Dear all,
I apologize for the delayed response and fragmented personal replies. I apologize that not all of your responses were selected for further comments, only those that were the first to come and those that look as the most relevant ones. I apologize that not all topics of these responses are regarded in my answers, only these that look to me as the most relevant ones. I apologize that the style of my answers is not always elegant and polite, (that is one of my problems), but the reason is not my bad character or bad temper, the reason is my bad knowledge of English. Sorry. And here are the replies: ===================================== To Krassimir Markov, (September 24, 2015). Thank you for your response. Yet I dont like it you force me to repeat commonplace banalities again and again. I have no stomach for this sort of things, but you insist and so I have to repeat: Every scientific discourse or dialogue begins with establishing some initial basic assumptions, which do not need to be solid or substantial (therefore, I dare to call them axioms). In the course of a subsequent reasoning, the initial assumptions are being transformed into a set of hypotheses, which are being applied to explain the existence or to predict results of observations of some natural phenomenon. If the hypotheses successfully pass this trial, the initial assumptions become regarded as true and sustainable. Then the next round of hypotheses ramification and complication comes into being until a full-blown new theory has become available. This is the way of thinking and reasoning which I am familiar with. Your question What is data? does not meet the conventions of such a discourse. Reading some of your previously published papers, I can guess what are the basic assumptions that you adhere to. But you do not declare them by yourself. Why should I do that instead of you? Do that, defend their validity by making prediction tests (as it is described above), and do not ask smart questions. Meanwhile I will ignore and discard your response. ======================================== To Günther Witzany, (September 24, 2015). Thank you very much for your response. I am a great admirer of your publications. Long before they become available on the Research Gate, I was really a stubborn hunter for them, happy with any piece of text (mainly abstracts) that I was lucky to catch (I am an engineer and thus biological publications usually are not accessible to me). As it was just stated above (in my answer to Krassimir), the only way to develop a new theory is to validate and justify its initial assumptions by applying them to an explanatory description of an observable natural phenomenon. In this regard, your publications were exactly what I was needed. (Although long before your papers become available to me, I gained my inspirations from the papers of Eshel Ben-Jacob, published a couple of years earlier). Never mind, his and your explorations were thought provoking, inspiring and really helpful to me. However, some reservations regarding their subject would be worth to mention here. In Eshels and your early publications, the term model/modeling is often encountered on various occasions. In contemporary science, the term has a pure mathematical connotation and usually implies data modeling. What follows from this is that modeling (and your engagement with it) explicitly presumes mandatory data processing. In the context of my assumptions-speculations, data processing is tightly bound to physical information processing. And that is the point you all all the time are busy with physical information processing, despite you even dont recognize the notion of it. (Semantic information processing also remains a terra incognita for you). In this regard, your description of the marvels and the mysteries of the chemical Auxin are missing their argument strength. First, Auxin is not a chemical (as you call it); it is a plant hormone (Wikipedia), a hormonal messenger. The message that a messenger is carrying is actually a piece of text written in a language (which is still unknown to us) with a chemical alphabet (that is also unknown to us). The message as a rule contains physical and semantic information subparts (text pieces). I apologize for drawing you into this mishmash, but the time is ripe to clarify some of the matters. For a long time, you Gunter, on various occasions assert the following statement: The Modern Synthesis regards the genetic code as a lineup of molecules that can be investigated through physics and chemistry and mathematics (for sure). And this is it. However, we know the genetic content of organisms is about communication, which cannot be reduced simply to physics and chemistry. Since the 1970s, Manfred Eigen has insisted that the genetic code is really a language, not just metaphorically, but a real language. (In an Interview given to Susan Mazur, 2015). On another occasion: Today, everyone speaks about the genetic code genes encoded in DNA that serve as the information-bearing molecules for all biological entities In the 1970s, Manfred Eigen insisted that the genetic code really represents a natural language and is not just metaphorical (Life is physics, and chemistry, and communication <http://onlinelibrary.wiley.com/doi/10.1111/nyas.12570/full> , 2015, p. 1). Although you do not completely support Manfred Eigens claim (and you even propose a refinement for it in your Pragmatic turn in biology, 2014), your primary assumption remains unchanged: The question remains how to define nucleic acid sequences as a real natural language/code (ibid, p. 6). Sorry, but this is a wrong and a misleading statement: nucleic acid sequences are not real natural language/code they are pieces of text bearing an information description. They are pieces of text written in some certain language using some certain alphabet (codes). To clarify further my claim, I would like to propose a gedanken experiment: imagine you have to provide a description of the water molecule structure. In English language using Latin alphabet letters, this description (text) would look like this: Water is made up of two hydrogen atoms and an atom of oxygen. Then you can decide to re-write this text using another alphabet, say, a chemical alphabet. Craig Venter has done such a thing inserting English text messages written as a sequence of letters C, G, A, and T (he called them watermark messages) into the DNA sequence of a bacterial genome. The purpose of the watermarks was to distinguish the synthetic genome from its natural counterpart. But what is interesting to us is that the bacterium and its watermarks were viable, that is, capable to replicate themselves in the course of bacterial reproduction and multiplication. That is, English text messages have behaved exactly the same way as all other genetic information sequences. I hope my basic assumption endorsed by Craig Venters experiments is quite clear to you now: the current wave of gene screening experiments is busy with high-throughput data (code) gathering only. It has nothing to do with information texts embedded in the code sequences. Therefore, text meaning is out of reach of contemporary gene screening experiments. In context of my basic assumptions (speculations), the bottom line can be summarized like this: contemporary biological research is busy with physical information processing only. Semantic information processing is out of its scope. I apologize again for such a long and late response. =================================================== To Pedro C. Marijuan, (September 25, 2015). Dear Pedro, I do not wish to be in a discord with you, but I do not share your praise for the Gunters response (the reasons for that I hope are somehow explained above). I also disagree with your assessment of the Encode project. Because my arguments on this subject overlap with comments to Howard Blooms response, I would further expand my explanation (on this subject) in the following comments upon the Blooms letter. ======================================== To Howard Bloom, (September 26, 2015). Dear Howard, I disagree with your assessment of Gunters wonderful description of auxin's many functions, but I am in accordance with you when you declare that the Encode project is an ambitious and primitive (however, I disagree with you about its necessity). As it was explained above (in my reply to Gunter), contemporary biological science does not accept the notion of information. It does not recognize the duality of information, its physical and semantic subdivision. And therefore, it is doomed to fall into the trap of its own unawareness continue to put extensive money and effort resources in data/code gathering (that is, physical information processing) hoping to arrive in such a way at the encoded texts meaning/interpretation (semantic information). Functional features of the code are the declared goals of the Encode project. They cannot be and never would be reached in a frame of mind of data processing. A similar situation is in the Human Brain Project launched by the European Community in 2014. The HBP has proudly declared that one of its prime goals is neuron communication study. A special line of research is devoted to neuron communication modeling, that is to an endless and exhausting data processing enterprise. The data gathered in neuron communication studies are the action potential pulse train propagation records. But if the brain is processing information what information is conveyed in the course of interneuron communication? What information is carried by action potentials pulse train? In my view, the pulse train of action potentials could be equated with noise following an actual train passage, a passage of heavy freight train. From the train noise records, would you like to extract the knowledge about the nature of the trains payload? Are you serious? That does not work and never would not (work). It would be nice if FIS discussions would help the Human Brain Project participants to overcome their generic cognitive biases. (Cognitive as you remember is an ability to process information). =================================================== I apologize again for such a long and unbalanced reply. Best regards, Emanuel. =========================================== From: howlbl...@aol.com [mailto:howlbl...@aol.com] Sent: Saturday, September 26, 2015 6:40 AM To: pcmarijuan.i...@aragon.es; witz...@sbg.at Cc: r...@howardbloom.net; fis@listas.unizar.es; emanl....@gmail.com Subject: Re: [Fis] Information is a linguistic description of structures wonderful description of auxin's many functions, gunther. may i suggest that auxin--or gaba and glutamate in animals--is like the word "a" in the english language. the meaning of "a" depends entirely on context. just as Gunther has said in many of his papers. and context changes as developmental stages pass by, just as pedro has emphasized. a project like ENCODE is ambitious and necessary, but primitive. it's the equivalent of breaking down Shakespeare to its component words, then putting those words in a list. doing that to shakespeare would lose everything for the sake of gaining almost nothing. this reductionist approach, while of value, is what babara ehrenreich in her introduction to the upcoming paperback version of my book the god problem: how a godless cosmos creates, calls "unacknowledged necrophilia." her quote: I was educated in this scientific tradition, ending up in cell biology, which proposed that you cannot understand, say, the flight of a hummingbird until you have killed the bird, cut its wing muscles into slices a few microns thick, and subjected them to electron microscopy. Thus a kind of unacknowledged necrophilia runs through modern laboratory biology: to study something you first have to kill it. You know you have understood it when you arrive at a theoretical description that contains no hint of agencyjust a series of mechanisms involving organelles, which you have isolated through high-speed centrifugation, and molecules, identified by a series of fractionation processes. The hummingbirds speed and grace is explained by the density of mitochondria in its wing muscles, leading to an abundant flow of ATP to the myosin. to reduce shakespeare to a list of words would be to kill it. our task is to understand its life. with warmth and oomph--howard =========================================== From: Pedro C. Marijuan [mailto:pcmarijuan.i...@aragon.es] (6) Sent: Friday, September 25, 2015 2:38 PM To: Günther Witzany Cc: Emanuel Diamant; fa...@howardbloom.net; 'fis' Subject: Re: Information is a linguistic description of structures Dear FISers and all, I include below another response to Immanuel post (from Guenther). I think he has penned an excellent response--my only addition is to expostulate a doubt. Should our analysis of the human (or cellular!) communication with the environment be related to linguistic practices? In short, my argument is that biological self-production becomes "la raison d'etre" of communication, both concerning its evolutionary origins and the continuous opening towards the environment along the different stages of the individual's life cycle. It is cogent that the same messenger plays quite different roles in different specialized cells --we have to disentangle in each case how the impinging "info" affects the ongoing life cycle (the impact upon the transcriptome, proteome, metabolome, etc.) There is no shortcut to the endless work necessary--wet lab & in silico. So I think that Encode and other big projects are quite useful in the continuous exploration of biological complexity and provide us valuable conceptual stuff--but looking for hypothetical big formalisms (I quite agree) is out sight. Molecular recognition which is the at the fundamentals of biological organization can only provide modest guidelines about the main informational architectures of life... beyond that, there is too much complexity, endless complexity to contemplate, particularly when we try to study multicellular organization. Anyhow, this topic of the essential informational openness of the individual's life cycle appears to me as the Gordian knot to be cut for the advancement of our field: otherwise we will never connect meaningfully with the endless info flows that interconnect our societies, generated from the life cycles of individuals and addressed to the life cycles of other individuals. Info sources, channels for info flows, and info receptors are not mere Shannonian overtones, they symbolically refer to the very info skeleton of our societies; or looking dynamically it is the engine of social history and of social complexity. Well, sorry that I could not express myself better. all the best--Pedro ================================================== From: Günther Witzany [mailto:witz...@sbg.at] (1) Sent: Thursday, September 24, 2015 11:21 AM To: Emanuel Diamant Cc: Pedro C. Marijuan; fa...@howardbloom.net Subject: Re: Information is a linguistic description of structures Dear all! What is the opposite of a linguistic description? a non-linguistic description? Please tell me one possible explanation of a non-linguistic description. So Im not convinced of the sense of the term "information". Concerning the "difference" of physical and semantic information: What would you prefer in the case of plant communication. Does the chemical Auxin represent a physical or a semantic information? Auxin is used in hormonal, morphogenic, and transmitter pathways. As an extracellular signal at the plant synapse, auxin serves to react to light and gravity. It also serves as an extracellular messenger substance to send electrical signals and functions as a synchronization signal for cell division. At the intercellular, whole plant level, it supports cell division in the cambium, and at the tissue level, it promotes the maturation of vascular tissue during embryonic development, organ growth as well as tropic responses and apical dominance. In intracellular signaling, auxin serves in organogenesis, cell development, and differentiation. Especially in the organogenesis of roots, for example, auxin enables cells to determine their position and their identity. These multiple functions of auxin demonstrate that identifying the momentary usage (its semantics) is extremely difficult because the context (investigation object of pragmatics) of use can be very complex and highly diverse, although the chemical property remains the same. Yes, mathematics is an artificial language. Last century the Pythagorean approach, mathematics represents material reality, (if we use mathematics we reconstruct creators thoughts) was reactivated: Exact science must represent observations as well as theories in mathematical equations. Then it would be sure to represent reality, because brain synapse logics then could express its own material reality. But this was proven as error. Prior to all artificial languages we learned how to interconnect linguistic utterances with practical behavior in socialisation; therefore the ultimate meta-language is everyday language with its visible superficial grammar and its invisible deep grammar that transports the intended meaning. How should computers extract deep grammar structures out of measurable superficial syntax structures? In the case of ENCODE project (to find the human genome primary data structures) this was the aim which got financial support of 3 billion dollars with the result of detecting the superficial grammar only, nothing else. Best Wishes Guenther =========================================== From: Krassimir Markov [mailto:mar...@foibg.com] (2) Sent: Thursday, September 24, 2015 11:40 AM To: Emanuel Diamant; fis@listas.unizar.es Cc: fa...@howardbloom.net; witz...@sbg.at Subject: Re: [Fis] Information is a linguistic description of structures Dear Emanuel, What is DATA? Best regards Krassimir =========================================== From: Emanuel Diamant [mailto:emanl....@gmail.com] (0) Sent: Thursday, September 24, 2015 8:47 AM To: 'fis@listas.unizar.es' Cc: 'pcmarijuan.i...@aragon.es'; 'witz...@sbg.at'; 'fa...@howardbloom.net' Subject: Information is a linguistic description of structures Dear FIS colleagues, As a newcomer to FIS, I feel myself very uncomfortable when I have to interrupt the ongoing discourse with something that looks for me quite natural but is lacking in our current public dialog. What I have in mind is that in every discussion or argument exchange, first of all, the grounding axioms and mutually agreed assumptions should be established and declared as the basis for further debating and reasoning. Maybe in our case, these things are implied by default, but I am not a part of the dominant coalition. For this reason, I would dare to formulate some grounding axioms that may be useful for those who are not FIS insiders: 1. Information is a linguistic description of structures observable in a given data set 2. Two types of data structures could be distinguished in a data set: primary and secondary data structures. 3. Primary data structures are data clusters or clumps arranged or occurring due to the similarity in physical properties of adjacent data elements. For this reason, the primary data structures could be called physical data structures. 4. Secondary data structures are specific arrangements of primary data structures. The grouping of primary data structures into secondary data structures is a prerogative of an external observer and it is guided by his subjective reasons, rules and habits. The secondary data structures exist only in the observers head, in his mind. Therefore, they could be called meaningful or semantic data structures. 5. As it was said earlier, Description of structures observable in a data set should be called Information. In this regard, two types of information must be distinguished Physical Information and Semantic Information. 6. Both are language-based descriptions; however, physical information can be described with a variety of languages (recall that mathematics is also a language), while semantic information can be described only by means of natural human language. This is a concise set of axioms that should preface all our further discussions. You can accept them. You can discard them and replace them with better ones. But you can not proceed without basing your discussion on a suitable and appropriate set of axioms. That is what I have to say at this moment. My best regards to all of you, Emanuel. ====================================================
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