Author: Mike White

Genomes, Books, and Science Fiction

ENCODE is devouring the rest of biomedical science

A new NIH RFA:

PsychENCODE: Identification and Characterization of Non-coding Functional Elements in the Brain, and their Role in the Development of Mental Disorders (R01)

The Encyclopedia of DNA Elements (ENCODE) project, by systematically cataloging transcribed regions, transcription factor binding sites, and chromatin structure, has recently found that a larger fraction of the human genome may be functional than was previously appreciated. However, our understanding of the role of these functional genomic elements in neurodevelopment and mental disorders is at an early stage. This funding opportunity will support studies that identify non-coding functional genomic elements and elucidate their role in the etiology of mental disorders.

Suddenly, the ENOCDE model is now the way to do science. It’s hard to disagree with Dan Graur on what the consequences are: Continue reading “ENCODE is devouring the rest of biomedical science”

Great scientists don’t need math

So says E.O. Wilson in the Wall Street Journal.

But don’t just read the headline – be sure to catch the nuance in Wilson’s piece. He’s saying don’t let fear of math drive you from science, because you don’t need straight A’s through four semesters of calculus to be a good scientist.

I don’t quite agree with Wilson when he says you can always find a mathematician as a collaborator to handle the math you need. A mathematically illiterate biologist working with a biologically illiterate mathematician is usually not a fruitful combination. But good scientists pick up the necessary mental toolkit as it’s needed, including mathematical and statistical knowledge (as long as they’re willing to put some serious effort into gaining that knowledge, as opposed to, say, figuring out how to mindlessly apply t-tests).

Sean Eddy calls this approach “ante-disciplinary science”: Continue reading “Great scientists don’t need math”

Some light reading for fellow science fiction junkies

amisnewmapsofhellAt last: I’ve got an author index of my science fiction reviews here at The Finch and Pea. If you compulsively read vintage science fiction like me (my interests mostly fall in the ~1945 to 1986 range), then you may just find something to your liking here.

Why vintage science fiction? It is a literature that has a lot to say about our culture’s relationship with science and technology, one that has developed some striking metaphors for science and nature.

Over the last few years I’ve managed roughly 30 reviews, fewer than I’d hoped, but not too shabby. Up next is a series on Big Dumb Object science fiction, already begun with Rendezvous with Rama. Coming up soon will be a discussion of Niven’s Ringworld, Varley’s Titan, Bob Shaw’s Orbitsville, Greg Bear’s Eon, and finally, once I finish working my way through the Polish original, Lem’s Solaris. Continue reading “Some light reading for fellow science fiction junkies”

How to reference a rejected paper on your CV

From Rob Phillips’ list of publications on his lab website:

A First Exposure to Statistical Mechanics for Life Scientists. (with Hernan G. Garcia, Jane’ Kondev, Nigel Orme and Julie A. Theriot), Rejected by Am. J. Phys., 2007. [online full text]

The paper itself is a great read, with some important ideas for anyone who thinks about how to incorporate more quantitative/physical concepts into our program of biology education. It also tells you that stat mech is almost effortless once you understand the Boltzmann distribution: Continue reading “How to reference a rejected paper on your CV”

Retraction rate increases with impact factor – is this because of professional editors?

Folks have long noted the strong positive correlation between high impact factor and retraction rate. There are three primary theories I’ve run across that attempt explain why Nature, Science, Cell, etc. have substantially higher retraction rates than other journals:

1) Acceptable risk/fame and glory theory: High impact factor journals are willing to publish riskier, but potentially higher-impact claims ASAP – more retractions are the price for getting high-impact science out early. The more negative version of this theory is that high impact factor journals care more about a high impact factor than about the integrity of what they publish.

2) Heightened scrutiny theory: papers published in high visibility journals get more scrutiny and thus flaws/fraud are more likely to be detected, but fraud/errors happen roughly equally everywhere. An associated theory is the high-stakes fraud theory: if you’re going to commit fraud, you need to make the payoff worth the risk, so you’re going to submit to Nature and not BBA.

Anthony Bretscher, in an MBoC commentary on editors, proposes a new theory, which, based on personal experience, I believe accounts for most of the correlation between retraction rate and high impact factor journals:

Continue reading “Retraction rate increases with impact factor – is this because of professional editors?”