Re: 2nd law clarifications

On Tue, 7 Jan 2025 11:58:24 +0000, MarkE wrote:

On 5/01/2025 8:08 pm, LDagget wrote:

On Thu, 2 Jan 2025 6:53:02 +0000, MarkE wrote:
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Are these statements correct? Could they be better expressed?
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Local entropy can decrease in an open system with an input of free
energy.
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Free energy alone is not sufficient to maintain or further decrease low
local entropy: an energy capture and transformation mechanism is also
needed.
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Extant life *maintains* low local entropy through its organisation and
processes.
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Evolving life *decreases* low local entropy through the ratcheting
mechanism natural selection acting on random mutations in instances
where that evolution increases functional complexity and organisation.
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There is no other known mechanism apart from natural selection that does
this. For example, neutral drift alone increases entropy.

>
There's so much fuzzy language in there that replying is bound to
explode
things into an extended attempt to us clean up the language enough  for
one to understand the claims in scientific language.
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So let's bypass that, besides, it's been done before.
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Instead, consider this. The broad objection is that creationists or
their
bedfellows try to claim that evolution is somehow a decrease in entropy.
Such a claim is superficially nonsensical. Here's why.
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Evolution is a result. In a simple example of adaption, an initial
population of bacteria begin with an enzyme that is effective against
one antibiotic but has very low efficacy against a related antibiotic.
These things work such that at very low concentrations of the antibiotic
the low efficacy is sufficient to allow the bacteria to keep growing
but at higher concentrations bacterial cell wall growth is inhibited
and the bacteria stop growing.
>
so the usual processes take place because they can't be stopped.
Imperfect
DNA replication occurs, mutations of the antibiotic resistance enzyme
occur, most have little effect but occasionally there are mutations that
result in increased activity against the related antibiotic (a new
drug).
So now bacteria with the mutation can grow faster than those without
the mutation. The process repeats, the gene pool evolves to have more
and more of the antibiotic resistance gene with higher efficacy and
that's evolution.
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Now where and how do people claim that is a violation of the 2nd law?
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Let's help with that. The process involves millions of bacteria growing,
reproducing, and sometimes dying. The process is the sum of all of these
events. Each and every cell consumed food, and metabolized it. The sum
of their life processes can be cartooned like the metabolism of glucose
C6H12O6 + 6 O2 ==> 6 CO2 + 6 H2O    This reaction increases entropy.
It still increases net entropy when coupled to charging ADP to ATP.
The sum of all of the chemical reactions that have to take place for a
cell to grow and replicate represents a relentless increase in entropy
comparing the reactants to the products.
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Now how do the creationists claim that summing up all of these millions
of positive increases in entropy represents a decrease in entropy?
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That's the essence of their nonsensical claim. At each and every step
along the way, all the chemical reactions are increasing entropy.
Entropy increases when DNA is replicated. There's negligible difference
between a perfect copy of a gene and a copy with a mutation. Either
way, it's an increase in entropy.
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The only way that evolution can be considered a decrease in entropy is
thus revealed to be by a failure to look at the actual processes
involved
and to instead resort to hand waving about loosey-goosey attempts to
invoke related concepts like __disorder__.
>

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Entropy is a difficult concept, especially its application to OoL and
evolution. I get the frustration. My own understanding in incomplete.
The examples you give point to a question of where exactly is the
"local" boundary of the claimed entropy decrease?

It doesn't need to be difficult. It's possible to make it seem
difficult, and you work hard at that below.

What about this approach as starting point. Take configuration entropy,
which relates to the arrangements or positions of components within a
system, but ignores energy distributions, i.e. it's a subset of
thermodynamic entropy, and can be calculated for systems where the
spatial distribution dominates the behavior. Configuration entropy can
be calculated using the Boltzmann entropy equation:

It has already been established in my example that the process of
evolution produces a large increase in entropy. So you attempt a
"let's ignore what we know and try to wave our hands and pretend
otherwise."  Seriously, that's what you're doing.

     𝑆 = 𝑘𝐵.ln(𝑊)
>
where:
     𝑆 is Entropy
     𝑘𝐵 is the Boltzmann constant
     𝑊 is the Number of possible microstates (configurations)
        consistent with the macrostate
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Microstate: A specific arrangement of the system's components.
Macrostate: The overall state of the system, described by observable
properties like temperature, pressure, or composition.
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A macrostate with a larger number of possible microstates has higher
configuration entropy." (ChatGPT-4o; also
https://en.wikipedia.org/wiki/Configuration_entropy)
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For an ensemble of molecules that could form a living entity, the
"nonliving macrostate" is composed of many more possible microstates
(Wn) than the "living macrostate" (Wl). E.g., if say Wn/Wl = 10^10, then
the local configuration entropy *decrease* to go from nonliving to
living is
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     Sn - Sl = kB(ln(Wn) - ln(Wl))
             = kB.ln(Wn/Wl)
             = kB.ln(10^10)
             = 3.2E-22 joules per kelvin

Thus we get an AI regurgitating things it doens't understand. I rather
doubt you understand all this either or you wouldn't be wasting yours
and other people's time like this.

Now, assuming that a similar result would apply for the other component
of thermodynamic entropy (i.e. energy distributions), then a protocell
or living cell represents a local region of greatly reduced entropy. The
process of abiogenesis has given rise to a region of reduced entropy
(albeit at the expense of an overall entropy increase in the
environment).
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And...so what, that's surely a given. You wouldn't dispute that, would
you?

I dispute that it's remotely relevant.
Here's a simple illustration. You know about the fact that complementary
DNA strands fold up into the triple helix. It's well known that paired
strands of DNA can be melted apart at higher temps but that they will
re-anneal when the temp is dropped, or if complementary pairs are
re-introduced to each other below the melting temperature.
It should be obvious that two independent strands have vastly higher
conformational entropy than the two of them paired up in a matched
double helix. And yet --- the folding is spontaneous and represents a
decrease in entropy. The conformational entropy may seem hugely
decreased
to you in concept. And if you run a statistical mechanic style
calculation
and estimate a W (as above) for the number of states available for
different conformations you can model the effect on just the DNA
strands.
The commensurate change in the solvent, in the other direction, happens
to overwhelm that of  the DNA strands. Broadly speaking, this is the
hydrophobic effect. Understanding it is essential to understanding
biochem.
The point? Babble away all you want about conformational entropy in DNA
strands, the process of forming the mated double helix is a spontaneous
process that increases entropy. There's no violation of the 2nd law.
Introducing some discussion about the conformational entropy of just the
DNA strands that ignores the entropy of the solvent interacting with the
DNA is a way to hide the truth of what happens in solution.
Don't do that. It's not honest. You were already shown that evolution is
the result of the addition of many increases in entropy. Retorting with
     "but but but, whatabout ...."
is nonsensical deflection. Don't do that. Whatabout-isms are no better
in science than they are in politics.
But you won't let it go, will you? Very well then.
We can compute, using W as with the above equations, the difference in
entropy for DNA synthesis that synthesizes a specific product strand vs.
a completely random strand. It's a large change in W when instead of
just
one base added at each position one can add any of 4. In fact it becomes
4^N where N is the length of the polymer synthesized. So we can plug in
the comparison of 1^N (also known as 1) to 4^N.
And what happens? It's minuscule compared to the entropy change from the
hydrolysis of the reactant nucleotide triphosphates.
An AI is dumb enough to be able to tell you how to calculate the entropy
different between synthesizing a random DNA strand of length N and a
specific DNA strand of length N.   But it doesn't know enough to tell
you
that it was, in fact, a stupid question if you're worried if the process
is problematic respective to the 2nd law of thermodynamics. It doesn't
understand.
Try to be better and understand.

Therefore, the issue is, are the mechanisms available to say OoL capable
of driving this required entropy reduction? There does not appear to be
simple yes/no answer. Are redox couples, proton gradient, etc
sufficient, and in what form?
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"In 1924 Alexander Oparin suggested that sufficient energy for
generating early life forms from non-living molecules was provided in a
"primordial soup".[31] The laws of thermodynamics impose some
constraints on the earliest life-sustaining reactions that would have
emerged and evolved from such a mixture. Essentially, to remain
consistent with the second law of thermodynamics, self organizing
systems that are characterized by lower entropy values than equilibrium
must dissipate energy so as to increase entropy in the external
environment.[32] One consequence of this is that low entropy or high
chemical potential chemical intermediates cannot build up to very high
levels if the reaction leading to their formation is not coupled to
another chemical reaction that releases energy. These reactions often
take the form of redox couples, which must have been provided by the
environment at the time of the origin of life.[33] In today's biology,
many of these reactions require catalysts (or enzymes) to proceed, which
frequently contain transition metals. This means identifying both redox
couples and metals that are readily available in a given candidate
environment for abiogenesis is an important aspect of prebiotic
chemistry.
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"The idea that processes that can occur naturally in the environment and
act to locally decrease entropy must be identified has been applied in
examinations of phosphate's role in the origin of life, where the
relevant setting for abiogenesis is an early Earth lake environment. One
such process is the ability of phosphate to concentrate reactants
selectively due to its localized negative charge.[34]
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"In the context of the alkaline hydrothermal vent (AHV) hypothesis for
the origin of life, a framing of lifeforms as "entropy generators" has
been suggested in an attempt to develop a framework for abiogenesis
under alkaline deep sea conditions. Assuming life develops rapidly under
certain conditions, experiments may be able to recreate the first
metabolic pathway, as it would be the most energetically favorable and
therefore likely to occur. In this case, iron sulfide compounds may have
acted as the first catalysts.[35] Therefore, within the larger framing
of life as free energy converters, it would eventually be beneficial to
characterize quantities such as entropy production and proton gradient
dissipation rates quantitatively for origin of life relevant systems
(particularly AHVs)."
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https://en.wikipedia.org/wiki/Entropy_and_life
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As far as I understand then, it does seem to be an oversimplification to
say the development of life (origin and evolution) violates the second
law. On the other hand, a supply of free energy is not in and of itself
sufficient to explain life.
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However, the ratio of the nonliving macrostate's number of possible
microstates (Wn) to the nonliving macrostate's (Wl) I suspect is grossly
underestimated, and the corresponding difficulty/improbability of matter
self-organising into life. A research avenue would be to further
quantify and analysise this.