Group Discussions in Biosemiotics
2012 Discussion of the paper Organic semiosis and Peircean semiosis
Marcello Barbieri
Dear Colleagues, In 2009, as you may remember, I asked Søren Brier and Cliff Joslyn to edit a Special Issue on the concept of “Information in Biosemiotics”, and after a long saga, that project has now been completed. The articles will soon appear online and in a few months will also come out on paper. Three of them explicitly claim that the cell is fully capable of interpretation, and criticize my view that organic semiosis is based exclusively on coding and decoding. They have been written by (1) Søren Brier and Cliff Joslyn, (2) Anton Markoš and Fatima Cvrčková and (3) Argyris Arnellos, Luis Emilio Bruni, Charbel Niño El-Hani and John Collier. This surely means that there is pluralism in our field, but that issue is too important and I could not let the criticism go unanswered. I have decided therefore to reply with the article that I am now sending in attachment. This too is pluralism. All the best Marcello
2 Stanley N Salthe
Musing upon the coding-interpretation controversy as presented by Marcello:
We have here a lively dialectic between those that hold interpretive semiosis to be the only kind (Peircean) of semiosis, and Marcello, who denies that biological codings are interpretive.
Both sides restrict semiosis to living systems and their social creations. There is a third position -- glancingly acknowledged by Marcello in a nod to Taborsky -- and this is that Peircean semiosis can be found throughout nature, as held by both Peirce and Sebeok, and given a label by Deely -- ‘physiosemiosis’.
This latter is my own position as well (laid out in a paper that is awaiting publication in Cybernetics and Human Knowing). The burden of my position is that certain abiotic locales, emergent from local energy flows, have a primitive (proto)semiosis as a result of their form. It would be such locales, in my view, that would have been the sites of the first living systems. My purpose in this is twofold: (1) to bring in evolutionary and materialist perspectives (nothing comes from nothing; everything has a precursor); (2) to urge an expansion of physicochemical discourse toward a more naturalistic and less technologically-oriented purview.
Like most scientists, Marcello is dubious of generalizing, and this, I feel, forms the basis of his opposition to attributing Peircean semiotics outside of the productions of nervous systems. He seems here to be saying, in effect, that if we can outline in detail the mechanistic steps involved in what could be viewed by a Peircean as interpretive semiosis, then we will have ‘explained away’ interpretation, which is then no longer needed in a purely naturalistic perspective. This is the traditional perspective of scientific reductionism. Well, then, if interpretive semiosis mediated by nervous systems in animals could be given a step-by-step microscopic description, I suppose we would have disposed of interpretation here as well!
STAN
3 Peter Harries-Jones
Dear Stan, Yes of course thermodynamic entropy creates patterned gradients which create specific sites in ecosystems. But does this have the same pattern characteristics as the affordance that the site gives to living organisms? Let us take a clear example of cyanobacteria which is site specific but whose evolutionary integration with other living organisms who become aerobic-dependent follows a very different pattern than that of the initial thermodynamic biochemical soup in which cyanobacteria arose.
That pattern can be derived from a study of bioentropy rather than thermodynamic entropy, bioentropy characteristics originally identified by Norbert Wiener and called (in a not very satisfactory term) "islands of order." What he meant was to point to characteristically different feedback patterns.
Now I suppose that it is possible -for a while at least- to engage in a double description of thermodynamic and bioentropic entropy, or even, as Taborsky does, create a functional equation for the two, but eventually one simply has to go to the optician to buy a new set of spectacles to register the consequences of feedback divergence. This might even lead to a search for new equations registering divergence in fractal dimensions some sort of equation that ladders fractals "upwards" rather than "downwards" as a result of ecosystem interaction .
All the best, Peter.
4 Stanley N Salthe
Peter -- Thanks for this feedback! Thermodynamics must indeed be 'up front' here, though I did not signal that. I think my main response to you is that the organization of a locale is indeed more detailed and persistent when it is a living one, and this difference was the result of evolution. But from the point of view of physical organization, I see no difference thermodynamically. Both -- for the abiotic, a tornado is a convenient example -- utilize the energy gradients that they destabilize to build and enhance their own form.
Both dissipate the gradients as fast as possible given the constraints of form that must be maintained and not destroyed by the energy flows. What the living have contributed to this perspective is their relative stability, which, importantly, implies also detailed organization modifiable into different forms aimed at different energy gradients. This means that living systems participate in the grand Big Bang scenario by becoming specialized for energy gradients that are not susceptible to spontaneous conduction (diffusion and mass wasting) or susceptible to abiotic dissipative structures (like tornadoes). Indeed, the presence of such unused gradients on a planet would have to have been an important pre-condition for the origin of life.
'Bioentropy', if I understand you aright, would be a form of informational entropy, not the physical entropy I discuss above. But it IS quite important in my proposal here, in the sense that informational entropy (information carrying capacity, or variety) is what has been produced by the evolution of living things, as we picture it as a tree of life. Thermodynamically, this reflects the different energy gradients each kind is dependent upon for its continuance. STAN
5 Howard Pattee
Dear Marcello and colleagues, I agree with you in the usage of code as a syntactic mapping that is independent of interpretation, because that is the case for the genetic code and all cryptographic codes. Of course there are other meanings, as in dress codes or legal codes. However, I define interpretation more broadly as any dynamical actions that are constrained by symbols to execute a function or other meaningful symbolic expressions. The most primitive case is the symbolically constrained dynamic folding that results in a functioning protein.
Attached is a brief explanation of why I use this broader definition. Regards to all, Howard
Attachment – Pattee’s Answer to Marcello- Interpretation
H. H .Pattee : The Dynamics of Interpretation—a Brief Response to Barbieri (5 April 2012)
I have not read the papers that use “code” and “interpretation” in ways with which Barbieri disagrees, so I cannot address what was said. Barbieri is of course correct that we should recognize the differences between genetic symbols and human symbols. It is no wonder that two symbol systems separated by billions of years of evolution have obvious differences in interpretation. What I wonder at are the fundamental processes of interpretation that are similar throughout evolution. In fact, I think the motivation for biosemiotics is based more on these similarities than on the differences. The basic similarities are (1) in both genes and human text, information is recorded in a structurally simple one-dimensional sequence with no intrinsic dynamics using a small, fixed set of arbitrary symbol vehicles, (2) these simple quiescent sequences manage somehow to constrain ineffably complex dynamical systems resulting in adaptive functions or meanings, and (3) in both cases, relatively little information controls endlessly complex coordinated behaviors.
I define all functional processes resulting from symbolic constraint of dynamics as an agent’s interpretation of the symbolic information. I define a code as a syntactic mapping that (like copying) is independent of interpretation. There is nothing novel about these definitions. I am simply describing what we can observe using words with their conventional meanings.
Even if you are not interested in the folding problem, I urge you to watch what I call the first level of interpretation of a gene that has been coded into its amino acid residue sequence. This folding can convert a quiescent sequence to an enzyme that speeds up a specific reaction by factors like 1012 to 1016. The folded is simulated at http://www.youtube.com/watch?v=gFcp2Xpd29I. This visual simulation is not as simple as it looks. It requires one of the largest computing systems in the world (thousands of distributed computers) that you can read about at http://folding.stanford.edu/. Many diseases are caused by misinterpretation of the genetic symbols, i.e., incorrect folding.
The higher levels of interpretation or function of this protein are only partially understood. When triggered by environmental changes like temperature and humidity and in cooperation with many other proteins it causes the leaves of plants to die and send their resources to the roots and seeds for the winter. Most biologists simply call this adaptive behavior. They do not call it predictive, purposeful, or altruistic behavior, although it is not easy to say why it is not.
We do not know very much about how the human brain interprets even simple sentences, but the best models at present are artificial neural nets. Barbieri mentions Kohonen networks that have an artificial discrete dynamics. I urge you to also try out the Demonstration of a net searching for an optimum pattern at http://www.cs.bham.ac.uk/~jlw/sem2a2/Web/Kohonen.htm. These are two very different models, but you will see similar patterns of behavior and common features that I claim are characteristic of all processes of interpretation of symbols as I define it. Here are a few common features.
1. The symbolic information is simple, stable, energy-degenerate, and can be unambiguously stored, copied, coded, and communicated without interpretation. 2. The constrained dynamical details appear to us as ineffably complex. That is, we need powerful computers for useful simulations for even the simplest protein function and sensorimotor control. 3. The process of interpretation requires intermediate stages. Folding involves metastable sub-structures that may change under the final fold. Words are recognized before sentences, but may change meaning as the sentence and text is completed. 4. Iterative competitive trial-and-error search is necessary with results (interpretations) that are statistical. Many details may be arbitrary. Knowing the details does not reveal function or meaning. 5. Interpretations of sentences are influenced by context, just as the functions of proteins are influenced by their environment. 6. Interpretation is a global property of the constrained dynamics that may exhibit many types of behavior including generic stability, metastable states, attractors, bifurcations, frustration, and chaos, all of which have corresponding functional consequences in both cells and brains.
6 Peter Wills
Dear Stanley, Peter, Howard and Marcello,
In 1993 (JTB 162, 267) I described a simple chemical system that undergoes a dynamic phase transition as a result of a purely symbolic condition. By "symbolic condition" I mean that the set of possible conditions (different possible polymeric sequences present in the system) are energetically equivalent. Thus, the thermodynamic driving force for the transition depends on a constraint that has "nothing" to do with the energy gradient that enables it. The constraint is purely formal or "informational" (not definable in terms of the quantities defined in physics). "Bioentropy" beyond thermal entropy perhaps. The result of the particular transition I describe is a molecular code: an operational system in which molecular sequences have acquired an arbitrary "meaning". I have described the more general evolutionary consequences of this possibility in my 2009 paper (JTB 257, 345).
In my elementary system, one molecular sequence gets "translated" into another, but it is the systemic effect of the latter (as an enzyme - the result of Howard's "folding" process, but this could, as he says, be any largely thermally constrained dynamic pathway in a more general system) which introduces something different from simple information transmission, what some want to call "interpretation". It seems clear to me that some systems in the universe (brains must be examples) evolve symbolic representations of other representational codes and even eventually representations of interpretations. Peter
7 Jesper Hoffmeyer
Dear folks I think it might be a good idea to establish a field of protosemiotics, a field to which this highly interesting system described in Peter's mail would surely belong. Protosemiotics would then be the field studying such processes of abiotic systems that might explain how life and semiosis could have occurred on Earth (or elsewhere).
But it is important that we stay sharp in our use of semiotic terms such as symbols. A symbol is a high level sign that presupposes a conventional (e.g. historically acquired) relation between the representamen (the primary sign or sign vehicle) and its supposed referent. I would submit that such a historical convention is at play at the level of genes, i.e. genes refer to proteins in the historically evolved context of a cellular system (the whole cellular apparatus being the interpreting system).
Now, I haven't read Peter's full paper, but judging from the hints given in the mail his system is still very far from the kind of historical agency implied by the term symbol. Nevertheless we must try to establish the ways such symbols were eventually created, and as far as I can see, this is exactly the important problem addressed in Peter's paper. Best wishes, Jesper
8 Re: semiosis at work before life
John Deely
Jesper, how does this proposal of a "protosemiotics" area differ from the proposal in the 6th chapter of all editions of my Basics of Semiotics of "physiosemiosis" as the manner in which was brought about the 'scaffolding' of the physical universe whereby it went from lifeless to able to support life to actually supporting life?
9 Dario Martinelli and Günther Witzany 06 aprile 2012 14:34 Dear colleagues, Please, kindly remove my address from this discussion. I have neither competence nor interest on the topic, to be able to contribute to it. Thank you All the best Dario
Dear Collegues! Please be so kind and remove my address from this discussion also. I am interested in empirical biosemiotics not in metaphysics or similar confusions. Best Wishes Guenther
10 Small clarification (Dario and Günther removed)
Peter Wills
Yes, Jesper, I think you have correctly interpreted what I have attempted. I used the word "symbol" in an extremely limited syntactic sense, meaning no more than "a letter in a given alphabet". Amino acids or nucleotides are good chemical examples. Individuals have some moieties in common with others that make them practically identical for some processes (defining the class/alphabet to which they belong) but show variation in other parts of their structure that make them distinguishable. On the basis of this distinguishability strings (or other arrangements) of letters can contain Shannon information, but much more is required before the information can be said to "mean" anything, a problem I tried to pose about these simple systems in my 1994 paper "Does information acquire meaning naturally?"
When information is used in biological systems it usually involves translation from one alphabet to another, a code. There are many classes of different states of biological subsystems (not just covalently bonded molecules) that serve as functional alphabets for different purposes, as Marcello has amply demonstrated. Then comes the function-generating part of the business (championed by Howard for so long) whereby the information serves as an initial condition for some "folding" process - often a dynamic pathway of potentially enormous complexity that may be largely constrained by "thermal" conditions - order which is inherent in the chemical composition of the system. It is the way in which such order is harnessed (as a result of historical evolution) to become inherent in systems that I want to call "Informed Generation".
I am yet to catch up with the possible distinction between protosemiosis and physiosemiosis. Greetings, Peter
11 About Howard's point
Marcello Barbieri
Dear Howard, I must say that your letter did surprise me! Do you really believe that protein folding is a form of interpretation? You know as much as I do that good honest biologists will never accept that, so why? Just to say that “it’s interpretation all the way down?” Please think about that. Best regards and Happy Easter! Marcello
12 Howard Pattee
Dear Howard, I must say that your letter did surprise me! Do you really believe that protein folding is a form of interpretation?
I don't "really believe" statements in the sense that you ask the question. I am simply defining the word "interpretation" generally as the action of symbols (as information vehicles) on physical systems (as matter and energy). Additionally, the action must be functional for the physical system as agent. I hope you are not objecting to my defining my words even though we may have different definitions. By this general definition (consistent with the basic Peircean triadic relation) there are obviously many levels of interpretation with an endless variety of functions. My brief comment was meant to emphasize that all levels of interpretation are exceedingly complex, and each level will require its own model.
You know as much as I do that good honest biologists will never accept that, so why?
"Honest biologists" who remember their first-year physics will accept that protein folding is the first level where information (as an energy-degenerate non-dynamic sequence) controls an energy and rate- dependent physical activity than has a function (for the cell as agent). I call this interpretation. What do you wish to call it?
Just to say that “it’s interpretation all the way down?”
I certainly do not say interpretation is "all the way down." On the contrary, I know of no level of interpretation below protein folding where information is converted to functional action. That is why I call it the first level. I agree that below the first level there is unknown territory.
Please think about that.
But not over Easter weekend! Also best regards, Howard
13 Marcello Barbieri
Dear Howard,
“…I hope you are not objecting to my defining my words even though we may have different definitions.”
You are certainly free to defining your words as you please. The problem is “who is going to believe them? (a part from Peircean fundamentalists)
"Honest biologists" who remember their first-year physics will accept that protein folding is the first level where information (as an energy-degenerate non-dynamic sequence) controls an energy and rate- dependent physical activity than has a function (for the cell as agent). I call this interpretation.
Yes, “honest biologists” will accept that protein folding is the first level etc. etc…but NONE of them would call that interpretation. Just make a simple test – ASK anybody, students and researchers (again “honest”) and see for yourself.
No, Howard, it is not enough to say “It’s interpretation because I define it that way” It’s like the old lady saying “It’s turtles because that is what I call them” Happy Easter again Marcello
14 DON FAVAREAU
15 Peter Harries-Jones
Dear Jesper, Thanks for the support. After listening ten years and watching biosemiotics go round and round on this point, it seems to me that the Peircian definitions of interpretation, symbol etc., are not robust enough -on their own- to accomplish what we would like them to accomplish so far as the definition of living systems is concerned. Therefore I suggest that they should be accompanied by another set pertaining to "connectivity." The reason for this is that the more one moves towards an ecosystemic interpretation, as compared to a single bio- agency, the more evident is the salience of connectivity to life. A single bio-agency cannot live on its own and is dependent on many sorts of reciprocity. In ‘Biosemiotics’ you identified membranes as the building blocks of life -and not the gene alone. This seems an important contribution, for membranes are reciprocation and exchange nodes. They are, in effect, interfaces which include and exclude. However membranes and interfaces incorporate a different sort of maths. and logic than the explorations of Peirce, a maths, which Mandelbrot called "rough" over "smooth." The "rough" are fractal dimensions with feedback. One thing that they do explain in a very concrete manner is Peirce 'law of habit." One needs then to explore connectivity further to see how fractal self-similarity changes. All the best, Peter.
16 Stanley N Salthe
Howard, Marcello --
Here is the way that protein folding can be seen as interpretation: If cells can control to some extent their internal milieu and if at least some proteins have alternative folding possibilities according to conditions then cells can control the folding of proteins according to their requirements, and are therefore interpreting the genetic material that they have been provided by their species. STAN
17 Günther Witzany
18 Alexei Sharov
Dear biosemioticians,
(1) Although biosemiotics is indeed science (here I agree with Marcello) it does not mean that we have to use the language (and ontology) of physics to describe semiosis. Science is a family of languages, not just one language of physics. The language of physics does not include the notion of agent (agency), thus it cannot capture semiosis. The only agent in physics is a human who designs and implements experiments. Simple semiotic systems can be described in physical terms but this description does not capture evolutionary potential and semiotic freedom. Thus "physiosemiotics" is a self-contradictory term.
(2) Protosemiotics is indeed a very important sub-field within biosemiotics. But it is not the same as "physiosemiotics" because protosemiosis requires agency. Protosemiotic agents (e.g., bacteria) use signs to directly control their functions, whereas eusemiotic agents associate signs with ideal objects, which are systemic internal states not reducible to specific signaling pathways. I will talk about it in Tartu. Of course, there is a transition zone between protosemiosis and eusemiosis (as between non-life and life).
(3) Peirce's classification of signs works in eusemiosis but it is not fully applicable to protosemiosis (because there are no objects and interpretants in protosemiosis). When we (humans) study protosemiosis we can assign objects and interpretants to molecular signs, which helps us to understand it. We say that a triplet of nucleotides "encodes" an aminoacid in a protein, but a cell has no idea of aminoacids. A triplet of nucleotides is a command to sub-agents (ribosome and tRNA) to perform specific actions. Moreover, the cell operates not at the level of triplets but at the level of full coding sequences (or exons in the case of alternative splicing). However, there is some parallelism between proto- and eusemiosis: sign molecules that function due to their shape are similar to icons (proto-icons), sign molecules that combine different shapes (and therefore make an association between two functions) are similar to indexes (proto-indexes), and finally, heritable sets of adaptors can support the existence of proto-symbols (e.g., coding DNA sequences) because they represent an "evolutionary convention". Of course, evolutionary convention is different from human convention because it is inherited rather than learned. Genetic language can be viewed as a proto-language.
(4) Any definition of a "sign", "code", or "information" as a "relationship" or "correspondence" is confusing because it does not refer to agents who developed these relationships and use them to organize and improve their functions. This pragmatic aspect of semiosis is largely ignored by many of our colleagues. Peirce's definition of sign is semantic, not pragmatic (despite the fact that Peirce was the first to talk about "pragmaticism"). He did not accept the notion of "creative evolution" (Henri Bergson) and de-emphasized agency. I agree with Günther Witzany that semiotics of Charles Morris is more relevant for biosemiotics because it is based on pragmatics.
(5) If you are interested in these topics, I present them in my short virtual course on biosemiotics at the seminar moderated by Dick Gordon: http://embryogenesisexplained.com/incoming-lectures The first lecture was on March 14. Slides and discussion are available here: http://embryogenesisexplained.com/2012/03/a-short-course-on-biosemiotics-1.html The next lecture will be on April 18.
Alexei
19 Howard Pattee
Dear Marcello and colleagues,
This is my answer to your test question ("ASK anybody . . . and see for yourself") whether folding is the first step in interpreting genetic information. First, I would say that just asking anybody is not a reliable test. I usually ask experts who know more than I do. As I recall, the first I heard the suggestion that folding is the first step in the interpretation of genetic information was from the geneticist Joshua Lederberg. That would have been at the Karolinska Institute in 1959, the year after Lederberg shared the Nobel Prize (fortranduction) with Beadle and Tatum (for one-gene one-enzyme). Lederberg's suggestion was very controversial at the time. Even after Christian Anfinsen the next year demonstrated that one-dimensional information determined three-dimensional folding (and function in ribonuclease), it still took 12 more years before its fundamental importance was recognized and Anfinsen was awarded the Nobel Prize.
Today, fifty years later, it is generally accepted that the first cellular function mediated by genetic information results from the act of folding. That is why the protein folding problem is so important. All of the steps of genetic information processing before folding (including copying, transcription, translation, synthetase adaptors, ribosome synthesis, and most editing processes) do not involve theinterpretation of the information. One way to understand this is that these are operations on one-dimensional polymer sequences. They are also rate-independent processes. That is, you get the same protein no matter how fast or slow it is synthesized. The first specific rate-controlling function is the 3-dimensional folded enzyme. Therefore it is the first level of interpretation of the genetic information.
Hoffmeyer’s concept of semiotic causation as bringing about effects through interpretation of symbols is useful to distinguish interpretation from the non-interpreted steps before folding. However, the same concept of interpretation can be expressed explicitly physical terms as the non-dynamic, arbitrary (energy- degenerate) symbol structures acting to constrain a functional dynamical process. It is useless to search for an interpretation or meaning in symbols without complementary knowledge of the energy dependent dynamics being constrained by the symbols.
You need not fear my word usage will lead to a plague of pansemioticians and hylozoists. I am not, as you say, “defining words as I please.” I choose my words to conform with standard biological and physical terminology, except where I wish to stimulate some creative thinking. I believe my usage of interpretation conforms with common dictionary definitions, e.g., from Abridged Oxford:Interpretation 1 The result of an action orprocess that expresses the meaning of symbols (as in the performance of a musical score). Of course there are many special narrower usages, e.g.: Interpreter 2 a computer program thatexecutes coded instructions.
I agree it is obvious that genetic interpretation has great differences from cognitive interpretation, but to support the biosemiotic principle of the coexistence of symbols and life, the important point is the fundamental similarities of interpretive processes (see my list of 6 in attached file in my last post).
Sincerely, Howard
20 Reply to Howard (New Mailing List)
Marcello Barbieri
Dear Howard, When I suggested “Ask anybody...and see for yourself”, I did not mean “Ask biologists their opinion” – I knew that you wouldn’t find that useful. What I meant – and I explicitly underlined it – was “Ask biologists if they BELIEVE you when you say that protein folding is interpretation”. Allow me to elaborate. Biologists are quite accustomed to make a “free” use of words in order to describe their discoveries – that’s why they talk of transcription, translation, messengers, tape- reading, splicing, processing, editing etc... those terms are useful because they deliver a clear message and are intuitively appealing. Biologists “believe” them because they understand what they mean and know that they are good at describing what happens. But ask them if they “believe” that protein folding is interpretation, and what you will get – if they are polite – is a laugh. The most usual answer I got is “physicists simply do not understand what biology is about”. Now you may say that you are not interested in such gut-feeling-reactions, but you should. Why would people who are perfectly happy to using fancy words every day, should object so strongly to using the word “interpretation”rather than simply “gene expression” or “epigenesis”? The point is that biologists use words as tools to find real solutions to the problems of life and instinctively reject any attempt to play tricks with them, to solve problems by name-giving. The word “interpretation” is loaded because it means Peircean ideology, and most biologists still genuinely believe in a “honest search of the truth” (how terribly old-fashioned, that is, isn’t it?).
Let me end by saying that I have always admired your work, to the point that I have dedicated a whole volume of our Book Series to a collection of your best essays (publication is imminent). But not even you, Howard, are allowed to play tricks with words. You may well dismiss the gut reactions of ordinary biologists, but they mean a lot, believe me. Your old admirer Marcello
21 DON FAVAREAU
22 Marcello Barbieri
23 DON FAVAREAU
Thank you, my friend! And everyone! :)
24 NEW Mailing List without DON and ANTON
Marcello Barbieri
Dear Søren, I will reply to your email, but first of all I am re-directing it to the LAST MAILING LIST (without Don and Anton, as they explicitly asked). From now on, please make sure to avoid the names of those who have opted out of our discussion group. And if somebody else wants to opt out, please say so NOW. Thank you. Marcello
Søren Brier
Dear Marcello Though I do not have much time presently I cannot resist answering part of this mail. It is especially the sentence “The word “interpretation” is loaded because it means Peircean ideology, and most biologists still genuinely believe in a “honest search of the truth” (how terribly old-fashioned, that is, isn’t it?).” This must mean Marcello that you do not have an ideology but are just interpreting “the facts” and that those can be had objectively and not influenced by any paradigmatic presumptions about reality including the nature of knowledge. Am I wrong in interpreting it thus that it means that scientist know what reality is (Das Ding an Sich) and therefore cannot be tricked or fooled? Thus the received view of biology is ideology free and any other interpretation is not. Would that then include code‐semiotics ? Or does it only go for the Peirceans? Or are we in the situation – as I believe – that there is not simple way to create and interpret data, thus everybody needs an explicit paradigm and have to be reflected about it and it is those reflections along with how we interpret and produce data that we need to discuss in order to search for the truth. Thus those who just rely un‐reflected on a received view are the ones to be distrusted? They are ideologists or fundamentalist that think they have already found the truth in “data”?! Venlig hilsen/best wishes Søren Brier doc. RNDr. Anton Markoš, CSc.
25 Marcello Barbieri
Dear Søren, Let me come now to your points. We all agree that science is about building models, and models of the world are not the world (“the map is not the territory”). Which means that scientists are not the foolish people who “… know what reality is (Das Ding an Sich) and therefore cannot be tricked or fooled”. You are making cheap irony on this point. We all agree that any view of the world is based on metaphysical hypotheses (for example that “there is a world out there”), but this does not mean that all such hypotheses are equivalent. The hypothesis of Intelligent Design, for example, is not equivalent to the hypothesis that life arose by natural means. The discovery of the genetic code raised the problem of understanding how it came into being, and we do NOT want “just-so-stories”. We can use all sorts of terminology but we do not want to solve the problem by name-giving. Let me be more specific. It is an experimental fact that animals are capable of interpretation, so we all accept that interpretive semiosis is a reality. It is also an experimental fact that a genetic code exists in every cell and does not depend on interpretation, so organic semiosis too is a reality. What do we conclude from these two realities? The “common sense” conclusion is that (1) there are two distinct types of semiosis in Nature, (2) that organic semiosis was the first to appear, and (3) that interpretive semiosis came into being much later in animals. What are the Peircean people saying? They say that “it’s interpretation all the way down”, that what is valid for animals is valid for all living creatures, that semiosis always requires interpretation. I agree with you that BOTH answers are equally legitimate from a metaphysical point of view, but don’t ask people to accept that they are equally “believable”. Now, what do we want to do with Biosemiotics? Do we want a “honest search of the truth” in a field that is largely grounded in mystery, or do we want to impose a cultural model of semiosis to all living creatures? I am committed to Biosemiotics as much as you are, Søren, and I am also committed to pluralism, so much so that I have promoted ALL answers, including yours. But what Biosemiotics are we going to build for our children? Best Marcello
26 Vinicius Romanini
I am pressed with deadlines too, but feel obliged to say something at this point. Peircean semeiotics is much more elaborated than the rough caricature you offered in your article. Since I have not read the articles you are responding to, I do not know if you got those strange ideas by yourself or second handed.
Peirce would never oppose himself to "real discontinuity", for instance, which is real secondness. Your article turns Peirce into some sort of Hegelianist, which he was not. Peirce would indeed oppose himself to any metaphysics based on ultimate constitutive parts of reality. The real is the immediate object of a true opinion, and the true opinion is the general ultimate effect (interpretant) that would be produced by the efforts of an ideal community of interpreters.
So there can be no "last word" on any scientific topic, only a falibilistic continuous approach to the truth. "Do not block the way of inquiry" - was one of Peirce´s favorite dictum. Semiotic interpretation is just the production of effects by something that is representing another. There is nothing mysterious about that. As Wittgenstein would say, let´s not argue about words only. Peirce does not say that everything must be semeiotic, but he leaves the inquiry open because there seems to be semeiosis in every corner of reality, and it is up to us to discuss this hypothesis. This is what scientists and phylosophers do. This hypothesis must not be discarded because you do not like it, because you think serious people will never believe it or because you find it obscene and don´t want to show to your children. This sort of argumentation is not fair. It carries a lot of individual prejudice. Remember that what is considered "scientific" in one age might change a lot in another.
We do NOT need a Torquemada throwing "Peircean people" to the fire. If you try to divide biosemioticians into those of "opera buffa" and of "opera seria", you might turned out to be classified where you did not expect to be! With my warmest regards, Vinicius
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27 Reply to Vinicius and three papers
Marcello Barbieri
Dear Vinicius and all, I am sending in attachment the three papers in question, but frankly the real issue is not about them. It is about the difference between organic semiosis and interpretive semiosis, a much larger issue that goes back all the way to the two origins of biosemiotics, one in molecular biology and the other in the humanities. This is the most important problem in our field, today, because it concerns the very essence of biological semiosis. The distinction between protosemiosis and eusemiosis is simply not enough because it is a distinction between two versions of interpretive semiosis, one more primitive and the other more complex, but both based on interpretation. In reality, all that we know suggests that it took a real macroevolution to bring interpretation into existence, that interpretation is based on abduction and that organic semiosis was not a simplified version of it – it was a completely different type of semiosis.
What you say about Peirce is perfectly ok to me, but you missed the point. What I object to is not Peirce but Peircean fundamentalism. I have the highest respect for Peirce, and I was not joking when I compared him to Aristotle – I do believe that abduction is the logical description of a real and immensely important biological mechanism.
You also miss the point when you write that I try to “…divide biosemioticians into those of "opera buffa" and of "opera seria"…” When I created the Editorial Board of our Journal (with complete freedom from the publisher) I invited many humanists and more than 90% of the Board were (and still are) Peirceans . What is that if not a sign of respect and the hope for a real dialogue with the people who have discovered interpretive semiosis? Yes, I was frustrated by those three papers, but not all Peirceans are fundamentalists and I still hope that one day we can reach a real synthesis in our field. Best regards Marcello
3 allegati
A-Anton Markos and Fatima (17 Mar 2012).pdf 273K
B-Soren Brier and Joslyn (10 Mar 2012).pdf 633K
C-Arnellos, Bruni et al (14 Mar 2012).pdf 981K
28 Kalevi Kull
Dear friends and colleagues, There are certainly different types of semiosis. And a possible solution to the controversy of this discussion has been proposed, for instance, in the papers
Vegetative, animal, and cultural semiosis: The semiotic threshold zones. In: Cognitive Semiotics 4 (2009). and Umwelt and modelling. In: Cobley, Paul (ed.), The Routledge Companion to Semiotics. (2010)
What Marcello is calling organic semiosis, is here called vegetative semiosis, and what Marcello calls interpretative semiosis, is here called animal semiosis. Also, as it is argued in these papers, vegetative semiosis is using the operation of recognition, whereas animal semiosis is based on association. These are related to different mechanisms of learning - the animal one requires associative learning. The appearance of new type of semiosis in this case is due to a principally new mechanism of learning (note that learning produces codes). It is also shown in these papers, that vegetative semiosis (close to Marcello's 'organic') can be put into correspondence with iconic semiosis, and animal semiosis (Marcello's 'interpretative') with indexical semiosis. Because, indeed, only the ability to associate signs (icons) and to make new signs from these (indexes) can create cognitive spacial maps, and spatial umwelt. Symbolic semiosis, in this case, will be left for "symbolic species" (i.e., human language, according to Tom Sebeok and Terry Deacon). As minimum, I think, an attempt to put into correspondence different semiotic models is a method that helps to understand each other. With all best wishes Kalevi
29 Paul Cobley
Dear Marcello, Of course, two wrongs do not make a right, but I don’t think that Søren was guilty of cheap irony in his response. In your previous email you actually did oppose ‘science’ to (Peircean) ‘ideology’, an artificial binary construction which can only ever privilege ‘science’. And even as you eschew the idea of a science that claims access to ‘reality’, you then invoke in your reply to Søren the notion of ‘common sense’, the most ideological figure of all. Notwithstanding the retirement of some people from the list, the discussion of how far interpretation might go down appears to me to be one of the most important tasks of biosemiotics now and in the future, as you state. Indeed, in your article you present a very persuasive case for this, as well as a measured picture of the two different positions on the matter in biosemiotics. Yet, if the humanities can shed any light on science, their most important contribution must be the idea that the way the sciences describe themselves is crucial. It’s all very well being careful about methodology and knowing the parameters of current arguments in the philosophy of science, but if the sciences revert to describing themselves informally in terms of ‘verities’, ‘truths’, ‘the bottom line’ and, yes, ‘common sense’, then we know that ideology is at work. You make a good point in your article about discontinuities; but many, especially in the humanities, feel that biology too often mounts an obsessive search for ‘origins’ which is of a piece with ‘ideology’. (This may be why Darwinian evolutionary biology in the last few decades – e.g. Dawkins - has been absolutely forthright about gradualism. Oddly, in one way, that is an affinity that is shared with the ‘interpretation camp’ of biosemiotics). I hope that you don’t think I’m setting the ‘language police’ on you, here. But since the question of the threshold of interpretations is central to the biosemiotics we are trying to “build for our children”, we cannot accomplish anything lasting through rhetoric, only through the dialogue inherent in the ongoing pluralism that you promote. Best, Paul
30 Biosemiotics and discontinuities
Marcello Barbieri
Thank you, Kalevi and Paul! It was a nice change getting POSITIVE letters from two Peircean scholars! Kalevi is right in saying that his distinction between vegetative, animal, and cultural semiosis corresponds to organic, interpretive and cultural semiosis. It is true that his description of vegetative semiosis is completely different from my description of organic semiosis, but that is another matter. The most important point is the recognition that there have been three major discontinuities in the history of life. Paul accepts the discontinuities but does not like the term “origins”, and yet it is such a nice word! A discontinuity after which something completely new comes into existence can rightly be called an “origin”, in my opinion. But that is a mere question of taste – “a rose is a rose by whatever name you call it”. The real issue at stake here is the very concept of discontinuity, and this is where the humanities could give a real contribution . The only discontinuity that has been accepted so far is God. Apart from that, we have had only two great paradigms based on continuity: either the idea that it is chemistry all the way up (materialism) or the idea that it is mind all the way down (idealism). Of course many people have proposed all sorts of discontinuities, but the problem is that they have never been convincing – we seems programmed to reject the idea that absolute novelties can come into existence (“nothing comes out of the blue”, in Stanley’s words). And yet a “logical” answer does exist – artifact-making does bring absolute novelties into existence, and all it takes is the spontaneous appearance of molecular machines (copymakers and codemakers). That would be an excellent point for philosophers to dwell into. The idea that life is artifact-making, that mind is artifact-making, that culture is artifact-making. That, in my opinion, is what Biosemiotics is about, and that is all in the future. Bon voyage! Marcello
31 Daniel Mayer
Dear friends and colleagues, I have been mulling over how to respond to this discussion, which, given my own background in philosophy, I believe is fundamental. It is at the very heart of our understanding of what we are hoping to build. Despite its length, if I may, I would like to share a few (slightly adjusted) paragraphs from my PhD dissertation (forthcoming). (By the way this is why I found my way to biosemiotics in the first place...) Though framed in relation to primatology, under discussion is the very same set of problems we are confronting here.
Metaphysical options[1]
Very schematically, when zoology is founded on a monistic ontology, such as the one that operates for Descartes in relation to animals, its object of study is reduced to entities of a single type, in his case mechanical entities. Descartes was not an innovator by being a dualist, but by abandoning dualism for all animals except humans, which also made him the first systematic mechanist.[2] This is not the only possible version of monism: animals and humans can also be reduced to spirits, in that way too denying all difference and thereby any problem of discontinuity.
On the other hand, when the foundation is equivocal or a dualist ontology, like the one that operates for Descartes in relation to humans, two substances, rex cogitans and res extensa, are irreducible and irreconcilable to each other, which brings about the paradoxes of all dualism: insurmountable discontinuities.
In contrast to these two options, if the foundation is an analogical ontology, in the sense that it poses the existence of different kinds of substances – to which underlies, for instance, the notion of structural variation – then different levels of being can exist, as well as their interrelation. This is the case with Aristotelian, and thereby Thomistic thought. The problem for such foundation is not incompatibility but integration: to account for each moment of development of the substance, its interrelations and transitions. That is, to account for both continuities and discontinuities. Only from such an ontology is it possible to identify and integrate the different levels of being that constitute the objects of study of zoology and of biology in general, in their full layered complexity. What is meant by “levels of being”? The schemes of recurrence intelligible for different disciplines that are constitutive of living beings; that is, the various levels that conform an object that may be studied by physics, chemistry, physiology, zoology, sociology, history, etc. But since these levels are at once autonomous, semi-autonomous and integrated, these levels may only be studied independently up to a point because the method for the study of the object as a whole must contemplate how to integrate what is understood by each discipline. To the extent that monistic foundations prevail in science – generally materialist monism – the tendency is for each discipline to consider its own field as privileged: the one whose content is that to which of all others are reducible. Inquiry into natural groups of nonhuman primates, for instance, may be within many fields, from environmental biology to cognitive ethology to genetics, etc., with each of these tending to treat itself as the proper frame for all the others. In the meantime, the development of a method appropriate to the study of nonhuman primates in their own terms is indefinitely postponed. In other words, what is postponed is the fashioning of the general frame of a discipline whose ideal of knowledge must be proportionate to their nature, and thereby capable of accounting not only for all pertinent levels of study of primates but also their integration.
With primates, for instance, the question arises, What kind of substance is psychic activity? What makes it different from other substances? And how is it integrated with them? Such questions lack sense in the context of a monistic ontology, and hardly make more sense in a dualistic context. In contrast, a science of primates founded on an analogical ontology will first seek to describe and then explain the different levels of degrees of development of each substance: it will differentiate sensibility, sensitivity, understanding, etc. to then ask itself to what extent and how these integrate a primate as a whole. (It is well worth keeping in mind that a living primate does not have a problem of integration at all, it carries on quite well with all these levels functioning at once and fully integrated!)
Again, the method of zoology, within the general context of evolutionary biology, must take up two dimensions: synchronically, it must explain animals as beings operating on different levels simultaneously; diachronically, it must explain how higher level structures emerge from and integrate with lower level structures, without the former violating the laws of the latter. When studies of non-human primates at all levels demonstrate their pertinence, including those that point to their high degree of sensitivity and understanding, one would suppose that the intellectual integrity of researches would demand that they ask themselves questions about the issue of integration, which would in turn lead to questions about their own underlying metaphysical stance. In fact, it was the search for answers to these questions that originated this study, and it is also what explains its framing and method. While it did start with question about primates, its own method gradually led to a focus on the conditions for the possibility of all possible forms of knowing.
With regard to it’s framing, from the start the project took shape as an analogical ontology. Having been born of an intense relationship with nonhuman primates, it took a life of its own as it became increasingly clear that what was needed was an appropriate foundation to an understanding of their emergence as subjects. In fact, is not hard to understand why there is a tendency to indefinitely postpone the development of a methodology capable of integrating the multiple levels of inquiry when the object of study is living beings. The difficulties begin at the very outset with the most basic dearth of terms by which to differentiate and characterize the various levels of being, let alone their integration. It is proposed here that distinctional process offers precisely this possibility. At the very least it suggests what a discipline with such an ideal of knowledge might look like: a discipline appropriate to the nature of living beings, any living being, one that takes into account and integrates all levels of study pertinent to them. Principally, a discipline for which the capacity to distinguish, the capacity to know – whatever that may be – takes center stage.
A key obstacle any such project must confront is the [depth of the] problem of anthropomorphism …belonging as it does to the general problem of subjects and their knowing of the world, as well as their knowing of other subjects, which is our knowing of others' knowing both of the world and of other subjects; what, in different terms, is the general problem of interpretation. The problem which is raised by interpretationis not some incidental problem; it belongs to the groundswell of the centuries; it is something which has been building up over the past four or five centuries. Because it is a first-class problem, it is not something that is going to be solved in any simple fashion.[1]
[1] This section is a modified version of section 2.14 of my MA dissertation ¿Qué es el primate? Hacia una epistemología Lonerganiana para entender el animal (What is a primate? Towards a lonerganian epistemology to understand the animal), Mexico D.F., 2004.
[2] Stephen Walker, Animal thought, Routledge & Kegan Paul, London, 1985, p. 5.
[3] Lonergan, Bernard, “Exegesis and Dogma” in Philosophical and Theological Papers 1958- 1964. Collected Works of Bernard Lonergan (CWL) Vol. 6. (Toronto: University of Toronto Press, 1996), p157.
32 Søren Brier
I do not think we disagree very much on these basic things. But on a deeper level, what worries me is that "the scientific world view" in the form of "the received view of science" hold so much implicit metaphysics in such a foggy way that we are unable to have fruitful discussions about it.What I for instance like about John Archibald Wheeler is that he actually - like Peirce - works explicit on the metaphysical dimension with his "it from bit" vision. I was fascinated by the book "Science and Ultimate reality" for his 90 years birthday conference 2004 edited by Barrow, Davies and Harper, Cambridge university Press. then there is the book that both Jesper and Terrance contributed to ed. Davies and Gregersen "Information and the nature of reality" I find McMullin's chaper " From matter to materialism" fascinating reading about how our ontological underpinnings of the material scientific wold view has developed so drastically.This is the stuff at the back of my head when we discuss these matters I agree that the is something existing which we have named "the genetic code", but as Shapiro wrote so nicely in his short and popular article, which Stan sent to us, then our view of that something has changed very much over time into a much more diverse and dynamic hierarchical picture already partly foreseen by Barbara McClinttoc, who fascinated me in a lecture many years ago.
But much of the discussion in the sciences seems to be based on undeclared old fashion ontological views. As a philosopher of science I still wonder how we are going to reflectively integrate the phenomenological view in our understanding of scientific knowledge. This is what Peirce tried through the making logic we now know only an aspect of an evolutionary and pragmaticist semiotics, which I almost understand now. But I find it very difficult to evaluated from the received view of science these days. Did he go wrong? Or where did he wrong and where did modern scientific, logics and mathematical metaphysics go wrong? And how can we mend that by making a new framework.
I do find your work interesting and admirable and most often very clear. But I think you have not really finished your paradigmatic framework yet - I know it takes many years. But do not just talk about "science" as that was something taken for granted. I am presently teach around 18 different paradigms in philosophy of natural and social science, and humanities most of which are involved in a heated discussion about what science and interpretation are and how we can determine if we are making true progress. Whit what criteria are we going to chose between competing theories or research programs as Lakatos calls them. He and Popper has some good suggestion, but they are not sufficient. Our situation is most interesting because that is where we are presently. On what criteria do we determine which research program or paradigm will be the most fruitful for biosemiotics. It is a very difficult choice.
Personally I am still wondering about how we are going to define "interpretation" if we combine the new views on the physical and the genetic ontology I mentioned here with a phenomenological reflection on realism and universals, which Peirce tried to carry through in his developing of pragmaticism.
I am presently looking at the very fascinating and expensive new book "Charles Sanders Peirce: The logic of Interdisciplinarity" with Elize Bizanz as editor which is a study book on pragmaticism publishing the Monist series in full. I recommend Kentner's short chapter on p.35 "Charles Sanders Pierce: Interdisciplinary Scientist" based on a self-description of Pierce of his own work. It gives a good understanding of what Peirce was actually up to in a very short space.
Venlig hilsen/best wishes Søren Brier
33 Re: Biosemiotics and discontinuities - On comparison of models
Kalevi Kull
Dear colleagues,
This is good if the models fit. Because our understanding is almost entirely based on our ability to find the match between (partly) unidentical models. (And this usually requires that we should not pay attention to the differences in names used by the different models. Already Ch. Morris and L. Bertalanffy have taught us this via the general systems approach.) If we find the right and effective match, then the particular differences between the models become useful, since these are then the points where one model can teach the other.
The same is true for Peirce’s model of semiosis - its usefulness depends on how we put it to the correspondence with other models. And here I am: IF one accepts Sebeok’s Thesis, then it is reasonable to limit the Peirce’s model with living systems. And Peirce himself might like this.
In this respect, I would suggest to read "Man's glassy essence" by Peirce (CP 6.238ff) (though it requires some knowledge of physics). Because this is where Peirce speaks about biophysics, and explicitly attempts to find the minimum molecular mechanism of protoplasm that is responsible for habit. From this text, one can see that (a) Peirce tends to believe that specific molecular constitution of protoplasm is responsible for semiosis, and (b) there was still so little known about the physical structure of matter, the energetics of the cell and nonlinear thermodynamics at that time that his further hesitations about the lower semiotic threshold are forgivable. Thus - have you ever noticed these passages of Peirce:
I have to elucidate [..] the relation between the psychical and physical aspects of a substance. The first step towards this ought, I think, to be the framing of a molecular theory of protoplasm. (CP 6.238-9) [..] physical property of protoplasm is that of taking habits. (CP 6.254) The problem is to find a hypothesis of the molecular constitution of this compound which will account for these properties, one and all. (CP 6.256) The truth is that, though the molecular explanation of habit is pretty vague on the mathematical side, there can be no doubt that systems of atoms having polar forces would act substantially in that manner, and the explanation is even too satisfactory to suit the convenience of an advocate of tychism. For it may fairly be urged that since the phenomena of habit may thus result from a purely mechanical arrangement, it is unnecessary to suppose that habit-taking is a primordial principle of the universe. (CP 6.262) [..] unless we are to accept a weak dualism, the property must be shown to arise from some peculiarity of the mechanical system. (CP 6.264)
Peirce indeed is trying to find the mechanical model for the necessary conditions of habit, and he more-or- less succeeds. He then, however, turns to the primordial origin of habit because he cannot explain some other things ... which, as I see it, can be explained due to the physics of the second half of the 20th century...
I mean first the dissipative systems, and second what Howard Pattee, Peter Wills and Terry Deacon (and some others) have understood and described as the emergence of semiosis. Would Peirce know this, he would come to the Gatherings in Biosemiotics. (And would tell that now he sees that what Kalevi and Marcello call codes would be habits in his terminology.) :-) Kalevi
34 Kalevi Kull
Dear colleagues, An abstract of my previous sending is this:
IF one accepts Sebeok's Thesis ("the phenomenon that distinguishes life forms from inanimate objects is semiosis" - Sebeok 2001) THEN it is reasonable to interpret Peirce's model of semiosis as limited to living systems WHICH IS SUPPORTED BY Peirce's statement that "since the phenomena of habit may [..] result from a purely mechanical arrangement [of molecular constitution of protoplasm], it is unnecessary to suppose that habit-taking is a primordial principle of the universe" (CP 6.262). In this case, the concept of habit corresponds closely to the concept of code. Best Kalevi :-)
35 Vinicius Romanini
Dear Kalevi and colleagues,
If we accept Sebeoks thesis (as you put it) then we should not search for quotations from Peirce to justify what has already been accepted. Let´s keep it with Sebeok´s - which I think had a poor understanding of Peirce´s mature semeiotic, which should be undestood as an attempt of deny nominalism and give an answer to Kant´s most important question: How are a priori synthetical judgements possible? Uexkull did not know Peirce, but is more Peircean than Sebeok when it comes to the fundamental question of semeiosis: life is a continuous synthesis of qualities which allows for diversification and growth. How should explain this? Starting from nominalism in his youth, Peirce was driven by the facts to admit that realism is the only possible mataphysics able to give an answer to this questions. And the answer is that habit-taking is primordial:
"Evolution means nothing but growth in the widest sense of that word. Reproduction, of course, is merely one of the incidents of growth. And what is growth? Not mere increase. Spencer says it is the passage from the homogeneous to the heterogeneous -- or, if we prefer English to Spencerese -- diversification. That is certainly an important factor of it. Spencer further says that it is a passage from the unorganized to the organized; but that part of the definition is so obscure that I will leave it aside for the present. But think what an astonishing idea this of diversification is! Is there such thing in nature as increase of variety? Were things simpler, was variety less in the original nebula from which the solar system is supposed to have grown than it is now when the land and sea swarms with animal and vegetable forms with their intricate anatomies and still more wonderful economies? It would seem as if there were an increase in variety, would it not? And yet mechanical law, which the scientific infallibilist tells us is the only agency of nature, mechanical law can never produce diversification. That is a mathematical truth -- a proposition of analytical mechanics; and anybody can see without any algebraical apparatus that mechanical law out of like antecedents can only produce like consequents. It is the very idea of law. So if observed facts point to real growth, they point to another agency, to spontaneity for which infallibilism provides no pigeon-hole. And what is meant by this passage from the less organized to the more organized? Does it mean a passage from the less bound together to the more bound together, the less connected to the more connected, the less regular to the more regular? How can the regularity of the world increase, if it has been absolutely perfect all the time? . . . Once you have embraced the principle of continuity no kind of explanation of things will satisfy you except that they grew. The infallibilist naturally thinks that everything always was substantially as it is now. Laws at any rate being absolute could not grow. They either always were, or they sprang instantaneously into being by a sudden fiat like the drill of a company of soldiers. This makes the laws of nature absolutely blind and inexplicable. Their why and wherefore can't be asked. This absolutely blocks the road of inquiry. The fallibilist won't do this. He asks may these forces of nature not be somehow amenable to reason? May they not have naturally grown up? After all, there is no reason to think they are absolute. If all things are continuous, the universe must be undergoing a continuous growth from non-existence to existence. There is no difficulty in conceiving existence as a matter of degree. The reality of things consists in their persistent forcing themselves upon our recognition. If a thing has no such persistence, it is a mere dream. Reality, then, is persistence, is regularity. In the original chaos, where there was no regularity, there was no existence. It was all a confused dream. This we may suppose was in the infinitely distant past. But as things are getting more regular, more persistent, they are getting less dreamy and more real." (CP 1. 175-176)
Sebeok puts the meaning of sign on its object (as I have shown in my paper presented by Richmond during the Biosemiotics Gathering of NY), which is sheer nominalism and the mature Peirce would never accept it. I think much of the ongoing dispute about the "origins" of life and the extension of biosemiotics has to do with nominalism x realism. For a good introduction about this in Peircean terms, I suggest the reading of the book review by Nathan Houser on "The threat of nominalism", here attached.
BOOK REVIEW Forster 030812.docx 23K
36 Howard Pattee
He says, “And yet mechanical law, which the scientific infallibilist tells us is the only agency of nature, mechanical law can never produce diversification. That is a mathematical truth -- a proposition of analytical mechanics; and anybody can see without any algebraical apparatus that mechanical law out of like antecedents can only produce like consequents. It is the very idea of law.”
This is the most common misconception of physical laws-- that is, because no event can disobey laws, the (false) assumption is that laws determine all events. That is demonstrably not the case! Most of the structures in the universe are undeterminable by laws, or else are chance. For example, choice of initial conditions cannot be determined by laws. Measuring agents and instruments obey physical laws but are not determined by laws. Sir Arthur Eddington (1929) emphasized this fact in The Nature of the Physical World (p. 260): “There is nothing to prevent the assemblage of atoms constituting a brain from being of itself a thinking object [including free will and consciousness] in virtue of that nature which physics leaves undetermined and undeterminable.” Murray Gell-Mann (1994) again emphasized this pointed in The Quark and the Jaguar (p. 134): “the effective complexity [of the universe] receives only a small contribution from the fundamental laws. The rest comes from the numerous regularities resulting from‘frozen accidents.’”
Howard
37 Vinicius Romanini
38 Peirce's model without primordiality of habit
Kalevi Kull
Dear colleagues!
Please note, Vinicius, that Pattee’s point here is different from Peirce's understanding of laws - Howard says that physical laws (however strict) do not determine everything, they leave something free (like initial conditions, or construction of instruments - which obey strict physical laws but are not determined by these). Peirce, however, applied fallibilism to physical laws, meaning that physical laws themselves need not to be strict but have exceptions. He needed this in order to explain diversification. Acceptance of the primordiality of habit in its extreme actually means that there are no physical laws in the sense physics deals with them, instead they are all habit-like, i.e., as if mental sensu lato. Important thing - we should distinguish between our talk on the history of science (if reconstructing what Peirce exactly said in context) and our talk on science itself (if using some models formulated by Peirce and decontextualising them in order to apply where relevant). I mean to do the latter here, thus we need not buy everything that Peirce has said. Analogically, when anybody is effectively using Darwinian model of natural selection, then it is used (since neodarwinians) completely abandoning Darwin's concept of inheritance (called pangenesis, assuming gemmules that would diffuse in the body and aggregate in the reproductive organs). Due to the knowledge that came much after Peirce on modelling of diversification, it is now possible completely to abandon the hypothesis of primordiality of habit. We may call this neo-Peirceanism, if one likes. The model of diversification as described by Prigogine is one that does not require primordiality of habit. Its freedom for diversification stems from fluctuations that can be thermal, in an autocatalytic system. Its mathematics necessary to explain self-organization was not available yet for Peirce. (However note that self- organisation is necessary but not sufficient for semiosis.) So there are models that now solve the problem of diversification without an assumption that physical laws themselves have to be habit-like. And we are still with Peirce’s realism when we speak about life. Best regards Kalevi
39 Vinicius Romanini
Dear all, Thanks Kalevi. Helmut Pape, talking to Prigogine in the early 1980´s, introduced this quote from Peirce: "You have all heard of the dissipation of energy. It is found that in all transformations of energy a part is converted into heat and heat is always tending to equalize its temperature. The consequence is that the energy of the universe is tending by virtue of its necessary laws toward a death of the universe in which there shall be no force but heat and the temperature everywhere the same. ... But although no force can counteract this tendency, chance may and will have the opposite influence. Force is in the long run dissipative; chance is in the long run concentrative. The dissipation of energy by the regular laws of nature is by these very laws accompanied by circumstances more and more favorable to its reconcentration by chance. There must therefore be a point at which the two tendencies are balanced and that is no doubt the actual condition of the whole universe at the present time." Prigogine found it "remarkable" and quoted it his 1984 book (with Stengers) "Order out of Caos". So I think we can say that Peirce´s cosmology is not so different from Prigogine´s. I am not a Peircean fundamentalist and, as Vincent Colapietro once wrote, the best way to do justice to Peirce is to go beyond Peirce. I hope there will be a day in which we will not be divided by Peirceans (or neo-Peirceans) and non- Peirceans, but will only be good semioticians. Nevertheless, going beyond is quite different from going backwards into mechanistic positivism. Peirce´s notion of habit-taking and mind goes much deeper than the concept of dissipative structures made out of particle interactions, for instance. Those who reject them usually think these concepts in terms of folk psychology - which is wrong. They are logical instances thought as to guide us out of the Metaphysical nebula of positivism, and I think they are still very necessary. My whole work (the Solenoid of Semeiosis and the Periodic Table of Classes of Signs) is a tentative to go beyond Peirce while keeping his fundamental and important lessons. All the best, Vinicius
40 Stanley N Salthe
41 Joachim De Beule
Dear Vinicius (and others), Forgive my ignorance on these matters but – even though Prigogine may have found it remarkable -- I do not understand what it means that "chance may and will have the opposite influence [and] is in the long run concentrative."? Is this an empirical law of nature, in the sense of e.g. the second law of thermodynamics? And what is meant by "in the long run"? Relative to what time scale? And what by "concentrative"? Best, Joachim.
42 Replies to Stan and Joachim.
Peter Wills
On 17/04/2012, at 10:28 PM, Stanley N Salthe wrote:
Vinicius, all -- Peirce's use of "chance" in this thermodynamic context is just right, in the sense that all dissipative structures, abiotic or living, are the products of history. That is to say, the formal causes of their appearance are various non-lawful (nonholonomic) constraints, including the genetic information in the genomes of the living and the laboratory arrangements of scientific observers. Thus it is history that channels the energy flows so as to maximize the energy dispersion from the energy gradients to the degree allowed by the organization of the dissipative structures, while paying the entropy 'tax' to the universe as a whole. STAN
Dear Stan
I would disagree that ALL dissipative structures have this quality of historical contingency. The typical physical ones (like patterns in the Zhabotinski reaction) are as predictable, given simple boundary conditions) as most equilibrium structures (like whether water is a solid, liquid or gas, given the temperature). That is, the formal causes of their appearance are lawful: they appear in exactly the same way whenever the constraints are the same. The same is not true for systems that depend on some arbitrary, contingent mapping from the constraints to the structure (as is the case in genotype-phenotype relationships). And it is true in a weaker sense for dissipative structures whose dynamics is chaotically divergent - but in that case, the magnituide of the divergence is lawlike. So what you say is true of organisms, but not of dissipative structures in general. As I see it, this pins down the task of biosemiotics exactly - to explicate the difference precisely and accurately. (Prigogine took one step too many in generalising his conclusions about dissipative structures to biology: his attempt to incorporate Eigen's work failed, but Eigen himself has never said so, I think because he does not have a clear idea of why it fails. We will see in his forthcoming magnum opus.) Peter
On 18/04/2012, at 12:59 AM, Joachim De Beule wrote: Dear Vinicius (and others),
Forgive my ignorance on these matters but --even though Prigogine may have found it remarkable-- I do not understand what it means that "chance may and will have the opposite influence [and] is in the long run concentrative."? Is this an empirical law of nature, in the sense of e.g. the second law of thermodynamics? And what is meant by "in the long run"? Relative to what time scale? And what by "concentrative"? Best, Joachim.
Dear Joachim,
The Peircian concentrative influence of chance seems to me to be a philosophical assumption. I cannot categorically contradict it. Nor can I see any way of testing it empirically. But what if there were some residual informatic order, some "meaningful connection", left as quantum decoherence apparently destroyed the fantastic array of temporary correlations that exist between possible outcomes during the next femptosecond ….? Could there be a cosmic code …? At this stage, I think we can believe what we like and I cannot see how it will impact on the natural sciences. The idea appealed to Prigogine because it gave his irreversible thermodynamics (in his interpretation) the appearance of a fairly full explanation of biology, which I do not think is the case (see above). Peter
43 Sorry for the unwanted mail
Marcello Barbieri
Cc: Alexei Sharov
Dear Anton, You and Don have explicitly asked to be taken out of the Mailing List, and, on April 12, I have done just that, in a letter which had the specific heading “Without Don and Anton”. After that, however, Kalevi has reintroduced your name (but not DON’s) into the Mailing List, so you have received an additional number of unwanted mail. The issue of unwanted mail is a serious one (a violation of privacy) and I always insist that we must respect the desire of those who opt out. Please let me and everybody else clearly know what you want to do about our Mailing List. Thank you Marcello
44 Joachim De Beule
45 Marcello Barbieri
Dear Joachim, Your idea is excellent, and indeed there already are a few blogs in Biosemiotics, but this case is different. This is mailing list that I use for annual consultations with the members of the Editorial Team of our Journal and with a few other people who have explicitly asked to join our discussion group. And since I am NOT technology-oriented I keep using the old fashioned system of the emails. Which is why I keep asking people NOT to use this mailing list for other purposes and to respect the decision of those who opt out. I hope that Anton will soon tell us what he intends to do. Best regards Marcello
46 Timo Maran
47 Joanna Rączaszek-Leonardi
48 Stanley N Salthe
The "long run concentrative" aspect means that if the new system is able to utilize its available energy gradients successfully, it will be able to use a portion of that energy to build its own concerns. The Second Law of thermodynamics calls for the dispersion of energy gradients, but will 'tolerate' some build- up of local gradient if that is funded by greater destruction of other gradients.
Dissipative structures are not taken as a law of nature, despite some suggestions about a 'Fourth Law' of thermodynamics. The prediction that they will appear everywhere in the universe is rather a local consequence of the Second Law itself. It might be reasonable to refer to their necessity wherever there are energy gradients not susceptible to dissipation by spontaneous conduction as a 'law of matter' (Heisenberg; reference lost). STAN
49 Stanley N Salthe
My point here is that these 'constraints' themselves depend upon the the contingent cultural evolution of the scientific social structure that produces it. No Law can predict the results of any evolution. And no law is determining the similarities among these experimental results. To the extent that they are predictable, they are the result of engineering, which it can be argued, is harnessing certain natural laws. Engineering itself is an historical emergent.
The same is not true for systems that depend on some arbitrary, contingent mapping from the constraints to the structure (as is the case in genotype-phenotype relationships). And it is true in a weaker sense for dissipative structures whose dynamics is chaotically divergent - but in that case, the magnituide of the divergence is lawlike. So what you say is true of organisms, but not of dissipative structures in general.
I disagree. Abiotic dissipative structures are dependent for their existence upon the various conditions of weather and geography, which are historically determined. As well, their exact form is never duplicated; tornadoes, for example, are no more identical in detail than any two organisms of the same species. Their 'identities' will have been the result of meteorological classification schemes.
As I see it, this pins down the task of biosemiotics exactly - to explicate the difference precisely and accurately.
And if there is no difference between abiotic and biotic dissipative structures -- AS dissipative structures - - then the next step would be to seek out the origins of semiosis in protosemiosis! This of course would require the "explication" you refer to. STAN
50 A few conclusions
Marcello Barbieri
Dear Colleagues, It is clear that Anton Markos is sending our letters directly to the waste-paper basket, so his name is out for good. He will no longer receive unwanted mail from us. It seems to me that this group discussion is coming to a close so let me say a few words about it. The object of the discussion was the claim of three papers that interpretation goes on at the molecular level, and I answered with another paper which argued that that claim was not based on anything vaguely resembling a scientific argument. It was based exclusively on the decision to say that some molecular processes can be “labelled” interpretation, something that I called “Peircean fundamentalism”. I believe that nobody has changed his or her mind in the course of the discussion, but perhaps we will be a bit more careful in the future about playing with words. Another result that I found interesting is the admission that we must go “beyond Peirce”, but clearly “in this way, not in your way”. So we have reached the point where the Holy Scriptures must be “interpreted” (what else?). This too is a little step forward. In my opinion we can close the discussion at this point, but of course it is possible to send a few more letters if somebody has something else to add. Thank you all for your cooperation! Best Marcello
51 Joachim De Beule
Dear All, I at least would like to say something still. With Marcello, I regret that we were unable to make any real progress on the important issues. I also wished that I had more time to contribute myself, but unfortunately this was not the case this time. But so in order to at least understand a bit more why progress is apparently so hard, I would like to ask you all to formulate what you think is at stake, so that we can at least have a better idea of what issues there really are and still need resolving before real scientific progress does become possible.
I think that the fundamental issue is whether our current scientific toolbox and vocabulary is sufficient to capture life, or rather that we must introduce some new fundamental observables and laws of Nature. I think that most of us agree that something is missing, but not on what. To put it bluntly: is it interpretation or is it coding, and what are these exactly?
So far, nobody has been able to convince me of what exactly interpretation should be. I have asked the "Peircians" to clarify and clearly define related concepts and terms on several occasions, not only what is "interpretation", but also "agency", ""long run concentrative forces", what are the time scales, etc. It seems almost as if some of these things, according to some at least, resist any definition or formalization. This cannot be the case, as it simply means the end of (scientific) progress, and I refuse to settle for this.
I am convinced that by including learning --which is a rudimentary form of coding or agency-- into our models of macro-evolution, evolutionary dynamics are changed in fundamental ways compared to what is possible with only differential reproduction (see also the paper in attachment which I intend to present at the Gatherings). The issue that remains for me is whether coding also requires us to extend our (meta-)physical and scientific toolbox, or change them in fundamentally new ways. If I understand correctly, Marcello even proposes that coding *continuously* leads to absolute novelties, to "new laws of nature" one could say (see his mechanisms of evolution paper). I think Marcello might be on to something here, but I am not sure myself yet, and I hope that we will eventually be able to resolve these issues after all!
The best to all, Joachim.
Tragedy_of_the_commune.pdf 426K
52 Joachim De Beule
From Victoria N. Alexander
Dear Joachim, I'm a Peircean who does not like the term "interpretation." I use the term "response" to a sign instead. A "response" is always "purposeful," and in this way it is different from a "reaction." I define agency as semiotic-poietic behavior. I attach selections from a paper I'm currently writing on this problem and look forward to speaking about it in July in Tartu. I hope you find it useful. I have a completely different take on "interpretation," so far as I can tell. My definition is designed to work for describing semiotic process, emergence, and intentionality, the three areas I work in. ( In the section below I quote Alexei Sharov, who understands the concept of cybernetic "agency" very well, in my opinion. Here I happened to be disagreeing about interpretation, but in general I find his work clear and useful.) The main thrust of my argument is that while biosemioticians understand semiosis; poiesis is less well understood. We have so much trouble with the term "interpretation" because it involves poiesis. I'm cc'ing Gerald and Stan too because they are implicated in my paper. There is too much controversy going on right now for me to send this to the whole list. Tori
...an "interpretation" is a response to something as if it were a sign, but whose semiotic object does not, in fact, exist. If the response-as-interpretation turns out to be beneficial for the system after all, there is biopoiesis. When the response is not "interpretive," but self-confirming in the usual way, there is biosemiosis...... Barbieri assumes (as many do) that interpretation is equal to flexibility or indeterminacy in the response. This is inaccurate. A system's response to a sign is always determined by previous selection, that is, all purposeful, semiotic responses tend to exist in the organism (or cybernetic system) because of the selective advantages they have had. Thus all responses are determined, evolutionarily speaking. It is not an "indeterminate response" that gives rise to "interpretation." It is not, as Sharov (2010) contends, that "agents select specific action out of multiple options." The type of response we call "interpretation" occurs when the type of objective (semiotic object), which has previously selected the response, does not exist. In short, all so-called "interpretations" are mistaken responses, or what we might call mis-responses. The response to the sign is still determined, even if the sign's objective does not exist. [Note: according to the philosophy of intentionality, all semiotic objects must be potentially inexistent; otherwise purposeful behavior is impossible.] If the mistaken response turns out to be advantageous, the agent will develop greater flexibility insofar as it has acquired a new goal, a new way to survive or self-affirm. Responses are not flexible in and of themselves. Flexibility is a product of the nature of triadic semiosis, which is always about the past. Every semiotic response is based on what has happened before. A response to a present situation can be "wrong," but better. Machine-like behavior occurs in all organisms if the arrows of the triad (Fig. 2) successfully point back to self, reconfirming the response. Every time the arrow makes a complete semiotic cycle, without difference, we have regular, habitual or instinctive behavior, which is more or less robotic. Such automation is the essence of semiosis. Such semiotic responses exist because they have been selected by evolutionary processes. As Sharov (1998) writes, "Relations are useful only if they preserve and augment the same relations in the future, i.e., if these relations are self-reproducing. This idea was first formulated by Pattee (1982, 1995) and was called "semantic closure". Semantic closure is a new criterion for autonomy (or wholeness) of systems. A set of elements connected by relations is autonomous only if it is semantically closed, i.e., it reproduces itself in the future and defines its identity in the process of self-production. The value of each component or relation in an autonomous system corresponds to its contribution to the ability (or probability) of the system to reproduce itself." Creative behavior will be different from this semiotic process that is closed to novelty. It will require an interloping new “objective” that will be made possible by a usual, but mistaken, response. What we call "interpretation," to reiterate, is a regular response to a sign of a semiotic object that turns out not to be a sign of that object, but which may lead to a new one: the response may obtain the objective of self- preservation in a novel way. Certainly a useful response may have to avoid strict self-reference if changed conditions demand adaptability.....
______Victoria N. Alexander, PhD www.dactylfoundation.org www.torialexander.com
53 ------Forwarded message ------From: Joachim De Beule
Dear Victoria, Thank you very much for your mail, I very much appreciate it, and it does make a number of things more clear to me. As you might remember from my contribution to the previous gathering, I like to take a cybernetic account myself as well because It brings the notion of purpose into our models and I agree that the idea of closure is fundamental for semiosis. I am with von Neumann, Rosen, Pattee, Varella etc., and you on this one -- I even wrote an editorial about it for the biosemiotics journal not so long ago. But I do not think that Marcello has any fundamental objections to this view either? So what is really at stake then? Anyway, I do not fully understand why and I find it a petty that this kind of constructive dialog is apparently not possible through the whole list, but as said I do appreciate your response. Thanks again! Joachim.
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