Author: Mike White

Genomes, Books, and Science Fiction

Energy and information (or lack thereof) in biological thinking

Eric Smith, “Thermodynamics of Natural Selection” (PDF):

The two paradigms dominating biological theory are the machine-like functioning of componentry (increasingly elaborated in molecular biology) (Alberts, 2002), and the Darwinian framework for understanding the stochastic dynamics of death and reproduction (Gould, 2002; Lewontin, 1974). The representation of biological processes as machines is often by way of models, which represent control flow and causation, and for which the goal is to conceptually or quantitatively reproduce typical observed behaviors (mechanisms of binding, Stormo and Fields, 1998, transcription or translation, Berman et al., 2006, cell cycling, Novak et al., 2001, regulation of cell division, Tyson et al., 2002 or metabolic pathways, Holter et al., 2001, etc.). Energy naturally appears in these contexts as an input, as a quantitative constraint, or as a medium of control. However, models constructed for the purpose of illustrating causality often diminish the importance of the incursion of error at all levels of organization and the consequent energetic costs of systemic error correction, and so are not suited to composition into a system-level description of either emergence or stability. At the other extreme, Darwinian selection is a purely informational theory, concerned with emergence and stabilization through statistical processes. Yet, for lack of a comprehensive theory of individual function, models of the dynamics resulting from selection inevitably take for granted (Hartl and Clark, 1997) the platform of physiology, growth, development, and reproduction, decoupling the problem of information input from energetic constraints on the mechanisms by which it occurs.

Sunday Poem

This week it’s more of a prose poem, from the great Argentine author Julio Cortázar’s book From the Observatory. This book is a stream of reflections on two scientific images, one of an 18th century Indian prince who built a marvelous, Escher-like obsveratory; and the other of the epic migration of the European eel from continental freshwater streams to the Sargasso sea.

In this passage, the Indian prince Jai Singh “confronts the cosmic bull”, and is portrayed, not completely without irony, as someone who uses the scientific tools of his eccentric observatory to break free of human slavery to nature, or human slavery to superstition in the face of nature’s overwhelming force. In the book, Jai Singh stands in contrast to the pedantry of those myopic scientists who study the minutiae of the eels without any appreciation for the majestic scope of the eels’ life cycle.

Jai Singh must have dreamed something else raised like a guerrilla of the absolute against the astrological fatality that guided his lineage, that decided births and deflowerings and wars; his instruments stood up to a destiny imposed from outside, the pentagon of galaxies and constellations colonizing the free man, his stone and bronze devices were the machine guns of real science, the great reply to the total image facing the tyranny of planets and conjunctions and ascendants;

the man Jai Singh, little prince of a declining kingdom, stood up to the many-eyed dragon, answered the inhuman fatality as a mortal provoking the cosmic bull, decided to channel the astral light, trap it in retorts and spirals and ramps, clipped the nails that bled his species;

and all that he measured and classified and named, all his astronomy on illustrated parchments was an astronomy of the image, a science of the total image, a leap from the brink to the present, of the astrological slave to the man who stands in dialogue with the stars.

Sunday Poem

The Two Apes of Brueghel (1957), Wisława Szymborska (1923-2011)

So appears my big graduation exam dream:
In a window sit two monkeys fixed by chains,
Beyond the window the sky flies
And the sea splashes.

The subject is the history of mankind.
I stammer and flail.

One monkey, gazing at me, ironically listens,
The second seems to doze –
But when after a question comes silence,
It prompts me
By softly clinking the chain.

Translation from the Polish by yours truly.
All I have to say about this poem is that a monkey rattling a chain is never a good thing, especially at a thesis committee update. See the original Brueghel painting here.

Biomedical science… is there a problem?

The big news around the ‘net today, as far as the life sciences are concerned, is the dramatic increase in the number of papers that are retracted, as documented (yet again) in this paper, and told in this NY Times piece by Carl Zimmer. (Check out some of the buzz here and here and here.) This story is primarily about the biomedical sciences, and so the question naturally arises, is the biomedical science community dysfunctional?

I’m going to say yes – but perhaps not in the way you think. As someone at a vulnerable career stage, whose future career path depends on the health of the biomedical community, I’ve experienced some of the problems in the community, and so I will offer you my opinion based on anecdotal evidence, for whatever it’s worth:

The biomedical community is dysfunctional because it has increasingly become a system based on a rigged lottery. Continue reading “Biomedical science… is there a problem?”

How to find your way in E. coli without stopping for directions

One of the keys to success in life is to regulate your genes properly. Genes are regulated by transcription factor proteins, which have to navigate their way around the genome and bind particular DNA targets. The problem is that there are only a few correct targets and the genome is large. So an obvious question is, why don’t transcription factors get lost? Do they stop and ask for directions? Where is the information for genome navigation coming from?

The answer to this question is still being worked out for eukaryotes, but it has been solved for E. coli. Peter von Hippel and Otto Berg largely figured out the answer in their classic 1986 paper “On the specificity of DNA protein interactions.” E. coli’s solution for making gene regulation manageable is simple and elegant, because this bacterium has the virtue of possessing a small genome. Let’s take a look at how genome navigation works in a bacterium: Continue reading “How to find your way in E. coli without stopping for directions”