Category Archives: PeerJ
Posted by PeerJin
As a scientist, are you always focused on improving your metrics by such means as getting papers into prestigious journals? Do your funders and institutions add to that pressure to get ahead? If so, you may be at risk of a new psychiatric condition known as “Publiphilia Impactfactorius” — or, simply, PI, described in a PeerJ […]
The post Obsessed with getting cited? You may have “Publiphilia Impactfactorius” appeared first on Retraction Watch.
Pretty much every person who ever read a dinosaur book or went to a natural history museum learned that Brontosaurus is just an outdated name for a big long-necked dinosaur that should be called Apatosaurus. Two different names were applied to the … Continue reading
The papers were
The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types
- [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.
- 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.
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
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.