William W. Cohen

As promised in the prologue, the book reads like a student’s class notes for an introductory course.

Professor Cohen is an expert in Machine Learning who took an interest in the applicability of his subject to bioinformatics and wrote this short book as a summary of his preliminary reading. It is not accessible to someone lacking a good high-school background in biology and organic chemistry; neither will it adequately refresh the details for one for whom the subjects have lain dormant for long. It will, however, prime the mind beautifully for the rest of the journey which it is presumed one to whom this book appeals intends to undertake.

The first section sketches DNA transcription and replication; the long middle section is a very detailed overview of some modern experimental techniques and the final brief section touches on the applications of computer science to bioinformatics.

I was struck particularly by Prof. Cohen’s metaphor for experimental biology: we are rather like giants smashing up great collections of minute and complicated machines and coarsely examining the aggregate detritus for a rough sense of the composition of the machines. (His metaphor is delightful extended: imagine a pile of personal computers laid out on a shag carpet, crushed by steamrollers, blown by the fan of a jet engine; the lighter parts blow further before the carpet snags them. We are left with bands of material graded from heavier to lighter and might conclude that a computer is composed of two or three sorts of metal and plastic organized in concentric shells.)

An illuminating section on reaction rates discusses molecular motion, the relative viscosities of cellular membrane and plasma (as butter to water), distances covered by diffusion (under random walk motion the time to cover a certain distance is as the square of the velocity, not linear with velocity) and contact probabilities, which may explain why diffusion is adequate in bacteria but that in larger cells reactions often take place along two dimensional membrane surfaces, where constrained motion increases the chances for reaction.

Other highlights: the behaviour of ion channels in nerve cells is nicely explained, protein gated channels a little less so (they are more complicated), discussion of energy transfer is too large a topic; the notes are merely a starting point.

In short; exactly as advertised, an excellent re-orientation and a guide to what to study next.… (més)