[Fis] [External Email] Re: Fwd: Entropy, the Second Law, and Life

Thu Jan 21 16:21:01 CET 2021

Pedro has written:

Thanks to Arieh and Stan. I agree that given the sheer variety of cases
--or systems-- where physical entropy may be meaningfully considered, and
calculated, a common interpretation for all of them is problematic.

But thinking in the ordinary chemical reactions and molecules present in
life, my proposal of "freedom" or "dynamic freedoms of the system" has the
advantage that brings to light --and dovetails-- the other factor in Gibbs
free energy: the enthalpy, the energy change in bonds. So on the one side
we have the increased (or decreased) motions status (position & momenta,
also including vibrations & oscillations), thus the degrees of freedoms.
And on the other side the change in internal energy associated to that
"making and breaking of bonds". Freedoms versus bonds. Entropy versus
enthalpy. And depending on the respective signs they should be added,
rested, etc. At least it has the advantage of being clearly explainable to
students without the usual mystical-mystery-tour.

    S: For living systems, I think we can assume a relatively stable
enthalpy, with which we can then see that energy changes created by system
activity will result in a USUAL and continuing entropy production, which
will institute a necessary search for more sources of energy by the system.
In the best cases (the living system survives) that search is successful.
Enthalpy considerations seem to me to delver no freedom from energy loss
that must be replenished (by way of, at least temporarily, producing MORE
loss (entropy)

PM: What Stan says is OK, but it has implicit the proverbial (scientific?
informational?) observer. We have had plenty of discussions on that...

    S: It is observations (of one kind or other) that generate information,
giving this discussion club much to consider!

 PM: Joseph and Jerry made mention, if I don't remember it wrongly, to
Pauli´s exclusion principle as counteracting entropy.

    S: Since we here descend into the Quantum level, it’s not clear to me
that the observable entropy of an ordinary system will be significantly
changed by PALPABLE CHANGES at this level. Is there evidence for that
changeably adding to the disorder of a system?

PM: By opening the possibility of bonding between heterogeneous atoms &
molecules, there is evident entropy decreases, but at the same time the
heterogeneity of the matter systems is remarkably increased, at least as
"entropy of mixing."

     S: So here we have more entropy production!  I don’t see how these
considerations negate my championing *what I would call” the Realm of
Entropy!

STAN

On Thu, Jan 21, 2021 at 7:45 AM Pedro C. Marijuan <pcmarijuan.iacs en aragon.es>
wrote:

> Dear All,
>
> Thanks to Arieh and Stan. I agree that given the sheer variety of cases
> --or systems-- where physical entropy may be meaningfully considered, and
> calculated, a common interpretation for all of them is problematic. But
> thinking in the ordinary chemical reactions and molecules present in life,
> my proposal of "freedom" or "dynamic freedoms of the system" has the
> advantage that brings to light --and dovetails-- the other factor in Gibbs
> free energy: the enthalpy, the energy change in bonds. So on the one side
> we have the increased (or decreased) motions status (position & momenta,
> also including vibrations & oscillations), thus the degrees of freedoms.
> And on the other side the change in internal energy associated to that
> "making and breaking of bonds". Freedoms versus bonds. Entropy versus
> enthalpy. And depending on the respective signs they should be added,
> rested, etc. At least it has the advantage of being clearly expalinable to
> students without the usual mystical-mystery-tour.
> What Stan says is OK, but it has implicit the proverbial (scientific?
> informational?) observer. We have had plenty of discussions on that...
> Joseph and Jerry made mention, if I don't remember it wrongly, to Pauli´s
> exclusion principle as counteracting entropy. By opening the possibility of
> bonding between heterogeneous atoms & molecules, there is evident entropy
> decreases, but at the same time the heterogeneity of the matter systems is
> remarkably increased, at least as "entropy of mixing." It may be tricky
> depending on the initial/final conditions considered to establish the
> entropy balance. Shu-Kun worked years ago on the paradoxes associated to
> that entropy of mixing.
>
> Best greetings to all!
> --Pedro
>
> it is El 18/01/2021 a las 21:28, Stanley N Salthe escribió:
>
>   Pedro -- Regarding entropy definitions in respect to information, I have
> found it useful to consider that what in Information Theory
> is often/typically referred to as 'information' ought, instead, to be
> referred to as 'information carrying capacity', while a sample taken
> from this would then be 'information' neat. In other words, any system we
> encounter will have a capacity to deliver information upon
> investigation.
> STAN
>
> On Mon, Jan 18, 2021 at 6:32 AM Arieh Ben-Naim <ariehbennaim en gmail.com>
> wrote:
>
>> Dear Pedro,
>> Sorry  for the long delay in my answer.
>> I will answer briefly since a long answer would take too much time and
>> space.
>> 1. I fully agree that entropy and SMI should be given different names.
>> The fact that Shannon called his measure ( the SMI ) entropy, was a grave
>> mistake.
>> This has caused great confusion in both thermodynamics and information
>> theory. ( confusing entropy with SMI and SMI with “information” is very
>> common)
>> 2. I agree that in some specific processes the entropy change may be
>> associated with increase in “freedom” or with “spreading.”
>> This is also true for “disorder” however, none of these interpretations
>> can be derived from the definition of entropy. So, in general, they are not
>> correct interpretation of entropy.
>> 3.  Of course the Gibbs energy is the quantity which is more fundamental
>> in a system at constant T and P. The formulation of the second law in terms
>> of entropy is valid only for isolated systems.
>> Best wishes
>> Arieh
>>
>> On Wednesday, January 13, 2021, Pedro C. Marijuan <
>> pcmarijuan.iacs en aragon.es> wrote:
>>
>>> Dear Arieh and FIS Colleagues,
>>>
>>> Again, regarding the interpretation of entropy as information or
>>> uncertainty (respect locations & momenta), my suggestion is that we should
>>> call "something else" to the extensive magnitude we are measuring.
>>> Otherwise, we easily give room to all those pseudo-interpretations you
>>> wonderfully describe and the general confusion with information. When I was
>>> teaching a bio-discipline for engineer students, I was using the term
>>> "freedom". You are measuring the degrees of freedom of the system, I was
>>> telling, how much they have changed either increasing or decreasing along
>>> the process. And that quantity of degrees of freedom when multiplied by the
>>> temperature gives the energy gained or lost via entropy change. So, the
>>> application of SMI to the system what tells us is about the degrees of
>>> freedom statistical measurement. In short: the new freedom status of the
>>> system. It may not be a terrific theoretical interpretation, but my
>>> students loved it (I confess that previously I was using Lambert's
>>> "dispersal", until I saw your criticisms in the web).
>>>
>>> All of this is well depicted in Gibbs' formula for the free energy of
>>> chemical reactions, with the part due to ENTHALPY change (basically
>>> internal energy), and the part due to ENTROPY change x Temp. Given than
>>> most biological --all!-- occur to room temperature (or far lower), the
>>> resulting contribution of entropy is pretty moderate. Actually I was
>>> checking chemical tables of many biological reactions, and the contribution
>>> of entropy was generally an order of magnitude lower than enthalpy--around
>>> 10% or less. I wonder --following Howard's comment days ago-- all the
>>> obsession with entropy and the universal neglect of enthalpy. It is
>>> enthalpy (or internal energy, or free energy) the big concern of all
>>> biological systems, "the food of today", rather than the negentropy or low
>>> entropy you graciously comment.
>>>
>>> I had also a comment regarding Joseph's and Jerry's on Pauli Exclusion
>>> Principle, but better for another day.
>>>
>>> Best wishes to all--Pedro
>>>
>>> El 08/01/2021 a las 19:22, Arieh Ben-Naim escribió:
>>>
>>> Dear Pedro and everyone else interested.
>>>
>>> I will briefly answer your questions, as I have discussed these in more
>>> details in my previews publications.
>>> Regarding the interpretation of entropy as a measure of information and
>>> as uncertainty.
>>> In my view these are the only valid interpretations of entropy, provided
>>> that one specifies information about what, and uncertainty with respect to
>>> what. Both of these are discussed in my book on “Information Theory” and in
>>> “Entropy: the Greatest Blunder in the History of Science.”
>>>
>>> Regarding the question of dimensions for entropy, I have also discussed
>>> that in my book on “Farewell to Entropy.”
>>> In my view this is a result of historical “accident” that temperature
>>> was given a special dimensions that were not used before in
>>> physics:”degrees”
>>> If temperature was given the dimensions of energy, then entropy would
>>> become dimensionless. This would ease the acceptance of the only correct
>>> interpretation of entropy either as a measure of information or a measure
>>> of uncertainty (in both cases the information and uncertainty with respect
>>> to the distribution of locations and momenta of all particles of the system
>>> at equilibrium)
>>>
>>> In my recent book I have criticized both Shermer’s and Pinker’s misuses
>>> of the concept of entropy in their books.
>>>
>>> I hope I have answered your questions, though very briefly.
>>> Best regards
>>> Arieh
>>>
>>> On Fri, Jan 8, 2021 at 15:40 Pedro C. Marijuan <
>>> pcmarijuan.iacs en aragon.es> wrote:
>>>
>>>> Dear Arieh & FISers,
>>>>
>>>> My appreciation for your elegant and lively contribution. Reading about
>>>> labeling the food on their "negentropy content"  or advising on low
>>>> entropy food (icy water!) was a most humorous way to criticize all the
>>>> nonsense and "mystical mystery tours" around entropy. Particularly,
>>>> Atkins (& Dawkins) quasi-religious views have always been unswallowable
>>>> for me. Anyhow, two further aspects I would like to hear from you.
>>>>
>>>> First, to put it most briefly, what basic, visual image would you
>>>> convey
>>>> for an intuitive understanding of entropy beyond the technicality of
>>>> SMI? Uncertainty, chaos, disorder, diffusion, dispersal... some many
>>>> terms around!  I could see years ago some heated exchanges you had with
>>>> Frank Lambert, the champion of entropy as energy dispersal. There is
>>>> also a longish comment on how Steven Pinker approaches
>>>> entropy-information-evolution-cognition as the four fundamental
>>>> concepts
>>>> in our scientific understanding of the world. He is wrong (IMO) in all
>>>> of them! Although it he is an extraordinary social psychologist the
>>>> basic sci. background he proposes is tainted. If we could give a more
>>>> sound "tetrad" even with those same concepts, it would be a great
>>>> outcome. Clarifying entropy in all aspects we could advance would a
>>>> terrific step.
>>>>
>>>> And second (maybe to be discussed later on) do you accept "dimensions"
>>>> for entropy? The units of jules/degreeK aren't they derived from having
>>>> entered the Boltzmann's constant? Why do we need at all separate units
>>>> for temperature and energy?
>>>>
>>>> Thanks for all the exchanges so far!
>>>>
>>>> Best--Pedro
>>>>
>>>> --
>>>> -------------------------------------------------
>>>> Pedro C. Marijuán
>>>> Grupo de Bioinformación / Bioinformation Group
>>>>
>>>> pcmarijuan.iacs en aragon.es
>>>> http://sites.google.com/site/pedrocmarijuan/
>>>> -------------------------------------------------
>>>>
>>>>
>>>> --
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>>> --
>>> Prof. Arieh Ben-Naim
>>> Department of Physical Chemistry
>>> The Hebrew University of Jerusalem
>>> Jerusalem, 91904
>>> Israel
>>>
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>>>
>>> --
>>> -------------------------------------------------
>>> Pedro C. Marijuán
>>> Grupo de Bioinformación / Bioinformation Group
>>> pcmarijuan.iacs en aragon.eshttp://sites.google.com/site/pedrocmarijuan/
>>> -------------------------------------------------
>>>
>>>
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>>
>>
>> --
>> Prof. Arieh Ben-Naim
>> Department of Physical Chemistry
>> The Hebrew University of Jerusalem
>> Jerusalem, 91904
>> Israel
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> --
> -------------------------------------------------
> Pedro C. Marijuán
> Grupo de Bioinformación / Bioinformation Group
> pcmarijuan.iacs en aragon.eshttp://sites.google.com/site/pedrocmarijuan/
> -------------------------------------------------
>
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