Friday's reading

Reading

Catching up on journal table-of-contents/rss readings.

News

Australia Researchers unhappy (unknown, 2011)

Climate change and Open Science

Nature debate on the Berkeley climate team’s (BEST) press release in advance of publication. (unknown, 2011) Editor critiques the stunt:

Richard Muller, the physicist in charge, even told the BBC: “That is the way I practised science for decades; it was the way everyone practised it until some magazines — particularly Science and Nature — forbade it.”

This is both wrong and unhelpful. It is wrong because for years Nature has explicitly endorsed the use of preprint servers and conferences as important avenues for scientific discussion ahead of submission to this journal, or other Nature titles.

And suggests they might have posted the result on a preprint server and solicited input, rather than announcing a definitive conclusion:

To solicit input on results before publication is not a guerrilla action against a shadowy scientific elite. Witness the posting on a preprint server last month of the paper reporting neutrinos that apparently travel faster than light: the authors made it clear that they were seeking help from the wider community to explain the findings, and the media stories (if not the headlines) mostly reflected that. To pretend otherwise can only erode public trust in science, as it is practised by all.

Education

A provocative letter on the lack of empirical support behind NSF’s recently closed G-12 initiative (Cormas, 2011)

Phylogenetics

Interesting study of branching models in treebase, including constant rate birth-death models and some time-dependent models (Jones, 2011)

From Bioinformatics, Spatial spread from phylogenies software (Bielejec et. al. 2011) and some treevis software (Pirrung et. al. 2011) I haven’t had a chance to look at.

Theoretical Ecology

Analysis of the global population dynamics database: uncertainty in abundance may drive the lack of signal of density dependence (Knape & de Valpine, 2012). The literature on this has been mixed, I wrote an F1000 comment on an earlier eco let paper that didn’t find density dependence, in which I called for just this kind of study, so it’s nice to see, if not surprising, that the conclusions here are largely a lack of signal. (Ziebarth et. al. 2010)

Critical transitions

Things I’ve been meaning to give a closer look into: (McClanahan et. al. 2011), (Franklin & Johnson, 2011), (Hirota et. al. 2011), (Staver et. al. 2011),

and still have to replicate the methodology of Ditlevsen & Johnsen, 2010

These regime shift videos are quite cute.

And this “database” is a great idea, but would be more useful if it had data, not just descriptive metadata.

Open Science Blogs

And catching up on some definite highlights from the open science blogs.

  • Cameron Neylon: on building useful databases. insightful, practical, an so right.
  • Michael Nielsen gives the best description of the state of Open Access publishing I’ve seen, including stories of some of the most exciting recent changes.
  • Heather Piwowar describes their total-impact project.
  • Our own open science community is getting going on Jason’s provocative post on getting scooped in open science. Jonathan Eisen shares his experiences and Law Professor Mario Biagioli shares a preprint on Openness, secrecy, and priority in science.

References