Re: "Algorithms" in Molecular Biology?

dougwedel@xxxxxxxxxxxxx wrote:
"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."

So far, the second law of thermodynamics in play. Prigogine dealt with this in
terms of "dissipative structures" rather than of "information". And there is
nothing requiring the reality of information posited here.

The laws of physics dictate what is possible. But they do not predict what
will be exactly. This is either a limitation of our ability to specify
physical states or it depends on quantum indeterminacy but for our purposes it
doesn't matter. The point is that S was correct to say we can't predict the
outcomes of biological processes purely in terms of physical laws.

That said, we certainly *can* say that order is the result of physical, and
only physical, processes after the fact. Our inability to reduce them is not
the point. An irreducible theory may be irreducible simply because the states
are multiply realised. Or they may be downwardly caused (i.e., caused by
higher level phenomena, like, say, ecological selection). This is a fact about
explanation, not a fact about the things themselves...

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.

The idea that aspects of the world that are not actual information processing
machines (like computers, teleph networks, and nervous systems) are algorithms
is a category error. A popular one, I grant you, but no more probative than
the pulley and lever mechanism metaphor of earlier times. Each generation
takes whatever is cool and uses it as a substantive heuristic so long as it
can. This is the "information age" but that doesn't make physical systems of
the ordinary kind computers.

Shannon's ideas were published in the late 1940s and almost as soon as it was
published, people started making use of it to "explain" everything from brain
behaviour to genes. But they, and we when we do it, are mistaken the metaphor
for the object, the abstract for the concrete, and the explanation for the
explanans.



--
John S. Wilkins, Postdoctoral Research Fellow, Biohumanities Project
University of Queensland - Blog: evolvethought.blogspot.com
"He used... sarcasm. He knew all the tricks, dramatic irony, metaphor, bathos,
puns, parody, litotes and... satire. He was vicious."

.

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