HDTenEightyP/NetNews huggingface dataset:
From: tolman%asylum.cs.utah.edu@cs.utah.edu (Kenneth Tolman)
Subject: Information content of cellular automata?
Date: 20 Nov 92 16:15:18 MST
Organization: University of Utah, CompSci Dept
Distribution: bionet


 What is the information content of a particular configuration for a CA?
 What are references which would discuss this? (see below)


 One could define the information content for a cellular automata to be 
-log(probability of state)  Is this correct?

 In S. Amoroso he suggests that the information content
does not change for a reversible deterministic CA, which seems agreeable.
This would also correspond to the above metric, for any later state would
have the same probability as its predecessor. (1)

 In T. Toffoli, he suggests that the information content depends
on the initial state for irreversible deterministic CA.  If one has enough
detail to construct the initial state, then one has preserved the information
but if there is not enough to reconstruct then one has lost information. (2)

 Wolfram suggests that the "entropy" of a CA can be given by the logarithm
of the "average number of possible states of a system", or as

  SUM p(i) log (p(i))

  Then he shows a graph with the entropy decreasing for an irreversible
CA, which is based on the probabilities for each of the possible states the
system can be in.....  this is not entirely clear to me, for the INITIAL
state would appear to have an equal distribution, and any later states would
have an unequal probability distribution.. so is he calculating probabilities
on the infinite limit of that state or what? (the alternative is of course
that he calculates the probability for a state from all possible initial
states for a particular time interval)  It appears here that the information
content of a particular state then WOULD be the -log(probability of state) (3)

  So what IS the information content of a particular state in a cellular 
automata?


1 S. Amoroso, Journal Comp. Sys. Sciences, Vol 6, pp. 448-464.

2 T. Toffoli, Journal Comp. Sys. Sciences, Vol. 15, pp. 213-231

3 S. Wolfram, Rev. Mod. Phys. Vol. 55, No. 3, July 1983, pp. 601-644
From: tolman%asylum.cs.utah.edu@cs.utah.edu (Kenneth Tolman)
Subject: Re: Journalist in search of DNA metaphors
Date: 15 Nov 92 19:04:52 MST
Organization: University of Utah, CompSci Dept

>After all there are so many different intricate mechanisms  from molecular 
>transport within cells to large structures like organs and limbs and there is
>the 
>three dimensional structure of the whole organism that has to be specified 
>somewhere.  Has anyone counted up all the different types of mechanisms and 
>then calculated how much information is needed to specify all of this. (I 
>nderstand that for e-coli you only need a hundred or so genes to specify the 
>entire organism)

There is not all that much to encode, we humans are pretty simple :)  A lot
of what you mention is implicit in the coding.. for instance if I were to
say "make the whole thing 5 feet high" then all of the rest of the body
parts would be made proportionately... there is not a unique command for
each piece.

Most of the mechanisms are repeated throughout the whole body, and thus
one coding gets spread all over.

The mechanisms are not "described" per se, they are started.  for instance,
there is no part of the body that understands the relationship of the
mitochondria's DNA to the cellular DNA, it merely is constructed that way
and it functions.  Thus, as long as the laws of physics are obeyed quite
intricate looking mechanisms can be encoded simply.
From: hybl@umbc4.umbc.edu (Dr. Albert Hybl (UMAB-BIOPHYS))
Newsgroups: bionet.info-theory
Subject: Re: What is a "perfect" crystal?
Summary: 0K folks - funny money -- MOLECULAR PENNIES!
Keywords: X-ray_Diffraction Single_Crystals Disorder Twinning Entropy
Date: 16 Nov 92 16:09:12 GMT
Organization: Univ. of MD, Baltimore County

In message <BxsBHq.364@ncifcrf.gov> dated Mon, 16 Nov 1992 01:15:26 GMT
from: toms@fcs260c2.ncifcrf.gov, Tom Schneider writes
>In other words, it's a perfect example of molecular pennies!
>
>This example is also neat because it relates to the OK problem.
>Could we cool this "twinned" crystal to 0K?
Probably.  While your near 0K, collect a set of X-ray data; I
would like to see that changes to the translational and
rotational vibration tensors.  [For details, see section (v)
in the original paper.]

>Your results imply that the position of the oxygen has no energetic
>implication.  Yet one could store 1 bit of information in each of
>the molecules!
Long range order might show up as a super lattice; we saw none.

>What is a "perfect" crystal?

A crystallographer normally works with a mosaic crystal,
many little "mosaic" blocks approximately aligned in an
aggregate that looks like a crystal.  The mosaic block are
thankfully in sufficient disregistry to scatter independently.
[See the discussion in section 5.4 of "Mosaic Theory" in Vol. III
of the International Tables for X-ray Crystallography page 313.]
I think that a perfectly entropy twinned crystal would not
look "perfect" to an X-ray beam.  X-rays know perfection when
they see it :-)

The discussion in section 2.6 of "Thermal Expansion in Relation
to Structure" in Vol. II of the Internation Tables for X-ray
Crystallography page 125 states: "A more fundamental quantity
would be the unit-cell size either for an unperturbed state of
absolute rest, or at 0K.  Neither of these are, in fact
attainable and therefore linear thermal-expansion coefficients
(alpha) and their variation with temperature should be
determined whenever possible. 
  Thermal-expansion coefficients are also useful:
(a) As an indication of interatomic and intermolecular forces
and their variations with direction, temperature, impurity,
vacant sites, spin orientations, electronic transitions, etc.
(b) For the detection of second-order transformations and of
the crystal directions principally concerned in such
transformation."

There is a caldron full of additional facts to spice up the
chowder.

Albert Hybl (hybl@umbc4.umbc.edu)
Newsgroups: bionet.info-theory
Subject: Re: dna replication
From: robison1@husc10.harvard.edu (Keith Robison)
Date: 17 Nov 92 14:29:13 GMT
Distribution: bionet.info-theory

pw@cubmol.bio.columbia.edu (Paul Wakenight) writes:



>So my question is this.  Considering that DNA polymerase cannot distinguish
>between dTTP and dUTP, how is it that dUTP is incorporated at such low rates?
>I have read the literature and it seems that there is no satifactory explana-
>tion.
>Viruses often encode their own set of enzymes for nucleotide synthesis, which
>in some cases is specialized to incorporate modified bases.  But in most other
>cases, they encode thy. synthetase, etc. for the production of dTTP.  This 
>looks like a clue to me.                 

>I would greatly appreciate your thoughts and
>esp. any material you could point me toward so I could get a mathematical
>perspective on nucleotide synth. and dna replication.

>thanks.

>Paul Wakenight
>.

	Uridine incorporation into DNA is not regulated at the level
of the polymerase, but by two other routes.  First, UTP levels are
kept low by a deoxyuridyltriphosphatase (dut), and if uridine is
incorporated into DNA it is excised by uracil-DNA glycosylase (ung) 
and the gap repaired by the DNA gap repair system.  If both of 
these systems are non-functional (such as in dut-ung strains of
E.coli), then DNA containing significant amounts of U will result.
This is critical part of the most commonly used site-directed 
mutagenesis scheme -- that of Kunkel (a name you might feed into
MedLine to find more information on this stuff).


Keith Robison
Harvard University
Department of Cellular & Developmental Biology
Department of Genetics / HHMI

robison@biosun.harvard.edu 


Newsgroups: bionet.info-theory
From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Subject: Re: What is a "perfect" crystal?
Summary: OK folks - check this out!  MOLECULAR PENNIES!
Keywords: X-ray_Diffraction Single_Crystals Disorder Twinning Entropy
Organization: Frederick Cancer Research and Development Center
Date: Mon, 16 Nov 1992 01:15:26 GMT

In article <1992Nov15.210817.20886@umbc3.umbc.edu>
hybl@umbc4.umbc.edu (Dr. Albert Hybl (UMAB-BIOPHYS)) writes:

>  You should add some FAT to you chowder, after all, every living cell
>contains some lipids.  I intended this to be an example for
>something being discused--I forgot what.  Oh, well--just toss
>it into chowder pot.
> 
>>
>>      CH2OR               CH2OR          (below plane)
>>      .                   .
>>      .                   .
>>   HO-C-H     and       H-C-OH
>>      .                   .
>>      .                   .
>>      CH2OR               CH2OR          (below plane)
>>  (a)                 (b)
>
>                   O  H   H
>             R =  -C-(C)9-C-Br
>                      H   H
>>
>>The disorder results from the competitive occupancy for each
>>site by rotational isomers (a) and (b). 

Ok (not 0K! :-) now it makes sense - Perhaps you brought this up as a nice
example of the penny analogy.  If I take 100 pennies and throw them down on a
table, after they have stopped bouncing around - that is, after they have
"cooled" - some will be heads and others will be tails.  As in your example,
the orientation doesn't matter, and does not have long range effects.  Because
there are two equally likely orientations of the molecules, uncertainty of the
orientation of each molecule is log 2(2) = 1 bit.  You expressed this as "1.38
cal/mole degree", which is the same thing (a trivial derivation is in
Schneider.edmm).

In other words, it's a perfect example of molecular pennies!

This example is also neat because it relates to the OK problem.  Could we cool
this "twinned" crystal to 0K?  Your results imply that the position of the
oxygen has no energetic implication.  Yet one could store 1 bit of information
in each of the molecules!  What is a "perfect" crystal?

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms@ncifcrf.gov
From: samodena@csemail.cropsci.ncsu.edu (S. A. Modena)
Newsgroups: bionet.info-theory
Subject: Further trouble at the OK corral
Date: 18 Nov 92 19:14:22 GMT
Organization: Crop Science Dept., NCSU, Raleigh, NC 27695-7620

"
Noise from Quantum Mechanics

ven at T=0, in the absence of thermal noise, most coordinates remain
random variables.  This noise arises from quantum mechanics and can be
qualitatively understood in terms of Heisenberg's uncertainty principle,
which constrains the reliability of simultaneous measurements of
complementary variables, such as position and momentum.........The
'quantum noise' that enforces the uncertainty principle provides an
independent limit to the reliability of measurements."

Annual Review of Biophysics and Biophysical Chemistry 16:455-78 1987

I interpret this to mean that I can not be certain that H(x)=0 at
Absolute Zero due to the Uncertainty Principle.

Steve
---
+------------------------------------------------------------------+
|     In person:  Steve Modena     AB4EL                           |
|     On phone:   (919) 515-5328                                   |
|     At e-mail:  nmodena@unity.ncsu.edu                           | 
|                 samodena@csemail.cropsci.ncsu.edu                |
|                 [ either email address is read each day ]        |
|     By snail:   Crop Sci Dept, Box 7620, NCSU, Raleigh, NC 27695 |
+------------------------------------------------------------------+
         Lighten UP!  It's just a computer doing that to you.    (c)
OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
Newsgroups: bionet.info-theory
Subject: Re: Journalist in search of DNA metaphors
From: robison1@husc10.harvard.edu (Keith Robison)
Date: 16 Nov 92 01:04:06 EST
Organization: Harvard University Science Center

In article <1992Nov15.190453.10654@hellgate.utah.edu> tolman%asylum.cs.utah.edu@cs.utah.edu (Kenneth Tolman) writes:
>
>The mechanisms are not "described" per se, they are started.  for instance,
>there is no part of the body that understands the relationship of the
>mitochondria's DNA to the cellular DNA, it merely is constructed that way
>and it functions.  Thus, as long as the laws of physics are obeyed quite
>intricate looking mechanisms can be encoded simply.

This is a very important point which is often lost in biology classes,
popular texts, etc.  While the DNA encodes an awful lot, there is much
it does NOT encode, but which is rather inherited from one's parents
in other ways.  A major example is the early three-dimensional patterning
of humans (and all other metazoans) -- the mother essentially generates
a template for the early coordinate system, one which she got from her
mother (and so and so on...).  While the information contained in the
DNA is critical for acting on this system to generate the final product,
the three dimensional structure is not encoded _in toto_ in the DNA.
Similarly, the fact that our cells are surrounded by a lipid bilayer 
is something which has been handed down epigenetically since the urcritter.


Keith Robison
Harvard University
Department of Cellular & Developmental Biology
Department of Genetics / HHMI

robison@biosun.harvard.edu
From: pw@cubmol.bio.columbia.edu (Paul Wakenight)
Subject: dna replication
Organization: Columbia University, Dept. of Biological Sciences.
Distribution: bionet.info-theory
Date: Mon, 16 Nov 1992 23:20:00 GMT



So my question is this.  Considering that DNA polymerase cannot distinguish
between dTTP and dUTP, how is it that dUTP is incorporated at such low rates?
I have read the literature and it seems that there is no satifactory explana-
tion.
Viruses often encode their own set of enzymes for nucleotide synthesis, which
in some cases is specialized to incorporate modified bases.  But in most other
cases, they encode thy. synthetase, etc. for the production of dTTP.  This 
looks like a clue to me.                 

I would greatly appreciate your thoughts and
esp. any material you could point me toward so I could get a mathematical
perspective on nucleotide synth. and dna replication.

thanks.

Paul Wakenight
.
From: lobry@evoserv.univ-lyon1.fr (Jean Lobry)
Newsgroups: bionet.info-theory
Subject: macrodescription of sequences
Date: 20 Nov 1992 14:09:58 GMT
Organization: biometry laboratory
Distribution: world
NNTP-Posting-Host: evoserv.univ-lyon1.fr

So is my question,

i)   Consider an alphabet of P different symbols.
ii)  Consider a sequence of L symbols from this alphabet.
iii) Count the number of differents K-tuple in the sequence.
     (a K-tuple is a subsequence of length K and overlapping
      of K-tuples is allowed).

Now you get a "macro-description" of the sequence in terms of
K-tuple frequency. For instance, with an alphabet of two
symbols '0' and '1' and the sequence of 5 symbols '00100', the
"macro-description" for K=2 is 
       00 -> 2 times
       01 -> 1 time
       10 -> 1 time
       11 -> 0 time

For a given "macrodescription", how many different sequences 
can be found ?
From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Newsgroups: bionet.info-theory
Subject: Re: What is a "perfect" crystal?
Summary: experiment possible!
Keywords: X-ray_Diffraction Single_Crystals Disorder Twinning Entropy
Date: 16 Nov 92 19:43:13 GMT
Organization: Frederick Cancer Research and Development Center

In article <1992Nov16.160912.14556@umbc3.umbc.edu> hybl@umbc4.umbc.edu
(Dr. Albert Hybl (UMAB-BIOPHYS)) writes:

>Probably.  While your near 0K, collect a set of X-ray data; I
>would like to see that changes to the translational and
>rotational vibration tensors.

Wow!  An experiment that actually can be done!  Hey you folks - it's not
counting angles on pin heads any more!  Anybody want to help convince Albert
that he should rev up his old gear and do the experiment?  :-)

>There is a caldron full of additional facts to spice up the chowder.

Perhaps you could mention a few choice ones?

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms@ncifcrf.gov
From: ahouse@hydra.rose.brandeis.edu (jeremy john ahouse)
Newsgroups: bionet.general
Subject: class-L list?
Date: 16 Nov 92 21:13:25 GMT
Organization: Brandeis - Center for Complex Systems
X-Xxdate: Mon, 16 Nov 92 21: 15:36 GMT
X-Useragent: Nuntius v1.1.1d12

I am trying to subscribe to the list server called Class-L, 
a mailing list and file server for researchers in classification, 
clustering, phylogenetic estimation, and related areas of data analysis.

        I have the addresses: 
        LISTSERV@SBCCVM and CLASS-L%SBCCVM.BITNET@CUNYVM.CUNY.EDU
        
        but neither of these works from my internet site.

        Do any of you have a non-bitnet address for this list?

A second question.  I have access to newsgroups, and in
fact can see a number of bionet groups, but not bionet.info-theory.  
So I subscribe via email.  Do others have this situation?

        Thank you.

        jeremy
From: s1400067@nickel.laurentian.ca
Newsgroups: bionet.general
Subject: info request Ra-226 in lake herring
Date: 18 Nov 92 22:15:03 GMT
Organization: Laurentian University

I have recently undertaken a project examining the dynamics of radium-226
uptake in Lake Herring from a lake contaminated by U tailings. If anyone has any
information to this end, it would be greatly appreciated.
Any information that could be posted to my email address directly would be even
more greatly appreciated (as I have limited access to the network)

Thank you in advance,
Greg Pyle
s1400067@nickel.laurentian.ca
Laurentian University
Dept. of Biology
Sudbury, Ont.
Canada
Newsgroups: bionet.general
From: refried@med.unc.edu (Howard M. Fried)
Subject: pUC119
Originator: refried@ocean
Organization: UNC-CH School of Medicine
Date: Sat, 21 Nov 1992 14:46:44 GMT

Someone wanted information on plasmid pUC119.  The reference is Vieira &
Messing, Methods in Enzymology, vol 153, pp3-11, 1987.


Newsgroups: bionet.general
From: danj@merlot.gwu.edu (Dan Jacobson )
Subject: Re:  info request IGD database
Originator: danj@merlot.gwu.edu
Organization: George Washington University, Washington, D.C.
Date: Fri, 20 Nov 1992 02:01:30 GMT


In article <1992Nov18.172914.25335@alchemy.chem.utoronto.ca> fbignone@alchemy.ch
em.utoronto.ca (Franco Bignone) writes:
>
>I am currently looking for information about a Human Database:
>IGD, Integrated Genomic Database, that I understand should be related
>to the Human Genome project, does anyone have more information about it?
>Who developed it, where is available by ftp etc.


I'm not sure but could you be thinking of the Genome Database (GDB)?

If so there are a variety of ways to access it - for more information
send a message to:

GDB USER SUPPORT
----------------
please contact GDB User Support by:

	Internet:   help@welch.jhu.edu
	Phone:      (410) 955-7058
    Fax:        (410) 614-0434



Best of luck,


Dan Jacobson

danj@chablis.gwu.edu
From: stoehr@embl-heidelberg.de
Newsgroups: bionet.general
Subject: Re: info request IGD database
Date: 20 Nov 92 11:17:28 +0100
Organization: EMBL, European Molecular Biology Laboratory

In article <1992Nov18.172914.25335@alchemy.chem.utoronto.ca>,
fbignone@alchemy.chem.utoronto.ca (Franco Bignone) writes:
> 
> I am currently looking for information about a Human Database:
> IGD, Integrated Genomic Database, that I understand should be related
> to the Human Genome project, does anyone have more information about it?
> Who developed it, where is available by ftp etc.
> Tx

Contact Dr Otto Ritter, DKFZ, Im Neuenheimer Feld 280, 6900 Heidelberg, Germany
E_mail: dok261@cvx12.dkfz-heidelberg.de  Fax: +49 6221 401271
Newsgroups: bionet.general
From: francis@monod.Biol.McGill.CA (Francis Ouellette)
Subject: Re: class-L list?
Organization: McGill University
Date: Tue, 17 Nov 1992 02:45:52 GMT

ahouse@hydra.rose.brandeis.edu (jeremy john ahouse) writes:

>I am trying to subscribe to the list server called Class-L, 
>a mailing list and file server for researchers in classification, 
>clustering, phylogenetic estimation, and related areas of data analysis.

>        I have the addresses: 
>        LISTSERV@SBCCVM and CLASS-L%SBCCVM.BITNET@CUNYVM.CUNY.EDU
>        
>        but neither of these works from my internet site.

did you try:

listserv@sbccvm.BITNET

(case not important, just used for emphasis)?

>A second question.  I have access to newsgroups, and in
>fact can see a number of bionet groups, but not bionet.info-theory.  
>So I subscribe via email.  Do others have this situation?

this is strange, maybe an oversight on the bart of your news administrator.
Check with your computing center.


best of luck,

francis


--
| B.F. Francis Ouellette  
| manager, yeast chromosome I project
| dept of biology, McGill university, Montreal, Qc, Canada
| francis@monod.biol.mcgill.ca
From: ACKROYD@UTSW.BITNET
Newsgroups: bionet.general
Subject: discontinue subscription
Date: 17 Nov 92 21:23:00 GMT
Distribution: bionet

Please end my subscription. Thanks Alison Ackroyd
Newsgroups: bionet.general
Subject: Re: pUC119 : Info wanted.
From: robison1@husc10.harvard.edu (Keith Robison)
Date: 20 Nov 92 14:28:26 GMT

wetsel_r@wums.wustl.edu writes:

>In a previous article, proberts@castle.ed.ac.uk (P Roberts) wrote:
>>I'm looking for information on the plasmid pUC119.  None of the
>>databases to which I have access have heard of it.  Does anyone out
>>there have any information they could let me have?  I would like to know
>>things like marker (presumably ampicillin), polylinker and any other
>>bits and bobs that it has.  A complete sequence would be great if
>>someone has a copy on-line that they could mail me.
>>  Thanks very much for any help you can offer.
>> 
>>          Paul (proberts@uk.ac.ed.castle)
>----=
>Paul:

>Forgive the stupid question... are you sure it's pUC119 as in *119*????  
>I've heard of pUC19, as in *19*, but not 119.  If it is in fact pUC19 that 
>you need, I think I can provide it to you but having been in mol-bio for 5 
>years, I've never heard of pUC119.

I believe that you will find that pUC119 DOES exist -- it is pUC19 with
an M13 ori added to convert it to a phagemid.


Keith Robison
Harvard University
Department of Cellular & Developmental Biology
Department of Genetics / HHMI

robison@biosun.harvard.edu
From: shibumi@net.bio.net (Kenton A. Hoover)
Newsgroups: bionet.general
Subject: Re: class-L list?
Date: 18 Nov 92 22:59:58 GMT
Reply-To: shibumi@net.bio.net
Organization: BIOSCI International Newsgroups for Biology

ahouse@hydra.rose.brandeis.edu (jeremy john ahouse) writes:
>A second question.  I have access to newsgroups, and in
>fact can see a number of bionet groups, but not bionet.info-theory.  
>So I subscribe via email.  Do others have this situation?

Messages are sent out every month to the 'control' and 'news.admin.misc'
groups (to sites that take distribution 'bionet') to verify that they are
taking all of the bionet newsgroups.  If you have any further questions
about this, please mail me directly, or discuss this issue with your
local systems administration staff (you may also pass my address along to
your local systems staff, and I can consult with them on your problem).


| Kenton A. Hoover                                 |      shibumi@net.bio.net |
| BIOSCI Network Administrator                     |                          |
| BIOSCI/IntelliGenetics, Inc.                     |          +1 415 962 7300 |
|=========== net.bio.net -- The New Home of the bionet Newsgroups ============|
|         The only thing necessary for the triumph of evil is for good        |
|                men to do nothing.  -- Edmund Burke (1729-1797)              |