HDTenEightyP/NetNews huggingface dataset:
From: mroussel@alchemy.chem.utoronto.ca (Marc Roussel)
Subject: Re: Mead and Conway (Section 9.11)
Organization: Department of Chemistry, University of Toronto
Distribution: bionet
Date: Tue, 29 Sep 1992 12:48:04 GMT

In article <1992Sep29.093739.12409@bnr.co.uk> pgh@bnr.co.uk (Peter Hamer)
writes:
>Surely, in a fairly weak sense, entropy does have something to do with
>the observer, and their beliefs?
>
>* Entropy is defined as a function of probabilities.
>
>* These probabilities are assigned with respect to some hypothesis.
>
>* Hence entropy is not an absolute measure, but conditional on the
>  hypothesis used in assigning probabilities to events.
>
>* So the *measured* entropy change of a ribosome would differ between
>  observers holding different hypotheses.
>
>... of course, the hypothesis you use to assign probabilities may be
>so widely accepted that this is a philosophical point rather than a
>practical one.

     I hope I don't offend Peter, but this sounds like mumbo-jumbo to
me.  What hypothesis are you talking about?  When I write down a
partition function, I make no hypotheses at all.  I just use the most
basic definition of probability and count up the number of states
accessible to a system.  If you see any bias in the way we compute
partition functions, please say so.  Otherwise, I'm really not sure I
understand this discussion.

				Marc R. Roussel
                                mroussel@alchemy.chem.utoronto.ca
From: mshute@cs.man.ac.uk (Malcolm Shute)
Newsgroups: bionet.info-theory
Subject: Re: More wacky theory
Date: 5 Oct 92 14:22:19 GMT
Distribution: bionet
Organization: Dept Computer Science, University of Manchester, U.K.

>In article <6078@m1.cs.man.ac.uk>, I wrote:
>> This then comes back to my comment last week, from Richard Dawkins' "The Blind
>> Watchmaker".  Mont Blanc is a complex structure... with millions of fragments
[etc]...

In article <1992Oct2.191214.48248@embl-heidelberg.de> croft@embl-heidelberg.de writes:
>Take th Nile delta for instance.  For thousands of years, people [...]
>So, I would claim that functionality is something with which we can invest
>something quite natural, as well as something that is designed!

Yes, true.
And this, or course, is the main thrust of Richard Dawkins' book...
that the human eye, or the bat's ear, or whatever has functionality and
structure... but no designer.

(NB: this is Richard Dawkins' thesis... don't assume that I concur with
him, just because I quote him :-).
--

Malcolm SHUTE.         (The AM Mollusc:   v_@_ )        Disclaimer: all
Newsgroups: bionet.info-theory
From: tolman%asylum.cs.utah.edu@cs.utah.edu (Kenneth Tolman)
Subject: Re: Prigogine's theories-- comments, anyone?
Date: 6 Oct 92 15:33:19 MDT
Organization: University of Utah, CompSci Dept

>   A layperson here, wondering about any connections between the
>info-biological ideas being tossed about here and the theories of Dr. Ilya
>Prigogine.  Is the similarity in language ("self-organization",
>"dissipative systems", "order from chaos", etc.) superficial, or are there
>parallels, points of intersection?

From my point of view, Prigogine is exactly correct.  When a system
bifurcates, it increases its informational content (locally, although it
is a dissipative system)
Newsgroups: bionet.info-theory
Subject: Re: Mead and Conway (Section 9.11)
From: z_madsenka@ccsvax.sfasu.edu
Date: 30 Sep 92 11:33:06 CST
Organization: Stephen F. Austin State University

{}{}{}{}{}{}{}{}{}{}{}{}{}{}{}{}{}{}{}{}{}{}}}{}}{}{}{}{}{}{}{}{}{}{}{}{}{}
What is known amount of information exanding into?

Kris Madsen
z_ccsvax.sfasu.edu
From: BIOCUKM@MVS.UCC.OKSTATE.EDU
Newsgroups: bionet.info-theory
Subject: J Theor Biol OK?
Date: 2 Oct 92 16:03:00 GMT
Distribution: bionet

Does anyone know whether the Journal of Theoretical Biology is
having problems?
I submitted a ms in March and have not yet received an evaluation
of it.  In recent weeks, I get no answer at the phone no. I have.
I also did not get a response to a letter I sent to Santa Fe.
Thanks in advance for any info or advice.
Ulrich Melcher

Newsgroups: bionet.info-theory
From: tolman%asylum.cs.utah.edu@cs.utah.edu (Kenneth Tolman)
Subject: Questions for a thermo person
Date: 6 Oct 92 15:40:00 MDT
Organization: University of Utah, CompSci Dept
Distribution: bionet


1) How do you choose parititions?

2) How do you choose partitions?

(I realized I needed two to make questions)

Seriously, I am curious how you choose partitions.
From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Newsgroups: bionet.info-theory
Subject: Yockey's book
Date: 29 Sep 92 21:41:16 GMT
Organization: Frederick Cancer Research and Development Center

Dr. Hubert Yockey's book has come out finally.  Dr. Yockey was one of
the first, perhaps THE first person to use information theory for
biological problems.  He was editor of this book:

@inproceedings{Quastler1958a,
author = "H. Quastler",
title = "A primer on information theory",
pages = "3-49",
editor = "H. P. Yockey and R. L. Platzman and H. Quastler",
booktitle = "Symposium on Information Theory in Biology",
publisher = "Pergamon Press",
address = "New York",
year = "1958"}

His new book is "Information Theory in Molecular Biology", available from:

Cambridge Univ. Press
40 West 20th Street
New York, N. Y.  10011-4211
1-800-827-7423
order number 350050

I have not seen a copy yet.

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms@ncifcrf.gov
From: jessec@yang.earlham.edu
Newsgroups: bionet.info-theory
Subject: Prigogine's theories-- comments, anyone?
Date: 6 Oct 92 18:34:33 GMT
Organization: Earlham College, Richmond, Indiana

Hello.

   A layperson here, wondering about any connections between the
info-biological ideas being tossed about here and the theories of Dr. Ilya
Prigogine.  Is the similarity in language ("self-organization",
"dissipative systems", "order from chaos", etc.) superficial, or are there
parallels, points of intersection?


   --Jesse.


-------------------------------------------------------------------------------
The double integral stood in Etzel Olsch's subconscious for the method of
finding hidden centers, inertias unknown, as if monoliths had been left
for him in the twilight, left behind by some corrupted idea of
"Civilization," in which eagles cast in concrete stand ten meters high at
the corners of the stadiums where the people, a corrupted idea of "the
People" are gathering, in which birds do not fly, in which imaginary
centers far down inside the solid fatality of stone are thought of not as
"heart," "plexus," "consciousness," (the voice speaking here grows more
ironic, closer to tears which are not all theatre, as the list goes on...)
"Sanctuary," "dream of motion," "cyst of the eternal present," or
"Gravity's gray eminence among the councils of the living stone." No, as
none of these, but instead a point in space, a point hung precise as the
point where burning must end, never launched, never to fall...

                                --Thomas Pynchon
                                  *Gravity's Rainbow*
From: pgh@bnr.co.uk (Peter Hamer)
Newsgroups: bionet.info-theory
Subject: Re: Mead and Conway (Section 9.11)
Date: 30 Sep 92 09:28:28 GMT
Reply-To: pgh@bnr.co.uk (Peter Hamer)
Distribution: bionet
Organization: BNR Europe Limited, London Road, Harlow, Essex, GB

In the referenced article mroussel@alchemy.chem.utoronto.ca (Marc Roussel) writes:
>In article <1992Sep29.093739.12409@bnr.co.uk> pgh@bnr.co.uk (Peter Hamer)
>writes:
>>Surely, in a fairly weak sense, entropy does have something to do with
>>the observer, and their beliefs?
>
>I hope I don't offend Peter, but this sounds like mumbo-jumbo to me.

None taken, but it rather forces me into a public response.

>What hypothesis are you talking about?  When I write down a
>partition function, I make no hypotheses at all.  I just use the most
>basic definition of probability and count up the number of states
>accessible to a system.

So you use Laplace's "Principle of Insufficient Reason". From a 
frequentist position 'this assumption may appear as arbitrary as
any other that might be made' [Janes]. From a Bayesian position
this is a *strong* statement about prior ignorance. Either way
you are making assumptions.

>If you see any bias in the way we compute partition functions,
>please say so.

If you genuinely are in complete prior ignorance my Bayesian component
says you are doing exactly the right thing.

>Otherwise, I'm really not sure I understand this discussion.

I was defending a position attacked by a previous poster; and did say -

>>... of course, the hypothesis you use to assign probabilities may be
>>so widely accepted that this is a philosophical point rather than a
>>practical one.

Regards, Peter
From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Newsgroups: bionet.info-theory
Subject: Re: Mead and Conway (Section 9.11)
Date: 29 Sep 92 21:54:39 GMT
Organization: Frederick Cancer Research and Development Center

In article <6210@m1.cs.man.ac.uk> mshute@cs.man.ac.uk (Malcolm Shute) writes:

>However, despite disagreeing with M&C's argument, I'm still not convinced
>that Fredkin type dissipationless computing is possible.

If EcoRI finds G and A and A and T and T and C, then it does a Boolean
operation.  "Computation" is merely large numbers of Boolean operations.  For
EcoRI to bind to GAATTC, it must dissipate energy.  However, if I put EcoRI
with a DNA that has no GAATTC, it will continue to "compute", but the result
will always be false - that is, it doesn't cut the DNA.  Hence dissipationless
(and rather useless!!!) computation happens all the time.  Useful computation
always requires dissipation to capture the results.  See Schneider.edmm.

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms@ncifcrf.gov
Newsgroups: bionet.info-theory
From: mroussel@plumbum.chem.utoronto.ca (Marc Roussel)
Subject: Re: Mead and Conway (Section 9.11)
Organization: Department of Chemistry, University of Toronto
Distribution: bionet
Date: Tue, 6 Oct 1992 19:56:24 GMT

In article <4057@fcs280s.ncifcrf.gov> toms@fcs260c2.ncifcrf.gov (Tom Schneider) writes:
>Yes, that is an important point, that we should usually be discussing changes
>of state.  However, I'm not sure I agree with your idea that entropy itself is
>dependent on people, since I can look up the entropy of copper in CRC - I did
>that for the calculation given in Schneider.edmm!  So there is a way to get the
>entropy of copper.  I think this is relative to absolute zero though.

     Obtaining absolute entropies requires a belief in the third law of
thermodynamics.  To be honest, other than the desire to put an absolute
number on entropies, I've never been able to fathom the value of this
"law".  Perhaps someone else can enlighten me.

				Marc R. Roussel
                                mroussel@alchemy.chem.utoronto.ca
Newsgroups: bionet.info-theory
From: samodena@csemail.cropsci.ncsu.edu (S. A. Modena)
Subject: Re: Mead and Conway (Section 9.11)
Organization: Crop Science Dept., NCSU, Raleigh, NC 27695-7620
Date: Wed, 7 Oct 1992 02:47:41 GMT

In article <4059@fcs280s.ncifcrf.gov> toms@fcs260c2.ncifcrf.gov (Tom Schneider) writes:
>In article <1992Sep30.190402.25351@beaver.cs.washington.edu> pauld@cs.washington.edu
>(Paul Barton-Davis) writes:
>
>|In article <4000@fcs280s.ncifcrf.gov> toms@fcs260c2.ncifcrf.gov (Tom Schneider) writes:
>|>If EcoRI finds G and A and A and T and T and C, then it does a Boolean
>|>operation.  "Computation" is merely large numbers of Boolean
>|>operations.  
>|
>|Minor nitpick, Tom. Computation can be *performed* by carrying out large
>|numbers of boolean operations, but the two are not the same.
>|.........etc....
>
>Sure.  I mean that what EcoRI does is equivalent to a Boolean operation, not
>that it really does direct AND operations the way one designs them in a.....
.....etc....
>operations - since one can write a computer program which simulates a Turing
>machine, and the program runs on Boolean logic gates.  So for me everything...
....etc....
>.....................  It's a lot of work to demonstrate that one has
>something equivalent to a Turing machine.   Why make life difficult??
>
>  Tom Schneider

Well, Tom, you're in good company with Nick Metropolis' clear opinion
that Claude Shannon preempted everyone when he showed the feasibility
of electronic digital computers by showing the relationship of series-type
and parallel-type switching circuits to OR and AND logic.  And Nick *did*
say that the Turing tour-de-force was unnecessarily overcomplicated.

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.
OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
From: kristoff@net.bio.net (David Kristofferson)
Newsgroups: bionet.info-theory
Subject: Re: FAQ - no changes
Date: 1 Oct 92 05:33:13 GMT
Organization: BIOSCI International Newsgroups for Biology

Actually there should be one small change in the FAQ.  Please change
all references to genbank.bio.net to net.bio.net.

Thanks,

Dave K.
From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Newsgroups: bionet.info-theory
Subject: Re: Mead and Conway (Section 9.11)
Date: 6 Oct 92 17:35:59 GMT
Organization: Frederick Cancer Research and Development Center

In article <1992Sep30.190402.25351@beaver.cs.washington.edu> pauld@cs.washington.edu
(Paul Barton-Davis) writes:

|In article <4000@fcs280s.ncifcrf.gov> toms@fcs260c2.ncifcrf.gov (Tom Schneider) writes:
|>If EcoRI finds G and A and A and T and T and C, then it does a Boolean
|>operation.  "Computation" is merely large numbers of Boolean
|>operations.  
|
|Minor nitpick, Tom. Computation can be *performed* by carrying out large
|numbers of boolean operations, but the two are not the same.
|
|Various network-based computing systems can only be described as
|performing boolean operations in a symbolic sense - there are no
|gates, no boolean logic to their operation (or rather, there *need*
|not be), at least while you remain at the level at which computation
|is nominally occuring. Summation of inputs to cross a threshold is not
|a boolean operation in the sense that conventional electronic circuits
|perform them.

Sure.  I mean that what EcoRI does is equivalent to a Boolean operation, not
that it really does direct AND operations the way one designs them in a
computer.  To me computation is always equivalent to a set of Boolean
operations.  Thus I do not see why the fuss about Turing machines:  they are a
VERY COMPLICATED way to express computation.  That is, it is not obvious how to
construct one.  Yet surely whatever they do can be expressed in Boolean
operations - since one can write a computer program which simulates a Turing
machine, and the program runs on Boolean logic gates.  So for me everything
reduces to NOT and AND:  NAND will do the job.  If one can build a NAND gate,
one can do any computation desired.  It's easy to demonstrate whether or not
one has a NAND operation.  It's a lot of work to demonstrate that one has
something equivalent to a Turing machine.   Why make life difficult??

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms@ncifcrf.gov
From: mroussel@ALCHEMY.CHEM.UTORONTO.CA (Marc Roussel)
Newsgroups: bionet.info-theory
Subject: Re: Mead and Conway (Section 9.11)
Date: 30 Sep 92 12:16:45 GMT
Distribution: bionet

In a recent posting, I wrote
>>				If you see any bias in the way we compute
>> partition functions, please say so.  Otherwise, I'm really not sure I
>> understand this discussion.

to which you replied
>No bias at all. Two observers with the same information about the same
>system will deem the same set of states accessible, and therefore calculate
>the same entropy. 

     In that case, I don't understand the fuss.  This is self-evident,
isn't it?  There must be more of a point to this discussion than simply
a question of how much data you need to fully describe a system.

                                Sincerely,

				Marc R. Roussel
                                mroussel@alchemy.chem.utoronto.ca
From: bdest+@pitt.edu (Benoit Desjardins)
Newsgroups: bionet.info-theory
Subject: information request: biomathematics / mathematical biology
Date: 6 Oct 92 05:23:35 GMT
Organization: University of Pittsburgh

I would like to know what are the good research centers (for
graduate training and postdocs) in biomathematics (mathematical
biology).  Can someone provide me with this information? Also, does
anyone know about the research activities of Oxford's Center for
Mathematical Biology?

                                       Thank you

                                       B. Desjardins
                                       benoit@med.pitt.edu

P.S. Please reply to "benoit@med.pitt.edu"
Newsgroups: bionet.info-theory
From: tolman%mindblow.cs.utah.edu@cs.utah.edu (Kenneth Tolman)
Subject: Re: Mead and Conway (Section 9.11)
Date: 26 Sep 92 19:50:04 MDT
Organization: University of Utah, CompSci Dept

>Yes, I've heard about this... Fredkin gates and all that... but never really
>looked into it.  Does it work, though?

Very good question.  And if it DID work, why doesn't current bacteria
use it?  Especially at least for things like DNA transcription, which is
clearly a computer-like process.  For bacteria and other living things,
they are constrained to operate in a thermal enviroment, which limits
the limit.  It has been suggested by Bennett that there is a minimal
driving force needed to produce forward computation (or transcription)
requiring heat dissipation.  Also he has suggested that proofreading errors
requires a minimal heat dissipation.

>However, I don't think that their reasoning works.
>In section 9.5.1, they argue that a reversible computer would know whether
>it was coming or going... and therefore can't be possible.  

??? It would know which way it was going?  I am not sure how that pertains..

>However, despite disagreeing with M&C's argument, I'm still not convinced
>that Fredkin type dissipationless computing is possible.

Perhaps it is not, but perhaps it is.  Fredkin's model has a flaw- it
requires perfectly determinism with no noise at all- which is effectively
impossible.  However, it is conceivable this could be attained through
a form of quantum computation, as Deustch and  Benioff have independently?
suggested.  In this, the Hamiltonian evolves in a deterministic computation,
and then is "observed" to get the answer.  Of course, you only get the 
answer some of the time :)

Keep in mind todays logic gates dissipate around 10^10 Kt per gate, and
so we could have practically dissipationless computing just by cleaning
up our technology.  I believe the current dissipation in transcription
is very low.... 100 kT??  (Bennett)

>The Turing Machine would, if built in the most perfect technology, still
>dissipate energy (heat) whenever it erased a square on the tape, to overwrite
>it with something else.

Keep in mind there are many equivalent models of computation, of which
the Turing machine is merely the "base model".  Fredkin's model
basically avoids "erasing squares" by keeping them all around....
I believe Toffoli once produced a reversible Turing machine, which kept
the old information around somewhere... I am thinking of building one
myself, embedded in a reversible cellular automata.

Charles Bennett "Dissipation-Error Tradeoff in Proofreading", Biosystems
11 (1979) pp. 85-91.

Paul Benioff "The Computer as a Physical System: A Microscopic Quantum
Mechanical Hamiltonian Model of Computers as Represented by Turing
Machines", Journal of Statistical Physics, 22, No. 5, (1980) pp. 563-591.

(Benioff deals specifically with the questions you raised about erasing
squares and so forth)

David Deutsch "Quantum theory, the Church Turing principle and the
universal quantum computer", Proc. R. Soc. London A400 (1985) pp.97-117.
From: jcollier@ariel.its.unimelb.EDU.AU (John Donald Collier)
Newsgroups: bionet.info-theory
Subject: Re: J Theor Biol OK?
Date: 4 Oct 92 05:27:19 GMT
Distribution: bionet
Organization: University of Melbourne, Australia

In <9210021604.AA03840@net.bio.net> BIOCUKM@MVS.UCC.OKSTATE.EDU writes:

>Does anyone know whether the Journal of Theoretical Biology is
>having problems?

Stu Kauffman was in a bad auto accident, which has set back 
publication of his book. It is possible that this has also
affected JTB.

-- 
John Collier 			Email: jcollier@ariel.ucs.unimelb.edu.au
HPS -- U. of Melbourne		  	Fax:   61+3 344 7959
Parkville, Victoria, AUSTRALIA 3052
From: mshute@cs.man.ac.uk (Malcolm Shute)
Newsgroups: bionet.info-theory
Subject: Re: Mead and Conway (Section 9.11)
Date: 29 Sep 92 09:20:52 GMT
Distribution: bionet
Organization: Dept Computer Science, University of Manchester, U.K.

In article <3988@fcs280s.ncifcrf.gov> toms@fcs260c2.ncifcrf.gov (Tom Schneider) writes:
>In article <9209250126.AA04548@eureka.buc.edu.au> kjm@buc.edu.au (Kevin Moore) writes:
>| Entropy itself is anthropomorphic, in the sense that it depends on how much we
>| know about a system. (Jaynes, in "Gibbs vs. Boltzmann entropies" American
>| Journal of Physics 1965 demonstrates this rather well)
>This is wrong (or "not right" for those with weak hearts... :-) - the
>entropy change of a ribosome has nothing whatsoever to do with humans.
>Entropy changes are only anthropomorphic when you are discussing humans!!
Tom, I'm disappointed!
What you said is correct *because* you made an important change in your wording...
but omitted to remind us what and how important this distinction is.
Can I therefore do it for you (hoping that you will correct me if I have got
this wrong):

Entropy *is* anthropomorphic to the extent that it depends how deep you
are prepared to study the object in question.  It's a bit like potential
energy.  Here... here is a 1kg lump of coal, being held 1m off the ground...
how much potential energy has it got?  The answer depends on whether you
are about to drop it to the ground, burn it, or split its atoms.

A more meaningful question is... in Process-A, by how much does its
potential energy *change*.  If Process-A involves dropping it to the
ground, you can safely answer "9.81J", without needing to rush to look
up the bonding energy of carbon atoms, or the masses of its atomic
particles.  By concentrating on *change of potential energy*, all the
irrelevent types cancel out, and the question becomes objective, and
deterministic.

Similarly with asking what the *change* in entropy is during Process-A,
rather than asking the less useful question of "how much entropy does
a given system have".
--

Malcolm SHUTE.         (The AM Mollusc:   v_@_ )        Disclaimer: all