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

Karl Javorszky karl.javorszky at gmail.com
Sat Feb 5 11:43:18 CET 2022

Dear Colleagues,

The Lecture by Youri has opened many approaches towards understanding the
general concept of information, specifically in a biologic context. The
participants address the specifics of interdependence *in biology. *The
overall sentiment appears to be that we are not yet there, because the
rules governing the interdependence are way far out too complicated. Not
explicitly stated but included between the lines is the admission that
biology appears to work according to rules which we simply have no way,
presently, to understand, lacking a general conceptual framework.

Once again, I have to bore you with empty formalities. If everything else
fails, look in the grammar of logical sentences. The sentences you
manipulate with the goal of assembling a coherent system, based upon
observations, which resulting system is rational and reasonable.

Whether one likes it or not, any rational explanation of any of the
manifold mysteries of Nature will boil down to be a question of
expressibility in a formal language, this requirement being equivalent to
computability. The term ‘rational’ is understood, since Wittgenstein, to
mean that a system of relations exists among elements of a collection of
ideas the meaning of which ideas is interpersonally clear. This means: if
you can model it by using natural numbers, then you have said something
rational. It works, if it counts. If it doesn’t count, it won’t work.

Presently, the attitude of the honourable learned friends is, that there is
no strategy available to massage that what we observe to be biology into a
form or shape so, that it could be made a question of whether it counts or
not. This defeatism is based on timidity and discouragement with regard to
the grammar of logical sentences. The current belief is, that there is no
method to translate idealised, schematised proceedings in biology into a
system of symbols which agree to Wittgenstein’s requirement that the words
used be interpersonally understood, because well defined. In other words,
the opinion in FIS seems to be, that biology cannot be modelled by numbers.
We can’t know, whether any concept or theory about biology is rational,
because we can’t calculate it, the problem being that there are no words
and no techniques to model biologic entities in a mathematically oriented
framework. We can’t count the relations among the elements of our thought
model, therefore we don’t know if our assumptions are reasonable.

The axiom: if it won’t count, it won’t work can be reversed. Biology
obviously works, therefore the system counts. (There are sufficiently many
of such logical sentences describing the proceedings, which use commonly
known concepts.) We just don’t know or recognise yet that grammar which
allows us to construct such logical sentences that describe biological

We have to change to a level of exactitude which is higher than that we
presently use. (Spoiler alert: consolidating the statements that refer to
similarities with those that refer to diversities yields an improvement in
a linear understanding of counting of roughly 3.4EE-92 %. We improve the
overall exactitude (reliability) of our testing apparatus by a percentage
of Zero-point: here follow ninety-two Zeroes three percent.) The inner
*reliability* of the testing system is improved by a very minuscule amount,
but the *validity* of our measurement becomes dramatically higher, as we
are able to predict occurrences of Nature also in domains which have not
yet been subject to testing of hypotheses. (We already know how to use the
system to predict occurrences in the realm of Physics, Chemistry,
Astronomy, etc. By using a slightly more exact version of the counting
system, we shall be able to predict occurrences also in Physiology and

Was it Archimedes who said: “Give me a fixed point and I will move the
whole world”? Here, we need a fixed discongruence and we can explain the
whole world. We present the whole system of unified and matching classical
logical sentences, in use presently, to be a special, idealised case.

For didactic and rhetorical reasons, we have to establish the idea of
the *existence
*of an inner {deviation, inexactitude, incongruence, contradiction} within
the counting system presently in use. This idea has to be the first in the
chain of thoughts that follows. The conjurer has to state he shall pull a
rabbit out of the cylinder before he proceeds to pulling out the rabbit.
One has to show: see, here is our *good old numbering system*, here
are our *good
old natural numbers* and *now watch my hands*. I shall show how things grow
and shrink, unfold and collapse, expand and construct, have fixed places or
have no fixed places, merge or don’t merge. One has to prepare the audience
for the trick. The existence of the possibility of the trick is
demonstrated in *oeis.org/A242615 <http://oeis.org/A242615>. *For ease of
human understanding, we simplified the two opposing mental constructs
as *‘similarity’,
‘diversity’ *and have shown that we perceive sequences (collections of
diversities) before a background of similar units, and that we perceive
groups (collections of commutative symbols) before a background of diverse
units. The fact is that there are differently many backgrounds available in
dependence of the number of interacting elements. Like in a theatre there
are differently many coulisses for plays with *n *actors. If the stage is
subdivided in *6 *substages, each with *11 *actors, there are plenty of
coulisses of the similarity kind, if *66 *actors are in *one *play, they
are severely restricted in their interactions because of a shortage of
coulisses before which they can act differently. It is important to
establish the idea that there *exists* an inner incongruence within the
numbering system, before one can go into discussing how to make use of the
inbuilt relative inexactitude.

One can use the linear contradiction (a deviation between two combinatorial
functions to the tune of 1/1094) to introduce an improved counting system.
In one such, there is a *third *measurement value which relates to the
discongruence between the two measurements. We not only have a) how similar
the elements of the collection are among each other and b) how diverse the
elements of the collection are among each other, but also c) how the
difference between a) and b) relates to the overall number of how many
elements are included in the collection. So far, only the measurement based
on a) has been in use. In the improved system, one counts in really small
units, which are in their nature predictabilities (extents of probability).
The system works best on collections that are axiomatically subject to
periodic changes.

This contribution to the closure of the current Session is an optimistic
one. It is possible to speak about the processes we observe in biology in a
rational fashion, using such words, the meaning of which is interpersonally
clear. The only requirement is a change of procedures within one’s own
brain, no need to buy or build new microscopes or spectrometers.

Sorry to be the voice sounding discordant. Think of me as the metronome
accompanying your concert of minds. The metronome doesn’t contribute to the
music, it is actually disturbing during performances, but it does have its
small practicalities, specifically in phases when the musicians have not
decided yet, according to which rhythm and melody they shall intone their
Te Deum, having found the rational explanation of the workings of biology.


Am Mi., 2. Feb. 2022 um 20:51 Uhr schrieb Stanley N Salthe <
ssalthe en binghamton.edu>:

> and, as such, self-referential'
> 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.
>> 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
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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
>>> --
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>>> 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
>>> ----------
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> Recuerde que si está suscrito a una lista voluntaria Ud. puede darse de
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