Evolvable molecular machines

Jim Toerresen jimtoer at idt.unit.no
Wed May 22 02:50:45 EST 1996


Thanks to all of you who replied on my requests on evolvable molecular
machines:

> 
> As a part the finalizing PhD we are in Norway assigned a subject 14 days in
> advance. In two weeks we shall collect available research publications and
> give an overview of the subject for the Ph.D. committee.  I have been
> assigned the very interesting subject "Evolvable Hardware".
> 
> I am doing computer architecture and know nothing about molecular biology.
> However, I have heard about people talking about molecular biology
> "machines". Probably none exits today but is there anyone coming up??
> If you know about this topic or can give me a good Web-pointer
> I would be happy to hear from you!
> 
> Please email me and I will summarize to this newsgroup.

Date: Tue, 14 May 1996 13:58:59 -0500
From: zauhar at xhost5.tripos.com (Randy Zauhar)

   A somewhat hot topic right now is Adelman's work on computing 
 with DNA. Here is the reference:

Adleman ["Molecular Computation of Solutions to Combinatorial
Problems", Science, 11 November 1994]

   This is not however an "evolvable" machine. There is also a review by 
 Tom Schneider (which I have not seen):

@article{Schneider.nano2,
author = "T. D. Schneider",
title = "Sequence Logos, Machine/Channel Capacity,
{Maxwell}'s Demon, and Molecular Computers:
a Review of the Theory of Molecular Machines",
journal = "Nanotechnology",
volume = "5",
number = "1",
pages = "1-18",
year = "1994"}

   You might also want to look at Drexler's semi-popular book on 
 Nanotechnology.

     Best of luck,

     Randy


All opinions expressed here are mine, not my employer's

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Date: Wed, 15 May 96 01:15 MET
From: chbarry at mackiller.llnl.gov

I hope you aren't too disapointed with this pointer but I heard Steven
Jobs is working on computer storage that uses DNA. Perhaps you could
learn a little about how molecular evolution works in living organisms
and apply it to computers the same way using the same/similar
mechanism... DNA storage that evlolves programs to fit a given task ?!
Good luck.

Chris

Date: Wed, 15 May 1996 17:13:14 -0500
From: podar at UTSW.SWMED.EDU (The Yeastie Boys)

There are plenty of so-called molecular machines today. This term is
somewhat arbitrary and I have not found a definition in a textbook , but it
usually reffers to complex macromolecular systems that do a certain
function. They do not have a membrane, which distinguishes them from
organelles (like the mitochondria, the lysosome and so on) which do have
one. The ribosome and the spliceosome are examples of molecular machines
and they might very well suit your needs.

Good luck,

Mircea Podar
Dept of Biochemistry
U.T.SW.Med.Ctr. Dallas

podar at utsw.swmed.edu

Date: Thu, 16 May 1996 15:31:50 -0400
From: Marcel TURCOTTE <turcotte at biochem9.chem.ufl.edu>
To: jimtoer at idt.unit.no
CC: turcotte at biochem9.chem.ufl.edu
Subject: Evolvable molecular machines
Content-Type: text
Content-Length: 1649


Jim,

Adleman (Science 266:1021-1024 Nov 1994) realized a molecular computer
and solved an instance of the `Hamiltonian path problem'.  You can
find a paper for a computer science audience at:

	ftp://usc.edu/pub/csinfo/papers/adleman/molecular_computer.ps

This experiment generated so much excitement that a Mini DIMACS
Workshop was organized 5 months later at Princeton, it was hosted by
Lipton (Princeton) and Baum (NEC).  Richard J. Lipton has a paper
available on the net:

	ftp://ftp.cs.princeton.edu/pub/people/rjl/bio.ps

Warren D. Smith and Allan Schweitzer {wds, als}@research.nj.nec.com at
NEC have worked on ``DNA computers in vitro and vivo'' they fetched
for life forms capable of large Turing universal computations.

Otherwise there is a Journal called ``Bio Systems'' from Elsevier
dedicated to this area of research, you can look for papers by Nikolay
G. Rambidi.

There is also a technical paper by Willem P. C. Stemmer in Science
270, Dec 1995 on ``The Evolution of Molecular Computation'' which has
some pointers to the literature.

This is it, I hope this might help!
Good luck with your exam!
-- 

Jim Toerresen                                # E-mail: jimtoer at idt.unit.no
Dept. of Computer Systems and Telematics     # Tel: +47-73594458 (office)
The Norwegian Institute of Technology        # Tel: +47-73886676 (home)
N-7034 Trondheim, NORWAY		     # Fax: +47-73594466 (office)


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