Using the logical language to understand Nature


The discussion in this group refocuses on the meaning of the terms
“symbol”, “signal”, “marker” and so forth. This is a very welcome
development, because understanding the tools one uses is usually helpful
when creating great works.

There is sufficient professional literature on epistemology, logical
languages and the development of philosophy into specific sub-philosophies.
The following is just an unofficial opinion, maybe it helps.



Wittgenstein has created a separate branch within philosophy by
investigating the structure and the realm of true sentences. For this, he
has been mocked and ridiculed by his colleagues. Adorno, e.g. said that
Wittgenstein had misunderstood the job of a philosopher: to chisel away on
the border that separates that what can be explained and that what is
opaque; not to elaborate about how one can express truths that are anyway
self-evident and cannot be otherwise.

The Wittgenstein set of logical sentences are the rational explanation of
the world. That, which we can communicate about, we only can communicate
about, because both the words and what they mean are self-referencing. It
is true that nothing ever new, hair-raising or surprising can come out of a
logical discussion modi Wittgenstein, because every participant can only
point out truths that are factually true, and these have always been true.
There is no opportunity for discovery in rational thinking, only for an
unveiling of that what could have been previously known: like an
archaeologist can not be surprised about a finding, he can only be
surprised about himself, how he had been able to ignore the possibility of
the finding so long.

As the Wittgenstein collection uses only such concepts that are
well-defined, these concepts can be easily enumerated. In effect, his
results show, that if one uses well-formulated, clearly defined logical
words, the collection of all explanations is the solution of a
combinatorial problem. This is also the reason why he says that his
philosophy is just a tool of sharpening the brain, and contains nothing
whatsoever noteworthy in a semantic fashion.

One may summarise that the pariah state among philosophers that
Wittgenstein suffered on this his insight, is owed to the conclusion that
real philosophy has either nothing to do with the grammar of true logical
sentences or otherwise it is degenerating into a technique outside
philosophy, namely number theory. If every concept can be represented by a
number, and valid sentence are those for which the rules that govern
numbers are satisfied, then one can work with the numbers as such and
figure out later for what they stand.

This is the situation as per today. There is no change whatsoever. The only
noteworthy development is, that one can indeed teach new tricks to that old
dog, number theory. The sand that has to be swiped away is the covering
layer of attitudes that are too clever by half. By keeping the nose not too
high, one may look before one’s feet and reconsider simple operations that
one executes by routine.

We know how to sort and how to order, and we are intelligent and flexible
enough to change priorities if circumstances dictate such. We know how to
order and how to reorder. If we only had a brain like a computer, we could
memorise all the patterns that appear as we transform from priority
readiness One into priority readiness Two.

There are many opportunities for number theory to jump into action in the
field of organising and reorganising. As one intensifies one’s hobby of
reordering the contents of one’s office, one will now have arrived at the
concept of sequenced groups of elements that change place together during a
reorder. Cycles that constitute a reorder connect elements with each other.
Learning is based on the concept of associations. Being an element in the
corpus of a cycle may well be the formal explanation for a property of
being associated with.

Whether one calls the elements’ {position, amount, sequential place,
relation to potential successors, …} {symbol, signal, mass, impact,
chemical valence, predictability, energy level, information content,…} is
of secondary importance. As we look into a kaleidoscope, the first step is
to make sure *that* we all look at a kaleidoscope, and preferably the same
one. The next task is to make sure that we all perceive the *same picture*.
As the kaleidoscope produces natural numbers, this should be a challenge
that one can be expected to match. Only after it has been agreed that we
all observe the same patterns is it reasonable to start discussing how to
name the facts of perception.

The present problem is not with the inability of the logical language to
process that what we wish to discuss.  The present task is to realise that
one needs a clear idea before one enters the struggle to express it
clearly. The unveiling has been done. Now the interested public is invited
to look at the picture.

Once one has answered the dilemma: “On Tuesdays, this here cup is to the
left of the screen, because Tuesdays I order things on their colour; on
Wednesdays the same cup is to the right of the screen for its size, because
on Wednesdays I order things on their size: so, which is the correct place
of this cup, actually?”; once on has figured this out – that namely the cup
would be oscillating between its two places, or take up a position on a
plane with axes: colour, size -, then one has done great strides towards
understanding that “symbol”, “sign”, “signal” etc. are surface concepts,
while the underlying deep concepts have to do with sequencing and the
mechanics of re-sequencing, which means cycles, rhythms and periodicities.



We all know that the DNA is a *sequence*. Then, if one wants to understand
how the DNA functions, one had better resign to the fact that one has to
deal with *sequences*, whether one likes the topic or not. As there can be
nothing philosophically new in the explanation of how the DNA works, the
only subject that needs investigation is, why one has such a reticence to
deal with places, priorities, rankings, order, first and last becoming last
and first, etc. Maybe the door to the edifice of insights on how the
interplay between mixtures and sequences actually works and what this
interplay produces; maybe this door opens from a well-barricaded corridor
within the cellar of the sub-conscious, hidden among some skeletons of {to
have sunken low, defeats of self-esteem, to have been downgraded, to be
among the last, to be a low-ranking individual, etc.}. One of the
techniques of influencing people with low self-esteem is to encourage them
to find the discipline in which they are really good. In how many ways can
a person be classified and how many of these ranking results are
contradictory? Is the concept of cognitive dissonance linked to the
similarity of two orders? Number theory should jump onto the subject of
intermediate states between two differing permutations, as it is intimately
connected with the subject of how DNA functions. Which names fit best the
patterns we observe while doing manifold re-orderings is presently of a
secondary importance. Of primary importance is presently to observe, what
happens if a *sequence* is turned into a different *sequence*. After all,
we deal with *sequences*, don’t we.


2018-02-10 16:24 GMT+01:00 Stanley N Salthe <ssal...@binghamton.edu>:

> Xueshan -- I think one can condense some of your insights hierarchically,
> as:
>
> In a system having language, information seemingly may be obtained in
> other ways as well. It would be a conceptually broader category. Thus
> (using the compositional hierarchy):
>
>         [information [language [signal]]]
>
> Meaning that, when a system has language, all information will be
> understood or construed by way of linguistic constructs.
>
> (Here I am using ‘signal’ as being more specific than Peirce’s ‘sign’,
> where:
>
>         [sign [information [...]]] )
>
> Then, more dynamically (using the subsumptive hierarchy):
>
>         {language {signal {information}}}
>
> Information in a languaged system is derived by way linguistic formations,
> so that, even though it is an extremely broad category, information
> (informing) only emerges by way of linguistically informed transformations.
>
> STAN
>
> On Sat, Feb 10, 2018 at 3:21 AM, Xueshan Yan <y...@pku.edu.cn> wrote:
>
>> Dear Colleagues,
>>
>> I have read the article "The languages of bacteria" which Gordana
>> recommended, and has gained a lot of inspiration from it. In combination
>> with Sung's comparative linguistics exploration on cell language and human
>> language, I have the following learning feelings to share with everyone:
>>
>> In this article, the author recognized that bacteria have evolved
>> multiple languages for communicating within and between species. Intra- and
>> interspecies cell-cell communication allows bacteria to coordinate various
>> biological activities in order to behave like multicellular organisms. Such
>> as AI-2, it is a general language that bacteria use for intergenera
>> signaling.
>>
>> I found an interesting phenomenon in this paper: the author use the
>> concept *information* 3 times but the concept *signal* (signal or
>> signaling) 55 times, so we have to review the history and application of
>> “information” and “signal” in biology and biochemistry, it is helpful for
>> us to understand the relationship between language, signal, and information.
>>
>> The origin of the concept of signal (main the signal transduction) can be
>> traced back to the end of the 1970s. But until 1980, biochemist and
>> endocrinologist Martin Rodbell published an article titled: “The Role of
>> Hormone Receptors and GTP-Regulatory Proteins in Membrane Transduction" in 
>> *Nature,
>> *in this paper he used the "signal transduction" first time. Since then,
>> the research on signal transduction is popular in biology and biochemistry.
>>
>> As for any information transmission system, if we pay more attention to
>> its transmission carrier instead of its transmission content, we are used
>> to employing "signal transmission" instead of "signal transduction". From
>> the tradition of the early use of information concept, the signal
>> transduction study of cells is only equivalent to the level of
>> telecommunications before 1948. Outwardly, before the advent of Shannon's
>> information theory, the central issue of telecommunications is "signal"
>> rather than "information". After that, the central issue of
>> telecommunications is "information" rather than "signal".
>>
>> According to the application history of information concept, nearly all
>> the essential problems behind the concepts of communication, messenger,
>> signal and so on may be information problems. Just as the language problem
>> what we are discussing here, our ultimate goal is to analyze the
>> information.
>>
>>
>>
>> For the same reason, I recommend another two papers:
>>
>> 1. Do Plants Think?  (June 5, 2012, *Scientific American*)
>>
>> (http://www.scientificamerican.com/article/do-plants-think-d
>> aniel-chamovitz/#rd?sukey=fc78a68049a14bb24ce82efd8ef931e640
>> 57ce6142b1f2f7b919612d2b3f42c07f559f5be33be0881613ccfbf5b43c4b)
>>
>> 2. Plants Can Think, Feel and Learn  (December 3, 2014, *New Scientist*)
>>
>> (http://www.newscientist.com/article/mg22429980-400-root-int
>> elligence-plants-can-think-feel-and-learn)
>>
>> From which we can judge whether or not a plants informatics can exists.
>>
>>
>>
>> Best wishes,
>>
>> Xueshan
>>
>>
>>
>> *From:* fis-boun...@listas.unizar.es [mailto:fis-boun...@listas.unizar.es]
>> *On Behalf Of *Sungchul Ji
>> *Sent:* Thursday, February 8, 2018 9:10 PM
>> *To:* Francesco Rizzo <13francesco.ri...@gmail.com>; Terrence W. DEACON <
>> dea...@berkeley.edu>
>> *Cc:* Fis, <fis@listas.unizar.es>
>> *Subject:* Re: [Fis] The unification of the theories of information
>> based on the cateogry theory
>>
>>
>>
>> Hi Terry,  and FISers,
>>
>>
>>
>> Can it be that "language metaphor" is akin to a (theoretical) knife that,
>> in the hands of a surgeon, can save lives but, in a wrong hand, can kill?
>>
>>
>>
>> All the best.
>>
>>
>>
>> Sung
>> ------------------------------
>>
>> *From:* Francesco Rizzo <13francesco.ri...@gmail.com>
>> *Sent:* Thursday, February 8, 2018 2:56:11 AM
>> *To:* Terrence W. DEACON
>> *Cc:* Fis,; Sungchul Ji
>> *Subject:* Re: [Fis] The unification of the theories of information
>> based on the cateogry theory
>>
>>
>>
>> Caro Terry estensibile a tutti,
>>
>> è sempre un piacere leggerTi e capirTi. La  general theory of
>> information è preceduta da un sistema (o semiotica) di significazione e
>> seguita da un sistema (o semiotica ) di comunicazione. Tranne che quando si
>> ha un processo comunicativo come il passaggio di un Segnale (che non
>> significa necessariamente 'un segno') da una Fonte, attraverso un
>> Trasmettitore, lungo un Canale, a un Destinatario. In un processo tra
>> macchina e macchina il segnale non ha alcun potere 'significante'. In tal
>> caso non si ha significazione anche se si può dire che si ha passaggio di
>> informazione. Quando il destinatario è un essere umano (e non è necessario
>> che la fonte sia anch'essa un essere umano) si è in presenza di un processo
>> di significazione. Un sistema di significazione è una costruzione semiotica
>> autonoma, indipendente da ogni possibile atto di comunicazione che
>> l'attualizzi. Invece ogni processo di comunicazione tra esseri umani -- o
>> tra ogni tipo di apparato o struttura 'intelligente, sia meccanico che
>> biologico, -- presuppone un sistema di significazione come propria o
>> specifica condizione. In conclusione, è possibile avere una semiotica della
>> significazione indipendente da una semiotica della comunicazione; ma è
>> impossibile stabilire una semiotica della comunicazione indipendente da una
>> semiotica della significazione.
>>
>> Ho appreso molto da Umberto Eco a cui ho dedicato il capitolo 10. Umberto
>> Eco e il processo di re-interpretazione e re-incantamento della scienza
>> economica (pp. 175-217) di "Valore e valutazioni. La scienza dell'economia
>> o l'economia della scienza" (FrancoAngeli, Milano, 1997). Nello mio stesso
>> libro si trovano:
>>
>> - il capitolo 15. Semiotica economico-estimativa (pp. 327-361) che si
>> colloca nel quadro di una teoria globale di tutti i sistemi di
>> significazione e i processi di comunicazione;
>>
>> - il sottoparagrafo 5.3.3 La psicologia genetica di Jean Piaget e la
>> neurobiologia di Humberto Maturana e Francesco Varela. una nuova
>> epistemologia sperimentale della qualità e dell'unicità (pp. 120-130).
>>
>> Chiedo scusa a Tutti se Vi ho stancati o se ancora una volta il mio
>> scrivere in lingua italiana Vi crea qualche problema. Penso che il dono che
>> mi fate è, a proposito della QUALITA' e dell'UNICITA',  molto più grande
>> del (per)dono che Vi chiedo. Grazie.
>>
>> Un saluto affettuoso.
>>
>> Francecso
>>
>>
>>
>>
>>
>> 2018-02-07 23:02 GMT+01:00 Terrence W. DEACON <dea...@berkeley.edu>:
>>
>> Dear FISers,
>>
>>
>>
>> In previous posts I have disparaged using language as the base model for
>> building a general theory of information.
>>
>> Though I realize that this may seem almost heretical, it is not a claim
>> that all those who use linguistic analogies are wrong, only that it can be
>> causally misleading.
>>
>> I came to this view decades back in my research into the neurology and
>> evolution of the human language capacity.
>>
>> And it became an orgnizing theme in my 1997 book The Symbolic Species.
>>
>> Early in the book I describe what I (and now other evolutionary
>> biologists) have come to refer to as a "porcupine fallacy" in evolutionary
>> thinking.
>>
>> Though I use it to critique a misleading evolutionary taxonomizing
>> tendency, I think it also applies to biosemiotic and information theoretic
>> thinking as well.
>>
>> So to exemplify my reasoning (with apologies for quoting myself) I append
>> the following excerpt from the book.
>>
>>
>>
>> "But there is a serious problem with using language as the model for
>> analyzing other
>>
>> species’ communication in hindsight. It leads us to treat every other
>> form of communication as
>>
>> exceptions to a rule based on the one most exceptional and divergent
>> case. No analytic method
>>
>> could be more perverse. Social communication has been around for as long
>> as animals have
>>
>> interacted and reproduced sexually. Vocal communication has been around
>> at least as long as frogs
>>
>> have croaked out their mating calls in the night air. Linguistic
>> communication was an afterthought,
>>
>> so to speak, a very recent and very idiosyncratic deviation from an
>> ancient and well-established
>>
>> mode of communicating. It cannot possibly provide an appropriate model
>> against which to assess
>>
>> other forms of communication. It is the rare exception, not the rule, and
>> a quite anomalous
>>
>> exception at that. It is a bit like categorizing birds’ wings with
>> respect to the extent they possess or
>>
>> lack the characteristics of penguins’ wings, or like analyzing the types
>> of hair on different mammals
>>
>> with respect to their degree of resemblance to porcupine quills. It is an
>> understandable
>>
>> anthropocentric bias—perhaps if we were penguins or porcupines we might
>> see more typical wings
>>
>> and hair as primitive stages compared to our own more advanced
>> adaptations—but it does more to
>>
>> obfuscate than clarify. Language is a derived characteristic and so
>> should be analyzed as an
>>
>> exception to a more general rule, not vice versa."
>>
>>
>>
>> Of course there will be analogies to linguistic forms.
>>
>> This is inevitable, since language emerged from and is supported by a
>> vast nonlinguistic semiotic infrastructure.
>>
>> So of course it will inherit much from less elaborated more fundamental
>> precursors.
>>
>> And our familiarity with language will naturally lead us to draw insight
>> from this more familiar realm.
>>
>> I just worry that it provides an elaborate procrustean model that assumes
>> what it endeavors to explain.
>>
>>
>>
>> Regards to all, Terry
>>
>>
>>
>>
>>
>>
>>
>> On Wed, Feb 7, 2018 at 11:04 AM, Jose Javier Blanco Rivero <
>> javierwe...@gmail.com> wrote:
>>
>> In principle I agree with Terry. I have been thinking of this, though I
>> am still not able to make a sound formulation of the idea. Still I am
>> afraid that if I miss the chance to make at least a brief formulation of it
>> I will lose the opportunity to make a brainstorming with you. So, here it
>> comes:
>>
>> I have been thinking that a proper way to distinguish the contexts in
>> which the concept of information acquires a fixed meaning or the many
>> contexts on which information can be somehow observed, is to make use of
>> the distinction between medium and form as developed by N. Luhmann, D.
>> Baecker and E. Esposito. I have already expressed my opinion in this group
>> that what information is depends on the system we are talking about. But
>> the concept of medium is more especific since a complex system ussualy has
>> many sources and types of information.
>> So the authors just mentioned, a medium can be broadly defined as a set
>> of loosely coupled elements. No matter what they are. While a Form is a
>> temporary fixed coupling of a limited configuration of those elements.
>> Accordingly, we can be talking about DNA sequences which are selected by
>> RNA to form proteins or to codify a especific instruction to a determinate
>> cell. We can think of atoms forming a specific kind of matter and a
>> specific kind of molecular structure. We can also think of a vocabulary or
>> a set of linguistic conventions making possible a meaningful utterance or
>> discourse.
>> The idea is that the medium conditions what can be treated as
>> information. Or even better, each type of medium produces information of
>> its own kind.
>> According to this point of view, information cannot be transmitted. It
>> can only be produced and "interpreted" out of the specific difference that
>> a medium begets between itself and the forms that take shape from it. A
>> medium can only be a source of noise to other mediums. Still, media can
>> couple among them. This means that media can selforganize in a synergetic
>> manner, where they depend on each others outputs or complexity reductions.
>> And this also mean that they do this by translating noise into information.
>> For instance, language is coupled to writing, and language and writing to
>> print. Still oral communication is noisy to written communication. Let us
>> say that the gestures, emotions, entonations, that we make when talking
>> cannot be copied as such into writing. In a similar way, all the social
>> practices and habits made by handwriting were distorted by the introduction
>> of print. From a technical point of view you can codify the same message
>> orally, by writing and by print. Still information and meaning are not the
>> same. You can tell your girlfriend you love her. That interaction face to
>> face where the lovers look into each others eye, where they can see if the
>> other is nervous, is trembling or whatever. Meaning (declaring love and
>> what that implies: marriage, children, and so on) and information (he is
>> being sincere, she can see it in his eye; he brought her to a special
>> place, so he planned it, and so on) take a very singular and untranslatable
>> configuration. If you write a letter you just can say "I love you". You
>> shall write a poem or a love letter. Your beloved would read it alone in
>> her room and she would have to imagine everything you say. And  imagination
>> makes information and meaning to articulate quite differently as in oral
>> communication. It is not the same if you buy a love card in the kiosk and
>> send it to her. Maybe you compensate the simplicity of your message by
>> adding some chocolates and flowers. Again, information (jumm, lets see what
>> he bought her) and meaning are not the same. I use examples of social
>> sciences because that is my research field, although I have the intuition
>> that it could also work for natural sciences.
>>
>> Best,
>>
>> JJ
>>
>> El feb 7, 2018 10:47 AM, "Sungchul Ji" <s...@pharmacy.rutgers.edu>
>> escribió:
>>
>> Hi  FISers,
>>
>>
>>
>> On 10/8/2017, Terry wrote:
>>
>>
>>
>> " So basically, I am advocating an effort to broaden our discussions and
>> recognize that the term information applies in diverse ways to many
>> different contexts. And because of this it is important to indicate the
>> framing, whether physical, formal, biological, phenomenological,
>> linguistic, etc.
>>
>> . . . . . . The classic syntax-semantics-pragmatics distinction
>> introduced by Charles Morris has often been cited in this respect, though
>> it too is in my opinion too limited to the linguistic paradigm, and may be
>> misleading when applied more broadly. I have suggested a parallel, less
>> linguistic (and nested in Stan's subsumption sense) way of making the
>> division: i.e. into intrinsic, referential, and normative
>> analyses/properties of information."
>>
>>
>>
>> I agree with Terry's concern about the often overused linguistic metaphor
>> in defining "information".  Although the linguistic metaphor has its
>> limitations (as all metaphors do), it nevertheless offers a unique
>> advantage as well, for example, its well-established categories of
>> functions (see the last column in *Table 1*.)
>>
>>
>>
>> The main purpose of this post is to suggest that all the varied theories
>> of information discussed on this list may be viewed as belonging to the
>> same category of ITR (Irreducible Triadic Relation) diagrammatically
>> represented as the 3-node closed network in the first column of *Table 1*
>> .
>>
>>
>>
>> *Table 1.*  The postulated universality of ITR (Irreducible Triadic
>> Relation) as manifested in information theory, semiotics, cell language
>> theory, and linguistics.
>>
>> *Category Theory*
>>
>>
>> *   f            g*
>>
>>
>>
>>
>> *   A -----> B ------>
>> C    |                           ^    |                            |    
>> |______________|*
>> *   h*
>>
>>
>>
>> *ITR (Irreducible Triadic Relation**)*
>>
>> *Deacon’s theory of information*
>>
>> *Shannon’s*
>>
>> *Theory of*
>>
>> *information*
>>
>> *Peirce’s theory of signs*
>>
>> *Cell language theory*
>>
>>
>> *Human language(Function)*
>>
>> A
>>
>> *Intrinsic *information
>>
>> Source
>>
>> Object
>>
>> Nucleotides*/
>> Amion acids
>>
>> Letters
>> (Building blocks)
>>
>> B
>>
>> *Referential *information
>>
>> Message
>>
>> Sign
>>
>> Proteins
>>
>> Words
>> (Denotation)
>>
>> C
>>
>> *Normative *information
>>
>> Receiver
>>
>> Interpretant
>>
>> Metabolomes
>> (Totality of cell metabolism)
>>
>> Systems of words
>> (Decision making & Reasoning)
>>
>> f
>>
>> ?
>>
>> Encoding
>>
>> Sign production
>>
>> Physical laws
>>
>> Second articulation
>>
>> g
>>
>> ?
>>
>> Decoding
>>
>> Sign interpretation
>>
>> Evoutionary selection
>>
>> First and Third articulation
>>
>> h
>>
>> ?
>>
>> Information flow
>>
>> Information flow
>>
>> Inheritance
>>
>> Grounding/
>>
>> Habit
>>
>> *Scale*
>>
>> *Micro-Macro?*
>>
>> *Macro*
>>
>> *Macro*
>>
>> *Micro*
>>
>> *Macro*
>>
>>
>>
>> *There may be more than one genetic alphabet of 4 nucleotides.  According
>> to the "multiple genetic alphabet hypothesis', there are n genetic
>> alphabets, each consisting of 4^n letters, each of which in turn
>> consisting of n nucleotides.  In this view, the classical genetic
>> alphabet is just one example of the n alphabets, i.e., the one with n = 1.
>> When n = 3, for example, we have the so-called 3rd-order genetic alphabet
>> with 4^3 = 64 letters each consisting of 3 nucleotides, resulting in the
>> familiar codon table.  Thus, the 64 genetic codons are not words as widely
>> thought (including myself until recently) but letters!  It then follows
>> that proteins are words and  metabolic pathways are sentences.  Finally,
>> the transient network of metbolic pathways (referred to as
>> "hyperstructures" by V. Norris in 1999 and as "hypermetabolic pathways" by
>> me more recently) correspond to texts essential to represent
>> arguement/reasoning/computing.  What is most exciting is the recent
>> discovery in my lab at Rutgers that the so-called "Planck-Shannon plots" of
>> mRNA levels in living cells can identify function-dependent "hypermetabolic
>> pathways" underlying breast cancer before and after drug
>> treatment (manuscript under review).
>>
>>
>>
>> Any comments, questions, or suggestions would be welcome.
>>
>>
>>
>> Sung
>>
>>
>>
>>
>> _______________________________________________
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>> Fis@listas.unizar.es
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>>
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>>
>>
>>
>>
>>
>> --
>>
>> Professor Terrence W. Deacon
>> University of California, Berkeley
>>
>>
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