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

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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:

>>>>>>>>>>>>>>>>>>>>>

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.

smart_alloyz

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.

memry_foam

Fig.2. 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.

Protein Synthesis (HT: Wiki Media)
Protein Synthesis (HT: Wiki Media)

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:

  1. Wikipedia.
  2. 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

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

  1. 1
    kairosfocus says:

    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.

    KF

  2. 2
    Dionisio says:

    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?

  3. 3
    EugeneS says:

    KF, Dionisio,

    Spasibo! And BTW I am currently hailing from the UK 😉

  4. 4
    Dionisio says:

    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. 🙂

  5. 5
    rvb8 says:

    “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.

  6. 6
    kairosfocus says:

    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. KF

  7. 7
    gpuccio says:

    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! 🙂

  8. 8
    EugeneS says:

    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?

  9. 9
    EugeneS says:

    GP,

    Thanks very much!

    Yes, I know this website. And, yes, it is very similar.

    ES

  10. 10
    bornagain77 says:

    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/2.....38811.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/.....nisms-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/2.....89651.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.....08728_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/crea.....-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

  11. 11
    bornagain77 says:

    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/2.....ellig.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/2.....93851.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/.....-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:
    http://www.uncommondescent.com.....ent-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

  12. 12
    Silver Asiatic says:

    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.

  13. 13
    Silver Asiatic says:

    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?

  14. 14

    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?

  15. 15
    EugeneS says:

    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.

  16. 16
    Silver Asiatic says:

    WJM

    Why give them the satisfaction of disrupting discussions in order to get banned yet again to replenish their reserve of self-righteous outrage?

    That would not be very good, true.

    I’ve been away from UD for a while and upon returning it just seems that some very good posts here do not get challenged from opposition. I assumed that it was because we lost many opponents from banning – and perhaps they learned a lesson on how to interact appropriately here.

    But perhaps the better reason is that ID arguments are so much stronger that nobody can really challenge them.

    The sound of quietness from our opposition is a sound of victory for ID. So, that’s a very good thing! (I wouldn’t want trolling, empty arguments just for the sake of activity anyway).

  17. 17
    bornagain77 says:

    ES as to:

    “Decisions are what is not there in physics
    ,,,the agent configures the physical system by instantiating rules of behaviour.”

    This may be of related interest for you:

    Forever quantum: physicists demonstrate everlasting quantum coherence – October 14, 2016 by Lisa Zyga
    Excerpt: “The trick lies in the fact that local decoherence acts in a preferred direction, which is perpendicular to the one in which coherence is measured,” Adesso explained. “Consequently, the resulting quantum states are overall degraded by such noise, but their observed coherence remains unaffected during the dynamics if the initial conditions are suitably chosen.
    http://phys.org/news/2016-10-q.....rence.html

    ‘Suitably chosen’ being the key phrase. In other words, ‘suitably chosen’ means to intelligent design the initial conditions in such a way so as to maintain quantum coherence in spite of noise.

    Just how ‘suitably chosen’ life is in order to maintain quantum coherence in spite of noise is touched upon here:

    Quantum criticality in a wide range of important biomolecules
    Excerpt: “Most of the molecules taking part actively in biochemical processes are tuned exactly to the transition point and are critical conductors,” they say.
    That’s a discovery that is as important as it is unexpected. “These findings suggest an entirely new and universal mechanism of conductance in biology very different from the one used in electrical circuits.”
    The permutations of possible energy levels of biomolecules is huge so the possibility of finding even one that is in the quantum critical state by accident is mind-bogglingly small and, to all intents and purposes, impossible.,, of the order of 10^-50 of possible small biomolecules and even less for proteins,”,,,
    “what exactly is the advantage that criticality confers?”

    https://medium.com/the-physics-arxiv-blog/the-origin-of-life-and-the-hidden-role-of-quantum-criticality-ca4707924552

    further notes as to ‘suitably chosen’ initial conditions
    http://www.uncommondescent.com.....ent-619243

  18. 18
    Silver Asiatic says:

    Thanks, ES. Very good OP by the way also.

    For me, the biggest challenge on this topic is in providing clarity, and I think you did it here. The concept of retention of information in memory is important, and the memory foam is a great example of a purely physical analogy that doesn’t work (although we see from rvb8’s response that it is the analogy that materialists would use).

    It’s too easy to think of language as merely an exchange of symbols, which then can be equated to something like chemical bonds.

    But the use of language requires memory storage of the language rules. Both sender and receiver have the same rules stored. And language necessarily requires the use of logic – which also requires memory storage and retrieval.

    There is “if then” logic found in many instances in biology, where organisms not only receive messages and apply them, but give feedback (if a flower, and rich in nectar and non-toxic, tell the hive about it).

    Now the entire reason, supposed by evolution, for a feedback loop where information is gathered, stored and then shared in a two-way process is … the preservation of the species?

    If so, then evolution is optimized to prevent diversification into new species. It’s not enough to ask why organisms are driven, fighting against hostile pressures, to survive and reproduce — but we have to ask why they are driven to preserve their own species to such a degree that they learn languages used to communicate about dangers and threats, not to the individual, but to the hive (or with some birds, even to birds of not their own species).

  19. 19
    EugeneS says:

    SA

    Thanks! Yes, as you walk up the organization ladder in the bioshere, you get progressively more complexity, layers and layers of overlaid complexity.

    What is important for me, is the transition between life and non-life is not just chemistry, not just a matter of degree, but a matter of kind. There is no gradualism here, there is a chasm.

    “although we see from rvb8’s response that it is the analogy that materialists would use”

    I do believe though that provided one has no strong a priori philosophical bias towards materialism, it is possible to demonstrate using exclusively material means that naturalism already fails to account for life as we know it today.

  20. 20
    Silver Asiatic says:

    ES

    Yes, as you walk up the organization ladder in the bioshere, you get progressively more complexity, layers and layers of overlaid complexity.

    Greater complexity, organization and interactivity is more costly — and evolution would necessarily seek lower costs not greater. The same result (survival and reproduction) can be achieved for much less. The massive complexity and order is extravagant and unnecessary.

    What is important for me, is the transition between life and non-life is not just chemistry, not just a matter of degree, but a matter of kind. There is no gradualism here, there is a chasm.

    In classical metaphysics, it’s an ontological difference. Because, as you write, there are decision-making functions, this cannot be the result of an entirely deterministic process.

    I do believe though that provided one has no a priori philosophical bias towards materialism, it is possible to demonstrate using exclusively material means that naturalism already simply fails to account for life as we know it today (and progressively more so in the future).

    I would enjoy and appreciate seeing your argumentation on this.

  21. 21
    AhmedKiaan says:

    “I’ve been away from UD for a while and upon returning it just seems that some very good posts here do not get challenged from opposition. I assumed that it was because we lost many opponents from banning – and perhaps they learned a lesson on how to interact appropriately here.”

    There’s not a lot to talk about here. I tried to get PaV to post about how the whole HIV/AIDS/Medical/Scientific establishment is committing fraud, which he seems to think, but he doesn’t want to.

    In the meantime, News posts x number of science links a week, bornagain does his cut and paste thing, Kairosfocus talks about his unique sciency acronyms, there’s a few people dorm-room philosophizing, and…that’s about it…..

  22. 22
    AhmedKiaan says:

    I don’t know what more this place could do, actually.

  23. 23
    gpuccio says:

    AhmedKiaan;

    What do you think of this thread? Just to know.

  24. 24
    Pindi says:

    Just to echo what AhmedKiaan is saying, I don’t think any of the banned people would be very interested in returning as there is very little scientific discussion here anymore. Gpuccio is an exception, as is HeKS, but the overt theists are running rampant here now. Thee is more debate at TSZ where 3 or 4 very strong ID commentators are a regular part of the discussions there now. For that matter the anti-ID commentators at TSZ have pretty strident debates amongst themselves also and pull no punches with each other, which is something that doesn’t happen much here – you all tend to agree and support each other, so not much interesting comes out. My 2 cents.

  25. 25
    Dionisio says:

    gpuccio @23:

    Oh, what a question! Well done!

    🙂

  26. 26
    Dionisio says:

    Pindi @24:

    If it’s so much more interesting in another blog, why are you hanging on here for so long?
    What keeps you from leaving this allegedly ‘boring’ forum and enjoying the real discussions somewhere else?
    Really puzzling, isn’t it?

  27. 27
    Pindi says:

    Dionisio, yes, it’s almost like an addiction. Pretty harmless one though I guess. Better than cigarettes..

  28. 28
    Dionisio says:

    Pindi @27:

    it’s almost like an addiction. Pretty harmless one though I guess. Better than cigarettes..

    Addiction to what specifically?

  29. 29
    Pindi says:

    Dionisio, good question.

  30. 30
    Dionisio says:

    Pindi @29:

    And what’s your answer to that good question?

    Again, what is the addiction (@27) that keeps you so active for so long in this allegedly ‘boring’ blog ?

    Are you telling us that you cannot answer such an easy question?

  31. 31
    Dionisio says:

    gpuccio:

    I’m curious to know AhmedKiaan’s answer to your question @23.

  32. 32
    EugeneS says:

    SA

    “Greater complexity, organization and interactivity is more costly — and evolution would necessarily seek lower costs not greater.”

    I agree. As David Abel puts it, evolution chooses from among already available alternatives. It does not choose for a future function.

    “I would enjoy and appreciate seeing your argumentation on this.”

    Thank you for your credit. This is how I see it. Basically, in inanimate matter we have a very limited set of scenarios: chaos, regularity and phase transitions in between.

    Life, on the contrary, is characterized by complex pragmatic function, open-endedness and creativity. With open-endedness, living systems are empowered by the ability to adapt. However, I view evolution as only oscillations around the already existing functional basins. No genuine function novelty is achievable in real life just by means of biological evolution. Simply because biological evolution has no foresight. As soon as one adds foresight to the equation, it stops being evolution. It is something else, a progression of states towards a set goal. Evolution has no goal by definition.

    In cellular automata there is a theoretic result proving the existence of so called gardens of Eden, i.e. automaton states S* that are not reachable by a given automaton other than by setting its initial state to be S*: S(t=0) = S*.

    This relates, BTW, to BA’s appropriately chosen initial conditions.

    There is no adequate naturalistic explanation for the semiotic core of the organization of life, i.e. of the tuple {data,protocol,interpreter} I mention in the OP.

    In order for something (e.g. an oligomer) to serve as information medium there must be inherent arbitrariness, multiplicity of alternative states to choose from in order to achieve some goal meaningful at a system level. This is why I think no attempt to explain life origin exclusively in terms of chemistry or physics will ever be successful.

    No such attempt addresses the most important question, i.e. the question about the origin of the first instruction to the first processor. Since for an instruction instantiated into physical medium there must be no particular physical or chemical bias, there is no exclusively physical or chemical way towards the first complex {data,protocol,interpreter}. It needs deliberate tuning. Inanimate nature does not do anything in order to. It could not care less if anything works as a system. For a system to appear it takes a unifying principle, pragmatic purpose which is embodied in the form of rules of behaviour. Rules are not constraints of physical necessity. Rules are arbitrary (not contrary) to natural regularities. Consequently, rules are not reducible to physical necessity. However, life is organized based on rules.

    A scientist who wants to account for life only by means of physics or chemistry is trying to enthusiastically build a house knowing that there are dozen other people demolishing, as enthusiastically as himself, what he has just managed to build…

  33. 33
    Dionisio says:

    EugeneS,

    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?

  34. 34
    Silver Asiatic says:

    AhmedKiaan

    I disagree that there’s not much to talk about here. On the contrary, there seems to be a lot of new material daily. But as I said earlier, I do notice that there is not as much opposition to ID here as in the past.

  35. 35
    Silver Asiatic says:

    Pindi

    I agree that debates here have cooled down somewhat and you’re probably right that banned people wouldn’t want to return anyway. At the same time, I do recall arguments here that went far beyond respectful exchanges, so I fully support the actions to ban those individuals.

    I checked out TSZ (noticing a number of UD names) and much of it does not seem to be hard science at all. In fact it seems to be a parallel of UD. I certainly don’t see the kind of original research that AhmedKiaan seems to think needs to be part of this blog. But the dialogue is lively in several places, true.

    Where there is widespread agreement that will reduce the activity, so that may be the case here also.

  36. 36
    Pindi says:

    Dionisio, I am not sure why I keep coming here. Entertainment I think. I used to enjoy watching the contest between opposing views, and I guess I keep checking in in case that kind of thing starts up again.

  37. 37
    rvb8 says:

    EugeneS,

    “evolution chooses from among already available alternatives.”

    No, it does not, as it can not ‘choose’ anything. The ‘already available alternatives’, are changing (increasing, decreasing) all the time, its called mutation followed by selection.

    This one sentence is so egrgious as to bring its writer into question. Here’s the question; ‘Do you not understand the equation RM+NS=Evolution?’

    This communication between cells is also not linguistic. Proteins in one cell are made of molecules which naturally (following the laws of physics) bind to the protein locks in another part of the cell, and your woo ‘information” is transferred; big deal? It’s the most natural process and is understandable. Which is a lot more than can be said of this psudo-intellectual drivel.

  38. 38
    Dionisio says:

    Silver Asiatic @34:

    I do notice that there is not as much opposition to ID here as in the past.

    Could that have anything to do with gpuccio and other serious folks here always winning the debates with the politely dissenting interlocutors?

    Besides, as more research papers get published less room is left for the politely dissenting interlocutors to maneuver with their just-so stories.

  39. 39

    rv,

    When Evgeny says “evolution chooses from among already available alternatives”, he is merely saying that evolution doesn’t select for future function (which is the very next sentence in his post). If you’re freaking over the word “choose” (as opposed to select), you can rest assured that ES is merely using “choose” as the outcome of selection. Moreover, the point he is making is one that you wouldn’t argue with, so whatever.

    … its called mutation followed by selection

    I believe you are one of the people I saw lamenting a lack of scientific topics on UD, so I have a science question for you. In 1955, Francis Crick proposed a yet unknown set of “adapter” molecules that he predicted would be necessary to connect the pattern of nucleic acids in DNA to the amino acids they specify during translation. Three years later Mahlon Hoagland and Paul Zamecnik discovered the tRNA adapters that Crick predicted would exist. They also found the complex proteins (aaRS) that are required to bind those tRNA with their individual amino acid cargo – establishing the Genetic Code. This all makes sense with the physicalist axiom (as naturalist philosopher Alex Rosenberg puts it) that “no clump of matter is about any other clump of matter”. In other words, a codon in DNA is obviously not “about” the amino acid it specifies during translation, and thus, Crick’s adapter molecule is required to establish a systematic association within the process of translation.

    And of course, all of this is exactly what is found inside the cell; there is an “adapter” tRNA for every amino acid, and there is an aaRS to load every adapter with its correct amino acid (in accordance with the code). The association of anticodon-to-amino acid is made when the aaRS loads the correct amino acid to the tRNA adapter (establishing the genetic code), and then the codon-to-anticodon association is made when the charged tRNA adapter enters the ribosome to deliver its amino acid cargo (to be bound to the new protein). None of this is even slightly controversial, and is taught in every biology textbook on the surface of the planet. In the genetic translation process, the sequence of codons in DNA establishes the order of amino acids to be bound to the nascent protein, and in a separate process, the aaRS establishes which amino acid will be associated with each codon.

    My question to you is: Do you think Crick, Rosenberg (and the rest of the planet) have it right? Given that a codon cannot be “about” an amino acid, is a correctly loaded tRNA adapter required to establish the systematic association?

  40. 40

    Evgeny, congratulations on a truly fine OP.

  41. 41
    EugeneS says:

    Dionisio,

    Unfortunately I cannot comment on morphogenesis as this is not my topic. I only know that other biologic codes apart from genetic code have been identified recently (membrane code is one of them).

  42. 42
    EugeneS says:

    Upright BiPed,

    Thanks very much!

    Yes, I was a bit baffled by the criticism against my use of “choose” instead of “select”. It is void of any substance 😉

  43. 43
    EugeneS says:

    Rvb8,

    You may choose to use “select” instead of “choose”. It does not make any difference to my argument.

    The remainder of your comment 37 is void of any meaning, I am afraid. No information translation is possible without the said arbitrariness. Genetic information translation is only possible due to absence of any chemical bias in nucleotide polymerization (any of {A,C,U,G} can polymerize any other).

    Your criticism would have been meaningful if you had shown a purely naturalistic way for the complex {data,protocol,interpreter} to arise. The RNA world hypothesis does not achieve that.

    Ask yourself why it is not possible to play chess on a vertically positioned wooden chessboard.

  44. 44
    Silver Asiatic says:

    rvb8

    Proteins in one cell are made of molecules which naturally (following the laws of physics) bind to the protein locks in another part of the cell, and your woo ‘information” is transferred; big deal?

    It should be pretty easy to falsify ID theory on this point. All you have to do is explain the precise laws of physics (or what chemical properties if you want) that determine how DNA codes for proteins.

    You’re also saying that a claim that an information transfer occurs in that process is ‘woo’, right?

  45. 45
    Silver Asiatic says:

    I was thinking (#16) why there was so little challenge or opposition. Then rvb8 comes along. 🙂 Come on, rvb — you really need to do a lot better than that.

  46. 46
    Silver Asiatic says:

    EugeneS

    As David Abel puts it, evolution chooses from among already available alternatives. It does not choose for a future function.

    Ok, choose, select … that’s the language evolutionists use so it shouldn’t be a problem, even though it creates an intelligent agent out of an unthinking process.

    Life, on the contrary, is characterized by complex pragmatic function, open-endedness and creativity. With open-endedness, living systems are empowered by the ability to adapt.

    Interesting and good argumentation here and following – thanks. I like to consider this ability to adapt as emerging from “the desire to survive”. Supposedly, inanimate life “wants to survive” somehow? A drop of water wants to preserve itself and not merge into the larger puddle? The clay under our feet is struggling not to be dissipated into dust?

    Ok, then by abiogenesis we have all of these living organisms that will actually change shapes and grow new functions just to prevent themselves from returning back into the non-living compounds they started from … ??? Just some of the insanity of evolutionary thought, as I see it.

    However, I view evolution as only oscillations around the already existing functional basins. No genuine function novelty is achievable in real life just by means of biological evolution. Simply because biological evolution has no foresight. As soon as one adds foresight to the equation, it stops being evolution. It is something else, a progression of states towards a set goal. Evolution has no goal by definition.

    Questions (for which I have my own answers but would like to hear yours): Why do you propose that evolution needs foresight? Why wouldn’t the appearance of a new function merely be established to meet a present need?

    No such attempt addresses the most important question, i.e. the question about the origin of the first instruction to the first processor. Since for an instruction instantiated into physical medium there must be no particular physical or chemical bias, there is no exclusively physical or chemical way towards the first complex {data,protocol,interpreter}. It needs deliberate tuning.

    For the first instruction to the first processor, rules have to be established and agreed-upon by sender and receiver in order to share the same data and translate. So, all of that would have to emerge simultaneously.

    It could not care less if anything works as a system. For a system to appear it takes a unifying principle, pragmatic purpose which is embodied in the form of rules of behaviour. Rules are not constraints of physical necessity. Rules are arbitrary (not contrary) to natural regularities. Consequently, rules are not reducible to physical necessity. However, life is organized based on rules.

    That is beautifully stated – excellent!

  47. 47
    Dionisio says:

    EugeneS @41:

    […] other biologic codes apart from genetic code have been identified recently (membrane code is one of them).

    Yes, that’s very interesting indeed. Thank you for mentioning such an exciting topic.

    Do those novel biologic codes open up new areas for intensive/extensive biology research that could enrich your topic too?

    BTW, I appreciate your honesty and humility in your comment regarding morphogen gradients being seen as another biologic code. Your honest and humble comment is in sharp contrast with some academics who have commented in this same site, but did not seem willing to admit their lack of knowledge in a particular area.
    Honesty and humility are required virtues in serious science in order for it to advance.
    Morphogen gradient formation and interpretation does not seem settled yet. It’s a “work-in-progress” issue. There are still outstanding questions and new unknowns may arise in the future. However, as new discoveries shed more light on the subject, the big picture seems increasingly pointing to a very fascinating information-processing subsystem.

  48. 48
    Dionisio says:

    Upright BiPed @39:

    In 1955, Francis Crick proposed a yet unknown set of “adapter” molecules that he predicted would be necessary to connect the pattern of nucleic acids in DNA to the amino acids they specify during translation. Three years later Mahlon Hoagland and Paul Zamecnik discovered the tRNA adapters that Crick predicted would exist. They also found the complex proteins (aaRS) that are required to bind those tRNA with their individual amino acid cargo – establishing the Genetic Code. This all makes sense with the physicalist axiom (as naturalist philosopher Alex Rosenberg puts it) that “no clump of matter is about any other clump of matter”. In other words, a codon in DNA is obviously not “about” the amino acid it specifies during translation, and thus, Crick’s adapter molecule is required to establish a systematic association within the process of translation.

    And of course, all of this is exactly what is found inside the cell; there is an “adapter” tRNA for every amino acid, and there is an aaRS to load every adapter with its correct amino acid (in accordance with the code). The association of anticodon-to-amino acid is made when the aaRS loads the correct amino acid to the tRNA adapter (establishing the genetic code), and then the codon-to-anticodon association is made when the charged tRNA adapter enters the ribosome to deliver its amino acid cargo (to be bound to the new protein). None of this is even slightly controversial, and is taught in every biology textbook on the surface of the planet. In the genetic translation process, the sequence of codons in DNA establishes the order of amino acids to be bound to the nascent protein, and in a separate process, the aaRS establishes which amino acid will be associated with each codon.

    Excellent description. Thank you.

  49. 49
    gpuccio says:

    Pindi:

    “the overt theists are running rampant here now”.

    Well, just a reflection about that.

    I think that one of the reasons why “the overt theists” seem to be more active here than before, is that each time we have tried to focus on science, and only science, “the overt atheists” have been very active in trying to move the debate to philosophical and anti-religious points which were not in any way implied in the argument being made.

    That has happened to me many times.

    You may be aware that most of the “answers” which are usually given to specific biological arguments for ID are of the “anti-religious” kind. The infamous “God of the gaps” pseudo argument is a good example, and I could not count the times that arguments about “Why would a good God allow evil and suffering” or similar non pertinent aspects suddenly arise when there is no more interest (or ability) to answer the scientific reasonings that point to design.

    And how many times just an appeal to “extreme materialism” has been given as an answer to any argument about information, as though appealing to “physical laws, and physical laws only” could easily erase all problems connected to information, meaning, and so on. See, for example, post #5, by rvb8, here.

    Add to that the easy shift to personal offence, derisive attitude, and so on, which is so frequent on both sides.

    Nothing of that helps what I would consider desirable and interesting: a peer to peer confrontation between people with different scientific views, who agree to respectfully share their arguments and their convictions about science.

    Is it so impossible to debate the theory of design in biology without being labeled as “creationist” or worse? Is it so impossible to consider the arguments about functional complexity, or semiosis, as serious scientific arguments? That does not mean that anybody has to agree: there are many serious scientific arguments which may simply be wrong, and in the end each person has to choose what he considers credible.

    However, serious scientific and intellectual confrontation is always a reward, and I believe that we can have it here, but only if a number of people on both sides are interested to have it.

    Just to be clear: I am not saying that nobody in the “anti-ID” field has seriously contributed to the discussions here: indeed, many very good opponents have been the main inspiration in my personal development of my ideas about ID and science. I am grateful to them all. But there is a crowd of other people who behave very differently. And even the best, sometimes, choose to find refuge in religious antireligious arguments, if they find it can help in some difficult context! 🙂

    Just to be clear: I have nothing against healthy confrontations between “overt theists” and “overt atheists”. They can be good and interesting, even if I am not personally a fan. My only point here is that they do not help a scientific discussion, where no reference to personal worldviews should be necessary, except in some very particular cases.

  50. 50
    Phinehas says:

    rvb8:

    No, it does not, as it can not ‘choose’ anything.

    It doesn’t “select” anything either. If you feel strongly enough about this to start a campaign to change the term “natural selection” to something more appropriate to what is actually happening, you will have my full support.

  51. 51
    EugeneS says:

    SA

    “Why wouldn’t the appearance of a new function merely be established to meet a present need?”

    Evolution with foresight is not evolution any more. I think that foresight is necessary in order to produce new function. Like I say, there are no naturalistic means to select for a not-yet available function. In order for a system to be capable of reacting to present needs, these needs must have been previously foreseen.

    One of absolutely stunning manifestations of bio-design is the existence of multiple fail-safe protein mechanisms, whereby individual mechanisms are so different in their implementation on the molecular level (so consequently they are not sharing any thinkable common ancestors) and yet they are unified by a single purpose. Probably I am not the best person to give specific examples but they do exist. I am sure GP will not allow me to make it up 🙂

    Say we have a chemical factory, there is a technological process that aims at producing this much of X. However, this X is not available in nature and is a product of a reaction between Y and Z under specific conditions (heat, pressure). So in order to produce X I as a chemist use foresight. I have a target state in mind which I pursue using material means (mixing so much of Y and Z). I am here a decision maker.

    Decision making is absolutely key in producing multi-component systems that are unified by a function to which all its components contribute and which is unavailable other then by means of the system acting as a whole. Inanimate nature is absolutely void of any decision making capability. I am aware of attempts to reduce intelligence to naturalistic factors. They are nothing but speculation.

  52. 52
    gpuccio says:

    EugeneS:

    Very good points!

    I always say that the inner conscious experiences that allow design are:

    a) Understanding of meaning.

    b) Desire, the experience of feeling, of what is “good”.

    c) The application of desire to understanding produces purpose.

    d) That generates the output of some meaningful configuration, which has the function to implement the desired thing, to the outer world.

    I think this is, more or less, what you call “foresight”.

    None of that can happen in a non conscious system. That’s why the design process, and its connected properties of functional complexity and semiosis, can only be the result of the intervention some conscious intelligent being.

  53. 53
    EugeneS says:

    GP

    Thought provoking as usual 😉

  54. 54
    EugeneS says:

    Dionisio

    “Do those novel biologic codes open up new areas for intensive/extensive biology research that could enrich your topic too?”

    Yes. There’s work by Marcello Barbieri specifically on this (see his Code biology).

    Well, I wish I could say ‘yes’ to the second part of your question. But it is not my subject unfortunately. I think that biology will drastically change in the future. Well, if not in the capacity of researcher, but at least as an onlooker, I think I will enjoy watching the process 🙂

  55. 55
    Silver Asiatic says:

    EugeneS 51

    Great response – thanks!

    Like I say, there are no naturalistic means to select for a not-yet available function. In order for a system to be capable of reacting to present needs, these needs must have been previously foreseen.

    The gradualist notion will claim that when new needs arise, adaptations occur simultaneously – but that’s impossible. Beyond this, a coordinated process required for a function cannot come together accidentally. That’s where the foresight comes into play, right? One part of the function has to join with another – and neither part has any usefulness (with regards to the new, present need) on its own.

    Probably I am not the best person to give specific examples but they do exist. I am sure GP will not allow me to make it up 🙂

    It would be great to see a real life example of this — if you or GP can come up with one. But the concept remains clear in the simulation you gave anyway.

    Decision making is absolutely key in producing multi-component systems that are unified by a function to which all its components contribute and which is unavailable other then by means of the system acting as a whole.

    That is an excellent and very clear explanation of what is actually required for a functional process. Parts which are entirely independent of each other on their own, are unified and coordinated into a whole – which only can be ordered, or organized by a principle outside of itself.

    Inanimate nature is absolutely void of any decision making capability. I am aware of attempts to reduce intelligence to naturalistic factors. They are nothing but speculation.

    Naturalistic processes are deterministic whereas there is a sense of free choice among options where there is intelligence.

  56. 56
    Dionisio says:

    gpuccio @49:

    Add to that the easy shift to personal offence, derisive attitude, and so on, which is so frequent on both sides.

    Nothing of that helps what I would consider desirable and interesting: a peer to peer confrontation between people with different scientific views, who agree to respectfully share their arguments and their convictions about science.

    Good point. Well stated. Thank you.

  57. 57
    Dionisio says:

    EugeneS @54:

    I think that biology will drastically change in the future. Well, if not in the capacity of researcher, but at least as an onlooker, I think I will enjoy watching the process

    I would enjoy watching it from the sideline too! 🙂

  58. 58
    EugeneS says:

    SA

    “Naturalistic processes are deterministic”

    Actually Abel argues that the word “process” already assumes some kind of ‘processing’ or teleology and is therefore, strictly speaking, inappropriate in relation to natural (including stochastic) phenomena. However, “stochastic process” is already a widely accepted misnomer.

    Even so, I would not say that natural ‘processes’ are necessarily deterministic. However, they are not teleological, they are not choice-contingent.

    Intelligence, on the contrary, has the unique ability to choose with intent.

  59. 59
    bornagain77 says:

    as to:

    “Say we have a chemical factory,,,”

    OK, let’s say we do. What would the comparison truly be like?

    “To grasp the reality of life as it has been revealed by molecular biology, we must magnify a cell a thousand million times until it is twenty kilometres in diameter and resembles a giant airship large enough to cover a great city like London or New York. What we would then see would be an object of unparalleled complexity and adaptive design. On the surface of the cell we would see millions of openings, like the portholes of a vast space ship, opening and closing to allow a continual stream of materials to flow in and out. If we were to enter one of these openings with find ourselves in a world of supreme technology and bewildering complexity. We would see endless highly organized corridors and conduits branching in every direction away from the perimeter of the cell, some leading to the central memory bank in the nucleus and others to assembly plants and processing units. The nucleus of itself would be a vast spherical chamber more than a kilometer in diameter, resembling a geodesic dome inside of which we would see, all neatly stacked together in ordered arrays, the miles of coiled chains of the DNA molecules. A huge range of products and raw materials would shuttle along all the manifold conduits in a highly ordered fashion to and from all the various assembly plants in the outer regions of the cell. We would wonder at the level of control implicit in the movement of so many objects down so many seemingly endless conduits, all in perfect unison. We would see all around us, in every direction we looked, all sorts of robot-like machines. We would notice that the simplest of the functional components of the cell, the protein molecules, were astonishingly, complex pieces of molecular machinery, each one consisting of about three thousand atoms arranged in highly organized 3-D spatial conformation. We would wonder even more as we watched the strangely purposeful activities of these weird molecular machines, particularly when we realized that, despite all our accumulated knowledge of physics and chemistry, the task of designing one such molecular machine – that is one single functional protein molecule – would be completely beyond our capacity at present and will probably not be achieved until at least the beginning of the next century. Yet the life of the cell depends on the integrated activities of thousands, certainly tens, and probably hundreds of thousands of different protein molecules.
    We would see that nearly every feature of our own advanced machines had its analogue in the cell: artificial languages and their decoding systems, memory banks for information storage and retrieval, elegant control systems regulating the automated assembly of parts and components, error fail-safe and proof-reading devices utilized for quality control, assembly processes involving the principle of prefabrication and modular construction. In fact, so deep would be the feeling of deja-vu, so persuasive the analogy, that much of the terminology we would use to describe this fascinating molecular reality would be borrowed from the world of late twentieth-century technology.
    What we would be witnessing would be an object resembling an immense automated factory, a factory larger than a city and carrying out almost as many unique functions as all the manufacturing activities of man on earth. However, it would be a factory which would have one capacity not equaled in any of our own most advanced machines, for it would be capable of replicating its entire structure within a matter of a few hours. To witness such an act at a magnification of one thousand million times would be an awe-inspiring spectacle.”
    Michael Denton PhD., Evolution: A Theory In Crisis, pg.328

    And to make the comparison complete, further suppose that we live in a bizarro world in which ‘educated’ scientists insist that this unrivaled chemical factory that we were staring at arose via one lucky accident at a time completely by chance.

    Seinfeld – Elaine discovers Bizarro World
    https://www.youtube.com/watch?v=IcjSDZNbOs0

  60. 60
    Dionisio says:

    Perhaps this is off topic but wanted to see if this VR stuff could have any application in biosemiotics or Systems Biology research and/or presentations?

    https://www.wired.com/2016/11/vr-totally-changing-architects-dream-buildings/?mbid=nl_11916_p7&CNDID=44828754

    Just curious.

  61. 61
    Dionisio says:

    EugeneS @54:

    There’s work by Marcello Barbieri specifically on this (see his Code biology).

    Thank you for the interesting reference.

    Code Biology: A New Science of Life by Marcello Barbieri

    This book is the study of all codes of life with the standard methods of science. The genetic code and the codes of culture have been known for a long time and represent the historical foundation of this book. What is really new in this field is the study of all codes that came after the genetic code and before the codes of culture. The existence of these organic codes, however, is not only a major experimental fact. It is one of those facts that have extraordinary theoretical implications. The first is that most events of macroevolution were associated with the origin of new organic codes, and this gives us a completely new reconstruction of the history of life. The second implication is that codes involve meaning and we need therefore to introduce in biology not only the concept of information but also the concept of biological meaning. The third theoretical implication comes from the fact that the organic codes have been highly conserved in evolution, which means that they are the greatest invariants of life. The study of the organic codes, in short, is bringing to light new mechanisms that have operated in the history of life and new fundamental concepts in biology.
    […]
    We arrive in this way at the conclusion that coding is not reducible to copying or to self-assembly, and the close relationship that exists between organic codes and macroevolution tells us that coding is indeed a fundamental mechanism. Code biology is truly a new science in the making, the exploration of a vast and still largely unexplored dimension of the living world, the real new frontier of biology.

  62. 62
    Silver Asiatic says:

    EugeneS @ 58

    Fascinating and important distinctions – thanks.
    It tells us how important the philosophical/semantic foundations to science really are. Yes, a ‘stochastic process’ is a misnomer. But we can notice how powerful that terminology can be in shaping (the wrong) understanding.
    Scientists become convinced that random outputs have innovative power. It’s compared to something like when humans do brainstorming. We supposedly think of random ideas, and then a good one arises and we select it.
    But a stochastic output alone cannot make those kinds of decisions, obviously.

    As to whether natural phenomena are necessarily deterministic – it could be argued both ways. Ultimately, in a materialistic universe, everything is reducible to physics. So, even stochastic outputs are traceable to the deterministic elements of matter, energy, forces, laws, etc.

    In other words, there is no freedom to select from options.

    However, using a more local understanding of randomness, it would probably be better to say that randomness does exist and events of that sort are not deterministic. A variety of outputs can be achieved, not in a linear dependence on previous causes.

    It’s with this that we see attempts to explain intelligence as a product of purely natural factors. But again, there can be no goal-seeking in that, and therefore no coordinated processes to achieve function.

  63. 63
    EugeneS says:

    SA

    We have nicely coherent views on the subject 😉

    BA

    “And to make the comparison complete, further suppose that we live in a bizarro world in which ‘educated’ scientists insist that this unrivaled chemical factory that we were staring at arose via one lucky accident at a time completely by chance.”

    As one of the commentators here aptly said many moons ago, I cannot believe that a code error correction system arose from a code error 😉

    Naturalists live in a different reality.

  64. 64

    At this point I think it’s safe to say that rv and others were never really interested in having a science discussion.

    No surprise.

  65. 65
    Origenes says:

    RVB8: The ‘already available alternatives’, are changing (increasing, decreasing) all the time, its called mutation followed by selection.
    Here’s the question; ‘Do you not understand the equation RM+NS=Evolution?’

    I don’t understand this equation. Allow me to illustrate my unenlightenment with an example:

    Suppose a DVD copy machine which produces a few random copy-errors every time it makes a copy. Suppose this machine makes 10 copies of a newly purchased Windows 7 DVD. Now remove the original DVD and repeat the imperfect copy process starting with functional second generation “mutated” copies (dysfunctional copies are removed from the process after testing). Next remove all second generation copies and repeat the copy process starting with functional third generation mutated copies. And so forth.

    Who of us would expect that this imperfect copy process to be anything other than the degeneration of Windows 7 eventually leading to mutated copies which are, without exception, dysfunctional? Who of us expects versions of Windows 7 with improved functionality?

    Of course a DVD with copy errors does not want to be functional, it really doesn’t care whether it is functional or not. But what exactly is the difference with an organism under materialism? Similar to a DVD who does not want to be functional, the organism does not want to live. The fermions and bosons that are the organism don’t give a hoot about life.

  66. 66
    gpuccio says:

    UB:

    “At this point I think it’s safe to say that rv and others were never really interested in having a science discussion.

    No surprise.”

    Indeed! 🙂

    We are certainly overwhelmed by the many and thoughtful comments of AhmedKiaan and rvb8 on the important subject of semiosis in this thread. Maybe they think that semiosis is a pillar of christian apologetics!

    Even the “addicted” Pindi seems to have found recovery… 🙂

  67. 67
    Silver Asiatic says:

    I’d draw some conclusions:

    1. The OP and related supportive commentary here is irrefutable.
    2. We don’t have any serious opposition.
    3. ID wins entirely on science here. There is no religious or apologetic dimension to the argument.
    4. Even if this was the only ID argument, materialism would fail, but there are others also.
    5. Materialists cannot even pretend to engage in the topic since to do so only makes things worse for them. Their only options are to ignore it, or claim things like “information does not exist”.

  68. 68
    kairosfocus says:

    SA, I have to get to the info is a fiction issue. KF

  69. 69
    kairosfocus says:

    Folks, Interesting what happens when several science- of- ID OP’s are put up; given the objection oh, UD is not posting on “science.” Surprise (not), it seems — from what was addressed and what has been by and large passed by, multiplied by want of cogency and a lit bluff or two . . . — objectors are not really focussed on the science and warrant of scientific claims issues. KF

  70. 70
    kairosfocus says:

    PS: Let us now refocus Dr. Selensky’s 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.

    What causal explanation — per observation and implied search challenge — best accounts for the cluster: messages, codes, signals, and communication networks?

    Why is that so? (By contrast with say nitinol or memory foam.)

    What does this then say, to the observed case . . . cell-based, biological life?

    KF

  71. 71
    kairosfocus says:

    F/N:

    I would suggest, we are more addressing:

    PHASE I:

    chance variation (CV)
    + differential reproductive success (DRS) –>

    descent with incremental modification (DWIM);

    PHASE II:

    DWIM + grand continent of life thesis (GCLTh) –>

    incrementally branching tree of life descent (IBTOLD)

    PHASE III:

    IBTOLD + assumed OoL by spontaneous abiogenesis (AOSA) –>

    Grand macrotheory of evolution (GME)

    PHASE IV:

    GME + methodological naturalism –>

    ideological, a priori lab coat clad evolutionary materialism (IALCCEvMat)

    The points where questionable theses and ideological a prioris are being injected will be readily apparent.

    KF

  72. 72
    Dionisio says:

    EugeneS:

    Does this paper relate to your topic?

    Biosemiotics is devoted to establish a paradigmatic background for research on the evolution of cognition and communication in all living systems going beyond mechanical molecular biology.

    The central research question is in what way it is possible to add a semiotic view to the modeling of biological science(Cobley,2010) in order to get out of the rigid mechanistic understanding of living systems and make it possible to integrate a first person view to living systems.

    The dynamics of semiotic freedom (Brier, 2012a) is adding the interactions of forms to the mechanical as well as the informational view of the world as differences.

    Can biosemiotics be a “science” if its purpose is to be a bridge between the natural, social and human sciences?
    Brier S
    Prog Biophys Mol Biol. 119(3):576-87.
    doi: 10.1016/j.pbiomolbio.2015.08.001.

  73. 73
    EugeneS says:

    Dionisio

    Thanks. I think it does. Basically, biosemiotics considers an organism as symbolically controlled matter. That is its main contribution to the discourse as far as I can tell.

  74. 74
    Dionisio says:

    EugeneS
    Thanks for the clarification.
    Is this also related to your topic?
    See paper reference posted @2194-2196 here:
    http://www.uncommondescent.com.....ent-620648

  75. 75
    EugeneS says:

    Dionisio

    These don’t seem closely related, at first glance.

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