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Writing Biosemiosis.org

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In September of 2009 I started a new document on my computer entitled “A System of Symbols”, where I was going to write about the part of design theory that interested me the most – that is, the representations that are required for self-replication (von Neumann, Pattee). My goal was to inventory all the physical conditions necessary for one thing to represent another thing in a material universe. I wrote and rewrote that essay for more than four years — reading, learning, and sharing along the way. As it turns out, writing that essay was my way of coming to understand the issues, and I spent a great deal of that time trying to articulate things I had come to understand conceptually, but could not yet put into words. Eventually I came into contact with the types of scientists and researchers who had substantial experience with these issues, up to and including those who had spent their entire careers on the subject. It was a humbling experience to share my thoughts with people of that caliber, and have them respond by sending me papers of their own that reflected the same concepts.

Then In 2014, I retired that essay and began writing Biosemiosis.org in its place. Since that work is available to any reader, I won’t recapitulate it here, but there are a couple of concepts I’d like to highlight – particularly the discontinuity found in the translation of recorded information. Read More

[I’d like to thank Barry and Uncommon Descent for allowing me to publish this introduction to my two projects]

Comments
Well, it seems that there is some problem with the update of the "recent comments" section.gpuccio
November 2, 2015
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Dionisio: Very good questions! And I would be really happy if we could have some answers, even partial. The problem of what controls the epigenetic procedures, as you well know, is still completely unsolved. We have a number of different layers of control (at least: DNA methylation, Histone modifications, Chromatin remodeling, 3D chromatin structure, Transcription Factors, Post transcriptional regulations, Post-translational modifications), which seem to act in a redundant and strictly intertwined pattern. As you always say, that is complex complexity indeed! Do those layers configure semiotic codes? Absolutely! Unfortunately, those codes are so complex that we scarcely understand them. For example, take the Histone code. Histone modifications have a recognizable, repetitive meaning. The most universally known meanings are the activating effect of H3K4me3 and the inhibitory effect of H3K27me3, and the double pattern (activation + inhibition) in many stem cell genes. I quote from the Wikipedia page:
Unlike this simplified model, any real histone code has the potential to be massively complex; each of the four standard histones can be simultaneously modified at multiple different sites with multiple different modifications. To give an idea of this complexity, histone H3 contains nineteen lysines known to be methylated — each can be un-, mono-, di- or tri-methylated. If modifications are independent, this allows a potential 419 or 280 billion different lysine methylation patterns, far more than the maximum number of histones in a human genome (6.4 Gb / ~150 bp = ~44 million histones if they are very tightly packed). And this does not include lysine acetylation (known for H3 at nine residues), arginine methylation (known for H3 at three residues) or threonine/serine/tyrosine phosphorylation (known for H3 at eight residues), not to mention modifications of other histones. Every nucleosome in a cell can therefore have a different set of modifications, raising the question of whether common patterns of histone modifications exist. A recent study of about 40 histone modifications across human gene promoters found over 4000 different combinations used, over 3000 occurring at only a single promoter. However, patterns were discovered including a set of 17 histone modifications that are present together at over 3000 genes.[10] Therefore, patterns of histone modifications do occur but they are very intricate, and we currently have detailed biochemical understanding of the importance of a relatively small number of modifications. Structural determinants of histone recognition by readers, writers and erasers of the histone code are revealed by a growing body of experimental data.[11]
Transcription factors act in a very complex combinatorial patterns. Complexes made by transcription factors and other proteins, which may include even 10-15 different molecules, connect enhancers to promoter regions, and modify dynamically 3d chromatin structure. So, do those layers configure semiotic codes? Absolutely! Where is the information which controls those layers? We really don't understand that, at present. But, wherever it is, it is extremely complex and very functional.gpuccio
November 2, 2015
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Steve @ 39 Sorry to disappoint you, but those folks are probably very busy trying to answer the "where's the beef?" questions for the evo-devo pseudoscientific nonsense that is published out there. :)Dionisio
November 2, 2015
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UB Where is the information on how to form the morphogen gradients for morphogenesis (important part of organogenesis) stored in? Does the morphogen gradient formation have to be done according to the protocols used by the cells for morphogen gradient interpretation? Does all this somehow relate to the semiotic concepts? Where is all that information stored in?Dionisio
November 2, 2015
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The septic zone is still in code denialism and they are also in science denialism. And to top it all off they could be awarded 3.1 million dollars if they could just support their claim tat the genetic code can be accounted for via physicochemical processes- but they won't even attempt to collect it! Talk about cowardice...Virgil Cain
November 2, 2015
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Where are the TSZ regulars to congratulate UB? If I am not mistaken, they were so sure UB's website would never materialize. So keiths, Sir Richard, Liz, petrushka, the 2 als, et all?? No comments? none??Steve
November 2, 2015
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Thanks UB for the info. FYI, the ghost of ben franklin just dropped by biosemiosis.org for tea. Great work, indeed! Look forward to lots more!Steve
November 2, 2015
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Mapou and UB: Very interesting thoughts about representations. I will try to add some personal reflections, to keep the discussion going. Mapou says: "I ask these questions because the conscious mind can only sense an internal representation of the environment constructed from sensory data." That's absolutely true. We could say that the whole sensory system is a "machine" whose purpose is to generate a physically ordered representation of physical events, in a form which can be "perceived" by our consciousness. Let's imagine that our consciousness is a subject which can only see what is on a specific monitor. And the monitor is fed by a complex recording system, which takes different shots of different things by some set of sensors, and transforms the information into the correct physical stimuli which can build an image on that monitor. The point is: the conscious representation (in the sense of perception) exists only when our consciousness "sees" what is in the monitor, but we can also say that the recording system generates a "representation" (in the sense of an ordered physical system which "takes on" the form of other physical events) which is then "passed" to the subject to be "represented" (in the sense of "perceived") in the consciousness. So, maybe we should distinguish between two different meanings of "representation": 1) A passive physical ordering of some physical substrate whose purpose is to catch some specific information and retain it in a specific form. 2) The conscious event which transforms representation of that first type into conscious events. Now, the important point IMO is that the conscious events which take place in 2) are not representations in the sense of 1). So, just to say, the experience of red is not the same thing as the physically coded impulse which corresponds to the experience of red in my consciousness. I would not necessarily say that it is a "spiritual entity", because that would bring the discussion to the ontologic philosophical level, but we can certainly say that it is a "conscious event", an event where an I represents something as a conscious perception. Another point is that representations of the first kind do not imply conscious events in the actual process of their generation (a video camera can work without any conscious contribution), but the systems which generate them do require an act of design to come into existence. Why? Because they are functionally complex. In particular, to go back to UB's main argument, all the systems which generate and use representations (in the first sense) which are symbolic and use a code to transmit their information and generate a specific semiotic and functional outcome are always, always, always the result of conscious design. IOWs, their origin is traceable to representations of the second type.gpuccio
November 1, 2015
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UB @30, Thanks for the clarification. I was obviously mistaken. I prefer to use the term "decoder" because I believe that a representational system consists of 3 things: the code creator, the code (representation or pattern) and the decoder. All 3 are part of the same system. Furthermore, the code creator must think of both the pattern and the decoder at the time of creation. While it is obvious that a code is an intelligent artifact, it is possible to use strict rules in order to automate code creation in an AI program during learning. For example, I have implemented a spiking neural network that can automatically discover and create internal patterns from signals (spikes) arriving at a set of input sensors. The discovered patterns can still be called representations (or codes) even though they were not directly made by an intelligent coder.Mapou
November 1, 2015
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How do I get my donation back? ;)Mung
November 1, 2015
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Hi Steve, Right below the "Contribution" button, there is a link that allows someone to up their contribution if they'd like. Many Many Many Thanks!Upright BiPed
November 1, 2015
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UB, your site has a donation page. but looks like the donation is set at 18 bucks. But what if someone like me thought 18 bucks was too little to give? How about unlocking the donation amount? This is a limited offer and will self-destruct if the secret password in not decoded in time. Tick-tock. :)Steve
November 1, 2015
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And this is important because at root we are not talking about the effect of a nucleotide, we are talking about the effect of a sequence. It wasn't called "the sequence hypothesis" for nothing.Mung
November 1, 2015
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One can learn very interesting things from reading this discussion. :)Dionisio
November 1, 2015
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Hi Mapou, I think we are on the same page. I have tried to pick out what I might have said to make you think that I see a representation as "causal agent", and I think I know what it is...
The pattern itself becomes the causal object in the system, and the primacy of the pattern over the medium results in a representational system with two distinct properties. These two properties are fundamental to an open-ended self-replicating system.
I am here pointing out the pattern becomes the very thing that the system (the decoder in your vernacular) recognizes and responds to. This point is being presented in the context of the pattern being independent of the minimum total potential energy state of the medium. I have gone to great lengths to show just how "passive" a representation is (in regard to determining what effect is produced by its recognition), and it was not my intent to reverse all that work with that one sentence. That pattern must still be recognized by the system (the decoder) and that recognition must still be acted upon by the organization of the system. Read in context, I don't see a reason that our individual understandings differ. Edit: Representations evoke effects, but they do not determine what those effects will be.Upright BiPed
November 1, 2015
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Think of the music box analogy. There are different levels of causation. That which causes the tine to vibrate is not the same as what causes this song to play rather than some other song. My .02Mung
November 1, 2015
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Mapou, the code gets used in controlling machinery which is causal. KFkairosfocus
November 1, 2015
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U.B. After briefly surfing through the material at the links provided, something in your ideas immediately struck me as odd. You seem to think of a representation as a causal agent. I say it's odd because my long held understanding calls for a representation to be entirely passive. The only active thing that I can see is the decoder. A representation is a passive symbol, IMO. A symbol written on a 2000 year-old papyrus is a representation, not a causal agent. PS. It's very possible that I am misreading your ideas. So correct me if I'm wrong.Mapou
November 1, 2015
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UB, I will be following your work closely because it is directly relevant to my work in artificial intelligence. Knowledge representation is the biggest unsolved problem in AI. The goal in AI is to come up with a universal knowledge representation scheme that can potentially model any kind of real world phenomena. The two big questions in my mind right now are: When does a structure become a representation? Can it be an intrinsic or self-supporting representation or is it a representation only in the conscious mind of an observer? I ask these questions because the conscious mind can only sense an internal representation of the environment constructed from sensory data. We never sense the world directly regardless of how "real" everything seems to us. Everything we see is in our visual cortex. But it gets very confusing from this point on because, for example, the colors that we see are neither in the environment nor the brain. Our consciousness somehow attaches color sensations to certain neuronal activities in the visual cortex. One cannot claim that colors are abstract symbols because they are directly known by our minds. At the same time, color sensations are triggered by the environment and can be said to represent environmental phenomena. It's complicated. Edit: But then again, maybe colors are abstract (non-physical) entities after all. Maybe they are not of this world. Maybe, they are spiritual entities.Mapou
November 1, 2015
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Should read - DEAD ARGUMENTS still used by our opponents and DEFLECTIONS/DISTRACTIONS still used by our opponents That puts it in contextVirgil Cain
November 1, 2015
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DEAD ARGUMENTS: It’s just chemistry It’s only a metaphor There is nothing symbolic in the cell There is no way to test for intelligence There is no evidence of design in biology There is no way to objectively detect ID ID can’t define what it means by intelligence ID proponents never offer evidence Evolution did it DEFLECTIONS/DISTRACTIONS: What is information? What is arbitrary? What is a code? What is intelligence? - - - - - - - - - -
In common parlance we refer to these sites as containing “information” in the form of specific nucleotide sequence. It’s a very useful analogy and I think everyone knows what we mean when we use it. Nobody expects it to conform to the meanings of “information” in other disciplines. Nobody, that is, except some IDiots who like to play semantic word games instead of addressing real science. I hope you’re not one of those people. -- Larry Moran
Yes, I'm afraid I am. :)Upright BiPed
November 1, 2015
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The sentence you quote is from the opening text of the site. I do not merely “declare” it, but go into substantial detail.
Then the proper thing to do is add a footnote at the end of that sentence that references the evidentiary support. The point is I agree with what you say. I also know that opening statements can capture an audience or lose one. Reference your statement so that you capture more than you lose. And even if Darwinian evolution had a genome all it could do is degrade it-> Spiegelman's Monster is what darwinian evolution can produce. ;)Virgil Cain
November 1, 2015
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VC, The sentence you quote is from the opening text of the site. I do not merely "declare" it, but go into substantial detail. Darwinian evolution require a genome. The site describes the material conditions that allow the genome to exist. If A requires B for A to exist, A cannot be the source of B. Will people argue anyway? Of course they will.Upright BiPed
November 1, 2015
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Mung:
The system is what is required for open-ended evolution to even occur.
Even if it is, and that is debateable, that alone doesn't mean Darwinian evolution could not have produced it.
So claiming it is the product of Darwin evolution doesn’t help.
Doesn't help what? It helps Darwinism and neo-Darwinism. Look, all I am saying is that it isn't enough to just declare things. Doing so makes us as guilty as the position we oppose.Virgil Cain
November 1, 2015
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Virgil Cain:
You have to do more than just baldly declare that [this system is not the product of Darwinian evolution.] as there are Darwinists who baldly declare the opposite-
The system is what is required for open-ended evolution to even occur. So claiming it is the product of Darwin evolution doesn't help.Mung
November 1, 2015
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Box, Thank You. I remember our first meeting here on UD. I was in the middle of a raging argument, and you were asking questions, attempting (as I saw it) to relate what I was saying to your own conceptions of the issues. I remember this because the distance between our conceptions interested me, as we both stand on the same side of the argument. You (in many ways like GPuccio) are very tuned to the realities of consciousness and purpose and intentionality, while I was interested in the material nuts and bolts of information in the natural world. I hope you will find the meeting of our two views in the writing I have presented. There is nothing at all difficult about the argument I am making. I do not know how the mind interacts with matter, but I cannot even type this sentence without knowing that it does. I do not know where the “I” is, or the soul. But I do know that effects of information aren't determined by the dynamic properties of the representations that evoke and constrain those effects -- thus, the reason to inventory the material conditions that allow that constraint to occur. The distance between our interests and conceptions is short. Again, thanks.Upright BiPed
November 1, 2015
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KF, There are a lot of different kinds of arguments and conversations that take place here at UD (evolution, fossil record, descent, genetics, etc). And then there are the arguments specifically about information. There is a whole class of these objections regarding information that are simply (and very rationally) emptied by the observations of semiosis. For some, the information on Biosemiosis.org will clarify the issues, and it will actually matter to them. But unfortunately, there are many who will simply continue on as if nothing had ever been presented. Not much can be done about that. People do what profits them.Upright BiPed
November 1, 2015
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I’d like to say a special “Thank You” to GPuccio. Early on, it was GP who made me understand how the issues of semiosis applied to genetic translation. He was the person who turned the light on. After that, I could find my way to the relevant literature by the relevant researchers. Thank you GP.Upright BiPed
November 1, 2015
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Hello All, GP, KF, ES, WJM, Andre, Dio… Thank you all for the kind words. It is truly appreciated.Upright BiPed
November 1, 2015
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UB, It's good to see the introduction to your projects published here. Excellent topic! Very timely! I look forward to enjoy reading this thread in the days ahead (D m). Thank you.Dionisio
November 1, 2015
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