Hello Terry, Sung, FIS colleagues

There is a notion of “body language”.

Perhaps it might be possible to develop a general theory of language that can 
take into account bacteria and dogs (according to Nature 
http://www.nature.com/news/dogs-can-tell-when-praise-is-sincere-1.20514) as 
well as plants https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2634130/ & 
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2688289/ cognitive agents with 
different levels of cognition which communicate and process information in 
order to survive.

One may build a theory of communication of information by just paying attention 
to what has been sent with respect to the cognitive structures of a sender and 
what has been received with respect to the cognitive structure of a receiver. 
Here cognitive means embodied and should include all sensors, actuators, memory 
and information processing mechanisms. As in biology thre are different kinds 
of organisms there are also different kinds of “languages”. There are small 
languages communicated in relatively simple ways between simple agents (like 
cells) and big languages used by complex agents like humans.

Why not?

Best wishes,

On 2018-02-13, 06:33, "Fis on behalf of Terrence W. DEACON" 
<fis-boun...@listas.unizar.es<mailto:fis-boun...@listas.unizar.es> on behalf of 
dea...@berkeley.edu<mailto:dea...@berkeley.edu>> wrote:

To claim that:

"without a language, no communication would be possible"

one must be using the term "language" in a highly metaphoric sense.

Is scent marking a language?
Sexual displays, like a peacock's tail?
How about a smile or frown?
Is the pattern of colors of a flower that attracts bees a language?
Was the evolution of language in humans just more of the same, not
something distinct from a dog's bark?
When a person is depressed, their way of walking often communicates
this fact to others; so is this slight modification of posture part of
a language?
If I get the hiccups after eating is this part of a language that
communicates my indigestion?

Is this usage of the term 'language' simply referring to the necessity
of a shared medium of communication? Is it possible to develop a
general theory of information by simply failing to make distinctions?

― Terry

On 2/12/18, Sungchul Ji 
<s...@pharmacy.rutgers.edu<mailto:s...@pharmacy.rutgers.edu>> wrote:
Hi FISers,

(1) I think language and communication cannot be separated, since without a
language, no communication would be possible (see Figure 1).

                                              Sender ------->  Message
-------->  Receiver



“Language and communication are both irreducibly triadic; i.e., the three
nodes and three edges are essential for communication, given a language or
code understood by both the sender and receiver.”   f =  encoding; g =
decoding; h = information flow.

Figure 1.  A diagrammatic representation of the irreducibly triadic nature
of communication and language.

(2) I think it may be justified and useful to distinguish between
anthropomorphic language metaphor (ALM) and non-athropomorphic language
metaphor (NLM).  I agree with many of the members of this list that we
should not apply ALM to biology uncritically, since such an approch to
biology may lead to  unjustifiable anthropomorphisms.
(https://en.wikipedia.org/wiki/Homunculus) and the anthropocentric theory of

(3) Table 1 below may represent one possible example of NLM.  Although the
linguistic terms such as letters, words, sentences, etc. are used in this
table, they  are matrially/ontologically  different from their molecular
coutner parts; e.g., letters are  different from nucleotides, protein
domians , etc.,and  words are different from genes, proteins, etc., but
there are unmistakable common formal features among them.

Table 1.  The formal and material aspects of the cell language (Cellese).

\      Material Aspect
     \    (Function)
Formal Aspect     \
    (Function)             \

DNA Language
Information transmission in time)

RNA Language
Information transmission in space, from DNA to proteins)

Protein Language
Energy transduction
from chemical to mechanical; i.e., conformon production)

Chemical Language
Source of free energy)

(To build)

4n nucleotides
n = 1, 2, 3, 4, . . .
Exons (?)

Protein domains

Partial chemical reactions

(To denote)



Full chemical reactions

(To decide)

cis-Genes (?)**

Metabolic pathways

Chemical gradients

(To reason/compute)

trans-Genes (?)**

‘Hypermetabolic pathways’

Chemical waves (?)

*I recently proposed that there are n (with n = 1 ~103?) genetic alphabets,
each containing 4^n letters and each letter in turn consisting of n
nucleotides.  In this view, the 64 codons are the so-called 3rd-order
letters , not words as widely assumed.
**cis-Genes are here defined as those genes covalently linked to each other
and hence being in the same chromosome, whereas trans-genes are defined as
those genes that are located in different chromos

(4)  The terms, DNese, RNese, and proteinese were coined by a young American
biochemist from Mexico City whom I met at the International Workshop on the
Linguistics of Biology and the Biology of Language held in Cuernavaca,
Mexico, in 1998, where I had presented the cell language ('cellese') theory,
prior to the young biochemist’s lecture  which followed mine the next day.
In his lecture, he surprised me by announcing these neologisms, which I did
not quite know how to justify.   But it took almost 20 years for me to
finally realize the utility of these terms for entirely different reasons, I
am sure, from those of the young biochemist from Mexico City.   I am
responsible for the coinage of cellese and  chemicalese in Table 1.

(5) If Table 1 is right, the cellese and its sub-languages, DNese, RNese,
proteinese and chemiclaese, are complemetary unions of form and matter.

If  you have any questions or comments, pleae let me know.

All the best.

(My time is out.  I am signing out in a hurry.)

From: Fis <fis-boun...@listas.unizar.es<mailto:fis-boun...@listas.unizar.es>> 
on behalf of Xueshan Yan
Sent: Monday, February 12, 2018 6:31 AM
To: FIS Group
Cc: 'Jose Javier Blanco Rivero'
Subject: Re: [Fis] The unification of the theories of information based on
the cateogry theory

Dear Javier and Dear Stan,


1. I very much agree with you as follows:

“I think that only signals can be transmitted, not information. Information
can only be gained by an observer (a self-referential system) that draws a

A Chinese scholar Dongsheng Miao’s argument is: There is no information can
exists without carrier, i.e. No naked can exists.

I think both of you two are expressing a principle of information science.

2. According to Linguistics, the relationship between language and
communication is:

Language is a tool of communication about information.

Of course, this is only limited to the human atmosphere. So I think that all
(Human) Semiotics ((Human) Linguistics), (Human) Communication Study should
be the subdisciplines of Human Informatics.


Dear Xueshan,

Thanks for sharing your interesting remarks and references. I think no one
really wants to deny the crucial role the language metaphor has played in
the thinking of communication and information models. But I believe the
crucial point is to distinguish between language and communication. Language
is for us humans the main communication medium, though not the only one. We
tend to describe other communication media in society and nature by mapping
the language-like characteristics they have. This has been useful and
sucessful so far. But pushing the language metaphor too far is showing its
analytical limits. I think we need to think of a transdisciplinary theory of
communication media. On the other hand, I agree with you that we need to
check the uses of the concepts of signal and information. I think that only
signals can be transmitted, not information. Information can only be gained
by an observer (a self-referential system) that draws a distinction.





According to Peirce, language is only one of the systematic signs. Here we
consider sign, signal, symbol as the same thing. So, more precisely in my

{signal {information}},   or   {substrate {signal {information}}}

But not

{language {signal {information}}}

If you remember, in our previous discussions, I much appreciate the

The hierarchy idea is very important to our study which is initially
introduced by Pedro, Nikhil and you.


Xueshan -- I think one can condense some of your insights hierarchically,

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’,

         [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.


Best wishes to all,



El feb 10, 2018 5:23 AM, "Xueshan Yan"
<y...@pku.edu.cn<mailto:y...@pku.edu.cn><mailto:y...@pku.edu.cn>> escribió:

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

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

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)


2. Plants Can Think, Feel and Learn  (December 3, 2014, New Scientist)


From which we can judge whether or not a plants informatics can exists.

Best wishes,


On Behalf Of Sungchul Ji
Sent: Thursday, February 8, 2018 9:10 PM
To: Francesco Rizzo
Cc: Fis, 
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.



From: Francesco Rizzo
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.


2018-02-07 23:02 GMT+01:00 Terrence W. DEACON

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

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

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

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

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.



El feb 7, 2018 10:47 AM, "Sungchul Ji"

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,

. . . . . . 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

Category Theory

    f            g
    A -----> B ------> C
     |                           ^
     |                            |

ITR (Irreducible Triadic Relation)

Deacon’s theory of information


Theory of


Peirce’s theory of signs

Cell language theory

Human language


Intrinsic information



Amion acids

(Building blocks)


Referential information






Normative information



(Totality of cell metabolism)

Systems of words
(Decision making & Reasoning)




Sign production

Physical laws

Second articulation




Sign interpretation

Evoutionary selection

First and Third articulation



Information flow

Information flow










*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.


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Professor Terrence W. Deacon
University of California, Berkeley

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