Notes from the biomass

If we follow Pedro Beltrao’s proposal to create virtual journals by tagging in Connotea to the end, we should start an online competition to create the journal with the highest impact factor. After all, the fantasy baseball and soccer manager games out there seem to be highly popular.

You probably need to select a minimum number of entries, may be 50 for a year or 5 - 10 a month and limit the subject area. The winner receives free scorn and secret envy from the scientific community.

The Altar des Alltags is a shrine currently installed in Munich by assorted Riesenmaschine followers to address our everyday gods. My non-German speaking readers are invited to pray to the Pantheon of Communication to catch the gist of the powers of the God for the Simple Solution of Complex Problems, the God for Forgotten Passwords and Merciful Amnesia, and their colleagues or just bow down, all of which can be done conveniently over the internet.

Sequencing a eukaryote organism apparently needs to pay back the effort with the initial publication, just like Hollywood blockbuster needs to bring its money on the opening weekend.
The problem is just that there are rarely exploitable surprises found in the sequence. At best, we bump into are harsh reminders of our ignorance. The genome of Mycobacterium tuberculosis told us that the PE/PPE genes, a large group of species-specific proteins were missed in 100 years of research on the bug. And remember that the main message of the human genome was that we had fewer genes than expected. Breaking news: estimates were wrong.
So, do the 222 Toll-like receptors found in the sea urchin’s genome (special Science issue) tell us much about the development of innate immunity? It rather shows that it will be nearly impossible to make simple inferences for these systems of the sea urchin and metazoans – which is certainly highly interesting yet somewhat unpleasant.

The conclusions of the review of the TLRs in Science include the following.
First, this genome sequence significantly refines our understanding of deuterostome immunity.
Which is a nice way of saying that many previous assumptions need to be jettisoned. Sequencing a genome is a good way of supplementing our lack of understanding with another myriad of unanswered questions - and a necessary framework to answer them. But didn’t yesterday’s ignorance feel more knowledgeable when the question/answers ratio suddenly increases dramatically?

N.B. Check Jonathan Eisen’s comment on justifying the efforts of sequencing.

Browsing any protein-protein interaction screen, the number of obvious false positives you can tell from simply assessing the function and cellular role of the two proteins is substantial. Hands up: If your screen would come up with a gyrase interacting with a glutamate racemase, would you put it in the abstract as a cool example?
After all, if you run two-hybrid, the gyrase obviously interacts with the DNA. If your screen is based on co-immunoprecipitation or another biochemical technique, the high abundance of an enzyme like glutamate racemase drives an obviously unspecific interaction. Obviously, you’d be discarding something interesting.

Despite an explosion of schemes for publishing research, our most important question remains unanswered. What constitutes a significant publication?We could have settled the problem a long time ago. However, evil capitalist publishers for monetary reasons, science magnates (re-styled as revolutionaries) to keep their established position and blue-eyed bloggers for causes they are unsure about all but promote their own style of selecting important works by interaction with other scientists or even the mass media. This only promotes preferential attachment, not absolute importance.
At best, the current discussion wastes trees and electricity in amounts that brings us closer to the entropic death of the universe but does not get us closer to objective publishing criteria. (more…)