Re: "Algorithms" in Molecular Biology?


"kramer" <kodream@xxxxxxxxx> wrote in message
news:e4l1dr$2l0c$1@xxxxxxxxxxxxxxxxxxxxxx

dougwedel@xxxxxxxxxxxxx wrote:
Many scientists have talked about the need to start thinking about
molecular
biology in terms of algorithms (I first encountered this from Sydney
Brenner
in Horace Freeland Judson's "Eighth Day of Creation" -- and that was more
than a quarter of a century ago).

What we are finding about the way genes actually work, such as the
workings
of the genes of immunology, reek of algorithmic characteristics. The
different genetic cassettes line up in the gene text itself like so many
sections of a switch statement in a program module.

Yet I wonder: do serious biologists talk in terms of "algorithms"? Can
anyone direct me to such a discussion? And if not, why not?

Lets everybody draw a chair. Unless you are an art school student you
probably all drew something that you can sit in. Is it the algorithm
of sitting which defines the chair property?

Lets all draw a DNA unless it folds up properly your organism is DEAD.
And we all know from the theory of evolution that biologists are only
interested in live things, and things that will reproduce and live a
long time.

There can be lots of DNA sequences, but unless they behave in a certain
way they are DEAD.

I guess my point is, you can't define the term algorithm, because the
concept subsumes the concept of definition. If you can't sit in it,
its not a chair, if it doesn't fold up into a double helix its not DNA.
If it can't be measured it can't exist. If a cell doesn't produce and
consequently consume ATP it doesn't live. If a virus doesn't rewire
the operation of a cell its not a virus.

The unusually-brilliant moderator of this group will probably censor my
post, but I have a comment: asking whether molecules "use algorithms" is the
same thing as asking "does the Moon calculate its orbit?" It is troublesome
that the latter (as well as the former) are not more widely recognized as
stupid. Individual sciences may still move forward, but this mistake
conceals something important about the conduct of science; the product of
science is verbal behavior that allows us to act upon the world in a
successful way. The "laws of physics" control the behavior of
appropriately-trained listeners, not the "behavior" of magnets, steam
engines, and black holes.

[moderator's note: Brilliant or not, this does seem to wandering
a bit far afield, although I certainly agree with the sentiment.
Perhaps we've done as much as we can with this thread? - JAH]




.

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