Introduction
This section is devoted to commentary on an idiosyncratic collection of papers in ‘systems biology’, (a sadly vitiated term), that have caught my attention. Its mostly critical. Biology, unlike Physics has a very hierarchical publication structure, perhaps because the volume and nature of material make it hard for those not involved in the subject to see the problems. Hence publication pedigree replaces a close reading. The problems are compounded for systems biology, where the mathematician may assume the pretty pictures plus gene names mean something while the biologist might be too respectful of equations (or go to the other extreme of damming them all). Physics papers are easier for most professionals to judge right/wrong or interesting/trivial and when I was last involved an interdisciplinary subject, ‘chaos’ and fluid mechanics, there was healthy skepticism between experiment and theory. Kudos were bestowed for experimentally proving something wrong. Negative results in Biology are not accorded much respect since they generally do not lead anywhere.
Logically there should be more blogging in emerging areas. The referees sometimes are the most careful readers a paper ever gets (and here the culture that makes for nitpicking on prospective work ie NIH grants is productive) but referee insights are lost. There are existing web protocols that allow linkage from a paper to all later commentaries that the PLoS journals use. Ideally this content should be collected in an open source version of Faculty of 1000. Wordpress seems a reasonable software option.
For the moment, my picks are organized here by year of publication. I try to ask one of the authors for feedback as to what I missed.