[Fis] How Molecules Became Signs

[Karl Javorszky]

There appear to be problems with the generation of a DOI for this, so let
me include the text of my remarks on Terrence's work.

Terrence Deacon’s „How Molecules Became Signs?” – remarks

Dear Terrence,



Thank you for sharing this excellent piece of work with FIS. You give us
insight into your epistemological system of concepts and present results
from experiments, attaching explanations to the observed results.

Your system of thoughts is the state of the art. Please allow me now to
send a message to you from the avant-garde. The relation between cutting
edge research, behind microscopes and basic research behind paper and
pencil, is one of mutual exchanges. You have discovered in vitro the DNA
and that it carries information. We now, some 70 years later, return with
the dossier *‘Information Transmission: Linear vs Multidimensional Forms’ *with
the proud label: *SOLVED. *We know now, what underlying facts reduce the
apparent complexities to a long series of combinatorial considerations.

Just as basic research gives you back the last question solved, you pose
new ones to us. You speak about *self-repairing mechanisms, *expressing the
idea in many forms. This will translate for us into the properties of
the *Target
Value as such*. So far, we have used the target value always in tandem with
an actual value and maintained than an oscillation (exchanging the posts)
between the two is a characteristic of life. Now we have to assume that
there are *objectively existing, interpersonally communicable *entities
that embody the concept of Nirwana. If the cell tends to maintain its
physiological state, and humans have self-preservation instincts, then
there must be a unique property to that state towards which our mental
creations tend to strive. After reading your article, one has been alerted
to the relevance of there being differing extents of measurements on a
dimension of desirability of states the world can be in. We shall come back
on this in due course (expect about 70 years.)



The message from the avant-garde is embedded in lots of noise. Efficiency
may in such circumstances prevail above politeness; a short, pregnant
message is better style if chances for misunderstandings are many. Let me
offer some feedback thoughts on the fundaments of your thinking. I wish to
talk about the setup and hypotheses of your experiments, not about their
validity.

1) Basic problem

*“What sort of process is necessary and sufficient to treat a molecule as a
sign?” This requires focusing on the interpreting system and its
interpretive competence.*

The properties of the objects can not be independent from the procedure of
assignments of characteristics by the observer, is being said here. This
echoes the old materialistic question, whether a geyser in Yellowstone had
been beautiful, forceful, regular, rationally caused before there were
humans who have given names of these properties to the natural processes to
which we later gave the name Yellowstone Geyser. It is true that our
conceptual problems are within our heads, therefore dealing with the
mechanism that the interpreter uses, is of great necessity and utility. Yet
it is also true, that objects have their properties and forms,
independently of any human ascribing a meaning or names to their properties
and forms.

The author concentrates on the spectator side of the interpretational
experiment and discusses the capabilities of the spectator. This is in the
tradition of investigating spontaneous, individual contributions of the
probands’ neurology, which are generally called *projections. *The author
discusses – like he should – the relations of the answers to the Rorschach
tables to the properties of the proband.

This restriction is pointed out and acknowledged by the author. He avoids
the subject, whether there are any actual properties to the objects. This
would be correct, if we were dealing with an idealised Rorschach type
input, where we define that there is no meaning behind the ink blots as
such. The author deals with molecules – which have an a-priori existence
and are not made-up creations of humans -, without addressing the side of
the recognition problem with regard to he objects that are to be
recognised. Why and how molecules are actually different, is a subject he
does not address.

When conducting an experiment in ascribing of properties to stimuli, (here:
“sign” to “molecules”), one should discuss or give reasons for not
discussing the properties of the stimuli. (In the experiments to create
neuroses, the proband is taught to differentiate between ellipses and
circles. Then, the ratio of the axes is gradually brought towards unity.)
Author should state clearly, whether molecules are in his views by their
nature different and recognisably different, that is: whether what he
discusses is self-exploration about the difficulties of deciding whether
input is a carrier of a message or not, in circumstances where it is not
clear whether the elements of input are recognisably different.

A contemplation about certitudes connected to recognisance of possible
signs is definitely in order. One should establish, whether one’s
perception bias causes blind spots or projections. As the author discusses
difficulties of recognising the “sign” property observable on “molecules”
without stating that such a property does indeed exist on the stimuli, the
treatise belongs in the category of *Confessiones, *meditations about the
limit of human knowledge, and has no bearing on any subject of natural
science.



2) Chromosomes as carriers of information

*“ …Crick … “central dogma” of molecular biology (i.e. that information in
the cell flows from DNA to RNA to protein structure and not the reverse) it
was taken for granted that that DNA and RNA molecules were “carriers” of
information.”*

The central fallacy in the central dogma is, that that it is linear, not
circular. DNA *carries *the information, and then what? The carrier
*downloads* the cargo and disappears. The carrier will be re-assembled in
the gonads and its load will be again *uploaded *unto it. The load is the
information, which has been *downloaded *into the organism during its early
phases of growth and development. There its linear form remains stored and
will be *uploaded *again as soon as the individual reaches sexual maturity.

Had the circular idea of the content of the information remaining basically
identical been used, the weak point of the to-fro copying idea would have
become an eyesore. Rather than address the problem, it was tabooed and
repressed.

If the contents of *Source S *are copied unto *Target T*, the capacity of *T
*to carry information must be minimally slightly above the capacity of the
source *S. *Otherwise the contents would not fit. Even if we think target
and source to be ideal, some properties of the exchange run counter to our
ideas of capacity and measures. The products of gonads of a grown organism
of 60.000 g weigh less than 1 g. Nature obviously uses *two *kinds of
measures for counting capacity, one for the unfolded, realised version and
one for the stored construction plans. Yet, in whichever counting system
Nature operates, there is a *one-to-one *relation between an unfolded
organism and their DNA. Maybe the mass of the carriers is different, but
the *number of alternatives *and the methods of identifying *one
specific *among
the alternatives needs to be identical, for the *load *for the carrier to
remain unchanged. (Say there is an *Enigma-style* coding and decoding
algorithm attached to the DNA in order to do the *into unfolding *part of
the job, and an *Enigma-style* coding and decoding algorithm in the gonads,
doing the *into registering *part of the job, then these two machines must
evaluate an identical number of alternatives so that they can yield a
result matching source and target, in both directions.) This problem being
fundamental and thinking about it severely restricted by systems of
tradition and belief, the problem was left aside.



3) Interpretations and algorithms

Both mental processes lead to a final stage, where there is (are)
satisfactory explanations, interpretations, exegeses, methods, techniques
having been shown to or conducted by the subjects themselves until a
cognitive dissonance has become dissolved and the subject reports that he
has understood the interpretation and/or the algorithm. In Terrence’s
formulation:

*A physical pattern by itself is not **about anything. The sequence of
nucleotides in a DNA molecule is just a molecular structure considered
outside the context of a living cell. For this structure to be **about
something there must be a process that interprets it.*

There is a touch of a teleological thinking in the part: *For this
structure to be **about something. *In science, it is outdated to see
Nature as a wish fulfilment centre. It is the subject’s decision, whether
he places the molecular structure inside or outside his own context (which
context resides in the skull of the spectator). Either there is a relation
between the molecular structure and the living organism, or there is none.

The interpretation and the algorithm have in common that they deconstruct
previous relations among the objects discussed and provide a newer set of
relations, which newer set makes more sense for the subject. This the
subject validates by saying Aha. The difference between interpretations and
algorithms is, that we are used to the idea that there are several
interpretations, each equally legitimate and reasonable, but there is – by
convention – only *one *algorithm that brings forth the desired solution.

The fallacy of the traditional way of treating the differences between
several interpretations and one algorithm lies in the opportunistic
observance of received attitudes towards tautologies. The algorithm shows
the problem to be reducible to a tautology. The interpretations show the
problem not to be reducible to *one *tautology, but to be a bouquet of
alternatives of tautologies. The timidity shows itself in the reluctance to
redesign the system of tautologies, so that alternatives of tautologies are
possible. Because we can not picture it on our millimetre paper background,
we are helpless. The creative solution is to take *two *sheets of
transparent millimetre papers, which are slightly in discongruence relative
to each other and *hola!* there you have a patterned millimetre paper on
which any number of tautologies can be pictured.

The part …* there must be a process that interprets it… *can be deeply and
enthusiastically supported. The process that interprets the written form
and translates it into the unfolded form is that what is interesting us,
because this is what is to be explained by words and in the form of
algorithms.



4) Innate, immanent properties of symbols

*In what sense are the intrinsic properties of a communication medium able
to be about anything?*

The term *‘about’ *appears to confirm a legitimacy to some properties to
some stimuli. Whether symbols have intrinsic properties or have no
intrinsic properties is one question. It is a completely different
question, whether the intrinsic properties – if any such are there at all –
have a dark foreboding, convey a hidden meaning, relate to a greater
something, are in a context of *‘about’*.

Again: it is one thing to perceive whether one sees an oval or a circle. It
is a different thing what happens if one cannot distinguish the two, and
why these are sometimes hard to distinguish.

The author does not disclose his opinion on whether the object he
discusses, communication medium’s intrinsic properties, does exist or does
not exist. This would be a promising path.



5) Unlimited

*Determination is not operative here, since there are unlimited classes of
similarity and correlational relationships in the world.*

Careless use of the word *unlimited *appears to signify a belief not
renounced with the necessary inner serenity of the idea of *unlimited. *People
should be expelled from any self-respecting Faculty of Biology, if they
even carelessly use ideas connected to *unlimited. *How would people react
in the Faculty of Mechanical Engineering if tutors were referring to *miracles,
the Devil’s work, talismans, *and be it by loose choice of words, in a
paper? If anyone has ever seen something biologic, this person should know
that trees do not grow to the sky. The un-biologic belief system connected
to the contrast *limited – unlimited *is easily shown by the growth of
cells that are usual and then cells that are cancerous. It is a part of the
canon that in biology everything is limited and under constraints.



6) Social success and scientific merit, important and relevant

*Often the semiotically relevant property of a sign vehicle is only one of
its many attributes, and not necessarily the one most salient. What matters
is how the relevant property is incorporated into an interpretive process,
because being interpreted is what matters.*

Very positive is the author’s wish to assign different words to different
aspects of sign vehicles. There have been suggestions published to
distinguish *important, relevant. *(See: Learn to Count in Twelve Easy
Steps, webinar in FIS 2013). The *position *of a term in the description of
the state of the world is *important *(the property referred to is nested
hierarchically among other properties that can be referred to, a version of
rank or priority), while the *actual use *of the term in a description
determines its *relevance *in the description. (That Joe can swim is not a
very important detail in his CV, and this would be normally not of first
importance in a description of Joe. In a situation, where the ability to
swim will restrict or expand alternatives, that property is *relevant.) *The
sequence of search criteria is *important, *but it remains, once set, the
property of the object. The* relevance* is a product of the situation, of
the spectator’s needs, not of the object.

The author correctly splits *{properties of the object **↔ needs of the
spectator}*, but then the two aspects become conflated again. In a humorous
interpretation, this sentence fits excellent into the background of
Hollywood, Berkeley and Facebook. The *Malleus Maleficarum *of 1486 was
widely interpreted and mattered much. Many academic careers were advanced
by educated treatises on the subject. Being interpreted much is *relevant *for
the career needs of the spectator, but is not of the first *importance *when
discussing properties of objects as such, in a detached, scientific way. In
everyday life, it is important, how much the thing is marketable, whether
it can become the focus of social attention, etc. Wittgenstein’s ideas
greet us again, as he says (2.0122): ~ “The thing is the completeness of
its relations”. In this sense, being discussed much was indeed the most
*important* property of the concept *phlogiston, *and in hindsight it
appears that *phlogiston *has never had any other *relevant *properties.



7) Defeatism and Timidity

*In this way the concept of biological information lost its aboutness but
became safe for use in a materialistic science that had no place for what
seemed like a nonphysical property. *

It appears that the author feels a great social responsibility. If a
concept loses its aboutness, it has lost one of its most important and
relevant properties. Aboutness appears to be meaning ‘placed in a
practical, useful, advantageous, innovative, fruitful context’. The
attitude is praiseworthy, as its goals are apparently a furthering of
well-being and quality of life.

The point is, that even without the relevance of aboutness, the concept of
biological information does have remarkable properties about which it is
worth maintaining a discussion. It is with a belittling aside, that the
author notes, that the concept has degenerated into a discussion of
relations of symbols among each other as such, and has no social, economic
or patriotic value. It is true, that the sense of reason diminishes as one
wants to discuss biologic information, but is forced, for lack of better
alternatives, to use that language which is suited for communication about
such occurrences that can be interpersonally spoken about while reasonably
maintaining the idea that those who communicate mean the same things.
Translating biology into Physics or Mathematics is bad, because these lack
the subtlety of language, e.g. by not being able to speak about
non-physical occurrences.

Once one knows that one has something to say which is interpersonally
communicable and one believes that this message should indeed be
communicated, one stands before the same problem as was addressed by the
author: …* materialistic science that had no place for what seemed like a
nonphysical property. *Specifically, it appears, it is the reluctance of
materialistic science to acknowledge *a-priori existing structures *to,
indeed, a-priori exist, that makes the task formidable. In such a case, one
has to rewrite the catechism in force until it allows for such observations
that we wish to share, to be expressible. This is indeed possible. You *know
*that there is a rational solution to the transmission methods of
biological information, because the thing evidently works.

Egon Friedell writes in Cultural History, that great innovations can by
their nature not originate from mainstream research. He who is mainstream,
is by definition not an outside freak who could dream up such an unusual
concept.

The unusual concept is not that much unusual, merely a suggestion to use
the properties of the background alongside the properties of the
foreground. The DNA being a *linear, sequential *collection, and the
organism being a *multidimensional, concurrently existing *collection, it
is but a small step to see the one being the foreground of the other, and
then the roles reversed. It helps to have found the underlying numeric
fact, that there are differently many similarity and diversity relations on
a collection of *n *objects, *in dependence of n. (oeis.org/A242615
<http://oeis.org/A242615>).*

All of sudden, *materialistic science *has a well-defined, numeric extents
supported, access to *what seemed like a nonphysical property. *

Once we set up *two *orientation reference senders, we are able to
triangulate our position to a much greater exactitude, compared to the
traditional model where everything is measured from the one and only
*Zero *away.
Our *two *reference senders broadcast distance and density signals. The are
situated near *11, 66 *to make use of maximal distortion (inexactitude,
relative deviance), and their two repeaters at *32, 97 *to make use of
maximal congruence. Their message is: *“If you are <so many: ni> expect
terms of trade for diversity/similarity 1/3, 1, 3, 1} for ni: {11, 32, 66,
97}”. *In the *Bazar *there is a *three-way trade *between *n, n!, n?.*

If there are any social controversies regarding the idea, that the world is
in many respects a compromise between many parts (and these many are best
studied at first in their most simple form of *a,b*), because there exist
mathematical facts of combinatorics, which our brain uses but does not
recognise (cf Wittgenstein: The eye cannot see itself), then these
controversies are to be suffered stoically. The interdependence between
foreground and background, diversity and similarity, exists irrespective of
our acknowledgement of its existence. The duality expressed by *A242615 *offers
lots of affordances, is highly *relevant *but in the present social context
relegated to an outsider position, not being *important *for social success
(yet). But do not blame the language and the keepers of the lexica and of
the grammar rules. You are allowed to speak your mind, even if it appears
agrammatical at first. The only way you can make yourself understood, then,
is to deictically define each and all of the steps you take. If the
sequence of the deictic definitions is correct, and any reasonable person
would (and does) understand what you are saying, then it is indeed the
level of social desirability which determines whether science merits
rewards. The author’s main idea, that it is more lucrative to have a trendy
idea people talk about than a profound idea that is a conversation stopper,
is empirically verified.

For the record: materialistic science *does have *a place for what seems a
nonphysical property.



8) Central Tautology

*Any property of a physical medium can serve as a sign vehicle of any type
(icon, index, or symbol) referring to any object of reference for whatever
function or purpose because these properties are generated by and entirely
dependent upon the form of the particular interpretive process that it is
incorporated into.*

It is praiseworthy that the author maintains the required rigidity in
logical texts, namely that they are basically a tautology. Of course, the
spectator can set any sign vehicle in any relation with any other vehicle,
and this will reflect nothing else but the acts of the spectator. This is
like saying that any answer to the Rorschach table is a property of the
proband and not of the table.

The definition may be formally in order and in everyday economic reality
reasonable. There is, however, the small detail about which the author does
not speak, namely the properties of the Rorschach tables themselves and in
what respects these are different and similar among each other. It is a
pleasing definition that the tables contribute nothing towards the
imagination, that ascribing is unprovoked and unbiased. Practitioners know
and theory deals with the fact that tables I – X are in themselves
different and offer each a different *sujet* to talk about. With the
improved version of the same idea, the TAT is an even better example.

The author states, that given an assembly of diverse objects, he is free to
order and group the objects as he sees fit, and that’s all. This statement
is true, but misses the point by far and wide. The point is not, how the
spectator can order the objects, but how the objects are ordered *by
themselves*. Do the objects show a *natural tendency *to assemble into
groups? Will there appear *archetypical constellations *due to the
artefacts of the objects being that many and so diverse cum similar? The
answer to both questions is *yes, *but the author does not discuss the
central problem of biological information, namely that there are *rules,
structures, limits, thresholds and constraints* for the procedure to
function. This may be the result of a subjective hopelessness, *falsely
believing* that because it is not expected that one uses sentences of an
innovative grammar, such a grammar is somehow unappetizing, wrong,
unheard-of, not listed in the lexicon of idioms, therefore *illegitimate*.



9) Full support

*But as a relatively inert linear molecule, the structural properties of
nucleotide polymers make them ideal to serve as templates. This is because
conformation differences along the length of the molecule caused by the
local nucleotide sequence provides a heterogeneous linear surface onto
which other molecules can weakly bind. These structural differences will
determine corresponding differences in how other molecules will tend to
attach to the polymer due to their shape and charge complementarities.
Since there will be both catalysts and polynucleotides within the inert
autogen capsid, free catalysts will tend to associate with free nucleotide
polymers with respect to these structural complementarities. The attached
catalysts will therefore tend to be arranged into distinct sequences along
the length of an extended nucleotide.*

This appears to be a very reasonable general chart of relations among
objects. Lacking the necessary knowledge in cell chemistry, this person can
only express his general support of the idea that *heterogeneous surface …
structural differences … structural complementarities … tend to be arranged
… distinct sequences … *are terms which refer to concepts which can be
naturally and easily integrated into the system of natural numbers (well,
maybe after some massaging).



Congratulations on this great work. In the body of the article, the author
introduces several realisations of a *circular and self-referencing *mechanism.
The idea is present in the lexicon of concepts in the hard sciences, under
the name *cycles. *You are discussing something that can be reasonably
expressed, nothing metaphysical about cycles.



Thank you for sharing this work with us.

Karl




Am Sa., 19. Feb. 2022 um 22:12 Uhr schrieb Pedro C. Marijuán <
pedroc.marijuan en gmail.com>:

> Dear FISers,
>
> We are going to start the new discussion modality based on specific
> publications. The initial contribution to comment is:
>
> *"How Molecules Became Signs**."* By *Terrence W. Deacon*, recently
> appeared in Biosemiotics.
>
> At his earlier convenience, Terry will send a leading text to start the
> discussion.
> Now, given that there is a doi https://doi.org/10.1007/s12304-021-09453-9
> (for freely downloading the paper),
> interested parties may read in advance the publication.
>
> Best greetings to all,
> --Pedro
>
> PS. Given that there are another three contributions tentatively arranged,
> a time span of around 2-3 weeks could be adequate. But we will see on the
> spot.
>
>
> <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
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