Criticizing neo-Darwinism

The main problem with ID as a science is that not only is this lack of consensus here on the forums but in the ID establishment. While a number of ID proponents may agree on some vague terms that they believe are relevant, i.e. irreducible complexity or complex specified information. The actual details of these terms and how they can be used to detect design are highly variable from proponent to proponent and even over time from one proponent, see for instance Behe's evolving definitions of what constitutes irreducible complexity.So while these debates are not likely to ever lead to a final determination on the metaphysical aspects of the question they do serve to highlight why ID cannot be considered a suitable scientific theory. It sounds like you are saying this site is pointless since neither side will ever be able to convince the other.TTFN,WKEdited by Wounded King, : Typos, including some pretty meaning changing ones.

Yes, oops! Nothing like a bit of sloppy typing to totally reverse your position on an issue.TTFN,WK

NWR has finally gotten around to formulating and posting his alternative theory to neo-darwinism. Since he is currently inactive on this forum you can find his post over on Dreamcatcher.The main thrust of the idea, as I understand it, is that junk DNA acts as a genetic reservoir allowing for complex genetic variation to be produced without being subject to natural selection which can then be transposed into a region where it becomes functional allowing an organism to exploit novel niches (the invasive part of the theory). The junk DNA is also a potential area where once successful genes can be archived in some way against possible future deployment when they might be beneficial once again.I think there are a number of problems with NWRs theory. My main objection is that it seems to have added an unnecessary level of teleology and un-evidenced and unnecessary genetic mechanisms to explain things that I at least consider already well explained by understood genetic and evolutionary mechanisms.TTFN,WKEdited by Wounded King, : No reason given.

I'm not sure that the mechanisms he posits are well enough defined for this to be true, certainly I don't think that there is any particular evidence supportive of this theory that isn't better explained by already understood mechanisms. This is a complicated question. The most obvious thing in this line would be pseudogenes. There are lots of cases where non-coding copies of genes which are coding in other species are known to exist but I don't see how there is any way to differentiate in NWR's theory between a gene being prototyped, as it were, in the junk DNA and an 'archived' gene.So looking at the cluster of olfactory receptor (OR) genes and pseudogenes in the primates for example (Rouquier et al., 2000) we see a pattern of phylogeny, adopting the idea that pseudogenes are genes in the process of development rather than degradation, almost exactly opposite that suggested by all other phylogenetic methods with humans being the most primitive (with ~70% of putative OR sequences lacking an open reading frame (ORF)) and a new work monkey like the marmoset the most derived (with 100% of putative OR sequences posessing an ORF).If we consider the pseudogenes to be archived no longer necessary sequences then our expectations are the same as with the neo-darwinian view of pseudogenisation except that for the pseudogenes to be 'recommissioned' will require a large number of mutations to combat the genetic degradation from conserved functional sequence which has occurred.So while the answer to your question is strictly 'yes', I don't think that the pattern in which such active and inactive copies between species occur fits with NWR's theory.TTFN,WKEdited by Wounded King, : No reason given.Edited by Wounded King, : No reason given.

Its know that genes can become pseudogenes and that some of what we consider pseudogenes are functional, but I don't know of any example where a pseudogene is thought to have reacquired functionality as a protein coding gene. I'm not sure how we would detect such a thing except as an anomaly in a set of phylogenies, i.e. a species which for all other genes trees out as being highly derived trees out as primitive for a particular gene which is a pseudogene in all the most closely related species. It would be a similar pattern to that seen for flight in the Whiting paper on the re-evolution of flight in stick insects (Whiting et al, 2003), but for a genetic rather than a phenotypic trait. That was one of my principal objections, in his efforts to try and overcome what he saw as an inability of neo-Darwinism to combat arguments regarding irreducible complexity NWR has in fact come up with a theory which really is susceptible to the arguments Behe and Dembski make, but which they only address to a strawman version of current evolutionary theory.By removing natural selection in an effort to maintain some potentially useful genetic variation, specifically by moving the focus to sequences in the Junk DNA in regions to which selection is blind, NWR has also done away with its ability to maintain currently useful variation.TTFN,WKEdited by Wounded King, : No reason given.Edited by Wounded King, : No reason given.

What exactly do you mean by 'stems'? 'Stems' is a rather imprecise term. Natural selection is necessary but not sufficient for the evolution of functional genetic complexity as it is understood in modern evolutionary theory.While natural selection cannot create novel variation it has a key role in maintaining variation which is beneficial to an organism's reproductive success.The creation of genetic variation relies on mutation.I don't see how you can have been discussing evolution on this site for several years and not understand what Percy was saying, its the very basic formulation that adaptive evolution is principally the result of Random Mutation and Natural Selection acting on a population.TTFN,WK

Hi Randman,I'll try and address points from a number of your posts. Well this seems very bizarre to me, I can't recall having seen this happening on this forum but I'll take your word for it. Yes, but there is not a 1 to 1 linear correspondence. Morphological evolution certainly depends on genetic evolution but there can be a large amount of genetic evolution independent of morphology per se, i.e. evolution of genes involved with cellular metabolism and biochemistry or even elements of the immune system. I disagree and you would have to present substantial evidence to support this claim. Complex genetics in morphologically simple organisms is not sufficient as thee are other levels of complexity which may necessitate it, such as the metabolic or biochemical complexity I mentioned previously.I'm assuming that the sort of thing you are talking about in terms of 'simple organisms with genes and genetic sequences for for complex functions the simple organisms don't have' you are thinking of things like homologues of the pax genes involved in eye development being expressed in sponges or various elements of the developmental gene network associated with the eye being found in 'primitive' organisms such as the platyhelminthes. I don't know of any examples of this sort of thing that would support your contention however. This is true to some extent, but we would also expect these genetic traits to be principally based upon already extant genetic material. We would expect genetic networks related to complex nerve function to be highly integrated and derived from any simpler network involved in the development of simpler nerve function. I'll revisit this in the context of the paper you reference about A. millipora. Percy was quite right not to promote a thread whose very title 'Acropora millepora and it's human genes' conveys a gross misrepresentation of the papers results, one you persist with in your frequent references to 'human gene sequences' and 'human genetic expressions'. The genes were present in humans and A. millipora and not in Drosophila or C. elegans. That doesn't make them 'human genetic sequences'.The fact that a species carries genes related to the those involved in the development of the nervous system does not imply we should expect to see something resembling the human nervous system in the organism. your argument relies heavily on the idea that these genes have no other conceivable function, this is easily shown to be false simply doing a literature search on the gene that the paper identifies as 'bilaterian genes whose specialized functions are associated with highly differentiated nervous systems' but which are not know to be present in any invertebrates. Of the three genes so identified 2 of them, Tumorhead and Churchill, are also involved in early morphogenetic movement in the developing embryo even in the first few cleavage stages in the case of Churchill in Zebrafish (Londin et al., 2007). Tumorhead has been shown to be similarly expressed at early stages in Xenopus (Traverso et al., 2006). Did you notice that neither of those species were human and yet had the genes you have been passing off as 'human gene sequences' in A. millipora.As we gain more and more knowledge about the genomes of various species our understanding improves. In the absence of contrary evidence it was the most parsimonious interpretation to assume that genes only found in the vertebrate lineage evolved in that lineage after it diverged from the invertebrates. The data you refer to show this was not true in several cases and in those case the most parsimonious explanation becomes that they have been lost at some point in the evolutionary lineages of Drosophila and C. elegans.Modern evolutionary biology has no problem with genetic loss, it is just another form of mutation. Whether such loss is actively adaptive in some way or simply serves to alleviate some burden on the cell is a moot point. Did the Drosophila lineage lose certain genes and concomitantly lose some morphological feature or did those genes simply become redundant for some reason and get discarded as excess baggage? It is an interesting question and not one really susceptible to an answer until we have wider body of genomic information to draw on.Is our understanding of the evolution of life on earth being altered by this kind of research, yes it is. Is our understanding of the processes of evolution? Not so much. This doesn't require any rethinking of the mechanisms of random mutation and natural selection as the primary ones in adaptive evolution. It implies that the common ancestor of invertebrates and vertebrates is more complex than simply being the overlapping set of their gene complements but I see little if any support for your contention that... ... viewed even in the best possible light this is still pure hyperbole.I look forward to your response when you can post again.TTFN,WK

The point is that any mutation, or 'genetic accident' if you insist, which isn't functionally neutral will produce a biological feature, i.e. a change in the observed phenotype of the organism. Most of these changes will themselves be effectively neutral, the majority of the rest will be detrimental and a slim few may be beneficial to the organisms reproductive success. It is the variation in these phenotypic traits that allows natural selection to occur as mutations increasing reproductive success will tend to be favoured.To make your question work the way you seem to intend I think you need to expand upon what you mean by a 'biological feature', i.e. perhaps a complex feature of multiple independent parts.TTFN,WK

Just bumping this since Randman is back on the boards and he was involved on this thread.TTFN,WK

Yup, any time Bolder-Dash is telling you how right you are and Brad McFall tells you how clear and understandable you are, you better check to see that you aren't just talking unintelligible hooey. In the case of the statement Larry Moran makes that seems mostly to be because he has made up his own idiosyncratic meaning for the term, as representing an ultra-adaptationist view. You could maybe make a tiny fragile case if you think of Darwinism being exactly derived from what Darwin formulated in the 19th century and no further, but in terms of neo-darwinism its just balderdash.And as for Alan MacNeill , he says he isn't a Darwinist in the same way a physicist isn't an Einsteinian. That doesn't seem to say anything about faults or flaws in neo-darwinism, and again is an idiosyncratic approach to what Darwinsm is, and it should be noted this is a different interpretation to what Larry Moran says Darwinism is.Why didn't you stick Lynn Margulis in there, at least she has a substantive and scientifically profitable alternative (even if she does over sell it, seeing most diversity in life as a biological nail for her endodymbiosis hammer.)Does this mean you still have the same opinion of Neo-Darwinism and are still fermenting your own 'invasive theory'?TTFN,WK

Well I know I didn't. NWR was using neo-Darwinism to refer principally to the mathematical formulations of Sewall, Fisher and Haldane which dealt with population genetics and preceded the elucidation of the structure of DNA by some decades. They didn't have any of our knowledge of modern molecular genetics and the specific nature of genetic mutation.When he says that others use neo-darwinism more broadly he refers to the fact that neo-darwinism is commonly used synonymously with both the 'modern evolutionary synthesis' and to embrace the various evolutionary genetic disciplines which have risen in profile subsequently including evolutionary aspects of developmental biology.Only a creationist would think that a scientific discipline which adjusts to fit reality was therefore flawed. It isn't even clear from what you are saying here what you do think it means. This is a good contrast to make. Our understanding of evolutionary theory does change regularly as our knowledge base expands, and consequently things do need revision. Behe on the other hand keeps changing back and forth between what definition of IC he uses depending on what he wants to do. If he wants to weasel out of actually having to make an ID case in support of it he uses the weak version where IC systems can evolve, he just thinks it unlikely, if he is preaching to the faithful then it is the 'strong' version where an IC system can't evolve because by definition any change will render it 'non-functional' even if it still performs some other related function. PaulK recently linked to an article discussing this behaviour, here. I'm interested in whether nwr still thinks that IC is a good argument against gradual evolution. You are mistaken, I didn't call him an idiot because that isn't something I tend to do directly, even to the most idiotic creationists. I doubt anyone reading this thread could fail to see how idiotic I thought many of the things nwr was saying were however. Specifically that the public perception of a scientific theory should have any sway in the scientific acceptance of that theory and that the existence of putatively IC systems was a problem for modern evolutionary theory/neo-darwinism. No it doesn't, this whole post comes across as if you have never heard of the modern synthesis and have no idea what it is. Certainly I would concede that in modern biological terms evolutionary theory now touches every aspect and I would refer you to Dobzhansky's seminal thoughts on the matter, PDF. Yeah, and no doubt the collapse of evolutionary theory is only about 5 years away, same as it has been for the last ~150 years.TTFN,WK

You know what, I agree with you, but subsequent discussions with nwr did tend to make it clear that this did seem to be what he was saying, you are the one who thinks his OP was clear and understandable. I have always thought that his attempts in this thread were fairly incoherent and based on a very idiosyncratic and unclear understanding of what neo-darwinism is. Sheesh, do I even have to explain your own posts to you?You suggested I pulled up short of calling nwr an idiot ... I was pointing out that it isn't a case of name tags, because I don't call creationists or IDists idiots either. This is not as simple a question as you might believe. I believe that molecular evolutionary change is gradual and occurs principally in steps of one mutation, however molecular genetics has massively broadened the scale of what 1 mutation can mean. 1 mutational event might produce a whole genome duplication, or a chromosomal duplication, it might create a whole new functional ORF by a frame shift as is hypothesised in the case of one of the Nylonase enzymes, it might be the swapping of exons between genes creating a novel combination of functions, it might be a transposition event introducing a novel transcriptional start site upstream of a gene and substantially altering its expression. Moving from the genotype to the phenotype adds another level of complexity since there is no simple linear relationship between the size of phenotypic effect of any individual mutation of a particular type. A single base pair substitution may produce an embryonic lethal while a whole genome duplication has no apparent phenotypic effect.In what way do you feel the modern sythesis is moving away from a gradualist theory? Lots of other things including contingency, endosymbiosis, genetic drift (including that resulting from large scale catastrophic events) and depending on your approach you might consider horizontal gene transfer or heritable epigenetic changes to be non-Darwinian mechanisms. No I haven't, I often say what various aspects of the modern synthesis say about specific topics, but as the name implies the modern synthesis is a synthesis of different disciplines. There is no simple formula for you to learn to understand the modern synthesis. If you understood the formulae of Fisher, Wright and Haldane you wouldn't understand the modern synthesis any more than someone who understood Einstein's theory of relativity would therefore understand modern quantum theory.The modern synthesis is commonly used as a term describing the contribution of a wide panoply of biological sciences as they relate to evolution, these include molecular genetics, developmental biology, population genetics, bioinformatics, biochemistry, paleontology, comparative biology, anatomy, ..., in fact pretty much any field of biology has evolutionary aspects which contribute. There was an original 'modern synthesis' in the 40s, but that has continued to expand as more has been learnt from the various fields which contribute to our knowledge of evolution. Of modern biology, hence why I was speaking in modern biological terms, I admit this whould have been clearer if I had said 'in terms of modern biology'. Of course to understand it all you had to do was follow the link and read what Dobzhansky said, for anyone else who is both lazy and ignorant here is the precis "Nothing in Biology Makes Sense Except in the Light of Evolution." How convenient for you, since nwr used IC as the basis of one of his criticisms I would have thought it would be quite on topic, but have it your own way. Take your time though, it might take some doing to find any evidence that what I am saying is false since it is so patently true from things that Behe has said himself. Consider me devastated, if Brad McFall turns up and tells me it was unintelligible as well I might just have to cry.TTFN,WKEdited by Wounded King, : No reason given.Edited by Wounded King, : No reason given.

Another stunning piece of science journalism . What were essentially identical were the mitochondrial 12S rDNA and 16S rDNA sequences.TTFN,WK