Evolution needs a library of Platonic forms?

_{Denyse O'Leary

March 17, 2015

Evolution, Intelligent Design, News}

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Well, then it sure isn’t “evolution” as National Geographic understands it.

This just in from Andreas Wagner at Aeon:

How do random DNA changes lead to innovation? Darwin’s concept of natural selection, although crucial to understand evolution, doesn’t help much. The thing is, selection can only spread innovations that already exist. The botanist Hugo de Vries said it best in 1905: ‘Natural selection can explain the survival of the fittest, but it cannot explain the arrival of the fittest.’ (Half a century earlier, Darwin had already admitted that calling variations random is just another way of admitting that we don’t know their origins.)

A metaphor might help to clarify the problem. Imagine a giant library of books containing all possible sequences of letters in the alphabet. Such a library would be huge beyond imagination, and most of its texts would of course be pure gibberish. But some would contain islands of intelligibility – a word here, a Haiku there – in a sea of random letters. Still others would tell all stories real and imagined: not only Dickens’s Oliver Twist or Goethe’s Faust, but all possible novels and dramas, the biography of every single human, true and false histories of the world, of other worlds as yet unseen, and so on. Some texts would include descriptions of countless technological innovations, from the wheel to the steam engine to the transistor – including countless innovations yet to be imagined. But the chances of choosing such a valuable tome by chance are minuscule.

Just think, even in the age of National Geographic, someone is actually looking at the problems seriously.

But then, didn’t Aeon also publish “Die, Selfish Gene, Die”?

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Comments

We try to make claims for which we have scientific support.
Unfortunately you don't seem to know what "scientific support" entails.
They tried to evolve a cat into a dog, when the theory of evolution doesn’t posit such a transition.
Please link to this alleged theory of evolution so we can see what it says. And what prevents such a transition?Joe_{March 23, 2015
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Silver Asiatic: basically, make a bold statement with a tremendous sense of confidence – knowing it is unsupported by fact. We try to make claims for which we have scientific support. However, we are always willing to listen to arguments and look at contrary evidence.Zachriel_{March 23, 2015
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Box
creating the illusion that there is some kind of debate going on
That's it. He's pretty good at it, if you don't pay attention to what is really said. The best trick he uses is to make assertions on highly-contested topics as if he has the final (and only) answer. It's a tactic similar to what is found in Rules for Radicals ... basically, make a bold statement with a tremendous sense of confidence - knowing it is unsupported by fact. You'll win over some undecideds by the sheer force of your conviction. Darwinian evangelization.Silver Asiatic_{March 23, 2015
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Aurelio, you and Zachriel are clueless. This is similar to black-and-white arguments that neither mutation nor natural selection are ‘creative’, when the claim is that it is the interaction between the two that leads to adaptation. Umm natural selection INCLUDES mutations, Zachriel. It is sad to see evos being ignorant of their own position's concepts. But it is typicalJoe_{March 23, 2015
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Zachriel #50, If I were a moderator of this forum I would delete the kind of posts you produce. To the perceptive onlooker it should be obvious that you are not addressing my arguments. You quote me and write something irrelevant in return, creating the illusion that there is some kind of debate going on, but actually there is nothing there.Box_{March 22, 2015
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Box: Collections of particles without any sophisticated level of organization, like in your examples, is exactly what we can expect given purely natural unguided forces – nothing more and nothing less. Your original contention concerned dynamic equilibrium – homeostasis. In any case, most materialists consider life to be expected given purely natural unguided forces. Box: ‘Rain’ or ‘sun’ are agglomerations of parts, no entities. The Sun's not an entity? It even has a name, Sol. Box: And a pile of rocks can be in stasis for even longer periods of time. You were discussing dynamic equilibrium. Box: Answer me this: why do organisms “don’t fall completely apart — as they do, in fact, at the moment of death. What power holds off that moment — precisely for a lifetime, and not a moment longer?” Your "moment longer" is tautological. The North Atlantic Gyre has had a longer life than any human. Metazoans apparently have a limited lifespan. This is thought to be insurance for continued evolution. Box: "Rather than becoming progressively disordered in their mutual relations (as indeed happens after death, when the whole dissolves into separate fragments), the processes hold together in a larger unity." Sure. Even bacteria cooperate. Box: Clusters of particles with rather easy to explain (by natural law) structures is IMO exactly what can be expected by blind particles in motion. Ease of explanation is not a valid reason to discount the possibility of explanation for something complex. Or the flooding of the Nile is due to the good graces of Hapi. http://upload.wikimedia.org/wikipedia/commons/thumb/1/1e/Hapy_tying.svg/2000px-Hapy_tying.svg.png gpuccio: Everything is possible. But here, we must look for what is likely, and for what can explain as a general principle the emergence of tons of complex functional information. Scenario c is a valid counterargument to "Either genes evolve according to scenario a), or they evolve according to scenario b). Furthermore, it illustrates your black-and-white thinking. Gene promiscuity is an overlap between your false dichotomy. As for what is possible, many, if not most, enzymes are promiscuous. gpuccio: Drift and selection are different. I don’t know what you mean by “mutually exclusive”, but selection is not drift. This, again, illustrates your black-and-white thinking. A gene may drift a little, then be subject to selection, then drift a little more. This is similar to black-and-white arguments that neither mutation nor natural selection are 'creative', when the claim is that it is the interaction between the two that leads to adaptation. gpuccio: That paper is very good work. They tried to evolve a cat into a dog, when the theory of evolution doesn't posit such a transition. Rather, cats and dogs share a common ancestor. Furthermore, point mutation is almost always going to be insufficient to cross functional spaces.Zachriel_{March 22, 2015
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DNA_Joke:
What is it with IDists and false dichotomies? Here’s something to consider gpuccio: the genes might be “somewhat functional”.
What is it with evos and their inability to read? When gpuccio said that is being and remaining functional until they change to another functional form,, that encompasses DNA_Joke's " the genes might be “somewhat functional”". As for being fatally flawed, conceptually, that would be unguided evolution. The posited mechanisms are known to be impotent so it doesn't matter how many needles there are, they are all safely out of the reach of the blind watchmaker- see "waiting for two mutations"Joe_{March 21, 2015
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Piotr @47 has already dealt with your misconceptions re ‘selection’ and ‘drift.’ I think there’s a more general problem here. Gpuccio @30
Excuse me, but you cannot have it both ways. Either genes evolve according to scenario a), that is being and remaining functional until they change to another functional form, or they evolve according to scenario b), from non functional forms which are free to change “neutrally” by definition, because they are not functional.
What is it with IDists and false dichotomies? Here’s something to consider gpuccio: the genes might be “somewhat functional”. Your insistence that it must be either (a) or (b), steadfastly ignoring the continuum between (a) and (b), is sad. We understand quite well how promiscuous enzymes can diverge to perform quite distinct, highly specific functions following gene duplication. Hold that thought in your mind for a minute. When Piotr notes
The Gauger–Axe paper is a joke — comparable to a demonstration that since a bat can’t evolve into a whale or vice versa, they can’t be related. The “splendid isolation” of functional islands is exaggerated
Gpuccio replies
You are very unfair. That paper is very good work. It shows exactly what it shows: that two very similar structures, with very similar functions, are more that 2 mutation distant. The authors derive some conclusions from that, with which I essentially agree. You can derive different conclusions. That is your privilege. But the paper itself is good and hard work, and it shows important facts, which everyone should seriously consider.
If anything, Piotr is being too kind. The paper represents a minimal amount of work, poorly designed and (this is the only criticism that matters) fatally flawed, conceptually. Piotr’s comparison to “bat-to-whale” evolution is absolutely correct. I am pretty sure that I have directed you [gpuccio] to my attempt to explain this to Mung. http://theskepticalzone.com/wp/?p=1472&cpage=7#comment-19065 Mung was also confused about dimensionality; but he’s an IDist, so it pretty much goes without saying.DNA_Jock_{March 21, 2015
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Gpuccio (on selection vs. drift),
I absolutely disagree. Maybe it is sometimes difficult to separate them in some experimental context (but it is probably possible to do that), but it is certainly possible, and dutiful, to separate them as concepts and models. What you say is like saying that it is not correct to regard gravitation and electromagnetism as separable processes. Different mechanisms and different things must be conceived and modeled and analyzed as separate processes. What do you mean?
Evolution = changes in allele frequency in a population over a large number of generations. If you concentrate on the alleles of a given locus, what happens from generation to generation is repetitive resampling -- a stochastic process, which leads to the fixation of some alleles and to the elimination of others. If there is no bias in the process (fixation or eliminations takes about as much time as you would expect simply as a consequence of the size of the effective population), we regard is as neutral "random drift". If there is a bias (fixation or elimination happens faster than the neutral expectation), we call it "selection". If the effective population is huge, you can say that the effect of drift is minimal (though you can't say it doesn't exist), and its easier for bias to take effect. In real-world populations we have a bit of the one and a bit of the other. It would be wrong to reify drift and selection as different separable "components": you can't say, for a given fixation, that it was caused only by drift or only by selection, or 26% by drift and 74% by selection (their joint effect is not even strictly additive!). You can say that a given evolutionary process is more "drift-like" or "selection-like", but there is no natural cut-off point between them. Note also that a locus may be "under selection" for reasons other than being advantageous or deleterious (it may be linked to a selected allele at another locus -- the hitchhiking effect), and that there can also be a bias against fixation (balancing selection). Resampling is reality. Drift, draft, positive/negative/balancing selection are our convenient labels for various typical "special scenarios". They help us to analyse and understand the stochastic process, but one shouldn't read too much into them.Piotr_{March 21, 2015
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Piotr: "The Gauger–Axe paper is a joke — comparable to a demonstration that since a bat can’t evolve into a whale or vice versa, they can’t be related. The “splendid isolation” of functional islands is exaggerated." You are very unfair. That paper is very good work. It shows exactly what it shows: that two very similar structures, with very similar functions, are more that 2 mutation distant. The authors derive some conclusions from that, with which I essentially agree. You can derive different conclusions. That is your privilege. But the paper itself is good and hard work, and it shows important facts, which everyone should seriously consider.gpuccio_{March 21, 2015
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Zachriel: "Genes can become promiscuous (have a secondary function), then duplicate, to form new genes. This was already mentioned above." Everything is possible. But here, we must look for what is likely, and for what can explain as a general principle the emergence of tons of complex functional information. Simply saying: "this could happen" is not an answer.gpuccio_{March 21, 2015
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Piotr: "There’s no reason why (a) and (b) should be mutually exclusive, any more than “drift” and “selection” are mutually exclusive" The problem is not that they are "mutually exclusive". They are simply different. The key point, as always, is the role of NS. If variation happens in a coding, or anyway functional, gene, NS can act, and often it will act. IOWs, we have functional consequences of the variation, whatever they are. If variation happens in a non functional sequence, the variation itself will be "invisible" to NS (unless a new function arises). The two things are quite different. Drift and selection are different. I don't know what you mean by "mutually exclusive", but selection is not drift. Selection implies an effect on reproductive fitness. Drift is by definition independent from that. So, if drift happens, it is not selection. If selection happens, it is not drift. Of course, both things can happen in some complex context, but still they are not the same process. You say: "it isn’t even quite correct to regard them as separable processes". I absolutely disagree. Maybe it is sometimes difficult to separate them in some experimental context (but it is probably possible to do that), but it is certainly possible, and dutiful, to separate them as concepts and models. What you say is like saying that it is not correct to regard gravitation and electromagnetism as separable processes. Different mechanisms and different things must be conceived and modeled and analyzed as separate processes. What do you mean?gpuccio_{March 21, 2015
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And “blind particles in motion” can form into galaxies, cyclones, snowflakes, fusion reactors, the Giant’s Causeway, buckminsterfullerenes, auroras, lightning, pulsars.
In an Intelligently Designed universe, yes.
Your argument would suggest that these forms can’t exist under materialism, which would probably surprise a lot of materialists.
Materialists cannot account for those forms other than saying they just happened. With materialism what isn't an accident emerged from accidents. It's sheer dumb luck all the way down...Joe_{March 21, 2015
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Here we go with the homeostasis nonsense again. -why do organisms “don’t fall completely apart — as they do, in fact, at the moment of death. What power holds off that moment — precisely for a lifetime, and not a moment longer?”- Are you kidding me? What a joke.Curly Howard_{March 21, 2015
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Zachriel,
Zach: Most materialists certainly don’t think life can’t be accommodated in their philosophy, or they probably wouldn’t be materialists.
Most materialists are not aware of the problems that homeostasis poses for their belief.
Box: Given materialism there is no particle or wave that gives a hoot about neither the organism nor its continued existence – homeostasis.

Zach: Particles and waves don’t give a hoot about whether the sun shines, or whether the rains come. That doesn’t mean these processes are “not what we can expect given purely natural unguided forces.”
Collections of particles without any sophisticated level of organization, like in your examples, is exactly what we can expect given purely natural unguided forces - nothing more and nothing less.
Zach: It turns out that particles and waves can do all sorts of interesting things even though they have neither interest nor give hoots about rain or sun.
‘Rain’ or ‘sun’ are agglomerations of parts, no entities. In my philosophy the distinction is essential – not in yours to be sure.
Box: Again: why would a bag of chemicals – the “organism” – perform a delicate balancing act GIVEN MATERIALISM?

Zach: Notably, cyclones can be in stasis for long periods of time. For instance, the Great Red Spot on Jupiter is centuries old, as is the North Atlantic Gyre.
And a pile of rocks can be in stasis for even longer periods of time. Obviously the solid structure and the stasis of these agglomerations can be explained by natural law. However most organisms are unstable structures – after death they readily disintegrate. Still these unstable structures don’t fall apart exactly for a life time. Answer me this: why do organisms “don’t fall completely apart — as they do, in fact, at the moment of death. What power holds off that moment — precisely for a lifetime, and not a moment longer?”
Stephen Talbott: In other words, despite the countless processes going on in the cell, and despite the fact that each process might be expected to “go its own way” according to the myriad factors impinging on it from all directions, the actual result is quite different. Rather than becoming progressively disordered in their mutual relations (as indeed happens after death, when the whole dissolves into separate fragments), the processes hold together in a larger unity.

Box: To be clear: this “larger unity” – the organism as a whole – is something that materialism cannot accommodate. As we all know, materialism can only accommodate blind particles in motion.

Zach: And “blind particles in motion” can form into galaxies, cyclones, snowflakes, fusion reactors, the Giant’s Causeway, buckminsterfullerenes, auroras, lightning, pulsars. Your argument would suggest that these forms can’t exist under materialism, which would probably surprise a lot of materialists.
No, my argument does not suggest that. Clusters of particles with rather easy to explain (by natural law) structures is IMO exactly what can be expected by blind particles in motion.Box_{March 21, 2015
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Box: you simply fail to address those arguments We did, but we'll respond in more detail. Most materialists certainly don't think life can't be accommodated in their philosophy, or they probably wouldn't be materialists. Box: Given materialism there is no particle or wave that gives a hoot about neither the organism nor its continued existence – homeostasis. Particles and waves don't give a hoot about whether the sun shines, or whether the rains come. That doesn't mean these processes are "not what we can expect given purely natural unguided forces." It turns out that particles and waves can do all sorts of interesting things even though they have neither interest nor give hoots about rain or sun. Box: Again: why would a bag of chemicals – the “organism” – perform a delicate balancing act GIVEN MATERIALISM? Essentially, life is a dissipative process, a sort of swirl in the flow of energy. Notably, cyclones can be in stasis for long periods of time. For instance, the Great Red Spot on Jupiter is centuries old, as is the North Atlantic Gyre. Box: To be clear: this “larger unity” – the organism as a whole – is something that materialism cannot accommodate. As we all know, materialism can only accommodate blind particles in motion. And "blind particles in motion" can form into galaxies, cyclones, snowflakes, fusion reactors, the Giant's Causeway, buckminsterfullerenes, auroras, lightning, pulsars. Your argument would suggest that these forms can't exist under materialism, which would probably surprise a lot of materialists.Zachriel_{March 21, 2015
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Zachriel: The continued existence of an organism – homeostasis & robustness – is not inconsistent with materialism. Nor is it utterly mysterious to materialists who can point, just as non-materialists can, to human scientific knowledge of biological organisms.
Sorry Zachriel, but I don't know what to say. This just about lacks any substance. You start off with an empty statement of faith and then act as if I claimed that materialists cannot point to "human scientific knowledge of biological organisms". In #33 I have provided arguments as to why materialism cannot accommodate an organism - specifically its continued existence - and you simply fail to address those arguments and it's typical.Box_{March 21, 2015
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Box: I simply did not write about abiogenesis. You're right. We read it, came back to it later, then responded incorrectly. Box: the continued existence of an organism – homeostasis & robustness – is utterly mysterious to materialism. The continued existence of an organism – homeostasis & robustness – is not inconsistent with materialism. Nor is it utterly mysterious to materialists who can point, just as non-materialists can, to human scientific knowledge of biological organisms.Zachriel_{March 21, 2015
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I was looking at the page with "Darwinian Debating Devices", but Zachriel's tactic, which he uses quite frequently, is not covered. Often Zachriel just posts something which at first glance looks responsive but really is not. I gather that Z's intention is to create the impression for the casual onlooker that an effective counter-argument is being offered. Post #35 is a good example.
Zachriel: Abiogenesis is not inconsistent with materialism.
This is totally unresponsive to what I wrote. I simply did not write about abiogenesis. Equally responsive would have been:
The earth is not a perfect sphere.
Box_{March 21, 2015
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Zachriel:
Genes can become promiscuous (have a secondary function), then duplicate, to form new genes.
There isn't enough time in the universe for unguided evolution to do that- see "waiting for two mutations"Joe_{March 21, 2015
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Box: It follows that the continued existence of an organism – homeostasis & robustness – is utterly mysterious to materialism. Abiogenesis is not inconsistent with materialism.Zachriel_{March 21, 2015
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gpuccio: Either genes evolve according to scenario a), that is being and remaining functional until they change to another functional form, or they evolve according to scenario b), from non functional forms which are free to change “neutrally” by definition, because they are not functional. Genes can become promiscuous (have a secondary function), then duplicate, to form new genes. This was already mentioned above.Zachriel_{March 21, 2015
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Homeostasis - and its subset robustness - is not what we can expect given purely natural unguided forces. Why would blind chemicals - lacking overview and bound by nothing but natural law – be motivated to uphold a dynamic equilibrium at the level of the organism as a whole, which is far beyond their reach? Given materialism there is no particle or wave that gives a hoot about neither the organism nor its continued existence – homeostasis. Again: why would a bag of chemicals – the “organism” – perform a delicate balancing act GIVEN MATERIALISM?
Talbott: (…) the question, rather, is why things don’t fall completely apart — as they do, in fact, at the moment of death. What power holds off that moment — precisely for a lifetime, and not a moment longer? (… ) In other words, despite the countless processes going on in the cell, and despite the fact that each process might be expected to “go its own way” according to the myriad factors impinging on it from all directions, the actual result is quite different. Rather than becoming progressively disordered in their mutual relations (as indeed happens after death, when the whole dissolves into separate fragments), the processes hold together in a larger unity.
To be clear: this “larger unity” – the organism as a whole – is something that materialism cannot accommodate. As we all know, materialism can only accommodate blind particles in motion. It follows that the continued existence of an organism – homeostasis & robustness – is utterly mysterious to materialism. Now what bothers me to no end is that Andreas Wagner – as a materialist – takes “robustness” as a cornerstone for his argument in favor of evolution and materialism. To me this is incoherent beyond any description. It’s like grounding the idea ‘absolutely everyone is an absolute egomaniac’ solely on the fact that altruism is being exploited – hey Andreas, how does your idea accommodate altruism?Box_{March 21, 2015
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Both drift and natural selection are impotent. No one cares if they are mutually exclusive as they are mutually impotent.
The Gauger–Axe paper is a joke — comparable to a demonstration that since a bat can’t evolve into a whale or vice versa, they can’t be related.
I challenge Piotr to say that to Axe and Gauger- we know he won't though because he can't stand to be corrected by the very people who actually know better.Joe_{March 21, 2015
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Gpuccio, I can very well have it both ways. There's no reason why (a) and (b) should be mutually exclusive, any more than "drift" and "selection" are mutually exclusive (it isn't even quite correct to regard them as separable processes). I have to do some work in the garden, so I'll leave a detailed answer for later.Piotr_{March 21, 2015
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Piotr: Excuse me, but you cannot have it both ways. Either genes evolve according to scenario a), that is being and remaining functional until they change to another functional form, or they evolve according to scenario b), from non functional forms which are free to change "neutrally" by definition, because they are not functional. I have nothing against the fact that many genes can be knocked out without obvious phenotypic consequences. That can easily be explained because: 1) Many functions are redundant, implemented in different ways. That is particularly evident in epigenetics. 2) Many phenotypic effects, although real, are not necessarily obvious in a general context. However, if a gene is no more functional, then it can evolve randomly in any possible direction: IOWs, it is no more visible to negative selection. That means that after a few changes it loses its connection to functionality, and therefore to any possible "genotypic network" of functional genes. So, if it "finds" a new functional configuration, there are only two possibilities: a) the new configuration is reasonably likely because its sequence is similar to the sequence of the original gene. But, in this case, homology will show clearly the relationship between the two genes. b) the new configuration is unrelated, at sequence level, to the original sequence. But in this case the transition is completely unlikely, and it cannot be the result of any "phantom" genotypic network of functional states, platonic or else. Why? Because again, functional states are privileged (probabilistically) only because they are visible to NS, and expanded and fixed by positive and negative NS. IOWs, if I start with a knocked out gene: A- And then it changes to: A1 A1 is sequence related to A. It can be still non functional, and then it is not part of any "network", platonic or else. Or it can be functional, and then it has to "enter" again a state of expression, expansion and fixation to be something more than a state like any other state. But then, negative selection again will act against variation. So, your reasoning can only work this way: A becomes A- to be free to change A- becomes A1 (related and functional) A1 is expanded and fixed. A1 becomes A1-, to be free to change... And so on. Myths, fairy tales? Once you accused me to believe in an imaginome at the level of cellular regulation of differentiation. I still do. But at least, cellular differentiation is something that we see happening all the time. Your imaginome of evolutionary processes is not only absurd: it is an absurd explanation for processes that have never been observed (shall I remind again that the main falsification of any darwinian process at the molecular level is the absence of observable functional intermediates in the proteome?). You cannot have it both ways. Functional states are "special" in the evolutionary process only because NS acts on them. You cannot invoke imaginary networks of functional states, and then ignore the role of NS. Neutral variation is exactly that: neutral. In neutral variation, probability acts without any reference to function. The only relationship between neutral variation and function is that negative selection limits neutral variation. And negative selection is a powerful force against evolution. Only positive NS "lowers" the probabilistic barriers. And positive NS implies functional intermediates, expanded and fixed.gpuccio_{March 21, 2015
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As I said, Piotr is just upset because I proved he doesn't understand nested hierarchies nor what they entail.Joe_{March 20, 2015
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You are a basket-case, Piotr. You have no idea and you think that your one-liner somehow means something. "Oh clades are nested in clades"- as if that helps you. Pathetic, Piotr, even for you.Joe_{March 20, 2015
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I rest my case.Piotr_{March 20, 2015
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Piotr, Andy lost. Obviously you are just a sad person. Also Jonny MS stopped me from posting- that is how they "win". My understanding of nested hierarchies is supported by everything I have referenced. OTOH you and yours have referenced nothing but yourselves and your misconceptions. Again- I have the support of references, you and Andy have nothing but to bastardize reality. Andy even admitted I was right but then said that all the transitionals existing at the same time is nonsense. which is true but that misses the point- all the transitionals still need to have a place when found and supposedly many have. Darwin, Mayr, Denton, and now Wagner all agree with me. Piotr has his arse and nothing more...Joe_{March 20, 2015
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