Does the Darwinian theory require modification or replacement?

I suppose I could do that, but I'm not sure I need to yet."Purifying selection" is not some random term that Shapiro coined. The term has a standard meaning. You can look it up on Wikipedia or find it defined in scientist papers.From Widespread purifying selection at polymorphic sites in human protein-coding loci, Austin L. Hughes et alia.Widespread purifying selection at polymorphic sites in human protein-coding loci - PMC

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One feature that can be indicative of the deleterious consequences of a given allele is evidence of purifying selection (13). Purifying selection is the form of natural selection that acts to eliminate selectively deleterious mutations.

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From WikipediaNegative selection - Wikipedia(natural_selection)

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In natural selection, negative selection[1] or purifying selection is the selective removal of alleles that are deleterious. This can result in stabilizing selection through the purging of deleterious variations that arise.

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Purging of deleterious alleles can be achieved on the population genetics level, with as little as a single point mutation being the unit of selection. In such a case, carriers of the harmful point mutation have fewer offspring each generation, reducing the frequency of the mutation in the gene pool.

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Wouldn't Shapiro have defined "purifying selection" if he was not using the term in its ordinary sense?

Shadow71,Can you indicate, in your own words, how this paper supports your argument? I could make some guesses about the Ho paper, but this Badyaev paper covers a lot of ground.

You seem to have a gross conceptual error regarding selection. Only the beneficial mutations are selected for what? You seem to believe that selection is something that occurs before the mutations are passed on to offspring. Am I reading you correctly?That is not what Shapiro or Wright present in their papers. Shapiro says that selection (i.e. purifying selection, or negative selection) happens due to competition for resources in a new ecology. That's clearly selection after creating/conceiving a new entity with a non-random mutation. I would think the answer to your question, as presented in Shapiro's paper ought to be obvious given the above, and an understanding of what natural selection means.

Shadow71, I hope you will molbiogirl's questions. But I did want to summarize my understanding.My own understanding is that the only thing presented so far that purports to explain evolution without natural selection is Ho's talk. Shapiro and Wright discuss non-random mutations acted on by natural selection. Cairns' Origin of mutants has been self refuted, and Zheng's paper was actually damaging to s71s cause.Non-random mutations plus natural selection, in my opinion, don't get us away from evolution as Darwin understood it.There are some other papers, but their relevance is still under discussion. (Ho, and Badyaev)What concerns me is that you do not seem to know what natural selection is, and cannot seem to recognize selection when scientist mention it in their papers. Yet, that's pretty much the portion of modern theory that Darwin did have a handle on in Origin of Species. How can a discussion of modifications to the current theory be meaningful without knowing what the current theory is?Also, it is helpful when you sprinkle some of your own commentary in between quotes from the papers when you present them. You do this sometimes, but not often enough. I have no idea what this sentence means. At some point, we need to agree on what definition of directed you are insisting on, so that we can meaningfully discuss it. In some sense, natural selection directs evolution.

Of course all terms are mere labels.Shapiro uses the term macro-evolution to refer to evolution by a different mechanism than that used for micro-evolution.On the other hand, in discussions here, we have typically used the term macroevolution to refer to an accumulated microevolution. Creationists have sometimes insisted that such accumulation is somehow limited from producing new kinds.I'm not sure which definition of macroevolution is the "correct" one, but I believe at least a couple authors cited in this discussion have used definitions similar to Shapiro's.

Shapiro speculates that macroevolution is ecological stress driven mutation mechanisms that generate complex structures. Microevolution is a slower mechanism that uses random mutations.Shadow71 has quoted sections of Shapiro's work using these definitions.

Perhaps I have overstated a bit. Shapiro's idea is that stress invokes mechanisms that are targeted at locations that will produce novel complex structures, while random mutation have a much lower likelihood of doing so. Shapiro discusses such might be the case.In any event, Shapiro describes that under stress there is a higher mutation rate, and higher likelihood of a mutation affecting a relevant biological function. When the stress is relieve, strictly random mutations at a lower rate occur.You'll have to read the paper to see if you believe that Shapiro is convincing.Wright describes some similar effects and some evidence. I don't recall if she uses the terms micro/macroevolutionI'm not defending either paper, but I don't call it word salad. If nothing else, macroevolution differs by using mutations that are responsive to stress (in frequency and/or location) and working faster than microevolution through strictly random mutation. And yes some evidence is cited.Shapiro's paper has a combination of speculation and some evidence. You'll have to judge credibility for yourself. I'm not a biologist, but I don't think the "word salad" criticism is justified.

Shadow71, this is ridiculous. How much of this data dump is actually relevant to this discussion. Most of this stuff is clearly not epigenetics related. We're not doing discovery here.

I'd never heard of the guy, but there are some videos on youtube with Pigliucci debating Kent Hovind and Robert Allen. Massimo handles himself pretty well.

Yet you don't even know what natural selection is. Shapiro talks about the role of negative selection on genetic engineering produced changes and his words won't enter your head.We know you are motivated reader who does not understand biology particularly well. You've been caught in any number of interpretation errors when reading these papers, all in favor of your own position. So why would anyone accept your reading of Pigliucci paper over Pigliucci's own interpretation?