[Fis] Fis Digest, Vol 108, Issue 5

Sun Jan 7 23:42:07 CET 2024

Dear colleagues,

Allow me to propose one more facet of life that adds to the central theme of Kantian Wholes: autonomous agency. Living organisms are "agential" materials, as Michael Levin puts it. They possess cognition, have agendas, and act purposefully.
This is how agency is explained by Stu in [1], and similarly in [2]:

"It is a stunning fact that the universe has given rise to entities that daily modify the universe to suit their own ends. We call this capacity 'agency' — the ability to act on one's own behalf."

But then one may ask: what must a physical system be such that it can act on its own behalf?
We propose a tentative five-part definition of a minimal molecular autonomous agent: such a system

  1.  should be capable of reproduction with heritable variation,
  2.  should perform at least one work cycle and have boundaries such that it
  3.  can be naturally individuated,
  4.  should engage in self-propagating work and constraint construction, and
  5.  should be able to choose between at least two alternatives.

(I reformatted the sentence into the numbered list).

References:
[1] Kauffman, S., Clayton, P. On emergence, agency, and organization. Biol Philos 21, 501–521 (2006). https://urldefense.com/v3/__https://doi.org/10.1007/s10539-005-9003-9__;!!D9dNQwwGXtA!WWIS2V8aSgvKYkrQRr725ec79RyfScFLmMNE8IsOuQH_2QEXOgrmSFAoTpy10_NrZIogCIJL_U0gt3mM7rtKVyxvUWJfKGhM$ 
[2] Kauffman, S.A. The origins of order: Self-organization and selection in evolution. New York: Oxford University Press, 1996.

To the above definition of agency of a minimal molecular autonomous agent, I would propose to add information processing which enables learning and adaptation.

It appears to me that points 1, 3, 4, and 5 above derive from the information processing capacity of these systems.
Goal-directedness, or agency, can be seen as based on information processing, which is enabled by memory and the mechanism of anticipation that is contingent on memory.

Evolutionarily, all cognitive (agential) mechanisms derive from material characteristics. As an illustration, see a very short account in the video The Biophysics of a Brainless Animal<https://urldefense.com/v3/__https://www.youtube.com/watch?v=ImKFUHJdcLE__;!!D9dNQwwGXtA!WWIS2V8aSgvKYkrQRr725ec79RyfScFLmMNE8IsOuQH_2QEXOgrmSFAoTpy10_NrZIogCIJL_U0gt3mM7rtKVyxvUQM960NL$ >.
More extended explanation can be found at:
https://urldefense.com/v3/__https://www.youtube.com/watch?v=O1VAIwcn7z8__;!!D9dNQwwGXtA!WWIS2V8aSgvKYkrQRr725ec79RyfScFLmMNE8IsOuQH_2QEXOgrmSFAoTpy10_NrZIogCIJL_U0gt3mM7rtKVyxvUS9S__8A$  Manu Prakash: The physics of biology, which addresses several of Stu’s questions.

Gordana

From: Fis <fis-bounces at listas.unizar.es> on behalf of Stuart Kauffman <stukauffman at gmail.com>
Date: Sunday, 7 January 2024 at 16:28
To: Louis Kauffman <loukau at gmail.com>, 0 <stukauffman at gmail.com>
Cc: "fis at listas.unizar.es" <fis at listas.unizar.es>, Andrea Roli <andrea.roli at unibo.it>
Subject: Re: [Fis] Fis Digest, Vol 108, Issue 5

Thank you Lou. I agree. Creativity is not deduction. Given what you write, Andrea and I claim to have shown that no laws at all entail the evolution of the biosphere which is a non-deducible, propagating, construction. Assume this is correct. But physics DOES HAVE LAWS THAT ENTAIL. So if Andrea and Stu are right and physics with laws is right, why can physics have entailing laws but not the evolving biosphere? One answer is that living organisms really are Kantian Wholes with Catalytic and Constraint closure, that can evolve new boundary conditions creating novel phase spaces, that can evolve and create ever-new phase spaces by selection on the whole, which is downward causation for those feature that survive and propagate best in the current context - and there is no prior description of what the current context will become.

But even if Andrea and I are right about evolving life, why can PHYSICS have entailing laws?

All very odd.

Stu

On Jan 7, 2024, at 2:00 AM, Louis Kauffman <loukau at gmail.com> wrote:

Dear Stu,

Think about physical laws.
Good principles like F = ma, Newton’s Law of Gravity,  and all that. Laws of E&M, Schrodinger equation, Dirac equation, Einstein’s modern geometric understanding of Gravity.
Some questions and thoughts.
1. Newton did not deduce the law of gravity. He guessed it and discovered that it explained Kepler’s Laws that were derived from observation. This made Newton’s guess very firm. There is no way to predict Newton’s Law of Gravity. In fact it is not even correct when one takes Einstein’s wider point of view. Einstein guessed that there should be a differential geometric law of gravity. He was lucky, the tensor expression in curvature that he sought was nearly unique and so in this case the mathematical constraints helped him find a physical law.
2. Once laws are given (or guessed) then some predictions are possible.
Clerk Maxwell guessed the laws of EM via Faraday’s experiments and Faraday’s field concepts. But then
Maxwell saw that in his theory the EM field could propagate like a wave and its velocity was the velocity of light! Who would have thought it? And this allowed Maxwell to further
guess (yes guess but some say ‘predict’) that light is an EM wave. Huge consequence for the physics and technology after that up through the present day. But this is being done by inventive discovery not by logical deduction.
3. No one could predict the structure of atoms or the later understood nuclear structure in terms of quarks. This is discovered and  verified and there are theories but there is no theory that predicts atoms. Once we know something about atoms we can understand how certain molecules could behave, but no one can predict the emergence and stability of
big molecules like DNA or their reproductive properties.
4. Physics is a big guesswork patchwork that uses mathematics and has some predictive abilities. But the main lines of its structure are guessed, discovered, invented, verified.
The logic comes last.

Mathematics is the same. It is a structural enterprise and we cannot predict where it will go and what will be proved. We knock around and invent or discover structures and sometimes get them into deductive frameworks.  Lots of ‘obvious’ things are not (yet) proved.

Best,
Lou

On Jan 6, 2024, at 3:49 PM, Stuart Kauffman <stukauffman at gmail.com<mailto:stukauffman at gmail.com>> wrote:

HI Pedro and All,

Thank you Pedro, perhaps we are at THE GREAT TRANSFORMATION. We begin to confront the vast, unprestatable, non-deducible becoming of the evolving biosphere. YET…yet, physics works also. We really can compute planetary orbits. If the biosphere is “governed by no laws” why do laws work so well in Physics?

And there is something very odd about, “Information”. Consider the information content of a Picasso painting. Cast it into 10,000 pixels, each reflecting  a wavelength specified by 4 bits. So 40,000 bits suffice and that 40,000 bits  can be sent by email all over the world to be printed out on physically different systems using different procedures and perhaps pigments to create a good copy of the Picasso. It seems information is not embodied but becomes physical to print, or to erase a bit in the 40,000 record.

Now think of a living cell, a Kantian Whole with Catalytic and Constraint Closure. There IS NO SEPARATE “description” of this reproducing system. It cannot be copied.  The living cell constructed itself, it did not create a description of itself sent to a distance assembly point.

Also in Boltzmann entropy can stay constant or increase. In Shannon, in parallel, information can be transmitted without or with loss. BUT..there is no creation of new information. That is due to the Newtonian Paradigm where the phase space of all the possibilities are stated beforehand. (In Shannon, the entropy of the source.) But in the evolution of the biosphere, co-evolving organisms are creating ever-new ways to get to co-exist for a while. This is the unprestable and non-deducible creation of new information. The emerging evolving increasing complexity of the biosphere is not via a channel transmitting information from some exogenous source. Andrea Roli and I are working on this. And this becoming is NOT AI, which is algorithmic.

Hm….

Stu

On Jan 5, 2024, at 2:20 PM, fis-request at listas.unizar.es<mailto:fis-request at listas.unizar.es> wrote:

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Today's Topics:

  1. Re: New Year Lecture - Stuart Kauffman (Terrence W Deacon)
  2. Re: Fis Digest, Vol 108, Issue 4 (Krassimir Markov)

----------------------------------------------------------------------

Message: 1
Date: Fri, 5 Jan 2024 08:47:37 -0800
From: Terrence W Deacon <deacon at berkeley.edu>
To: Pedro C. Mariju?n <pedroc.marijuan at gmail.com>
Cc: fis at listas.unizar.es, Skauffman <stukaufman at gmail.com>
Subject: Re: [Fis] New Year Lecture - Stuart Kauffman
Message-ID:
<CAOJbPRLC40bnKjupETxqd_tDLXziDZdwVTvXHVauFwcdwytxuA at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Beware of the cryptic Cartesianism of opposing informationalism to
physicalism (as in "it from bit").
By accepting this framing, we risk falling for the old idealism vs
materialism trap, just in a new form.

On Fri, Jan 5, 2024 at 3:59?AM Pedro C. Mariju?n <pedroc.marijuan at gmail.com>
wrote:

Dear Stuart and FIS colleagues,

We are honored that you impart the FIS New Year Lecture this time. In this
list, quite a few members share the impression that we are involved in a
historical transition in science. Maybe, as you and Andrea Roli state, it
could be the Third Great Transition. That it revolves around putting  into
question the predominance of physicalist views was coincidentally discussed
in a previous discussion session, when two pioneers of AI research (Yixin
Zhong from China and Eric Werner from Oxford) were arguing for a paradigm
change away for physicalism. Now you are providing strong arguments from
the biological self-construction and evolutionary points of view. An
important point is the argument on Kantian wholes, from the closure of
auto-catalitic sets. It could also be considered as the organizational
reliance on "cycles". In biological systems there is a towering presence of
cycles: from elementary reaction cycles, to enzyme work-cycles, to regional
reaction cycles, gene expression cycles (your Boolean networks!!), to
genetic macro-cycles... to the cell's entire life cycle. And an even larger
story could be told about cycles in complex organisms...

To put the argument in a nutshell: bye to physicalism (as a fundamental
meta-scientific vision). Yes, but what would substitute for it?
I dare say "informationalism". You mention the biosphere and the  global
economy, and even our cultures. Aren't all them based on the circulation of
"information flows"  (in vastly different forms, of course)??
Let us think, for instance, on the enormous disarray created by the new
social networks in our societies... we do not much understand the
psychological changes derived for the intertwining of natural vs artifical
info flows in our societies.

I am just reading Joseph's just arrived comments, philosophically and
formally oriented. Fine.  I would ad that we are lacking a vast
informational view that can help us to understand that strange world put
into action 3,000 million years ago, full of emergent realms. So, filling
in the gap that physicalim is unable to fill in consistently.

Best regards to all,
--Pedro

*PS. If anyone has doubts about the messages effectively  distributed in
the list, go please to the instantaneous archive:
http://listas.unizar.es/pipermail/fis/
<http://listas.unizar.es/pipermail/fis/>*

-------------------------------------------------------------------------------------------
El 04/01/2024 a las 23:54, Stuart Kauffman escribi?:

Hello to All,

I am truly grateful to have this opportunity to discuss with you the
recent Stuart Kauffman and Andrea Roli paper, ?A Third Transition In
Science?? J. Roy. Soc. Interface, 4/ 14 2023.  I attach a link below. It?s
eventual publication in a fine journal after almost two years has its own
wry history.

Andrea and I think we are correct, but we may be wrong. More, I only
slightly begin to understand what our results, if correct, mean.

I had thought that the First Transition in science was Newton?s invention
of Classical Physics in 1689 A.D. And I thought the Second Transition was
the reluctant discovery of quantum mechanics between 1900 and 1927 A.D.

I begin to suspect I was wrong.  The First Transition in science was in
1299A.D. when the first mechanical clock was invented and installed at the
Wallingford Abby. It was installed because the monks were often late for
prayers. Within less than a century, Europe was dotted by chuch towers with
ever - more impressive mechanical clocks. Modern people in 1379 A.D. must
have begun to wonder if the World itself was some amazing clockwork
machine. Then Copernicus, 1543 A.D., then Kepler, Galileo and Newton.

This, then, was the Second Transition in Science. Yes, yes, yes!  The
World is a vast clockwork machine. No room for God?s miracles ? the Deistic
God of the Enlightenment. No room for mind ? Descartes lost his Res
cogitans to Newton?s Res extensa. No Free Will.

With Planck, Heisenberg, and Schrodinger cam a loss of determinism, but
still within the Newtonian Paradigm. And no mind and no responsible Free
Will.

If Andrea and I are correct, this Third Transition demonstrates for the
first time since 1299AD, 725 years later, that the evolving biosphere is
not a clockwork machines. Evolving life is not a machine at all.

Are the two of us correct? If so, what does this Third Transition
portend?  These  issues now lies before us.

Merci a tous,

Stu Kauffman

A Third Transition in Science? Link

https://urldefense.com/v3/__https://royalsocietypublishing.org/doi/10.1098/rsfs.2022.0063__;!!D9dNQwwGXtA!QWqRy48IxgI7uqQVW1zW2bni_amdH6RTRyIDsnv2KVgCUL0gLsvl9TQg9-0nZwoqnXSch1vxIkH0HogQ-8uUlw$
<https://urldefense.com/v3/__https://royalsocietypublishing.org/doi/10.1098/rsfs.2022.0063__;!!D9dNQwwGXtA!RH-1N1FEJfqU41WdGgs7y8jJfe5UgMaHIJlh56CZUw76fWIEwZkUE9gIll06GR3L150IpC24ewV5iF7LveZK0HwbrDZ8$>

<https://urldefense.com/v3/__https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=emailclient__;!!D9dNQwwGXtA!RH-1N1FEJfqU41WdGgs7y8jJfe5UgMaHIJlh56CZUw76fWIEwZkUE9gIll06GR3L150IpC24ewV5iF7LveZK0Kbsj3yQ$> Libre
de virus.https://urldefense.com/v3/__http://www.avast.com__;!!D9dNQwwGXtA!QWqRy48IxgI7uqQVW1zW2bni_amdH6RTRyIDsnv2KVgCUL0gLsvl9TQg9-0nZwoqnXSch1vxIkH0HoiCeiZeGQ$
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Message: 2
Date: Fri, 5 Jan 2024 23:19:59 +0200
From: Krassimir Markov <itheaiss at gmail.com>
To: fis at listas.unizar.es
Subject: Re: [Fis] Fis Digest, Vol 108, Issue 4
Message-ID:
<CAKEQgkxjFRQ6=gw15cJ6DNN-BcU0soEHvi-42hxiJPC45wk1GA at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Dear Prof. Kauffman and FIS Colleagues,
Warm Wishes for health and happiness in (and not only!) New Year !

Dear Prof. Kauffman,
Thank you very much for the interesting article and the ideas presented in
it.
I fully agree that set theory cannot be used for the purposes you state in
the article.
I agree with all your conclusions and opinions ...

But ...

Only at the level of set theory!

Modern mathematics has already proposed theoretical foundations by which to
model the complexity and unpredictability you speak of.

This is the Category Theory.

I do not have the opportunity to go into details here, but I will try to
explain the difference in a sentence or two.

In set theory, we work with elements and functions from one element to
another element.

In category theory, we work with structures and morphisms (mappings) of
structures into structures, and a special place is occupied by functors,
which are mappings of categories into categories.

I have been using Category Theory for modeling information phenomena for
many years and I am satisfied with the results.
Maybe someday we'll have a chance to talk in more detail.

With respect,
Krassimir

<https://urldefense.com/v3/__https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail__;!!D9dNQwwGXtA!Tk1UTgfW-nil9p-FpOx_8br863v36zD2frnSNU3nLkVuQ3b4QFYWywpUTtXGpgeiMPnVfFr0lweo0pSd3bs$ >
????
??????https://urldefense.com/v3/__http://www.avast.com__;!!D9dNQwwGXtA!Tk1UTgfW-nil9p-FpOx_8br863v36zD2frnSNU3nLkVuQ3b4QFYWywpUTtXGpgeiMPnVfFr0lweoxbM1Dfw$
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<#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

?? ??, 5.01.2024??. ? 13:59 <fis-request at listas.unizar.es> ??????:

Send Fis mailing list submissions to
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When replying, please edit your Subject line so it is more specific
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Today's Topics:

  1. Re: New Year Lecture - Stuart Kauffman (joe.brenner at bluewin.ch)
  2. Re: New Year Lecture - Stuart Kauffman (Pedro C. Mariju?n)

---------- Forwarded message ----------
From: "joe.brenner at bluewin.ch" <joe.brenner at bluewin.ch>
To: Skauffman <stukaufman at gmail.com>
Cc: pedroc.marijuan at gmail.com, fis at listas.unizar.es, plamen at simeio.org
Bcc:
Date: Fri, 5 Jan 2024 12:41:33 +0100 (CET)
Subject: Re: [Fis] New Year Lecture - Stuart Kauffman

Dear Stuart (if I may), Pedro and Plamen,

Happy New Year and best wishes for 2024 to All! As Pedro and Plamen may
recall, I have been ?at home in Stuart?s Universe? for some time. His
article, however, brings clearly into focus the issues to be resolved in
science and philosophy, including logic.

As you may not recall, however, I have been arguing for all this time, *contra
vents et mar?es*, in favor of some very specific additions. Among other
things these, have their ground in the very much neglected Buddhist
insights into the relational structure of reality (co-dependence or
co-instantiation) in the work of both Nagarjuna (2nd - 3rd Centuries
C.E.) and Yamauchi Tokuryu (19th -20th Centuries).

To be as brief as possible here, Stuart?s article refers to or implies
needed changes in the following areas:

-        Free will as necessary for individual and collective
responsibility;

-        Total separability in the part-whole relation:

-        Inapplicability of standard set theory;

-        Dynamic implications of the Axiom of Choice; (I have sent my
philosophical-logical interpretation of this Axiom to some 45 people
without  an answer, not that I was wrong or ignorant ? nothing.)

-        Non-algorithmic, but regular features of the real world;

I look forward very much to a dialogue on these and other issues,

Cheers, as far as possible,

Joseph

----Message d'origine----
De : stukauffman at gmail.com
Date : 04/01/2024 - 23:54 (E)
? : fis at listas.unizar.es
Cc : pedroc.marijuan at gmail.com, plamen at simeio.org
Objet : [Fis] New Year Lecture - Stuart Kauffman /Pedro and Plamen is this
what you need? stu

Hello to All,

I am truly grateful to have this opportunity to discuss with you the
recent Stuart Kauffman and Andrea Roli paper, ?A Third Transition In
Science?? J. Roy. Soc. Interface, 4/ 14 2023.  I attach a link below. It?s
eventual publication in a fine journal after almost two years has its own
wry history.

Andrea and I think we are correct, but we may be wrong. More, I only
slightly begin to understand what our results, if correct, mean.

I had thought that the First Transition in science was Newton?s invention
of Classical Physics in 1689 A.D. And I thought the Second Transition was
the reluctant discovery of quantum mechanics between 1900 and 1927 A.D.

I begin to suspect I was wrong.  The First Transition in science was in
1299A.D. when the first mechanical clock was invented and installed at the
Wallingford Abby. It was installed because the monks were often late for
prayers. Within less than a century, Europe was dotted by chuch towers with
ever - more impressive mechanical clocks. Modern people in 1379 A.D. must
have begun to wonder if the World itself was some amazing clockwork
machine. Then Copernicus, 1543 A.D., then Kepler, Galileo and Newton.

This, then, was the Second Transition in Science. Yes, yes, yes!  The
World *is* a vast clockwork machine. No room for God?s miracles ? the
Deistic God of the Enlightenment. No room for mind ? Descartes lost his Res
cogitans to Newton?s Res extensa. No Free Will.

With Planck, Heisenberg, and Schrodinger cam a loss of determinism, but
still within the Newtonian Paradigm. And no mind and no responsible Free
Will.

If Andrea and I are correct, this Third Transition demonstrates for the
first time since 1299AD, 725 years later, that the evolving biosphere is
not a clockwork machines. Evolving life is not a machine at all.

Are the two of us correct? If so, what does this Third Transition
portend?  These  issues now lies before us.

Merci a tous,

Stu Kauffman

A Third Transition in Science? Link

https://urldefense.com/v3/__https://royalsocietypublishing.org/doi/10.1098/rsfs.2022.0063__;!!D9dNQwwGXtA!Tk1UTgfW-nil9p-FpOx_8br863v36zD2frnSNU3nLkVuQ3b4QFYWywpUTtXGpgeiMPnVfFr0lweoI7pfKPU$
<https://urldefense.com/v3/__https://royalsocietypublishing.org/doi/10.1098/rsfs.2022.0063__;!!D9dNQwwGXtA!Qqk-MU8YHDOqCRFRhl7TeX1dkVGTkGVguvuvh9b0bDsQA5fo9VckJgLmoyonQDdvxMbEBRHMUpOBTww1u06J-5k$>

---------- Forwarded message ----------
From: "Pedro C. Mariju?n" <pedroc.marijuan at gmail.com>
To: Skauffman <stukaufman at gmail.com>, fis at listas.unizar.es
Cc:
Bcc:
Date: Fri, 5 Jan 2024 12:59:18 +0100
Subject: Re: [Fis] New Year Lecture - Stuart Kauffman
Dear Stuart and FIS colleagues,

We are honored that you impart the FIS New Year Lecture this time. In this
list, quite a few members share the impression that we are involved in a
historical transition in science. Maybe, as you and Andrea Roli state, it
could be the Third Great Transition. That it revolves around putting  into
question the predominance of physicalist views was coincidentally discussed
in a previous discussion session, when two pioneers of AI research (Yixin
Zhong from China and Eric Werner from Oxford) were arguing for a paradigm
change away for physicalism. Now you are providing strong arguments from
the biological self-construction and evolutionary points of view. An
important point is the argument on Kantian wholes, from the closure of
auto-catalitic sets. It could also be considered as the organizational
reliance on "cycles". In biological systems there is a towering presence of
cycles: from elementary reaction cycles, to enzyme work-cycles, to regional
reaction cycles, gene expression cycles (your Boolean networks!!), to
genetic macro-cycles... to the cell's entire life cycle. And an even larger
story could be told about cycles in complex organisms...

To put the argument in a nutshell: bye to physicalism (as a fundamental
meta-scientific vision). Yes, but what would substitute for it?
I dare say "informationalism". You mention the biosphere and the  global
economy, and even our cultures. Aren't all them based on the circulation of
"information flows"  (in vastly different forms, of course)??
Let us think, for instance, on the enormous disarray created by the new
social networks in our societies... we do not much understand the
psychological changes derived for the intertwining of natural vs artifical
info flows in our societies.

I am just reading Joseph's just arrived comments, philosophically and
formally oriented. Fine.  I would ad that we are lacking a vast
informational view that can help us to understand that strange world put
into action 3,000 million years ago, full of emergent realms. So, filling
in the gap that physicalim is unable to fill in consistently.

Best regards to all,
--Pedro

*PS. If anyone has doubts about the messages effectively  distributed in
the list, go please to the instantaneous archive:
http://listas.unizar.es/pipermail/fis/
<http://listas.unizar.es/pipermail/fis/>*

-------------------------------------------------------------------------------------------
El 04/01/2024 a las 23:54, Stuart Kauffman escribi?: