Danny Amor's Online Library/Danny Amor's Online Library - Volume 1.iso/html/faqs/faq/biology/info-theory

Text File | 1995-07-25 | 25.6 KB | 754 lines

Subject: Biological Information Theory and Chowder Society FAQ
Newsgroups: bionet.info-theory,news.answers
From: [e-mail] (Tom Schneider)
Date: Tue, 1 Nov 1994 03:38:58 GMT

Archive-name: biology/info-theory

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

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

             Biological Information Theory and Chowder Society

version = 1.64 of bionet.info-theory.faq  1994 October 31

***********************************************************
- What is the History of The Biological Information Theory and Chowder Society?
- What Kind of Questions Are Appropriate For Discussion?
- How Can I Learn More About Information Theory and Biology?
- How Do I find Sequence Logos on the Web?
- Is There a Shell Script for Making Sequence Logos?
- Is There a Mosaic Page for Making Sequence Logos?
- Will Authors Send Me Papers?
- Can You Just Point My Mosaic To The FAQ and the Archives?
- How Do I obtain bionet.info-theory BY EMAIL?
- Where Did I Get This FAQ File From Originally?
- What is the IP number of the FAQ archive?
- Where Are the Bionet Archives?
- What Can I Do About Inappropriate Postings?
- What is the official word on copyright of this FAQ?
- Who Takes Care of This Group?
***********************************************************

* What is the History of The Biological Information Theory and Chowder Society?

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
  the limits of computation
  "dissipationless" (?) computation
  Maxwell's demon
  anecdotes and humor about all these topics
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
([e-mail]), usually makes the arrangements.

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

* What Kind of Questions Are Appropriate 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?

What does Maxwell's Demon have to do with all of this?

What are the limits of computers?

What are the limits of nanotechnology?

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

* How Can I Learn More About Information Theory and Biology?

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.

By arrangement, books that have prices listed can be ordered over Internet from:
  Reiter's Scientific & Professional Books
  2021 K Street, NW
  Washington, DC  20006
  1-800-537-4314
  1-202-223-3327
  1-202-296-9103 FAX
  [e-mail]

Shipping and handling charges are:
in the DC metropolitan area $4.00 for one item, $0.50 for each additional item,
outside the area $4.50 for one item, $0.50 for each additional item.

The prices are current as of October 1994; because publishers are constantly
changing their prices, they should be considered estimates rather than
guaranteed prices.  To open an account you must first either phone or FAX them
and provide a credit card number.  Book orders can be then placed at any time
over the Internet.
        **DO NOT SEND CREDIT CARD NUMBERS OVER THE INTERNET!**

Reiter's carries all of the books on this list except "Information Theory:
Saving Bits", and that one can be special ordered.  If enough interest in this
book is generated by the FAQ, it will be added as regular stock.  (It can also
be ordered directly from the company using the information given.)

# Gonick's Wonderful books (Don't be shy!  They are worth the money!!):

@book{Gonick.computers,
author = "L. Gonick",
title = "The Cartoon Guide to Computers",
edition = "second",
publisher = "HarperCollins",
address = "New York, NY",
isbn = "0-06-273097-5",
price = "price as of 1994 October 31: \$11.00",
year = "1991"}

@book{Gonick.genetics,
author = "L. Gonick",
title = "The Cartoon Guide to Genetics",
edition = "updated",
publisher = "Barnes \& Nobel",
address = "New York, NY",
isbn = "0-06-273099-1",
price = "price as of 1994 October 31: \$12.00",
year = "1991"}

@book{Gonick.physics,
author = "L. Gonick
 and A. Huffman",
title = "The Cartoon Guide to Physics",
publisher = "HarperPerennial",
address = "New York, NY",
isbn = "0-06-273100-9",
price = "price as of 1994 October 31: \$12.00",
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",
publisher = "The Benjamin/Cummings Publishing Co., Inc.",
address = "Menlo Park, California",
isbn = "0-8053-9614-4",
price = "price as of 1994 October 31: \$59.95",
year = "1987"}

# This book describes LaTex and BiBTeX:

@book{Lamport1994,
author = "L. Lamport",
title = "\LaTeX: A Document Preparation System,
User's Guide \& Reference Manual",
edition = "second",
publisher = "Addison-Wesley Publishing Company",
address = "Reading, Massachusetts",
isbn = "0-201-52983-1",
price = "price as of 1994 October 31: \$32.95",
year = "1994"}

# ***********************************************************
# 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",
publisher = "Dover Publications, Inc.",
address = "New York",
isbn = "0-486-24061-4",
comment = "
original copyright 1961
Ordering information:  Pierce1980 is currently available by mail from:
   Dover Publications, Inc.
   31 East 2nd street
   Mineola, New York 11501
order:
   Pierce, An Introduction to Information Theory: Symbols, Signals and Noise
   code number: 24061-4
$7.95 + charges.  Payment in full, no telephone or credit card orders.
Postage and Handling charges are:
Bookrate: $3 (US only)
UPS: $4.50 (US only, not Alaska or Hawaii or PO boxes)
Foreign orders: add 20% of total (minimum $2.50)
Sales Tax (Ny residents only)
Foreign Orders Note: Remittances must be sent by international money order or
in U.S. funds via Federal Wire System to Chemical Bank, N. Y.  ABA #021000128.
Mark all remittances `For the account of Dover Publications, Inc.  #001 053
272'.  This information is from the Dover Math and Science Catalogue 9/92",
price = "price as of 1994 October 31: \$8.95",
year = "1980"}

Christopher Hillman ([e-mail]) suggests that this one is a
better starting point:  Thomas Cover and Joy A. Thomas, Elements of Information
Theory, Wiley, 1991.  People who have seen both could post their opinions.

# 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.",
comment = "original address was Providence, Rhode Island",
address = "Dedham, MA",
isbn = "0-939765-25-X",
phone = "[phone]",
price = "price as of 1994 October 31: \$11.95",
year = "1988"}

# Important originals:

@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",
isbn = "0-252-72548-4",
price = "price as of 1994 October 31: \$9.95",
year = "1949"}

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

# For the committed: The Complete Works!

@inproceedings{Shannon1993,
author = "C. E. Shannon",
editor = "N. J. A. Sloane and A. D. Wyner",
booktitle = "Claude Elwood Shannon: Collected Papers",
publisher = "IEEE Press",
address = "Piscataway, NJ",
isbn = "0-7803-0434-9",
comment = "IEEE Order Number: PC0331-9
  To order directly by charge card (eg Visa works) you can call
  (908)-981-0060
  $69.95 + $5 handling charge
  delivery in about 2 weeks",
price = "price as of 1994 October 31: \$69.95",
year = "1993"}

# How locks work and other cool stuff:

@book{Macaulay1988,
author = "D. Macaulay",
title = "The Way Things Work",
publisher = "Houghton Mifflin Company",
address = "Boston",
isbn = "0-395-42857-2",
price = "price as of 1994 October 31: \$29.95",
comment = "This book is also available on Windows-Compatible CD-ROM
  cdrom isbn = 1-56458-901-3  Price as of 1994 October 31: \$99.95",
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)",
price.hard = "price as of 1994 October 31: \$80.00",
isbn.paper = "0-691-08727-X (paperback)",
price.paper = "price as of 1994 October 31: \$26.95",
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"}

# A version of Jaynes' new book "PROBABILITY THEORY -- THE LOGIC OF SCIENCE"
# is available in the archive in the jaynes directories.

# ***********************************************************
# 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"}

@article{Stephens.Schneider.Splice,
author = "R. M. Stephens
  and T. D. Schneider",
title = "Features of spliceosome evolution and function
inferred from an analysis of the information at human splice sites",
journal = "J. Mol. Biol.",
volume = "228",
pages = "1124-1136",
year = "1992"}

@article{Papp.helixrepa,
author = "P. P. Papp
 and D. K. Chattoraj
 and T. D. Schneider",
title = "Information Analysis of Sequences that Bind
the Replication Initiator {RepA}",
journal = "J. Mol. Biol.",
comment = "Cover of 233, number 2!",
volume = "233",
pages = "219-230",
year = "1993"}

@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"}
ftp://ftp.ncifcrf.gov/pub/delila/nano2.ps

# ***********************************************************
# 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",
publisher = "Pergamon Press",
address = "New York, London",
comment = "out of print",
year = "1958"}

@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",
isbn = "0-521-35005-0",
comment = "40 West 20th Street,
New York, N. Y.  10011-4211,
order number 350050",
phone = "1-800-827-7423",
price = "price as of 1994 October 31: \$74.95",
year = "1992"}

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

* Will Authors Send Me Papers?

Tom Schneider will mail you copies of his papers.  Send your physical address
to him at [e-mail].  Some papers are on line already, see also the
README file in the ftp archive ftp.ncifcrf.gov in pub/delila.

If you are willing to send out papers or have papers you would like listed
here, please contact Tom Schneider.

You can request them by Mosaic from the page
http://fconvx.ncifcrf.gov:2001/~toms/papers.html

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

* How Do I find Sequence Logos on the Web?

http://fconvx.ncifcrf.gov:2001/~toms/sequencelogo.html

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

* Is There a Shell Script for Making Logos?

Yes, you will find the one Shmuel Pietrokovski wrote in the ftp archive
ftp.ncifcrf.gov in pub/delila/logoaid.  (Also available in
bioinformatics.weizmann.ac.il/pub/software/logoaid.)
***********************************************************

* Is There a Mosaic Page for Making Sequence Logos?

Yes, Steve Brenner has done it!

http://www.bio.cam.ac.uk/seqlogo/

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

* Can You Just Point My Mosaic To The FAQ and the Archives?

This file and the postings may be obtained by Mosaic through the world wide web
at:

<UL>

<H2>
<LI> <A HREF="ftp://ftp.ncifcrf.gov/pub/delila/bionet.info-theory.faq.Z">
FAQ (Frequently Asked Questions)</A>
about the Biological Information Theory and Chowder Society
</H2>

<H2>
<LI> <A HREF="gopher://net.bio.net/11/BIO-INFO">
Gopher Link to Archive of All Postings.</A>
This archive contains the most recent postings
as separate documents.</H2>

<H2>
<LI> <A HREF="ftp://net.bio.net/pub/BIOSCI/BIO-INFO">
Archive of Monthly Postings.</A>
This archive (currently) contains postings
from each month as a single document.</H2>

<H2>
<LI> <A HREF="ftp://ftp.bio.indiana.edu/usenet/bionet/info-theory/">
Gopher link to Archive of Postings at IUBO.</A>
This archive contains individual postings.
Older postings are collected by the month as a single document.
There is an index for each month.
</H2>

</UL>

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

* How Do I obtain 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 [e-mail] 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:
     Using the computer account in which you want to receive mail
     messages, please send an email message to the e-mail server at
     [e-mail].  Leave the Subject: line blank.
     In the body of the message include the line

     subscribe bio-info

     to add yourself to the mailing list or

     unsubscribe bio-info

     to cancel an existing subscription.  If you need personal
     subscription assistance, please contact [e-mail].

   Europe, Africa, and Central Asia:
       Send a email message to the person at
      [e-mail]
   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:
      [e-mail]

   Europe, Africa, and Central Asia:
      [e-mail]

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
[e-mail].

DO NOT CONTACT TOM SCHNEIDER FOR SUBSCRIPTIONS OR UNSUBSCRIBING!

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

* Where Did I Get This FAQ File From Originally?

The latest version of this FAQ is stored in the anonymous ftp archive
ftp.ncifcrf.gov in pub/delila under the name bionet.info-theory.faq and also as
bionet.info-theory.faq.Z (The .Z means it is compressed; remember to use the
binary transfer mode if you pick up the latter.  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 [e-mail]

This file is also posted monthly on news.answers and bionet.info-theory.

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

* What is the IP number of the FAQ archive?

For ftp.ncifcrf.gov you can use 129.43.1.11

***********************************************************
* Where Are the Bionet Archives?

The entire collection of BIOSCI/bionet messages from inception are
available via the biosci.src WAIS source at net.bio.net.  Contact
[e-mail] for further help with accessing this WAIS source.

FTP archives of all the BIOSCI/bionet messages are available at net.bio.net
[134.172.2.69] in /pub/BIOSCI.  bionet.info-theory is in pub/BIOSCI/BIO-INFO.
Files are in mailbox format, with names of the form YYMM (YY=last 2 digits of
the year, MM=cardinal number of the month, zero padded).  The current months
postings are in the file 'current'.  Contact [e-mail] for
further help with or comments on the archives.

All the bionet.* newsgroups, including info-theory, are also archived for
Gopher retrieval from the IUBIO Gopher hole and for anonymous ftp from
ftp.bio.indiana.edu, directory usenet/bionet/...

The archives can be accessed by gopher or ftp running under the Mosaic
interface.  The URL (Universal Record Locator) for gopher is:
   gopher://net.bio.net/11/BIO-INFO
This gives individual postings.  By ftp one can use:
   ftp://net.bio.net/pub/BIOSCI/BIO-INFO
Unfortunately this gives the entire month in a single document.

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

* What Can I Do About Inappropriate Postings?

The short form of this news group's name, bio-info, can be a little confusing
to some people inexperienced in network communications or with little knowledge
of the discipline (if there is any :-) of biological information theory.  It
can and has been mistaken as a news group for general biological information.
Our readers should be aware that when such postings come to our attention, we
do attempt to inform, privately, the people who make these inappropriate
postings of the error of their ways and suggest alternative or more appropriate
venues.

Subjecting the writers of inappropriate posting to public excoriation is not a
good policy because the mistake is usually inadvertent and the follow-up
postings add further to the irritation of our regular readers.  When others
publicly reply to such posts in this news group, although they may think they
are being polite to the original poster, they are still annoying our regular
readers.  We suggest that a better policy for readers who do wish to reply to
inappropriate posts is to do so privately or to an appropriate news group.

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

* What is the official word on copyright of this FAQ?

This FAQ fits the description in the U. S. Copyright Act of a "United States
Government work".  It was written as a part of my official duties as Government
employee.  This means it cannot be copyrighted.  The article is freely
available without a copyright notice, and there are no restrictions on its use,
now or subsequently.  I retain no rights in the FAQ.

Thomas D. Schneider

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

* Who Takes Care of This Group?

John S. Garavelli
Protein Information Resource
National Biomedical Research Foundation
Washington, DC  20007
[e-mail]

Tom Schneider
National Cancer Institute
Laboratory of Mathematical Biology
Frederick, Maryland  21702-1201
[e-mail]

John L. Spouge
National Center for Biotechnology Information
National Library of Medicine
Bethesda, MD  20894
[e-mail]

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

John Garavelli (who also answers to "Steve" if you want to avoid confusion)
often organizes dinner speakers.

John Spouge often arranges dinner locations.

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