BIO-INFO group is now active, come join us!

toms at NCIFCRF.GOV toms at NCIFCRF.GOV
Fri Jan 24 17:52:52 EST 1992


The BIO-INFO news group, otherwise known as the Biological Information Theory
and Chowder Society is now fully operational at all BIOSCI distribution sites.
This is the official announcement of the availability of the newsgroup even
though it has been in partial operation at GenBank and Daresbury for about a
month now, and we've already had a few interesting rows.  Below is the latest
version of the FAQ (Frequently Asked Questions), which will tell you how to
pick up the previous posts and other goodies.  Feel free to comment on them.
Please join us!  Hors d'oeuvres anyone?

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms at ncifcrf.gov


Frequently Asked Questions (FAQ) for bionet.info-theory

version = 1.14 of bionet.info-theory.faq  1992 January 24
This file is stored in the anonymous ftp archive ncifcrf.gov in pub/delila.
Please send questions and comments to: Tom Schneider toms at ncifcrf.gov

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PURPOSE

The news group bionet.info-theory is a forum for discussion of information
theory in biology.

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OBTAINING bionet.info-theory BY EMAIL

If you have access to USENET news YOU DO NOT NEED AN E-MAIL SUBSCRIPTION!!  We
strongly encourage all interested users to explore getting USENET news at your
site.  Please consult your systems manager or contact biosci at genbank.bio.net
for assistance if needed.

The BIOSCI (email) name for the forum is BIO-INFO.

Depending on where you are, you have to do different things to subscribe or be
removed from the email subscription list:

SUBSCRIBING / UNSUBSCRIBING
   North or South America or Pacific Rim:
   Send a email message to the person at
      biosci at genbank.bio.net
   requesting a subscription or removal from the BIO-INFO forum.

   United Kingdom:
   Send a email message to the person at
      biosci at uk.ac.daresbury
   requesting a subscription or removal from the BIO-INFO forum.

   Europe except the United Kingdom:
   To subscribe, send the message "SUBSCRIBE BIO+INFO your name" to the machine at:
      LISTSERV at IRLEARN.BITNET
   To unsubscribe, send the message "SIGNOFF BIO+INFO" to the machine (must
   be sent from the same address as the sign-on).

SENDING OUT POSTINGS
Thereafter, address email messages for this forum to one of:

   North or South America or Pacific Rim:
   BIO-INFO at genbank.bio.net

   United Kingdom:
   BIO-INFO at uk.ac.daresbury

   Europe except the United Kingdom:
   BIO-INFO at IRLEARN.BITNET

You can post to any of the above address if you want.  We only request that you
sign up at your local node in order to optimize the use of the network
resources for message distribution.

Do not send subscription requests to any of these addresses, or you will have
sent it to everybody on the planet (to your great embarrassment, and we will
drub you with food cake)!  Let me say that again:  please do not post requests
for subscription or being removed from the list to the list itself, that takes
up bandwidth all over the world!

If you have problems, contact the subscription site manager who you signed up
with.  If your problem is not resolved, please contact biosci at genbank.bio.net.

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ARCHIVES

All the bionet.* newsgroups, including info-theory, are now archived
for anonymous ftp from ftp.bio.indiana.edu, directory usenet/bionet/...

GenBank/IG also has the entire collection of bionet messages from inception,
which are available via the biosci.src WAIS source at genbank.bio.net.  Contact
biosci at genbank.bio.net for further help with this.

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HISTORY

The Biological Information Theory and Chowder Society (BITCS) is a group of
scientists interested in the biological applications of information theory
(thus the "BIT") who meet informally for dinner (thus the "CS") from time to
time in the Washington, DC, area.  At our dinners we have only one rule ---
food fights are discouraged.

The guys who started this thing did it because we weren't certain we understood
the biological implications of information theory.  Some of us are more
comfortable with the mathematical machinery and assemble biological systems
into grand canonical ensembles whether they want to be there or not; and some
of us think they understand what the biological systems are doing but can't
take a log to base 2.  What we try to do is pry from one another the bits of
knowledge that will help us understand what's going on.

Some of the topics up for discussion in our group are:
  biological applications of information theory
  biochemical molecular machines
  computer methods for recognition of molecular structure and function
  database organization for biomolecular information
  nanotechnology
A few relevant papers are listed below.

The group started when Tom Schneider was introduced to John Spouge in 1988.
Tom bounced his ideas about molecular machines off John, and John kept finding
flaws.  Tom would go away rather unhappily for a month and then find a
solution.  But John was always one step ahead...  (and still is, on last
account.)  Tom gave a talk about molecular machines at the Lambda Lunch meeting
on the Bethesda NIH campus, and John introduced John (Steve) Garavelli.  We all
got together with Peter Basser for dinner once in a while to talk about
information theory.  Steve brought in one of the first people to apply
information theory to biology, Hubert Yockey.  Steve Garavelli dubbed the group
the "Biological Information Theory and Chowder Society", which it is still
called.  We are known sometimes as 'chowderheads', and talk about food fights,
but so far have only had electronic food fights!  We hold dinners in Bethesda
Maryland on random occasions.

When our informal mailing list became difficult to handle, we petitioned to
start a bionet news group.  We hope to hold roaring discussions, and everyone
is welcome to join.  If you are uncertain about something, quit lurking and ask
on the net.  It may well be that what bothered you is the key to a new piece of
information theory in biology.  (The major advances so far have been by things
that REALLY bugged people.)

We will also announce when and where our (irregular) eatings are and you are
welcome to join if the travel is not too far.  John Spouge
(spouge at ncbi.nlm.nih.gov), usually makes the arrangements.

***********************************************************
SOME QUESTIONS FOR DISCUSSION

This faq sheet answers simple questions about this group.  The BIG questions
should be discussed on the net, where we can all haggle over them.  Here are a
few for starters:

What is the role of theory in biology today?
What should be the role of biological theory?

What is information?  How should it be defined?

What bothers you when you read the two papers on the theory of molecular
machines?  (It is only from the things that bother us that we can make progress
in understanding.)  (See references below.)

What are flaws in the theory of molecular machines?

How is ATP used to drive molecular machines?

All communication systems are associated with living things, so is it true that
information theory is really a theory about living things?  Was Shannon really
a great biologist?

***********************************************************
REFERENCES - General

There are a huge number of papers related to this topic, just about everything
in molecular biology, lots of chemistry, physics, electronics, evolutionary
theory, thermodynamics, statistical mechanics and the kitchen sink ...  You can
get a pretty good overview by combining the references of Schneider.ccmm,
Schneider.edmm and Leff1990.  References are given in BiBTeX format, the
bibliography program associated with LaTeX, the powerful and portable
typesetting program.

@book{Leff1990,
author = "H. S. Leff and A. F. Rex",
title = "Maxwell's Demon: Entropy, Information, Computing",
publisher = "Princeton University Press",
address = "Princeton, N. J.",
phone = "1(800) 777-4726",
isbn.hard  = "0-691-08726-1 (hard cover)",
isbn.paper = "0-691-08727-X (paperback)",
year = "1990"}

# Wonderful books:

@book{Gonick.computers,
author = "L. Gonick",
title = "The Cartoon Guide to Computer Science",
publisher = "Barnes \& Nobel",
address = "N. Y.",
year = "1983"}

@book{Gonick.genetics,
author = "L. Gonick",
title = "The Cartoon Guide to Genetics",
publisher = "Barnes \& Nobel",
address = "N. Y.",
year = "1983"}

@book{Gonick.physics,
author = "L. Gonick
 and A. Huffman",
title = "The Cartoon Guide to Physics",
publisher = "HarperPerennial",
address = "N. Y.",
isbn = "0-06-273100-9",
year = "1990"}

# This book describes LaTex and BiBTeX:

@book{Lamport1986,
author = "L. Lamport",
title = "\LaTeX: A Document Preparation System,
User's Guide \& Reference Manual",
publisher = "Addison-Wesley Publishing Company",
address = "Reading, Massachusetts",
callnumber = "Z253.4.L38L35",
isbn = "0-201-15790-X",
year = "1986"}

# ***********************************************************
# REFERENCES - Information Theory

# The best starter book:

@book{Pierce1980,
author = "J. R. Pierce",
title = "An Introduction to Information Theory:
Symbols, Signals and Noise",
edition = "second",
year = "1980",
publisher = "Dover Publications, Inc.",
address = "New York"}

# The original:

@article{Shannon1948,
author = "C. E. Shannon",
title = "A Mathematical Theory of Communication",
year = "1948",
journal = "Bell System Tech. J.",
volume = "27",
pages = "379-423, 623-656"}

@book{ShannonWeaver1949,
author = "C. E. Shannon
 and W. Weaver",
title = "The Mathematical Theory of Communication",
publisher = "University of Illinois Press",
address = "Urbana",
year = "1949"}

# The basis of molecular machine theory:

@article{Shannon1949,
author = "C. E. Shannon",
title = "Communication in the Presence of Noise",
year = "1949",
journal = "Proc. IRE",
volume = "37",
pages = "10-21"}

# How locks work and other cool stuff:

@book{Macaulay1988,
author = "D. Macaulay",
title = "The Way Things Work",
publisher = "Houghton Mifflin Company",
address = "Boston",
year = "1988"}

# ***********************************************************

# REFERENCES - Jaynes

@article{JaynesI,
  author = "Edwin T. Jaynes",
  title = "Information Theory and Statistical Mechanics",
  year = 1957,
  journal = "Physical Review",
  volume = "106",
  pages = "620-630"}
 
@article{JaynesII,
  author = "Edwin T. Jaynes",
  title = "Information Theory and Statistical Mechanics. {II}",
  year = 1957,
  journal = "Physical Review",
  volume = "108",
  pages = "171-190"}
 
# ***********************************************************
# REFERENCES - Schneider

@article{Schneider1986,
author = "T. D. Schneider
 and G. D. Stormo
 and L. Gold
 and A. Ehrenfeucht",
title = "Information content of binding sites on nucleotide sequences",
journal = "J. Mol. Biol.",
volume = "188",
pages = "415-431",
year = "1986"}

@inproceedings{Schneider1988,
author = "T. D. Schneider",
editor = "G. J. Erickson and C. R. Smith",
title = "Information and entropy of patterns in genetic switches",
booktitle = "Maximum-Entropy and Bayesian Methods in Science and Engineering",
volume = "2",
pages = "147-154",
publisher = "Kluwer Academic Publishers",
address = "Dordrecht, The Netherlands",
year = "1988"}

@article{Schneider1989,
author = "T. D. Schneider
 and G. D. Stormo",
title = "Excess Information at Bacteriophage {T7} Genomic Promoters
Detected by a Random Cloning Technique",
year = "1989",
journal = "Nucl. Acids Res.",
volume = "17",
pages = "659-674"}

@article{Schneider.Stephens.Logo,
author = "T. D. Schneider
 and R. M. Stephens",
title = "Sequence Logos: A New Way to Display Consensus Sequences",
journal = "Nucl. Acids Res.",
volume = "18",
pages = "6097-6100",
year = "1990"}

@article{Schneider.ccmm,
author = "T. D. Schneider",
title = "Theory of Molecular Machines.
{I. Channel} Capacity of Molecular Machines",
journal = "J. Theor. Biol.",
volume = "148",
number = "1",
pages = "83-123",
note = "{(Note: The figures were printed out of order!
Fig. 1 is on p. 97.)}",
year = 1991}

@article{Schneider.edmm,
author = "T. D. Schneider",
title = "Theory of Molecular Machines.
{II. Energy} Dissipation from Molecular Machines",
journal = "J. Theor. Biol.",
volume = "148",
number = "1",
pages = "125-137",
year = 1991}

# Copies of these and of earlier papers (ie, level 0 theory)
# are available; send your physical address to Tom Schneider.
# (His address is given below.)
# 
# See also the README file in the ftp archive ncifcrf.gov in pub/delila.

# ***********************************************************
# REFERENCES - Yockey

@book{Yockey1958a,
  editor = "Hubert P. Yockey and Robert P. Platzman and Henry Quastler",
  title = "Symposium on Information Theory in Biology",
  booktitle = "Symposium on Information Theory in Biology",
  year = 1958,
  publisher = "Pergamon Press",
  address = "New York, London"}

@article{Yockey1981,
  author = "Hubert P. Yockey",
  year = 1981,
  title = "Self-organization Origin of Life Scenarios and Information Theory",
  journal = "J. Theor. Biol.",
  volume = "91",
  pages = "13-31"}

***********************************************************

John S. Garavelli
Protein Identification Resource
National Biomedical Research Foundation
Washington, DC  20007
garavelli at gunbrf.bitnet

Tom Schneider
National Cancer Institute
Laboratory of Mathematical Biology
Frederick, Maryland  21702-1201
toms at ncifcrf.gov

John L. Spouge
National Center for Biotechnology Information
National Library of Medicine
Bethesda, MD  20894
spouge at frodo.nlm.nih.gov

Please email comments and suggestions on this faq sheet to Tom.

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