[Fis] CODE DISCUSSION. A Mini-Synthesis

Sun Oct 3 09:31:18 CEST 2021

he error rate during DNA replication is as low as 10−9 to 10−11 errors 
per base pair.
Source: 
https://www.google.com/search?client=firefox-b-d&q=error+dna+replication

Yet, this is the source of mutation and drives evolution.
Best, Loet

<https://www.springer.com/gp/book/9783030599508>Loet Leydesdorff

________________________________

Professor emeritus, University of Amsterdam
Amsterdam School of Communication Research (ASCoR)

loet en leydesdorff.net <mailto:loet en leydesdorff.net>; 
http://www.leydesdorff.net/

"The Evolutionary Dynamics of Discursive Knowledge" at

https://link.springer.com/book/10.1007%2F978-3-030-59951-5 (Open Access)
https://www.springer.com/gp/book/9783030599508 (Hardcopy)

http://scholar.google.com/citations?user=ych9gNYAAAAJ&hl=en

ORCID: http://orcid.org/0000-0002-7835-3098;

------ Original Message ------
From: "Louis Kauffman" <loukau en gmail.com>
To: joe.brenner en bluewin.ch
Cc: robert.marty98 en gmail.com; ehres en u-picardie.fr; ricottam en etrovub.be; 
jerry_lr_chandler en icloud.com; fis en listas.unizar.es; 
pcmarijuan.iacs en aragon.es
Sent: 10/3/2021 8:02:16 AM
Subject: Re: [Fis] CODE DISCUSSION. A Mini-Synthesis

>Indeed recursive change is essentially always on a spiral where there 
>is change both in what acts and what is acted upon.
>Overly simple models may give the impression that the results are just 
>cycles or that the processes themselves are not subject to change.
>There has been a lag between what are good actual depictions of change 
>and recursion and the oversimplified models.
>For example, in economics it has long been assumed that the markets can 
>be described objectively in terms of actors who behave entirely 
>rationally an all have the same information.
>This is nonsense but makes some calculations easier for the economists. 
>In practice, the very theories and ideas of the participants in the 
>markets are part of the action of that market and so
>contribute to its change and evolution. The same remarks apply to 
>biological evolution.
>
>
>>On Oct 2, 2021, at 10:39 AM, joe.brenner en bluewin.ch wrote:
>>
>>Dear All,
>>
>>This note addresses several of the issues raised in your recent notes 
>>at once. It is a non-mathematical attempt to describe a single 
>>recursive change rather than to model a complete process. It requires 
>>a different picture of recursion in that a spiral and not circular 
>>path is followed. Interdependence is present but it is between the 
>>different parts of the spiral. The term cycle is acceptable only if it 
>>understood that, in reality, no perfect loop, cycle or circle is 
>>possible.
>>
>>  I am looking, then, at a single realization, exactly, something that 
>>was potential becoming realized, actual, but with the capacity also to 
>>go from actual to potential. A “bird’s-eye view” shows a certain 
>>dynamic quasi-symmetry, or quasi-periodicity, as the parts of the 
>>system repeat, but not absolutely.
>>
>>The fact that, as we all know, biological replication is correct most 
>>of the time does not invalidate my thesis. First of all, it is subject 
>>to error, and more importantly, at our macroscopic level, errors are 
>>as much the rule as the exception.
>>
>>I would very much welcome your comments, especially, Plamen, a 
>>reference to HoTT that might be relevant.
>>
>>Thank you and best wishes,
>>
>>Joseph
>>
>>>----Message d'origine----
>>>De : pcmarijuan.iacs en aragon.es
>>>Date : 28/09/2021 - 19:34 (E)
>>>À : fis en listas.unizar.es
>>>Cc : ricottam en etrovub.be, ehres en u-picardie.fr, 
>>>robert.marty98 en gmail.com, jerry_lr_chandler en icloud.com, 
>>>joe.brenner en bluewin.ch
>>>Objet : Re: [Fis] CODE DISCUSSION. A Slice of Life. OM
>>>
>>>Dear All,
>>>
>>>As the discussion is getting more complex, I can only give a couple 
>>>of brief responses to the issues raised by Lou and Jerry (I agree 
>>>with Joseph's comments and appreciate them). Responding first to Lou, 
>>>indeed distinctions are a fundamental issue, also in the 
>>>bioinformation world. Actually I have been considering --these last 
>>>two decades or so-- that for living agents information appears as 
>>>"distinction on the adjacent". Expressing distinctions as a result of 
>>>recursion is new for me: I was following Karl's partitions, and was 
>>>much interested in his notion of a limited number of multidimensional 
>>>partitions depending on set size. This alternative (or complementary) 
>>>recursive conceptualization can also be very interesting regarding 
>>>two biological approaches I was recently intrigued with: the work on 
>>>the emergence of syntax/meaning in the RNA sequences world by 
>>>Witzany's, and in the algorithmic challenge of vertebrate immune 
>>>systems having to distinguish between self and non-self--in a true 
>>>Godelian puzzle (ongoing work by Sheri Markose). Probably the latter 
>>>would accept presenting in our list. If there are expressions of 
>>>interest I could tell her.
>>>
>>>And about Jerry's eleven paragraphs, I am afraid that such general 
>>>questions may open excessively the discussion. Somehow, I was 
>>>reminded of some past Century philosophers: Ortega y Gasset, 
>>>Merleau-Ponty, and A.N. Whitehead. I am more familiar with the former 
>>>--his "perspectivism". My personal translation is the "doctrine of 
>>>limitation". Given the iron-limits of our cognition, every scientific 
>>>approach becomes limited, specialized, and forced to 
>>>multidisciplinary dialog. This rubbing among disciplines is a potent 
>>>recombination engine that creates and destroys models, paradigms, and 
>>>even entire fields. So, disciplines of natural science are not only 
>>>formal/experimental constructs, but also social-historical bodies 
>>>with singular idiosyncratic trajectories. Just looking at this very 
>>>list we can watch what has happened with information discussions in 
>>>last decades...   Well, this is an indirect response. to Jerry's well 
>>>crafted points and I would need more time to make a decent criticism.
>>>
>>>Finally, going back to codes, maybe they are the inner "constraints" 
>>>to vehiculate the external information flows, versus the internal 
>>>ones, so that the former are conveniently matched, processed, and 
>>>solved. Talking in terms of "intelligence", both the natural 
>>>intelligence  of biological systems and the artificial intelligence 
>>>of computer systems cannot handle their respective external 
>>>information flows except by relying on a multitude of multi-level 
>>>channeling codes. (??)
>>>
>>>Best regards,
>>>--Pedro
>>>
>>>in the way El 27/09/2021 a las 19:34, Jerry LR Chandler escribió:
>>>>Pedro, List:
>>>>>
>>>>>>So, there are formal, logical, philosophical, semiotic arguments 
>>>>>>to make about codes--OK, but if they do not consider this real 
>>>>>>world aspect of heterogeneity of processing architectures am 
>>>>>>afraid they will be of limited usefulness to approach the reliance 
>>>>>>of computers and living beings on codes.
>>>>>>
>>>>>>Best regards,
>>>>>>--Pedro
>>>>>
>>>>
>>>>This sentence, in my mathematical judgement, gets to the essence of 
>>>>communication of artificial actions within humanity as a whole by 
>>>>using artificial symbol systems to create meaning that is informed 
>>>>by the intentions of the communicator with respect the capacities of 
>>>>potential receivers.
>>>>
>>>>In short, mathematics itself is merely one of the multitude of 
>>>>synthetic symbol systems that have emerged as a critical component 
>>>>of human cultures.
>>>>
>>>>The role of mathematics in human cultures started at least 4 
>>>>millennia BC and has continued to grow.
>>>>The parallel role of a second synthetic symbol representing sounds, 
>>>>alphabets and other alphabet-like encoding systems, lead to methods 
>>>>to record human history, human emotions, humans desires for the 
>>>>future (planning and philosophies of actions, such as anticipation.)
>>>>
>>>>Pedro, your brilliant sentence captures the very essence, in my 
>>>>opinion, of the central issue that is overlooked in most of the FIS 
>>>>exchanges because it identifies the common source of the diverse 
>>>>assertions that separate the meanings of the assertions to different 
>>>>recipients.
>>>>
>>>>The “lingua franca” of this List Serve is a theory of mathematically 
>>>>grounded “messages”, augmented with symbols for sounds.  One might 
>>>>even conjecture that if we all had a homogeneous understanding of 
>>>>how these iconic forms are understood, such as mathematical category 
>>>>theory, we would have complete foundation for the foundations of the 
>>>>information sciences!
>>>>
>>>>As you so adroitly point out, Pedro, the heterogenous membership 
>>>>understand that symbol systems other than mathematics and alphabets 
>>>>are used in the natural sciences and natural philosophy to 
>>>>communicate information between participants of this list. [" 
>>>>formal, logical, philosophical, semiotic arguments to make about 
>>>>code”]
>>>>
>>>>Why?
>>>>Why are heterogenous symbol systems used in scientific 
>>>>communications about nature?
>>>>Historically, how have the multitude of symbol systems emerged from 
>>>>alphabets and mathematics?
>>>>How are these emergent properties of symbol systems used in the 
>>>>pragmatic work of the natural scientists?
>>>>
>>>>The philosophy of science of physics embraces the mathematical 
>>>>symbol system and asserts that all logical natural truths can be 
>>>>expressed in this language (Galileo). This philosophy has been 
>>>>embraced by many FIS contributors and grounds linguistically the 
>>>>forms of the encoded messages of both agreement and disagreement.  
>>>>The focus of the disagreements tend to be limited to such 
>>>>mathematical/physical terms, as entropy, excluded middle, number 
>>>>sequences, and meanings of formal logical terminology.
>>>>
>>>>The philosophy of the natural sciences rests on the pragmaticisms. 
>>>>Natural scientists assign meaning to semantic terms in order to 
>>>>identity the objects of nature understudy. To this end, natural 
>>>>scientists (including physicians) assign direct one to one 
>>>>correspondence relationships between semantic terms and sensory 
>>>>experiences (in addition to sensory experiences of sight and sound 
>>>>used for mathematical symbolic communications), other sensory 
>>>>experiences, such as smell, taste, touch, temperature, pressure, and 
>>>>intuitive feelings (for example, the touch of a loved one) are 
>>>>routinely used.
>>>>
>>>>In short, the ontology and epistemology of the symbolic forms of 
>>>>human symbolic codes extend far beyond narrow boundaries of the 
>>>>meanings of theological terms associated with the logics of 
>>>>mathematics and physics.
>>>>
>>>>In closing, Pedro I would pose a singular interrogative.
>>>>Do these eleven paragraphs, taken as a whole, capture the essence of 
>>>>your intended meaning of the sentence quoted at the beginning of 
>>>>this message? My premise would be that in the conceptual 
>>>>architecture of my pragmatic use of codes and symbols in these brief 
>>>>paragraphs, I probably missed certain critical features of your 
>>>>intended meaning.  Can you (or other readers) flag the multiplicity 
>>>>of defects?
>>>>
>>>>If so, you can move the conversation forward and expand on these 
>>>>concepts from your particular arithmetical, heterogenic, 
>>>>psychological, referential philosophy of communication (and also 
>>>>information) by either augmenting or rejecting parts of the 
>>>>architectures this semantic encoding of meanings of symbolic codes.
>>>>
>>>>Cheers
>>>>
>>>>Jerry
>>>>
>>>>Research Professor
>>>>Krasnow Institute for Advanced Study
>>>>
>>>>(BTW, the philosophical roots of the modern notions of the concepts 
>>>>of evolutionary emergences of symbolic differences that encode 
>>>>differences can be associated with the terms introduced by 
>>>>philosopher, C S Mills, heteropathy ca 1843)
>>>>
>>>>
>>>>
>>>
>>>
>>>--
>>>-------------------------------------------------
>>>Pedro C. Marijuán
>>>Grupo de Bioinformación / Bioinformation Group
>>>
>>>pcmarijuan.iacs en aragon.eshttp://sites.google.com/site/pedrocmarijuan/
>>>-------------------------------------------------
>>>
>>><https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=emailclient> 
>>>Libre de virus. www.avast.com 
>>><https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=emailclient>
>>><https://rich-v01.bluewin.ch/#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>>>
>>
>>
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