[Fis] FW: New Year Lecture. Logic of Recursive Transductions

[Joseph Brenner]

Dear Mark, Dear FISers



Mark's term "logic of recursive transductions" cuts to the heart of the
current debate. If one objects that this is 'just' physics or biology, my
answer is that it is both logic and physics and biology, and that many
problems have come simply from our separation of them, and characterizing
them without including their dynamics as processes.



Energy is involved when I "go back over something", as I have with John
Torday's stimulating approach, in order to see what is in it that I must
take into account (and vice versa I hope).



At this point, I feel I need a 'refresher' on Loet Leydesdorff's important
distinction, with reference to information, between recursion and incursion.
Loet?



When one thinks outside the box, as Bob U. will have us do, the air may seem
a little thin, for a while. However, one can soon get acclimatized, with
some good will.



Cheers,



Joseph



-Original Message-
From: Fis [mailto:fis-boun...@listas.unizar.es] On Behalf Of Mark Johnson
Sent: mercredi, 10 janvier 2018 11:08
To: JOHN TORDAY
Cc: fis
Subject: Re: [Fis] New Year Lecture



Dear John,



Thank you very much for this - a great way to start the new year!



I'd like to ask about "communication" - it's a word which is

understood in many different ways, and in the context of cells, is

hard to imagine.



When you suggest that "the unicellular state delegates its progeny to

interact with the environment as agents, collecting data to inform the

recapitulating unicell of ecological changes that are occurring.

Through the acquisition and filtering of epigenetic marks via meiosis,

fertilization, and embryogenesis, even on into adulthood, where the

endocrine system dictates the length and depth of the stages of the

life cycle, now known to be under epigenetic control, the unicell

remains in effective synchrony with environmental changes." It seems

that this is not communication of 'signs' in the Peircean sense

supported by the biosemioticians (Hoffmeyer). But is it instead a

recursive set of transductions, much in the spirit of Bateson's

insight that:



"Formerly we thought of a hierarchy of taxa-individual, family line,

subspecies, species, etc.-as units of survival. We now see a different

hierarchy of units-gene-in-organism, organism-in environment,

ecosystem, etc. Ecology, in the widest sense, turns out to be the

study of the interaction and survival of ideas and programs (i.e.,

differences, complexes of differences, etc.) in circuits." (from his

paper "Pathologies of Epistemology" in Steps to an Ecology of Mind)



Recursive transduction like this is a common theme in cybernetics -

it's in Ashby's "Design for a Brain", Pask's conversation theory, and

in Beer's Viable System Model, where "horizon scanning" (an

anticipatory sub-system gathering data from the environment) is an

important part of the metasystem which maintains viability of the

organism (It's worth noting that Maturana and Varela's autopoietic

theory overlooks this).



"Communication" would then be much more like "conversation".

etymologically, "con-versare". "to turn together". dancing! Does this

fit?



A further point is to then ask whether a logic of evolutionary biology

is a logic of recursive transductions over history. The critical point

is what Joseph Brenner argued before Christmas in objecting to Peirce:

we struggle to express the specificity and basis for change in our

logic. Do we need a different kind of logic?



Best wishes and Happy new year,



Mark



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Re: [Fis] New Year Lecture

[Francesco Rizzo]

Cari tutti,
i messaggi di Pedro e Sungchul sono decisivi e riportano il dibattito
nell'alveo della scienza che si proietta nel futuro. Ho elaborato una
Nuova economia in cui la biologia dell'informazione o l'informazione della
biologia è fondamentale per l'esistenza e la conoscenza umane in-centrate
sulla triade semiologica o semiotica della significazione, informazione,
comunicazione. Per quanto gli studiosi abbiano fatto di tutto per separare
e contrapporre campi diversi  del sapere, la legge dell'informazione li
unisce e univoca tutti.
Grazie e auguri.
Francesco. .

2018-01-11 23:25 GMT+01:00 Sungchul Ji :

> Hi Pedro, John and other FISers,
>
> (*1*)  Thank you John for the succinct summary of your cell-based
> evolutionary theory.  As I indicated offline, I too proposed a cell-based
> evolutionary theory in 2012 [1] and compared it with the gene-centered
> evolutionary theory of Zeldovich and Shankhnovich (see Table 14.10 in [1]).
>
>
> (*2*) I agree with Pedro that
>
> ". . . ..  essential informational ideas are missing too, and this absence
> of the informational perspective in the ongoing evo discussions is not a
> good thing. . . . "
>
>
> I often wonder if this situation has arisen in biology because biologists
> blindly apply to their problems the information theory as introduced by
> Shannon almost 7 decades ago in the context of communication engineering
> without due attention paid to the fact that  the Shannon-type information
> theory is not designed to handle the "meaning" or semantics of messages but
> only the AMOUNT of the information they carry.  If we agree that there are
> three essential aspects to information, i.e., *amount* (e.g., my USB
> stores 3 Megabytes of information), *meaning *(e.g., the nucleotide
> triplet, ACG, encodes threonine),  and *value* (e.g., the same message,
> 'Yes', can have different monetary values, depending on the context), we
> can readily see that the kind of information theory most useful for
> biologists is not (only) the Shannon-type but (also) whatever type that can
> handle the semantics and pragmatics of information.
>
>
> (*3*) One way to avoid the potential confusions in applying information
> theory to biology may be to recognize two distinct types of information
> which, for the lack of better terms, may be referred to as the "meaningless
> information" or I(-)  and "meaningful information" or I(+), and what Pedro
> regarded as the missing "essential informational ideas" above may be
> identified with I(+) (?)
>
>
> (*4*)  There may be many forms of the I(+) theories to emerge in the
> field of "new informatics" in the coming decades.  Based on my research
> results obtained over the past two decades, I am emboldened to suggest that
> "linguistics" can be viewed as an example of the I(+) theory. The term
> "linguistics" was once fashionable in Western philosophy and humanities (
> https://en.wikipedia.org/wiki/Linguistic_turn) in the form of "linguistic
> turn" but apparently became outmoded (for some unknown reason to me, a
> non-philosopher), but I am one of the many (including Chargaff who
> discovered his two parity rules of DNA sequences; https://en.
> wikipedia.org/wiki/Chargaff%27s_rules) who believes that linguistics
> provide a valuable tool for elucidating the workings of living structures
> and processes [2, 3].  In fact we may refer to the emerging trend in the
> early 21st century that explore the basic relations between linguistics and
> biology as the "Linguistic Return", in analogy to the "Linguistic Turn"
> referring to the  "major development in Western philosophy during the
> early 20th century, the most important characteristic of which is the
> focusing of philosophy and the other humanities primarily on the
> relationship between philosophy and language." ((https://en.wikipedia.org/
> wiki/Linguistic_turn)
>
> (*5*)  So, linguistics played an important role in philosophy in the
> early 20th century and may play a similarly important role in biology in
> the coming decades of the 21st century.  What about physics?  Does physics
> need linguistics to solve their basic problems ?   If not
> linguistics, perhaps semiotics, the study of signs?  The latter possibility
> was suggested by Brian Josephson in his lecture
>
> "*Biological Organization as the True Foundation of Reality"*
>
>
>  given at the 66th Lindau Nobel Laureate Meeting held in Lindau, Germany,
> stating that
>
>
> “*Semiotics will eventually overtake quantum mechanics in the same way **as
> quantum mechanics overtook classical physics.”*
>
> I referred to this statement as the "Josephson conjecture" in [3].  When I
> visited him in Cambridge last summer to discuss this statement, he did not
> object to his name being used in this manner.
>
>
> (*6*)  If the concepts of the "Linguistic Return" in biology and
> the Josephson conjecture  in physics prove to be correct in the coming
> decades and centuries, it may be possible to 

Re: [Fis] New Year Lecture

[Sungchul Ji]

Hi Pedro, John and other FISers,


(1)  Thank you John for the succinct summary of your cell-based evolutionary 
theory.  As I indicated offline, I too proposed a cell-based evolutionary 
theory in 2012 [1] and compared it with the gene-centered evolutionary theory 
of Zeldovich and Shankhnovich (see Table 14.10 in [1]).


(2) I agree with Pedro that

". . . ..  essential informational ideas are missing too, and this absence of 
the informational perspective in the ongoing evo discussions is not a good 
thing. . . . "


I often wonder if this situation has arisen in biology because biologists 
blindly apply to their problems the information theory as introduced by Shannon 
almost 7 decades ago in the context of communication engineering without due 
attention paid to the fact that  the Shannon-type information theory is not 
designed to handle the "meaning" or semantics of messages but only the AMOUNT 
of the information they carry.  If we agree that there are three essential 
aspects to information, i.e., amount (e.g., my USB stores 3 Megabytes of 
information), meaning (e.g., the nucleotide triplet, ACG, encodes threonine),  
and value (e.g., the same message, 'Yes', can have different monetary values, 
depending on the context), we can readily see that the kind of information 
theory most useful for biologists is not (only) the Shannon-type but (also) 
whatever type that can handle the semantics and pragmatics of information.


(3) One way to avoid the potential confusions in applying information theory to 
biology may be to recognize two distinct types of information which, for the 
lack of better terms, may be referred to as the "meaningless information" or 
I(-)  and "meaningful information" or I(+), and what Pedro regarded as the 
missing "essential informational ideas" above may be identified with I(+) (?)


(4)  There may be many forms of the I(+) theories to emerge in the field of 
"new informatics" in the coming decades.  Based on my research results obtained 
over the past two decades, I am emboldened to suggest that "linguistics" can be 
viewed as an example of the I(+) theory. The term "linguistics" was once 
fashionable in Western philosophy and humanities 
(https://en.wikipedia.org/wiki/Linguistic_turn) in the form of "linguistic 
turn" but apparently became outmoded (for some unknown reason to me, a 
non-philosopher), but I am one of the many (including Chargaff who discovered 
his two parity rules of DNA sequences; 
https://en.wikipedia.org/wiki/Chargaff%27s_rules) who believes that linguistics 
provide a valuable tool for elucidating the workings of living structures and 
processes [2, 3].  In fact we may refer to the emerging trend in the early 21st 
century that explore the basic relations between linguistics and biology as the 
"Linguistic Return", in analogy to the "Linguistic Turn" referring to the  
"major development in Western philosophy during the early 20th century, the 
most important characteristic of which is the focusing of philosophy and the 
other humanities primarily on the relationship between philosophy and 
language." ((https://en.wikipedia.org/wiki/Linguistic_turn)

(5)  So, linguistics played an important role in philosophy in the early 20th 
century and may play a similarly important role in biology in the coming 
decades of the 21st century.  What about physics?  Does physics need 
linguistics to solve their basic problems ?   If not linguistics, perhaps 
semiotics, the study of signs?  The latter possibility was suggested by Brian 
Josephson in his lecture

"Biological Organization as the True Foundation of Reality"


 given at the 66th Lindau Nobel Laureate Meeting held in Lindau, Germany, 
stating that

“Semiotics will eventually overtake quantum mechanics in the same way as 
quantum mechanics overtook classical physics.”

I referred to this statement as the "Josephson conjecture" in [3].  When I 
visited him in Cambridge last summer to discuss this statement, he did not 
object to his name being used in this manner.


(6)  If the concepts of the "Linguistic Return" in biology and the Josephson 
conjecture  in physics prove to be correct in the coming decades and centuries, 
it may be possible to conclude that philosophy, biology, and physics are 
finally united/integrated in the framework of semiotics viewed as a generalized 
linguistics.


All the best.


Sung








  [1] Ji, S. (2012).  The Zeldovich-Shakhnovich and MTLC Models of 
Evolution: From Sequences to 
Species.  In: Molecular Theory of the Living Cell: concepts, Molecular 
Mechanisms, and Biomedical Applications.  Sprinter, New York.  Pp. 509-519. PDF 
at http://www.conformon.net/model-of-evolution/
   [2] Ji, S. (2012).  The Isomorphism between Cell and Human Languages: The 
Cell Language Theory. In: 
Molecular Theory of the Living Cell: Concepts, Molecular Mechanisms, and 
Biomedical Applications.  

[Fis] Code Biology

[Pedro C. Marijuan]

 Dear FISers, this Conference in Code Biology may be of interest to 
some parties. It will be in beautiful Granada (Spain), next June. 
Although the deadline for abstract submission is too close, there would 
be a longer term if requested to the organizers.


I hpe to see you there. Best--Pedro

--



*Fifth International Conference in Code Biology*





/Call for Papers /

The /International Conferences in Code Biology/ aim at bringing together 
scholars and researchers who are interested in the study of all codes of 
life, from the genetic code to the codes of culture.


The /Fifth International Conference in Code Biology/ will take place in 
Granada (Spain)from 5 to 9 June 2018. The Conference will host 
individual talks, poster sessions, a roundtable discussion and the 
Annual General Assembly of the Code Biology Society.


People who wish to deliver individual talks are invited to email an 
Abstract of between 200-500 words to granada-abstra...@codebiology.org 



Abstracts should be sent as one-page files written in a format such as 
.doc or .rtf (no PDF please).


The deadline for Abstract submission is *15 January 2018*.

Earlier submission is highly recommended.

More details are available in the Conference homepage

http://www.codebiology.org/conferences/Granada2018/

Looking forward to receiving your Abstract and to seeing you in Granada

/Julyan Cartwright, Marcello Barbieri and Jannie Hofmeyr/

Julyan Cartwright

/Local Conference organizer /
Instituto Andaluz de Ciencias de la Tierra (IACT) CSIC- Universidad de 
Granada

Av. de las Palmeras, 4.
18100 Armilla, Granada, Spain
julyan.cartwri...@csic.es //

Marcello Barbieri and Jannie Hofmeyr

/On behalf of the Code Biology Society/


--
-
Pedro C. Marijuán
Grupo de Bioinformación / Bioinformation Group
Instituto Aragonés de Ciencias de la Salud
Centro de Investigación Biomédica de Aragón (CIBA)
Avda. San Juan Bosco, 13, planta 0
50009 Zaragoza, Spain
Tfno. +34 976 71 3526 (& 6818)
pcmarijuan.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
-

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