<div dir="ltr">
<p class="MsoNormal" style="margin:0cm 0cm 8pt;font-size:12pt;font-family:"Times New Roman",serif"><span lang="DE-AT">Dear
Colleagues,<span></span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;font-size:12pt;font-family:"Times New Roman",serif"><span lang="DE-AT"><span> </span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;font-size:12pt;font-family:"Times New Roman",serif">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 <i>in
biology. </i>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.<span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;font-size:12pt;font-family:"Times New Roman",serif"><span> </span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;font-size:12pt;font-family:"Times New Roman",serif">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. <span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;font-size:12pt;font-family:"Times New Roman",serif"><span> </span></p>
<p class="gmail-MsoNoSpacing" style="margin:0cm;font-size:12pt;font-family:"Times New Roman",serif">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. <span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;font-size:12pt;font-family:"Times New Roman",serif"><span> </span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;font-size:12pt;font-family:"Times New Roman",serif">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.<span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;font-size:12pt;font-family:"Times New Roman",serif"><span> </span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;font-size:12pt;font-family:"Times New Roman",serif">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 processes. <span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;font-size:12pt;font-family:"Times New Roman",serif"><span> </span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;font-size:12pt;font-family:"Times New Roman",serif">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 <b><i>reliability</i></b> of the testing system is improved by a very
minuscule amount, but the <b><i>validity</i></b> 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 Genetic.)<span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;font-size:12pt;font-family:"Times New Roman",serif"><span> </span></p>
<p class="gmail-MsoNoSpacing" style="margin:0cm;font-size:12pt;font-family:"Times New Roman",serif">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.
<span></span></p>
<p class="gmail-MsoNoSpacing" style="margin:0cm;font-size:12pt;font-family:"Times New Roman",serif"><span> </span></p>
<p class="gmail-MsoNoSpacing" style="margin:0cm;font-size:12pt;font-family:"Times New Roman",serif">For didactic and rhetorical reasons, we have to establish
the idea of the <i>existence </i>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 <b><i>good old numbering system</i></b>,
here are our <b><i>good old natural numbers</i></b> and <b><i>now watch my
hands</i></b>. 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 <i><a href="http://oeis.org/A242615">oeis.org/A242615</a>. </i>For ease
of human understanding, we simplified the two opposing mental constructs as <i>‘similarity’,
‘diversity’ </i>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 <i>n </i>actors. If the stage is subdivided in <i>6
</i>substages, each with <i>11 </i>actors, there are plenty of coulisses of the
similarity kind, if <i>66 </i>actors are in <i>one </i>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 <i>exists</i> an inner incongruence within the numbering system, before one can go
into discussing how to make use of the inbuilt relative inexactitude.<span></span></p>
<p class="gmail-MsoNoSpacing" style="margin:0cm;font-size:12pt;font-family:"Times New Roman",serif"><span> </span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;font-size:12pt;font-family:"Times New Roman",serif">One can use the linear contradiction (a deviation between
two combinatorial functions to the tune of 1/10<sup>94</sup>) to introduce an
improved counting system. In one such, there is a <i>third </i>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. <span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;font-size:12pt;font-family:"Times New Roman",serif"><span> </span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;font-size:12pt;font-family:"Times New Roman",serif">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.<span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;font-size:12pt;font-family:"Times New Roman",serif"><span> </span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;font-size:12pt;font-family:"Times New Roman",serif">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.<span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;font-size:12pt;font-family:"Times New Roman",serif"><span> </span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;font-size:12pt;font-family:"Times New Roman",serif">Karl<span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;font-size:12pt;font-family:"Times New Roman",serif"><span> </span></p>
</div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Am Mi., 2. Feb. 2022 um 20:51 Uhr schrieb Stanley N Salthe <<a href="mailto:ssalthe@binghamton.edu">ssalthe@binghamton.edu</a>>:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">and, as such, self-referential'<div>STAN</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Feb 2, 2022 at 12:17 PM <a href="mailto:joe.brenner@bluewin.ch" target="_blank">joe.brenner@bluewin.ch</a> <<a href="mailto:joe.brenner@bluewin.ch" target="_blank">joe.brenner@bluewin.ch</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><font size="3">This is a poetic statement.</font><div><font size="3">Joe<br></font><blockquote style="margin-right:0px;margin-left:15px">----Message d'origine----<br>De : <a href="mailto:ssalthe@binghamton.edu" target="_blank">ssalthe@binghamton.edu</a><br>Date : 02/02/2022 - 16:23 (CEST)<br>À : <a href="mailto:Jerry_LR_Chandler@me.com" target="_blank">Jerry_LR_Chandler@me.com</a>, <a href="mailto:fis@listas.unizar.es" target="_blank">fis@listas.unizar.es</a><br>Objet : Re: [Fis] [External Email] Re: Fis Digest, Vol 85, Issue 16--CLOSING<br><br><div dir="ltr">
Some limitations upon language are overcome in poetry.
<div>
STAN
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</div>
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<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">
On Tue, Feb 1, 2022 at 8:23 PM Jerry LR Chandler <
<a style="text-decoration:underline;color:blue">jerry_lr_chandler@me.com</a>> wrote:
<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div style="overflow-wrap: break-word;">
Youri, Pedro, List:
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Perhaps a short footnote to the discussion.
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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.
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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.
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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.
</div>
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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.
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How serious is this limitation of expressibility within human languages? How much meaning can one compress into a few propositional terms?
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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”.
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Spring is only a few weeks away; I am looking forward to the pleasures of working my garden!
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Cheers
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Jerry
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<br>
<blockquote type="cite">
<div>
On Feb 1, 2022, at 2:12 PM, Pedro C. Marijuán <
<a style="text-decoration:underline;color:blue">pedroc.marijuan@gmail.com</a>> wrote:
</div>
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<div>
<div>
<div>
Dear Youri and FIS Colleagues,
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<div>
Many thanks for all your personal reflections. It is a great closing of the New Year Lecture.
</div>
<div>
What a pity you have been sequestered these weeks by the guardians of orthodoxy!
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<div>
For those interested in biological information, the sober realization is that there is a whole world of phenomena to analyze, reinterpret, and cohere.
<br>
</div>
<div>
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.
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</div>
<div>
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</div>
<div>
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.
<br>
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It is curious, but somehow these are also social "informational problems."
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Anyhow, I was motivated by Youri reflections. Hope having not been too rambling.
</div>
<div>
And now we have to continue our FIS discussions--in a few days I will send the received proposals so far.
</div>
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Best wishes to all, and I join Gordana's greetings to our Chinese Colleagues for their Spring Festival & New Year.
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--Pedro
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<div>
El 31/01/2022 a las 11:42, Youri Timsit escribió:
<br>
</div>
<blockquote type="cite">
<pre>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,
<a href="https://doi.org/10.1017/S0033583517000117" target="_blank">https://doi.org/10.1017/S0033583517000117</a>).
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, « <a style="text-decoration:underline;color:blue">fis-bounces@listas.unizar.es</a> on behalf of
<a style="text-decoration:underline;color:blue">fis-request@listas.unizar.es</a> » <a style="text-decoration:underline;color:blue"><fis-bounces@listas.unizar.es on behalf of
fis-request@listas.unizar.es></a> a écrit :
</pre>
<blockquote type="cite">
<pre>Send Fis mailing list submissions to
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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)
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Message: 1
Date: Wed, 26 Jan 2022 13:45:57 +0100
From: Pedro C. Mariju?n <a style="text-decoration:underline;color:blue"><pedroc.marijuan@gmail.com></a>
To: "'fis'" <a style="text-decoration:underline;color:blue"><fis@listas.unizar.es></a>
Subject: [Fis] Fwd: NEW YEAR LECTURE--from Jerry Chandler
Message-ID: <a style="text-decoration:underline;color:blue"><54419d99-ed1b-3da4-384e-845765c1917e@gmail.com></a>
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_Mssg. from Jerry Chandler_
List, Pedro, Youri,
</pre>
<blockquote type="cite">
<pre>On Jan 19, 2022, at 12:55 PM, Pedro C. Mariju?n
<<a style="text-decoration:underline;color:blue">pedroc.marijuan@gmail.com</a><a style="text-decoration:underline;color:blue"><mailto:pedroc.marijuan@gmail.com></a>> 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:<a href="https://www.mdpi.com/1422-0067/22/21/11965" target="_blank">https://www.mdpi.com/1422-0067/22/21/11965</a>, 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.
</pre>
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<pre>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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Message: 2
Date: Wed, 26 Jan 2022 22:30:45 -0600
From: Jerry LR Chandler <a style="text-decoration:underline;color:blue"><jerry_lr_chandler@me.com></a>
To: fis <a style="text-decoration:underline;color:blue"><fis@listas.unizar.es></a>
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