Progress report

The Results section of the Sxy manuscript-in-progress has been revised, and I'm waiting for results and figures from the grad students before doing more work on it.

The CRP-S manuscript has been provisionally accepted, with reviews that were both complimentary and useful. Over the next few days the grad student whose work it reports will make the minor corrections it requests and do the new analyses suggested by one especially helpful reviewer, and we'll compose a response for the Editor. Then we'll resubmit and wait for the acceptance email telling us where to send our $1900 payment of the journal's 'Open Access Charge'.

A paragraph (oops, it's turning into an essay) about such publication charges. Until 10-20 years ago, almost all research was published in print journals whose costs of publication were covered by subscription fees and often by advertising revenue. Because only specialists read most journals, the subscription fees were high for individuals (often well over $100 for 12 issues per year) and exorbitant for institutions such as university libraries. Some journals were published by non-profit professional societies, and some by profit-seeking publishers. This arrangement was bad for science, because articles were only available to people whose grants or institutional libraries could pay for a subscription.

Now, much research is published electronically as well as or instead of on paper, and most of it is available free online, either immediately or after a profit-allowing delay (often 6 or 12 months). This is good - research results are much more widely available - but it has reduced the incentive to pay for a subscription, so journal revenues are down. Journals have responded by requiring large financial contributions from the authors of the papers they publish.

This smells like payola, and my knee-jerk reaction to the $1900 charge is outrage, but in fact it's a move in the right direction. The costs of disseminating research should be treated as part of the costs of doing science, and it makes much more sense to pay them as publication charges ($ from research grants) than as subscription fees ($ from university libraries). The 'usual' way (pay for the privilege of reading the papers) was the wrong way. It was the standard only because, before the internet, we didn't have the technology to make our findings widely available. (Readers interested in this issue should check out the Public Library of Science.)

Now, where was I? Oh yes, progress... We're still waiting for the final decision on our revised and resubmitted USS-2006 manuscript, but we don't expect any problems. The Perl project needs attention (the WestGrid server has unexpectedly given our requested runs the cold shoulder), so I'll try to sit down with the post-docs today to sort out where the bugs are and what to do next. I'll also get back into my 'unbiased' search for USS-related motifs in the genome sequence. And maybe I'll get back to the bench for a change - a collaborating grad student needs me to run an assay for him.