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-daniel-chamovitz/ #rd?sukey=fc78a68049a14bb24ce82efd8ef931e64057ce6142b1f2f7b919612d2b3f42c07f 559f5be33be0881613ccfbf5b43c4b） 2. Plants Can Think, Feel and Learn (December 3, 2014, New Scientist) (http://www.newscientist.com/article/mg22429980-400-root-intelligence-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 < <mailto:13francesco.ri...@gmail.com> 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 <mailto: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 <mailto: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 <mailto: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 _______________________________________________ Fis mailing list Fis@listas.unizar.es <mailto:Fis@listas.unizar.es> http://listas.unizar.es/cgi-bin/mailman/listinfo/fis <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flistas.uniz ar.es%2Fcgi-bin%2Fmailman%2Flistinfo%2Ffis&data=02%7C01%7Csji%40pharmacy.rut gers.edu%7Cca4905ddbcb943df537b08d56ec96c4c%7C927347c284584fde99b9ca9ba94d96 e0%7C1%7C0%7C636536733755726637&sdata=ir%2FcgnTkNiV8YXWkbn3T4FULEtrqVHFhg%2F FFVuDc9IA%3D&reserved=0> _______________________________________________ Fis mailing list Fis@listas.unizar.es <mailto:Fis@listas.unizar.es> http://listas.unizar.es/cgi-bin/mailman/listinfo/fis <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flistas.uniz ar.es%2Fcgi-bin%2Fmailman%2Flistinfo%2Ffis&data=02%7C01%7Csji%40pharmacy.rut gers.edu%7Cca4905ddbcb943df537b08d56ec96c4c%7C927347c284584fde99b9ca9ba94d96 e0%7C1%7C0%7C636536733755726637&sdata=ir%2FcgnTkNiV8YXWkbn3T4FULEtrqVHFhg%2F FFVuDc9IA%3D&reserved=0> -- Professor Terrence W. Deacon University of California, Berkeley _______________________________________________ Fis mailing list Fis@listas.unizar.es <mailto:Fis@listas.unizar.es> http://listas.unizar.es/cgi-bin/mailman/listinfo/fis <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flistas.uniz ar.es%2Fcgi-bin%2Fmailman%2Flistinfo%2Ffis&data=02%7C01%7Csji%40pharmacy.rut gers.edu%7Cca4905ddbcb943df537b08d56ec96c4c%7C927347c284584fde99b9ca9ba94d96 e0%7C1%7C0%7C636536733755726637&sdata=ir%2FcgnTkNiV8YXWkbn3T4FULEtrqVHFhg%2F FFVuDc9IA%3D&reserved=0>
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