Re: "Algorithms" in Molecular Biology?


"John Wilkins" <john@xxxxxxxxxxxxx> wrote


Schrodinger's (can't safely do umlauts in Thunderbird, sorry) claim is not
that maths is going on in the biologist organisms, but rather a denial
that
biology "was much too involved to be fully accessible to mathematics"
(p3).
mathematics was the tool of physics, not the reason physical processes
occurred. His metaphor of the "aperiodic crystal" as the basis for
heredity
certainly (ahem) crystallised thinking, but he notes that the "four
dimensional structure" of living things (i.e., extended organisms over
time
and space) is determined by the structure of the nucleus (in particular
chromosomes). It's clear that he does not mean that the chromosomes form
an
actual "code-script" as he calls it (p22) but that it is a metaphor to aid
understanding. He calls a gene "the hypothetical material carrier of a
definite hereditary feature". He doesn't appear to make much of the
immaterial
informational aspect of genes.

Schrodinger not only predicted the "code-script" 10 years before Watson and
Crick published its structure, he also predicted that from what was already
then (1943) known of the enormous complexity and precise order of biological
molecules that the unfolding science of the living cell would require NEW
LAWS OF PHYSICS. This is a part of "What is Life?" that often is left
undiscussed -- after all, what can the man be talking about? Here's three
snippets from the final chapter of the published version of "What is Life?"
The chapter begins with a question:

"Is Life Based on the Laws of Physics?

"NEW LAWS TO BE EXPECTED IN THE ORGANISM

"What I wish to make clear in this last chapter is, in short, that from all
we have learnt about the structure of living matter, we must be prepared to
find it working in a manner that cannot be reduced to the ordinary laws of
physics. And that not on the ground that there is any 'new force' or what
not, directing the behaviour of the single atoms within a living organism,
but because the construction is different from anything we have yet tested
in the physical laboratory... The unfolding of events in the life cycle of
an organism exhibits an admirable regularity and orderliness, unrivalled by
anything we meet with in inanimate matter. ... An organism's astonishing
gift of concentrating a 'stream of order' on itself and thus escaping that
decay into atomic chaos -of 'drinking orderliness' from a suitable
environment -seems to be connected with the presence of the 'aperiodic
solids', the chromosome molecules, which doubtless represent the highest
degree of well-ordered atomic association we know of -much higher than the
ordinary periodic crystal -in virtue of the individual role every atom and
every radical is playing here. To put it briefly, we witness the event that
existing order displays the power of maintaining itself and of producing
orderly events."

At the very time that Schrodinger was giving his lecture Shannon was writing
some of his key papers, but it was classified work at the time by the war
department. Information theory had not yet been born, and Schrodinger
therefore did not have at his disposal the conceptual equipment necessary to
discuss the nuts and bolts of the new laws of physics that would be required
to encompass life within its folds. But perhaps now with the tremendous
flowering of information theory and computer science we can begin to imagine
that the new laws of physics that Schrodinger was talking about were the
laws of algorithmic processing in the living cell, yet to be discovered, and
indeed, as this thread has seemed to indicate, not yet really even discussed
with any specificity.


.

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