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,



From: [] On
Behalf Of Sungchul Ji
Sent: Thursday, February 8, 2018 9:10 PM
To: Francesco Rizzo <>; Terrence W. DEACON
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
< <> > 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. 



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

. . . . . . 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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