Do preprints count for anything? Not according to Elife & G3 & some authors ..

Well, just got pointed to this paper: Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms | eLife by Martial Marbouty, Axel Cournac, Jean-François Flot, Hervé Marie-Nelly, Julien Mozziconacci, Romain Koszul.  Seems potentially really interesting.

It is similar in concept and in many aspects to a paper we published in PeerJ earlier in the year (see Beitel et al., 2014 Beitel CW, Froenicke L, Lang JM, Korf IF, Michelmore RW, Eisen JA, Darling AE. (2014) Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products. PeerJ 2:e415 http://dx.doi.org/10.7717/peerj.415.

Yet despite the similarities to our paper and to another paper that was formally published around the time of ours, this new paper does not mention these other pieces of work any where in the introduction as having any type of “prior work” relevance.  Instead, they wait until late in their discussion:

Taking advantage of chromatin conformation capture data to address genomic questions is a dynamic field: while this paper was under review, two studies were released that also aimed at exploiting the physical contacts between DNA molecules to deconvolve genomes from controlled mixes of microorganisms (Beitel et al., 2014; Burton et al., 2014).

Clearly, what they are trying to do here is to claim that since they paper was submitted before these other two (including ours) was published, that they should get some sort of “priority” for their work.  Let’s look at that in more detail.  Their paper was received May 9, 2014.  Our paper was published online May 27 and the other related paper by Burton et al. was published online May 22.  In general, if a paper on what your paper is about comes out just after you submit your paper, while your paper is still in review, the common, normal thing to be asked to do is to rewrite your paper to deal with the fact that you were, in essence, scooped.  But that does not really appear to be the case here.  They are treating this in a way as “oh look, some new papers came out at the last minute and we have commented on them.”  The last minute would be in this case, 6 months before this new paper was accepted.  Seems like a long time to treat this as “ooh – a new paper came up that we will add a few comments about”.

But – one could quibble about the ethics and policies of dealing with papers that were published after one submitted one’s own paper.  From my experience, I have always had to do major rewrites to deal with such papers.  But maybe E-Life has different policies.  Who knows.  But that is where things get really annoying here.  This is because it was May 27 when our FINAL paper came out online at PeerJ. However, the preprint of the paper was published on February 27, more than two months before their paper was even submitted.  So does this mean that the authors of this new paper do not believe that preprints exist?  It is pretty clear on the web site for our paper that there is a preprint that was published earlier.  Given what they were working on – something directly related to what our preprint/paper was about, one would assume they would have seen it with a few simple Google searches.  Or a reviewer might have pointed them to it.  Maybe not.  I do not know.  But either way, our preprint was published long before their paper was submitted and therefore I believe they should have discussed it in more detail.

Is this a sign that some people believe preprints are nothing more than rumors?  I hope not.  Preprints are a great way to share research prior to the delays that can happen in peer review.  And in my opinion, preprints should count as prior research and be cited as such.  I note – the Burton group in their paper in G3 also did not reference our preprint in what I consider to be a reasonable manner.  They add some comments in their acknowledgements

While this manuscript was in preparation, a preprint describing a related method appeared in PeerJ PrePrints (Beitel et al. 2014a). Note added in proof: this preprint was subsequently published (Beitel et al. 2014b). 

Given that our preprint was published before their paper was submitted too, I believe that they also should have made more reference to it in their paper.   But again, I can only guess that both the Burton and the Marbouty group just do not see preprints as being respectable scientific objects.  That is a bad precedent to set and I think the wrong one too.  And it is a shame.  A preprint is a publication.  No – it is not peer reviewed.  But that does not mean it should not be considered part of the scientific literature in some way.  I note – this new paper from the Marbouty group seems really interesting.  Not sure I want to dig into it any deeper if they are going to play games with the timing of submission vs. published “papers” as part of how they are positioning themselves to be viewed as doing something novel.

Article by Amy Maxmen "Preserving Research" on ways to share unpublished manuscripts

There is a nice article by Amy Maxmen in The Scientist titled “Preserving Research” on ways to share unpublished manuscripts. It includes some discussion of pros and cons of various archives including arXiv, Figshare, ResearchGate and more. Definitely worth a look.  There are of course many many many ways to share your articles before and after you publish them.

For more about sharing PDFs/articles see my post: The Tree of Life: Ten simple ways to share PDFs of your papers.  And of course, don’t forget that just posting your paper somewhere does not mean that it will continue to be available to all.  Also – the license that you use when sharing your article affects how people can use and reshare it so pay attention to the fine print and use as broad a license as possible …

Some new preprints of interest and comments on "The case for preprints in biology"

Getting more and more into preprints (see for example these posts Guest post from Jake Scott: Building trust: a sine qua non for successful acceptance of preprints in the biological sciences and More bio preprint discussion sites …).  So am starting to browse preprint servers a bit more and I have found some recently posted preprints of interest:
http://arxiv.org/abs/1306.1206

From arVix:

From PeerJ preprints

I wondered – where else might one find Biology themed preprints.  And a little google searching let me to this new PLOS Biology paper which somehow I had missed a few weeks ago: The Case for Open Preprints in Biology
(Full citation: Desjardins-Proulx P, White EP, Adamson JJ, Ram K, Poisot T, et al. (2013) The Case for Open Preprints in Biology. PLoS Biol 11(5): e1001563. doi:10.1371/journal.pbio.1001563)
Wow – how perfect.  In their paper they not only lay out the case for why preprints would be a good thing in biology but discuss some of the options.  And in addition to PeerJ and arXiv they point to Figshare, Github, and ResearchGate.
Below is Figure 1 from their paper:
Figure 1. It can take several months before a submitted paper is officially published and citable.. Meanwhile, few people are aware of the research that has been done since, typically, only close colleagues are given access to the preprints. With public preprint servers, the science is immediately available and can be openly discussed, analyzed, and integrated into current research. doi:10.1371/journal.pbio.1001563.g001
They also show that in arXiv submissions in the qBio section are going up but not nearly as much as submissions in other fields
Figure 2. Submissions to the quantitative biology section lag behind physics, mathematics, and computer science.  Data from [19]. doi:10.1371/journal.pbio.1001563.g002.  The reference to 19 is to Warner S (2012) Data for arXiv submissions by subject and year. Available: http://dx.doi.org/10.6084/m9.figshare.96​966. Accessed 14 April 2013.
I think this paper is worth a look for anyone interest in scientific publishing.  I like their last line and will end my post with it:

Preprints are simply bypassing this model for what we believe is the progress of science: they speed up the dissemination of scientific discoveries and put on readers’ shoulders the responsibility to judge originality and pertinence.

Guest post from Jake Scott: Building trust: a sine qua non for successful acceptance of preprints in the biological sciences

Today I am happy to have a guest post from my friend and colleague Jake Scott.  The topic of the day is preprints in biology and medicine.




Hi – I’m Jake Scott.  I met Jonathan last year when he and I spoke at TEDMED 2012. Both Jonathan and I have posted recently about the need for, and (slowly) growing movement in the biological sciences to post #preprints of manuscripts in openly accessible fora to circumvent some problems associated with standard academic publishing.  Most worrisome are the issues surrounding #openaccess and the length of time it takes to get information from one’s brain to the literature – drastically slowing down the pace of science.

This has worked GREAT in the physics community, where this trend really began quite some time ago when the high energy physicists started the arXiv.  Now, the precedent is set, and no one in physics bats an eye about sticking their paper on the arXiv, and cite other works presented there as standard publications.

The climate in biology, sadly, is much different. Whether this is because of a more competitive climate for funding, or just a field diluted by more talented scientists, I don’t know.  But there is a pervasive attitude of fear and mistrust around the idea of preprints.

Before you read on (and become biased by my opinions) take a few second (really, probably 1.5 minutes) and take this quick survey:

When I preach to my biological colleagues about the virtue of pre-print servers, I most often, I hear:

Why should I post my papers on a pre-print server where anyone can see it before it is published!?  They could scoop me!

I honestly don’t understand this argument, but I hear it all the time.  By nature of pre-print servers, like the arXiv, the idea is yours! Time and date stamped. And, better yet, it is completely #openaccess, free of charge, and helps move science along at a better pace.  Only a very few journals have problems with posting of pre-prints before they get their (greedy) hands on the results of all your hard work, but most are totally OK with it.

The arXiv isn’t really interested in shopping its (free) service out to the biological sciences, not because they don’t think it would be of value, but because it just doesn’t have the infrastructure to support it.  This is a problem that is being with newly created repositories like Nature Precedings, PeerJ and soon, the bioRxiv.  So, the only thing holding us up is, IMHO, trust.

How can we rectify this?

I think the way forward is to create something that we are all missing now, except when we are at our home conference, among friends or if we got into a time machine and went back 100 years – community.

Science is such a juggernaut now that putting your work onto a pre-print server where anyone in the world can see your as of yet unvetted work can be daunting.  Worse, the idea of commenting on it is a tough sell when the world is a witness.  I think we need to (re)create micro-communities of our specialist peers where these initial discussions can be held.  Two examples of this are Haldane’s Sieve and more recently created, an initiative I’m involved with, Warburg’s Lens.  These two sites are micro-communities where population and evolutionary biologists, and mathematical oncologists (respectively) congregate to discuss pre-prints culled from any repository but necessarily of interest to the micro-community.

This does two things: it allows a common place for easy browsing in topics of interest to a specialist (like reading your favorite journal), and increases the chances that the readers and commenters are your (at large) peers.

So, those are my two cents. #Openaccess for all is coming, and preprints are a part of the wave.  The sooner we all adopt an open science attitude, the sooner we’ll come to the conclusions and make the discoveries that make doing science AWESOME.  There is no better job than science, and sharing and communication are central to it

So START SHARING your science.  Commit to this – when you are ready to submit your next paper, put that version on a pre-print server as you start the submission process. Then tweet about it, G+ about it, blog about it, do whatever, but let your peers know!

Anyone else interested in starting a micro-community discussion forum, or to just discuss this issue further, please contact me.

If you are against it – please leave some comments about why, I’d love to try to convince you otherwise!  If you are a biologist (or know one) who DOES post pre-prints, weigh in and share your good experiences!

About me: I am a radiation oncologist and I approach the understanding of cancer like my original training in physics taught me – from the ground up, using the descriptive language of mathematics.  Using established mathematics in new ways, guided by the principles of evolution, I hope to better understand (and maybe treat!) cancer.  I am a proud member of the Integrated Mathematical Oncology group at the Moffitt Cancer Center and the Centre for Mathematical Biology at Oxford University.  You can follow me on twitter @CancerConnector or read my blog Connecting the Dots.

More bio preprint discussion sites …

Another Bio-related preprint discussion site has popped up: Connecting the Dots: Warburg’s Lens: A pre-print discussion forum for the mathematical oncology community.  From my friend and colleague Jacob Scott.  A good addition to Haldane’s Sieve.  Seems to me preprints are the next wave in open access in biology …

Thank you Google Scholar Updates for finding me two new papers to read

Am really liking the Google Scholar Updates system.   Have written about it before: The Tree of Life: Wow – Google Scholar “Updates” a big step forward … and continue to be impressed.  Today the system suggested two papers for me

Dead on accurate in terms of papers I would be interest in.  #1 is on Drosophila associated microbes and it is a paper from Dmitri Petrov’s group: Bacterial diversity associated with Drosophila in the laboratory and in the natural environment.  #2 is on computational normalization of shotgun genome sequence data from Titus Brown and others.  As these are both preprints I almost certainly never would have found them without Google Scholar Updates.

Nature Precedings – a preprint server for biology akin to arXiv – shutting down as of April 3

Just got this email regarding Nature Precedings.

Dear registrant:

As you are an active user of Nature Precedings, we want to let you know about some upcoming changes to this service. As of April 3rd 2012, we will cease to accept submissions to Nature Precedings.  Submitted documents will be processed as usual and hosted provided they are uploaded by midnight on April 3rd.  Nature Precedings will then be archived, and the archive will be maintained by NPG, while all hosted content will remain freely accessible to all.

Be assured that Nature and the Nature research journals continue to permit the posting of preprints and there is no change to this policy, which is detailed here.

Nature Precedings was launched in 2007 as NPG’s preprint server, primarily for the Life Science community.  Since that date, we have learned a great deal from you about what types of content are valued as preprints, and which segments of the research community most embrace this form of publication.  While a great experiment, technological advances and the needs of the research community have evolved since 2007 to the extent that the Nature Precedings site is unsustainable as it was originally conceived.

Looking forward, NPG remains committed to exploring ways to help researchers, funders, and institutions manage data and best practices in data management, and we plan to introduce new services in this area.  We have truly valued your contributions as authors and users to Nature Precedings and hope that you will actively participate in this research and development with us.

Interestingly, there is no announcement at the Nature Precedings site itself.  I assume the email I received is real (it really looks real) though you never know these days.  It’s too bad.  I like the concept of a preprint server for biology.  Interestingly, one of the alternatives to NP is FigShare (which is pretty cool) which recently became part of the Digital Science group which is a sister group to Nature.  Hmm … wonder what the conversations at joint tea parties between Nature and Digital Science group are like.  Could be fun.