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Alife Digest Number 016
Artificial Life Digest, Number 16
Tuesday, April 17th 1990
Issue's Topics:
Brain Waves generated by model
artificial life research
Update on SRL
Theoretic Protein Folding Work
----------------------------------------------------------------------
Subject: Brain Waves generated by model
Date: Mon, 09 Apr 90 14:37:02 PDT
From: rpandey@mist.cs.orst.edu
Communications of the ACM 33(4), April 1990 p.387 has a Newstrack brief that
reads:
"BRAIN WAVES...A supercomputer model for studying the brain has
unexpectedly produced--on its own--electrical waves like those
actually found in the brain itself. The model, developed by IBM
scientist Roger Traub and Columbia University researchers Richard
Miles and Robert K.S. Wong, was designed to imitate 10,000 cells
in the brain's hippocampus, the origin of many epileptic episodes.
The most startling aspect of these waves is that no one understands
precisely how they are generated either by the supercomputer model
or by the brain. However, their existence does provide the
scientists with potent evidence their brain model is accurate."
Anyone have any more information than appears above?
-----------
Rajeev Pandey | Department of Computer Science
Internet: rpandey@cs.orst.edu | Computer Science Building 100
UUCP: hp-pcd!orstcs!rpandey | Oregon State University
Phone:(503) 737-3273 Fax: (503) 737-3014 | Corvallis, OR 97331-3902 U.S.A.
------------------------------
Date: Thu, 12 Apr 90 08:56:50 -0400
From: fritz_dg%ncsd.dnet@gte.com
Subject: artificial life research
Assuming that the emergence of complex entities with the characteristics of
life requires the interaction of organizing code with an environment or medium
capable of evolving complexity, there are efforts underway to study:
algorithmic code with computer environments (GA's, AL programs), organic code
with laboratory/biosphere environments (genetic engineering), and
memetic/culturgenetic code with social environments (clearinghouse
at U. of Miami?).
The question is, is anyone working the AL principle on any other media?
Inorganic non-computational would be of interest. This notion must at least
have been grist for many SciFi story mills, but I'm not up on this sort of
thing. In any event, the development of an actual, not fanciful,
genesis is the thing. Anyone?
Dave Fritz fritz_dg%ncsd.dnet@gte.com
------------------------------
Date: Sat, 14 Apr 90 16:22:46 CDT
From: kurt@happy.csg.uiuc.edu (Kurt)
Subject: Update on SRL
A friend just sent me some information about upcoming Survival Research
Labs performances which was posted to the Crash mailing list. Enjoy.
kurt
Really From: Mason Jones <mason@haedx.UUCP>
>From: hoptoad!xerox.com!minneman.pa
>
>I talked to Mark Berger (who runs the COCA) when I was up in Seattle. He
>said that Mark Pauline had rejected the hangar site (can't remember why)
>but that he had been happy with an abandoned railroad yard just south of
>the Kingdome. It sounded pretty definite at that point; the flyers
>certainly have been printed up with that date.
That makes sense. The hangar site was what I heard last year. I
suspect Mark wanted to avoid anything indoors. The last show here
in SF was a bit confined because it was under the freeway. I'm glad
to hear it'll be an outdoor thing (as long as it doesn't rain).
>Mark Pauline talked at EE380 at Stanford today. He mentioned an upcoming
>performance this summer or early fall at Heart Park in Lewiston (sp?), New
>York (near Niagra Falls). Sounds like road trip material for everybody
>east of the Mississippi! He also said there was one more San Francisco
>show planned for this calandar year.
Yeah, last I talked to him about it, the Buffalo one is sometime
around August. The SF one may actually be in San Luis Obispo at
Cal Poly, if it's the one I think he was probably talking about.
That wasn't at all definite as of a few weeks ago, though.
>He also mentioned a running machine they're working on. It looks like it
>will be a six-legged machine with alternating tripod gait. Unlike the
>Raibert machine, which uses compliant legs, they intend to dynamically
>adjust the leg length with hydraulics. He mentioned a figure of > 10
>m.p.h. as a target. This is supposed to be done for the N.Y. performance.
The hydraulic leg length is similar to the way the current walking
machine operates (the huge one that had one of the flame throwers
at the SF show). That one moves the diagonally-opposed legs up at
the same time, thus leaning forward a little, then lifts the other
two legs. That one's only got four legs, of course, not six like
this new one will have.
He didn't say anything about the whistles? I don't know what the
status of those is right now... I've been too busy to stop by
and check on things lately.
------------------------------
Date: Tue, 17 Apr 90 10:03:31 EDT
From: hunter@nlm.nih.gov (Larry Hunter)
Subject: Theoretic Protein Folding Work
"David A. Honig" <honig@bonnie.ics.uci.edu> writes in Alife-digest #15:
... some computational chemists found that *many sequences* of amino
acids yield the same shape when the protein folds. Now, no doubt there
may be critical sequences, but their point was that nature gives you
some slack (my interpretation), since shape matters a lot for enzymatic
activity.
So it may be not only useful but perhaps realistic to have redundancy
in geno to pheno expression.
I think this refers to work by Ken Dill and Kit Fun Lau at UCSF. This
is VERY interesting stuff. The idea is to use a simple model of
protein folding (driven only by polar vs. non polar residues in a 2D
conformation space) so that the free energies of the entire space of
conformations for short (< length 18) "peptides" can be searched in
(semi-) reasonable amounts of computer time. Given the ability to
determine conformations from sequence, they investigate the
relationship between changes in sequence space and changes in
conformation space. David is correct in noticing that one of the take
home messages is that most mutations are neutral in terms of
conformation. Some refs:
Lau, Kit Fun & Dill, Ken, "Theory for protein mutability and
biogenesis," Proc. Nat. Acad. Sci. USA, Vol. 87, pp. 638-642, January
1990 Biophysics.
Lau, Kit Fun & Dill, Ken, "A lattice statistical mechanics model of
the conformational and sequence spaces of proteins," Macromolecules,
Vol 22, No. 10, pp. 3986-3997, 1989.
Also interesting in this vein is the empirical work done by Bob Sauer
and colleagues at MIT. They have systematically changed each residue
in lambda repressor and measured functional changes. There results
are remarkably similar to Dill's theoretical ones: namely, most
mutations are neutral with respect to function, and that the ones that
matter most are the in the core residues. Refs:
Bowie, J., Reidhaar-Olsen, J., Lim, W. & Sauer, R., "Deciphering the
Message in Protein Sequences: Tolerance to Amino Acid Substitutions,"
Science, vol. 247, pp. 1306-1310, 16 March 1990.
Reidhaar-Olsen, J. & Sauer, R., "Combinatorial Cassette Mutagenesis as
a Probe of the Information Content of Protein Sequences," Science,
vol. 241, pp. 53-57, 1 July 1988.
As a CS person, I find Dill's work especially compelling. His method
suggests all kinds of computer-based experiments....
Larry
Lawrence Hunter, PhD.
National Library of Medicine
Bldg. 38A, MS-54
Bethesda. MD 20894
(301) 496-9300
(301) 496-0673 (fax)
hunter@nlm.nih.gov (internet)
------------------------------
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