From: samodena@csemail.cropsci.ncsu.edu (S. A. Modena)
Subject: Re: entropy??
Organization: Crop Science Dept., NCSU, Raleigh, NC 27695-7620
Distribution: bionet
Date: Thu, 12 Nov 1992 08:38:27 GMT

In article <9211111438.AA09019@net.bio.net> MCCAINKW@DUVM.OCS.DREXEL.EDU (Kate McCain) writes:
>Please excuse the intrusion of a lurker on bio-info.  With respect to Steve's
>flame -- isn't _one_ definition of entropy the degree of _structure_ in
>a system and isn't it then reasonable to measure the degree of structure
>"frozen" in the ultimately cooled crystal?
>
>
>Kate McCain   <a potentially crispy critter if the flamethrower points her way>
>College of Information Studies
>Drexel University
>
>mccainkw@duvm.ocs.drexel.edu

I used up most of the kerosine last night and I'm saving what's left for
Marc.  :^)

I see no problem with your thought *provided* you call the figure of
merit something like COMPLEXITY or HETEROGENEITY. You might use Shannon's
measure to characterize stretches or domains of DNA sequences that way.
(There is a another lurker at NCBI who could expand the idea beautifully.)

If I use Shannon's calculation for a stretch of a particular (singular)
strand of DNA, that is not a calculation about ENTROPY, but rather
structural complexity.  On the other hand, suppose I posed this question:

What are the ENTROPY-associated characteristics that a ribosome must accomodate
as it translates a particular m-RNA Ferritin allele?

I've entered (IMHO) an area of ENTROPY-based biophysics that most other people
seemed to have missed and therefore need to talk in extended fashion
about copper crystals approaching ZERO Kelvin, which might spark a new
dicussion forum: alt.physics.state.solid.

To answer my own question: I might define a "word" framelength, do
experiments to characterize the real in vivo range of translation
rates, and thence think about calculating a single ENTROPY number, which
is a *kind* of figure of merit, but also I need to calculate an upper
bound bandwidth number and a lower bound.  Thinking along these lines
might lead one to then explore such ideas as: is the lower bound on
bandwidth zero, or is it non-zero because at a certain slow rate the
translation process collapses or experiences fidelity problems....and
at the high end, the same but for different mechanical reasons?

IN EITHER CASE, this might lead one to model the translation process
in the tradition spectral-decade-of-frequency rolloff formulation
characteristic of AC and RF electrical circuits containing networks of
lumped reactances...thereby moving real-world bio-physics closer
to a single paradigm.  But, of course, since I'm not a mathematician nor 
a bio-physicist...coupled with the notion of NOT-INVENTED-HERE...would
lead to the immediate dismissal of the concept with a "Huh?"

But of course, what will actually happen is the discussion about
whether the *definition* of ZERO Kelvin permits "freezing in" of
crystal dislocations OR rigorously excludes imperfect crystal
localities from reaching Ok, will remain unresolved.  

And that is why the Constantinople Branch
of Apologetics relocated to bionet.info-theory: it needed the kind of
thinkers that can overlook that their professional piling of superstition upon
conjecture upon assumption has been cleaved from the underlying requirement
of checking one's logic by proceeding from first/primal axiom toward
outer-most/most-ramified postulate, rather than reverse order. In human
perception and in thermodynamics, time-space transitions forward and
backward may appear linearly correlated to the *observer*, but
simultaneously appear hysteretic to the *outside* observer. Notice that
my proposition above does not suffer the critical flaw of a first
axiom incoherently defined: since I rely on no axioms whatever.

I guess I still have the nasties.  ;^)

Oh, yes, Kate: note that my ribosomal model clearly involved dynamics
(i.e., something changes with time). 

Just for imaginative sake: if I were to look at the universe of all
ferritin DNA sequences that exist in nature at this microsecond: is
that an entropy calculation, or a complexity calculation?  If I
take the same set of DNA sequences and add in both weighting by
living population magnitudes and observations over a 1 million-year
stretch of time: is that an entropy calculation or a complexity
calculation?  (And I do mean a Shannon calculation.) 

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