Introducing James Barham (Introduction)
by David Turell 
, Monday, August 17, 2015, 14:17 (3385 days ago)
He is a philosopher of science mentioned in my last book. In this first essay he introduced and discusses the intelligent agency of life:-http://jamesabarham.com/my-blog/33-seeing-past-darwin-i-The official explanation of the nature of living things---and therefore of human beings---that we've all been led to believe in for the past 60 or 70 years turns out to be dead wrong in some essential respects.-What have we been so wrong about? It's complicated, but in a phrase, it's this:-The machine metaphor was a mistake---organisms are not machines, they are intelligent agents.-What does that mean? That's what's hard to explain in a brief compass, but here's one way of putting it:-We are finally beginning to realize, on the basis of irrefutable empirical evidence, as well as more careful analysis of Darwinian theory itself, that purposeful action in living things is an objectively real phenomenon that is presupposed, not explained, by the theory of natural selection.-What do I mean by purpose?-Purpose is the idea that something happens, not because it must tout court, according to physical law, but rather because it must conditionally, in order for something else to happen. This ubiquitous property lies at the heart of living systems, and it's what makes them so puzzling, from a physical point of view.-*****-This way of thinking proposed to solve the problem of purpose by denying it was real. Living systems were just accidental conglomerations of parts that happened by pure chance to work together as a functioning whole. And all the changes that organisms have undergone during the process of evolution---ditto.-In other words, nothing in organisms happens so that the whole organism may live. Rather, stuff happens, and organisms just happen to live as a result.-A pretty nifty theory, that---if it made sense.-The trouble is, it never made any sense. For one thing, it meant that all purpose is an illusion, even in ourselves, which is absurd. We know that is not true from the direct evidence of our own experience.-So, one important difficulty with the theory of natural selection is that it contradicts everything we understand about how we ourselves work.-But that is only the beginning of the trouble with Darwinism. An even bigger shortcoming of the theory is that it simply took all the hardest parts of the problem of purpose as given.- How did those incredibly complicated systems imbued with purpose through and through, which we call "cells," come to be in the first place? Nobody has a clue.-***-Finally, we now know that living systems are autonomous agents, capable of highly flexible intelligent behavior. For example, even the simplest, single-celled organisms, such as bacteria, are able to adjust themselves to altered circumstances in a purposeful way. And they can do this even if the circumstances are unlike any ever encountered by their ancestors during their evolutionary history.-How are systems physically capable of this sort of intelligent, adaptive behavior? Again, all the Darwinist has to say is: Intelligent agency would be a great thing to have from the point of view of natural selection, therefore natural selection will see to it that it comes into existence.-In summary, for the Darwinian explanatory framework to make sense, we have to suppress all the toughest questions about living things and simply take their adaptive capacity, their robustness, and their very existence for granted. Then---and only then---does natural selection make sense.-But in that case, we are just assuming that organisms are intelligent agents. We are not explaining how there can be such a thing as intelligent agents.
James Barham introduces James Shapiro
by David Turell , Monday, August 17, 2015, 23:21 (3385 days ago) @ David Turell
Barham thinks Shapiro's contributions to understanding genetics is extremely important:-http://jamesabarham.com/my-blog/34-seeing-past-darwin-ii-james-a-shapiro-"A molecular biologist at the University of Chicago by the name of James A. Shapiro recently published a masterly synthetic work which constitutes the most substantial contribution to date to post-Darwinian thinking in contemporary biology.(1)-The volume in question is entitled Evolution: A View from the 21st Century (FT Press, 2011), and it is simply stunning in every respect.-***- "the importance of bringing the insights of Shapiro and others to a wider audience can scarecely be exaggerated. Much in our culture depends upon the public's being made aware that Darwinian theory as standardly interpreted is intellectually bankrupt.(2) And little that I have encountered communicates this fact so well as the work of James A. Shapiro.-***-"Throughout the whole remarkable series of Huff Post essays, Shapiro stresses the importance of a key concept for understanding how both life and evolution work---"natural genetic engineering." While the technical details of this phenomenon can be forbidding, the basic idea is simple enough. In a nutshell, the phrase "natural genetic engineering" refers to cells' ability to "reprogram" their genomes as necessary---that is to say, purposefully---in order to meet changed environmental conditions.-***-"How do cells with finite DNA, and finite coding capacity, produce a virtually infinite variety of antibodies? The answer is that certain immune cells (B cells) become rapid evolution factories. They generate antibodies with effectively limitless diversity while preserving molecular structures needed to interact with other parts of the immune system.-"Immune cells achieve both diversity and regularity in antibody structures. They accomplish this by a targeted yet flexible process of natural genetic engineering: they cut and splice DNA.(2/6) . . .-"Three remarkable things about [two particular types of natural genetic engineering] are explicitly excluded from the prevailing philosophy of genetic change. First, they are adaptive and purposeful genome changes. Second, they are functionally targeted. Third, for [one of the types], targeting involves intercellular signals that depend on how other cells in the immune system perceive a particular infection.-"If immune cells can do all the above, is there any scientific reason we would assume that other cells cannot do the same? Coupling DNA restructuring to transcription is of major significance. All cells can target transcription to functionally relevant sites in the genome. Given that the immune system is how evolution evolved rapid protein evolution, should we not look to it for clues about basic evolutionary processes?(4/3)-***-"From these quotes, the reader can see that Shapiro does not mince words. He knows the vision of evolution he proposes is revolutionary---it does not "extend" the standard Darwinian account of evolution, it completely overturns it---and he is not afraid to say so.-"But what does "natural genetic engineering" really amount to?-"Clearly, it cannot be explained by natural selection, because it is the motor of all morphological and physiological variation, and thus is presupposed by the concept of natural selection. On Shapiro's view, natural selection is reduced to a superficial description of the evolutionary process, not an explanation of anything of much interest. (my bold)
More James Barham introduces James Shapiro
by David Turell , Monday, August 17, 2015, 23:26 (3385 days ago) @ David Turell
A comment by Barham concerning unanswered questions raised by Shapiro:-http://jamesabarham.com/my-blog/35-reply-to-james-shapiro-further-thoughts-on-natural-genetic-engineering-and-vitalism-"But Darwinism has never been just another scientific theory. It has always been dear to its proponents as a complete metaphysical system. All along, Darwinists have seen it as their task to "reduce" the manifest teleological and normative characteristics of life to mechanical interactions. That is what the theory of natural selection is all about.-"Therefore, Shapiro is being a bit ingenuous if he thinks he can simply forswear the philosophical implications of his position as none of his responsibility. He is tangled up with them, whether he likes it or not.-"Either cells are machines made of inherently inert parts cobbled together by natural selection, or they are . . . something else. No one who denies the first alternative should be surprised if he is asked what that "something else" could possibly be. "Besides, if we don't at least ask that question, how will we ever make any progress towards answering it? "-Comment: And, of course, for me that 'something else' is intelligent information imbued in organisms by God.
More James Barham introduces James Shapiro
DAVID: Barham thinks Shapiro's contributions to understanding genetics is extremely important:-http://jamesabarham.com/my-blog/34-seeing-past-darwin-ii-james-a-shapiro-The following quote seems to me to sum up Shapiro's approach to the problem of how evolution has progressed:-"Throughout the whole remarkable series of Huff Post essays, Shapiro stresses the importance of a key concept for understanding how both life and evolution work---"natural genetic engineering." While the technical details of this phenomenon can be forbidding, the basic idea is simple enough. In a nutshell, the phrase "natural genetic engineering" refers to cells' ability to "reprogram" their genomes as necessary---that is to say, purposefully---in order to meet changed environmental conditions.”-Shapiro is convinced that cells are sentient, cognitive beings: “Living cells and organisms are cognitive (sentient) entities that act and interact purposefully to ensure survival, growth, and proliferation. They possess corresponding sensory, communication, information-processing, and decision-making capabilities.”(p. 143) Put the two together, and you could scarcely have a clearer indication that their ability to “reprogram” their genome is autonomous (Barham used that very word) and is the driving force behind evolution.-However, Barham has his own agenda: "From these quotes, the reader can see that Shapiro does not mince words. He knows the vision of evolution he proposes is revolutionary---it does not "extend" the standard Darwinian account of evolution, it completely overturns it---and he is not afraid to say so.” -What follows is an attack on the concept of natural selection, which you David, have seized upon as if you also thought it was fundamental:-"But what does "natural genetic engineering" really amount to? Clearly, it cannot be explained by natural selection, because it is the motor of all morphological and physiological variation, and thus is presupposed by the concept of natural selection. On Shapiro's view, natural selection is reduced to a superficial description of the evolutionary process, not an explanation of anything of much interest.(David's bold)-How many times do we have to agree that natural selection only selects from what exists? It's true that some atheistic evolutionists would like to think it solves all the problems, but you and I know that not even Darwin claimed that natural selection produced innovation. His theory was that this was done by random mutations (which we also agree has been discredited by all the modern discoveries relating to DNA). You and Barham are flogging the dust left behind by the skeleton of a dead horse. Move on.-And move on you and Barham eventually do: "But Darwinism has never been just another scientific theory. It has always been dear to its proponents as a complete metaphysical system. All along, Darwinists have seen it as their task to "reduce" the manifest teleological and normative characteristics of life to mechanical interactions. That is what the theory of natural selection is all about. "Either cells are machines made of inherently inert parts cobbled together by natural selection, or they are . . . something else. No one who denies the first alternative should be surprised if he is asked what that "something else" could possibly be. (David's bold)-David's comment: And, of course, for me that 'something else' is intelligent information imbued in organisms by God.-It is you, David, who have insisted that cells are machines, and both Barham and Shapiro disagree with you. If cells are not machines, they are sentient, cognitive, intelligent, autonomous beings, not automatons programmed with “intelligent information” by God. Barham seems to be asking Shapiro to denounce the atheistic approach to Darwinism and acknowledge the teleology of evolution and perhaps tell us the source of this cellular intelligence. Shapiro has graciously replied as follows: “I took pains in the book to say that origins-of-life questions are still beyond rigorous scientific investigation. We do not yet understand enough about life as we find it. This gap in understanding includes the issues of agency and teleology so fascinating to Barham.” And of course to my dear friend, David Turell. I don't know Barham or Shapiro's religious leanings, but as an agnostic, I can only repeat that Darwin's theory of evolution does NOT preclude the existence of God, and the thrust of both Barham and Shapiro's argument so far is to favour the hypothesis that evolution is driven by the intelligence of the cell. As for God's purpose (if he exists), it will be interesting to see if Barham's view is as anthropocentric as your own. -I will look at Parts 3 & 4 tomorrow.
More James Barham introduces James Shapiro
by David Turell , Wednesday, August 19, 2015, 22:52 (3383 days ago) @ dhw
> David's comment: And, of course, for me that 'something else' is intelligent information imbued in organisms by God. > > dhw: It is you, David, who have insisted that cells are machines, and both Barham and Shapiro disagree with you. If cells are not machines, they are sentient, cognitive, intelligent, autonomous beings, not automatons programmed with “intelligent information” by God.-And I repeat, if the cells follow the information carefully as automatons they will look exactly as if they care intelligent. > > I don't know Barham or Shapiro's religious leanings, but as an agnostic, I can only repeat that Darwin's theory of evolution does NOT preclude the existence of God, and the thrust of both Barham and Shapiro's argument so far is to favour the hypothesis that evolution is driven by the intelligence of the cell. -I don't know about Barham, but I have suspected from previous associations he may be a Christian. Shapiro at one time was President of his Jewish temple.
James Barham 5
by David Turell , Wednesday, August 19, 2015, 23:07 (3383 days ago) @ David Turell
In this essay he attempts to explain life as an emergent property run by intelligent agency:-http://jamesabarham.com/my-blog/38-seeing-past-darwin-v-life-and-emergence-"In contrast to what happens inside a machine, everything that goes on within a living being possesses an inherent purpose---namely, maintaining the organism in existence. That is the essential difference between living and nonliving things.-"And that, above all, is what requires scientific explanation.-"The pseudo-explanation of natural selection has blinded us to the importance of functional stability for too long. But the phenomenon is there, right in front of our eyes---both in the massive coherence and coordination of the biochemistry of life, and in the amazing adaptivity of living things to perturbation.-"All the empirical evidence points to the existence of a fundamental power of intelligent agency underlying life. All we have to do is throw aside our mental blinders and look.-"This does not mean that we currently possess the conceptual resources to explain intelligent agency as an emergent property of the living state of matter. It does mean that we need to start trying to develop such resources, if we ever wish to understand life and evolution in a fundamental way."
Introducing James Barham
DAVID: He is a philosopher of science mentioned in my last book. In this first essay he introduced and discusses the intelligent agency of life:-http://jamesabarham.com/my-blog/33-seeing-past-darwin-i-Thank you yet again, not only for a very stimulating article, but also for your openness in drawing attention to certain ideas that directly contradict your own. You will of course have your personal slant on all this, but I shall select the sections that particularly interest me. I am going to juxtapose quotes for the sake of clarity: -“The official explanation of the nature of living things---and therefore of human beings---that we've all been led to believe in for the past 60 or 70 years turns out to be dead wrong in some essential respects. What have we been so wrong about? It's complicated, but in a phrase, it's this: The machine metaphor was a mistake---organisms are not machines, they are intelligent agents.” “Finally, we now know that living systems are autonomous agents, capable of highly flexible intelligent behavior. For example, even the simplest, single-celled organisms, such as bacteria, are able to adjust themselves to altered circumstances in a purposeful way. And they can do this even if the circumstances are unlike any ever encountered by their ancestors during their evolutionary history.”-This is a key element of my own hypothesis, as opposed to your insistence, David, that bacteria are automatons merely obeying God's instructions. Barham seems to take it for granted that you are wrong. “We are finally beginning to realize, on the basis of irrefutable empirical evidence, as well as more careful analysis of Darwinian theory itself, that purposeful action in living things is an objectively real phenomenon that is presupposed, not explained, by the theory of natural selection.”-As all of us on this website have constantly reiterated, natural selection can only select from that which already exists. It does not produce anything. However, Darwin's theory does entail purpose: that of survival, which is as objectively real as a purpose can get. It does not, however, entail a divine purpose for creation. I would like to add improvement to survival, which takes us firmly into Darwinian territory, but without the random mutations and the gradualism which are key elements for him but which we have long since agreed are highly suspect. Instead we have intelligent, autonomous beings (Barham's “simplest, single-celled organisms”) purposefully cooperating in order to produce increasing complexity. Natural selection ensures that efficient combinations and processes survive and are passed on. Darwin concludes: “from so simple a beginning endless forms have been, and are being, evolved.” In my edition he even talks of life “having been originally breathed by the Creator into a few forms or one”. Is there anything there for a theistic evolutionist to object to?-“How did those incredibly complicated systems imbued with purpose through and through, which we call "cells," come to be in the first place? Nobody has a clue.”-Darwin's concern was with Chapter 2 of life, not Chapter 1: “How a nerve comes to be sensitive to light, hardly concerns us more than how life itself originated.” (Difficulties on Theory). Barham is right, nobody has a clue. Neither theist nor atheist. So each comes up with his own speculative hypotheses. It will be interesting to see the continuation of this essay, especially as he intends to cover the work of James A. Shapiro, a dedicated believer in the autonomous intelligence of bacteria. Thank you again, David. *** I drafted this last night, but I see you have already posted the second part. I'll try to read it and comment tomorrow.
Introducing James Barham
by David Turell , Tuesday, August 18, 2015, 16:46 (3384 days ago) @ dhw
dhw: “Finally, we now know that living systems are autonomous agents, capable of highly flexible intelligent behavior. For example, even the simplest, single-celled organisms, such as bacteria, are able to adjust themselves to altered circumstances in a purposeful way. And they can do this even if the circumstances are unlike any ever encountered by their ancestors during their evolutionary history.”[/i] > > This is a key element of my own hypothesis, as opposed to your insistence, David, that bacteria are automatons merely obeying God's instructions. Barham seems to take it for granted that you are wrong.-Barham is not what he seems. The ID folks love him. And again 'highly flexible intelligent behavior' can be from onboard highly intelligent instructions. > > dhw: “We are finally beginning to realize, on the basis of irrefutable empirical evidence, as well as more careful analysis of Darwinian theory itself, that purposeful action in living things is an objectively real phenomenon that is presupposed, not explained, by the theory of natural selection.” > > As all of us on this website have constantly reiterated, natural selection can only select from that which already exists. It does not produce anything. However, Darwin's theory does entail purpose: that of survival, which is as objectively real as a purpose can get. It does not, however, entail a divine purpose for creation. I would like to add improvement to survival, which takes us firmly into Darwinian territory, -To which I would note again: bacteria are highly successful. There is no driving necessity to go beyond their level of existence, but it happened. I see purpose. > > It will be interesting to see the continuation of this essay, especially as he intends to cover the work of James A. Shapiro, a dedicated believer in the autonomous intelligence of bacteria. Thank you again, David. -It is published. Look.
Introducing James Barham; Parts 3 & 4
by David Turell , Tuesday, August 18, 2015, 21:04 (3384 days ago) @ David Turell
These two essays cover amazing phenotypical adaptations and brain plasticity adaptation:-http://jamesabarham.com/my-blog/36-seeing-past-darwin-iii-mary-jane-west-eberhard-West-Eberhard's ideas are crucial for one main reason: The Darwinian project is intended, more than anything else, to demonstrate that teleology, or purpose, can be eliminated from our theoretical understanding of the living world.-archerWest-Eberhard's work helps to upend that project by showing how purposiveness (or goal-directedness) lies at the heart of any realistic explanatory framework in evolutionary biology. In other words, her contribution consists in demonstrating that, far from eliminating purpose from nature, evolution in fact presupposes it.-In a nutshell, West-Eberhard's thesis is contained in the title of her magnum opus, Developmental Plasticity and Evolution.-***-In cases like Slijper's goat and Faith the Dog, we can see the power of these phenomena in action. But they are equally active in less extreme cases, as well. In fact, whenever any change whatsoever is introduced at the genetic level, some goal-directed compensation must take place in order for a viable adult form to be attained.-In a phrase: Responsive phenotype structure is the primary source of novel phenotypes. -This means that the process of natural selection presupposes the phenomena of developmental plasticity and phenotypic accommodation. Therefore, far from being cast out of biology, teleology turns up at its very heart. In this way, evolution is vindicated, but Darwinism is turned on its head.-To avoid teleology, Darwinism must posit random genetic changes that result in random phenotypic changes. But West-Eberhard's work shows us there is no such thing as a random phenotypic change. Instead, we can now see that all phenotypic change is goal-directed.-Thus, the evolutionary process has depended upon the inherent, teleological capability of all living things to adapt themselves to circumstances, within and without. It is this capability that explains evolution, not the other way around.-Essay 4: more experiments that show adaptability:-http://jamesabarham.com/my-blog/37-seeing-past-darwin-iv-some-experiments-What is the bearing of these experiments on the controversy surrounding evolution?-The point is simply this: Organisms of all sorts are capable of intelligent, goal-directed, adaptive behavior that cannot possibly be accounted for on the basis of the theory of natural selection.-Never in the evolutionary history of human beings was there selection for "seeing" with the tongue.-Never in the evolutionary history of fruit flies was there selection for adaptation to an inverted visual field.-Never in the evolutionary history of ferrets was there selection for the brain reorganization necessary to see with the auditory cortex.-And never in the evolutionary history of the slime mold was there selection for solving mazes.-***-The main task of Darwinian theory is to "reduce" teleology and normativity to mechanism.-Therefore, as soon as the Darwinist admits the reality of a general capacity for adaptivity extending throughout all of the living world, he has already given away the whole ballgame.-Of course, the Darwinist will say that there is no need to posit past selection for plasticity. Instead, we will be invited to view plasticity as a "spandrel"---an accidental side effect of other abilities that were selected for.-But that would be entirely ad hoc. There is absolutely no evidence to support such a claim.-Moreover, it would be absurd, in terms of the relative significance of cause and effect.-My comment: Obviously organisms have built-in adaptation guides; source?
Introducing James Barham; Parts 3 & 4
Again I'll cherrypick from Parts 3 & 4:-“To avoid teleology, Darwinism must posit random genetic changes that result in random phenotypic changes. But West-Eberhard's work shows us there is no such thing as a random phenotypic change. Instead, we can now see that all phenotypic change is goal-directed.”-We need to think carefully about this term “teleology”. Does he mean purpose, or does he mean divine purpose? “Thus, the evolutionary process has depended upon the inherent, teleological capability of all living things to adapt themselves to circumstances, within and without. It is this capability that explains evolution, not the other way around.”-Evolution doesn't explain anything; it's a process. Darwin tried to explain evolution through the sequence of random mutations and natural selection, i.e. chance dictated the first, but whatever was not fit for purpose perished, so natural selection was not chance but purpose orientated. Of course I agree with Barham that random mutations are highly dubious, and that it is more likely that organisms themselves purposefully make the changes that will enable them to adapt or improve. So instead of random mutations and natural selection explaining evolution, we now have purposeful mutations and natural selection as our explanation. We do not have an explanation for the intelligence that organizes the purposeful mutations. “The point is simply this: Organisms of all sorts are capable of intelligent, goal-directed, adaptive behavior that cannot possibly be accounted for on the basis of the theory of natural selection.”-Of course they can't. The argument is a non sequitur. Their intelligent behaviour is accounted for by their intelligence. Natural selection merely decides which of their behaviours will survive. It seems to me that Barham is conflating random mutations and natural selection in his desperation to discredit the atheistic view of Darwin's theory. As is so often the case with agenda-driven arguments, much of what he says is true, but it is undifferentiated.-“The main task of Darwinian theory is to "reduce" teleology and normativity to mechanism.”-Interestingly, the main task of Turellian theory is to promote teleology through mechanism, since David believes God's purpose could only be achieved by preprogramming and dabbling, which would make all organisms into automatons: the exact opposite of Barham and Shapiro's claims.-“Therefore, as soon as the Darwinist admits the reality of a general capacity for adaptivity extending throughout all of the living world, he has already given away the whole ballgame.”-Hold on, who said this capacity extended throughout all of the living world? Adaptivity only comes into play when conditions change, and throughout the history of the living world, changing conditions have resulted in death to much of the living world. This particular agnostic Darwinist can therefore point out that although cells may apply their adaptive intelligence, it is natural selection that will decide which of them will survive. Thus evolution progresses through a combination of chance and purpose: chance dictating changes in the environment and which organisms have the right sort of intelligence to cope with them or exploit them; purpose, because those organisms have deliberately sought to change themselves appropriately. How much of the ballgame has been given away? Not common descent. Not natural selection. Only random mutations, which have now become purposeful mutations. DAVID: My comment: Obviously organisms have built-in adaptation guides; source?-Not obvious at all, since clearly Barham and Shapiro attribute autonomous intelligence to organisms. Source? Shapiro refuses to be drawn. I am perfectly willing to acknowledge the possibility of a designer God. I don't believe in it, but I don't believe in any of the alternatives either, though one of them must be true!-Xxxxxxxxxxxxxxxxxxxxxx-Part 5 does not seem to me to add anything to the discussions we have already had, though I regard emergence as a very fruitful subject that is highly relevant to our own discussions on consciousness in general and cellular intelligence in particular.
Introducing James Barham; Parts 3 & 4
by BBella , Thursday, August 20, 2015, 17:51 (3382 days ago) @ dhw
I missed reading the last post on the thread dhw and I were discussing about the possibility of older beings, etc. I can't remember what subject heading it was under...any help? Thanks
Introducing James Barham; Parts 3 & 4
by David Turell , Thursday, August 20, 2015, 18:18 (3382 days ago) @ BBella
I missed reading the last post on the thread dhw and I were discussing about the possibility of older beings, etc. I can't remember what subject heading it was under...any help? Thanks-I don't think this is it, but:-Ruminations on origin of life; Paul Davies (Introduction)-by BBella @, Saturday, August 15, 2015, 22:56 (5 days ago) @ David Turell
Introducing James Barham; Parts 3 & 4
by David Turell , Thursday, August 20, 2015, 18:10 (3382 days ago) @ dhw
> dhw: We need to think carefully about this term “teleology”. Does he mean purpose, or does he mean divine purpose?-As I read him it is purposeful activity by the organism. > > dhw: “Thus, the evolutionary process has depended upon the inherent, teleological capability of all living things to adapt themselves to circumstances, within and without. It is this capability that explains evolution, not the other way around.” > > Evolution doesn't explain anything; it's a process.-He is not having evolution explain anything. Look again. He is saying the teleology of adaptation appears to explain the process of evolution. - > dhw: So instead of random mutations and natural selection explaining evolution, we now have purposeful mutations and natural selection as our explanation. We do not have an explanation for the intelligence that organizes the purposeful mutations.-Agreed. but we have the problem of explaining the source of the intelligent information the organisms are using. > > dhw: “The point is simply this: Organisms of all sorts are capable of intelligent, goal-directed, adaptive behavior that cannot possibly be accounted for on the basis of the theory of natural selection.” > > Of course they can't. The argument is a non sequitur. Their intelligent behaviour is accounted for by their intelligence.-Which developed how?-> “The main task of Darwinian theory is to "reduce" teleology and normativity to mechanism.”-> > dhw: Interestingly, the main task of Turellian theory is to promote teleology through mechanism, since David believes God's purpose could only be achieved by preprogramming and dabbling, which would make all organisms into automatons: the exact opposite of Barham and Shapiro's claims.-Not exactly. Neither provide us with a source of the intelligence. If naturally developed, it would require immediate analysis of experienced stimuli quickly enough to survive rapid changes in stressful environment changes, either in climate or new predators.-> > DAVID: My comment: Obviously organisms have built-in adaptation guides; source? > > dhw: Not obvious at all, since clearly Barham and Shapiro attribute autonomous intelligence to organisms. Source? Shapiro refuses to be drawn. I am perfectly willing to acknowledge the possibility of a designer God. I don't believe in it, but I don't believe in any of the alternatives either, though one of them must be true!-Since you accept cause and effect, list in your head the possible causes or the intelligence and tell me which is most realistic from your viewpoint.
Introducing James Barham; Parts 5 & 6
by David Turell , Thursday, August 20, 2015, 19:26 (3382 days ago) @ David Turell
dhw: Part 5 does not seem to me to add anything to the discussions we have already had, though I regard emergence as a very fruitful subject.-It is a lead in to a very complicated view of how life persists in the organism.- http://jamesabarham.com/my-blog/39-seeing-past-darwin-vi-f-e-yates-s-homeodynamics-I constantly refer to feed-back:-> "Yates's idea was to apply some of the concepts of qualitative dynamics to the problem of understanding the stability of living systems---in particular, physiological feedback systems. In order to understand why Yates's ideas are so original, it is important to understand that the conventional way of modeling the "homeostatic" behavior of various physiological systems is by means of an altogether different set of ideas---those of cybernetics, or feedback-control theory."-Adaptation:-> "'Robustness' refers to the ability of a living system to return to an earlier functional regime following perturbation, while "plasticity" means the ability to find a novel functional regime that maintains overall system viability, in case a perturbation is so great as to make a robust response impossible.-> "According to this way of using the terms, the ability of a broken bone to heal would be an example of robustness, while the ability of a dog to shift to a three-legged gait upon losing a limb would be an example of plasticity."-Metabolism works in cycles, organized as required:-> "we recognize that most physiological processes are periodic, or cyclical, in nature. This is no mere accident, but rather is a deep insight into the nature of living, as opposed to nonliving, systems. In Yates's words:-> "In any persistent system, whose operations are sustained over periods of time very long compared to the characteristic process and interactional times within it, cyclic energy transformations must be present. Certain processes must occur again and again if the system is to persist. Otherwise we would observe only relaxational trajectories to equilibrium death. Thus, limit cycle--like, nearly periodic, oscillatory behavior is the signature of energy transformations in open, complex, thermodynamic systems"-Built-in mathematical system:-> "Finally, perhaps the most important aspect of homeodynamics---at least from a philosophical perspective---is the way it helps us to rationalize the phenomenon of teleology.-> "Teleology---or goal-directedness, or purposiveness---is a manifest property of practically all biological phenomena. It has been considered anathema since the time of Francis Bacon, because it has seemed impossible to square with ordinary physical causation. Homeodynamics is valuable, above all, as a way of reconceptualizing teleology in biology.-> "Traditionally, teleology has been considered unacceptable because it seems to presuppose either "backwards causation" or else a mind capable of forming conscious intentions.-> "The former is unacceptable because it seems impossible that a non-actual, future state of affairs (the goal state) should causally influence the present. The latter is unacceptable because most biological systems apparently lack a mind in the relevant sense of a capacity for forming conscious intentions. (my bold) > "Homeodynamics solves this riddle by injecting the mathematical apparatus of nonlinear dynamics into the discussion, which introduces the element of virtuality. Virtuality---a notion well attested in physical science---is built into the concept of an attractor, in regard both to equifinality and to metastability."-Note he removes 'mind', which is my point.-His conclusion:-> "'I have attempted to provide a glimpse of a general, physical "theory" (more correctly, an heuristic) for a fundamental understanding of the complex dynamic character of energetic metabolic networks and their regulations. The heuristic, [homeodynamics], is free of unjustified intentional or "smart" elements, of vitalisms, or of Kiplingesque Just So Stories about causalities. It is synoptic and level-independent. It supports both reductionist and holistic approaches to complex systems and avoids two dominant intellectual constraints of recent times, viz., genetic determinism from molecular biologists, and the notion that contemporary particle physics has the wherewithal to come up with a "theory of everything.'"
Barham; Part 7; Looking at cells dynamically
by David Turell , Friday, August 21, 2015, 20:06 (3381 days ago) @ David Turell
This is a wholly different way of looking at cells and the way they function:-http://jamesabarham.com/my-blog/40-seeing-past-darwin-vii-some-physical-properties-of-life-"Too often, we envision the cell as a "factory" containing a fixed complement of "machinery" operating according to "instructions" (or "software" or "blueprints") contained in the genome and spitting out the "gene products" (proteins) that sustain life.-"Many things are wrong with this picture, but one of the problems that needs to be discussed more openly is the fact that in this "factory," many if not most of the "machines" are themselves constantly turning over---being assembled when and where they are needed, and disassembled afterwards. The mitotic spindle (top) is one of the best-known examples, but there are many others.-"Funny sort of "factory" that, with the "machinery" itself popping in and out of existence as needed!-***-"Paradoxically, extraordinary advances in our understanding of the parts do not seem to bring about significant progress in our understanding of the whole. In fact, it appears that the design of the cell becomes increasngly elusive as experimental data accumulate. . . . Quantitative visualization of fluorescently tagged proteins inside living cells shows that most, perhaps all, sub-cellular structures and macromolecular complexes exist not as pre-assembled and relatively stable structures, but as highly dynamic steady-state macromolecular organizations, conceptually similar to a treadmilling actin filament but of greater complexity.-***-" ...it should be pointed out that, in reality, the internal resource distribution/transport systems of biological organisms (at all scales) are not mechanistic pipes built according to a preconceived design, but dynamic and adaptive fluxes of energy/matter in themselves, shaped by both internal and external influences. And their main purpose is not to deliver resources and remove waste---that is the limited interpretation of the mechanistic paradigm---but to integrate energy/matter and space into one scale-free continuum of energy/matter circulation.-***-"DNA is a stable template by means of which some proteins generate other proteins, as required. Proteins, not genes, are the active agents in the cell. Therefore, it would be far closer to the truth to say that genes are proteins' way of making more proteins.-"Still closer to the truth, of course, would be to say that both proteins and genes are cells' way of making more cells. But be that as it may, the question that arises from a right understanding of causality within the cell is this: How can proteins be "active agents"?-***-"First, proteins are frustrated systems. "Frustration" is a technical term in physics meaning that a system in incapable of relaxing into a single lowest-energy state. The reason for this is a myriad of competing self-interactions among different parts of the system. As a result, the system as a whole incessantly and rapidly traverses a very large set of nearly isoenergetic, conformational substates.-"In other words, proteins resemble not so much the traditional static structures depicted by X-ray diffraction (which are only averages), as essentially dynamic, writhing masses of fleeting configurations that have been described as "kicking and screaming."-***-"In summary, proteins are far from being the static molecular "machines" of popular imagining. Rather, their behavior is dominated by their intrinsic dynamics (frustration) and thermodynamic coupling to their environment (slaving).-***- "Considered as a whole, cytoplasm must have physical properties that are very different from those of ordinary liquid water---properties that make of cytoplasm an intermediate state of matter in between a liquid and a solid, like a gel or a liquid crystal.-"This is what one would expect on theoretical grounds from the sheer fact of cell crowding, but experimental evidence is also not lacking. For example, relatively large sections of the cell membrane may be excised with no visible effect on the functioning of the cell, and with no leakage of cell contents."-Comment: Living cells are extremely complex and dynamic, not the bobs Darwin envisioned.
Introducing James Barham; Parts 3 & 4
dhw: We need to think carefully about this term “teleology”. Does he mean purpose, or does he mean divine purpose? DAVID: As I read him it is purposeful activity by the organism.-I think so too, but there is a degree of ambiguity in the word, and the question of the source of cellular intelligence is always in the background.-BARHAM: “Thus, the evolutionary process has depended upon the inherent, teleological capability of all living things to adapt themselves to circumstances, within and without. It is this capability that explains evolution, not the other way around.” Dhw: Evolution doesn't explain anything; it's a process.-DAVID: He is not having evolution explain anything. Look again. He is saying the teleology of adaptation appears to explain the process of evolution.-“The other way round” would mean evolution explaining the capability, and I am pointing out that nobody would claim that it does, because evolution doesn't explain anything. This is one of several devices used to try and discredit the theory (like pretending that natural selection is offered as an explanation for cellular intelligence). dhw: So instead of random mutations and natural selection explaining evolution, we now have purposeful mutations and natural selection as our explanation. We do not have an explanation for the intelligence that organizes the purposeful mutations. DAVID: Agreed. but we have the problem of explaining the source of the intelligent information the organisms are using.-That is what I mean by not having an explanation for the intelligence, which you prefer to call “intelligent information”.-BARHAM: “The point is simply this: Organisms of all sorts are capable of intelligent, goal-directed, adaptive behavior that cannot possibly be accounted for on the basis of the theory of natural selection.” DHW: Of course they can't. The argument is a non sequitur. Their intelligent behaviour is accounted for by their intelligence. DAVID: Which developed how?-Same problem. Nobody knows the source. This discussion is about how evolution works: Chapter 2 of life, not Chapter 1.-BARHAM: “The main task of Darwinian theory is to "reduce" teleology and normativity to mechanism.” dhw: Interestingly, the main task of Turellian theory is to promote teleology through mechanism, since David believes God's purpose could only be achieved by preprogramming and dabbling, which would make all organisms into automatons: the exact opposite of Barham and Shapiro's claims. DAVID: Not exactly. Neither provide us with a source of the intelligence. If naturally developed, it would require immediate analysis of experienced stimuli quickly enough to survive rapid changes in stressful environment changes, either in climate or new predators.-Same again, and again. The issue between you and Barham/Shapiro/me is your insistence that cells are automatons and not autonomous, intelligent beings. The source is a different subject.-DAVID: My comment: Obviously organisms have built-in adaptation guides; source? dhw: Not obvious at all, since clearly Barham and Shapiro attribute autonomous intelligence to organisms. Source? Shapiro refuses to be drawn. I am perfectly willing to acknowledge the possibility of a designer God. I don't believe in it, but I don't believe in any of the alternatives either, though one of them must be true!-DAVID: Since you accept cause and effect, list in your head the possible causes or the intelligence and tell me which is most realistic from your viewpoint.-From my point of view, there is no “most realistic”. I acknowledge the possibility of your God, of some sort of panpsychist evolution, and of chance (given an eternity and infinity of material combinations). I can't go further than that.-QUOTE: "Teleology---or goal-directedness, or purposiveness---is a manifest property of practically all biological phenomena. It has been considered anathema since the time of Francis Bacon, because it has seemed impossible to square with ordinary physical causation. Homeodynamics is valuable, above all, as a way of reconceptualizing teleology in biology.-"Traditionally, teleology has been considered unacceptable because it seems to presuppose either "backwards causation" or else a mind capable of forming conscious intentions." (MY BOLD)-"The former is unacceptable because it seems impossible that a non-actual, future state of affairs (the goal state) should causally influence the present. The latter is unacceptable because most biological systems apparently lack a mind in the relevant sense of a capacity for forming conscious intentions.”(David's bold)-David: Note he removes 'mind', which is my point.-You have ignored the paragraph that precedes your bold (and which I have now put in bold). He is explaining why teleology has been traditionally rejected (whereas he accepts it): namely, backward causation or the APPARENT lack of a mind. He does NOT agree with these “traditional” reasons. You are clutching at straws. He has already said explicitly that he shares Shapiro's view of cells as autonomous intelligent beings.
Introducing James Barham; Parts 3 & 4
by David Turell , Friday, August 21, 2015, 21:34 (3381 days ago) @ dhw
dhw: He does NOT agree with these “traditional” reasons. You are clutching at straws. He has already said explicitly that he shares Shapiro's view of cells as autonomous intelligent beings.-On re-reading you are correct.