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: Thu, 8 Oct 1992 00:50:35 GMT

In article <6375@m1.cs.man.ac.uk> mshute@cs.man.ac.uk (Malcolm Shute) writes:
>Err.  I don't understand.
>Suppose I have 63.5g of copper here...
>you say that you could tell me its entropy at 0K.

     That's right...  S(Cu,0K)=0.

>But... I thought entropy was a measure of disorder,
>and was proportional to the log-to-base-2 of the number of permutations
>of its components.

     Sort of.  "Disorder" is a bad word which should almost never be used
in connection with entropy.  Also, physical scientists almost never use
base 2, preferring the much more logical base e :-).  In any event, entropy
is the log of the number of different microstates which correspond to a
given macrostate.  At 0K, the crystal should have collapsed to its
ground state.  There is exactly one way to put a crystal in its ground
state, namely to have a perfect lattice with all the electrons filling
the bands up to the Fermi level.  (If you want to get into excruciating
details, the nuclei also have to be in their lowest energy levels, the
nuclear spins all have to be aligned, etc.)  It follows that
S = k ln(1) = 0.
     This is all covered in standard physical chemistry textbooks under
the heading "third law of thermodynamics".

                                Sincerely,

				Marc R. Roussel
                                mroussel@alchemy.chem.utoronto.ca
From: mshute@cs.man.ac.uk (Malcolm Shute)
Newsgroups: bionet.info-theory
Subject: Re: Mead and Conway (Section 9.11)
Date: 7 Oct 92 10:40:59 GMT
Distribution: bionet
Organization: Dept Computer Science, University of Manchester, U.K.

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.

Err.  I don't understand.
Suppose I have 63.5g of copper here...
you say that you could tell me its entropy at 0K.

But... I thought entropy was a measure of disorder,
and was proportional to the log-to-base-2 of the number of permutations
of its components.

So, 63.5g of Cu has 6.023e23 atoms, so its entropy = lg( factorial(6.023e23) )

But hang on, each atom is itself composed of 29 protons, 29 electrons and on
average 34.5 neutrons.  So perhaps its entropy = lg( factorial(5.57e25) )

But hang on, each electron/proton/neutron is composed of 3 quarks... or what
ever the correct breakdown is, so its entropy = lg( factorial(1.671e26) )

But hang on... in the year 2016, Professor Joe Scientist is going to discover
that quarks are each composed of 7 malcons...

etc

Surely, my definition of the entropy of 63.5g of Cu is going to be dependent
on how much I know about the make-up of matter.  The more I know, the more
particals there are to take into account?
--

Malcolm SHUTE.         (The AM Mollusc:   v_@_ )        Disclaimer: all
Newsgroups: bionet.info-theory
From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Newsgroups: bionet.info-theory
Subject: H-trees
Date: 13 Oct 92 19:07:10 GMT
Organization: Frederick Cancer Research and Development Center

In article <6432@m1.cs.man.ac.uk> mshute@cs.man.ac.uk (Malcolm Shute) writes:

|This, to me, seems very much like Tom's question, how much information do you
|need to deliver a letter, or to wander down to stores?  How much information
|needs to be on the envelope, and how much is 'encoded' by the maze (by the
|road network, or the corridor layout).

|I've tried a couple of times to provoke response, with a picture of an H-tree
|layout, and asked how much information is contained in the layout itself.
|No one has ever responded, either positively, or negatively.  Was I really
|way off course, and into the realms of irrelevence with my suggestion?
|You can tell me... I can take it :-)

I've answered (twice now!) but evidently something is still bothering you (or
you are missing postings!).  You could define your H-tree in bits - if it is a
50 by 50 array of bits then you have 2500 bits.  Compress it.  Alternatively,
you could use the program complexity (Kolmoragov).  But I'm not clear why you
want to know this.  What will it tell you if you know how many bits are needed
to define the layout of an H-tree?

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms@ncifcrf.gov
Newsgroups: bionet.info-theory
From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Newsgroups: bionet.info-theory
Subject: Re: The Dualism in info theory
Date: 13 Oct 92 19:02:43 GMT
Organization: Frederick Cancer Research and Development Center

In article <1992Oct12.235329.12233@ncsu.edu> samodena@csemail.cropsci.ncsu.edu
(S. A. Modena) writes:

>Perhaps the fundamental short-coming of Tom's model: failure to
>capture fundament function behavior....perhaps a necessay extension
>to explain Rs/Rf ratios different than 1.0  (thinking of your latest
>posting which restricted itself to just two alternatives to explain
>the Rs/Rf contradiction).

What is "fundament function behavior" and how does Rs/Rf fail?

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms@ncifcrf.gov
From: jweimar@ulb.ac.be (Joerg Richard Weimar)
Newsgroups: bionet.info-theory
Subject: Re: AND gate puzzle for you
Date: 8 Oct 92 11:56:54 GMT
Distribution: bionet

In article <1992Oct6.233508.13111@hellgate.utah.edu>  
tolman%asylum.cs.utah.edu@cs.utah.edu (Kenneth Tolman) writes:

> Discussion of extremes:
> 
> The AND gate certainly loses information, so the
> information loss is greater than 0.  However, it does not
> lose all of its information, which is clearly 2 bits to
> start out.  Therefore, the information loss is somewhere
> greater than 0, and less then 2.   

What about the following argument: 

The AND gate gains information: Without AND gate, you
only know the probabilities of inputs A and B separately
(say 1/2 each). After combining them with an AND gate, you
also know the combined probability P(A=1 & B=1). You
gained information (by doing a calculation through the
AND gate) if you look at the inputs and the outputs
(assuming the AND gate to be idealized and reflecting at
the output always the value A & B  instantaneously).
--
                                Joerg Richard Weimar
jweimar@ulb.ac.be    Physique Nonlineaire et Mechanique Statistique
                                Universite Libre de Bruxelles
Tel +32-2-6505530               Campus de la Plaine, C.P. 231
Fax +32-2-6505767               B-1050 Bruxelles, Belgium
Newsgroups: bionet.info-theory
From: tolman%asylum.cs.utah.edu@cs.utah.edu (Kenneth Tolman)
Subject: Re: Adaptive Complexity
Date: 10 Oct 92 18:24:14 MDT
Keywords: entropy  complexity  adaptivity
Organization: University of Utah, CompSci Dept

>The following relayed item is self-explanitory.  Since it will be
>in the next building, you may be a book report, if it's good.

Hey, wait a second..... this is not fair!

>                           Dr. MURRAY GELL-MANN
>         Robert Andrews Millikan Professor of Theoretical Physics
>                    California Institute of Technology
>          "SIMPLICITY, COMPLEXITY, AND COMPLEX ADAPTIVE SYSTEMS"
>What makes one landscape or one work of art more complex than another?

Is there some way we can get access to this talk!  Maybe a summary?
Now I am just dying to know what was said, but have no way to find out :(

I seriously would like to know what was said here.... any help or
references would be great,

thanks

Newsgroups: bionet.info-theory
From: tolman%asylum.cs.utah.edu@cs.utah.edu (Kenneth Tolman)
Subject: Re: Questions for a thermo person
Date: 9 Oct 92 16:12:39 MDT
Organization: University of Utah, CompSci Dept
Distribution: bionet

>>1) How do you choose parititions?
>If your question contained a little more information it might map onto a
>better answer than this.

Alright, here is a little more entropy (information) :)  Please tell if
the following has correctly interpreted anything correctly, it may not!

Classically,  the entropy of a system is proportional to the log of the
number of microscopic "complexions" of a given macroscopic state.
Therefore, we set up a coarse grained system characterized by paritions,
and the partitions are chosen by a human attempting to understand what
will happen.  However, if we choose a partition differently the macrostate
is defined by a different class of microstates.  Entropy is said to
go up when we move into indistinguishable macrostates.... which apparently
depends on our partition set up.  My contention is that actual entropy goes
up without any sort of human intervention or understanding, and that it
should not rely on any partitions at all.... unless of course there is some
a priori reason for establishing partitions in some particular way.

Listen to this quote, it sounds ominous for the foundations of 
classical thermodynamics: " ... provided we adopt the correct counting
procedure, it does give correct thermodynamic results..  The apparent
success of Boltzmann's principle, provided we can justify our choice
of the expression of the thermodynamic probability....."*

Ummm... why do we have to provide for anything?  Physical law does not
depend in any way on us, or on our method of accounting... UNLESS the
only way it can work is for us to fudge our mathematics to support
experimental results.  However, that would be tautological, and I am sure
that I am misinterpreting something.  So the original question was,
"how do you choose a partition?"  

Lavenda, B. H., "Statistical Physics", Wiley Publication, New York, 1991,
 pp. 2-11.
Newsgroups: bionet.info-theory
From: tolman%asylum.cs.utah.edu@cs.utah.edu (Kenneth Tolman)
Subject: Interpreting Shannon
Date: 8 Oct 92 01:28:43 MDT
Organization: University of Utah, CompSci Dept
Distribution: bionet

Consider a source with 4 random possible outputs:  A, BJD, DHFDD, and HJKHHKJH
Assume the probability of each to be:

DHFDD       0.5
BJD         0.25
A           0.125
HJKHHKJH    0.125

Then the entropy of this source is 1.75 bits, with Shannon's measure.

Now, if the source produces one of these in particular, say BJD, how do
we measure the amount of information produced?  Would it not be the -log(0.25),
or in general -log p(i)?  Is this correct?

So in general, given any random source, the amount of information created would
be -log (probability of occurance of output)

Now, the Kolmogrov complexity of an object is its minimal description in bits,
so we could consider the entropy of any particular sequence as a combination
of Shannon and Kolmogrov...

We have to have a machine randomly produce sequences by making a 0 or 1 then
randomly (50%) stopping or continuing creation, and then let a Turing
machine operate on these sequences to produce the final sequences.
Unfortunately, it will be difficult to find out the probability of any
particular output sequence, for many reasons.  However, if we were to assume
that each input sequence produced a unique output sequence then the two
measures would appear identicle, as the probability of occurance would 
correspond to the probability of the input sequence.  The probability of 
the input sequence would then be 1/2^n and then the -log (1/2^n) would
give you the length of the thing.. perfect.  However, since the inputs
do not produce unique outputs it makes these measures somewhat different,
but not significantly...

Have I interpreted Shannon correctly?  Can the amount of information production
be given by the -log p(i) for a particular output sequence?
From: mshute@cs.man.ac.uk (Malcolm Shute)
Newsgroups: bionet.info-theory
Subject: Re: Mead and Conway (Section 9.11)
Date: 8 Oct 92 10:20:25 GMT
Distribution: bionet
Organization: Dept Computer Science, University of Manchester, U.K.

>In article <6375@m1.cs.man.ac.uk> mshute@cs.man.ac.uk (Malcolm Shute) writes:
>>Err.  I don't understand.
>>Suppose I have 63.5g of copper here...
>>you say that you could tell me its entropy at 0K.

In article <1992Oct8.005035.6012@alchemy.chem.utoronto.ca> mroussel@alchemy.chem.utoronto.ca (Marc Roussel) writes:
>     That's right...  S(Cu,0K)=0.
>[...]  At 0K, the crystal should have collapsed to its
>ground state.  There is exactly one way to put a crystal in its ground
>state, namely to have a perfect lattice with all the electrons filling
>the bands up to the Fermi level.  (If you want to get into excruciating
>details, the nuclei also have to be in their lowest energy levels, the
>nuclear spins all have to be aligned, etc.)  It follows that
>S = k ln(1) = 0.

Errrrrrrrrrrrr.  Now I'm really confused.
I thought Tom had said that he'd recently had to *look up* the entropy
for Copper at 0K.  If what you say is true, then the tables which he
consulted wouldn't have been very interesting ones :-)

	TABLE OF ENTROPIES OF ELEMENTS AT ABSOLUTE ZERO

	Aluminium, Al:	0.0000
	Copper, Cu:	0.0000
	Iron, Fe:	0.0000
	Lead, Pb:	0.0000
	Zinc, Zn:	0.0000
etc :-) :-)

What's going on?  Can you shed some light, Tom?
--

Malcolm SHUTE.         (The AM Mollusc:   v_@_ )        Disclaimer: all
From: MCCAINKW@DUVM.OCS.DREXEL.EDU (Kate McCain)
Newsgroups: bionet.info-theory
Subject: Stu Kauffman & JTB
Date: 7 Oct 92 14:28:19 GMT
Distribution: bionet


According to the voice-mail message for Stu's lab at Penn, he can be
reached at (505) 984-8800.  The new number for the Journal of Theoretical
Biology is (505) 984-0139.


Thanks,

Kate McCain

Newsgroups: bionet.info-theory
From: mshute@cs.man.ac.uk (Malcolm Shute)
Newsgroups: bionet.info-theory
Subject: Re: AND gate puzzle for you
Date: 9 Oct 92 13:35:11 GMT
Distribution: bionet
Organization: Dept Computer Science, University of Manchester, U.K.

In article <1992Oct8.155813.26894@hellgate.utah.edu> tolman%asylum.cs.utah.edu@cs.utah.edu (Kenneth Tolman) writes:
>This is an interesting analysis!  I do not agree with it, but it feels
>correct in a way, for why would we undertake computation unless we were
>given new information?
We could be doing it because we want to *reveal* information which,
though already present, is obscurred by a surfeit of other information.

>What would be the point of computation unless it
>told us something we did not know?
Because we were previously unable to see the wood for the trees.

>If computation lost information at
>every gate, what the heck would we be doing?
We'd be taking a chain-saw to all but the information that we wanted, so
that we could at last have an unobscurred view of the information of interest.

And it's not just computation which works as a metaphorical chain-saw.
I believe we are doing something similar when we are designing experiments.
The art of choosing a suitable experiment for a particular measurement
is to find some property of the universe which cause the characteristic
in question to be attenuated least, and all other characteristics to be
attenuated down into the noise level so that we can just about ignore them.

For instance, you want to verify Newton's law of cooling...
so you don't just play a bunsen burner on a patch of open sea, and watch it...
you close in a measured sample in a flask, you sheild it from drafts,
you would even have screened it from radio waves if you had any suspicions
that radio emisions from Alpha Centuria would have an effect above the
noise level of your experiment.

On the other hand, if you were interested in measuring the amount of radio
emision from Alpha Centuria, you'd build yourself a radio telescope, and
shield it from bunsen burners (and other heat sources), etc.

In a sense... all the information we could ever wish to know about the
universe is *already* around us, and in our possession.  We want to find
out about the orbit of the new planet, Smiley... well, just measure the
perturbations in the orbit of the moon, or the free fall of this apple
to the ground.  The information is there... the skill is in masking out
all the other stuff which over shadows it.

So yes, I believe that computers are designed to destroy information,
not to create it.
--

Malcolm SHUTE.         (The AM Mollusc:   v_@_ )        Disclaimer: all
From: ICEAB@ASUACAD.BITNET
Newsgroups: bionet.info-theory
Subject: Re: The Dualism in info theory
Date: 12 Oct 92 21:44:01 GMT
 <1992Oct11.072935.9685@ncsu.edu>
Organization: Arizona State University

When I first saw your subject, I thought that perhaps you were going to
start in on a topic of some interest to bacterial geneticists like myself -
namely, how do your information theories work if the encoded message is
actually an overlapping one? Many bacterial viruses show overlaps where one
gene begins or ends within another one. Sometimes they are in the same reading
frame and sometimes they are not. Even a full scale cell like Escherichia coli
displays some overlaps, although usually they are in the same frame and just
represent truncated forms of the longer gene.
From: kjm@buc.edu.au (Kevin Moore)
Newsgroups: bionet.info-theory
Subject: Parametrisation-dependence of entropy (was Re: Mead and Conway (Sect...
Date: 7 Oct 92 17:44:27 GMT
Distribution: bionet


In article <9210061831.AA18345@net.bio.net>
toms@fcs260c2.ncifcrf.gov (Tom Schneider) writes

> In article <9209300553.AA24276@eureka.buc.edu.au> kjm@buc.edu.au (Kevin Moore) writes:
> 
> >one observer knows the temperature, and the second knows the temperature
> >and magnetisation. The ensemble of the first observer contains the ensemble
> >of the second. Both observers see the second law hold, but both calculate
> >DIFFERENT entropies for the system. No hypotheses are involved here, merely
> >the fact that different information about the system is held by the two
> >observers.
> 
> Not quite.  In your example, the person who knew less about the system will
> eventually figure that they were missing something.  

How? Without access to the magnetisation information, I can't see a way for
the person to know that anything was up. Any energy input by the magnetic
field would have to be lumped in as heat by this observer.
 
						Get the observer out of
> your calculations, it messes things up.

And now to really set the cat among the pigeons, if you go back to the
first law,

	dU = dQ - dW

ask yourself the question, "What counts as work, and what counts as heat?"
the answer depends on what system parameters you measure. For each
parameter q_i, there is a generalised force F_i, and a contribution to the
work
	dW_i = F_i dq_i

Presumably dU has to be well-defined, in which case dQ (and hencs dS) IS
dependent on which parameters you measure.

Tom? Malcolm? If you can see a flaw, I'd like to know what it is.

***************************************************************************
Let there be light			*      	Kevin Moore
	Bomb number 20			*   kjm@eureka.buc.edu.au
***************************************************************************

Newsgroups: bionet.info-theory
From: samodena@csemail.cropsci.ncsu.edu (S. A. Modena)
Subject: Re: Adaptive Complexity
Keywords: entropy  complexity  adaptivity
Organization: Crop Science Dept., NCSU, Raleigh, NC 27695-7620
Date: Sun, 11 Oct 1992 06:20:31 GMT

In article <1992Oct10.182415.8563@hellgate.utah.edu> tolman%asylum.cs.utah.edu@cs.utah.edu (Kenneth Tolman) writes:
>>The following relayed item is self-explanitory.  Since it will be
>>in the next building, you may be a book report, if it's good.
>
>Hey, wait a second..... this is not fair!

What's unfair? A Cal Tech notable coming to Cow U?  [We are, after all,
a land grant university.  :^)  ]

>
>>                           Dr. MURRAY GELL-MANN
>>         Robert Andrews Millikan Professor of Theoretical Physics
>>                    California Institute of Technology
>>          "SIMPLICITY, COMPLEXITY, AND COMPLEX ADAPTIVE SYSTEMS"
>>What makes one landscape or one work of art more complex than another?
>
>Is there some way we can get access to this talk!  Maybe a summary?
>Now I am just dying to know what was said, but have no way to find out :(
                                  ^^^
Hey! I'm good but not that good: I haven't traveled into the future and back!
The presentation won't be until Oct. 19th!  |:^)

>
>I seriously would like to know what was said here.... any help or
>references would be great,

I've marked it on my calender and it really will be in the next building.
I can't guarentee that I'm going to be able to attend, but this is one
I'd be very interested in.  If I remember, I'll call around Monday and
see if someone this prestegious will play on Concert Net....

>
>thanks

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: Parametrisation-dependence of entropy (was Re: Mead and Conway (Sect...
Organization: Department of Chemistry, University of Toronto
Distribution: bionet
Date: Wed, 7 Oct 1992 20:08:53 GMT

In article <9210070244.AA04295@eureka.buc.edu.au> kjm@buc.edu.au (Kevin Moore)
writes:
>And now to really set the cat among the pigeons, if you go back to the
>first law,
>
>	dU = dQ - dW

     Ick!  I thought this particular sign convention had vanished into
the mists of history.  Far better to write

	  dU = dq + dw

so that all inputs to the system are positive.

>ask yourself the question, "What counts as work, and what counts as heat?"
>the answer depends on what system parameters you measure.

     There is an entirely satisfactory resolution to this question to be
found in the works of the so-called "rational thermodynamics" school
(see in particular the opening chapter of Truesdell's "Rational
Thermodynamics", 2nd ed.).  Heat is a type of energy that flows on
contact in the presence of a temperature gradient.  If you can physically
separate the system from the putative source of heat and still cause the
effect you claimed to be heat, or if you can cause the effect to continue
when a thermometer says that the temperature of system and agent are
equal, you know that the thing you initially claimed to be heat isn't.

>Presumably dU has to be well-defined, in which case dQ (and hencs dS) IS
>dependent on which parameters you measure.

     S is a state function.  You can't calculate it directly from heat
measurements so writing that "dQ (and hence dS) IS dependent on which
parameters you measure" is an unjustifiable leap in logic, even if we
allow you to separate work and heat terms in the arbitrary way you
described above.

				Marc R. Roussel
                                mroussel@alchemy.chem.utoronto.ca