer review process is
conducted in order to benefit particularly authors, but also those offering their
services for free: reviewers and associate editors.

The idea is that instead of sending a manuscript from journal to journal and a
separate review process being conducted each time, articles are submitted to PoS
and reviewed by volunteer reviewers only once. All that review the manuscript
rate the reviews of the other reviewers (a reviewer quality score) and the
authors then revise the manuscript and finally, any journal using the system
could make an offer to publish. If authors got multiple offers, they could then
choose the journal they wish to publish in. A (smallish) number of papers have
been accepted via the system now (mostly ecology journals).

The benefits for authors is that the time to acceptance should be shorter, and
more predictable, for reviewers, if you're a good reviewer and get a good score,
you can add it to your CV, for associate editors- you never have to find another
reviewer, but rather just scan reviewed manuscripts and make offers on the ones
that suit your journal.

I will not go into this further, but feel free to check out the website and
decide if you would like to be involved. The system is slowly gaining momentum in
ecology and evolution circles, but they are aiming to work across fields, so any
field where the main journals join the service could benefit.

I have joined the community there and reviewed an article, but I have not yet
submitted any papers. I have no conflicts of interest to declare other than
living in the same country as the founders and discussing the system with them
over a few beers ;)

Best

Craig Primmer

PS- I am just a messenger, so please direct questions to the founders via the
website. They are very keen to discuss this!

-------------------------------------------------
Craig Primmer


Academy Professor
Division of Genetics and Physiology
Department of Biology (Vesilinnantie 5)
20014 University of Turku
FINLAND


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From jgibson5une.edu.au  Thu Mar 28 07:49:04 2013 
From: John Gibson <jgibson5une.edu.au> 
Subject: RE: Publish or Perish? 
Postmaster: submission approved 
To: Multiple Recipients of <angenmapanimalgenome.org> 
Date: Thu, 28 Mar 2013 07:49:04 -0500 

One regret Max may have is that I agree with much that Max has articulated
(sorry Max, it is usually a much more interesting discussion when we
disagree). I see little evidence that the current system is fundamentally
broken but there is certainly every reason to push for it to continuously
evolve to better processes and structures.

While most correspondents have voiced concern about the costs of publishing
I have not seen an analysis of the real costs to the publisher (which
should include the profit they require to be interested in remaining in
business) of publishing under different models or the cost-benefits to the
research community of different models. Talk of paying reviewers for their
services might be considered more equitable but that will further increase
the cost of publication, and the cost of publication and/or access to
papers seems to be a bigger issue for most people than whether or not we
get paid for our services as reviewers.

It is useful to put the cost of publishing research results in the context
of the full cost of research. About 10 years ago an external review panel I
was working with stated that the average cost of research per publication
in biological/agriculture subjects in developed countries was in excess of
$100,000 per paper. In this context a fee of approx $2000 (i.e less than 2%
of total cost) to get the results published does not seem excessive. Based
on proposals I have reviewed in recent years I would guess the current full
cost (external grants + institutional costs) of the research behind each
per peer review publication is very much higher than $100,000. Has anyone
seen a recent assessment of research costs per peer review publication?

While not all funding agencies allow publication costs to be included, a
large number do, and in reality the cost to our institutions of publishing
in open access journals is trivial in relation to the costs of employing
the researchers. So for most researchers in developed countries the move to
open access can be budgeted for where there is the will to do so. The
challenge then is how to support researchers who genuinely have very
limited resources; for example (but not limited to) colleagues in
developing countries. Many but far from all journals have mechanisms to
reduce or remove costs for truly needy researchers and there remain many
journals that do not charge publication fees.

An issue to consider as a variety of electronic publishing systems emerge
is whether a given system is likely to be sustained in the long-term and if
not does that mean that all the papers on that system risk becoming
inaccessible at some future date?

 
 
John Gibson 
University of New England 
Armidale, NSW 2351 
Australia 

 
-----Original Message----- 
.From: Rothschild, Max F [AN S] [mailto:mfrothsciastate.edu]  
.Sent: Thursday, 28 March 2013 1:39 AM 
.To: Multiple Recipients of <AnGenMapanimalgenome.org> 
.Subject: RE: Publish or Perish 

Dear Colleagues,

I am sure I will regret this but.....

I have read most of the notes recently posted on Angenmap and on AGDG. Many
of the comments focus on complaints about the present system and the need
to find alternatives that are free, easy and open. I agree with many of the
complaints but the solutions proposed seem full of potholes.

While some insist quality will follow I have my doubts. As someone who has
published a number of papers in many journals let me state the obvious:

Reviews are often slow and on occasion poor. Journals are expensive to own
and many time publication costs seem excessive. Formatting is a pain in
the... it would be nice to write the work up and publish in a few days.

But let me remind you of the old saying "things are usually worth their
cost"

The new publishing model proposed has many flaws. If there is no peer
review and there is no cost how will these journals be any different than
the usual stuff on the web that no one really can verify?

Frankly, I am really disappointed in my colleagues who are such rigorous
scientists and conduct outstanding research and then at the finish line
don't want to publish in the usual way - as I said sure we all have
complaints BUT we can improve the system

 1) volunteer to do more reviews 
 2) do you reviews without bias 
 3) do your reviews in a more speedy manner 
 4) offer to be on editorial boards 
 5) if you don't like the cost find a different journal with lower costs 

Let's try to fix the system instead of trying to build a new one.

 
Max Rothschild 
Iowa State University 

From mfrothsciastate.edu  Thu Mar 28 10:17:51 2013
From: "Rothschild, Max F [AN S]" <mfrothsciastate.edu>
Subject: RE: Publish or Perish?
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Thu, 28 Mar 2013 10:17:51 -0500

Thanks John for the comments  ( I marked my colander as a day we agreed :-) ,
especially relating to the real cost of publications and the relationship of
publication cost to experimental costs.

Thanks also to the many people who wrote me privately and said they agreed but
didn't want to join the public discussion.

I was troubled by one remark yesterday that implied that as a more established
researcher I of course had more funds to support publication.  I don't see it
that way at all - as John said I write it into grants I get to do the work.
Without the work then no publications.

Now someone should calculate the number of researcher hours spent on this topic
and then consider the real cost of the discussion  ;-)

best to all

Max


-----Original Message-----
.From: John Gibson [mailto:jgibson5une.edu.au] 
.Sent: Thursday, March 28, 2013 7:49 AM
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: RE: Publish or Perish?

One regret Max may have is that I agree with much that Max has articulated (sorry
Max, it is usually a much more interesting discussion when we disagree). I see
little evidence that the current system is fundamentally broken but there is
certainly every reason to push for it to continuously evolve to better processes
and structures.

While most correspondents have voiced concern about the costs of publishing I 
have not seen an analysis of the real costs to the publisher (which should 
include the profit they require to be interested in remaining in business) of 
publishing under different models or the cost-benefits to the research community 
of different models. Talk of paying reviewers for their services might be 
considered more equitable but that will further increase the cost of 
publication, and the cost of publication and/or access to papers seems to be a 
bigger issue for most people than whether or not we get paid for our services as 
reviewers. 

It is useful to put the cost of publishing research results in the context of 
the full cost of research. About 10 years ago an external review panel I was 
working with stated that the average cost of research per publication in 
biological/agriculture subjects in developed countries was in excess of
$100,000 per paper. In this context a fee of approx $2000 (i.e less than 2% of 
total cost) to get the results published does not seem excessive. Based on 
proposals I have reviewed in recent years I would guess the current full cost 
(external grants + institutional costs) of the research behind each per peer 
review publication is very much higher than $100,000. Has anyone seen a recent 
assessment of research costs per peer review publication?

While not all funding agencies allow publication costs to be included, a large 
number do, and in reality the cost to our institutions of publishing in open 
access journals is trivial in relation to the costs of employing the 
researchers. So for most researchers in developed countries the move to open 
access can be budgeted for where there is the will to do so. The challenge then 
is how to support researchers who genuinely have very limited resources; for 
example (but not limited to) colleagues in developing countries. Many but far 
from all journals have mechanisms to reduce or remove costs for truly needy 
researchers and there remain many journals that do not charge publication fees.

An issue to consider as a variety of electronic publishing systems emerge is 
whether a given system is likely to be sustained in the long-term and if not 
does that mean that all the papers on that system risk becoming inaccessible at 
some future date?



John Gibson
University of New England
Armidale, NSW 2351
Australia


-----Original Message-----
.From: Rothschild, Max F [AN S] [mailto:mfrothsciastate.edu]
.Sent: Thursday, 28 March 2013 1:39 AM
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: RE: Publish or Perish

Dear Colleagues,

I am sure I will regret this but.....

I have read most of the notes recently posted on Angenmap and on AGDG.  Many of 
the comments focus on complaints about the present system and the need to find 
alternatives that are free, easy and open.  I agree with many of the complaints 
but the solutions proposed seem full of potholes.

While some insist quality will follow I have my doubts.  As someone who has 
published a number of papers in many journals let me state the obvious:

Reviews are often slow and on occasion poor.
Journals are expensive to own and many time publication costs seem excessive.
Formatting is a pain in the...
it would be nice to write the work up and publish in a few days.

But let me remind you of the old saying "things are usually worth their cost"

The new publishing model proposed has many flaws.
If there is no peer review and there is no cost how will these journals be any 
different than the usual stuff on the web that no one really can verify?

Frankly, I am really disappointed in my colleagues who are such rigorous 
scientists and conduct outstanding research and then at the finish line don't 
want to publish in the usual way - as I said sure we all have complaints BUT we 
can improve the system

 1) volunteer to do more reviews
 2) do you reviews without bias
 3) do your reviews in a more speedy manner
 4) offer to be on editorial boards
 5) if you don't like the cost find a different journal with lower costs

Let's try to fix the system instead of trying to build a new one.


Max Rothschild
Iowa State University

From ignacyuga.edu  Thu Mar 28 10:58:09 2013
From: Ignacy Misztal <ignacyuga.edu>
Subject: Re: Publish or Perish?
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Thu, 28 Mar 2013 10:58:09 -0500

Max and John make good argument about the cost of research versus the 
cost of publications. This argument looks different in some 
groups/countries where salaries are paid by the government but 
publishing costs need to come out of scarce operating budget.

We may ask ourselves why we publish. After all, we can publish on our 
own website. If titles are meaningful, google searches will find those.

We publish in refereed for a variety of reasons:
1. Summarize  a project that needs to end with paper(s).
2. Give young scientists tools for job search.
3. Claim credit for a new idea.
4. Share unclear results as a next incremental step towards a particular goal.
5. Have sufficient number of refereed publications / year as job requirement.
6. As above but to build CV for salary increase, better chance of grants, new 
   job opportunites, awards,...
7. Have paper in elite journal for benefits that come with publishing in
   elite journals.
8. ....

If we want to publish fast for reasons 4-6, we want fast yet cheap publishing.
If we want quality feedback, we want journals that are read and also with 
reviewers who value those journals. Such journals have limited space so they 
have to be selective.

I am sometimes frustrated with a slow review process, but I am even more 
happy when "nasty" reviewers insist on something and they are right. 
Better slow and find something exciting than realize later that a 
published paper is misleading or even harmful.

Some known groups published very little in reviewed journals. For instance,  
details of a multibreed model for beef, a big topic in beef at a time, were 
never published by Cornell in a refereed journal. Seems 1-7 did not apply. 
A friend of mine who managed to publish in Nature is eager to wait years 
without publishing for another high-impact publication. Only point 8 counts 
for him!


Ignacy


On 3/28/2013 8:49 AM, John Gibson wrote:

> One regret Max may have is that I agree with much that Max has articulated
> (sorry Max, it is usually a much more interesting discussion when we
> disagree). I see little evidence that the current system is fundamentally
> broken but there is certainly every reason to push for it to continuously
> evolve to better processes and structures.
> 
> While most correspondents have voiced concern about the costs of publishing
> I have not seen an analysis of the real costs to the publisher (which
> should include the profit they require to be interested in remaining in
> business) of publishing under different models or the cost-benefits to the
> research community of different models. Talk of paying reviewers for their
> services might be considered more equitable but that will further increase
> the cost of publication, and the cost of publication and/or access to
> papers seems to be a bigger issue for most people than whether or not we
> get paid for our services as reviewers.
> 
> It is useful to put the cost of publishing research results in the context
> of the full cost of research. About 10 years ago an external review panel I
> was working with stated that the average cost of research per publication
> in biological/agriculture subjects in developed countries was in excess of
> $100,000 per paper. In this context a fee of approx $2000 (i.e less than 2%
> of total cost) to get the results published does not seem excessive. Based
> on proposals I have reviewed in recent years I would guess the current full
> cost (external grants + institutional costs) of the research behind each
> per peer review publication is very much higher than $100,000. Has anyone
> seen a recent assessment of research costs per peer review publication?
> 
> While not all funding agencies allow publication costs to be included, a
> large number do, and in reality the cost to our institutions of publishing
> in open access journals is trivial in relation to the costs of employing
> the researchers. So for most researchers in developed countries the move to
> open access can be budgeted for where there is the will to do so. The
> challenge then is how to support researchers who genuinely have very
> limited resources; for example (but not limited to) colleagues in
> developing countries. Many but far from all journals have mechanisms to
> reduce or remove costs for truly needy researchers and there remain many
> journals that do not charge publication fees.
> 
> An issue to consider as a variety of electronic publishing systems emerge
> is whether a given system is likely to be sustained in the long-term and if
> not does that mean that all the papers on that system risk becoming
> inaccessible at some future date?
>  
>  
> John Gibson 
> University of New England 
> Armidale, NSW 2351 
> Australia 

From Matthew.McClureARS.USDA.GOV  Thu Mar 28 11:50:39 2013
From: "McClure, Matthew" <Matthew.McClureARS.USDA.GOV>
Subject: RE: Publish or Perish?
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Thu, 28 Mar 2013 11:50:39 -0500

While I realize that there are many hidden costs for both traditional and 
open access journals and that in the overall picture a $2,000 publication 
fee for a $250,000 funded project is not much, my major issue with many of 
the traditional journals is that I must pay to publish in the journal and 
then others must pay to read the manuscript.  Yes for society journals if 
you are a member then have access to the articles, but you still must pay 
the page charge to publish and then the membership fee or article fee to 
view the articles.

This double billing is what leads me to prefer publishing in an open access
manner when possible.  Yes, the publication fee for open access can be 
higher but this allows the public and other scientists to easily access the 
research results which ultimately was already paid for by the public if 
public grant money funded the work.

-Matt McClure


-----Original Message-----
.From: Ignacy Misztal [mailto:ignacyuga.edu]
.Sent: Thursday, March 28, 2013 11:58 AM
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: Re: Publish or Perish?

Max and John make good argument about the cost of research versus the cost 
of publications. This argument looks different in some groups/countries where
salaries are paid by the government but publishing costs need to come out of
scarce operating budget.

We may ask ourselves why we publish. After all, we can publish on our own
website. If titles are meaningful, google searches will find those.

We publish in refereed for a variety of reasons:
1. Summarize  a project that needs to end with paper(s).
2. Give young scientists tools for job search.
3. Claim credit for a new idea.
4. Share unclear results as a next incremental step towards a particular goal.
5. Have sufficient number of refereed publications / year as job requirement.
6. As above but to build CV for salary increase, better chance of grants, new 
job opportunites, awards,...
7. Have paper in elite journal for benefits that come with publishing in elite
journals.
8. ....

If we want to publish fast for reasons 4-6, we want fast yet cheap publishing.
If we want quality feedback, we want journals that are read and also with
reviewers who value those journals. Such journals have limited space so they 
have to be selective.

I am sometimes frustrated with a slow review process, but I am even more happy
when "nasty" reviewers insist on something and they are right.
Better slow and find something exciting than realize later that a published 
paper is misleading or even harmful.

Some known groups published very little in reviewed journals. For instance, 
details of a multibreed model for beef, a big topic in beef at a time, were 
never published by Cornell in a refereed journal. Seems 1-7 did not apply. 
A friend of mine who managed to publish in Nature is eager to wait years 
without publishing for another high-impact publication. Only point 8 counts 
for him!

Ignacy

From gianolaansci.wisc.edu  Thu Mar 28 12:15:16 2013
From: Daniel Gianola <gianolaansci.wisc.edu>
Subject: RE: Publish or Perish?
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Thu, 28 Mar 2013 12:15:16 -0500

John,

If your cost estimate of $100,000 per published journal is accurate, then I
infer that Max's published work has a lower bound estimated cost of about
4-5 x 10**7 US dollars (assuming he has published 400-500 dollars, which I
am sure is not a bad range estimate). The cost of the unpublished part is a
bit harder to estimate.

Now, if one assumes that there are 100 Max-types in the world (strong
assumption), and we add up their research capital (which must be much larger
than 4-5 x 10**7 US dollars), do you think this could help save Cyprus? If
so, we should send all Max-types to Nicosia for a few years and let the
research funds flow there. Problem solved.

Unfortunately, we do not have any quant guys who can match that (Dale Van
Vleck retired) and, also, our number crunching research is much cheaper...

[NOTE: this is intended to be humorous]

Enjoy the Easter break, if available.

Best wishes,

Daniel



-----Original Message-----
.From: John Gibson [mailto:jgibson5une.edu.au] 
.Sent: Thursday, March 28, 2013 7:49 AM
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: RE: Publish or Perish?

One regret Max may have is that I agree with much that Max has articulated
(sorry Max, it is usually a much more interesting discussion when we
disagree). I see little evidence that the current system is fundamentally
broken but there is certainly every reason to push for it to continuously
evolve to better processes and structures.

While most correspondents have voiced concern about the costs of publishing
I have not seen an analysis of the real costs to the publisher (which should
include the profit they require to be interested in remaining in business)
of publishing under different models or the cost-benefits to the research
community of different models. Talk of paying reviewers for their services
might be considered more equitable but that will further increase the cost
of publication, and the cost of publication and/or access to papers seems to
be a bigger issue for most people than whether or not we get paid for our
services as reviewers. 

It is useful to put the cost of publishing research results in the context
of the full cost of research. 
About 10 years ago an external review panel I was working with stated that
the average cost of research per publication in biological/agriculture
subjects in developed countries was in excess of
$100,000 per paper. In this context a fee of approx $2000 (i.e less than 2%
of total cost) to get the results published does not seem excessive. Based
on proposals I have reviewed in recent years I would guess the current full
cost (external grants + institutional costs) of the research behind each per
peer review publication is very much higher than $100,000. Has anyone seen a
recent assessment of research costs per peer review publication?

While not all funding agencies allow publication costs to be included, a
large number do, and in reality the cost to our institutions of publishing
in open access journals is trivial in relation to the costs of employing the
researchers. So for most researchers in developed countries the move to open
access can be budgeted for where there is the will to do so. The challenge
then is how to support researchers who genuinely have very limited
resources; for example (but not limited to) colleagues in developing
countries. Many but far from all journals have mechanisms to reduce or
remove costs for truly needy researchers and there remain many journals that
do not charge publication fees.

An issue to consider as a variety of electronic publishing systems emerge is
whether a given system is likely to be sustained in the long-term and if not
does that mean that all the papers on that system risk becoming inaccessible
at some future date?


John Gibson
University of New England
Armidale, NSW 2351
Australia


-----Original Message-----
.From: Rothschild, Max F [AN S] [mailto:mfrothsciastate.edu]
.Sent: Thursday, 28 March 2013 1:39 AM
.To: Multiple Recipients of <AnGenMapanimalgenome.org>
.Subject: RE: Publish or Perish

Dear Colleagues,

I am sure I will regret this but.....

I have read most of the notes recently posted on Angenmap and on AGDG.  Many
of the comments focus on complaints about the present system and the need to
find alternatives that are free, easy and open.  I agree with many of the
complaints but the solutions proposed seem full of potholes.

While some insist quality will follow I have my doubts.  As someone who has
published a number of papers in many journals let me state the obvious:

Reviews are often slow and on occasion poor.
Journals are expensive to own and many time publication costs seem
excessive.
Formatting is a pain in the...
it would be nice to write the work up and publish in a few days.

But let me remind you of the old saying "things are usually worth their
cost"

The new publishing model proposed has many flaws.
If there is no peer review and there is no cost how will these journals be
any different than the usual stuff on the web that no one really can verify?

Frankly, I am really disappointed in my colleagues who are such rigorous
scientists and conduct outstanding research and then at the finish line
don't want to publish in the usual way - as I said sure we all have
complaints BUT we can improve the system

 1) volunteer to do more reviews
 2) do you reviews without bias
 3) do your reviews in a more speedy manner
 4) offer to be on editorial boards
 5) if you don't like the cost find a different journal with lower costs

Let's try to fix the system instead of trying to build a new one.

Max Rothschild
Iowa State University
  

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