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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.

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

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

Comments
Dionisio These don't seem closely related, at first glance.EugeneS
November 14, 2016
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EugeneS Thanks for the clarification. Is this also related to your topic? See paper reference posted @2194-2196 here: https://uncommondescent.com/intelligent-design/mystery-at-the-heart-of-life/#comment-620648Dionisio
November 14, 2016
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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.EugeneS
November 14, 2016
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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.
Dionisio
November 14, 2016
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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. KFkairosfocus
November 12, 2016
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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? KFkairosfocus
November 12, 2016
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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. KFkairosfocus
November 12, 2016
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SA, I have to get to the info is a fiction issue. KFkairosfocus
November 11, 2016
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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".Silver Asiatic
November 11, 2016
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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... :)gpuccio
November 10, 2016
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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.Origenes
November 10, 2016
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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.Upright BiPed
November 10, 2016
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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.EugeneS
November 10, 2016
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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.Silver Asiatic
November 10, 2016
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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.
Dionisio
November 10, 2016
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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.Dionisio
November 10, 2016
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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
bornagain77
November 10, 2016
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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.EugeneS
November 9, 2016
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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! :)Dionisio
November 9, 2016
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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.Dionisio
November 9, 2016
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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.Silver Asiatic
November 9, 2016
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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 :)EugeneS
November 9, 2016
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GP Thought provoking as usual ;)EugeneS
November 9, 2016
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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.gpuccio
November 9, 2016
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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.EugeneS
November 9, 2016
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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.Phinehas
November 9, 2016
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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.gpuccio
November 9, 2016
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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.Dionisio
November 9, 2016
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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.Dionisio
November 9, 2016
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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!Silver Asiatic
November 9, 2016
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