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Prominent NAS member trashes neo-Darwinism

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Natural selection …is not the fundamental cause of evolution.

Masatoshi Nei

Science continues to destroy Darwinism. A prominent member of the National Academy of Sciences, Masatoshi Nei, trashed neo-Darwinism in the recent peer-reviewed article: The new mutation theory of phenotypic evolution.

Haldane’s dilemma showed mathematically that natural selection could not be the major driving force of evolution. Haldane’s dilemma lead in part to the non-Darwinian theory of molecular evolution known as the “neutral theory of molecular evolution”. Neutral theory asserted natural selection was not the principal driving force of molecular evolution. However, when molecular neutral theory was presented to the world in the 1960’s, it was politically incorrect to assert the obvious consequence of the neutral theory of molecular evolution, namely: morphology, physiology, and practically anything else made of molecules would NOT be principally shaped by natural selection either.

In What are the speed limits of naturalistic evolution?, I pointed out:

And if Haldane’s dilemma were not enough of a blow to Darwinian evolution, in the 1960’s several population geneticists like Motoo Kimura demonstrated mathematically that the overwhelming majority of molecular evolution was non-Darwinian and invisible to natural selection. Lest he be found guilty for blasphemy, Kimura made an obligatory salute to Darwin by saying his non-Darwinian neutral theory “does not deny the role of natural selection in determining the course of adaptive evolution”. That’s right, according to Kimura, adaptive evolution is visible to natural selection while simultaneously molecular evolution is invisible to natural selection. Is such a position logical? No. Is it politically and intellectually expedient? Absolutely!

But now 4 decades later, the inevitable consequence of Haldane’s dilemma and Kimura’s neutral theory may be ending the uneasy truce between neo-Darwinists and neutralists.

Nei writes:

For the last six decades, the dominant theory of evolution has been neo-Darwinism, which was developed by the three founders of theoretical population genetics, Fisher (1), Wright (2), and Haldane (3), and was later supported by various evolutionists (4). Neo-Darwinism asserts that natural selection is the driving force of evolution,
….
In the last four decades, the study of molecular evolution has shown that a majority of amino acid substitutions in proteins are neutral or nearly neutral

However, most evolutionists still believe in neo-Darwinism with respect to phenotypic evolution and are not interested in neutral evolution (19,22).

Mayr (23) stated that neutral mutations apparently occur at the molecular level, but because they do not affect phenotypic characters, they are of little interest to evolutionists.
….

By contrast, Nei (17, 24, 25) argued that because phenotypic characters are ultimately controlled by DNA sequences, both molecular and phenotypic evolution must occur in similar [non Darwinian] ways. He also suggested that a considerable portion of morphological evolution is caused by neutral or nearly neutral mutations, and the driving force of evolution is mutation at both molecular and phenotypic levels.
….
As mentioned in the introduction, a majority of current evolutionists believe in neo-Darwinism. In one of the most popular textbooks on evolution, Futuyma (ref. 20, p. 10) states that evolutionary change is a population process in which one genotype replaces other ones, and for this process to occur, mutation is quite ineffective because of its low rate of occurrence, whereas even the slightest intensity of natural selection can bring about substantial change in a realistic amount of time. He also states “Natural selection can account for both slight and great differences among species, and adaptations are traits that have been shaped by natural selection.” Although this type of statement is quite common in the evolutionary literature, it is obvious that any advantageous genotype is produced by mutation including all kinds of genetic changes. Natural selection occurs as a consequence of mutational production of different genotypes, and therefore it is not the fundamental cause of evolution.

Historically, the word mutationism was used to refer to William Bateson’s saltationism or similar ideas, in which natural selection plays little role. Later Morgan (109) presented a more reasonable form of mutationism taking into account the role of natural selection. His view was abstract and based on a few lines of speculative arguments. However, recent molecular studies of phenotypic evolution support the basic ideas of his view and have extended it to a more comprehensive view presented in this article. If the new form of mutation theory described here is right, even in its crudest form, more emphasis should be given on the roles of mutation in the study of evolution.

Notes:

1. ID sympathizer Dr. John Davison, who has spent much of his recent life promoting the works of William Bateson, should be much encouraged with these developments. It was through Davison I learned of Bateson’s wonderful ideas.

2. Richard Dawkins wrote of Kimura in Blindwatchmaker. Dawkins argued Kimura’s ideas wouldn’t overturn Darwinism since Darwinism operated at the higher level of adaptation whereas Kimura’s non-Darwinian theory operated at the lower level of molecules. But the reductionists are now getting taste of their own medicine. If the Darwinism doesn’t operate at the molecular level, then why should we expect it to operate at much higher levels like morphology and physiology either?

3. Lewontin gives a powerful example of neutral evolution at the morphological level. Rhinos have either 1 horn or 2 horns. Did natural selection cause the evolution of one horn in one case, and 2 horns in another? Unlikely.

4. Salthe pointed out a fundamental contradiction in Fisher’s fundamental theorem of natural selection. Selection is the enemy of diversity. Salthe realized the obvious problem of trying to account for the abundance of diversity through a mechanism which reduces diversity.

5. At least 3 signatories of the Discovery Institute’s Dissent from Darwin list anticipated these recent developments. Davison, Salthe, and Ho. Ho managed to present echoes of these ideas 30 years ago in a peer-reviewed journal. See: An eloquent but bogus non-review by Dawkins.

a relative lack of natural selection may be the prerequisite for major evolutionary advance

Mae Wan Ho

Comments
We could go on forever with Bob shifting the terminology. The greater the environmental hardship, the more organisms of higher complexity (or anything other than bacteria) struggle in the battle for survival. In the long run, highly complex organisms will perish due to their lack of fecundity, robustness and the shear amount of time between generations. Moreover, NS does not merely select on the basis of reproductive success, but being a blind force is unable to foresee potential problems (which intelligence does) and thus (acting upon shuffling and segregation) evolves organisms down an ever narrowing cone of generalization – leading ultimately to extinction. [Re: my comments on the panda – Post 30]Acquiesce
July 26, 2007
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EDIT TO THE EDIT: BTW If you say 3, then you have to show how NS can select for organisms that survive less well than their competitors and produce fewer offspring per unit of time... (This I got it with that one)Atom
July 26, 2007
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EDIT: BTW If you say 3, then you have to show how NS can select for organisms that survive better than their competitors and produce fewer offspring per unit of time... (Before Bob serves up another uncharitable reading, I'll make myself crystal clear)Atom
July 26, 2007
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Again: Tell me which of these you disagree with: 1) Simpler organisms reproduce in greater numbers than more complex organisms. (In general.) Bacteria vs. insects vs. rodents vs. man 2) According to NDE, the general trend of life development in earth history is from simple organisms to more complex ones. 3) If NS only selects for survivability and reproductive success, and the simpler the organism the better they do in both respects (see 1 above), then we should expect a trend towards increasing simplicity of organisms. 4) Experimental evidence suggests this is indeed the case when replicators are allowed to mutate and are subject to NS, being selected by reproductive success. BTW If you say 3, then you have to show how NS can select for organisms that produce fewer offspring per unit of time...Atom
July 26, 2007
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Do they have more working parts? Yes. Some of them are carried in plasmids. More working parts or different working parts?tribune7
July 26, 2007
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I’ve already given an example to show that reproductive success does not necessarily predict fitness.
Excuse me? You're trying to get back into the fitness word game? I'm not playing that game with you. As I made clear, we're only talking about reproductive (replication) success now. (See my post 162) This can be compared across any class of replicators. And again you dodge the issue.Atom
July 26, 2007
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Atom - I've already given an example to show that reproductive success does not necessarily predict fitness. And also explained (several times) that you can't compare fitness of different species.
Bob seems to be defining complexity as simple change. Are bacteria that acquire resistance to antibiotics more complex than those that don’t? Do they have more working parts?
Yes. Some of them are carried in plasmids. PaV - fitness is there. Check the Red Queen stuff. Also, I hope you're aware of the tight connection between selection coefficients and fitness. BobBob O'H
July 26, 2007
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“Then note that the “expected” refers to a mathematical expectation”—Bob PaV responds: 'Expected on what basis? And, of course, the basis is………they’re more “fit”. (s=selection coefficient=fitness.) Circle now complete.' Bob: "Ah, OK. You’re not familiar with basic terminology in probability theory. I hope you don’t mind if I pass on explaining this: it really would take us off-topic." I've studied quantum mechanics. I know what an expected value is. But you're assuming fitness values for various outcomes. From Wikipedia: "In probability theory the expected value (or mathematical expectation, or mean) of a discrete random variable is the sum of the probability of each possible outcome of the experiment multiplied by the outcome value (or payoff)." Those values are all "a posteriori". That is the point I'm making. The values you "input", are drawn from experience. Thus, the input simply reproduces the output. Now, I suppose you could do a simulation using initial values, and you could say that's a prediction. But, if it doesn't match what is seen "a posteriori", then I suspect the temptation would be to change the "initial values" until you did get a match. IOW, circular reasoning.
I’ll just point out that fitness isn’t a tautology, because we can predict fitness (e.g. as I did here).
---Bob I'm reading your paper right now. But from the abstract, it appears you could make no conclusions about fitness. I don't see how that answers my assertion.PaV
July 26, 2007
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ok…so who here believes that Darwinian processes are incapable of producing complexity? I'll raise my hand. Actually, it's not so much that I think they are "incapable" of producing complexity but wondering why it should be assumed that they can based on the non-illustrations provided by Bob. Bob seems to be defining complexity as simple change. Are bacteria that acquire resistance to antibiotics more complex than those that don't? Do they have more working parts?tribune7
July 26, 2007
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Bob, Notice, in my last post I am talking about reproductive success (producing offspring in greater numbers), not your vague and shifting "fitness" (since you seem to want to play word games with that term.) I am simply making a factual point about which organisms produce offspring faster: simple vs. complex. I use examples of different organisms (bacteria, insects, rodents, man) to show that the general trend does in fact exist. There is no scientific law against comparing the reproductive output of two different kinds of replicators. It is becoming clear that you won't tackle the issue directly, so I won't press you any more on it. I am confident that this issue will remain in your mind after this. Whenever you see experimental results showing that simpler replicators outreproducing more complex ones, this thread will come to memory and eventually you will have to deal with the issue. AtomAtom
July 26, 2007
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ok...so who here believes that Darwinian processes are incapable of producing complexity?Patrick
July 26, 2007
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Patrick - as far as I can tell, people are arguing about the inability to produce complexity - see tribune7's post just before yours. I think tribune7 now has to show that all increases in complexity are responses to a change in the environment that can be reversed if his argument is to stand. If he wants to bring more conditions in, I think it's up to him to show that they always hold. BobBob O'H
July 26, 2007
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I don't think anyone is denying the basic ability to produce trivial complexity but not CSI. There's only a certain level of plasticity and personally depending on the design of system I think that plasticity can vary. An example is multiple GAs all designed to reach the same goal but only some are capable of it. Here's the question ID proponents have been asking for years: where's the evidence that underlies the assumption that trivial changes will somehow compound and get beyond the "edge"?Patrick
July 26, 2007
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yes. Surely any bacterium that gains a function is more complex. Resistence to antibiotics? The ability to eat oil? How are they more complex than other bacteria. Let's say you are right and these new functions increase complexity. Acquiesce points out in post 120 that these new functions cause a loss of fitness -- once the antibiotic is removed from the environment -- if fitness is defined as as the average number of surviving progeny of a particular genotype compared with average number of surviving progeny of competing genotypes after a single generation as per Jehu's wiki link.tribune7
July 26, 2007
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tribune7 - yes. Surely any bacterium that gains a function is more complex. I'll let you search Talk Origins for the relevant pages. :-) BobBob O'H
July 26, 2007
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What matters is whether a bacterium (say) that mutates to something more complex (perhaps it gets a gene with a new function) is fitter than the non-mutants without the added complexity. Bob, has a bacterium ever been observed mutating into something more complex?tribune7
July 26, 2007
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Bob: Enough has long since been said -- several times -- to show why many of us note several problems with the assumption that we can credibly get enhanced functionality through random mutation [etc], and that we can then see such an incrementally ever more and more complex organism competing with their parent populations and establishing itself in the ecological zone. Then, there is the problem that such incrementalism has to account for the onward fact of the implications of the weight of the fossil record: sudden appearances [and disappearances] and stasis. Cf here, Lonnig, 2004:
examples like the horseshoe crab are by no means rare exceptions from the rule of gradually evolving life forms . . . In fact, we are literally surrounded by 'living fossils' in the present world of organisms when applying the term more inclusively as "an existing species whose similarity to ancient ancestral species indicates that very few morphological changes have occurred over a long period of geological time" [85] . . . . Now, since all these "old features", morphologically as well as molecularly, are still with us, the basic genetical questions should be addressed in the face of all the dynamic features of ever reshuffling and rearranging, shifting genomes, (a) why are these characters stable at all and (b) how is it possible to derive stable features from any given plant or animal species by mutations in their genomes? . . . . A first hint for answering the questions . . . is perhaps also provided by Charles Darwin himself when he suggested the following sufficiency test for his theory [16]: "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." . . . Biochemist Michael J. Behe [5] has refined Darwin's statement by introducing and defining his concept of "irreducibly complex systems", specifying: "By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning" . . . [for example] (1) the cilium, (2) the bacterial flagellum with filament, hook and motor embedded in the membranes and cell wall and (3) the biochemistry of blood clotting in humans . . . . One point is clear: granted that there are indeed many systems and/or correlated subsystems in biology, which have to be classified as irreducibly complex and that such systems are essentially involved in the formation of morphological characters of organisms, this would explain both, the regular abrupt appearance of new forms in the fossil record as well as their constancy over enormous periods of time. For, if "several well-matched, interacting parts that contribute to the basic function" are necessary for biochemical and/or anatomical systems to exist as functioning systems at all (because "the removal of any one of the parts causes the system to effectively cease functioning") such systems have to (1) originate in a non-gradual manner and (2) must remain constant as long as they are reproduced and exist. And this could mean no less than the enormous time periods mentioned for all the living fossils hinted at above. Moreover, an additional phenomenon would also be explained: (3) the equally abrupt disappearance of so many life forms in earth history . . . The reason why irreducibly complex systems would also behave in accord with point (3) is also nearly self-evident: if environmental conditions deteriorate so much for certain life forms (defined and specified by systems and/or subsystems of irreducible complexity), so that their very existence be in question, they could only adapt by integrating further correspondingly specified and useful parts into their overall organization, which prima facie could be an improbable process -- or perish . . . . According to Behe and several other authors [5-7, 21-23, 53-60, 68, 86] the only adequate hypothesis so far known for the origin of irreducibly complex systems is intelligent design (ID) . . . in connection with Dembski's criterion of specified complexity . . . . "For something to exhibit specified complexity therefore means that it matches a conditionally independent pattern (i.e., specification) of low specificational complexity, but where the event corresponding to that pattern has a probability less than the universal probability bound and therefore high probabilistic complexity" [23]. For instance, regarding the origin of the bacterial flagellum, Dembski calculated a probability of 10^-234[22].
While of course Darwin indulged in a a bit of selective hyper-skepticism above [he was only going to accept absolute proof in a context where only abductive explanations are possible] but the point is clear enough. GEM of TKIkairosfocus
July 26, 2007
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Acquiesce - we're no further because people are still bringing up irrelevant details. It doesn't matter if bacteria produce more offspring that, say, polar bears. What matters is whether a bacterium (say) that mutates to something more complex (perhaps it gets a gene with a new function) is fitter than the non-mutants without the added complexity. I'm still waiting for someone to show that there is actually a problem: if there is no problem, there is no need for a solution. BobBob O'H
July 26, 2007
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H'mm: Onlookers -- it seems Bob will not directly respond to me here or in the July 6th thread -- it seems we have made little or no progress. (Other than to highlight that natural selection as a concept tends to fall into tautology/ circular argument, and that there are excellent reasons to think that simpler systems have obvious advantages.) As to the "you don't understand mathematical expectation and/or probability theory": --> Atom is an Engineer/Software Engineer. --> I am an Applied Physicist who also holds an MBA (as well as a third u/grad major in Math), who among other things has helped to design engineering undergraduate curricula, in partnership with people designing BSc computing curricula -- we had one of those Faculties that blended engineering and computing. --> Others here will have comparable exposure to the relevant mathematics and sciences generally. --> Many of us have significant design and development experience with hardware and/or software systems, in academic, military or commercial contexts. (That is a big part of why when we see the sorts of complexity being discussed, we know the hard way just how hard it is to make something complicated work by intent much less through random generation and probabilistic filtering.) Speaking for myself, I first met expectation in sixth form, before going to University proper, decades ago. In designing u/grad engineering curricula, the relevant statistics and probability would be covered in the first level course in that area, soon after doing the basic calculus or in the part of the computer people, intro discrete math sequence. In short, your remarks evidently betray a lack of understanding of the level of the people you are addressing. Our concern is not as to whether sum across outcome payoffs times probabilities will yield an expectation, but on [1] what the credible probabilities are and [2] what the likely payoffs to increments in complexity compatible with what mutations are observed to do will be. In particular, as already excerpted, there is a serious question as to whether body-plan level innovations of the sort of scope in the Cambrian revolution are within reasonable reach of NDT. Then, when we look at the mechanism that is held to generate the sort of complexity implied by that revolution and the rest of the fossil record and what we see in current life forms and ecosystems, we have a big problem with the idea that the incrementalist approach in NDT will credibly generate such diversification, starting with the basic issue of more complexity step by step leads to greater competitive fitness to the environment thus differential reproductive success. The bacteria - insects - man example is just one case in point of the trend, and the simulations on the matter underscore the point too. All of this gets back to what Nei highlights, as was excerpted in 127 above. GEM of TKIkairosfocus
July 26, 2007
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Atom [147]: I don’t want to lose focus of the basic point, so let’s go back to simple facts. Tell me which of these you disagree with: 1) Simpler organisms reproduce in greater numbers than more complex organisms. (In general.) Bacteria vs. insects vs. rodents vs. man 2) According to NDE, the general trend of life development in earth history is from simple organisms to more complex ones. 3) If NS only selects for survivability and reproductive success, and the simpler the organism the better they do in both respects (see 1 above), then we should expect a trend towards increasing simplicity of organisms. 4) Experimental evidence suggests this is indeed the case when replicators are allowed to mutate and are subject to NS, being selected by reproductive success. Please tell me which of those points is in error. and please get around to answering Aq’s intial question about how NS can form a trend of increasing complexity while selecting based on increasing reproductive success…
Bob: In point 1 Atom was merely asking you whether you accept that simple organisms reproduce in greater numbers than more complex organisms. Don’t try and evade the point. Insects, rodents and man were merely put there to give examples of higher organisms and their trend towards decreased fitness. BTW, bacteria (under favourable conditions) could produce enough offspring to equal the mass of our planet in around a week. Point 1 is a no-brainer. Now can you answer those points listed by Atom? And also my initial question: How can NS form a trend of increasing complexity while selecting based on increasing reproductive success. We are 150 posts on and you still cannot put forward any workable solution (at least I have tried – see 72).Acquiesce
July 26, 2007
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Sal - assuming a Poisson process, then the proportion that didn't have a mutation would be e^-1 = 0.37. So there should still be some signal. BobBob O'H
July 26, 2007
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Bob, I've appreciated your patience in answering question. I have a technical one pertaining to mutation rates. There is the jukes-cantor model for neutral mutation and divergence. At some point two identical sequences become fully divergent (well really 75%). But one problem I've not been able to resolve. If we have a 1 mutation per 10 million years per nucleotid position. Should the sequences be pretty much fully divergent in 10 million years. I can't seem to reconcile the math with the decaying explonential in the Juke-Cantor model. Any insights? The question related to neutral mutation in pseudo-genes. If the mutation rate is 1 nucleotide per 1 position per 10 million years, shouldn't the pseudo gene be trashed in 10 million years? Salvadorscordova
July 26, 2007
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Atom - I've tried to answer Acquiesce's point repeatedly, but you're repeating many of the same mis-conceptions. You can't compare the fitnesses of different species (competition between species is primarily a problem for ecologists to study). Even Acquiesce agrees with that. So your first point in wrong. You're obviously not understanding what I'm writing: in post 146 you quote me saying that we can only compare individuals of the same species, and then ask if we can compare rats and humans. Now, I'm not up on thought in baraminology, but I suspect even they don't think rats and humans are that closely related. BobBob O'H
July 25, 2007
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“Then note that the “expected” refers to a mathematical expectation”—Bob Expected on what basis? And, of course, the basis is………they’re more “fit”. (s=selection coefficient=fitness.) Circle now complete.
Ah, OK. You're not familiar with basic terminology in probability theory. I hope you don't mind if I pass on explaining this: it really would take us off-topic. There's an explanation here. Sorry it's not from TalkOrigins. :-) I'll just point out that fitness isn't a tautology, because we can predict fitness (e.g. as I did here). In essence, we can assign fitness to individuals, based on heredity (i.e. estimates of fitness of their ancestors). This would obviously be impossible if it were a tautology. BobBob O'H
July 25, 2007
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I don't want to lose focus of the basic point, so let's go back to simple facts. Tell me which of these you disagree with: 1) Simpler organisms reproduce in greater numbers than more complex organisms. (In general.) Bacteria vs. insects vs. rodents vs. man 2) According to NDE, the general trend of life development in earth history is from simple organisms to more complex ones. 3) If NS only selects for survivability and reproductive success, and the simpler the organism the better they do in both respects (see 1 above), then we should expect a trend towards increasing simplicity of organisms. 4) Experimental evidence suggests this is indeed the case when replicators are allowed to mutate and are subject to NS, being selected by reproductive success. Please tell me which of those points is in error. and please get around to answering Aq's intial question about how NS can form a trend of increasing complexity while selecting based on increasing reproductive success...Atom
July 25, 2007
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You would have to compare individuals of the same species competing in the same niche (OK, we can relax the “same” a bit, to allow for complex individuals invading new niches for example). Bob
If I am correct, the more unecessarily complex will be weeded out by NS before they can gain a foothold, unless they move to an entirely new niche as Aq suggsted, in which case you'd say their fitness cannot be compared. Where do we draw the (artificial) line of comparison? Can two different strains of a bacteria be compared? How about a bacteria and algae in the same habitat? How about rats and humans, both mammals, inhabiting the same village, competing for grain?Atom
July 25, 2007
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"Then note that the “expected” refers to a mathematical expectation"---Bob Expected on what basis? And, of course, the basis is.........they're more "fit". (s=selection coefficient=fitness.) Circle now complete. Q. "Why do you expect them to survive?" A. "Because they have traits that are more 'fit'." Q. "What do you mean by they're more 'fit'?" A. "They have traits that make you "expect" them to survive." Round, and round, we go.PaV
July 25, 2007
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How about an actual example where a more complex organism is less fit than its simpler counterpart?
Depends on the complexity being looked at it, does it not? Let's take a look at TO's example of people with "monkey tails". I have no problem calling that "complexity" in a generalized sense (as in, not CSI). I'm not sure what positive effects they do have. From what I remember they're not articulated and cannot serve as an additional limb. But I'm pretty sure they'd act as the opposite of a peacock's feathers, dramatically reducing those individual's chances of reproducing. Ditto goes for additional/non-functioning mammary nipples and other examples that turn off the opposite sex. I see your point, though. The situation is complicated enough that there can't be blanket statements. There can be increments in complexity where the tradeoff is more positive than negative. But that's why ID doesn't have blanket statement...there is a complexity threshold. And that's why Behe is trying to find an "edge of evolution". While an estimate has been arrived at I don't think that "edge" has been found yet. Personally I think it "might" be greater than where some ID proponents envision it to be. But I could be wrong. As an aside, the problem with these loose definitions comes about when any type of complexity itself is rewarded for the sake of complexity...then you get things like AVIDA.Patrick
July 25, 2007
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I’m assuming your use of the word precludes comparing, say, polar bears with bacteria?
Indeed. You would have to compare individuals of the same species competing in the same niche (OK, we can relax the "same" a bit, to allow for complex individuals invading new niches for example). BobBob O'H
July 25, 2007
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Bob: Atom - we’re not getting anywhere. How about survival? How about an actual example where a more complex organism is less fit than its simpler counterpart? Bob, what do you mean by "counterpart?" I'm assuming your use of the word precludes comparing, say, polar bears with bacteria? (If not, then the exercise becomes rather simple, doesn't it?) So, what are we allowed to compare in order for it to meet your "counterpart" standard?Phinehas
July 25, 2007
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