HDTenEightyP/NetNews huggingface dataset:
From: mroussel@alchemy.chem.utoronto.ca (Marc Roussel)
Subject: Re: Question on entropy at 0K
Organization: Department of Chemistry, University of Toronto
Distribution: bionet
Date: Wed, 11 Nov 1992 01:56:08 GMT

In article <9211101804.AA01955@hydra.rose.brandeis.edu>
ahouse@HYDRA.ROSE.BRANDEIS.EDU writes:
>>     Now if you cool copper to 0K, it should form a perfect crystal
>>PROVIDED THAT YOU COOL IT SUFFICIENTLY SLOWLY.  If you don't, you could
>>get any number of imperfections "frozen in" (that is the usual jargon)
>>and thus almost any number for the entropy.
>
>>                                Marc R. Roussel
>>                                mroussel@alchemy.chem.utoronto.ca
>
>        Couldn't you also wait long enough (infinite time?) so statistical
>fluctuations provide a "perfect" crystal?  Or is the claim here that the
>perfect crystal state is completely inaccessible from the "frozen in"
>imperfections?

     If you actually get to 0K with an imperfect crystal, the
imperfections will indeed be frozen in.  There are no fluctuations at 0K
because there is no available energy.  (If someone out there knows more
than I do about quantum field theory, perhaps they could illuminate me
on the possibility of inducing thermodynamic fluctuations from vacuum
fluctuations.  I have a hunch that this is impossible, but I don't know
enough to say for sure.)  The idea of waiting a long time is of course
implicit in the suggestion that the crystal should be cooled
sufficiently slowly.

				Marc R. Roussel
                                mroussel@alchemy.chem.utoronto.ca
From: shenkin@still3.chem.columbia.edu (Peter Shenkin)
Newsgroups: bionet.info-theory
Subject: Re: Question on entropy at 0K (was Re: Tom's Test Thu Nov  5 17:22:37 EST 1992)
Keywords: test posting, crossed fingers
Date: 11 Nov 92 21:12:47 GMT
Organization: Dept. of Chem, Columbia U, New York
X-Posted-From: still3.chem.columbia.edu
NNTP-Posting-Host: sol.ctr.columbia.edu

In article <1992Nov11.015108.16795@alchemy.chem.utoronto.ca>
 mroussel@alchemy.chem.utoronto.ca (Marc Roussel) writes:
>In article <1992Nov10.233836.22358@sol.ctr.columbia.edu>
> shenkin@still3.chem.columbia.edu (Peter Shenkin) writes:
>>By the way, the Third Law ultimately comes from the experimental observation
>>that DELTA-G for chemical processes approaches 0 as T approaches 0 K.
>
>     You mean d(Delta G)/dT, don't you?

Yes, I do;  apologies.  Or I could have said, "DELTA-G becomes independent
of T as T approaches 0 K," which amounts to the same thing.  Thank you, Marc.

And I should also have added, "... for processes taking place at constant 
T and P."

	Thanks again,
	-P.
-- 
************************f*u*cn*rd*ths*u*cn*gt*a*gd*jb*************************
Peter S. Shenkin  shenkin@still3.chem.columbia.edu   Columbia Univ., Chemistry
********* DEMOCRACY:  The theory that the people know what they want, ********
********** and deserve to get it good and hard.  -- H. L. Mencken ************
From: kjm@buc.edu.au (Kevin Moore)
Newsgroups: bionet.info-theory
Subject: Re:  Trouble at the 0K corral!
Date: 12 Nov 92 14:59:43 GMT
Distribution: bionet


In article  <9211111942.AA20920@net.bio.net>
toms@fcs260c2.ncifcrf.gov (Tom Schneider) writes
> 				Surely we must all agree that at zero Kelvin
> there could be alternative configurations frozen in?  

Tha alternative configurations generally represent higher energy states
than that of a perfect crystal. (I can't think of a counterexample...
anyone?) So these kinetically frozen in configurations do not represent an
equilibrium state at 0K.

							Ahh but now we have a
> contradiction!  For zero K is (apparently) defined only for a perfect crystal!
> So that means that a substance could lose all heat energy (which is impossible
> to do, but we'll imagine it anyway...) but have alternative configurations.  If
> zero K is defined only for a perfect crystal, then what temperature is the
> imperfect crystal that is in thermal equilibrium with the perfect crystal?
> Seems to me that they must have the same temperature!  Anybody see a way out of
> this puzzle?

Without a mechanism to allow the dissipation of the frozen in energy, an
imperfect crystal cannot be thought of as being in thermal contact, so the
idea of thermal equilibrium is somewhat irrelevant.

And just for steve,

|-----------\_ ______
|             |      \
|             |       )      Bite on this bullet. Feel better now?
|            _|______/
|-----------/

Kevin Moore	kjm@eureka.buc.edu.au


P.S. for Tom. If this appeared in your mailbox, it means I still haven't 
sorted out my mailing list problems.
From: jiri@pelagic.berkeley.edu (Jiri Weiss)
Newsgroups: bionet.info-theory
Subject: Journalist in search of DNA metaphors
Date: 13 Nov 92 02:00:27 GMT
Distribution: usa
Organization: University of California, Berkeley
NNTP-Posting-Host: pelagic.berkeley.edu
Originator: jiri@pelagic.berkeley.edu

I am a free-lance journalist  looking for your thoughts on how laymen like 
myself are supposed to understand what will be the end result of the human 
genome project. There is the DNA as a blueprint for life analogy or DNA as a 
book of life or the DNA as a whole library .  (All these bring up the problem 
of who reads the blueprints, the books and who checks out the books from the 
library. ) Then there is the DNA as computer program for a massively parallel 
computer (the cell) analogy .

What bothers me,  first of all, is the amount of information we are talking 
about.  I hear that written about in terms of a couple of hundred Manhattan 
telephone books or a hard disk full.

To a layman a hard disk full of information does not seem like much to 
determine as complex a mechanism as a human body.   If you ask Boeing for 
the blueprints for their 747 -- arguably the most complex thing human beings 
have ever designed, you will certainly get more than one large hard disk full.

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 
understand that for e-coli you only need a hundred or so genes to specify the 
entire organism)

How much will we understand once we have the DNA sequence?  I am told 
that having the sequence of the human genome will be the equivalent of 
having a hieroglyphic text before the Rosetta stone.  How much use will that 
be?  How close to being able to understand what is written will we be?  10 
percent, 20 percent? 

Given the fact that all we know is that one gene codes for one protein, are we 
going to be able to read the book of life and say:  Oh yes, here is the chapter
about the shape of the eye and here is the paragraph that determines the size of
the lens? Where is the information stored about the three-dimensional nature 
of the human body? Where will we read "the leg bone is connected to the 
thigh bone"?

I would appreciate any thought on the above. You can call me directly at (510) 
849-3992, if you like.  Thanks! This is my first Internet posting ever...

Jiri Weiss
Newsgroups: bionet.info-theory
From: kjm@buc.edu.au (Kevin Moore)
Newsgroups: bionet.info-theory
Subject: Re: Question on entropy at 0K
Date: 13 Nov 92 21:08:17 GMT
Distribution: bionet


In article <9211130141.AA00630@net.bio.net>
mshute@cs.man.ac.uk (Malcolm Shute) writes:

> So... really, my initial question was "What are these CRC tables able to state"?

The entropy of a perfect crystal at a particular temperature, and standard
pressure, under a particular model (which doesn't include subatomic
particles to my knowledge.) 

			[deletia]

> Then, someone says that the entropy of a substance is only 0 at 0K if it
> is a perfect crystal.

This is because the state of anything other than a perfect crystal cannot
be considered fully specified (zero information entropy) because of the
possibility of quantum tunneling to even out the dislocations. On sensible
experimental timescales, this is pretty much irrelevant, IMHO.

> But I am then lead to ask, what about NaCl?  If it has 0 entropy, then it
> ceases to have structure (?), and hence ceases to be NaCl, surely?
> A 58.4g lump of NaCl at 0K would then be indistinguishable from a 23g lump
> of Na lieing beside a 35.4g lump of Cl.  Is this correct?

Well, not indistinguishable. They still have different masses. Zero entropy
means that the structure can be fully specified for each. (Or if you like,
they can both be represented as a single point in the phase space for each.
The dimensionality of the phase spaces will be different though.)

> 
> Then, someone else says that some substances (H2O and CO2... interesting, they
> are both compounds, like NaCl) have >0 entropy at 0K.

Degeneracies in the ground state, presumably? I don't think I saw that
article.
							  In which case, my
> question about "how do you know how many sub-sub-sub-atomic particles there
> are in the structure?" rears its head again.

In general, you don't. The quantum states you consider are model-dependent.
The probabilities of these states are ipso facto model-dependent, and the
entropy, which is a function of the probabilities, is also model-dependent.
Actually, I don't think the sub^n-atomic particles would be relevant,
because nuclear transitions are high energy (X-ray and up) and are frozen
into their ground states in normal circumstances. So their contribution to
the entropy should be negligible. Still, if they are thermalised, then
there is a (very small) probability of a sub^n-atomic particle being in an
excited state, and therefore a non-zero contribution to entropy, but this
would be to small to bother with in normal circumstances. (I think I just
stuck my neck out far enough for Steve Modena to lop it, and in his current
mood....)

Anyway, cheers,

Kevin Moore	kjm@eureka.buc.edu.au
From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Newsgroups: bionet.info-theory
Subject: Re: Question on entropy at 0K
Keywords: coins
Date: 10 Nov 92 21:37:31 GMT
Distribution: bionet
Organization: Frederick Cancer Research and Development Center

In article <9211101804.AA01955@hydra.rose.brandeis.edu>
Jeremy John Ahouse (ahouse@HYDRA.ROSE.BRANDEIS.EDU) writes:

> Couldn't you also wait long enough (infinite time?) so statistical
> fluctuations provide a "perfect" crystal?

No, because those fluctuations mean that the system is >0K.  That is, if it
fluctuates, it has a temperature.  Although it may form a perfect crystal at
some instant, the atoms/molecules will have velocity and will bounce out to fly
around a moment later.

> Or is the claim here that the perfect crystal state is completely
> inaccessible from the "frozen in" imperfections?

I think that's what folks are talking about.  The interesting thing is that in
a large collection of systems (ie, an ensemble), some will be frozen in one
configuration and others will be frozen in a different one.  I think - and
would be happy to be corrected on this - that the entropy would be best
measured across this ensemble.

A nice way to think about this is a field of coins.  Take 100 pennies and throw
them down on a table.  (One landed on the edge?  Knock it over!  Another fell
off the edge?  Throw it back on.  Geez. :-)  The coins, although "frozen" in
place will have an uncertainty of 1 bit since half are heads and the other half
are tails.  (Recall that uncertainty is proportional to entropy; see
Schneider.edmm page 128 equation 6.)

By the way, if you would like a wonderful demonstrator for explaining things
like this, you can get coins that are 3 inches (7.7cm) in diameter!  I have a
copper (looking) penny that says "ONE CENT" with leaves on one side and an
Indian face with "UNITED STATES OF AMERICA 1877" on the other side.  I sent a
friend a coin with buffalo on one side with the words "UNITED STATES OF
AMERICA, E Pluribus unum" and "FIVE" on the bottom.  On the other side is an
Indian with the word "LIBERTY" and "1913".  The silver coin I have is a Kennedy
half dollar, it's the nicest of them all.  The company which sells these things
at Newark International Airport, National Airport and Dulles International
Airport is called News Emporium, Inc.  (703) 661-3550.  If anybody contacts
them and gets more information please post here for the rest of us.  Oh, they
cost about $3 each.

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms@ncifcrf.gov
Newsgroups: bionet.info-theory
From: msfuller@cc.utah.edu (MARC S. FULLER)
Subject: re: entropy estimates from a finite sample
News-Software: VAX/VMS VNEWS 1.4-b1  
Organization: University of Utah Computer Center
Date:  6 Nov 1992 09:05 MST  

I had similar questions when I was trying to esitmate entropy and information 
transfer rates in somatosensory neurons.  The problem is that not much is known 
about the acutal distribution of these functions so only general probability 
techniques can be applied.  A good reference to check is: Fagan, R. 1978. 
Information Measures:statistical confidence limits and inference. J. Theor 
Biol. v 73. p61-79.

Marc S. Fuller fuller@cardio.med.utah.edu
Newsgroups: bionet.info-theory
From: jiri@pelagic.berkeley.edu (Jiri Weiss)
Newsgroups: bionet.info-theory
Subject: Journalist in search of DNA metaphors
Date: 11 Nov 1992 22:53:37 GMT
Organization: University of California, Berkeley
Distribution: usa
NNTP-Posting-Host: pelagic.berkeley.edu
Originator: jiri@pelagic.berkeley.edu


Newsgroups: bionet.info-theory
From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Subject: Re: human mind, an ergodic source?
Keywords: artificial intelligence, probability, information theory, cognitive
Organization: Frederick Cancer Research and Development Center
Date: Thu, 5 Nov 1992 23:48:20 GMT

In article <1992Oct28.051730.3860@wixer.cactus.org> sparky@wixer.cactus.org
(Timothy Sheridan) writes:

>There is a nice volume called  'symbols signals and noise' by peirce i think.
>It discusses a variety of points on info theoy, learning, psycology...
>I think it is a classic.

The reference is:

@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"}

Definitely a classic, I recommend it for everybody who reads this group.

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms@ncifcrf.gov
Newsgroups: bionet.info-theory
From: samodena@csemail.cropsci.ncsu.edu (S. A. Modena)
Subject: Re: Question on entropy at 0K
Summary: No matter how long I wait, NOTHING CHANGES at zero Kelvin, ever!
Keywords: Pinheads PseudoScience FlameThrowers Reality-check 
Organization: Crop Science Dept., NCSU, Raleigh, NC 27695-7620
Distribution: bionet
Date: Wed, 11 Nov 1992 12:30:56 GMT


Ok Ok I'm going to make a few enemies by calling you all utterly stupid!

Are you ready?

FLAME THROWER ON:

You are all so @#$%@&#$*@^ stupid!

Entropy is a measure of a DYNAMIC process/system; no dynamics? ==> H(x) = 0!

Zero Kelvin BY DEFINITION == NO DYNAMICS == ENTROPY FIGURE OF ZERO!!!!

FLAME THROWER OFF!

If I have misunderstood the theoretical or spiritual or virtual meaning
of ZERO KELVIN, feel free to roast me.  Otherwise, I'm taking note
of all the pseudo-scientists/mathematicians who are, in effect, discussing
how many angels can stand on the head of a pin!....or something
approximating that.  I repeat it: at Absolute Zero, there can be no
H(before)-H(after) calculation, therefore this is a B.S. line of
discussion.

Will someone please email me some 2-penny nails to chew on, I'm fresh out
and having a fidget fit.  :^)

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
         
Newsgroups: bionet.info-theory
From: mroussel@alchemy.chem.utoronto.ca (Marc Roussel)
Subject: Re: Question on entropy at 0K (was Re: Tom's Test Thu Nov  5 17:22:37 EST 1992)
Keywords: test posting, crossed fingers
Organization: Department of Chemistry, University of Toronto
Date: Tue, 10 Nov 1992 15:56:07 GMT

In article <1992Nov10.010248.17290@husc3.harvard.edu>
robison1@husc10.harvard.edu (Keith Robison) writes:
>In article <6697@m1.cs.man.ac.uk> mshute@cs.man.ac.uk (Malcolm Shute) writes:
>>Just before your long silence, you mentioned that you had recently had cause
>>to consult some tables, to find out the entropy which a certain mass of copper
>>would have at 0K.
>>
>>I replied with some question, and someone replied to me to the effect that
>>he knew the entropy of all substances at 0K... namely, 'zero'
>>(all atoms, particles,
>>sub-particles, etc at ground state).
>>
>>I said that I was therefore confused as to what it was that you had consulted
>>in your tables on entropy of copper.
>
>The Third Law of Thermodynamics states that at 0 K, the entropy
>of a _pure perfect crystal_ is 0, not all substances.

     Copper is a pure substance.  If you don't have pure copper (within
some very tight specification determined by the accuracy of your
experiment), you can't claim that what you are measuring is the entropy
of copper.
     Now if you cool copper to 0K, it should form a perfect crystal
PROVIDED THAT YOU COOL IT SUFFICIENTLY SLOWLY.  If you don't, you could
get any number of imperfections "frozen in" (that is the usual jargon)
and thus almost any number for the entropy.
     To summarize my argument:  If you have a crystal of copper whose
entropy does not go to zero as you approach 0K, it either is not pure
copper (in which case its entropy depends on its composition) or it has
not been properly annealed (in which case its entropy depends on its
history).  Such a crystal would not be a good candidate from which to
prepare a tabulated entry.

				Marc R. Roussel
                                mroussel@alchemy.chem.utoronto.ca
From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Newsgroups: bionet.info-theory
Subject: Re: Trouble at the 0K corral!
Keywords: WE ARE IN TROUBLE FOLKS!!!!!!
Date: 11 Nov 92 22:16:44 GMT
Distribution: bionet
Organization: Frederick Cancer Research and Development Center

In article <1992Nov11.212802.16407@alchemy.chem.utoronto.ca>
mroussel@alchemy.chem.utoronto.ca (Marc Roussel) writes:

|     I don't think that an imperfect crystal can ever be described as
|having a temperature of 0K.  With every type of imperfection I can
|imagine (even isotopic heterogeneities) there has to be an associated
|energy term.

Perhaps you could give a few examples of what you imagined?  Where does
that energy term come from?

| If the crystal is in equilibrium at 0K, then every
|energetic degree of freedom has to have vanished.  This suggests that
|you in fact can't freeze in imperfections in the manner we have all been
|discussing.

This seems to make sense except for one thing:  I thought that 0K was
defined.  So here you are drawing a conclusion about what nature can
do based on a definition!

Whether or not the proton is stable, and whether or not vacuum fluctuations
destroy the possibility of 0K, there is still the question of whether a frozen
array of molecules in disarray has higher entropy than a frozen array of
molecules all lined "up".  It seems to me that this is reasonable, as to line
them all "up" would require some selections to be made.  Thus go get them into
the state would require some dissipation, but the odd thing is that it goes to
the rest of the universe.  So the frozen dis-array (arg, bad pun, sorry) itself
shouldn't carry any more entropy than the ordered array.  Strange.

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms@ncifcrf.gov
From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Newsgroups: bionet.info-theory
Subject: frustration
Date: 11 Nov 92 05:25:39 GMT
Organization: Frederick Cancer Research and Development Center

In article <1992Nov11.015108.16795@alchemy.chem.utoronto.ca>
mroussel@alchemy.chem.utoronto.ca (Marc Roussel) writes:

>     In the spirit of some of the examples given by Peter, I mention
>so-called frustrated systems for which conflicting energy-minimization
>demands result in degenerate ground states.  Consider a one-dimensional
>anti-ferromagnetic solid; the lowest energy configuration is

Just to throw a twist in here, I'd like to clarify the idea of frustrated
systems.  I understood the term to mean a system which has a distinct minimum
energy, but that can't be reached for some reason, such as topology.  Thus I
don't see how the ground state would be relevant.  The reason I bring this up
is that the concept seems to apply directly to the problems of molecular
machines.  In the before state, EcoRI is somewhere on the DNA, and is
"frustrated" in its binding attempts.  Only when it finds GAATTC will it bind
and dissipate.  The same model holds for DNA, rhodopsin and muscle.  The case
of muscle is particularly interesting to think about.

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