Monday, February 20, 2012

The role of textbooks in biology

"Hey, this is textbook knowledge, you should know that!"

This is what I would be told, if I were to ask a stupid question about microbiology in the laboratory. (And for the record, I believe that such things as "stupid questions" do in fact exist.) 

"Textbook knowledge" is often used to define the core knowledge that a biologist (or any scientist, as far as I can tell) should possess as a result of her education. When I was an undergraduate biology student, we used to talk about "the Campbell" and "the Alberts" to refer to our textbooks of general biology and molecular biology, respectively, and today I talk of "the Brock" to mention a reference textbook in microbiology. Textbooks are not only useful to students; personally, I often find relevant information in them, although most of my readings are scientific papers. 

A textbook should provide you with the background knowledge sufficient to operate in the current state of your discipline. (Although, of course, some will be more general or conversely will be more specific than others, depending on their goals.) 

The University of Chicago Press (Image source)
The reason I want to write about textbooks here is a consequence of my reading of "The structure of scientific revolutions" (1962), the landmark book by science philosopher Thomas Kuhn. Together with Popper, Kuhn is among the most famous philosophers of science: he coined the term "paradigm shift", which is not only a fascinating concept, but also a very catchy idea. Scientists like to use it often and in many different contexts. (Probably too often in my opinion, since paradigm shifts do not take place that frequentlyif they take place at all.) 

Kuhn's book is an excellent read because it is rather concise (my edition is about 200 pages, with a 30 pages postscript) and almost devoid of jargon, which makes it very engaging. My only regret was maybe that I felt I already knew too much of it, since Kuhn's ideas have been widely explained and discussed. For instance, I remember reading a very good recapitulation of Kuhn's theses in a French translation of Alan Chalmers' book "What is that thing called science?". Nonetheless, a lot of fascinating details were still to be found.

Sunday, February 12, 2012

Jacques Monod and the study of bacterial growth

Among the great scientists of the 20th century, Jacques Monod holds a prominent place. Together with François Jacob and André Lwoff he contributed to the creation of molecular biology through his study of genetic regulation, in particular the lac operon in E. coli. Before this achievement, which was awarded a Nobel prize in 1965, Monod helped define the nature of bacterial growth in a variety of experiments that took place during his doctorate. He published it in 1942, exactly seventy years ago, under the title "Recherches sur la croissance des cultures bactériennes" (a second edition, the one I read, was published in 1958).

In his experiments, Monod followed the growth of liquid bacterial cultures in flasks at controlled conditions of temperature and oxygenation. The turbidity of the culture, which was used as a surrogate value for bacterial biomass, was measured with a nephelometer (in laboratories, today, a spectrophotometer is usually employed, but the principle is the same). Bacteria were grown in complex (brain broth) or defined media with variable sources of carbohydrates. Monod used Bacillus subtilis and Escherichia coli (that he calls B. coliBacterium coli I suppose, which is the ancient taxonomy). 

Most notably, Monod showed that bacterial growth is limited by the amount of nutrients, but that the yield is independent of the concentration of these nutrients. The growth rate, however, is dependent of the nutrients' concentration and rapidly reaches a limit. What is more, this maximal growth rate can vary a lot with different carbon sources and temperatures. Today, we still talk about 'Monod kinetics' when we describe the growth of bacterial cultures.

Sunday, February 05, 2012

What news from the ‘arsenic life’ front?

Mono Lake, CA, photo by NASA
This story has already become sort of a case study. In December 2010, NASA held a press conference about its astrobiology research program and the discovery of a bacterium from Mono Lake (CA) allegedly capable of substituting phosphorus by arsenic in its DNA. The research was published in ScienceExpress and attracted a lot of attention from the media - mostly as a consequence of the ‘hype’ factor brought by NASA, which went as far as saying that “The definition of life has just expanded”. All life on Earth shares the same DNA, whose backbone is made of sugar and phosphate. If any organism could replace phosphate by arsenate, that indeed would be very surprising and exciting.