UD Guest Post: Dr Eugen S on “Biological memory vs. memory of materials”

_{kairosfocus
November 7, 2016

Engineering, Informatics, Intelligent Design

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UD has a broad and deep pool of readers and occasional contributors from across the world that have a lot to say, things that are well worth pondering. In this case, I am more than happy to host a guest post in which physicist and computer scientist ES (who hails from Russia) argues the thesis:

No linguistic processing occurs in the case of memory of a material that is exclusively explainable in terms of physical interactions between particles of that material, whereas the basic architecture of life is inherently linguistic.

Let us now ponder:

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Biological memory vs. memory of materials

[Eugen S, UD November 7, 2016]

Contemporary technology allows us to make self-deploying structures that can revert to their previous state. This kind of structures are used in space, medicine, forensic science, navigation, etc. They are said to have memory of shape or even possess heredity. Wait a minute… Everybody knows that heredity is a property of life. Isn’t that interesting?

Let’s take a quick look at the kind of memory a material like a smart alloy or a polymer foam has and compare it with biological memory. Let’s see if the common terminology reflects any inherent phenomenological similarities.

Materials with memory

The memory of a material is exclusively a result of physical interactions between its particles. A great many processes in nature, including memory of shape, can be thought of as manifestations of one powerful physical principle, the principle of minimum total potential energy.

The minimum total potential energy principle is a fundamental concept that describes the physical behaviour of matter. It dictates that (at low temperatures) a structure or body shall deform or displace to a position that (locally) minimizes the total potential energy, with the lost potential energy being converted into kinetic energy (specifically heat) [Wikipedia, Minimum total potential energy principle]. In other words, it is a tendency of a physical system towards an equilibrium state.

This principle is the basis of many natural phenomena:

mechanical or electromagnetic oscillations;
elliptic shapes of planetary orbits;
ellipsoidal shapes of planets and stars;
stability of mechanical structures;
stability of mechanical systems’ motion;
spherical shapes of soap bubbles;
crystallization;
precipitation;
convection patterns;
interference patterns;
sand dunes;
Moire stripes;
etc.

Smart alloys such as nickel titanium (nitinol) exhibit two closely related and unique properties: shape memory effect (SME) and superelasticity (SE) (also called pseudoelasticity (PE)) [Wikipedia, Shape memory alloys]. Shape memory is the ability of nitinol to undergo deformation at one temperature, then recover its original, undeformed shape upon heating above its transformation temperature. Superelasticity occurs at a narrow temperature range just above its transformation temperature; in this case, no heating is necessary to cause the undeformed shape to recover, and the material exhibits enormous elasticity, some 10-30 times that of ordinary metal [Wikipedia, Nickel-titanium].

In the case of memory foam, the effect of the long term preservation of shape is achieved by maximizing plasticity characteristics of an artificial polymer.

In all these cases, an elementary particle is mechanically stressed, which causes its deformation over time. Deformation may be caused by external force or temperature gradients in the alloy. Particles of matter under stress will tend to move in such a way that their total potential energy is minimal.

Fig.1. Smart alloys are used in mechanical structures where regaining the original form is critical. Source: GCSE Chemistry.

In more complex cases, the behaviour of a material may depend not only on its mechanical properties and the current state (temperature, alloy composition, etc.) but also on previous states. Examples of such systems and processes include:

self-induced oscillatory processes, such as the famous chemical clock (e.g. the Belousov-Zhabotinski autocatalytic reaction);
hysteretic effects;
fluctuations far from the thermodynamic equilibrium;
chaos.

The behaviour of these non-linear systems is also exclusively a result of particle dynamics even though its detailed scientific description would require far more sophisticated modelling than for some of the previous examples.

For example: Mechanical characteristics of memory foam are optimized for long term plasticity. These materials are heavily used in medicine, forensic science, fine arts, etc.

Biological memory

In organisms, in contrast, heredity is organized using symbolic memory that is non-existent in naturally occurring non-living systems. The functioning of biological heredity depends on interpretation of material tokens (signs) that prescribe the motion of elementary particles that the genetic information translation system consists of. Triplets of messenger RNA nucleotides (they are called codons) acting as tokens are interpreted by the translation system to evoke specific physical effects, i.e. the synthesis of a polypeptide foldable into functional proteins, in accordance with a translation protocol.

Fig.3. Genetic information translation process. Wikipedia.
The necessary condition a physical structure must satisfy to serve as a symbolic information storage is that it should be physically indeterminate (energy degenerate). Here is how physicist Howard Pattee formulates it: […A]ll symbol vehicles obey physical laws and have, in principle, a physical description, but that does not imply that they are physically determined. Quite the contrary is true. Such a degenerate sequence structure can have an immense number of physically indeterminate sequences [Pattee 2007]. An example of such symbolic information storage is messenger RNA. It is capable of serving as information medium because any of the four nucleotides (A, C, U or G) that are the building blocks of RNA oligomers can polymerize any other in aqueous solutions without any physico-chemical bias.

The codon-to-amino acid correspondence is realized by transport RNAs charged with the ‘correct’ amino acids corresponding to messenger RNA codons. The correspondence between codons and the twenty proteinogenic amino acids exists as a small set of formal rules known as the genetic code.

So the functioning of biological heredity is irreducible to exclusively the dynamics of elementary particles in the field of intermolecular forces. The dynamics of the system itself is prescribed by the sequence of codons in messenger RNA.

What does this all mean?

As we can see, there is no inherent similarity between the physical memory of shape in a material and the inherently formal, symbolic genetic memory of organisms. Biological memory as a phenomenon is totally different from memory of shape. Clearly, then, when we say that a material has memory we only draw a weak superficial analogy to the biological heredity mechanism.

Life is distinguished from non-life by its dependence on material construction under the control of coded symbolic description [Pattee 2007].

The messenger RNA translation system is a linguistic machine. A linguistic machine is the interpreter in the following tuple:

{data, protocol, interpreter}.

A linguistic machine takes as input signals from its environment or from a channel of communication with other linguistic machines and interprets them as data according to a specified protocol (a set of rules) and performs actions meaningful in the context where the machine operates. Examples of linguistic machines are artificial information processing systems (such as autopilots, automated decision support systems, etc.), computer language processors and even mathematics.

No linguistic processing occurs in the case of memory of a material that is exclusively explainable in terms of physical interactions between particles of that material, whereas the basic architecture of life is inherently linguistic.
Resources:

Wikipedia.
Howard Pattee. The Physics and Metaphysics of Biosemiotics. In Biosemiotics: Information, Codes and Signs in Living Systems. M. Barbieri (ed.), 2007, pp.219-234.

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A distinction well worth pondering. Let us now pause and discuss ES’s thesis and substantiation. END

Comments

BA77, SA, Very interesting comments. Decisions are what is not there in physics ;) Polymer foam does not make decisions. It trivially tends to an equilibrium with (locally) minimal potential energy. Physical laws are the same regardless. Yet, the organization of the semiotic complex {data,protocol,interpreter} is arbitrary (not contrary) to the laws of physics. Pattee even goes as far as saying 'complementary to physics'. At the core of information processing in this physical world lies arbitrariness i.e. the absence of any physico-chemical bias towards any particular one of multiple alternative system states. UB calls it discontinuity. Then the agent configures the physical system by instantiating rules of behaviour. The essence of these rules is bona fide decision making that physicality just provides a substrate for. In fact, I have recently started avoiding the use of "the laws of nature" ;) They are just natural regularities.EugeneS_{November 8, 2016
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Silver Asiatic asks:
Is it time for another amnesty period (say a 2-week trial) for banned posters to give us a try again?
Why give them the satisfaction of disrupting discussions in order to get banned yet again to replenish their reserve of self-righteous outrage?William J Murray_{November 8, 2016
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Suggestion for KF, Barry or mods ... Is it time for another amnesty period (say a 2-week trial) for banned posters to give us a try again?Silver Asiatic_{November 8, 2016
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rvb8
Biology follows different physical laws to Memory Foam? Which ones?
An information circuit does not follow the laws of physics. With memory foam, the shape that is retained is entirely dependent upon the exact shape that is pressed into it. Where there is information exchange, however, (as with living beings in biology) a signal is sent, but it must be received and interpreted and then a variety of actions can follow from the signal. The memory foam is determined by the shape, and no matter what shape it is, the foam is changed in exactly the same way. With a signals sent, a receiver filters noise and selects the coded message. In fact, some action from the receiver can trigger the sending of the message also, and can also give feedback to the sender to communicate that the signal was received and understood. That's what happens in biology. In a strictly a physio-chemical process, there is no translation or decoding of a message and then a logical decision-tree following to respond with actions.Silver Asiatic_{November 8, 2016
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In fact, tissue-specific spatial organization of genomes is found to be very nuanced,,,
Shoddy Engineering or Intelligent Design? Case of the Mouse's Eye - April 2009 Excerpt: -- The (entire) nuclear genome is thus transformed into an optical device that is designed to assist in the capturing of photons. This chromatin-based convex (focusing) lens is so well constructed that it still works when lattices of rod cells are made to be disordered. Normal cell nuclei actually scatter light. -- So the next time someone tells you that it “strains credulity” to think that more than a few pieces of “junk DNA” could be functional in the cell - remind them of the rod cell nuclei of the humble mouse. http://www.evolutionnews.org/2009/04/shoddy_engineering_or_intellig.html Ask an Embryologist: Genomic Mosaicism - Jonathan Wells - February 23, 2015 Excerpt: humans have a "few thousand" different cell types. Here is my simple question: Does the DNA sequence in one cell type differ from the sequence in another cell type in the same person?,,, The simple answer is: We now know that there is considerable variation in DNA sequences among tissues, and even among cells in the same tissue. It's called genomic mosaicism. In the early days of developmental genetics, some people thought that parts of the embryo became different from each other because they acquired different pieces of the DNA from the fertilized egg. That theory was abandoned,,, ,,,(then) "genomic equivalence" -- the idea that all the cells of an organism (with a few exceptions, such as cells of the immune system) contain the same DNA -- became the accepted view. I taught genomic equivalence for many years. A few years ago, however, everything changed. With the development of more sophisticated techniques and the sampling of more tissues and cells, it became clear that genetic mosaicism is common. I now know as an embryologist,,,Tissues and cells, as they differentiate, modify their DNA to suit their needs. It's the organism controlling the DNA, not the DNA controlling the organism. http://www.evolutionnews.org/2015/02/ask_an_embryolo093851.html
Thus since form/shape clearly is not reducible the bottom up Darwinian explanations, then any claim that Darwinian explanations can explain 'transformation of form' is completely disconnected from the empirical evidence we now have in hand. Of supplemental note: Perhaps the most interesting demonstration that ‘form/shape’ is not reducible to ‘bottom up’ material explanations is by noting the fact that the ‘form/shape’ of an organism is almost immediately lost upon the death of an organism:
Rabbit decomposition time-lapse (higher resolution) – video https://www.youtube.com/watch?v=C6sFP_7Vezg
In the following article, Stephen Talbott asks this very important question about the relatively sudden loss of ‘form’ at the death of an organism. Specifically Talbott asks, “What power holds off that moment — precisely for a lifetime, and not a moment longer?”
The Unbearable Wholeness of Beings – Stephen L. Talbott Excerpt: Virtually the same collection of molecules exists in the canine cells during the moments immediately before and after death. But after the fateful transition no one will any longer think of genes as being regulated, nor will anyone refer to normal or proper chromosome functioning. No molecules will be said to guide other molecules to specific targets, and no molecules will be carrying signals, which is just as well because there will be no structures recognizing signals. Code, information, and communication, in their biological sense, will have disappeared from the scientist’s vocabulary. ,,, the question, rather, is why things don’t fall completely apart — as they do, in fact, at the moment of death. What power holds off that moment — precisely for a lifetime, and not a moment longer? Despite the countless processes going on in the cell, and despite the fact that each process might be expected to “go its own way” according to the myriad factors impinging on it from all directions, the actual result is quite different. Rather than becoming progressively disordered in their mutual relations (as indeed happens after death, when the whole dissolves into separate fragments), the processes hold together in a larger unity. http://www.thenewatlantis.com/publications/the-unbearable-wholeness-of-beings
As to answering the question, What power holds off that moment — precisely for a lifetime, and not a moment longer?, I hold that it is 'non-local' quantum information that is holding off that moment — precisely for a lifetime, and not a moment longer
excerpt: What Penrose and Hameroff are referring to is the fact that in quantum mechanics it is quantum information that is primarily conserved, and not necessarily energy and matter that are primarily conserved, as energy and matter are primarily conserved in classical mechanics: https://uncommondescent.com/intelligent-design/philosopher-of-science-roger-penrose-thinks-soul-may-survive-death/#comment-620372
And as I elucidated in a bit more detail at the listed link quoting Penrose and Hameroff, I hold that this 'non-local' quantum information gives us actual scientific evidence for a transcendent soul. Verse:
Mark 8:37 “Is anything worth more than your soul?”
Supplemental notes:
Jim Al-Khalili, at the 2:30 minute mark of the following video states, ",,and Physicists and Chemists have had a long time to try and get use to it (Quantum Mechanics). Biologists, on the other hand have got off lightly in my view. They are very happy with their balls and sticks models of molecules. The balls are the atoms. The sticks are the bonds between the atoms. And when they can't build them physically in the lab nowadays they have very powerful computers that will simulate a huge molecule.,, It doesn't really require much in the way of quantum mechanics in the way to explain it." At the 6:52 minute mark of the video, Jim Al-Khalili goes on to state: “To paraphrase, (Erwin Schrödinger in his book “What Is Life”), he says at the molecular level living organisms have a certain order. A structure to them that’s very different from the random thermodynamic jostling of atoms and molecules in inanimate matter of the same complexity. In fact, living matter seems to behave in its order and its structure just like inanimate cooled down to near absolute zero. Where quantum effects play a very important role. There is something special about the structure, about the order, inside a living cell. So Schrodinger speculated that maybe quantum mechanics plays a role in life”. Jim Al-Khalili – Quantum biology – video https://www.youtube.com/watch?v=zOzCkeTPR3Q Molecular Biology - 19th Century Materialism meets 21st Century Quantum Mechanics – video https://www.youtube.com/watch?v=rCs3WXHqOv8
bornagain77_{November 8, 2016
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Of related note to 'memory of shape'. It is important to note that the 'form/shape' that a particular organism may take is not reducible to 'bottom up' Darwinian explanations in the first place. Thus, since Darwinian explanations are at a complete loss to explain why a particular organism has any particular form/shape then, of course, Darwinian explanations are also at a complete loss to explain how 'transformation of form/shape' is even remotely possible. The insurmountable problem of ‘form/shape’ for reductive materialistic explanations of Darwinian evolution has now been demonstrated by a few different methods. One method that demonstrated this failure is by saturation mutagenesis:
Response to John Wise - October 2010 Excerpt: A technique called "saturation mutagenesis"1,2 has been used to produce every possible developmental mutation in fruit flies (Drosophila melanogaster),3,4,5 roundworms (Caenorhabditis elegans),6,7 and zebrafish (Danio rerio),8,9,10 and the same technique is now being applied to mice (Mus musculus).11,12 None of the evidence from these and numerous other studies of developmental mutations supports the neo-Darwinian dogma that DNA mutations can lead to new organs or body plans--because none of the observed developmental mutations benefit the organism. http://www.evolutionnews.org/2010/10/response_to_john_wise038811.html 'No matter what we do to a fruit fly embryo there are only three possible outcomes, a normal fruit fly, a defective fruit fly, or a dead fruit fly. What we never see is primary speciation much less macro-evolution' – Jonathan Wells Darwin's Theory - Fruit Flies and Morphology - video http://www.youtube.com/watch?v=hZJTIwRY0bs
Here are some other examples that are very good for clearly illustrating that 'form/shape' is not reducible to 'bottom up' Darwinian explanations:
What Do Organisms Mean? Stephen L. Talbott - Winter 2011 Excerpt: Harvard biologist Richard Lewontin once described how you can excise the developing limb bud from an amphibian embryo, shake the cells loose from each other, allow them to reaggregate into a random lump, and then replace the lump in the embryo. A normal leg develops. Somehow the form of the limb as a whole is the ruling factor, redefining the parts according to the larger pattern. Lewontin went on to remark: "Unlike a machine whose totality is created by the juxtaposition of bits and pieces with different functions and properties, the bits and pieces of a developing organism seem to come into existence as a consequence of their spatial position at critical moments in the embryo’s development. Such an object is less like a machine than it is like a language whose elements... take unique meaning from their context.[3]",,, http://www.thenewatlantis.com/publications/what-do-organisms-mean "Last year I had a fair chunk of my nose removed in skin cancer surgery (Mohs). The surgeon took flesh from a nearby area to fill in the large hole he’d made. The pictures of it were scary. But in the healing process the replanted cells somehow ‘knew’ how to take a different shape appropriate for the new location so that the nose now looks remarkably natural. The doctor said he could take only half the credit because the cells somehow know how to change form for a different location (though they presumably still follow the same DNA code) . — I’m getting the feeling that we’ve been nearly as reductionist in the 20-21st century as Darwin and his peers were when they viewed cells as little blobs of jelly." leodp - UD blogger
Moreover, this failure of Darwinian explanations to be able to explain the particular form/shape of a organism happens at a very low level. For example, the shape that a particular protein may take is, in many instances, found to be dependent on whatever particular context the protein is found to be in. i.e. The shape of the protein is not rigidly defined by its particular sequence:
“It was long believed that a protein molecule’s three-dimensional shape, on which its function depends, is uniquely determined by its amino acid sequence. But we now know that this is not always true – the rate at which a protein is synthesized, which depends on factors internal and external to the cell, affects the order in which its different portions fold. So even with the same sequence a given protein can have different shapes and functions. Furthermore, many proteins have no intrinsic shape, (intrinsically disordered proteins), taking on different roles in different molecular contexts. So even though genes specify protein sequences they have only a tenuous (very weak or slight) influence over their functions. ,,,,So, to reiterate, the genes do not uniquely determine what is in the cell, but what is in the cell determines how the genes get used. Only if the pie were to rise up, take hold of the recipe book and rewrite the instructions for its own production, would this popular analogy for the role of genes be pertinent. Stuart A. Newman, Ph.D. – Professor of Cell Biology and Anatomy Biology's Quiet Revolution - Jonathan Wells - September 8, 2014 Excerpt: In 1996, biologists discovered a protein that does not fold into a unique shape but can assume different shapes when it interacts with other molecules. Since then, many such proteins have been found; they are called "intrinsically disordered proteins," or IDPs. IDPs are surprisingly common (about 1/3 of the proteins in our body), and their disordered regions play important functional roles.,,, ,,, Huge unanswered questions remain, and they will only be answered by going beyond the discredited myth that "DNA makes RNA makes protein makes us." http://www.evolutionnews.org/2014/09/biologys_quiet_089651.html Not Junk After All: Non-Protein-Coding DNA Carries Extensive Biological Information - Jonathan Wells - May 2013 Conclusion:,, Protein function depends on three-dimensional shape, and the same sequence of amino acids can be folded differently to produce proteins with different three-dimensional shapes [144–147]. Conversely, proteins with different amino acid sequences can be folded to produce similar shapes and functions [148,149]. Many scientists have pointed out that the relationship between the genome and the organism - the genotype-phenotype mapping = cannot be reduced to a genetic program encoded in DNA sequences. http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0009
This finding holds for RNA molecules as well
The Strange Inevitability of Evolution - Philip Ball - Jan. 2015 Excerpt: Naively, you might expect RNAs with a similar shape, and thus presumably phenotype, to share a similar sequence, so that a map of the possible sequences—the sequence space, which can be represented as a many-dimensional space where each grid point corresponds to a particular sequence—is divided up into various “shape kingdoms” (See Not a Patch, a). But that wasn’t what Schuster found. Instead, RNAs with the same shape could vary very widely in sequence: You could get the same shape, and therefore potentially the same kind of catalytic function, from very different sequences. http://nautil.us/issue/20/creativity/the-strange-inevitability-of-evolution
In fact, instead of DNA sequences ultimately controlling what form/shape a particular organism may take, as is presupposed in Darwinian thought, it is now found that it is the organism itself controlling the form/shape of DNA and even controlling sequences within DNA:
Tissue-specific spatial organization of genomes - 2004 Excerpt: Using two-dimensional and three-dimensional fluorescence in situ hybridization we have carried out a systematic analysis of the spatial positioning of a subset of mouse chromosomes in several tissues. We show that chromosomes exhibit tissue-specific organization. Chromosomes are distributed tissue-specifically with respect to their position relative to the center of the nucleus and also relative to each other. Subsets of chromosomes form distinct types of spatial clusters in different tissues and the relative distance between chromosome pairs varies among tissues. Consistent with the notion that nonrandom spatial proximity is functionally relevant in determining the outcome of chromosome translocation events, we find a correlation between tissue-specific spatial proximity and tissue-specific translocation prevalence. Conclusion: Our results demonstrate that the spatial organization of genomes is tissue-specific and point to a role for tissue-specific spatial genome organization in the formation of recurrent chromosome arrangements among tissues. http://genomebiology.com/content/5/7/R44
bornagain77_{November 8, 2016
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GP, Thanks very much! Yes, I know this website. And, yes, it is very similar. ESEugeneS_{November 8, 2016
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RVB8, "Is someone now going to mock my poor understanding" I am not, as far as I am concerned. A linguistic machine does not necessarily 'talk' a human language. However, when you hear people say that computers talk to each other, remember what I wrote in this OP ;) Cells do communicate. Even though their communication language is different from human, it is a language all the same. This is why cells fall into the category of linguistic machines. A linguistic machine is a device. When you see a device in the street, how can you tell it is a device? Are there any properties that can help you classify things you see in the world? Once you come up with those properties, can you be confident in your classification? If so, what if you see a similar device in every living cell?EugeneS_{November 8, 2016
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Eugene: Very good work. Your argument seems similar to the semiosis argument many times made by Upright Biped. You may be interested in his site on the subject: http://www.biosemiosis.org/ The "quality" of rvb8's comment at #5 is the best possible confirmation of the value of what you say! :)gpuccio_{November 8, 2016
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RVB8, DNA and RNA are about code; machine code. Code is a linguistic phenomenon and it is embedded in the core of life in the cell, along with associated complex execution machinery built with molecular technology. Please face this and its import. KFkairosfocus_{November 7, 2016
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"whereas the basic architecture of life is inherently linguistic." Fish don't talk, they're alive. Come to think of it so are trees, with an abundent lack of language. Is someone now going to mock my poor understanding of the use of the word, 'linguistic'? Memory Foam mattresses are not living, got it. But they exhibit a property of memory, in returning to an original shape, got it, I think. These material things that go back to an original shape are not actively choosing this, but are merely obeying physics; got it, I think. These things bare no resemblance to 'Biological memory'! Really? Biology follows different physical laws to Memory Foam? Which ones? Nobels in the offing.rvb8_{November 7, 2016
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Dr. E. S. Pazhálusta! Mnyé budyet ochen priatno z vami razgavarivat. Zhelayu Vam vsevo nailuchshevo! Ok, since this is mainly an English language venue and you're in the UK, let's switch back to English. :)Dionisio_{November 7, 2016
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KF, Dionisio, Spasibo! And BTW I am currently hailing from the UK ;)EugeneS_{November 7, 2016
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KF, Glad to read this interesting OP topic. Thank you for posting it and for letting us interact with Dr. E.S. directly. Dobró pozhálovat Dr. E. S.! Do you think morphogenesis could be used as an illustration of interesting cases of the tuple {data, protocol, interpreter} associated with the morphogen gradient formation and posterior interpretation?Dionisio_{November 7, 2016
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ES argues:
No linguistic processing occurs in the case of memory of a material that is exclusively explainable in terms of physical interactions between particles of that material, whereas the basic architecture of life is inherently linguistic.
. Well worth pondering. KFkairosfocus_{November 7, 2016
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Biological memory vs. memory of materials

[Eugen S, UD November 7, 2016]

Materials with memory

Biological memory

What does this all mean?

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