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Following on from a thought that I expressed in the thread on mathematics, I wonder if a lot of argument might be avoided if we agreed that "existence" can occur in different degrees or categories? -For instance dhw and DT lay much emphasis on subjective experiences and anecdotal evidence that I would discount. Perhaps claims based on such experiences can be said to refer to concepts having "subjective existence". Perhaps this is another name for "faith". Is it possible to separate arguments about things in the subjective world from those in the objective world? Perhaps this is what is meant by Gould's NOMA (non overlapping magisteria).-Even in the objective world there are arguably degrees of existence depending on the amount and certainty of evidence backing them up. For instance historical and legendary characters or events. There is a sense in which the past fades away as evidence and memory is eroded by time.

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GPJ

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PART ONE-George wonders if we might avoid a lot of argument by agreeing that "existence" can occur in different degrees or categories, and he has raised two issues in particular that I'd like to focus on, one in relation to our discussions on evidence and faith, and the other more specifically on history and religion.-GEORGE: For instance dhw and DT lay much emphasis on subjective experiences and anecdotal evidence that I would discount. Perhaps claims based on such experiences can be said to refer to concepts having "subjective existence". Perhaps this is another name for "faith". Is it possible to separate arguments about things in the subjective world from those in the objective world?-That last question is the crucial one. In virtually every area under discussion, it's almost impossible to tell where subjective ends and objective begins, even if there's a consensus on what exists objectively. George always protests when I say that his belief in the chance origin of life, for instance, constitutes faith. By faith I understand belief in something even though there's no evidence for it. George fixes on the physical reality of life (objective), in my view quite rightly argues that there's no evidence (objective) for a divine creator, and concludes that chance is the most probable cause (subjective). I regard that as a perfectly reasonable argument. But I also argue that despite all the efforts of our highly intelligent scientists, there's no evidence (objective) that chance is capable of assembling the components for life. Consequently, in accordance with the above definition, belief in chance = faith. Both George and David look at all the factors that go to make up life (objective), and come up with diametrically opposed, but in my view equally reasonable conclusions (subjective), each of which requires a different kind of faith (subjective). My non-conclusion is also subjective, but without faith. One might therefore rephrase George's question: is it possible to separate subjective perception and/or interpretation from the objective world? -"Subjective experiences" and "anecdotal evidence" are attractive terms, but they sound far less reliable than "objective evidence", and so we need to ask: evidence of what? No-one will deny that in many areas of life, certain things can be proved by scientific experiment (objective) ... otherwise our technology wouldn't work. But there are other areas in which such practical tests are not possible, or where evidence appears objective but isn't, or where objective realities are open to subjective interpretation. Perhaps the nearest we can get to objectivity generally is consensus. For instance, I never saw a dodo, or the Battle of Hastings, or the Great Fire of London, or Napoleon, but there's a consensus concerning their reality, and so I believe they existed. However, once I would have believed that the sun went round the Earth, that Piltdown Man was a missing link, that junk DNA was useless, that global warming was a fact. There appeared to be a consensus. As a layman, I believe what I'm told if the experts agree and I see no reason to disbelieve them. (And if the pendulum swings hard enough, I'm liable to swing with it.) In a thousand years' time, how many of our facts will have been exposed as fiction? To put it another way, how many of our apparently "objective" realities will have been dismissed as "subjective" or "anecdotal"? Conversely, who knows how much evidence now dismissed as subjective and anecdotal will have come to be regarded as fact? The anthropomorphization of animals (a silly concept, in my view, since we are animals descended from animals) is no longer a matter of anecdote, as more and more evidence becomes available that they communicate, feel and think. Once upon a time, Europeans looked on Africans as subhuman. -In conclusion to Part One, then, while I can see the attractions of categorizing experiences as you suggest, I don't think that would stop us arguing about exactly the same things we're arguing about now, and for exactly the same reasons!

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Sir, I hope you will read this some day. (Its good - don't worry)-Your speculation about the objective/subjective "realities" discord was utterly outstanding! This is in light of my understanding of quantum mechanics' "SLIT" experiment, where electrons were shot through variously polarized slits, and moved towards their targets as though they had had a mind of their own - proving the "action at a distance" hypothesis (Now a law!?) (SLIT = Super-Luminal Information Transfer, if memory serves.) Thus, our subjectiveness isn't as SUB-jective as we think it is, and opens up brand new avenues in science.-For my purposes, however, my own subjectivity ends at the ends of the hairs on my body, because that is exactly where I can feel the objective world interacting with me. My body is an extension of my brain's desire to experience reality (and everything else...) As for sound, sight and smell...again, objective starts where my sensors pick it up. I also always allow for errors in transcription or transduction. We "see" because of our eyes' transduction, but we "perceive" because of our brains' transcription. When these are in parity, best reality happens.-Seems to work for me.-Please feel free to e-m me, personally, whenever.-Thanks!-Tim

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Tim has informed us about the SLIT experiment, in which electrons appear to have a mind of their own, casting new light on the concept of subjectivity. -First of all, Tim, a warm welcome to the forum, and many thanks for this very interesting post. No doubt our "resident" scientists will comment on the experiment, though it would be helpful if you yourself could tell us more about its significance in relation to the general topic of subjectivity. -In this context, I was particularly struck by your remark that "we "see" because of our eyes' transduction, but we "perceive" because of our brains' transcription. When these are in parity, best reality happens." This is a very neat way of framing our whole discussion, because all of us may "see" precisely the same set of apparently objective facts, but the brain may transcribe them into diametrically opposed conclusions, and nobody is in a position to say whose transcription is the objectively real one. In most cases, we rely on a consensus (intersubjective), practical experiments (as objective as can be), or personal experience (subjective). Certain "realities" can't be tested by practical experiment ... I'm thinking for instance of emotional and aesthetic processes which are every bit as real to us as material objects ... and the questions at the heart of our discussions come into this category. Even if science were eventually to produce a formula that led to life, evolution and consciousness, we still wouldn't be able to say whether the original came about by accident or by design. I wonder where you stand on this issue.-Thank you again for your post. I for one would welcome more!

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Tim has informed us about the SLIT experiment, in which electrons appear to have a mind of their own, casting new light on the concept of subjectivity. 
> 
> Thank you again for your post. I for one would welcome more!-So would I. Tim has reminded us that quantum reality, which undergirds our general appreciation of reality, really is a counterintuitive pool of quicksand, Einstein's 'spooky actions at a distance', two sister quanta responding to each other across the universe with an exact mimic of action.-Also, a new fossil find demonstrates an early simple form of multicellularity existed 2 billion years ago:-http://www.sciencedaily.com/releases/2010/06/100630171711.htm

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> Also, a new fossil find demonstrates an early simple form of multicellularity existed 2 billion years ago:
> 
> http://www.sciencedaily.com/releases/2010/06/100630171711.htm-There is already controversy about the above fossil find. They may represent stromatolites, massive collections of single-celled organisms, or pyrite deposits. Organic chemicals found in the area suggest they were living forms. The issue, of course, is the relation to the Cambrian Explosion, which Darwinism cannot explain, unless more complex fossils are found in prior layers. The Edicarans are simplistic sheets of cells which appear immediately prior to the Cambrian, and the jump to the complexity of the Cambrian is a huge gulf for Darwinism to swallow and explain.. The first Cambrians were found in the Burgess Shale above Emerald Lake in Canada in the late Nineteenth Century. There are now a number of similar shales in China with comparable organisms. Where is Darwin's gradualism? And don't tell me the fossils will be found. Burgess was found 120 years ago or so.

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David has referred us to a new fossil find that proves the existence of multicellular organisms 2.1 billion years ago. They are too big and too complex to be prokaryotes or eukaryotes, and predate the earliest known multicellular life forms by 1.5 billion years.-It's amazing how many recent discoveries represent a "major breakthrough" in our understanding of life, the universe, the descent of man, the nature of the genome ... and yet it seems to me that each one tends to deepen the mysteries rather than solve them. -David asks, in the light of the new discovery and its relation to the Cambrian Explosion, "Where is Darwin's gradualism?" This is a point of the theory that I have never quite understood. Darwin is unequivocal about its importance: "If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down." (Origin, p. 214) In some respects he is on safe ground, because no-one can ever prove that there were no transitional forms, just as no-one can ever prove that there is no God. The Eldredge-Gould concept of 'punctuated equilibrium', however, contradicts that of 'Natura non facit saltum' and it certainly seems to be more in keeping with the fossil record as we know it. What I don't understand is why gradualism should be so crucial to the theory as a whole. Mutations and new combinations would account for some innovations, and the impact of environmental changes for others. How and why else would new organs come into being? In both cases, there would be jumps, after which natural selection would certainly bring about gradual improvements, but how complex does an organ have to be before we call it complex? A single cell alone is staggeringly complex. Either innovations work or they don't, and if they do, they are already complex, even if they survive and later become even more complex. It therefore seems to me that evolution doesn't depend on gradualism at all. Perhaps someone can enlighten me.-
*** This will be my last post for ten days or so, as my two-year-old grandson insists on his parents, my wife and me taking him on holiday to Cornwall. I suspect he will be teaching us more about life than all the Gabonese fossils put together.

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dhw: "Either innovations work or they don't, and if they do, they are already complex, even if they survive and later become even more complex. It therefore seems to me that evolution doesn't depend on gradualism at all. Perhaps someone can enlighten me."-There is a section in Ernst Mayr's "What Evolution Is" that deals with this subject, though as I've said before I'm not a biologist and I find the language difficult to follow. He points out that: "individuals in a single population may differ by visibly different characters" (he cites eye colour and number of molars). He continues: "A successful mutation with a large phenotypic effect can be gradually incorporated into a population as long as it is able to pass through a period of polymorphism in which it coexists with the previous phenotype, until it has completely displaced the original gene." He ends with "it must be remembered that there is a considerable range in the size of the mutations that lead to evolutionary change". Later on he says: "Darwinian gradualism is due to the gradual restructuring of populations."

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GPJ

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In my post of 8 July at 21.24 I asked why Darwin (Natura non facit saltum) considered gradualism to be so essential that his theory would "absolutely break down" if it could be demonstrated "that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications." My point is threefold: (1) That even a single cell is staggeringly complex, so where does the scale of complexity begin? (2) That all mutations, innovations, adaptations to new conditions represent jumps in Nature, and if they didn't work ... even in their most rudimentary form ... they wouldn't survive. (3) That the theory of punctuated equilibrium fits in far better with the fossil record as we know it.-George has kindly offered me a possible explanation, quoting Ernst Mayr: -"Individuals in a single population may differ by visibly different characters" (he cites eye colour and number of molars). I don't think this has any bearing on the way complex organs arise out of mutations or adaptations.-"A successful mutation with a large phenotypic effect can be gradually incorporated into a population as long as it is able to pass through a period of polymorphism in which it coexists with the previous phenotype until it has completely displaced the original gene." 
That makes sense to me, but misses the point at issue, which is that a successful mutation will already entail complexity ... it will involve an innovation which works, i.e. a jump, not a gradual development. A light-sensitive nerve is a jump from a nerve which is not light-sensitive (and where did nerves come from in the first place?). In passing, one might also question why a phenotypic mutation should take place if the original gene is already well suited to its environment. -"It must be remembered that there is a considerable range in the size of the mutations that lead to evolutionary change."
Well, OK, maybe a small mutation is only a small jump, but a big mutation will be a big jump.-"Darwinian gradualism is due to the gradual restructuring of populations."
No it isn't. The gradualism so vital to Darwin is the formation of complex organs through mutation and adaptation. It seems reasonable to me to argue that new organs will gradually be refined and improved by natural selection. However, it does not seem reasonable to me to assert that mutations and adaptations are initially NOT complex, and that such innovations can only come about gradually. If an innovation is not successful, it will not survive. This does not in any way undermine the theory of evolution, and so I remain as mystified as ever by Darwin's insistence. All the same, I'm grateful to George for making the effort to enlighten me. Any other suggestions? -Coincidentally, there was an article in yesterday's Sunday Times, under the heading 'Conan' bug may be source of life. The bug, called Deinococcus radiodurans, is so tough that it could survive space travel. Professor Ivan Paulino-Lima, a biophysicist in Rio de Janeiro, has published a paper in Planetary and Space Science, describing the various tests on this bug, which was first discovered 50 years ago after a can of corned beef went rotten despite having been sterilized by radiation. "The discovery has excited astronomers, who have long speculated that the debris ejected into space when planets are struck by large meteorites might be able to transport such microbes between planets, thus spreading life." Scientists are therefore suggesting that "such organisms could have been the origin of life on Earth." Maybe, though that should not be confused with "the origin of life". -The sting is in the tail: "The most likely explanation for the germ's toughness is that each bug possesses four to 10 copies of its genome, rather than the usual single version. It also has a highly efficient repair system, so even if the DNA is ripped apart by radiation, bits can easily be spliced together again." Can you imagine a greater jump than that from inanimate matter to a bug that can reproduce itself, survive in any environment, and repair itself? And why would such an organism need to evolve into other organisms when it is already so perfectly equipped for survival? And why would its genome evolve into the far less efficient "usual single version"?

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Ernst Mayr wrote: "Individuals in a single population may differ by visibly different characters" (he cites eye colour and number of molars). -dhw, who is a great expert on these things assures us: "I don't think this has any bearing on the way complex organs arise out of mutations or adaptations."-So there. That's telling him! -Of course it has a bearing. It's by such minor changes that more major changes come about; for instance one can easily visualise teeth gradually developing into sharper points allowing for a change to a different diet, or what about the famous beaks of the finches.-dhw further expounds: "... the point at issue, ... is that a successful mutation will already entail complexity ... it will involve an innovation which works, i.e. a jump, not a gradual development."-Doesn't a slightly differently shaped beak more suited to opening certain nuts, say, constitute a successful mutation? This doesn't seem to involve any increase in complexity at all. dhw seems to have already decided in advance that any change however small is a "jump" and that jumps are impossible.-dhw gives the example: "A light-sensitive nerve is a jump from a nerve which is not light-sensitive (and where did nerves come from in the first place?)."-But why should any of the steps in this process be big jumps in complexity? A nerve is simply a piece of tissue that transmits a message in some form along its length. In a simple form it could just conduct heat, when its outer end touches a hot object. It would also be heated up when infrared rays impinged on it (heat being simply vibration of the molecules). A slightly greater sensitivity and it could detect red light rays.-dhw: "one might also question why a phenotypic mutation should take place if the original gene is already well suited to its environment." -This appears to assume that it takes place instantaneously, as opposed to being a gradual process. On the other hand there may be a rapid change in the environment that brings it on, out of the variation within the population; i.e. the individuals with the modification are better able to survive and propagate.-dhw admits: "Well, OK, maybe a small mutation is only a small jump, but a big mutation will be a big jump."-Yes and big mutations are usually unsuccessful mutations.-Erns Mayr wrote: "Darwinian gradualism is due to the gradual restructuring of populations."-dhw however ia a greater authority: "No it isn't."-That's telling him!-dhw: "The gradualism so vital to Darwin is the formation of complex organs through mutation and adaptation. ... it does not seem reasonable to me to assert that mutations and adaptations are initially NOT complex, and that such innovations can only come about gradually."-Well, this is absolutely denying Darwin's entire thesis!-dhw: "If an innovation is not successful, it will not survive."-Why not? If it is only a slight change, like a sharper tooth or a differently shaped beak it need make no difference, it will just add to the variation within the population.-dhw: "This does not in any way undermine the theory of evolution, and so I remain as mystified as ever by Darwin's insistence."-On the contrary, as dhw's original quote from Darwin himself says, dhw's insistence that evolution can only occur in big jumps entirely goes against Darwin's thesis.

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GPJ

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Of course it has a bearing. It's by such minor changes that more major changes come about; for instance one can easily visualise teeth gradually developing into sharper points allowing for a change to a different diet, or what about the famous beaks of the finches.-Beak size changes back and forth adapting to the climate. the species otherwise show no changes.-> 
> Doesn't a slightly differently shaped beak more suited to opening certain nuts, say, constitute a successful mutation? This doesn't seem to involve any increase in complexity at all.-Again we are discussing minor adaptations-
> But why should any of the steps in this process be big jumps in complexity? A nerve is simply a piece of tissue that transmits a message in some form along its length. In a simple form it could just conduct heat, when its outer end touches a hot object. It would also be heated up when infrared rays impinged on it (heat being simply vibration of the molecules). A slightly greater sensitivity and it could detect red light rays.-Remember ion exchange runs down the nerve. Nerves do not conduct heat or pain, just electrical impulses. The brain has to develop the mechanism to sort out interpretations of the stimuli received in the cortex. In human babies two-point identification of pricks on the skin is learned(!)as they grow and can see where the pricks are.-> 
> dhw admits: "Well, OK, maybe a small mutation is only a small jump, but a big mutation will be a big jump."
> 
> Yes and big mutations are usually unsuccessful mutations.-Just as in the Cambrian Explosion I presume.-> On the contrary, as dhw's original quote from Darwin himself says, dhw's insistence that evolution can only occur in big jumps entirely goes against Darwin's thesis.-Exactly the point. Current reearch in epigenetic controls brings Lamark back into the picture. Evolution occurred, no question. At least Ernst Mayr was right on that point when he rejected the mathematicians, in the 1967 Wistar Institute conference, who said gradual mutations were to slow for the time allotted for that to be the mechanism. Gould and punctuated equilibrium must be respected, as another point. By this time the missing fossils should have popped up.

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George has taken me to task over my post on gradualism. -I wrote that I did not regard different eye colours and number of molars as having any bearing on the way complex organs arise out of mutations or adaptations. George cites the famous beaks of finches as a further example. None of these are NEW ORGANS. They are variations on existing organs. I wrote: "If an innovation is not successful, it will not survive," to which George responds: "Why not? If it is only a slight change, like a sharper tooth or a differently shaped beak it need make no difference, it will just add to the variation within the population." A variation is not an innovation.-I wrote: "It seems reasonable to me to argue that new organs will gradually be refined and improved by natural selection", but you have ignored this sentence, which I would have thought makes the distinction clear. A new organ is a heart, a liver, a kidney, an eye, a penis. And no matter how rudimentary the innovation itself may be, even through exaptation or gene duplication, (a) it is still complex, (b) it still has to work, and (c) you still have to account for the original organ. -"For this reason Darwinism has concentrated on the evolutionary development of existing organs." -The above quote is taken from -[link=http://]http://creation.com/images/pdfs/tj/j19_2/j19_2_76-82.pdf[/link].-I have never claimed to be "a great expert on these things", and rely on others in the field. I suspect you do too, so please read the article. Try to ignore the word "creation". This is a straightforward account by an expert on the problem I have tried so inadequately to explain.-Still on the subject of complexity you wrote that "a nerve is simply a piece of tissue that transmits a message in some form along its length." Why SIMPLY? It has taken thousands of years for intelligent humans to refine their methods of transmitting messages. If you think nerves are "simple", have a look at 
http://en.wikipedia.org/wiki/Nerve-Here is a sample: "Each nerve is a cordlike structure that contains many axons. These axons are often referred to as "fibres". Within a nerve, each axon is surrounded by a layer of connective tissue called the endoneurium. The axons are bundled together into groups called fascicles, and each fascicle is wrapped in a layer of connective tissue called the perineurium. Finally, the entire nerve is wrapped in a layer of connective tissue called the epineurium." Simple?-I find it unreasonable to assert that mutations and adaptations are initially not complex, and that such innovations (see above) can only come about gradually. You responded: "Well, this is absolutely denying Darwin's entire thesis!"-It is not Darwin's entire thesis, but Darwin said his thesis depended on it, and this whole thread is my attempt to find out why. An essential element of Darwin's thesis is the argument that all life has descended from a few forms or one, and that natural selection will result in the survival of advantageous changes. The example of finches' beaks brilliantly illustrates how a modification can over time result in a different variety, but a beak is still a beak and a finch is still a finch. You wrote: "dhw's insistence that evolution can only occur in big jumps entirely goes against Darwin's thesis." That is a slight misrepresentation of my argument. Innovations ... as opposed to variations ... entail a jump (maybe big, maybe small), and they may gradually be refined and improved. What I do not understand is why Darwin insisted that there were no "jumps in Nature", or that any jumps would invalidate the theory that we are all descended from one or a few forms via a process of natural selection.

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A new organ is a heart, a liver, a kidney, an eye, a penis. And no matter how rudimentary the innovation itself may be, even through exaptation or gene duplication, (a) it is still complex, (b) it still has to work, and (c) you still have to account for the original organ. 
> 
> "For this reason Darwinism has concentrated on the evolutionary development of existing organs." 
> 
> The above quote is taken from 
> 
> [link=http://]http://creation.com/images/pdfs/tj/j19_2/j19_2_76-82.pdf[/link].-An absolutely brilliant article. It proves to me that unless a person is well-read in biology or has had deep biologic training, the objections we biologists have to Darwin are totally misunderstood as fairy tales. Take the circulatory system: the evolutionary tree shows simple spaces with fluid in say, the lobster, circulation by muscle movement stirring the liquid. Then pulsing tubes, one-chambered, two-chambered, three-chambered, and finally a four-chambered heart in dogs and us as examples. As an example of complexity, a four-chamber heart requires an electrical system to allow for proper temporal pumping in one direction! By chance mutation!? The valve system shows each type of valve is perfectly designed for its function, especially for the low pressure right side and the high pressure left side. Transitional forms from space to tube to four chambers, non-existent! 
> 
> Still on the subject of complexity you wrote that "a nerve is simply a piece of tissue that transmits a message in some form along its length." Why SIMPLY? If you think nerves are "simple", have a look at 
> http://en.wikipedia.org/wiki/Nerve
> 
> Here is a sample: "Each nerve is a cordlike structure that contains many axons. These axons are often referred to as "fibres". Within a nerve, each axon is surrounded by a layer of connective tissue called the endoneurium. The axons are bundled together into groups called fascicles, and each fascicle is wrapped in a layer of connective tissue called the perineurium. Finally, the entire nerve is wrapped in a layer of connective tissue called the epineurium." Simple?
> What I do not understand is why Darwin insisted that there were no "jumps in Nature", or that any jumps would invalidate the theory that we are all descended from one or a few forms via a process of natural selection.-Easy answer. Darwin did not know any better. He was using animal breeders as examples, and they made tiny changes in their attempts. Research has obviously refuted this aspect of Darwin's thinking. Evolution is an obvious event. Darwin's proposed mechanism is wrong.

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The PDF cited by dhw is a totally worthless paper from a creationist.-As you can tell from his conclusion: "... organs must be of a certain complexity before they can function, a concept called 'irreducible complexity'."
This is Behe's discredited idea from Darwin's Black Box.-The BCSE has:
"Jerry Bergman is another well known creationist in the USA. Bergman has put together a list of 3,000 scientists world-wide who he claims are sceptical about the Theory of Evolution. The list, which actually appears to have 2,000 names on it, is full of errors and inaccuracies and no systematic attempt at checking the information appears to have been made. / The list is full of people who are dead or are not scientists or who work for institutions that don't exist or closed down years ago. No attempt appears to have been made to check what their actual views are, where they work or what their qualifications are. There are cases where qualifications are attributed to people even though they don't have them."
His wikipedia page has been closed down.

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GPJ

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GEORGE: The PDF cited by dhw is a totally worthless paper from a creationist.-Thank you for your diligent research on Jerry Bergman. It was evident from the reference that he was a creationist, but I am prepared to consider his arguments rather than his background. If the Archbishop of Canterbury were to ignore Dawkins' scientific arguments on the grounds that he is an atheist, we would all laugh our socks off.-Perhaps, however, I can persuade you to concentrate on messages rather than on messengers. I had pointed out that new organs such as heart, liver, penis etc., even in their most rudimentary form, were immensely complex and had to function if they were to survive. (I also wrote a detailed challenge to your use of "simple" in relation to nerves.) Such innovations seem to indicate that, contrary to Darwin's thesis, Nature does sometimes "jump". I therefore asked why Darwin thought his theory of evolution ... that all life is descended from one or a few forms, and that these have developed into the present vast range through a process of natural selection ... depended absolutely on gradualism, i.e. on the principle that Nature does not "jump". Your response was to ignore the problem of innovation and restrict yourself to variation (which indeed is a gradual process). David Turell, who is certainly more qualified than either of us in the field of biology, thought Bergman's article was "absolutely brilliant". Perhaps, then, you could help me to solve my gradualism problem by explaining the biological fallacies in the argument. I'm afraid that criticism along the lines of "worthless" and "discredited" and "creationist" are no help to me at all.

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David Turell, who is certainly more qualified than either of us in the field of biology, thought Bergman's article was "absolutely brilliant". Perhaps, then, you could help me to solve my gradualism problem by explaining the biological fallacies in the argument. I'm afraid that criticism along the lines of "worthless" and "discredited" and "creationist" are no help to me at all.-Hear,hear! The points Bergman raised are valid and unanswered by the Darwin Theory. As I have said before: the complexities presentd by living organisms are mindboggling. I get the urge to describe some of that complexity here. But that is the wrong approach. Each person on this site with no biology background needs to read a simple high school text to get some tiny sense olf the biologic knowledge out there. Yes, in a sense I am a creationist, in that I feel I have found evidence for an intelligence controlling all we see and research. My theory is that the process of evolution from simple to complex is coded in the genome from the beginning. We are currently finding Lamarkian evidence in the epigenetic studies. That is why Altenberg happened. Neo-Darwinism is n ot the answer.

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The new studies, as with Behe, show gene losses and new gene gains with gaps in the record that deny Darwin gradualism:

https://inference-review.com/article/the-origin-of-novel-genes

The four studies find that organisms with different morphologies possess different sets of genes. Given that genes provide much of the information encoding the morphology of living organisms, this finding may not seem a surprise. That novel genes do not accumulate with Darwinian gradualism in the phylogeny is perhaps more surprising. The authors describe bursts of innovation: upon the origin of placental mammals, 357 novel genes; upon the origin of the metazoan, 1,189 novel genes; upon the origin of the land plants, 1,167 novel genes; and upon the origin of the flowering plants, 2,525 novel genes.

Equally surprising is evidence that the patterns of presence and absence of many genes in these studies do not form a nested hierarchy congruent with the accepted phylogeny. Particular genes often appear in more than one clade. This leads the authors to infer massive gene losses and frequent horizontal gene transfer in the history of life.

The unexpected nature of these findings was not lost on the authors of the studies. Three of the paper titles emphasize unexpected novelty and one emphasizes unexpected loss. But all four show similar patterns. More is revealed in each than a single title can convey.

IN THIS CONTEXT, the gene does not embody solely unique protein-coding sequences, nor groups of slightly different protein-coding sequences, but larger cohesive clusters that the authors term homology groups...According to the parameters applied by the authors, the homology groups in question are typically larger groupings than a gene family...Of the 87 homology groups examined, 15 exhibited detectable similarity with other homology groups in mammals and 39 with other homology groups in animals. This left 33 of the 87 homology groups with no detectable similarity to any other groups in their study. Even if all proteins that have any detectable similarity with BLASTP were joined together, the resulting sequence space would resemble an archipelago, rather than a continent.

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The largest of these four studies included more than nine million protein-coding sequences from 208 genomes, spanning eukaryotic life from yeast to humans to ash trees.3 Such a sample might be expected to show continuous variation. Instead, these nine million sequences clustered into 661,545 homology groups.

The evolution of novel genes is a subject with a substantial literature all its own, which has recently shifted from the view that all new genes begin as duplicates of pre-existing genes to a view that many genes evolve de novo from non-coding sequences.

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Rather than emerging gradually, a few at a time, the evidence presented in these four papers suggests the occurrence of punctuated bursts. At every major phylogenetic node that was examined, the appearance of hundreds, and in some cases thousands, of novel homology groups was detected.

Evolution by bursts is, of course, not expected if natural selection is the main driver. “[N]atural selection acts only by taking advantage of slight successive variations,” Darwin remarked; “she can never take a great and sudden leap, but must advance by short and sure, through slow steps.” The findings presented in these papers suggest otherwise. It seems that the evolution of life is characterized by leaps involving large numbers of novel homology groups.

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The fossil record depicts the appearance of the first angiosperms as a sudden event, with no clear progenitors. This was known, in part, to Darwin, who famously complained to the Director of Kew Gardens in 1879 that the origin of the dicotyledonous angiosperms was an “abominable mystery.”7 The mystery has since deepened to include all other angiosperms.

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ALL FOUR STUDIES under review found massive gene losses for phylogenetic nodes at the base of the major groups of living organisms. This suggests that major evolutionary transitions do not occur solely by means of tinkering with existing genes. Instead, it seems that vast numbers of existing genes are jettisoned and replaced by entirely different ones. Such processes would represent a radical overhaul in the genetic composition of organisms. (my bold)

***

The authors suggest that horizontal gene transfer could explain the incongruent patterns of gene presence or absence that give rise to some of the apparent losses. Bowles et al. found that 323 homology groups were present in fungal and land plant genomes, but absent from all other taxa. Instead of being lost in the lineages between fungi and land plants, the genes could simply have jumped.

The incongruence between patterns in the absence or presence of homology groups and widely accepted phylogenies raises a broader issue. A single phylogeny is clearly an inadequate model for the history of life, but there is no obvious replacement.

Comment: Genomic studies don't support Darwin. Behe is supported, and the Cambrian gap is not the only major gap to be explained. Certainly fits God in charge.

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DAVID: The new studies, as with Behe, show gene losses and new gene gains with gaps in the record that deny Darwin gradualism:
https://inference-review.com/article/the-origin-of-novel-genes

QUOTES: The evolution of novel genes is a subject with a substantial literature all its own, which has recently shifted from the view that all new genes begin as duplicates of pre-existing genes to a view that many genes evolve de novo from non-coding sequences.

Rather than emerging gradually, a few at a time, the evidence presented in these four papers suggests the occurrence of punctuated bursts.

Evolution by bursts is, of course, not expected if natural selection is the main driver.

ALL FOUR STUDIES under review found massive gene losses for phylogenetic nodes at the base of the major groups of living organisms. This suggests that major evolutionary transitions do not occur solely by means of tinkering with existing genes. Instead, it seems that vast numbers of existing genes are jettisoned and replaced by entirely different ones. Such processes would represent a radical overhaul in the genetic composition of organisms. (David’s bold)

DAVID: Genomic studies don't support Darwin. Behe is supported, and the Cambrian gap is not the only major gap to be explained. Certainly fits God in charge.

A month ago, on the thread “Evolution: a different view with loss of traits; not Behe”, I challenged the statement that “advances always result from loss of genes”. I wrote: “I suggest that the process is on-going, with a constant acquisition of new genes (or new functions for old genes) and loss of unwanted genes. Natural selection merely decides which genes are necessary and which are not.” Initially you pooh-poohed the very notion of new genes, but eventually withdrew your objection when you realized that modern research supported it. You and I have long since rejected Darwin’s gradualism, and I have long since supported Gould’s punctuated equilibrium. The above quote on natural selection is correct in relation to Darwin’s use of the term and his insistence on gradualism, but in itself is irrelevant once we acknowledge that natural selection doesn’t drive anything. It merely selects from what already exists. I suggest that Behe’s loss of genes IS the result of natural selection. The genes that are lost are those that are no longer of any use if new genes perform new functions. I agree that what is presented here fits your notion that God dabbles or preprogrammes every change. It also fits Shapiro’s notion that intelligent cells are inventive, together with the all-important concept of cell plasticity, through which “a cell can take on different and reversible identities”. The inventiveness of cells responding to changes in environmental conditions, whether global or local, explains all the gaps. And it allows for your God as the inventor of cellular intelligence.

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DAVID: The new studies, as with Behe, show gene losses and new gene gains with gaps in the record that deny Darwin gradualism:
https://inference-review.com/article/the-origin-of-novel-genes

QUOTES: The evolution of novel genes is a subject with a substantial literature all its own, which has recently shifted from the view that all new genes begin as duplicates of pre-existing genes to a view that many genes evolve de novo from non-coding sequences.

dhw: Rather than emerging gradually, a few at a time, the evidence presented in these four papers suggests the occurrence of punctuated bursts.

Evolution by bursts is, of course, not expected if natural selection is the main driver.

Sudden changes with bursts is NOT natural selection.

ALL FOUR STUDIES under review found massive gene losses for phylogenetic nodes at the base of the major groups of living organisms. This suggests that major evolutionary transitions do not occur solely by means of tinkering with existing genes. Instead, it seems that vast numbers of existing genes are jettisoned and replaced by entirely different ones. Such processes would represent a radical overhaul in the genetic composition of organisms. (David’s bold)

DAVID: Genomic studies don't support Darwin. Behe is supported, and the Cambrian gap is not the only major gap to be explained. Certainly fits God in charge.

dhw: A month ago, on the thread “Evolution: a different view with loss of traits; not Behe”, I challenged the statement that “advances always result from loss of genes”. I wrote: “I suggest that the process is on-going, with a constant acquisition of new genes (or new functions for old genes) and loss of unwanted genes. Natural selection merely decides which genes are necessary and which are not.” Initially you pooh-poohed the very notion of new genes, but eventually withdrew your objection when you realized that modern research supported it.

I don't remember the incident in the bold. I've always presented the issue of de novo genes as not supporting Darwin.

dhw: You and I have long since rejected Darwin’s gradualism, and I have long since supported Gould’s punctuated equilibrium. The above quote on natural selection is correct in relation to Darwin’s use of the term and his insistence on gradualism, but in itself is irrelevant once we acknowledge that natural selection doesn’t drive anything. It merely selects from what already exists. I suggest that Behe’s loss of genes IS the result of natural selection. The genes that are lost are those that are no longer of any use if new genes perform new functions.

You misunderstand Behe's main point. His gene loss made new species, not new functions, although taht can also happen.

dhw: I agree that what is presented here fits your notion that God dabbles or preprogrammes every change. It also fits Shapiro’s notion that intelligent cells are inventive, together with the all-important concept of cell plasticity, through which “a cell can take on different and reversible identities”. The inventiveness of cells responding to changes in environmental conditions, whether global or local, explains all the gaps. And it allows for your God as the inventor of cellular intelligence.

You've covered all the bases.

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dhw: A month ago, on the thread “Evolution: a different view with loss of traits; not Behe”, I challenged the statement that “advances always result from loss of genes”. I wrote: “I suggest that the process is on-going, with a constant acquisition of new genes (or new functions for old genes) and loss of unwanted genes. Natural selection merely decides which genes are necessary and which are not.” Initially you pooh-poohed the very notion of new genes, but eventually withdrew your objection when you realized that modern research supported it. (David’s bold)

DAVID: I don't remember the incident in the bold. I've always presented the issue of de novo genes as not supporting Darwin.

8 September:
DAVID: The acquisition of new genes in your statement now in red is not supported. […]

dhw: […] the acquisition of new genes has plenty of support.

I quoted three articles. You then replied:

DAVID: Your articles are from 2013, not current presentations. Research advances, and yes new genes appear, but it still appears major evolutionary changes….result in loss of DNA [….] it depends upon which genes you are looking at and how much new they create.

New genes are central to my proposal, and their non-existence was initially central to your rejection of it. You then switched your line of attack.

dhw: You and I have long since rejected Darwin’s gradualism, and I have long since supported Gould’s punctuated equilibrium. The above quote on natural selection is correct in relation to Darwin’s use of the term and his insistence on gradualism, but in itself is irrelevant once we acknowledge that natural selection doesn’t drive anything. It merely selects from what already exists. I suggest that Behe’s loss of genes IS the result of natural selection. The genes that are lost are those that are no longer of any use if new genes perform new functions.

DAVID: You misunderstand Behe's main point. His gene loss made new species, not new functions, although taht can also happen.

You misunderstand my main point. I don’t see how gene loss can MAKE new species, and am proposing that new genes or new functions for old genes make species, and the loss of genes is the RESULT of speciation, because natural selection roots out whatever is no longer required. Please explain why this is not feasible.

dhw: I agree that what is presented here fits your notion that God dabbles or preprogrammes every change. It also fits Shapiro’s notion that intelligent cells are inventive, together with the all-important concept of cell plasticity, through which “a cell can take on different and reversible identities”. The inventiveness of cells responding to changes in environmental conditions, whether global or local, explains all the gaps. And it allows for your God as the inventor of cellular intelligence.

DAVID: You've covered all the bases.

Thank you.

2361 views

dhw: A month ago, on the thread “Evolution: a different view with loss of traits; not Behe”, I challenged the statement that “advances always result from loss of genes”. I wrote: “I suggest that the process is on-going, with a constant acquisition of new genes (or new functions for old genes) and loss of unwanted genes. Natural selection merely decides which genes are necessary and which are not.” Initially you pooh-poohed the very notion of new genes, but eventually withdrew your objection when you realized that modern research supported it. (David’s bold)

DAVID: I don't remember the incident in the bold. I've always presented the issue of de novo genes as not supporting Darwin.

8 September:
DAVID: The acquisition of new genes in your statement now in red is not supported. […]

dhw: […] the acquisition of new genes has plenty of support.

I quoted three articles. You then replied:

DAVID: Your articles are from 2013, not current presentations. Research advances, and yes new genes appear, but it still appears major evolutionary changes….result in loss of DNA [….] it depends upon which genes you are looking at and how much new they create.

New genes are central to my proposal, and their non-existence was initially central to your rejection of it. You then switched your line of attack.

dhw: You and I have long since rejected Darwin’s gradualism, and I have long since supported Gould’s punctuated equilibrium. The above quote on natural selection is correct in relation to Darwin’s use of the term and his insistence on gradualism, but in itself is irrelevant once we acknowledge that natural selection doesn’t drive anything. It merely selects from what already exists. I suggest that Behe’s loss of genes IS the result of natural selection. The genes that are lost are those that are no longer of any use if new genes perform new functions.

DAVID: You misunderstand Behe's main point. His gene loss made new species, not new functions, although that can also happen.

dhw: You misunderstand my main point. I don’t see how gene loss can MAKE new species, and am proposing that new genes or new functions for old genes make species, and the loss of genes is the RESULT of speciation, because natural selection roots out whatever is no longer required. Please explain why this is not feasible.

This statement of yours is specifically totally incorrect. Behe clearly shows loss of genes speciates as does this new entry. The bold is a backward view of the process. The loss causes speciation. It can be seen as a rearrangement of genes and a restructuring of old gene expression in new gene networks of the remaining genes. And why do you drag in natural selection? Your Darwin bias is back.

dhw: I agree that what is presented here fits your notion that God dabbles or preprogrammes every change. It also fits Shapiro’s notion that intelligent cells are inventive, together with the all-important concept of cell plasticity, through which “a cell can take on different and reversible identities”. The inventiveness of cells responding to changes in environmental conditions, whether global or local, explains all the gaps. And it allows for your God as the inventor of cellular intelligence.

DAVID: You've covered all the bases.

dhw: Thank you.

I have to let you teeter atop the fence.

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DAVID: You misunderstand Behe's main point. His gene loss made new species, not new functions, although that can also happen.

dhw: You misunderstand my main point. I don’t see how gene loss can MAKE new species, and am proposing that new genes or new functions for old genes make species, and the loss of genes is the RESULT of speciation, because natural selection roots out whatever is no longer required. Please explain why this is not feasible.

DAVID: This statement of yours is specifically totally incorrect. Behe clearly shows loss of genes speciates as does this new entry. The bold is a backward view of the process. The loss causes speciation. It can be seen as a rearrangement of genes and a restructuring of old gene expression in new gene networks of the remaining genes. And why do you drag in natural selection? Your Darwin bias is back.

I haven’t read Behe, but you have told us that this is his theory. The new entry does not show that loss of genes CAUSES speciation, unless you have omitted something from the quotes. It says that all four studies “found massive gene losses….This suggests that major evolutionary transitions do not occur solely by means of tinkering with existing genes. Instead, it seems that vast numbers of existing genes bb are jettisoned and replaced by entirely different ones.” Do you really believe that there would be a new species if the jettisoned genes were not replaced by new ones? The existing genes that are jettisoned are not needed because they are replaced by the new ones! The genes that remain will indeed be restructured. All this fits in perfectly with my proposal that speciation is caused by the “acquisition of new genes (or new functions for old genes) and loss of unwanted genes. Natural selection merely decides which genes are necessary and which are not.” In my response to your post, I didn’t “drag in” natural selection. That was a follow-up to the quote “Evolution by bursts is, of course, not expected if natural selection is the main driver.” However, I must stress that I am not arguing with Behe – I can only discuss the points you raise. Now please tell me why my proposal is not feasible.

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DAVID: You misunderstand Behe's main point. His gene loss made new species, not new functions, although that can also happen.

dhw: You misunderstand my main point. I don’t see how gene loss can MAKE new species, and am proposing that new genes or new functions for old genes make species, and the loss of genes is the RESULT of speciation, because natural selection roots out whatever is no longer required. Please explain why this is not feasible.

DAVID: This statement of yours is specifically totally incorrect. Behe clearly shows loss of genes speciates as does this new entry. The bold is a backward view of the process. The loss causes speciation. It can be seen as a rearrangement of genes and a restructuring of old gene expression in new gene networks of the remaining genes. And why do you drag in natural selection? Your Darwin bias is back.

dhw: I haven’t read Behe, but you have told us that this is his theory. The new entry does not show that loss of genes CAUSES speciation, unless you have omitted something from the quotes. It says that all four studies “found massive gene losses….This suggests that major evolutionary transitions do not occur solely by means of tinkering with existing genes. Instead, it seems that vast numbers of existing genes bb are jettisoned and replaced by entirely different ones.” Do you really believe that there would be a new species if the jettisoned genes were not replaced by new ones? The existing genes that are jettisoned are not needed because they are replaced by the new ones!

Your declaration of 'there must be new genes' I view as a cry of despair! The article is not edited by me to hide gene gains. In that regard, all it discussed was gene loss!!!

The genes that remain will indeed be restructured. All this fits in perfectly with my proposal that speciation is caused by the “acquisition of new genes (or new functions for old genes) and loss of unwanted genes. Natural selection merely decides which genes are necessary and which are not.” In my response to your post, I didn’t “drag in” natural selection. That was a follow-up to the quote “Evolution by bursts is, of course, not expected if natural selection is the main driver.” However, I must stress that I am not arguing with Behe – I can only discuss the points you raise. Now please tell me why my proposal is not feasible.

Because the evidence presented does not support it for new genes. Where I agree is: new functions of old genes by reorganization of gene expression and redeveloped gene wide network associations may well be the cause of speciation.

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dhw: I don’t see how gene loss can MAKE new species, and am proposing that new genes or new functions for old genes make species, and the loss of genes is the RESULT of speciation, because natural selection roots out whatever is no longer required. Please explain why this is not feasible.

DAVID: This statement of yours is specifically totally incorrect. Behe clearly shows loss of genes speciates as does this new entry. The bold is a backward view of the process. The loss causes speciation. It can be seen as a rearrangement of genes and a restructuring of old gene expression in new gene networks of the remaining genes. […]

dhw: I haven’t read Behe, but you have told us that this is his theory. The new entry does not show that loss of genes CAUSES speciation, unless you have omitted something from the quotes. It says that all four studies “found massive gene losses….This suggests that major evolutionary transitions do not occur solely by means of tinkering with existing genes. Instead, it seems that vast numbers of existing genes are jettisoned and replaced by entirely different ones.” Do you really believe that there would be a new species if the jettisoned genes were not replaced by new ones? The existing genes that are jettisoned are not needed because they are replaced by the new ones! (dhw’s new bold)

DAVID: Your declaration of 'there must be new genes' I view as a cry of despair! The article is not edited by me to hide gene gains. In that regard, all it discussed was gene loss!!!

I wrote that the article did NOT show that loss of genes caused speciation, unless you’d missed something out. I had already bolded the relevant sentence: “existing genes are jettisoned and replaced by entirely different ones.” Do you think entirely different genes are old genes? And are you now going back to your earlier denial that new genes exist? Look again at the article: “The evolution of new genes is a subject with a substantial literature of its own […] many genes evolve de novo from non-coding sequences.” In the light of all this, why is my theory not feasible?

DAVID: Because the evidence presented does not support it for new genes. Where I agree is: new functions of old genes by reorganization of gene expression and redeveloped gene wide network associations may well be the cause of speciation.

The evidence presented emphasizes the existence of new genes, and the fact that they replace old genes. I agree that the remaining genes will be restructured. All this is an exact repeat of my proposal that speciation is caused by the “acquisition of new genes (or new functions for old genes) and loss of unwanted genes. Natural selection merely decides which genes are necessary and which are not.” However, I must stress that I am not arguing with Behe – I can only discuss the points you raise. Now please tell me why my proposal is not feasible.

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dhw: I don’t see how gene loss can MAKE new species, and am proposing that new genes or new functions for old genes make species, and the loss of genes is the RESULT of speciation, because natural selection roots out whatever is no longer required. Please explain why this is not feasible.

DAVID: This statement of yours is specifically totally incorrect. Behe clearly shows loss of genes speciates as does this new entry. The bold is a backward view of the process. The loss causes speciation. It can be seen as a rearrangement of genes and a restructuring of old gene expression in new gene networks of the remaining genes. […]

dhw: I haven’t read Behe, but you have told us that this is his theory. The new entry does not show that loss of genes CAUSES speciation, unless you have omitted something from the quotes. It says that all four studies “found massive gene losses….This suggests that major evolutionary transitions do not occur solely by means of tinkering with existing genes. Instead, it seems that vast numbers of existing genes are jettisoned and replaced by entirely different ones.” Do you really believe that there would be a new species if the jettisoned genes were not replaced by new ones? The existing genes that are jettisoned are not needed because they are replaced by the new ones! (dhw’s new bold)

DAVID: Your declaration of 'there must be new genes' I view as a cry of despair! The article is not edited by me to hide gene gains. In that regard, all it discussed was gene loss!!!

dhw: I wrote that the article did NOT show that loss of genes caused speciation, unless you’d missed something out. I had already bolded the relevant sentence: “existing genes are jettisoned and replaced by entirely different ones.” Do you think entirely different genes are old genes? And are you now going back to your earlier denial that new genes exist? Look again at the article: “The evolution of new genes is a subject with a substantial literature of its own […] many genes evolve de novo from non-coding sequences.” In the light of all this, why is my theory not feasible?

DAVID: Because the evidence presented does not support it for new genes. Where I agree is: new functions of old genes by reorganization of gene expression and redeveloped gene wide network associations may well be the cause of speciation.

dhw: The evidence presented emphasizes the existence of new genes, and the fact that they replace old genes. I agree that the remaining genes will be restructured. All this is an exact repeat of my proposal that speciation is caused by the “acquisition of new genes (or new functions for old genes) and loss of unwanted genes. Natural selection merely decides which genes are necessary and which are not.” However, I must stress that I am not arguing with Behe – I can only discuss the points you raise. Now please tell me why my proposal is not feasible.

Yes, we both agree new genes appear, but the evidence is still on the side that speciation involves loss of genes. To repeat: "new functions of old genes by reorganization of gene expression and redeveloped gene wide network associations may well be the cause of speciation." Your proposal covers the same ground. Our difference is I think God is doing the coding.

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dhw: In the light of all this, why is my theory not feasible?

DAVID: Because the evidence presented does not support it for new genes. Where I agree is: new functions of old genes by reorganization of gene expression and redeveloped gene wide network associations may well be the cause of speciation.

dhw: The evidence presented emphasizes the existence of new genes, and the fact that they replace old genes. I agree that the remaining genes will be restructured. All this is an exact repeat of my proposal that speciation is caused by the “acquisition of new genes (or new functions for old genes) and loss of unwanted genes. Natural selection merely decides which genes are necessary and which are not.” However, I must stress that I am not arguing with Behe – I can only discuss the points you raise. Now please tell me why my proposal is not feasible.

I would like to make a slight change to my proposal, in direct opposition to the theory I have been objecting to: Speciation is caused by the acquisition of new genes AND new functions for old genes, and is ACCOMPANIED by loss of unwanted genes etc.

DAVID: Yes, we both agree new genes appear, but the evidence is still on the side that speciation involves loss of genes. To repeat: "new functions of old genes by reorganization of gene expression and redeveloped gene wide network associations may well be the cause of speciation." Your proposal covers the same ground. Our difference is I think God is doing the coding.

I don’t know why you feel it is necessary to repeat everything I have said in my original proposal, but thank you for withdrawing your objection to new genes, dropping your insistence that loss of genes CAUSES speciation, and agreeing with me that old genes take on new functions. The argument has been about the cause of speciation, and I am perfectly happy, as I always have been, to acknowledge the possibility that there is a God who did the coding. If you now accept my revised proposal, I think we can close this thread.

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dhw: In the light of all this, why is my theory not feasible?

DAVID: Because the evidence presented does not support it for new genes. Where I agree is: new functions of old genes by reorganization of gene expression and redeveloped gene wide network associations may well be the cause of speciation.

dhw: The evidence presented emphasizes the existence of new genes, and the fact that they replace old genes. I agree that the remaining genes will be restructured. All this is an exact repeat of my proposal that speciation is caused by the “acquisition of new genes (or new functions for old genes) and loss of unwanted genes. Natural selection merely decides which genes are necessary and which are not.” However, I must stress that I am not arguing with Behe – I can only discuss the points you raise. Now please tell me why my proposal is not feasible.

dhw: I would like to make a slight change to my proposal, in direct opposition to the theory I have been objecting to: Speciation is caused by the acquisition of new genes AND new functions for old genes, and is ACCOMPANIED by loss of unwanted genes etc.

DAVID: Yes, we both agree new genes appear, but the evidence is still on the side that speciation involves loss of genes. To repeat: "new functions of old genes by reorganization of gene expression and redeveloped gene wide network associations may well be the cause of speciation." Your proposal covers the same ground. Our difference is I think God is doing the coding.

dhw: I don’t know why you feel it is necessary to repeat everything I have said in my original proposal, but thank you for withdrawing your objection to new genes, dropping your insistence that loss of genes CAUSES speciation, and agreeing with me that old genes take on new functions. The argument has been about the cause of speciation, and I am perfectly happy, as I always have been, to acknowledge the possibility that there is a God who did the coding. If you now accept my revised proposal, I think we can close this thread.

I do not agree fully with the bold above. Loss of genes appears to be one of causes of speciation along with a restructuring of expression of genes and may include new genes added. But based on Behe, some speciation changes are just deletion.

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dhw: I would like to make a slight change to my proposal, in direct opposition to the theory I have been objecting to: Speciation is caused by the acquisition of new genes AND new functions for old genes, and is ACCOMPANIED by loss of unwanted genes etc.
If you now accept my revised proposal, I think we can close this thread.

DAVID: I do not agree fully with the bold above. Loss of genes appears to be one of causes of speciation along with a restructuring of expression of genes and may include new genes added. But based on Behe, some speciation changes are just deletion.

A restructuring of expression of genes is what I call new functions for old genes. This whole discussion began with my disputing the claim that “advances always result from loss of genes”. I only know Behe’s theory from what you tell me, so I don’t know if his examples are minor variations or totally new species. I remember you picking on the example of the polar bear lacking two genes found in the grizzly and the brown bear. I wouldn’t call this an advance. They are all bears, but they live in different conditions, and had to adapt accordingly. The obvious inference is that genes which operate in a warm climate won’t be of any use in a cold climate. I can’t see the logic in the argument that losing useless genes will create a new fur coat. But I can only discuss the points you reproduce here. Since we do in fact call these different bears different species, perhaps we shouldn’t be using the word “speciation” at all and should stick to the term used in the latest article: “major evolutionary transitions”, which I would equate with innovation and which, you will remember, occur when “vast numbers of existing genes are jettisoned and replaced by entirely different ones”. But I would also expect loss of genes as a RESULT of minor transitions and not as the cause.

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dhw: I would like to make a slight change to my proposal, in direct opposition to the theory I have been objecting to: Speciation is caused by the acquisition of new genes AND new functions for old genes, and is ACCOMPANIED by loss of unwanted genes etc.
If you now accept my revised proposal, I think we can close this thread.

DAVID: I do not agree fully with the bold above. Loss of genes appears to be one of causes of speciation along with a restructuring of expression of genes and may include new genes added. But based on Behe, some speciation changes are just deletion.

dhw: A restructuring of expression of genes is what I call new functions for old genes. This whole discussion began with my disputing the claim that “advances always result from loss of genes”. I only know Behe’s theory from what you tell me, so I don’t know if his examples are minor variations or totally new species. I remember you picking on the example of the polar bear lacking two genes found in the grizzly and the brown bear. I wouldn’t call this an advance. They are all bears, but they live in different conditions, and had to adapt accordingly. The obvious inference is that genes which operate in a warm climate won’t be of any use in a cold climate. I can’t see the logic in the argument that losing useless genes will create a new fur coat. But I can only discuss the points you reproduce here. Since we do in fact call these different bears different species, perhaps we shouldn’t be using the word “speciation” at all and should stick to the term used in the latest article: “major evolutionary transitions”, which I would equate with innovation and which, you will remember, occur when “vast numbers of existing genes are jettisoned and replaced by entirely different ones”. But I would also expect loss of genes as a RESULT of minor transitions and not as the cause.

Behe is a pioneer in theory just like Shapiro. He does use the polar bear as a prime example of species change. You are correct. it is really a massive adaptation to specific environment. He also discusses the mammoth and its DNA differences from elephants, in which it is found between 500-800 genes were degraded. His book is filled with such examples of adaptation by gene degradation. His prime thought early in the book to quote is: "Darwin's mechanism works chiefly by squandering genetic information for short-term gain." By this he means adaptation which aids survival "by damaging or breaking genes." (pages 37-38) By no means does he says he is positive full speciation in evolution is the cause of speciation, but he feels he is offering strong evidence in a 342 page book filled with adaptive examples. All dog varieties are due to damaged/degraded genes, but following your thought they are still really mostly wolves, as shepherd/wolves exist. Susan and I have been to a local breeding/rescue ranch out of curiosity..

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dhw: This whole discussion began with my disputing the claim that “advances always result from loss of genes”. I only know Behe’s theory from what you tell me, so I don’t know if his examples are minor variations or totally new species. I remember you picking on the example of the polar bear lacking two genes found in the grizzly and the brown bear. I wouldn’t call this an advance. They are all bears, but they live in different conditions, and had to adapt accordingly. The obvious inference is that genes which operate in a warm climate won’t be of any use in a cold climate. I can’t see the logic in the argument that losing useless genes will create a new fur coat. But I can only discuss the points you reproduce here. Since we do in fact call these different bears different species, perhaps we shouldn’t be using the word “speciation” at all and should stick to the term used in the latest article: “major evolutionary transitions”, which I would equate with innovation and which, you will remember, occur when “vast numbers of existing genes are jettisoned and replaced by entirely different ones”. But I would also expect loss of genes as a RESULT of minor transitions and not as the cause.

DAVID: Behe is a pioneer in theory just like Shapiro. He does use the polar bear as a prime example of species change. You are correct. it is really a massive adaptation to specific environment. He also discusses the mammoth and its DNA differences from elephants, in which it is found between 500-800 genes were degraded. His book is filled with such examples of adaptation by gene degradation. His prime thought early in the book to quote is: "Darwin's mechanism works chiefly by squandering genetic information for short-term gain." By this he means adaptation which aids survival "by damaging or breaking genes." (pages 37-38) By no means does he says he is positive full speciation in evolution is the cause of speciation, but he feels he is offering strong evidence in a 342 page book filled with adaptive examples. All dog varieties are due to damaged/degraded genes, but following your thought they are still really mostly wolves, as shepherd/wolves exist. Susan and I have been to a local breeding/rescue ranch out of curiosity..

Thank you for this revealing summary. It's a far cry from “advances always result from loss of genes”, and indeed it is pretty clear that the examples don’t even deal with advances! A polar bear can hardly be called an advance on a grizzly bear! It is perfectly logical that adaptation should RESULT in loss of genes since genes necessary for one environment may be of no use in another. I would suggest that adaptations will primarily involve new functions for existing genes, though some new ones may be necessary, but major innovations will certainly require new genes.

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dhw: This whole discussion began with my disputing the claim that “advances always result from loss of genes”. I only know Behe’s theory from what you tell me, so I don’t know if his examples are minor variations or totally new species. I remember you picking on the example of the polar bear lacking two genes found in the grizzly and the brown bear. I wouldn’t call this an advance. They are all bears, but they live in different conditions, and had to adapt accordingly. The obvious inference is that genes which operate in a warm climate won’t be of any use in a cold climate. I can’t see the logic in the argument that losing useless genes will create a new fur coat. But I can only discuss the points you reproduce here. Since we do in fact call these different bears different species, perhaps we shouldn’t be using the word “speciation” at all and should stick to the term used in the latest article: “major evolutionary transitions”, which I would equate with innovation and which, you will remember, occur when “vast numbers of existing genes are jettisoned and replaced by entirely different ones”. But I would also expect loss of genes as a RESULT of minor transitions and not as the cause.

DAVID: Behe is a pioneer in theory just like Shapiro. He does use the polar bear as a prime example of species change. You are correct. it is really a massive adaptation to specific environment. He also discusses the mammoth and its DNA differences from elephants, in which it is found between 500-800 genes were degraded. His book is filled with such examples of adaptation by gene degradation. His prime thought early in the book to quote is: "Darwin's mechanism works chiefly by squandering genetic information for short-term gain." By this he means adaptation which aids survival "by damaging or breaking genes." (pages 37-38) By no means does he says he is positive full speciation in evolution is the cause of speciation, but he feels he is offering strong evidence in a 342 page book filled with adaptive examples. All dog varieties are due to damaged/degraded genes, but following your thought they are still really mostly wolves, as shepherd/wolves exist. Susan and I have been to a local breeding/rescue ranch out of curiosity..

dhw: Thank you for this revealing summary. It's a far cry from “advances always result from loss of genes”, and indeed it is pretty clear that the examples don’t even deal with advances! A polar bear can hardly be called an advance on a grizzly bear! It is perfectly logical that adaptation should RESULT in loss of genes since genes necessary for one environment may be of no use in another. I would suggest that adaptations will primarily involve new functions for existing genes, though some new ones may be necessary, but major innovations will certainly require new genes.

Relax from your old teachings and beliefs. The bold is specifically not proven. Much is shown to be accomplished by reduplication, alterations in expressions, and setting up of new genome-wide networks among existing genes.

The polar bear difference is somewhat more than fur color but I'll buy adaption along with you. The mammoth is very different in appearance, but again it is an elephant with a woolly hide and giant tusks. Phenotype used for classification is useless. DNA study is the true guide to evolution. We both know this. Behe, with his emphasis on DNA, is pursuing a valid approach to cracking open the issue of speciation.

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DAVID: Behe is a pioneer in theory just like Shapiro. He does use the polar bear as a prime example of species change. You are correct. it is really a massive adaptation to specific environment. He also discusses the mammoth and its DNA differences from elephants, in which it is found between 500-800 genes were degraded. His book is filled with such examples of adaptation by gene degradation. His prime thought early in the book to quote is: "Darwin's mechanism works chiefly by squandering genetic information for short-term gain." By this he means adaptation which aids survival "by damaging or breaking genes." (pages 37-38) By no means does he says he is positive full speciation in evolution is the cause of speciation, but he feels he is offering strong evidence in a 342 page book filled with adaptive examples. All dog varieties are due to damaged/degraded genes, but following your thought they are still really mostly wolves, as shepherd/wolves exist. Susan and I have been to a local breeding/rescue ranch out of curiosity..

dhw: Thank you for this revealing summary. It's a far cry from “advances always result from loss of genes”, and indeed it is pretty clear that the examples don’t even deal with advances! A polar bear can hardly be called an advance on a grizzly bear! It is perfectly logical that adaptation should RESULT in loss of genes since genes necessary for one environment may be of no use in another. I would suggest that adaptations will primarily involve new functions for existing genes, though some new ones may be necessary, but major innovations will certainly require new genes.

DAVID: Relax from your old teachings and beliefs. The bold is specifically not proven. Much is shown to be accomplished by reduplication, alterations in expressions, and setting up of new genome-wide networks among existing genes.

What old teachings and beliefs? Initially you were sceptical about the very existence of new genes! I didn’t say it was proven – it is my suggestion, but what else do you think new genes would be required for if not for innovation? The rest of what you say is covered by new functions for old genes.

DAVID: The polar bear difference is somewhat more than fur color but I'll buy adaption along with you. The mammoth is very different in appearance, but again it is an elephant with a woolly hide and giant tusks. Phenotype used for classification is useless. DNA study is the true guide to evolution. We both know this. Behe, with his emphasis on DNA, is pursuing a valid approach to cracking open the issue of speciation.

That may be so, but his theory as you have presented it quite patently does not even begin to prove that speciation is caused by loss of genes, or that "advances always result from loss of genes", which was the claim that started this discussion.

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DAVID: Behe is a pioneer in theory just like Shapiro. He does use the polar bear as a prime example of species change. You are correct. it is really a massive adaptation to specific environment. He also discusses the mammoth and its DNA differences from elephants, in which it is found between 500-800 genes were degraded. His book is filled with such examples of adaptation by gene degradation. His prime thought early in the book to quote is: "Darwin's mechanism works chiefly by squandering genetic information for short-term gain." By this he means adaptation which aids survival "by damaging or breaking genes." (pages 37-38) By no means does he says he is positive full speciation in evolution is the cause of speciation, but he feels he is offering strong evidence in a 342 page book filled with adaptive examples. All dog varieties are due to damaged/degraded genes, but following your thought they are still really mostly wolves, as shepherd/wolves exist. Susan and I have been to a local breeding/rescue ranch out of curiosity..

dhw: Thank you for this revealing summary. It's a far cry from “advances always result from loss of genes”, and indeed it is pretty clear that the examples don’t even deal with advances! A polar bear can hardly be called an advance on a grizzly bear! It is perfectly logical that adaptation should RESULT in loss of genes since genes necessary for one environment may be of no use in another. I would suggest that adaptations will primarily involve new functions for existing genes, though some new ones may be necessary, but major innovations will certainly require new genes.

DAVID: Relax from your old teachings and beliefs. The bold is specifically not proven. Much is shown to be accomplished by reduplication, alterations in expressions, and setting up of new genome-wide networks among existing genes.

dhw: What old teachings and beliefs? Initially you were sceptical about the very existence of new genes! I didn’t say it was proven – it is my suggestion, but what else do you think new genes would be required for if not for innovation? The rest of what you say is covered by new functions for old genes.

DAVID: The polar bear difference is somewhat more than fur color but I'll buy adaption along with you. The mammoth is very different in appearance, but again it is an elephant with a woolly hide and giant tusks. Phenotype used for classification is useless. DNA study is the true guide to evolution. We both know this. Behe, with his emphasis on DNA, is pursuing a valid approach to cracking open the issue of speciation.

dhw: That may be so, but his theory as you have presented it quite patently does not even begin to prove that speciation is caused by loss of genes, or that "advances always result from loss of genes", which was the claim that started this discussion.

Well, we have clarified Behe's theory and it is highly suggestive of gene loss playing a major role in speciation since adaptation is mainly from gene degradation. However adaptation does not lead to speciation in the fossil record. Speciation creates gaps. Darwin's gradualism is not proven. Shapiro's theory is another approach, bootstrapping by editing DNA. This is all we have and in comparison I like Behe's approach better since it encompasses a review of genetic evidence. Shapiro is an extrapolation from free-living bacteria. And all Lenski has shown in his E. coli studies is some mutational adaptations in the same species.

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DAVID: Well, we have clarified Behe's theory and it is highly suggestive of gene loss playing a major role in speciation since adaptation is mainly from gene degradation.

The examples you have given show that there is gene loss which can be explained by the fact that certain genes are no longer needed when conditions change. Existing genes will take on new functions. This is a far cry from gene loss playing a constructive role even in adaptation. Out of interest, I would like to know if Behe also found new genes in his examples, though I suspect that adaptation itself would not require them, whereas major innovations would. You did not answer my question: what else do you think new genes would be required for if not for innovation?

DAVID: However adaptation does not lead to speciation in the fossil record. Speciation creates gaps. Darwin's gradualism is not proven. Shapiro's theory is another approach, bootstrapping by editing DNA. This is all we have and in comparison I like Behe's approach better since it encompasses a review of genetic evidence. Shapiro is an extrapolation from free-living bacteria. And all Lenski has shown in his E. coli studies is some mutational adaptations in the same species.

We have long since agreed that Darwin was wrong to say that there are no jumps in Nature. Shapiro’s theory is that intelligent cells do the engineering, and it takes into account the research of others into cellular intelligence. I have offered you a proposal concerning the role of new genes, old genes and discarded genes in speciation, and although like all the other theories, it is not proven, I still don’t know why you object to it.

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DAVID: Well, we have clarified Behe's theory and it is highly suggestive of gene loss playing a major role in speciation since adaptation is mainly from gene degradation.

The examples you have given show that there is gene loss which can be explained by the fact that certain genes are no longer needed when conditions change. Existing genes will take on new functions. This is a far cry from gene loss playing a constructive role even in adaptation. Out of interest, I would like to know if Behe also found new genes in his examples, though I suspect that adaptation itself would not require them, whereas major innovations would. You did not answer my question: what else do you think new genes would be required for if not for innovation?

DAVID: However adaptation does not lead to speciation in the fossil record. Speciation creates gaps. Darwin's gradualism is not proven. Shapiro's theory is another approach, bootstrapping by editing DNA. This is all we have and in comparison I like Behe's approach better since it encompasses a review of genetic evidence. Shapiro is an extrapolation from free-living bacteria. And all Lenski has shown in his E. coli studies is some mutational adaptations in the same species.

dhw: We have long since agreed that Darwin was wrong to say that there are no jumps in Nature. Shapiro’s theory is that intelligent cells do the engineering, and it takes into account the research of others into cellular intelligence. I have offered you a proposal concerning the role of new genes, old genes and discarded genes in speciation, and although like all the other theories, it is not proven, I still don’t know why you object to it.

You know full well I think a designer is required for all advance in evolution at the speciation level. As we study it, it should require a careful definition of species. We have noted the differences in bears by fur color as not really species set apart..

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dhw: We have long since agreed that Darwin was wrong to say that there are no jumps in Nature. Shapiro’s theory is that intelligent cells do the engineering, and it takes into account the research of others into cellular intelligence. I have offered you a proposal concerning the role of new genes, old genes and discarded genes in speciation, and although like all the other theories, it is not proven, I still don’t know why you object to it.

DAVID: You know full well I think a designer is required for all advance in evolution at the speciation level.

That is not an answer! Your designer would have created the mechanism in the first place, but even if he dabbled, the process of inventing, restructuring and discarding cells would have been the same. So why do you think speciation cannot possibly have been caused (whether dabbled or not) by a combination of new genes with old genes taking on new functions, while other old genes are discarded because they are no longer of any use?

DAVID: As we study it, it should require a careful definition of species. We have noted the differences in bears by fur color as not really species set apart.

I made that point myself earlier in this discussion. It makes no difference to the feasibility of my proposal, and no matter how we define speciation, it would still leave wide open the question of how loss of genes can create anything new. Why do you think it is not feasible that the loss of genes RESULTS from speciation, as above?

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dhw: We have long since agreed that Darwin was wrong to say that there are no jumps in Nature. Shapiro’s theory is that intelligent cells do the engineering, and it takes into account the research of others into cellular intelligence. I have offered you a proposal concerning the role of new genes, old genes and discarded genes in speciation, and although like all the other theories, it is not proven, I still don’t know why you object to it.

DAVID: You know full well I think a designer is required for all advance in evolution at the speciation level.

dhw: That is not an answer! Your designer would have created the mechanism in the first place, but even if he dabbled, the process of inventing, restructuring and discarding cells would have been the same. So why do you think speciation cannot possibly have been caused (whether dabbled or not) by a combination of new genes with old genes taking on new functions, while other old genes are discarded because they are no longer of any use?

Your suggestion of the changes in genes is reasonable. Adding new genes which work in concert to create a new species, coordinating with loss of genes and changing some gene network expression is a complex design requirement. It also requires a concept of what it is that is wanted for the new species to be able to do. Only a designer can accomplish this. Your answer has no mechanism for coordination of all these steps except the nebulous concept that cells are innately intelligent, source of that intelligence unknown.

DAVID: As we study it, it should require a careful definition of species. We have noted the differences in bears by fur color as not really species set apart.

dhw: I made that point myself earlier in this discussion. It makes no difference to the feasibility of my proposal, and no matter how we define speciation, it would still leave wide open the question of how loss of genes can create anything new. Why do you think it is not feasible that the loss of genes RESULTS from speciation, as above?

Answered: Gene loss, gene network modifications, changes in gene expressions altogether are reasonably capable of of speciation. The absolute requirement of new genes is pure unproven assumption of Darwinism. The possible proof of this is the small human gene tiny size compared to other organisms. Analysis of chimp gene relationships found (described previously here) the gene bases are 98% similar to human, but really 79% different in organization. Also our chromosome number is different. There are studies that describe human gene losses compared to chimps in the process of speciation:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4298176/

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DAVID: You know full well I think a designer is required for all advance in evolution at the speciation level.

dhw: Your designer would have created the mechanism in the first place, but even if he dabbled, the process of inventing, restructuring and discarding cells would have been the same. So why do you think speciation cannot possibly have been caused (whether dabbled or not) by a combination of new genes with old genes taking on new functions, while other old genes are discarded because they are no longer of any use?

DAVID: Your suggestion of the changes in genes is reasonable. Adding new genes which work in concert to create a new species, coordinating with loss of genes and changing some gene network expression is a complex design requirement.

Thank you. I am not denying the complexity.

DAVID: It also requires a concept of what it is that is wanted for the new species to be able to do. Only a designer can accomplish this. Your answer has no mechanism for coordination of all these steps except the nebulous concept that cells are innately intelligent, source of that intelligence unknown.

I keep agreeing that the source is unknown, but God is one possibility. What is “wanted” is an awareness of the conditions in which the organism finds itself (as opposed to your own theory, which requires a crystal ball to anticipate future conditions) and the intelligence to find ways of coping with them (adaptation) or exploiting them (innovation) – though it’s sometimes difficult to draw a line between the two processes. The concept of cellular intelligence is no more nebulous than the concept of an unknown intelligent being providing the first cells with a programme for every single development in the history of evolution that he does not directly dabble.

DAVID: As we study it, it should require a careful definition of species. We have noted the differences in bears by fur color as not really species set apart.

dhw: …no matter how we define speciation, it would still leave wide open the question of how loss of genes can create anything new. Why do you think it is not feasible that the loss of genes RESULTS from speciation, as above?

DAVID: Answered: Gene loss, gene network modifications, changes in gene expressions altogether are reasonably capable of of speciation.

That is not an answer. Why is it not feasible that there will be genes which a new species will not require and will therefore jettison?

DAVID: The absolute requirement of new genes is pure unproven assumption of Darwinism.

I’m pleased to hear this, as I was under the impression from your earlier posts that the very concept of new genes was doubtful. (That was the first reason you gave for rejecting my proposal.) If we have biologists favouring new genes as essential to speciation, it would be silly to reject the possibility. And now that you have acknowledged the existence of new genes,please tell us what they might be used for if not for some kind of innovation. And your comment still does not answer my question, now bolded.

DAVID: The possible proof of this is the small human gene tiny size compared to other organisms. Analysis of chimp gene relationships found (described previously here) the gene bases are 98% similar to human, but really 79% different in organization. Also our chromosome number is different. There are studies that describe human gene losses compared to chimps in the process of speciation:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4298176/

Do these studies claim that evolutionary innovation is caused by loss of genes? And do they discount the possibility that evolutionary innovation is caused by new genes and new functions for old genes, while useless old genes are jettisoned? And do you happen to know if Behe has examined the incidence of new genes in new species?

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DAVID: Your suggestion of the changes in genes is reasonable. Adding new genes which work in concert to create a new species, coordinating with loss of genes and changing some gene network expression is a complex design requirement.

dhw: Thank you. I am not denying the complexity.

DAVID: It also requires a concept of what it is that is wanted for the new species to be able to do. Only a designer can accomplish this. Your answer has no mechanism for coordination of all these steps except the nebulous concept that cells are innately intelligent, source of that intelligence unknown.

dhw: I keep agreeing that the source is unknown, but God is one possibility. What is “wanted” is an awareness of the conditions in which the organism finds itself (as opposed to your own theory, which requires a crystal ball to anticipate future conditions) and the intelligence to find ways of coping with them (adaptation) or exploiting them (innovation) – though it’s sometimes difficult to draw a line between the two processes. The concept of cellular intelligence is no more nebulous than the concept of an unknown intelligent being providing the first cells with a programme for every single development in the history of evolution that he does not directly dabble.

At least I can accept a designer is required.

dhw: …no matter how we define speciation, it would still leave wide open the question of how loss of genes can create anything new. Why do you think it is not feasible that the loss of genes RESULTS from speciation, as above?

DAVID: Answered: Gene loss, gene network modifications, changes in gene expressions altogether are reasonably capable of of speciation.

dhw: That is not an answer. Why is it not feasible that there will be genes which a new species will not require and will therefore jettison?

Note the red above. I answered your suggestion with agreement.

DAVID: The absolute requirement of new genes is pure unproven assumption of Darwinism.

dhw: I’m pleased to hear this, as I was under the impression from your earlier posts that the very concept of new genes was doubtful. (That was the first reason you gave for rejecting my proposal.) If we have biologists favouring new genes as essential to speciation, it would be silly to reject the possibility. And now that you have acknowledged the existence of new genes, please tell us what they might be used for if not for some kind of innovation. And your comment still does not answer my question, now bolded.

I have answered:

DAVID: The possible proof of this is the small human gene tiny size compared to other organisms. Analysis of chimp gene relationships found (described previously here) the gene bases are 98% similar to human, but really 79% different in organization. Also our chromosome number is different. There are studies that describe human gene losses compared to chimps in the process of speciation:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4298176/

dhw: Do these studies claim that evolutionary innovation is caused by loss of genes? And do they discount the possibility that evolutionary innovation is caused by new genes and new functions for old genes, while useless old genes are jettisoned? And do you happen to know if Behe has examined the incidence of new genes in new species?

I've seen no mention from him of new genes. Why do you ignore the article on chimps and us? It says there was gene loss and reorganization!!!

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dhw: …no matter how we define speciation, it would still leave wide open the question of how loss of genes can create anything new. Why do you think it is not feasible that the loss of genes RESULTS from speciation, as above?

DAVID: Answered: Gene loss, gene network modifications, changes in gene expressions altogether are reasonably capable of of speciation.

dhw: That is not an answer. Why is it not feasible that there will be genes which a new species will not require and will therefore jettison?

DAVID: Note the red above. I answered your suggestion with agreement.

Your answer ranks gene loss alongside the other two factors in CAUSING speciation. I am proposing that gene loss is the RESULT of speciation – the genes are not needed and are therefore discarded.

dhw: Do these studies claim that evolutionary innovation is caused by loss of genes? And do they discount the possibility that evolutionary innovation is caused by new genes and new functions for old genes, while useless old genes are jettisoned? And do you happen to know if Behe has examined the incidence of new genes in new species?

DAVID: I've seen no mention from him of new genes. Why do you ignore the article on chimps and us? It says there was gene loss and reorganization!!!

I am not disputing the fact that there is gene loss! I am disputing the argument that gene loss CAUSES speciation, and this whole discussion began by my disputing the claim that evolutionary advances “always result from loss of genes”. All you have come up with is the fact that genes get lost during adaptation, and initially you disputed the concept of new genes. The fact that speciation must involve reorganization of genes is so obvious that it is barely worth stating.

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dhw: …no matter how we define speciation, it would still leave wide open the question of how loss of genes can create anything new. Why do you think it is not feasible that the loss of genes RESULTS from speciation, as above?

DAVID: Answered: Gene loss, gene network modifications, changes in gene expressions altogether are reasonably capable of of speciation.

dhw: That is not an answer. Why is it not feasible that there will be genes which a new species will not require and will therefore jettison?

DAVID: Note the red above. I answered your suggestion with agreement.

Your answer ranks gene loss alongside the other two factors in CAUSING speciation. I am proposing that gene loss is the RESULT of speciation – the genes are not needed and are therefore discarded.

dhw: Do these studies claim that evolutionary innovation is caused by loss of genes? And do they discount the possibility that evolutionary innovation is caused by new genes and new functions for old genes, while useless old genes are jettisoned? And do you happen to know if Behe has examined the incidence of new genes in new species?

DAVID: I've seen no mention from him of new genes. Why do you ignore the article on chimps and us? It says there was gene loss and reorganization!!!

dhw: I am not disputing the fact that there is gene loss! I am disputing the argument that gene loss CAUSES speciation, and this whole discussion began by my disputing the claim that evolutionary advances “always result from loss of genes”. All you have come up with is the fact that genes get lost during adaptation, and initially you disputed the concept of new genes. The fact that speciation must involve reorganization of genes is so obvious that it is barely worth stating.

We can stop here. Basically we do not know how speciation works. Just theories, not Darwin's

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dhw: I am not disputing the fact that there is gene loss! I am disputing the argument that gene loss CAUSES speciation, and this whole discussion began by my disputing the claim that evolutionary advances “always result from loss of genes”. All you have come up with is the fact that genes get lost during adaptation, and initially you disputed the concept of new genes. The fact that speciation must involve reorganization of genes is so obvious that it is barely worth stating.

DAVID: We can stop here. Basically we do not know how speciation works. Just theories, not Darwin's

You are happy to demolish Darwin’s theory of random mutations, but having championed Behe’s theory as if it were some kind of breakthrough, you would now prefer not to discuss it because I’ve questioned its premises. Yes, we can stop here. We can stop every discussion on every subject, because we don’t “know” the origin of life, if God exists, what are his nature, purposes, methods if he does exist, how to resolve the theodicy problem, how consciousness arose and functions, whether or not we have free will, whether cells are intelligent or not…etc. and how speciation happened. But I would like to think that both of us are constantly learning from these discussions, and if nothing else they are keeping our old brains ticking! :-)

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dhw: I am not disputing the fact that there is gene loss! I am disputing the argument that gene loss CAUSES speciation, and this whole discussion began by my disputing the claim that evolutionary advances “always result from loss of genes”. All you have come up with is the fact that genes get lost during adaptation, and initially you disputed the concept of new genes. The fact that speciation must involve reorganization of genes is so obvious that it is barely worth stating.

DAVID: We can stop here. Basically we do not know how speciation works. Just theories, not Darwin's

dhw: You are happy to demolish Darwin’s theory of random mutations, but having championed Behe’s theory as if it were some kind of breakthrough, you would now prefer not to discuss it because I’ve questioned its premises. Yes, we can stop here. We can stop every discussion on every subject, because we don’t “know” the origin of life, if God exists, what are his nature, purposes, methods if he does exist, how to resolve the theodicy problem, how consciousness arose and functions, whether or not we have free will, whether cells are intelligent or not…etc. and how speciation happened. But I would like to think that both of us are constantly learning from these discussions, and if nothing else they are keeping our old brains ticking!

I'm with you. your thoughts about areas of discussion are right on. All I meant was the current subject is rather beaten to death for the moment, so let's find other aspects with whic h to challenge each other.

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dhw: "Either innovations work or they don't, and if they do, they are already complex, even if they survive and later become even more complex. It therefore seems to me that evolution doesn't depend on gradualism at all. Perhaps someone can enlighten me."
> 
> There is a section in Ernst Mayr's "What Evolution Is" that deals with this subject, though as I've said before I'm not a biologist and I find the language difficult to follow. He points out that: "individuals in a single population may differ by visibly different characters" (he cites eye colour and number of molars). He continues: "A successful mutation with a large phenotypic effect can be gradually incorporated into a population as long as it is able to pass through a period of polymorphism in which it coexists with the previous phenotype, until it has completely displaced the original gene." He ends with "it must be remembered that there is a considerable range in the size of the mutations that lead to evolutionary change". Later on he says: "Darwinian gradualism is due to the gradual restructuring of populations."-The rediscovery of Tadpole shrimp in Scotland, a 200 million year-old species, unchanged for all that time is an example of what? How does an organism decide it is perfect for its environmnt and make no changes for 200 million years? Saying 'stasis' identifies the issue or does it? Punctuated equilibrium doesn't help either. This is not gradualism. Nothing before and nothing after. Mutation just disappears in this animal, or no mutation achieved a necessary change. This is really what the fossil record is like. Trilobites with their double eye lenses for 250 million years, appear and then disappear. Nothing in this view suggests gradualism.-http://www.guardian.co.uk/environment/2010/jul/29/rare-tadpole-shrimps-found-scotland

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David has drawn our attention to an article in The Guardian concerning the rediscovery of the Tadpole shrimp, and asks: "How does an organism decide it is perfect for its environment and make no changes for 200 million years?"-Two weeks ago I pointed out an article which claimed that the 'Conan' bug could have been the origin of life on Earth. The bug is so tough that it can survive space travel, having its DNA ripped apart by radiation, and virtually any other environmental hazard you can think of. The article explained that the most likely explanation for its toughness was that the bug "possesses four to 10 copies of its genome, rather than the usual single version." I asked why this remarkable organism would need to evolve into other organisms when it is so perfectly equipped for survival, and why the four to 10 copy genome would evolve into the far less efficient "usual single version". -We need a specialist in the field to supply us with plausible explanations. Can anyone help?

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Most of evolution shows gaps. How significant is the absence of gradual fossils:

https://aeon.co/ideas/the-missing-fossils-matter-as-much-as-the-ones-we-have-found?utm_...

"The coelacanths are an ancient group of lobe-finned fishes, with weird appendages that take the form of bony, fleshy, muscular stalks. They’re well-represented in the fossil record all the way back to the Devonian period, some 390 million years ago. However, about 66 million years ago – the time of the dinosaurs’ demise – coelacanths disappear completely. It looked like they went extinct. Then, in 1938, someone caught a coelacanth in a fishing net off the coast of South Africa.

"The lesson here is that the absence of evidence – in this case, the lack of coelacanth fossils – is not the same as evidence of an absence. Take a kookier example. There’s a subculture of ‘cryptozoologists’ who believe that populations of pterodactyls are hiding out in remote parts of the globe, such as Papua New Guinea or the Brazilian rainforest. Pterosaurs, too, disappeared from the fossil record around 66 million years ago, and there is no proof that any of them exist today. Should we apply the same test as for the coelacanths? Or in this case, for some reason, does the absence of evidence amount to the same thing as the evidence of an absence?

"Figuring out the meaning of these gaps is notoriously difficult when you study the deep past. The ‘historical sciences’ of geology, archaeology and palaeontology deal with sedimented layers of matter, much of which has been destroyed or degraded over time. It can’t be reconstructed on a lab-bench or in a particle accelerator. In response to this challenge, palaeontologists perform a kind of scientific jujitsu. They treat the blank spots in the fossil record as evidence of something in and of themselves.

"Consider the idea that evolutionary changes are slow and cumulative, a theory known as Darwinian Gradualism. The fossil record contains some lovely specimens that point to gradual evolutionary change à la Darwin. But more often than not, a certain type of fossil just shows up in the rock strata, persists for a while as it is, and then disappears. Should we take the absence of proof of gradual change as evidence of the fact that evolution is not gradual?

"Darwin himself lost sleep over this problem. He eventually decided that the absence of evidence of gradual change is not, in itself, evidence of the absence of gradualism.
Instead, he attributed the gaps to the record’s incompleteness.

"Fast forward to the next century. In the 1970s, the biologists Niles Eldredge and Stephen Jay Gould argued that the lack of proof of gradualism is itself an informational signal. ‘Stasis is data,’ they claimed. If the fossil record contains periods where nothing changes, that’s because nothing, in fact, has changed. The lack of evidence of gradual evolution is simply telling us that there wasn’t much of it going on. Instead, they suggested that evolution happened by way of rapid bursts of change before reaching a plateau, a theory they called ‘punctuated equilibrium’.

"In the ensuing debate, the ‘gradualists’ shot back with the claim that history was covering its tracks: that the lack of slow transformation in the fossil record pointed to the rarity of successful fossilisation. Those in favour of Eldredge and Gould’s idea about sudden jumps in evolution, meanwhile, considered absences as indicators of biological reality.They wanted scientists to take stasis in the fossil record at face value. Either way, absences matter.

***

"The case of the coelacanth and the pterodactyl are similar in one respect. Both fossils have been missing for the past 66 million years. But for pterosaurs, the best explanation is just that the animals went extinct. For the coelacanth, the message is more complex. Accounting for the gap might invoke the small population size, when and how fossilisation occurs in marine environments, and the fact that much of the rock on the ocean floor is quite young. For both creatures, at least one thing is clear: what doesn’t fossilise is often as revealing as what does."

Comment: the article makes a good philosophical point, but the evidence is that the gaps are as large as ever, specifically with the newer soft form fossils from the pre-Cambrian era. Gradual Darwinism is pretty much dead.

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They have evidence of gene transfer and transposon genes which are active:

https://phys.org/news/2021-02-fossil-coelacanth-evolved-dozens-genes.html

"The capture of the first living Coelacanth, a mighty ocean predator, off the coast of South Africa caused quite a stir in 1938, 65 million years after its supposed extinction. It became known as a "living fossil" owing to its anatomy looking almost identical to the fossil record. But while the Coelacanth's body may have changed little, its genome tells another story.

"Toronto scientists have now revealed that the African Coelacanth, Latimeria chalumnae, gained 62 new genes through encounters with other species 10 million years ago.

***

"What's even more fascinating is how these genes came about. Their sequences suggest they arose from transposons, also known as "selfish genes". These are parasitic DNA elements whose sole purpose is to make more copies of themselves, which they sometimes achieve by moving between species.

"The findings show the dramatic effect traveling transposon DNA can have on the creation of genes and provide a glimpse into some of the forces that shaped the genome of one of the most ancient and mysterious organisms.

"'Our findings provide a rather striking example of this phenomenon of transposons contributing to the host genome," says Tim Hughes, senior study author and a professor of molecular genetics....

"'We don't know what these 62 genes are doing, but many of them encode DNA binding proteins and probably have a role in gene regulation, where even subtle changes are important in evolution," says Hughes, who is Canada Research Chair in Decoding Gene Regulation and John W. Billes Chair of Medical Research at the Temerty Faculty of Medicine at U of T.

"Transposons are sometimes also called "jumping genes" because they switch location in the genome, thanks to a self-encoded enzyme that recognises and move its own DNA code via "cut and paste" mechanism. New copies can arise through serendipitous jumps during cell division when the whole genome is replicated.

***

"There are myriad examples of transposon-derived genes across species, but the Coelacanth stands out for the sheer scale of it.

"It was surprising to see coelacanths pop out among vertebrates as having a really large number of these transposon-derived genes because they have an undeserved reputation of being a living fossil," says graduate student Isaac Yellan who spearheaded the study.

"'The Coelacanth may have evolved a bit more slowly but it is certainly not a fossil," he says.

"After scanning all available genomes, Yellan was able to find related genes, but their distribution across species was patchy and not what you'd expect from common ancestry. In addition to the single CGGBP-like gene in all mammals, birds and reptiles, Yellan found copies in some, but not all, fish he looked at, as well as in lamprey, a primitive vertebrate, and a type of fungus. Worms, molluscs, and most insects had none. And then there were 62 in the Coelacanth, whose genome became available in 2013.

With common ancestry ruled out, it appears instead that the transposons came into various lineages at different times by being carried between species through what is known as horizontal gene transfer.

"Horizontal gene transfer fuzzies up the picture of where the transposons came from but we know from other species that it can occur via parasitism," says Yellan. "The most likely explanation is that they were introduced multiple times throughout evolutionary history."

"It remains unclear what the genes are doing but several lines of evidence point to a finely-tuned role in gene regulation. Computational modeling and test tube experiments established that the genes' products are proteins which bind unique sequence signatures on the DNA, suggests a role in gene expression, similar to the human counterpart. Furthermore, the genes are varyingly switched on across dozen or so Coelacanth organs for which data exist, suggesting finely-tuned roles that are tissue-specific."

Comment: Is gene horizontal transfer an organismal ability, or does God step in and make the changes? Since I think God speciates, I feel He steps in. Specifically, we observe the results of gene transfer, but do not know the underlying mechanism. The coelacanth didn't change its body form (phenotype) but other apparently necessary gene regulations.

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They are everywhere in genomes and advance evolution:

https://phys.org/news/2021-02-virally-derived-transposons-domesticated-evolve.html

"About half of our genome is made up of transposable elements (TEs), also known as transposons. These 'jumping genes' are short stretches of DNA that have the unique ability to duplicate themselves and change their position within our code. While these philanderings play an essential role in the evolution of the species, if unchecked, transposons can wreak havoc on the genome.

"Although the transcription and proliferation of TEs is usually constrained by DNA methylation or other repressive chromatin amendments, TEs sometimes escape these countermeasures. For example, at certain periods of germ cell gametogenesis and early embryonic development, many epigenetic controls are wiped clean during scheduled system-wide reboots. Fortunately, cells have a backup mechanism known as the PIWI/piRNA pathway which can repress TEs. A recent paper in Nature Reviews Molecular Cell Biology investigates the many ways in which piRNAs can silence TEs, and defines new mechanisms by which they might also control gene expression.

"In the PIWI/piRNA pathway, RNA molecules about 25-32 nucleotides long associate with the Argonaute proteins from the PIWI clade to form piRISC complexes. These complexes target TEs post-transcriptionally, and also through the induction of epigenetic changes at the loci from which they are expressed. Piwi is an abbreviation of "P-element Induced WImpy testis," with the "P" meaning paternal.

***

"Two main classes of TEs can be defined. Class I TEs are called retrotransposons, which generally function via reverse transcription of the DNA into an RNA intermediate, hinting at their retroviral ancestry. Retrotransposons are commonly grouped into three main orders of decreasing size and complexity; the retrotransposons with long terminal repeats (LTRs), the LINES (which have reverse transcriptase but not LTRs), and the SINEs (which have neither). Class II TEs are the DNA transposons, which typically encode several sequence curiosities including a special transposase used for insertion and excision.

"Lest we give the impression that the transposon hazard is something we should be better off without, consider that transposons are solely responsible for most, or at least many, of the higher evolutionary refinements we enjoy today. Everything from live birth to expansion of the neocortex appears to have been driven by genome-wide insertion of TEs into the promoter regions of key regulatory genes. No other evolutionary process capable of radically altering the expression of so many genes in such a short time has been identified, let alone imagined. (my bold)

***

"The magic sauce hidden in these transposable elements is that they happen to be good at creating transcription factor binding sites."

Comment: The article contains many specific types of genetic activity conducted by these TE's. Is this God's supreme method for advancing evolution?

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Mainly absent. Gunter Bechly in a video:

https://youtu.be/luxbHIF3MAU

It is over an hour long, but one of the many, many examples was the dinosaur explosion:

https://www.sciencedaily.com/releases/2018/04/180416105803.htm

Dinosaurs had originated much earlier, at the beginning of the Triassic Period, some 245 million years ago, but they remained very rare until the shock events in the Carnian 13 million years later.

***

First there were no dinosaur tracks, and then there were many. This marks the moment of their explosion, and the rock successions in the Dolomites are well dated. Comparison with rock successions in Argentina and Brazil, here the first extensive skeletons of dinosaurs occur, show the explosion happened at the same time there as well.

Lead author Dr Massimo Bernardi, Curator at MUSE and Research associate at Bristol's School of Earth Sciences, said: "We were excited to see that the footprints and skeletons told the same story. We had been studying the footprints in the Dolomites for some time, and it's amazing how clear cut the change from 'no dinosaurs' to 'all dinosaurs' was."

Comment: This is one prime example Bechly mentioned. Evolution runs in spirts, never slow and steady

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> David asks, in the light of the new discovery and its relation to the Cambrian Explosion, "Where is Darwin's gradualism?" This is a point of the theory that I have never quite understood. Darwin is unequivocal about its importance: "If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down." (Origin, p. 214) In some respects he is on safe ground, because no-one can ever prove that there were no transitional forms, just as no-one can ever prove that there is no God. The Eldredge-Gould concept of 'punctuated equilibrium', however, contradicts that of 'Natura non facit saltum' and it certainly seems to be more in keeping with the fossil record as we know it. What I don't understand is why gradualism should be so crucial to the theory as a whole. It therefore seems to me that evolution doesn't depend on gradualism at all. Perhaps someone can enlighten me.-
Eldridge-Gould disturb(ed)some old school rigid Darwinists. In the past I've mentioned Reznick's guppies, now studied 20 years. They can change size to avoid preditors in a two-year period. Now we find that sticklebacks can adapt to colder waters in a three-year period. Epigenetic change may drive evolution more importantly than 'gradual' Darwinian suppositions. -
http://www.publicaffairs.ubc.ca/2010/08/04/mr-10-111/

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I think the "gradualist Darwinian" answer to these abilities of the guppies and sticklebacks is that they have evolved these strategies by the usual gradual processes. Another example might be the way some plants conform to a cycle of a prime number of years to escape predation by insects that have another cycle.-The webpage linked to by DT states (my emboldening):
"Our study is the first to experimentally show that certain species in the wild could adapt to climate change very rapidly ... in this case, colder water temperature. However, this rapid adaptation is not achieved without a cost. Only rare individuals that possess the ability to tolerate rapid changes in temperature survive, and the number of survivors may not be large enough to sustain the population. It is crucial that knowledge of evolutionary processes is incorporated into conservation and management policy." So they are only able to adapt so quickly because the ability has already been evolved and there is sufficient of it in the population.-Concerning the Cambrian "Explosion" I've been looking at some evolutionary sites about this subject, and it wasn't so sudden or inexplicable as DT tries to suggest.-http://www.fossilmuseum.net/Paleobiology/CambrianExplosion.htm-"It is important to remember that geological history contains numerous periods of slow evolution punctuated by periods of rapid evolution, which Steven J. Gould called Punctuated Equilibrium. The rates of evolution generally depend on rates of selection, which in turn depend on rates of environmental change. It also depends upon the existing genomic diversity on which selection acts. Mutation rates tend to be slow and steady, and in the absence of environmental change, slowly accumulate in a population. It is selective pressure that weeds out the mutations that are detrimental or neutral to survival, and retains and multiplies the mutations that are beneficial within a population. For a population isolated in a new environment, rapid selection can lead to speciation, and in the Lower Cambrian, to radically new forms that we now group in the Phyla of modern times." Thus Gould's ideas do not contradict Darwin's gradualism. It's not a question of jumps but of speed.-
http://www.pbs.org/wgbh/evolution/library/03/4/l_034_02.html-"Internal, genetic factors were also crucial. Recent research suggests that the period prior to the Cambrian explosion saw the gradual evolution of a "genetic tool kit" of genes that govern developmental processes. Once assembled, this genetic tool kit enabled an unprecedented period of evolutionary experimentation -- and competition. Many forms seen in the fossil record of the Cambrian disappeared without trace. Once the body plans that proved most successful came to dominate the biosphere, evolution never had such a free hand again, and evolutionary change was limited to relatively minor tinkering with the body plans that already existed." I suppose this idea of the evolution of a "genetic tool kit" could be what DT calls pre-loading or design, but it doesn't contradict evolution.

--
GPJ

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I think the "gradualist Darwinian" answer to these abilities of the guppies and sticklebacks is that they have evolved these strategies by the usual gradual processes. -2 years for guppies to change and 3 years for sticklebacks is not gradual. -
>
> I suppose this idea of the evolution of a "genetic tool kit" could be what DT calls pre-loading or design, but it doesn't contradict evolution.-You misunderstand my theory. I am not contradicting evolution. Evolution happened, as much as I know I was born. I'm simply proposing that evolutionary advance is guided by the genetic code itsef, pre-planning.

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I think the "gradualist Darwinian" answer to these abilities of the guppies and sticklebacks is that they have evolved these strategies by the usual gradual processes. 
> 
> 2 years for guppies to change and 3 years for sticklebacks is not gradual. -My point is that the guppies and sticklebacks have evolved the ability, over earlier millennia, to make this quick adaptation.

--
GPJ

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I think the "gradualist Darwinian" answer to these abilities of the guppies and sticklebacks is that they have evolved these strategies by the usual gradual processes. 
> > 
> > 2 years for guppies to change and 3 years for sticklebacks is not gradual. 
> 
> My point is that the guppies and sticklebacks have evolved the ability, over earlier millennia, to make this quick adaptation.-And my point is that all organisms have had this ability from a very early time, in the first one-celled organisms.

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Wow. I wrote this very nice reply to you, and then hit Send (in reply mode), as if it were a personal e-m, without hitting the link to bring me to this forum. Sorry if I seem a shade late; I was awaiting a response from you.-1. EXISTENCE is subjectively relative, on two levels: True/Relevant(?) and False/Irrelevant(?). Existence, then, becomes similar to the "I'm OK, You're Ok" quadrant, in the book by the same name. In Functional Reality, the objective and subjective constantly merge, diverge, merge and diverge, ad infinitum. I was forced to liken it to a water-level with two cross-hairs; Where that bubble wanders, within our psychology/ies, IS "reality" (for that moment, period, era, eon....)-Example: I know that my car exists, in my driveway. I just looked out the window, and, as I type, I KNOW it is there. Yet, if I sell my car, I still know that it exists, but that someone else is driving it. The same can be said of my ex-wife!!!!!!) So, although both exist, in my mind, their relevancy is seriously questionable. This is the bubble in the True/IRrelevant square. Now, in the True/RELevant square.....My house is on fire. DOES the fire "exist"? ... YES! It exists and IS extremely relevant.-The True/Relevant category contains things like bills, job, traffic, food, your pets, YOU, your laundry, etc. These are both True AND Relevant, since you have to deal with them daily. These include things in which you mostly have no choice but to make them both true AND relevant, or else you're in trouble.-The False/IRrelevant square contains things like whatever is splattered onto the pages of the magazines you're forced to look at, as you wait to pay for your groceries, movies - anything we manufacture for entertainment, or is not impinging upon your freedom. Whenever you don't care about something, it (might be) irrelevant; Whenever you know something isn't true, it (might be) false. Please notice the question marks, above, behind the names of these categories. This is to indicate that a judgment must be made, to find out where that bubble is, if you care at all.
 
You can mix and match these four qualifiers any way you'd like, except as indicated in the below-following sentence.-Here they are:-True
False
Relevant
Irrelevant-Please notice that they are mutually exclusive polarities! I.e., something CANNOT be both true AND false, nor relevant AND irrelevant, simultaneously, and constitute the cross-hairs of this "psy-levelometer". -2. Our eyes, ears, noses, mouths, and skin are SENSORS for our brains, through which our brains experience their surroundings. The sensors pick up signals from the environment, and send them to the brain; The brains then respond in accordance with one or many essential routines, and (we hope, we try...) to adjust our responses as we go. That is really the whole story about our subjective/objective interaction.-3. MY answer to your question about whether there is or is not an Intelligent Design going on.... -What you are really asking is: How did the complex cell become extant? One might accept the simple cell as inevitable, given evolutionary pressures; But how did the complex cell evolve???? The complex cell seems to need the Intelligent Design argument to resolve the issue.-However, what you might consider is that, in the same way that there evolved a simple cell, out of biological necessity, came the complex cell, given the extant, stable structure of the simple cell. Necessity is the key to understanding this concept.-Think of your own brain, in desperate need. You are hungry, afraid, etc. What happens? The original, basic subsistence cells form-up and interact with one another, chemically/molecularly, to create/devise new relations = ideas/notions, and you think/do things that would otherwise not have been conceivable even moments before the action.-It is the notion of "Intelligence" that needs to be clearly defined before a rational answer can be attained here. "Intelligence" is, now, as we've attempted to understand it, NOT a strictly human attribute, but an attribute intrinsic to "life" itself, as we have come to know it. Life, as we know it, follows a type of logic that is not familiar to our minds, which is why we even question both Intelligence, and Design, and then try to squish them into one seemingly coherent phrase!-Sir, I tell you, clearly - ALL things and developments EVOLVE! Our only problem is in finding, presently, the beginnings of it.-Please tell me your sense of this answer.-t

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Wow. I wrote this very nice reply to you, and then hit Send (in reply mode), as if it were a personal e-m, without hitting the link to bring me to this forum. Sorry if I seem a shade late; I was awaiting a response from you.-Let me warn you. Occasonally this forum has a hiccup and a reply does not post. I copy it, if it is of any length before submitting, and then I am protected from re-doing some brilliant comment.
> 
> What you are really asking is: How did the complex cell become extant? One might accept the simple cell as inevitable, given evolutionary pressures; But how did the complex cell evolve???? The complex cell seems to need the Intelligent Design argument to resolve the issue.
> 
> However, what you might consider is that, in the same way that there evolved a simple cell, out of biological necessity, came the complex cell, given the extant, stable structure of the simple cell. Necessity is the key to understanding this concept.-Chance appearance of even a 'simple cell' is not so simple, since the most simple of cells is, of itself, an extremely complex entity. My contention is there are no simple cells. The list of requirements for the smallest Mycoplasma reaches hundreds of structural protein molecules, many enzymes, and many injesting and ejecting processes. So I remain of the opinion that intelligent design is a requirement for any appearance of first life. Necessity can only come from an underlying driving force to bring life from inorganic matter, which of itself has no demonstable driving force.

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Mr. Turell - I completely agree with you. Even the simplest of life is so durned complex that it taxes the very outer limits of human ability to comprehend.-I fully believe that it is NOT a choice about whether or not there IS Intelligence (or Design) behind life, as this just seems so obvious as to be an utter waste of precious time. Rather, this choice needs to be sorted into a box that has not yet been built.-We humans have our various gods, and these gods are imputed with intelligence that we lack (or seem to lack, or as yet lack, or can never attain....etc.), and thus, as responsible Agnostics, we must find clearer, cleaner definitions for both "intelligent/ce" and "design/er", so that we can absolutely minimize anthropomorphic bias - though, admittedly, this is difficult in the extreme.-OR, to the contrary, if there actually IS a, or several, gods, working together, find ways to form this defining process to give credit to him/her/it/them.-All beings upon this Earth have their own specific expression/s of their 'intelligence', and, in demonstrating it, they also define their limitations; Although wasps can build exquisite nests, and spiders can build near-perfect webs, still, neither of them can fly. They function within their domains in Nature, and can't stray much beyond these tight areas. The 'intelligence' demonstrated, although brilliant, is reduced in value by its own lonely specificity. We alone seem to be the only beings who are extreme generalists. I constantly come to terms with myself about why this is so.-As I have these internal arguments, I often revert to my historical understanding of religious evolution, and how it is SOOOO easy to impute to some deity the understanding that we lack - and even that act lies strictly within the imperial domain of human intelligence. As far as can be yet demonstrated, no other other being does this.-What thinketh ye?

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Mr. Turell - I completely agree with you. Even the simplest of life is so durned complex that it taxes the very outer limits of human ability to comprehend.
> 
> What thinketh ye?-From my first post to you: > So I remain of the opinion that intelligent design is a requirement for any appearance of first life. Necessity can only come from an underlying driving force to bring life from inorganic matter, which of itself has no demonstable driving force.-I am the resident panentheist on this website. There is a universal intelligence which religions, who know no more than I do, call God. I do also in discussing my beliefs with others, but no religion has the truth.

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Mr. Turell - I completely agree with you. Even the simplest of life is so durned complex that it taxes the very outer limits of human ability to comprehend.-
I've expressed the opinion in the past that most junk DNA will turn out to be important layers of control of gene function. Now a finding of how the creation of small peptides is in control of embryonal development:-http://www.nature.com/news/2010/100715/full/news.2010.356.html

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TINY ERROR!-After I had submitted my last, I noticed that I had stated that a wasp couldn't fly. What I MEANT was that neither of these critters could do each others' job in Nature. The spider builds the web; The wasp flies around killing other bugs; Both of them have a skill-set, yet they are not interchangeable. They comprise a niche - and yet, if memory serves, strangely, wasps and spiders are genetically related in some degree. Anyway, sorry for any confusion.

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Tim, I've just returned from a family holiday and have read your very interesting response to my post of 4 July and the interchange between yourself and David.*** -First of all, I'm sorry you've had trouble posting items on the forum. As David says, it's always best to make a copy. I usually draft responses in WORD and then copy and paste before clicking on "submit".-I don't think there is any disagreement between us on the topic of subjectivity/objectivity, and I particularly like your additional category of relevance/irrelevance, which I'll come back to in a moment.-Concerning intelligence/design, you wrote that all things evolve, and "our only problem is in finding, presently, the beginnings of it." That observation lies at the heart of our discussion, and David's response concerning the complexity of the simplest of cells is one aspect of my own basic dilemma. The materialist argument seems to me deliberately to minimize the problem ... start with something simple, and evolution will inevitably lead to greater complexity. Wrong, wrong, wrong. The cell is NOT simple. We start with something so complex that it is able not only to reproduce but also, ultimately, to vary itself and adapt to changing conditions. And it is THIS initial mechanism (what you call "the beginnings of it") that we are expected to believe somehow managed to assemble itself spontaneously.-In your response to David, you have commented on this: "I fully believe that it is NOT a choice about whether or not there IS Intelligence (or Design) behind life, as this just seems so obvious as to be an utter waste of precious time. Rather, this choice needs to be sorted into a box that has not yet been built." I presume your "box" is a definitive description of this intelligence (you wrote: "It is the notion of Intelligence that needs to be clearly defined"), and of course we have no way of knowing its nature. All we can do is speculate. The basis of our speculation can only be our subjective assessment of the evidence before us, and this has nothing to do with science, which can only attempt to explain the technology behind the so-called design. A conventional theist will look at life and claim that the world is filled with evidence of the creator's consciousness and love for his creation. A conventional atheist will see life as an utterly impersonal process in which the world is governed by blind chance and the unconscious laws of Nature (which you rightly call "a type of logic"). David's panentheism involves a conscious designer, but none of the anthropomorphic trappings of the established religions. You have also mentioned the need to minimize "anthropomorphic bias". I would put forward two separate points here: 1) If you believe in CONSCIOUS design, is it not feasible that the design might reflect elements of the designer? In other words, the anthropomorphic elements are perhaps not imposed by the product (us) on the designer, but are the designer's reflection in the product. Could love and hate, a sense of beauty, imagination, reason come into being within us if they did not already feature in the conscious intelligence that produced us? 2) If, however, you believe that the creative force is unconscious and hence impersonal and without such attributes, I would take up your own categories, and suggest that this is a combination of (subjective) truth and irrelevance, in so far as it is a force with which we can have no relationship. (The latter argument also applies to a conscious deist God.)-One further aspect of my agnostic dilemma lies in the inevitable question: If the Universal Intelligence is conscious, where did its consciousness come from? If you can believe in the spontaneous generation of such a UI, you might just as well believe in the spontaneous generation of life on Earth (= atheism). -And so there, in brief, you have the confusing jumble of irreconcilable factors and possibilities that form the basis of my agnosticism. I wonder if they are also the basis of yours.--*** I will try to work my way through the remaining posts in the next couple of days.

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I copied out some of your paragraphs to me, so I can work with them.-"The materialist argument seems to me deliberately to minimize the problem ... start with something simple, and evolution will inevitably lead to greater complexity. Wrong, wrong, wrong. The cell is NOT simple. We start with something so complex that it is able not only to reproduce but also, ultimately, to vary itself and adapt to changing conditions. And it is THIS initial mechanism (what you call "the beginnings of it") that we are expected to believe somehow managed to assemble itself spontaneously."-I very often ponder this same problem while staring at bug so tiny that I had to go get a magnifying glass just to see it at all. There it is, walking around down there, with a life all its own, utterly unaware of anything else that doesn't having any meaning to it, nor could it conceive of all of us, walking around, utterly unaware of its existence. A theist would then, naturally, follow-out that example as proof that G/god MUST exist, but that we are like that bug, unable to fathom Him. One bug saying to another, "YES there are humans!", while the others laugh at him, saying, "You ever SEE any of these humans?!" "No, but sometimes I get these feelings like I'm being WATCHED from 'out there, somewhere...'"-Also, you mentioned that materialists deliberately minimize this problem. I ardently agree with this, but with the additional statement that "This is just what we DO." I believe this is how G/god/s themselves evolved as they wove themselves into and throughout human social patterns of thought and behavior. Ever notice how, in every culture I have heard of, the religiosity moved from many gods, to a few important ones, and then, after thousands of years, merged into the one god most of us have today? This is minimalization, which is simply another version of "efficiency" of one's belief structure. Humans are superbly adept at finding simpler ways of doing things. In life, its just a way of making work easier and faster; In beliefs, its a way of reducing complexity, and directing ones efforts at obedience and reverence much simpler. That's why we have nicknames, abbreviations, acronyms, better and better tools and instruments, etc. So, when dealing with something as incomprehensively complex as Life, we just call it "Survival of the Fittest", and be on our merry way. That's another aspect of Functional Reality, especially with regard to capitalism, where, if one's company is not 'fit', it will be gobbled up by some fitter predator, vis., Walmart. In religion/s, whomever has the most efficient god, wins (minus the fear factor, present in Islam - I wonder how many "adherents" would pray five times a day without the peer pressure, or fear of their authority structure?!).-Re: Your philosophical (agnostic) consternation, given how difficult this way is. I agree, it is (or was, for me). I was driving myself MAD with all these imponderables. I vowed to devise a way for me to, basically, chill out, and to find some kind of solace in my emotional stultification. I did find a way out. I worked on what was truly essential and true in life, and tossed out the rest as being various degrees of irrelevance. I did this so that I could focus better in my life, and it has helped me. It also accidentally-on-purpose became the perfect acronym. I have, since ten years ago, mainly focused on six primary thought/behavior factors. These are: Science, Organization, Logic, Appreciation, Communication, and Edification (SOLACE). Every time I get too wound-up, I just say "SOLACE" to myself, and everything gets itself automatically "filed" into the "I'll get to that later. Right now, I have something of higher priority in mind."-Is that cool, or what?-Now, as to whether or not the Universe is "intelligent" (which we have not yet defined, BTW), I already know that it IS, but, like the bug I mentioned, is, as yet, beyond my ken, and so I just "play the ball where it lies" every day. It turns out to be a zen thing, really, as you just function within the on-going time-periods, as they pass by each day, while secretly hoping that we'll someday figure it out. Meanwhile, I just have to do my life the best I can figure it out.-However, I will state now, and I'm pretty sure we agree, that the God of the religions we have now is NOT the God of "how things actually are". Christians want us all to have a personal relationships with God; Jews just want us to read the Torah; Muslims, the Koran, etc., but, I get a whole different feel/think for the God thing. No time for that now, but some other time.-My neighbor's cow is out, and walking down the road. Have to get her back.-Hope to hear from you.-t

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Tim imagines one bug telling another that there are humans, while others laugh at him. 
If you care to scroll back to the thread An Analogy, you will find a little poem posted on Friday 23 October 2009 at 11.19, which may give you a chuckle.-You have extended my observation about materialists minimizing the problem of complexity to a general human tendency towards simplification, e.g. reducing multiple gods to one. You are right. It is said that even the many Hindu gods are in fact simply aspects of the one supreme being (Brahma). You also relate this principle to "Functional Reality" and capitalism. On an earlier thread we discussed the reductive manner in which we use language to kid ourselves that we understand phenomena which in fact are a total mystery to us. A typical example is our identification of mental faculties such as consciousness, the unconscious, reason, memory etc. Most people will assume that the terms actually explain the process, whereas in fact we haven't a clue how any of these areas of our mental activity work. 95% of the universe is unknown to us, so we call this "dark matter" and "dark energy", and we use the terms as if they actually meant something. "God" is probably the best example of all. No matter what name you give him, it is just a word to denote something unknowable. Perhaps this is the only way we can deceive ourselves into thinking we have a grasp of ultimate realities.-Your thought/behaviour acronym of SOLACE does indeed sound like a petty "cool" way of organizing priorities. Like George I enjoy puzzles, and you set me off on the trail of more general lifestyle priorities, though I'm going to cheat by making this plural as I have two indispensable Ss. How about Science, Orderliness, Love, Art (= the arts), Cash, Empathy, Sport? -As regards your feeling that if there is a God, it's not the God of the established religions, yes, we agree. But most religions may have a central core of truth in them, since there is certainly some kind of life force responsible for our existence. I include religions which we in the West arrogantly label primitive (why should a totem pole be seen as more primitive than a cross, or a dance as more primitive than the Eucharist?). I don't see much difference between venerating Jehovah, Allah, the Earth Diver or Mother Nature. What irks me is the arrogance of those who claim to know the precise nature of that life force and are intolerant of those who do not share their subjective vision of the worlds we know and don't know. This group ranges from religious to atheistic fundamentalists. -I hope you managed to recapture your neighbour's cow.

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dhw appears to have undergone some sort of conversion experience on his holiday: "As regards your feeling that if there is a God, it's not the God of the established religions, yes, we agree. But most religions may have a central core of truth in them, since there is certainly some kind of life force responsible for our existence." Agnostic no more!

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GPJ

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GEORGE: dhw appears to have undergone some sort of conversion experience on his holiday: "As regards your feeling that if there is a God, it's not the God of the established religions, yes, we agree. But most religions may have a central core of truth in them, since there is certainly some kind of life force responsible for our existence." Agnostic no more!-I thought that even the most rabid of atheists would have to acknowledge that there is some kind of "life force" at work, and I chose the expression carefully in order to avoid any link to the divine. Evidently I was not careful enough! I concluded: "What irks me is the arrogance of those who claim to know the precise nature of that life force", the range of which extended from religious to atheistic fundamentalists. I have no complaint if, for instance, theists believe the life force is conscious and caring, or atheists believe it is a mixture of unconscious chance and the impersonal laws of Nature. I only complain if they are "intolerant of those who do not share their subjective vision of the worlds we know and don't know." So rest assured, George, I remain, as ever, yours indecisively,
 
dhw.

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dhw thought that: "even the most rabid of atheists would have to acknowledge that there is some kind of "life force" at work".-Certainly not! There is no evidence for any such "elan vital". This is a reversion to primitive "vitalism".-dhw has no complaint if "atheists believe it is a mixture of unconscious chance and the impersonal laws of Nature".-Such a process cannot be described as a "life force". To give it such a name implies surely that it is purposive towards the creation of life, or that it is somehow motivated and possesses some primitive form of life within itself.

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GPJ

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PART TWO-GEORGE: Even in the objective world there are arguably degrees of existence depending on the amount and certainty of evidence backing them up. For instance historical and legendary characters or events. There is a sense in which the past fades away as evidence and memory is eroded by time. -It's insights like this that warm my heart, because in a few words George has encapsulated one of the great problem areas of human culture: memory. Before writing was invented, humans relied on oral tradition for stories to be handed down, and by the time the stories were written, who knows how many embellishments they'd undergone? David has pointed out that the gospels were written long after Christ's death. No-one knows exactly when ... I've read that it was between 60 and 100 AD, though Christians try to make it as early as possible! These are not first-hand accounts, and they are not based on authenticated evidence, and may even in part be based on each other. Josephus's two brief mentions of Christ are also highly suspect. I'm not saying Christ didn't exist, but how can we possibly know which stories are true? Let me offer you some titbits from Jan Assmann's monumental work on memory (not yet published in English), drawing here on Maurice Halbwachs: "Christian topography is pure fiction. The holy sites do not commemorate facts attested to by contemporary witnesses, but they represent ideas of faith whose roots were sunk there long after the events." "When Paul came on the scene...the focus of memory shifted from Galilee to Jerusalem. Here there are absolutely no 'authentic memories', because the trial and execution of Christ took place in the absence of the disciples." "The new idea, made binding by the Council of Nicea [325 AD], was that Jesus as the Son of God died to redeem the sins of mankind. This took on the status of memory, and became a memory figure as the story of the Passion." And it's not just Christian "history" that becomes a blur. The Exodus is absolutely central to Judaism, but its historicity is also a matter of great controversy. -Under "Refutation"...17 February at 18.42 (but do please put future posts on this thread), Matt says he can't recall many cases where "such a rich mythology was built round person(s) who didn't exist at all." When Christians read that Christ was born of a virgin in a manger, they probably regard that as history; but are they equally impressed when they hear that the Lord Krishna was born in a dungeon that shone with a mysterious light, or that my Dogon friends Amma and Nommo came out of an enormous egg, or that Minerva sprang fully armoured from the brain of Jupiter? All of these are associated with a rich mythology.-We can't even kid ourselves that modern history is objective. It's constantly been rewritten, and the more powerful the ruler(s), the less reliable the history. And so we finish with the same question as before: is it possible to separate subjective perception and/or interpretation from the objective world? The past fades away as evidence, and memory is eroded by time...(I'm only repeating this because I like it so much)...and human culture, like everything else in the history of our world from its very beginnings, becomes shrouded in mystery. Thank you, George.

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Following on from a thought that I expressed in the thread on mathematics, I wonder if a lot of argument might be avoided if we agreed that "existence" can occur in different degrees or categories? 
> 
> For instance dhw and DT lay much emphasis on subjective experiences and anecdotal evidence that I would discount. Perhaps claims based on such experiences can be said to refer to concepts having "subjective existence". Perhaps this is another name for "faith". Is it possible to separate arguments about things in the subjective world from those in the objective world? Perhaps this is what is meant by Gould's NOMA (non overlapping magisteria).
> 
> Even in the objective world there are arguably degrees of existence depending on the amount and certainty of evidence backing them up. For instance historical and legendary characters or events. There is a sense in which the past fades away as evidence and memory is eroded by time.-This is exactly the direction I wanted to go. Though, I hesitate at what kind of meaningful discussion can be had when there's a general disagreement on how we should treat subjective claims. Mayhaps we should lay a groundwork?

--
\"Why is it, Master, that ascetics fight with ascetics?\"

\"It is, brahmin, because of attachment to views, adherence to views, fixation on views, addiction to views, obsession with views, holding firmly to views that ascetics fight with ascetics.\"

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Anecdotal evidence from a senior policeman:-http://www.thisiswesternmorningnews.co.uk/news/PRAYER-CRACK-CRIME/article-1851685-detail/article.html?cacheBust=791v088PpHB9&success=true#community-Would you accept this as evidence?

--
GPJ

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Anecdotal evidence from a senior policeman:
> 
> http://www.thisiswesternmorningnews.co.uk/news/PRAYER-CRACK-CRIME/article-1851685-detai... 
> Would you accept this as evidence?-Only with a control group praying for the criminals or for more accidents )

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George has referred us to an article in which a senior policeman attributes reductions in accident rates and an increase in detection rates partly to the power of prayer. George asks if we would accept it as evidence.-This is a great idea. We can solve our national debt crisis at a single stroke. We'll get rid of the police force, health service, social welfare and armed forces, and hand control to the mighty monks at the Monastery of St Miraculoso.-My thanks to George for a fun post ... or it would be if Inspector Bartlett didn't expect to be taken seriously. Let's all pray to win the lottery, and when we don't, we can write and tell him we've proved God doesn't exist.-This could also be an exciting new game. We can call it TESTING CREDULITY. My turn now: how many chimpanzees with unlimited brushes and paints do you reckon it would take to produce Michelangelo's Sistine Chapel?

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> This could also be an exciting new game. We can call it TESTING CREDULITY. My turn now: how many chimpanzees with unlimited brushes and paints do you reckon it would take to produce Michelangelo's Sistine Chapel?-As long as they could be trained to lie on their backs for hours at an end doing the ceiling as Mike did, I think it would work. George took this, I think from the 'prayers for the sick' studies of about ten years ago. The anonymous studies were somewhat sugggestive (the patients didn't know they were prayed for) but it was impossible to set up control groups, one study was fudged, and finally I've not heard of more studies being done.

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DHW: This could also be an exciting new game. We can call it TESTING CREDULITY. My turn now: how many chimpanzees with unlimited brushes and paints do you reckon it would take to produce Michelangelo's Sistine Chapel?-DAVID: As long as they could be trained to lie on their backs for hours at an end doing the ceiling as Mike did, I think it would work. -No, no, no, David, you're breaking the rules! No training allowed. No trainers, you see. There's nothing/nobody/nichts/niemand/nada/nadie/niente/nessuno to give guidance. The chimps of chance are entirely on their own!

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DHW: This could also be an exciting new game. We can call it TESTING CREDULITY. My turn now: how many chimpanzees with unlimited brushes and paints do you reckon it would take to produce Michelangelo's Sistine Chapel?
> 
> DAVID: As long as they could be trained to lie on their backs for hours at an end doing the ceiling as Mike did, I think it would work. 
> 
> No, no, no, David, you're breaking the rules! No training allowed. No trainers, you see. There's nothing/nobody/nichts/niemand/nada/nadie/niente/nessuno to give guidance. The chimps of chance are entirely on their own!-Well then 100 if enough bananas are hanging from the ceiling at each picture site, especially in the center where God and Adam touch fingers solving the issue of origin of life.

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More anecdotal evidence people take seriously.-House of Commons Science and Technology Committee says National Health Service wasting millions promoting homeopathic hospitals.-http://news.bbc.co.uk/1/hi/health/8524926.stm-A speaker on the news today claimed that the committee was being "fundamentalist".-Real evidence: None dead in homeopathic overdose:-http://blog.newhumanist.org.uk/2010/02/none-dead-in-mass-homeopathic-overdose.html

--
GPJ

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More anecdotal evidence people take seriously.
> 
> House of Commons Science and Technology Committee says National Health Service wasting millions promoting homeopathic hospitals.
> 
> http://news.bbc.co.uk/1/hi/health/8524926.stm
> 
> A speaker on the news today claimed that the committee was being "fundamentalist".
> 
> Real evidence: None dead in homeopathic overdose:
> 
> http://blog.newhumanist.org.uk/2010/02/none-dead-in-mass-homeopathic-overdose.html-Had no idea such still existed anywhere. The one in N.Y. started homeopathic , by the 1920's added allopathic treatment, and by the time I applied to med school, was no longer homeopathic. Now called N.Y. Med., was "Flower & Fifth Ave" by common parlance back when I was a kid.

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My family and many of my friends have used homepathics for years. I know it works better in some situations than allopathic meds, and as mentioned below, no one (or animal) would ever die by an overdose, unlike many allopathic meds. I personally do believe in faith but do not believe faith is what is relieving the baby's teething or a horse/cat/dog's ailment, etc., when given homeopathics. I've too many years experience with it to fall for the placebo explanation. I'm sure many of those who are invested in big pharma will be doing whatever they can to campaign against anything that might take a bite out of their profits. I don't think it will change the opinions of those who have used these remedies and have very good experiences with them for years. --> More anecdotal evidence people take seriously.
> 
> House of Commons Science and Technology Committee says National Health Service wasting millions promoting homeopathic hospitals.
> 
> http://news.bbc.co.uk/1/hi/health/8524926.stm
> 
> A speaker on the news today claimed that the committee was being "fundamentalist".
> 
> Real evidence: None dead in homeopathic overdose:
> 
> http://blog.newhumanist.org.uk/2010/02/none-dead-in-mass-homeopathic-overdose.html

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My thanks to George for drawing our attention to another interesting example of "anecdotal evidence", in this case homeopathy.-Like BBella, I know several people who swear by it, and if didn't work at all, the practice would have died out long ago. However, what interests me in the context of our discussions is how it works if it really is a sham (I don't know enough about it to make a judgement). Yet again, it's language that makes us think we've got it covered. We talk of "placebos" and "autosuggestion" as if that were an explanation. It isn't. Those are just words to describe an extraordinary and incomprehensible process. Initially there's something wrong with the body. People are given a useless medication which they believe will help them, and just because they believe it.....what happens next? Certain cells in their brains release certain chemicals which set in motion the body's own remarkable mechanisms of self-healing. How's it done? Sometimes the trick doesn't work, and you may get the opposite, "nocebo" effect ... but it's still the same mystery of consciousness, of what controls the brain cells, and how the "will" of the cells can influence other areas of the body.-What is the "placebo effect" evidence of? Perhaps I should have objected earlier to the word "evidence", because it carries too much weight. In my subjective view, until we get a satisfactory physical explanation of how consciousness works, it suggests the possibility (no more) that the mind is not simply a matter of brain cells.

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dhw writes: "Thanks to George for drawing our attention to another interesting example of "anecdotal evidence", in this case homeopathy. / 
Like BBella, I know several people who swear by it, and if didn't work at all, the practice would have died out long ago."-The fact that people swear by it doesn't mean it actually works, only that they believe it does.-dhw asks: "However, what interests me in the context of our discussions is how it works if it really is a sham (I don't know enough about it to make a judgement)."-Homeopathy doesn't work. People come to think it does work by erroneous reasoning. They take the medicine and the problem clears up, so they attribute the cure to the medicine, when it probably got better quite naturally. In other cases the problem doesn't clear up, so they try something else.-The idea that people get better because of the psychological effect of their own belief in the efficacy of the medicine is another issue altogether. There does seem to be some truth in this, as experiment shows, but the effect can only work in a very limited range of problems, say where relaxation is an aid to the body's natural processes.

--
GPJ

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GEORGE: Homeopathy doesn't work. People come to think it does work by erroneous reasoning. They take the medicine and the problem clears up, so they attribute the cure to the medicine, when it probably got better quite naturally.-As I haven't done any research on the subject, and have no first-hand experience, I stated in my post that I couldn't make a judgement. I don't know how much research you've done yourself, George, to be able to make your authoritative statement, but in any case my post focused on the placebo effect, i.e. "the mystery of consciousness, of what controls the brain cells, and how the "will" of the cells can influence other areas of the body." Your only comment on this is that "the effect can only work in a very limited range of problems, say where relaxation is an aid to the body's natural processes." I don't suppose you would regard the body's self-healing processes as a mystery either, though I wonder how many man-made mechanisms you know of that can put themselves right with no outside intervention.-On a lighter note, yesterday's Guardian carried an article about the new president of the Flat Earth Society. Daniel Denton argues (seriously) that the Earth is flat because it appears flat, and the sun and moon (which are much smaller than mainstream science says) rotate around a plane of the Earth, because they appear to do so. His beliefs entail the non-existence of gravity, and the contention that most space exploration, including the moon landings, is faked. He also says, "There is no unified flat Earth model, but the most commonly accepted one is that it's more or less a disc, with a ring of something to hold in the water. [...] most people think it's mountains with snow and ice." -In my eagerness to help, I have been doing some intensive googling, and to my delight came across a book entitled: 
Homeopathy ... Beyond Flat Earth Medicine by Timothy R. Dooley.-Perhaps he can be persuaded to write a sequel: 
Flat Earth ... Beyond Homeopathy Medicine

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The following is a question set for a University of Arizona mid-term chemistry exam. The answer by one student was so 'profound' that the professor shared it with colleagues, via the internet, which is why we now have the pleasure of enjoying it as well:-Bonus Question: Is Hell exothermic (gives off heat) or endothermic (absorbs heat)?-Most of the students wrote proofs of their beliefs using Boyle's Law (gas cools when it expands and heats when it is compressed), or some variant. One student, however, wrote the following:-First, we need to know how the mass of Hell is changing in time. So we need to know the rate at which souls are moving into Hell and the rate at which they are leaving, which is unlikely. I think that we can safely assume that once a soul gets to Hell, it will not leave. Therefore, no souls are leaving. As for how many souls are entering Hell, let's look at the different religions that exist in the world today.-Most of these religions state that if you are not a member of their religion, you will go to Hell. Since there is more than one of these religions and since people do not belong to more than one religion, we can project that all souls go to Hell. With birth and death rates as they are, we can expect the number of souls in Hell to increase exponentially. -Now, we look at the rate of change of the volume in Hell because Boyle's Law states that in order for the temperature and pressure in Hell to stay the same, the volume of Hell has to expand proportionately as souls are added.-This gives two possibilities
1. If Hell is expanding at a slower rate than the rate at which souls enter Hell, then the temperature and pressure in Hell will increase until all Hell breaks loose.
2. If Hell is expanding at a rate faster than the increase of souls in Hell, then the temperature and pressure will drop until Hell freezes over. 
So which is it?-If we accept the postulate given to me by Teresa during my Freshman year that, 'It will be a cold day in Hell before I sleep with you', and take into account the fact that I slept with her last night, then number two must be true, and thus I am sure that Hell is exothermic and has already frozen over.-The corollary of this theory is that since Hell has frozen over, it follows that it is not accepting any more souls and is therefore, extinct...leaving only Heaven, thereby proving the existence of a divine being which explains why, last night, Teresa kept shouting 'Oh my God.'-The student was given an A+.

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dhw: "As I haven't done any research on the subject, and have no first-hand experience, I stated in my post that I couldn't make a judgement. I don't know how much research you've done yourself, George, to be able to make your authoritative statement,"-It seems dhw is unable to trust anyone, certainly not anyone calling themselves a scientist, and has to carry out his own experiments. There's plenty of literature on the subject from reliable sources. The report of the Science and Technology Committee being only the latest. Of course, statements from practitioners of homeopathy need to be treated with caution.

--
GPJ

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> ... but it's still the same mystery of consciousness, of what controls the brain cells, and how the "will" of the cells can influence other areas of the body.
> 
> What is the "placebo effect" evidence of? Perhaps I should have objected earlier to the word "evidence", because it carries too much weight. In my subjective view, until we get a satisfactory physical explanation of how consciousness works, it suggests the possibility (no more) that the mind is not simply a matter of brain cells.-Here is another article onthe thought that it is consciousnes that gives us an illusion that we have free will. The author states that a small part of the proof is how different identical twins are, raised in the same environment. This is garbage. All the studies show that identical twins, raised apart, are extremely similar.-http://www.physorg.com/news186830615.html

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David has referred us to an article by Anthony Cashmore, Professor of Biology at the University of Pennsylvania, who argues that:
 
"a belief in free will is akin to religious beliefs, since neither complies with the laws of the physical world. One of the basic premises of biology and biochemistry is that biological systems are nothing more than a bag of chemicals that obey chemical and physical laws."-And as far as he's concerned, for the rest of the article that's it! He assumes that because he considers physical explanation to be one of the basic premises of his subject, there can't be any other explanation. Presumably, then, there can be no such person as a religious or agnostic biologist or biochemist. I see no difference between this level of argumentation and the claim that because no answer has yet been found to the mystery of consciousness, we must all have souls.-Professor Cashmore's reflections on the justice system remind me of discussions in my schooldays about the degree to which humans can be held responsible for their actions. We argued then, as we argue now, that our characters are formed by heredity, environment and chance events, and even if we have free will, it's impossible to measure the extent to which our decisions are influenced by these factors, which are all outside our control. Long before the advances of neuroscience, I remember arguing that the purpose of the justice system should not be retribution but the protection of society (I agree with his opposition to the death penalty). The question of whether consciousness ... and by extension the will ... is or is not engendered by the "bag of chemicals" makes little difference to this overall argument, while Cashmore's assumption that science will eventually confirm his prejudgement tells us quite a lot about him and absolutely nothing about these unexplained phenomena.

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