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

[Stanley N Salthe]

and, as such, self-referential'
STAN

On Wed, Feb 2, 2022 at 12:17 PM joe.brenner en bluewin.ch <
joe.brenner en bluewin.ch> wrote:

> This is a poetic statement.
> Joe
>
> ----Message d'origine----
> De : ssalthe en binghamton.edu
> Date : 02/02/2022 - 16:23 (CEST)
> À : Jerry_LR_Chandler en me.com, fis en listas.unizar.es
> Objet : Re: [Fis] [External Email] Re: Fis Digest, Vol 85, Issue
> 16--CLOSING
>
> 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> a écrit :
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>> 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
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>> 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>
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