Tuesday, June 10, 2008

To wikify GenBank?

Further to the IPBiz post --Use of GenBank Accession numbers in patent applications --, note the "letter to the editor" in Science (320 Science 1289 (6 June 08)) commenting on the 21 March "News of the Week" story "Proposal to 'wikify' GenBank Meets Stiff Resistance". The letter states: "Serious users of GenBank use it as a starting point for in-depth analysis with new bioinformatic tools and reviews of more recent work. These users often learn more about the data than the initial depositors or curation staff. This valuable information--hidden in notebooks and rarely published is being lost to researchers."

The authors mention EcoliWiki and EcoliHub. Of alternatives, the authors write the challenge is not chaos but lack of participation. [IPBiz notes the USPTO seems to be bothered by the "changing" aspect of GenBank. Separately, the challenge to peer to patent is simply stupidity.]

Elsewhere, at page 1292: the "standard error" --- is the confusion of statistical with substantive significance (As Posner once wrote: correlation is not causation.)

At page 1297, in "The Scale of Prediction," we have "changes in individual factors (temperature, pH, O2, etc.) do not occur in isolation but in a temporally coupled and nonrandom manner for physicochemical reasons." There is discussion of an article by Tagkopoulos on page 1313. Also: an organism can migrate to a suboptimal environment and rapidly gain fitness through rewiring. Such a marginal increase in fitness might make the organism reasonably competitive while it undergoes a much longer process (lateral gene transfers and/or spontaneous mutations followed by selection) to fully adapt to its environment.

At page 1301, a discussion of eukaryotes.


Post a Comment

<< Home