Dave - Thanks. This physicist is learning a lot of biology by osmosis.
> My analyses are not optimizing a gene sequence, but rather seek to
> find an optimum network connecting known sequences (i.e., an
> evolutionary tree). The basic process is simple: Construct a
> network. Modify the network in various ways. If a better network is
> found, modify that network and try to improve on it. Stop when no
> better networks are found. Repeating the process several times
> helps. This finds greatly improved networks (though not necessarily
> the best network) much more efficiently than simply trying random
> networks. This seems to directly contradict the No Free Lunch
> principle. It does not involve any knowledge of the goal on the part
> of the program or programmer, and is applicable to any similar data
David, what criteria do your programs use to find a "better" network?
Our local group works with viruses, and stresses them. Then they let them
reproduce for several weeks in a chemostat under stress, and they
sequence them several
times a day. So at the end of the experiment, they know the detailed sequence
history, as well as the beginning and end points.
Then our computer guy takes the beginning and final sequence, and lets the
computer figure the optimum tree to get from here to there. But the
"best" pathway has always been far from the actual path.
Getting back to our NFL lecture, the next day I asked my C.S. friend
how he sized up
the NFL situation. He said, "well, than maybe Nature isn't
algorithmic" This really
surprised me because I took this to mean "Well, maybe the philosophy
isn't working". But by the next week he had thought of a number
of ways that his
faith in Naturalism could be preserved.. (too complex for me to remember)
I highly recommend Dembski"s book, No Free Lunch . It is closely
reasoned from a number of
different angles. And it has stood up well under the reviews it has received.
All God"s Best. Larry Johnston
"There is sufficient light for those who desire
to see, and there is sufficient darkness for those
of a contrary disposition."
-Blaise Pascal, Pensees 149 ~~~~~~~~~~~~~
Lawrence H. Johnston home:917 E. 8th st.
professor of physics, emeritus Moscow, Id 83843
University of Idaho (208) 882-2765
Fellow of the American Physical Society
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