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:

• [1305.7256] tRNA signatures reveal polyphyletic origins of streamlined SAR11 genomes among the alphaproteobacteria
• Coalescence, genetic diversity and adaptation in sexual populations from Neher et al. 
• Reducing assembly complexity of microbial genomes with single-molecule sequencing from Koren et al. 
• Antibiotic resistance landscapes: a quantification of theory-data incompatibility for fitness landscapes from Crona et al. 

From PeerJ preprints

• Supertrees based on the subtree prune-and-regraft distance from Whidden et al. 
• Microenvironmental variables need to effect intrinsic phenotypic parameters of cancer stem cells to affect tumourigenicity from Jake Scott et al.
• GenGIS 2: Geospatial analysis of traditional and genetic biodiversity, with new gradient algorithms and an extensible plugin framework from Rob Beiko et al. 

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.

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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: