Re: [ECOLOG-L] bioarxiv (questions about)

[Gregor Kalinkat]

Dear all,

as somebody who has been closely following the rise of preprint use in ecology 
I wanted to chime in and share this link list that I have been assembling over 
the last couple of years (note the chronological order of the linked articles 
and how much things have changed from 2012 to 2018): 

https://dynamicecology.wordpress.com/2012/07/19/esa-journals-and-ecology-letters-will-not-publish-papers-with-preprints/
 

http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001563

http://www.oikosjournal.org/blog/new-preprint-server  

https://jabberwocky.weecology.org/2014/07/07/which-preprint-server-should-i-use/
 

https://jabberwocky.weecology.org/2014/09/08/ecology-letters-now-allows-preprints-and-why-this-is-a-big-deal-for-ecology/
 

http://www.nature.com/news/biologists-urged-to-hug-a-preprint-1.19384   

http://www.sciencemag.org/news/2017/04/biorxiv-preprint-server-gets-funding-chan-zuckerberg-initiative

https://jabberwocky.weecology.org/2017/05/02/is-it-ok-to-cite-preprints-yes-yes-it-is/

https://twitter.com/cshperspectives/status/871005699798700032 

https://blogs.royalsociety.org/publishing/a-preprint-success-story/

https://twitter.com/cshperspectives/status/1002509448814977024

With regard to the original post I would also like to stress that the intention 
behind peprint servers never was to get rid of peer-review but rather 
attenuating the negative effects of the traditional publishing system (i.e. (1) 
delays due to repeated rejections and (2) closed access of the final products). 
Considering that the publishing systems is transforming (and likely will 
continue being transformed for many years to come) I think we will still need 
*some* type of quality control, curating service and excellence approval system 
similarily to the traditional journals. To what level this will integrate the 
exisiting infrastructure is still an open question. 

All the best
Gregor



---
Dr. Gregor Kalinkat
Scientist @LeibnizIGB Berlin, DE

email: kalin...@igb-berlin.de
skype: gregor.kalinkat
landline: +49 30 641 81 707
mobile: +49 157 870 21 304

Department of Ecosystem Research
Leibniz-Institute of Freshwater Ecology and Inland Fisheries
Müggelseedamm 310
12587 Berlin
GERMANY

www.gregorkalinkat.com | Institutional site at IGB: http://goo.gl/4hxVEL | 
Google Scholar profile: http://goo.gl/RI0a5 | Researchgate: 
http://goo.gl/hpdXbW | Publons: https://goo.gl/IBzEUk | Twitter: 
http://goo.gl/5hNgSL | Youtube channel: http://goo.gl/nbY6S6


-Original message-
> From:Alicia Krzton 
> Sent: Monday 4th June 2018 17:04
> To: ECOLOG-L@LISTSERV.UMD.EDU
> Subject: Re: [ECOLOG-L] bioarxiv (questions about)
> 
> I would just note that a comparison with publishing in a society journal is 
> not apples to apples. It’s free or nearly so to the author, but the reader 
> requires a subscription. The comparison here was to the cost to publish Open 
> Access, which is typically 1500-2000 dollars. Preprints get around that.
> 
> I believe the jury is still out on preprints, myself, but clearly some people 
> find value in them.
> 
> Ali K.
> Research Data Management Librarian 
> Auburn University 
> 
> On Sun, Jun 3, 2018 at 9:31 PM cruzan  <mailto:cru...@pdx.edu>> wrote:
> In response:
> 1. The submissions are not peer-reviewed. You can post anything
>   there. They just screen for stuff that is offensive or
>   "non-scientific." I wonder what percentage are ever published.
> 2. I wonder who is citing these papers and where and why? If they
>   are not reliable resources then why cite them. Im guessing people
>   want to get some results out quickly or maybe get some feedback to
>   make the review process go better.
> I dont see the point of posting anything on a website like this
>   one. The papers are suspect unless peer reviewed and I seriously
>   doubt that any search committee or any promotions committee would
>   accept a paper posted at this web site or any others like it as a
>   valid publication. The peer review process is not perfect, but in
>   most cases we get it right. If you publish in journals run by
>   non-profit professional societies it will cost you much less and
>   sometimes nothing at all. 
> Mitch Cruzan 
> 
> On 6/1/2018 12:24 PM, Malcolm McCallum
>   wrote:
> Hi, 
> Do many of you use bioarxiv?
> I recently became familiar with it, and in searching
>   literature, I noticed many papers deposited in it have
>   citations in excess of 100.  It brought me to wondering about
>   the role of a preprint server, and read about 30-40 different
>   commentaries and research articles about preprint servers last
>   night.  the parallel preprint server in physics and math,
>   arxiv, has been around since 1991. 

Re: [ECOLOG-L] bioarxiv (questions about)

[Alicia Krzton]

I would just note that a comparison with publishing in a society journal is
not apples to apples. It’s free or nearly so to the author, but the reader
requires a subscription. The comparison here was to the cost to publish
Open Access, which is typically 1500-2000 dollars. Preprints get around
that.

I believe the jury is still out on preprints, myself, but clearly some
people find value in them.

Ali K.
Research Data Management Librarian
Auburn University

On Sun, Jun 3, 2018 at 9:31 PM cruzan  wrote:

> In response:
>
> 1. The submissions are not peer-reviewed. You can post anything there.
> They just screen for stuff that is offensive or "non-scientific." I wonder
> what percentage are ever published.
>
> 2. I wonder who is citing these papers and where and why? If they are not
> reliable resources then why cite them. I'm guessing people want to get some
> results out quickly or maybe get some feedback to make the review process
> go better.
>
> I don't see the point of posting anything on a website like this one. The
> papers are suspect unless peer reviewed and I seriously doubt that any
> search committee or any promotions committee would accept a paper posted at
> this web site or any others like it as a valid publication. The peer review
> process is not perfect, but in most cases we get it right. If you publish
> in journals run by non-profit professional societies it will cost you much
> less and sometimes nothing at all.
>
> Mitch Cruzan
>
> On 6/1/2018 12:24 PM, Malcolm McCallum wrote:
>
> Hi,
> Do many of you use bioarxiv?
> I recently became familiar with it, and in searching literature, I noticed
> many papers deposited in it have citations in excess of 100.  It brought me
> to wondering about the role of a preprint server, and read about 30-40
> different commentaries and research articles about preprint servers last
> night.  the parallel preprint server in physics and math, arxiv, has been
> around since 1991.  There are a growing number of people who put their
> paper in the database, then update it, but don't ever publish it.  There
> are a number of op-eds and such that suggest these servers will never or
> absolutely will replace journals in the near future.
>
> I have to wonder how long it will be before this overtakes journals for
> scholarly communication.
>
> 1. some funders are requiring papers to be deposited in a preprint
> server..
> 2. there is no delay.
> 3. there is opportunity for feedback, sort of a post-peer review, and for
> you to revise the article, with all versiions freely available.
> 4. it is fully accessible by Google Scholar, probably the most used
> scholarly search engine at this time.
> 5. it is fully citable in a manuscript, I saw some that had over 150, and
> one with 180 citations.  A lot were in the 30's.
> 6.  outside of tenure and review committees, the purpose of pubs is
> communication, so if 1-5 are true, I have to wonder why I should fork out
> $1500 to some journal to put my findings behind a paywall.  Yes, I plan to
> publish what I have already posted, but it has crossed my mind as to
> whether there is even a point.  One could even question whether a typical
> tenure and review committee would even notice or care if these are
> preprints and not publications if one has been cited dozens or hundreds of
> times.  This is further reinforced by a trend to evaluating scientists
> based on their citations and their paper's citations rather than on the
> citations to the journals in which they have published (investigator impact
> instead of journal impact).
>
> Anyone else starting to wonder about this?
>
> --
> Malcolm L. McCallum
> Aquaculture and Water Quality Research Scientist
> School of Agriculture and Applied Sciences
> Langston University
> Langston, Oklahoma
>
>
> Link to online CV and portfolio :
> https://www.visualcv.com/malcolm-mc-callum?access=18A9RYkDGxO
> Google Scholar citation page:
> https://scholar.google.com/citations?user=lOHMjvYJ=en
> Academia.edu:
> https://ui-springfield.academia.edu/MalcolmMcCallum/Analytics#/activity/overview?_k=wknchj
> Researchgate:
>  
> https://www.researchgate.net/profile/Malcolm_Mccallum/reputation?ev=prf_rep_tab
> 
> Ratemyprofessor:
> http://www.ratemyprofessors.com/ShowRatings.jsp?tid=706874
>
> *Confidentiality Notice:* This e-mail message, including any attachments,
> is for the sole use of the intended recipient(s) and may contain
> confidential and privileged information.  Any unauthorized
> review, use, disclosure or distribution is prohibited.  If you are not the
> intended recipient, please contact the sender by reply e-mail and destroy
> all copies of the original message.
>
> “*Nothing is more priceless and worthy of preservation than the rich
> array of animal life with which our country has been blessed. It is a
> many-faceted treasure, of value to scholars, scientists, and nature lovers
> alike, and it 

Re: [ECOLOG-L] bioarxiv (questions about)

[cruzan]

In response:

1. The submissions are not peer-reviewed. You can post anything there. 
They just screen for stuff that is offensive or "non-scientific." I 
wonder what percentage are ever published.


2. I wonder who is citing these papers and where and why? If they are 
not reliable resources then why cite them. I'm guessing people want to 
get some results out quickly or maybe get some feedback to make the 
review process go better.


I don't see the point of posting anything on a website like this one. 
The papers are suspect unless peer reviewed and I seriously doubt that 
any search committee or any promotions committee would accept a paper 
posted at this web site or any others like it as a valid publication. 
The peer review process is not perfect, but in most cases we get it 
right. If you publish in journals run by non-profit professional 
societies it will cost you much less and sometimes nothing at all.


Mitch Cruzan


On 6/1/2018 12:24 PM, Malcolm McCallum wrote:

Hi,
Do many of you use bioarxiv?
I recently became familiar with it, and in searching literature, I 
noticed many papers deposited in it have citations in excess of 100.  
It brought me to wondering about the role of a preprint server, and 
read about 30-40 different commentaries and research articles about 
preprint servers last night.  the parallel preprint server in physics 
and math, arxiv, has been around since 1991.  There are a growing 
number of people who put their paper in the database, then update it, 
but don't ever publish it.  There are a number of op-eds and such that 
suggest these servers will never or absolutely will replace journals 
in the near future.


I have to wonder how long it will be before this overtakes journals 
for scholarly communication.


1. some funders are requiring papers to be deposited in a preprint 
server..

2. there is no delay.
3. there is opportunity for feedback, sort of a post-peer review, and 
for you to revise the article, with all versiions freely available.
4. it is fully accessible by Google Scholar, probably the most used 
scholarly search engine at this time.
5. it is fully citable in a manuscript, I saw some that had over 150, 
and one with 180 citations.  A lot were in the 30's.
6.  outside of tenure and review committees, the purpose of pubs is 
communication, so if 1-5 are true, I have to wonder why I should fork 
out $1500 to some journal to put my findings behind a paywall.  Yes, I 
plan to publish what I have already posted, but it has crossed my mind 
as to whether there is even a point.  One could even question whether 
a typical tenure and review committee would even notice or care if 
these are preprints and not publications if one has been cited dozens 
or hundreds of times.  This is further reinforced by a trend to 
evaluating scientists based on their citations and their paper's 
citations rather than on the citations to the journals in which they 
have published (investigator impact instead of journal impact).


Anyone else starting to wonder about this?

--
Malcolm L. McCallum
Aquaculture and Water Quality Research Scientist
School of Agriculture and Applied Sciences
Langston University
Langston, Oklahoma


Link to online CV and portfolio : 
https://www.visualcv.com/malcolm-mc-callum?access=18A9RYkDGxO
Google Scholar citation page: 
https://scholar.google.com/citations?user=lOHMjvYJ=en
Academia.edu: 
https://ui-springfield.academia.edu/MalcolmMcCallum/Analytics#/activity/overview?_k=wknchj
Researchgate: https://www.researchgate.net/profile/Malcolm_Mccallum/reputation?ev=prf_rep_tab 

Ratemyprofessor: 
http://www.ratemyprofessors.com/ShowRatings.jsp?tid=706874


*_Confidentiality Notice:_* This e-mail message, including any 
attachments, is for the sole use of the intended recipient(s) and may 
contain confidential and privileged information. Any unauthorized
review, use, disclosure or distribution is prohibited.  If you are not 
the intended recipient, please contact the sender by reply e-mail and 
destroy all copies of the original message.


“/Nothing is more priceless and worthy of preservation than the rich 
array of animal life with which our country has been blessed. It is a 
many-faceted treasure, of value to scholars, scientists, and nature 
lovers alike, and it forms a vital part of the heritage we all share 
as Americans./”
*-President Richard Nixon upon signing the Endangered Species Act of 
1973 into law.*


"/Peer pressure is designed to contain anyone with a sense of drive/" 
-*Allan Nation*

*
*
"...Every time they kick your teeth down your throat in this business, 
and believe me, they will, you get right back up and say that to 
yourself. Hey, it worked for me and the boys!” John Lennon*

*
*1880's: *"/There's lots of good fish in the sea/"  W.S. Gilbert
*1990's:*  Many fish stocks depleted due to overfishing, habitat 
loss,and pollution.
2000:  Marine reserves, 

[ECOLOG-L] bioarxiv (questions about)

[Malcolm McCallum]

Hi,
Do many of you use bioarxiv?
I recently became familiar with it, and in searching literature, I noticed
many papers deposited in it have citations in excess of 100.  It brought me
to wondering about the role of a preprint server, and read about 30-40
different commentaries and research articles about preprint servers last
night.  the parallel preprint server in physics and math, arxiv, has been
around since 1991.  There are a growing number of people who put their
paper in the database, then update it, but don't ever publish it.  There
are a number of op-eds and such that suggest these servers will never or
absolutely will replace journals in the near future.

I have to wonder how long it will be before this overtakes journals for
scholarly communication.

1. some funders are requiring papers to be deposited in a preprint server..
2. there is no delay.
3. there is opportunity for feedback, sort of a post-peer review, and for
you to revise the article, with all versiions freely available.
4. it is fully accessible by Google Scholar, probably the most used
scholarly search engine at this time.
5. it is fully citable in a manuscript, I saw some that had over 150, and
one with 180 citations.  A lot were in the 30's.
6.  outside of tenure and review committees, the purpose of pubs is
communication, so if 1-5 are true, I have to wonder why I should fork out
$1500 to some journal to put my findings behind a paywall.  Yes, I plan to
publish what I have already posted, but it has crossed my mind as to
whether there is even a point.  One could even question whether a typical
tenure and review committee would even notice or care if these are
preprints and not publications if one has been cited dozens or hundreds of
times.  This is further reinforced by a trend to evaluating scientists
based on their citations and their paper's citations rather than on the
citations to the journals in which they have published (investigator impact
instead of journal impact).

Anyone else starting to wonder about this?

-- 
Malcolm L. McCallum
Aquaculture and Water Quality Research Scientist
School of Agriculture and Applied Sciences
Langston University
Langston, Oklahoma


Link to online CV and portfolio :
https://www.visualcv.com/malcolm-mc-callum?access=18A9RYkDGxO
Google Scholar citation page:
https://scholar.google.com/citations?user=lOHMjvYJ=en
Academia.edu:
https://ui-springfield.academia.edu/MalcolmMcCallum/Analytics#/activity/overview?_k=wknchj
Researchgate:
 https://www.researchgate.net/profile/Malcolm_Mccallum/reputation?ev=prf_rep_tab

Ratemyprofessor: http://www.ratemyprofessors.com/ShowRatings.jsp?tid=706874

*Confidentiality Notice:* This e-mail message, including any attachments,
is for the sole use of the intended recipient(s) and may contain
confidential and privileged information.  Any unauthorized
review, use, disclosure or distribution is prohibited.  If you are not the
intended recipient, please contact the sender by reply e-mail and destroy
all copies of the original message.

“*Nothing is more priceless and worthy of preservation than the rich array
of animal life with which our country has been blessed. It is a
many-faceted treasure, of value to scholars, scientists, and nature lovers
alike, and it forms a vital part of the heritage we all share as Americans.*
”
*-President Richard Nixon upon signing the Endangered Species Act of 1973
into law.*

"*Peer pressure is designed to contain anyone with a sense of drive*" -*
Allan Nation*

"...Every time they kick your teeth down your throat in this business, and
believe me, they will, you get right back up and say that to yourself. Hey,
it worked for me and the boys!” John Lennon

*1880's: *"*There's lots of good fish in the sea*"  W.S. Gilbert
*1990's:*  Many fish stocks depleted due to overfishing, habitat loss,and
pollution.
2000:  Marine reserves, ecosystem restoration, and pollution reduction *MAY*
help restore populations.
2022: "Soylent Green is People!" Charleton Heston as Detective Thorn
2022: "People were always awful, but their was a world once, and it was
beautiful.' Edward G. Robinson as Sol Roth.

The Seven Blunders of the World (Mohandas Gandhi)
Wealth w/o work
Pleasure w/o conscience
Knowledge w/o character
Commerce w/o morality
Science w/o humanity
Worship w/o sacrifice
Politics w/o principle