Confusing data with theory

Maybe because experiments can be so much work, molecular biologists are just happy to have the data:

Krakauer, et al. “The challenges and scope of theoretical biology”, Journal of Theoretical Biology Volume 276, Issue 1, 7 May 2011, Pages 269–276:

The current absence of a strong theoretical foundation in biology means that there is weak guidance regarding what quantities or variables need to be understood to best inform a general understanding (an explanatory basis) for biological features of interest. An unfortunate result of the absence of theory is that some researchers confuse just having data with ‘understanding’. For example there is a base for collecting and analyzing the most microscopic data: experimental procedures and measurements in a high-throughput transcriptomics study are built around the assumption that transcripts are the primary data to be explained, and in neuroscience, recording from numerous individual neurons. This bias reflects a rather naive belief that the most fundamental data provide a form of explanation for a system, as if enumerating the fundamental particles were equivalent to the standard model in physics.

And here is this kind of thinking in action:

Nurse and Hayles. The cell in an era of systems biology. Cell (2011) vol. 144 (6) pp. 850-854: Continue reading “Confusing data with theory”

Most inappropriate sentence ever written in a biophysical chemistry textbook

In fact most of our modern interest in the structure of biological molecules and systems is the foreplay related to our passionate interest in function.

– P.R. Bergethon, The Physical Basis of Biochemistry

Michel Houellebecq does post-apocalyptic clones

I just read Michel Houellebecq’s novel The Possibility of an Island. It was a mistake for me to do so. Given my literary tastes (Pynchon, Nabokov, Kafka, Borges, Cortázar, Calvino, DeLillo, etc.) I’ve long thought that Houellebecq would just my style but unfortunately, instead of reading what is likely a better Houellebecq novel, Elementary Particles, I picked up up The Possibility of an Island. On the surface, this book sounds great – a provocative, imaginative French writer does a sci-fi-ish, post-human, post-apocalyptic novel. What’s not to love?

Well, the tedious writing for one. While there are some good riffs in here, in general the flat prose is repetitive and tiring, executed with a light ponderosity that quickly becomes boring. I’ve got nothing against ‘novels of ideas’, but my experience is that a novel centered around ideas (as opposed to say, one focused on plot or character sketches) is generally a failure unless it also succeeds as art, because without art this kind of a novel typically is about as compelling as the classic dinner party bore who spends the whole evening droning on with poorly articulated banalities. Continue reading “Michel Houellebecq does post-apocalyptic clones”

Why to avoid a science career…

Yep:

“Academia’s Crooked Money Trail”, by Beryl Lieff Benderly, over at Science Careers

The troubles plaguing academic science — including fierce competition for funding, dismal career opportunities for young scientists, overdependence on soft money, excessive time spent applying for grants, and many more — do not arise, Stephan suggests, from a shortage of funds. In 2009, she notes, the United States spent nearly $55 billion on university- and medical school–based research and development, far more than any other nation.

The problems arise, Stephan argues, from how that money is allocated: who gets to spend it, where, and on what. Unlike a number of other countries, the United States structures university-based research around short-term competitive grants to faculty members. The incentives built into this system lead universities to behave “as though they are high-end shopping centers,” she writes. “They turn around and lease the facilities to faculty in [exchange for] indirect costs on grants and buyout of salary…” Continue reading “Why to avoid a science career…”

Progress in biology?

“I came to work at the MRC Unit for the Study of Structure of Biological Systems in September of 1951…The then tiny unit, composed of Max Perutz, John Kendrew, Francis Crick, and Hugh Huxley, with Sir Lawrence Bragg, the Cavendish Professor, as its very involved patron, had as its objective the understanding of life at its deepest level, the molecular. By so doing, they hoped to transofrm biology from a morass of seemingly limitless and often boring facts into an intelectually satisfying discipline like physics and chemistry.”

– James Watson, “Minds That Live For Science”, in A Passion for DNA.

60 years later:

“Biology is entering a period where the science can be underlaid by explanatory and predictive principles, rather than little bits of causality swimming in a sea of phenomenology.”

– Eric Davidson, quoted in Erica Check Hayden,”Life is Complicated,” Nature April 1, 2010

Will we ever escape from the morass of limitless, boring facts?