[Fis] Fis Digest, Vol 108, Issue 4

Sat Jan 6 14:55:35 CET 2024

Hi. Rosen’s book, Life Itself, is superb. But/and does Rosen solve the problem of the emergence of non-deducible new affordances? In short, is there a sense in which the evolution of the biosphere is mathematizable? I may have stumbled upon one approach linking the TAP theory and the emergence of autocatalytic sets. Somehow this seems to be a theory of sufficient, but not necessary conditions. This cannot be used in the Aristotelian framework of the law of the Excluded Middle and Non Contradiction. But it can be used if “possibilities” are allowed, eg  “Possible uses of X”.

Stu

> On Jan 6, 2024, at 6:14 AM, Dr. Plamen L. Simeonov <plamen.l.simeonov at gmail.com> wrote:
> 
> Exactly. For conventional everyday tasks from math and engineering, physics too, standard CT is great.
> I have not been a professor in anything, but I dealt with these issues long enough, so I know the advantages and the limits. 
> For biology, CT has its limits despite the functor operators and the higher level abstractions of mapping functions and sets.
> Andree Ehresmann was well aware of this when she developed her MES (Memory Evolutive Systems) extension of CT.
> I worked with her for many years towards extending her formalism with higher-order logic and computation.
> It is not as easy as I thought. Otherwise others would have developed this combination already. 
> I did not obtain funding to elaborate further on these ideas. So, even this step is sleeping for the moment.
> Andree has formulated her approach very well and proved a number of theorems and lemmas.
> Unfortunately, these ideas remain unused beyond visualization. 
> Another  author and colab of Robert Rosen, Aloisus Louie, developed a different approach to handle impredicability. 
> However, his ideas which continue Rosen's approach to CT with new operators, also remain on paper for the moment.
> Very nice books continuing Rosen's volumes on "Life Itself", III and IV, by Aloisius. 
> All this needs education, elaboration and funding to deliver better results.
> The above works are not the perfect solution, but a step towards reaching it, I believe.
> 
> Best,
> 
> Plamen
> 
> 
> On Sat, Jan 6, 2024 at 8:54 AM Louis Kauffman <loukau at gmail.com <mailto:loukau at gmail.com>> wrote:
>> Dear Krassimir,
>> This is the other Prof Kauffman. I use both category theory and set theory.
>> The limitations are similar. We can work with patterns and we can deduce some things, but we are not prepared to predict
>> novelty in many many situations.
>> Best,
>> Lou Kauffman
>> 
>>> On Jan 5, 2024, at 1:19 PM, Krassimir Markov <itheaiss at gmail.com <mailto:itheaiss at gmail.com>> wrote:
>>> 
>>> 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$>	Няма вирусиhttps://urldefense.com/v3/__http://www.avast.com__;!!D9dNQwwGXtA!RKH7zd3szsvFUgmliDeXUjBADu9azf13wRBsWQgiEwP_ZhQ7wyxF3VOwTqP476WBUAJZFm5DzjI22WmcjNM-SWM$  <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$>
>>> На пт, 5.01.2024 г. в 13:59 <fis-request at listas.unizar.es <mailto:fis-request at listas.unizar.es>> написа:
>>>> Send Fis mailing list submissions to
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>>>> When replying, please edit your Subject line so it is more specific
>>>> than "Re: Contents of Fis digest..."
>>>> Today's Topics:
>>>> 
>>>>    1. Re: New Year Lecture - Stuart Kauffman (joe.brenner at bluewin.ch <mailto:joe.brenner at bluewin.ch>)
>>>>    2. Re: New Year Lecture - Stuart Kauffman (Pedro C. Mariju?n)
>>>> 
>>>> 
>>>> 
>>>> ---------- Forwarded message ----------
>>>> From: "joe.brenner at bluewin.ch <mailto:joe.brenner at bluewin.ch>" <joe.brenner at bluewin.ch <mailto:joe.brenner at bluewin.ch>>
>>>> To: Skauffman <stukaufman at gmail.com <mailto:stukaufman at gmail.com>>
>>>> Cc: pedroc.marijuan at gmail.com <mailto:pedroc.marijuan at gmail.com>, fis at listas.unizar.es <mailto:fis at listas.unizar.es>, plamen at simeio.org <mailto: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 marées, 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 <mailto:stukauffman at gmail.com>
>>>> Date : 04/01/2024 - 23:54 (E)
>>>> À : fis at listas.unizar.es <mailto:fis at listas.unizar.es>
>>>> Cc : pedroc.marijuan at gmail.com <mailto:pedroc.marijuan at gmail.com>, plamen at simeio.org <mailto: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!RKH7zd3szsvFUgmliDeXUjBADu9azf13wRBsWQgiEwP_ZhQ7wyxF3VOwTqP476WBUAJZFm5DzjI22WmcR2mREdI$  <https://urldefense.com/v3/__https://royalsocietypublishing.org/doi/10.1098/rsfs.2022.0063__;!!D9dNQwwGXtA!Qqk-MU8YHDOqCRFRhl7TeX1dkVGTkGVguvuvh9b0bDsQA5fo9VckJgLmoyonQDdvxMbEBRHMUpOBTww1u06J-5k$> 
>>>>>  
>>>>>  
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> ---------- Forwarded message ----------
>>>> From: "Pedro C. Marijuán" <pedroc.marijuan at gmail.com <mailto:pedroc.marijuan at gmail.com>>
>>>> To: Skauffman <stukaufman at gmail.com <mailto:stukaufman at gmail.com>>, fis at listas.unizar.es <mailto: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/
>>>> 
>>>> -------------------------------------------------------------------------------------------
>>>> El 04/01/2024 a las 23:54, Stuart Kauffman escribió:
>>>> 
>>>> 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!RKH7zd3szsvFUgmliDeXUjBADu9azf13wRBsWQgiEwP_ZhQ7wyxF3VOwTqP476WBUAJZFm5DzjI22WmcR2mREdI$  <https://urldefense.com/v3/__https://royalsocietypublishing.org/doi/10.1098/rsfs.2022.0063__;!!D9dNQwwGXtA!RH-1N1FEJfqU41WdGgs7y8jJfe5UgMaHIJlh56CZUw76fWIEwZkUE9gIll06GR3L150IpC24ewV5iF7LveZK0HwbrDZ8$>
>>>> 
>>>> 
>>>> 
>>>> 
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