From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Subject: FAQ
Organization: Frederick Cancer Research and Development Center
Date: Thu, 5 Nov 1992 23:38:19 GMT

Finally we are back on line!  Here is the FAQ.  There are minor changes and the
reference to Yockey's new book.

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

             Biological Information Theory and Chowder Society

version = 1.26 of bionet.info-theory.faq  1992 November 5

This file is stored in the anonymous ftp archive ncifcrf.gov in pub/delila
under the name bionet.info-theory.faq.Z (The .Z means it is compressed;
remember to use the binary transfer mode.  See the uncompressed README
file in the archive for where to get the uncompress program if you need it.)
Please send questions and comments to: Tom Schneider toms@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.  It's MUCH easier on you than an e-mail subscription!  Please consult
your systems manager or contact biosci@net.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@net.bio.net
   requesting a subscription or removal from the BIO-INFO forum.

   Europe, Africa, and Central Asia:
   Send a email message to the person at
      biosci@daresbury.ac.uk
   requesting a subscription or removal from the BIO-INFO forum.

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

   North or South America or Pacific Rim:
      bio-info@net.bio.net

   Europe, Africa, and Central Asia:
      bio-info@daresbury.ac.uk

You can post to either 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@net.bio.net.

DO NOT CONTACT TOM SCHNEIDER FOR SUBSCRIPTIONS OR UNSUBSCRIBING!

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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 net.bio.net.  Contact
biosci@net.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@ncbi.nlm.nih.gov), usually makes the arrangements.

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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?

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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.

# 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"}

# A good starting point if you don't know much molecular biology:
# (Two volumes)

@book{Watson1987,
author = "J. D. Watson
 and N. H. Hopkins
 and J. W. Roberts
 and J. A. Steitz
 and A. M. Weiner",
title = "Molecular Biology of the Gene",
edition = "fourth",
year = "1987",
publisher = "The Benjamin/Cummings Publishing Co., Inc.",
address = "Menlo Park, California"}

# 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"}

# A good introduction to the mathematics:

@book{Sacco1988,
author = "W. Sacco
 and W. Copes 
 and C. Sloyer
 and R. Stark", 
title = "Information Theory: Saving Bits",
publisher = "Janson Publications, Inc.",
address = "Providence, Rhode Island",
isbn = "ISBN 0-939765-25-X",
year = "1988"}

# 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"}

# Leff1990 gives a review of the Maxwell's Demon problem.
# See also Schneider.edmm, listed below.

@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"}

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

# 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}

@article{Herman.Schneider1992,
author = "N. D. Herman
  and T. D. Schneider",
title = "High Information Conservation Implies that at Least Three Proteins
Bind Independently to {F} Plasmid {{\em incD\/}} Repeats",
journal = "J. Bact.",
volume = "174",
pages = "3558-3560",
year = "1992"}

# 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"}

@book{Yockey1992,
author = "H. P. Yockey",
title = "Information Theory in Molecular Biology",
publisher = "Cambridge University Press",
address = "Cambridge",
callnumber = "",   
comment = "40 West 20th Street,
New York, N. Y.  10011-4211,
1-800-827-7423,
order number 350050",
year = "1992"}   

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

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

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

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

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