[Fis] Fwd: Re: Fis Digest, Vol 85, Issue 16. Onti and Epistemic Perspectives

Wed Feb 2 12:30:56 CET 2022

Cari Tutti,
Joseph ha ragione al 100%, senza de-qualificare o sotto-valutare l'apporto
di  chi la pensa diversamente, poiché nessuno
a questo mondo possiede la verità assoluta. Nell'altro mondo si vedrà.
Beninteso, il mondo della terra e il mondo del cielo sono essenzialmente
basati sull'amore, inteso  come la legge  delle leggi
della vita e della scienza o, se volete, della vita della scienza o della
scienza della vita.
Un saluto augurale a tutti.
Francesco

Il giorno mer 2 feb 2022 alle ore 09:52 joe.brenner en bluewin.ch <
joe.brenner en bluewin.ch> ha scritto:

> Dear Youri, Pedro and All,
>
> I have very much welcomed this exchange which I hope will continue past
> the "closing". One possible area for discussion is the relatiion of
> information to ontology and epistemology. Youri wrote:
>
> >In this respect, I have the impression that an epistemological perspective
> >on one's own activity is more conducive to a form of humour,
> >relativity and makes people less rigid and therefore less aggressive ?
>
> I beg to differ with Youri on this point. In my view, it has been the
> neglect of the ontological aspects of complex phenomena, of which humor and
> information are prime examples, that has led to reductionist,
> non-humanistic interpretations. I would look forward to the views of others
> on this issue, in which science and philosophy are conjoined.
>
> Best wishes,
>
> Joe
>
> >
> >----Message d'origine----
> >De : youri.timsit en mio.osupytheas.fr
> >Date : 31/01/2022 - 11:42 (E)
> >À : fis en listas.unizar.es
> >Objet : Re: [Fis] Fis Digest, Vol 85, Issue 16
> >
> >about Information, Editors, Humour and Life Metaphors
> >
> >
> >Dear all,
> >
> >
> >Thanks again to Pedro for allowing these interesting exchanges and thanks
> >to all for
> >your comments around the new year lecture.
> >
> >
> >First of all, I would like to point out that I am not an information
> >specialist at all,
> >nor am I a mathematician: I look modestly at the structure of biological
> >macromolecules. And by chance, I simply observed protein networks in the
> >ribosome that were analogous to neural networks. By transitivity, I
> >wondered if
> >these networks could also transmit signals and integrate them, like neural
> >networks: is it information? I don't know Š.
> >
> >
> >But that¹s how I came to ask the question, can the architecture of the
> >networks tell us
> >what they do? Can we deduce the 'function' of a network by the way it is
> >connected? If you look through the literature, you can find, for example,
> >these
> >famous "small world networks", the "scale-free" networks,
> >Uri Alon's FFL motifs, but if you look a little deeper, you can see that
> >it's
> >not that simple... the answer is not clear.
> >
> >I also asked myself a stupid question: is there a kind of
> >'proportionality' between the difficulty of
> >the tasks to be accomplished and the complexity of the networks that are
> >supposed to process them? If we look at the nervous system, from the
> >simplest
> >organisms to the most complex (which Cajal has started to do), we can see
> >that
> >the more complex the behaviour of organisms is, the more complex their
> >nervous
> >system is... but is there a simple law to describe this phenomenon? and do
> >things start from the ribosome, from LUCA (last universal common
> ancestor)?
> >
> >
> >This is why I called on my mathematical colleagues Daniel Bennequin, who
> >is also a nervous
> >system specialist, and his student Grégoire Sergeant-Perthuis. Ribosome
> >networks
> >and their properties have been described but, of course, this does not
> >allow us
> >to understand how they work. The famous 'structure-function relationships'
> >that
> >serve as the scaffolding for all modern biology have serious limitations.
> >
> >
> >And to answer Jerry's question, normally, if we knew the properties of
> >atoms and
> >molecules perfectly, the crystallographic structure of a bacterial
> ribosome
> >(take for example pdb code: 4y4p which contains 3 tRNAs and is very high
> >resolution): normally, this structure which contains "all the
> >information" should allow us to understand the ribosome completely... But
> >this is not the case. It also requires thousands of tedious biochemical
> >studies, the design of hundreds of mutants in various areas of the rRNA
> and
> >ribosomal proteins to test their 'functional' roles. And with all this
> work
> >over half a century, we have painfully arrived at a very mechanistic view
> >of
> >the ribosome and the whole of life... and the essentials still elude us.
> >The
> >conclusion of a recent review by one of the leading experts in the field
> >(Harry
> >Noller) on ribosome dynamics is: "an important unanswered question is: how
> >are intersubunit and head rotations coordinated with all of the other
> >dynamic
> >events of the ribosome during translocation?" (Noller et al., 2017,
> >https://doi.org/10.1017/S0033583517000117).
> >
> >
> >Thus, a purely mechanistic vision does not allow us to understand either
> >the ribosome
> >or living organisms in their entirety and misses entirely the "information
> >flow" that Pedro talks about.
> >
> >When we see that the entire human genome has been sequenced, that the PDB
> >is filled
> >with hundreds of thousands of macromolecule structures, that the
> >pharmaceutical
> >industry 'excels' in the design of targeted medicines and the belief in
> the
> >effectiveness of drug design, and that on the other hand, a tiny
> >coronavirus or
> >even an ebola virus containing only 6 genes can wipe out the whole of
> >mankind,
> >we have the right to ask ourselves whether we are not missing something
> >essential in our understanding of living organisms?
> >
> >
> >In my opinion, this is where the crucial question of living metaphors,
> >humour,
> >seriousness and aggressiveness of scientific editors comes in...
> >
> >It seems to me that certain forms of thought, and in particular the choice
> >of metaphors,
> >are more conducive to poetry, humour, and that humour, art and poetry, can
> >often mitigate the aggressive impulses, war and, among other things, the
> >implacable authority of scientific editors (this is in response to the
> >editor's
> >comments on Joe's article). I think S. Freud would not contradict me...
> >sublimation in art, is the last bastion against barbarism...
> >
> >
> >In biology, for the moment, it is very comfortable for the community of
> >biologists (and the
> >pharmaceutical industry that controls it) to compare living beings to
> >machines:
> >the whole edifice of molecular biology is based on this reductive analogy
> >that
> >simplifies living beings and their constituents to a mechanistic
> >functioning
> >drawn from analogies with engineering and industry. Genetic 'codes and
> >programmes',
> >and the notions of the famous 'structure/function' relationships that have
> >structured biological thinking since the death of Stalin, Prokofiev in
> >1953 and
> >the concomitant publication of the structure of the DNA double helix. Each
> >molecule has a specific function and its structure is responsible for it!
> >Of
> >course, there is some truth in this paradigm, but it is not so simple...
> >But
> >one prefers this simple system of thought to wandering in still
> ill-defined
> >spheres... wandering is very badly tolerated by science although it is its
> >deepest essence....
> >
> >
> >If we look at the literature on antibiotics, for example, we realise that
> >many
> >"antimicrobial molecules" are also neuromodulators ... ! We also
> >realise that proteins can have multiple functions, that others have no
> >structure.... etc: there is a huge task to be carried out in biology:
> >redefine
> >the notion of function!
> >
> >
> >On the subject of seriousness in science, there are few philosophical
> >works that
> >address this question: what is really serious? It is, however, a serious
> >question... Nietzche had already asked himself about humour and philosophy
> >when
> >he published his "gai savoir"... more recently, we find "en
> >quête du sérieux" by J.LH. Thomas. Rare are the philosophers and
> >scientists who question the seriousness of their approaches... is
> >sequencing
> >the entire human genome really serious? (this question is provocative... I
> >am aware of it) but one can ask the question in
> >view of what this project has really brought?
> >
> >In this respect, I have the impression that an epistemological perspective
> >on one's own activity is more conducive to a form of humour,
> >relativity and makes people less rigid and therefore less aggressive ?
> >
> >About competition between living beings (and researchers) ... the famous
> >"struggle for life"..., there are other systems of thought which are
> >still very much in the minority... see "la manifestation de soi" by
> >Jacques Dewitte (édition la découverte..; I don't know if it's translated
> >into
> >English?). Despite the dominant view, we know that ecosystems are based on
> >many
> >other laws than the prey/predator relationship... You only have to look at
> >how
> >a large whale can protect penguins, sea lions and its calf under its fins
> >against the attack of orcas.
> >
> >
> >This machine metaphor and all the simplifying ideology about living beings
> >that goes with it
> >is nevertheless dominant and authoritarian today: in my opinion, it
> >guarantees
> >the functioning of a biology at the mercy of the pharmaceutical industry,
> >which
> >wants to reduce living beings to obedient objects.
> >
> >It is based on a misunderstood Darwinian vision that exalts the survival
> >of the strongest
> >and the best adapted... see the "Darwinian programme for French
> >science" proposed by the president of the CNRS, A. Petit: we are not far
> >from the notion of degenerate art that was hunted down not so long ago by
> >certain regimes.
> >
> >
> >In short,there is a whole arsenal of concepts that are the pillars of a
> >neo-liberal
> >reductionist ideology, which, instead of understanding and contemplating
> >the
> >living, seeks to exploit it, if not destroy it. With the machine metaphor,
> >we
> >are not joking, there is no room for humour, we are 'efficient' and
> >'performing' and we assimilate ourselves to our object of study... we
> >ourselves
> >become machines for producing scientific facts... and multiple guardians
> >ambush
> >everywhere, making sure that this gigantic machine called science works
> >well...
> >That's why it took me a while to answer you, I was transformed for several
> >weeks into a machine asking for money to be able to do science...
> >
> >
> >Like any authoritarian system, it comes with a repressive apparatus to
> >enforce it, and
> >I'm taking the risk of proposing here that the main inquisitors are the
> >"scientific editors" and also a large part of our colleagues who
> >"know" where "right and wrong", "true and false",
> >lie on the basis of a supposed rationality.
> >
> >
> >One can imagine that showing Chaplin's film "Modern Times", having the
> >Milgram test or
> >listening to a Bach fugue to the editors of major scientific journals
> could
> >help them better understand the limits of the machine metaphor, understand
> >the
> >immeasurable complexity of life and its information flows and make
> >relations
> >between researchers more harmonious....
> >
> >
> >
> >
> >
> >
> >all the best
> >
> >Youri
> >
> >
> >
> >Le 27/01/2022 12:00, « fis-bounces en listas.unizar.es on behalf of
> >fis-request en listas.unizar.es » <fis-bounces en listas.unizar.es on behalf of
> >fis-request en listas.unizar.es> a écrit :
> >
> >>Send Fis mailing list submissions to
> >>      fis en listas.unizar.es
> >>
> >>To subscribe or unsubscribe via the World Wide Web, visit
> >>      http://listas.unizar.es/cgi-bin/mailman/listinfo/fis
> >>or, via email, send a message with subject or body 'help' to
> >>      fis-request en listas.unizar.es
> >>
> >>You can reach the person managing the list at
> >>      fis-owner en listas.unizar.es
> >>
> >>When replying, please edit your Subject line so it is more specific
> >>than "Re: Contents of Fis digest..."
> >>
> >>
> >>Today's Topics:
> >>
> >>   1. Fwd:  NEW YEAR LECTURE--from Jerry Chandler (Pedro C. Mariju?n)
> >>   2. Test Message No Content (Jerry LR Chandler)
> >>
> >>
> >>----------------------------------------------------------------------
> >>
> >>Message: 1
> >>Date: Wed, 26 Jan 2022 13:45:57 +0100
> >>From: Pedro C. Mariju?n <pedroc.marijuan en gmail.com>
> >>To: "'fis'" <fis en listas.unizar.es>
> >>Subject: [Fis] Fwd:  NEW YEAR LECTURE--from Jerry Chandler
> >>Message-ID: <54419d99-ed1b-3da4-384e-845765c1917e en gmail.com>
> >>Content-Type: text/plain; charset="utf-8"; Format="flowed"
> >>
> >>_Mssg. from Jerry Chandler_
> >>
> >>List, Pedro, Youri,
> >>
> >>> On Jan 19, 2022, at 12:55 PM, Pedro C. Mariju?n
> >>> <pedroc.marijuan en gmail.com <mailto:pedroc.marijuan en gmail.com>> wrote:
> >>>
> >>> So, my contention is that a new filed like bio-chemistry or
> >>> bio-physics would be needed concerning the biological-informational
> >>> themes, a bio-information discipline comparable to those just
> >>> mentioned. According to several authors? (me included), the
> >>> prokaryotic cell should be considered as the fundamental, basic unit
> >>> of biological cognition. Thereafter, there would be different ways to
> >>> characterize its informational processes, particularly along the
> >>> "information flow" conceptualization... interested parties may go to
> >>> the recent contribution of Jorge Navarro and
> >>> mine:https://www.mdpi.com/1422-0067/22/21/11965, it is in the special
> >>> issue coordinated by Youri.? I also discuss that the from the
> >>> informational thinking one could find the ways and means to renew the
> >>> outdated Modern Synthesis.
> >>>
> >>> Otherwise, without a clearer disciplinary framework, am afraid the new
> >>> biology will be reduced to bioinformatics and experimental "omic"
> >>> disciplines. Just another (advanced, "very advanced") technology.
> >>
> >>Pedro: ?Your comments are often intriguing and these sentences are no
> >>exception.
> >>I do not grasp what either your scientific or personal objectives are.
> >> ?One consistent theme in somehow tied to expectations about ?biologic
> >>codes? in relation to forms of communication. ?Can you be more explicit
> >>about what sorts of meaning you are seeking to understand?
> >>Youri has presented the FIS with an encoded diagram of one of the
> >>central apparati of all living organisms. ?Roughly speaking, the role of
> >>the ribosome is well-understood although finer structuring of the
> >>apparatus and its dynamics will continue to be studied ad infinitum. The
> >>logical role of the ribosome in transducing information into alternative
> >>dynamic forms has been clear for more than 40 years.
> >>
> >> ?This encoded diagram is based on the epistemology of the chemical code
> >>of life, the physical codes of mass and electricity and the mathematical
> >>codes of permutation groups, space groups, number theory, and so forth.
> >>Is it not clear that Youri?s work generates a diagram that is a logical
> >>constant of form?
> >>
> >>Somehow, I suspect that the epistemic gaps between mathematics and
> >>physics and chemistry lie at the root of your search for biological
> >>codes. ?Perhaps the effort is guided by a believe that the genesis of
> >>living dynamics, involving thousands of variables and literally hundreds
> >>of millions of *_unique_* biochemical reactions must necessarily be
> >>expressible in simplistic and other scientific, syntactical symbol
> >>systems? ?(Hundreds of millions of reactions BECAUSE every DNA base
> >>occupies a logically unique sequential position and undergoes unique
> >>reactions during transcription and duplication.)
> >>
> >> ?Is the concern semantics or semeoius? ?The syntax of Youri?s work is
> >>not seriously questioned, is it? ?Is the problem that Youri?s work does
> >>not fit into alternative theories of ?information? that can not be
> >>distorted to fit the biological codes?
> >>
> >>Youri - Can you refer to a data source that lists the physical-chemical
> >>data of an E coli ribosome in terms of the parts of the whole? ?(I am
> >>not referring x-ray data, just the chemical parameters used to compute
> >>the structure.). As time allows, I may do a few calculations to
> >>unconceal aspects of the scientific information content of a ribosome.
> >>
> >>Cheers
> >>
> >>Jerry
> >>
> >>
> >>
> >>
> >>
> >>--
> >>El software de antivirus Avast ha analizado este correo electr?nico en
> >>busca de virus.
> >>https://www.avast.com/antivirus
> >>-------------- next part --------------
> >>An HTML attachment was scrubbed...
> >>URL:
> >><
> http://listas.unizar.es/pipermail/fis/attachments/20220126/80b8cc16/attac
> >>hment-0001.html>
> >>
> >>------------------------------
> >>
> >>Message: 2
> >>Date: Wed, 26 Jan 2022 22:30:45 -0600
> >>From: Jerry LR Chandler <jerry_lr_chandler en me.com>
> >>To: fis <fis en listas.unizar.es>
> >>Subject: [Fis] Test Message No Content
> >>Message-ID: <4DD2D213-D3EC-4FDF-B1F7-FCC4FF9756CC en me.com>
> >>Content-Type: text/plain;     charset=us-ascii
> >>
> >>
> >>
> >>
> >>------------------------------
> >>
> >>Subject: Digest Footer
> >>
> >>_______________________________________________
> >>Fis mailing list
> >>Fis en listas.unizar.es
> >>http://listas.unizar.es/cgi-bin/mailman/listinfo/fis
> >>
> >>
> >>------------------------------
> >>
> >>End of Fis Digest, Vol 85, Issue 16
> >>***********************************
> >
> >_______________________________________________
> >Fis mailing list
> >Fis en listas.unizar.es
> >http://listas.unizar.es/cgi-bin/mailman/listinfo/fis
> >----------
> >INFORMACIÓN SOBRE PROTECCIÓN DE DATOS DE CARÁCTER PERSONAL
> >
> >Ud. recibe este correo por pertenecer a una lista de correo gestionada
> por la Universidad de Zaragoza.
> >Puede encontrar toda la información sobre como tratamos sus datos en el
> siguiente enlace:
> https://sicuz.unizar.es/informacion-sobre-proteccion-de-datos-de-caracter-personal-en-listas
> >Recuerde que si está suscrito a una lista voluntaria Ud. puede darse de
> baja desde la propia aplicación en el momento en que lo desee.
> >http://listas.unizar.es
> >----------
> >
> _______________________________________________
> Fis mailing list
> Fis en listas.unizar.es
> http://listas.unizar.es/cgi-bin/mailman/listinfo/fis
> ----------
> INFORMACIÓN SOBRE PROTECCIÓN DE DATOS DE CARÁCTER PERSONAL
>
> Ud. recibe este correo por pertenecer a una lista de correo gestionada por
> la Universidad de Zaragoza.
> Puede encontrar toda la información sobre como tratamos sus datos en el
> siguiente enlace:
> https://sicuz.unizar.es/informacion-sobre-proteccion-de-datos-de-caracter-personal-en-listas
> Recuerde que si está suscrito a una lista voluntaria Ud. puede darse de
> baja desde la propia aplicación en el momento en que lo desee.
> http://listas.unizar.es
> ----------
>
------------ pr�xima parte ------------
Se ha borrado un adjunto en formato HTML...
URL: <http://listas.unizar.es/pipermail/fis/attachments/20220202/990579df/attachment-0001.html>