[Fis] [External Email] Re: Fis Digest, Vol 85, Issue 16--CLOSING

[Stanley N Salthe]

Some limitations upon language are overcome in poetry.
STAN

On Tue, Feb 1, 2022 at 8:23 PM Jerry LR Chandler <jerry_lr_chandler en me.com>
wrote:

> Youri, Pedro, List:
>
> Perhaps a short footnote to the discussion.
>
> The remarkable success of linear mathematics is not to be denied.  We are
> all aware of its massive impact on our daily lives and the work that we do.
>
> That being said, the questions turn to evaluation of the ’net value’ of
> information theory/linear mathematics on the direction of social and
> cultural values.  In particular, the role of the individual has changed so
> dramatically.
>
> It seems to me that the nature of informational successes is wildly
> overestimated.  As Youri alludes, only small categories of issues and
> challenges can be addressed.  As Youri’s work illustrates, the widely
> issues of the extreme perplexity of nature remain unapproachable through
> linear mathematics.  And non-mathematics remains bound to a few variables,
> not the tens of thousands of factors that are operating in ribosomal
> information processing during molecular transcription and translations.
>
> One issue of deep concern is the very limitation of linguistic
> communication itself.  How many factors can one communicate in a sentence?
> How many quantities can one compare to describe a biological object?  To
> me, this is a very very serious problem.
>
> How serious is this limitation of expressibility within human languages?
> How much meaning can one compress into a few propositional terms?
>
> Beyond the limitations of any one language looms the larger issue of
> scientific meta-languages, several semeiotic versions used to describe
> singular natural processes. This also is a very serious challenge.  COVID
> has opened this issue to the general public and the public has sharply
> rejected “scientific wisdom”.
>
> Spring is only a few weeks away; I am looking forward to the pleasures of
> working my garden!
>
> Cheers
> Jerry
>
> On Feb 1, 2022, at 2:12 PM, Pedro C. Marijuán <pedroc.marijuan en gmail.com>
> wrote:
>
> Dear Youri and FIS Colleagues,
>
> Many thanks for all your personal reflections. It is a great closing of
> the New Year Lecture.
> What a pity you have been sequestered these weeks by the guardians of
> orthodoxy!
>
> For those interested in biological information, the sober realization is
> that there is a whole world of phenomena to analyze, reinterpret, and
> cohere.
> Almost anything in the "received wisdom" about biomolecular phenomena
> looks partial, biased, insufficient--notwithstanding all the great
> experimental achievements accumulated. Youri is very eloquent about that in
> his ribosome research. Something similar seems to be occurring in the
> neurosciences, also dumbfounded under the sheer accumulation of facts. We
> lack clarity, concision, coherence in all bio-info arenas. We might say the
> received wisdom (sequencing, structure/function, Darwinian selection,
> input/output) at least maintains a "floating line" that gives a shared
> coherence to international research programs--that at the same time work
> hard to stifle new thought. A genuine thinking bureaucracy.
>
> There is also a "mass bureaucracy" in the control and administration of
> research. All this surrounding bureaucracy has been engrossed by two new
> factors, presumably. One, not new actually, is the approximate duplication
> of scientific effort every 30 years or so; for each passing generation
> after the industrial revolution has doubled the scientific/technological
> workforce on average. Like in the evolution of central nervous systems we
> seem to have crossed a threshold in this engrossment of science
> practitioners. It is an ad hoc industry now, deprived more and more of
> vocational drivers and subject to a multilayered political/administrative
> command. There seems to be more than 10 million scientists in the world
> nowadays (from UNESCO report), and every year another 300,000 would be
> joining. They need institutions, labs, career development, journals,
> publications, etc. "Publish or perish"...No wonder a mammoth
> pseudo-publication system has taken off, degrading the whole system as a
> way to communicate new research and new thought. And the other factor would
> relate to the information technologies themselves. Their many advantages
> have also serious collateral damages for our scientific endeavor. The
> e-bureaucracy has become larger and larger, and insatiable, a painful sink
> of our research time. The new ways of e-thinking, influenced by the new
> communication tools, are superficial and lacking reflection, and at the
> same time plainly caught into the "identitary fragmentation." Less
> (serious) scientific books are written, and even less are read. "We
> students do not read books!", they say nonchalantly... But perhaps more
> than journals, books have been the fundamental vehicle of scientific
> thought.
>
> It is curious, but somehow these are also social "informational problems."
>
> Anyhow, I was motivated by Youri reflections. Hope having not been too
> rambling.
> And now we have to continue our FIS discussions--in a few days I will send
> the received proposals so far.
>
> Best wishes to all, and I join Gordana's greetings to our Chinese
> Colleagues for their Spring Festival & New Year.
>
> --Pedro
>
> El 31/01/2022 a las 11:42, Youri Timsit escribió:
>
> 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 offis-request en listas.unizar.es » <fis-bounces en listas.unizar.es on behalf of
> fis-request en listas.unizar.es> <fis-bounces en listas.unizar.esonbehalfoffis-request@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> <pedroc.marijuan en gmail.com>
> To: "'fis'" <fis en listas.unizar.es> <fis en listas.unizar.es>
> Subject: [Fis] Fwd:  NEW YEAR LECTURE--from Jerry Chandler
> Message-ID: <54419d99-ed1b-3da4-384e-845765c1917e en gmail.com> <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> <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> <http://listas.unizar.es/pipermail/fis/attachments/20220126/80b8cc16/attachment-0001.html>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 26 Jan 2022 22:30:45 -0600
> From: Jerry LR Chandler <jerry_lr_chandler en me.com> <jerry_lr_chandler en me.com>
> To: fis <fis en listas.unizar.es> <fis en listas.unizar.es>
> Subject: [Fis] Test Message No Content
> Message-ID: <4DD2D213-D3EC-4FDF-B1F7-FCC4FF9756CC en me.com> <4DD2D213-D3EC-4FDF-B1F7-FCC4FF9756CC en me.com>
> Content-Type: text/plain;	charset=us-ascii
>
>
>
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> Fis mailing listFis en listas.unizar.eshttp://listas.unizar.es/cgi-bin/mailman/listinfo/fis
>
>
> ------------------------------
>
> End of Fis Digest, Vol 85, Issue 16
> ***********************************
>
>
> _______________________________________________
> Fis mailing listFis en listas.unizar.eshttp://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
> ----------
>
>
>
>
> <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>
> _______________________________________________
> 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/20220202/7ff7e95e/attachment-0001.html>