Does the Darwinian theory require modification or replacement?

I'm not sure what distinction you are trying to make here. A species that disappears surely is an evolutionary dead end, or do you mean that they evolved into other distinct species, speciation isn't usually considered extinction. Obviously any species that hasn't disappeared isn't yet an evolutionary dead end.Can you give some examples of each class?TTFN,WK

What is 'missing' is that virtually all of this work has been done in bacteria or yeast.So what is missing is any connection between this research and evolution in metazoa where there is a germ/soma divide. The, as yet missing, basis for such a mechanism was something I was just speculating on.TTFN,WK

That is a bit unfair, he has done quite a bit of work on Mu bacteriophage transposable elements, and that also seems to be the principle basis for most of his claims.TTFN,WK

Mainly that it is one with a long history, having been characterised in the early 70s. There are also engineered strains which have a Lac operon, which makes for a very useful experimental system for identifying when insertions have occurred producing fusion proteins. As to that, you must have noticed that whenever IDists bring up these arguments they never care about the actual mechanisms involved, only that they can quote someone saying that adaptive mutations are non-random or directed.TTFN,WK

How have you looked?I'm not being facetious but it is not an easy thing to identify papers with differing opinions in the literature. Even in review papers, which one might hope would be comprehensive, there is often a heavy bias towards the authors chosen interpretation of the data which may include not mentioning data they consider inconsequential.The fact that you didn't find anyone specifically challenging his opinions can just as easily be interpreted as the result of his views being marginal rather than correct.TTFN,WK

You are right of course about the correct terminology, but it gets really tedious trying to correct every creationist IDist who turns up decrying the modern synthesis, when clearly they mean the current state of understanding of evolutionary biological science. Because, as you may have noticed, telling a creationist that they are wrong rarely leads to them revising their behaviour.I think you are exaggerating to call Dr. A's usage 'radically' non-standard. Perhaps the distinction here should be between the modern synthesis and "The Modern Synthesis".Part of the problem is perhaps that there isn't any catchy specific defining term for the current state of knowledge. Neo-Darwinism got taken in the century before the last one, and that is still widely bandied about.I tend to use modern evolutionary theory, but that is very easily confused with the modern synthesis.People have been proposing things like 'extended synthesis' or variations on Evo-Devo such as Eco-Evo-Devo, but as yet there is no clear winner.TTFN,WK

I heartily encourage every true born British man and woman on this site to do their patriotic duty and use the term Milliard to denote 10⁹. It serves both to emphasise our fraternal links with continental Europe and our independence from the insidious and creeping Americanisation of the English language, which even now tries to insert Zs into the word Americanisation as I type.TTFN,WK

Then I hope you have been brushing up on your pinyin. Personally I do not drink ... beer.TTFN,WK

Just to clarify the point several people have made. In other words Zheng is saying, far from our having no 'proof' of random mutations, that random mutation should be considered the default assumption.He is at pains to emphasise however that the fact that we observed results consistent with random mutation in a particular experiment or set of experiments does not preclude the existence of 'directed' mutation in some cases.His conclusion is that the fluctuation test may be an insufficient method either to prove that, in the case of the Luria-Delbruck experiment, "All phage-resistant bacteria in nature resulted from mutations that occurred independently of stimulation of the phage." or that "Some of the observed mutants were due to mutations caused by stimulation of the phage."TTFN,WK

Proven is a rather imprecise phrase if you mean absolute proof in that case no, but absolute proof is rarely if ever a standard attained by scientific investigation. It also manages to staggeringly miss the point of his essay if that is the main thing you took from it.What there is is a vast wealth of evidence showing that the overwhelming majority of mutations are random with respect to fitness. What Zheng says reflects this, given the strong evidence for random mutation being the common mode of mutation it should be our default assumption. The main point of his paper, which you seem to have entirely missed, is ... It is impossible to entirely preclude directed mutations occurring with most of the currently used approaches, except when using some instantly lethal selective agent. But there is a staggering paucity of evidence for directed mutation. At best we see evidence for natural systems which may marginally effect the probabilistic distribution of fitness effects.TTFN,WKEdited by Wounded King, : Added attribution to quote

Wow, so Shapiro agrees with Shapiro as well, all we need now is Shapiro to agree and we'll have a universal scientific consensus.TTFN,WK

That isn't what Wright means by derepression. Derepression is simply a form of gene regulation where a gene that is constitutively repressed, usually by the binding of some transcription factor, has that repressive element removed. Derepression usually allows for a more rapid transcriptional response than the traditional program of transcriptional activation.Wright's argument is simply that when genes are specifically derepressed in response to some environmental factor, in most of her examples this is starvation for a specific metabolite, then genes relevant to the metabolism of that factor will often be derepressed and their expression strongly upregulated. Since transcriptional activity makes DNA more susceptible to mutation these newly transcriptionally active sites wil be significantly more prone to mutation than they were in the non-starved environment.She then argues that by increasing the level of mutation in a specific locus related to that metabolic pathway you will generate more mutants relevant to that pathway and therefore have a higher chance of generating beneficial mutants in that pathway.Just to add futher to what I said previously in the thread about these mechanisms not being relevant to evolution out of the microbial sphere. I seem to have previously missed Wright stating this outright in her own paper ... So she acknowledges that while multi-celled organisms show transcriptional responses to starvation there is no apparent mechanism for that to feedback to the genome as she proposes in bacteria.TTFN,WKEdited by Wounded King, : No reason given.

Well we try, but it gets tedious when you continually ignore our corrections and repeat the same mistaken arguments again and again.For instance your description of 'purifying selection' is nonsense. Purifying selection doesn't take over, it is simply one result of ongoing natural selection, and by acknowledging its role in this situation you are conceding that your fabulous "directed mutation" mechanisms are producing deleterious mutations which need to be weeded out.Which is essentially what everyone has been telling you all along when we point out that there is still a whole spectrum of beneficial and deleterious mutations being produced. The spectrum of mutations after selection is a completely different issue and we would expect it to be strongly weighted towards beneficial mutations.I think you need to realise that Wright's "direction" is regardless of the fitness benefits of the resultant mutation. The "direction" is simply to a specific genetic locus. Wright makes a reasonable argument that this will give an increased chance of a beneficial mutation occurring at that locus since it has an increased chance of all mutations associated with its transcriptional state. We can easily point out that this will also produce an increased chance of deleterious mutations at this locus, and this is where selection plays its part by favouring the proliferation of the beneficial mutations and tending to eliminate the deleterious ones. Again, simply wrong. The whole point of acknowledging the role of selection is that it means that evolution is not totally random or accidental. Evolution is a feedback between the genomes of organisms and their environment with the environment constraining and filtering the form of the evolving genome. Really? Excellent! Can you provide us references for 5 papers published in the last month which lead to this conclusion? So far you have managed a handful, mostly review papers, covering about a decade.It seems that you are slipping into hyperbole here.Perhaps what you meant was that every day scientists are putting forth new studies which you insist on fitting into your preconceived notions of how things should be. Which would explain why you are throwing Cairns' name around even though he has produced several papers which have effectively shown that the phenomenon he observed was not directed mutation.TTFN,WKEdited by Wounded King, : No reason given.

The selection is what imparts the direction you describe through the selective maintenance of the beneficial mutations. How can you say all that and still not realise that what you are describing is explicitly not directed for fitness at the locus, because it relies on selection to weed out the deleterious mutations which is simply classical neo-darwinian evolution.The best you can say is that the increase in the mutation rate at that specific locus might produce more beneficial mutations related to the environmental trigger that caused the derepression than would otherwise have ocurred.TTFN,WK

We recently had a whole thread devoted to this topic, All Human Beings Are Descendants of Adam . You should read through that to find out many of the ways in which what you say here is incorrect, the principal one being that modern humans have thousands of ancestor in common not just one. No they seriously don't, you could probably count on the fingers of one hand the number of biologists who would disagree that humans share common ancestors with chimpanzees and Gorillas. What they may do is debate the specifics of the timing and nature of the diversification of the apes, but that isn't what you were describing.TTFN,WK