Joe’s post this week on the need for wholesale reform of the current peer-reviewed journal system caused a stir – following links from BoingBoing, Reddit and Hacker News it’s already our second most popular post ever in terms of traffic, and the comments thread currently sits at 86 comments. It’s (unsurprisingly) a topic that aroused passion among scientists, with strong arguments being made both for and against the current system. [DM]
A paper in Nature this week is that rarest of creatures: a high-impact genomics paper with only two authors. Heng Li and Richard Durbin show that the information contained in a single human genome sequence is sufficient to reveal a surprising amount of information about our recent evolutionary history. For the lay summary, Razib Khan has a typically thorough dissection of the paper and its implications. [DM]
Mary Carmichael has a fantastic piece in Nature (free registration required, annoyingly) about a Minnesotan woman who has devoted her life to attacking newborn screening programs. It’s a suitably balanced article: while the anti-screening activists engage in brazen hyperbole against a system that has unquestionably saved many lives, Carmichael doesn’t shirk away from noting that there have also been abuses of privacy. It’s not a debate that will be going away any time soon. [DM]
Colm O’Dushlaine, a scientist at the Broad Institute, has been analysing his 23andMe data in various ways and documenting his methods and results online. If you’re savvy enough to use the Unix command line you’ll find some useful tips for mining your own data. [DM]
Various Genomes Unzipped members have made the transition to Google’s much-discussed new social media platform, Google Plus. You can find Daniel here, Dan here, Joe here, Luke here and Vince here. [DM]
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Joe’s argument can be summarized simply: open source peer review over academic peer review.
Open source codebases on github are FAR more robustly peer reviewed than the vast majority of academic papers.
Did anyone do “academic peer review” of Linux? Of Rails? Of Django, JQuery, Protobuf, or any of the things on this list:
https://github.com/popular/watched
Answer: no. Yet many of those projects are not only used in academic papers, they are the foundation for huge websites that all of us use on a daily basis.
Reason #1: for one thing, open source code usually actually works, whereas most papers are written to obscure exactly what the academic is doing so that they can retain that edge over the competition. Just try getting a raw dataset or key reagent out of some of these people.
Reason #2: no one can stop you from putting something on github. We recognize at the beginning that there will always be haters for every project. Fine, this work isn’t for them, ignore. Can you imagine if a Python developer had to please some randomly chosen Java developer before showing his work to a mass audience?
Yet that’s what academic peer review is. It’s 2-3 guys who often want to torpedo your stuff. It’s just statistically provably less robust than 1000 eyes of experts cloning and forking your git repository.
Funding models need to catch up, but the technological counterexample is already there: open source peer review, not academic peer review.
Also, that Heng Li/Durbin paper took two years to get published. Who knows what the backstory was, but it’s probably a pretty good case study for the Pickrell proposal.
thanks for the link! and i appreciate the term “lay summary,” i get a lot of crap for being too abstruse ;-)