Does the Darwinian theory require modification or replacement?

Just to clarify, I don't think the insertion site into the bacterial genome is as non-specific as you seem to be making out here, although it may be and it is certainly subject to errors since the review details cases where the CRISPR locus has lost its leader sequence and consequently cannot incorporate new spacers or initiate the immunity effect. My main point is that the PAM motifs are not highly specific. As an example I searched the genome of Enterobacteria phage lambda for the NNGGNG motif and got 748 hits just for that one motif, the longer motif (NNAGAAW) has 111 matches.I certainly see no reason why a substantial bacterial population, probably in the millions or billions of cells, couldn't rapidly incorporate all of such a small number of protospacer sequences into the complementary CRISPR locus for that PAM.Reading another review (Al-Attar et al., 2011) brings up a particularly relevant point ... So in fact the PAM sequence may not have a role in which spacer sequences are incorporated but only in which persist.TTFN,WKEdited by Wounded King, : No reason given.

As I understand it the system is more specific than that and new spacer sequences and their accompanying repeat sequence are incorporated directly adjacent to the leader sequence (Figure 2, Karginov and Hannon, 2010). In this case proximal and distal are being used to describe the distance of elements from the leader sequence.The things from Al-Attar et al. are in reference to the nature of the proto-spacer sequences themselves in their native genomic context, they don't seem to favour any particular type of sequence and they have no apparent bias for a particular DNA strand.The conclusion to the Shah paper states ... The orientation in which they are incorporated into the CRISPR locus is apparently determined by the orientation of the PAM sequence. Though given the other speculation in that paper perhaps we should term it the orientation that confers a fitness effect from the spacer.It may also be the case that there are a whole lot of cases selected against where the spacer inserted into another region entirely or into a distal region of the CRISPR locus or on the wrong side of the leader. The actual existence of such cases seems purely hypothetical at the moment and there is nothing in the literature we have discussed to suggest it. Ain't that the truth!TTFN,WK

Like Percy said, if you want to discuss whether the system qualifies as "dedicated, nonrandom and beneficial" then you should join the conversation Percy and I were having.I think I have made a reasonable case that the choice of sequences incorporated is not non-random in any meaningful sense, beyond perhaps a variable specificity for certain common motifs occurring hundreds of times even in the small genomes of bacteriophages.I think there is a good argument to be made that the site of incorporation seems to be directed by whatever the incorporation mechanism is. But this is no more non-random than many already widely accepted mechanisms such as VDJ recombination. There is a slight distinction given that any derived benefit is heritable in this case, but then as I have already said many times, there is a good case to be made that the majority of bacterial evolution is Lamarckian in terms of being the inheritance of acquired characteristics.I think there is also considerable reason to doubt that every incorporation into the CRISPR loci is necessarily beneficial on the basis of post-hoc surveys of incorporations in populations under selective pressure. What would be required is to remove the selective pressure using some sort of bacteriophage that was non-lytic and didn't put a significant strain on the host cell, or alternatively to co-infect with such a strain if stress from infection was required to trigger the system. The population could then be assayed for incorporation of sequences at CRISPR loci which came from the non-selective strain.As to dedicated, this seems somewhat subjective. Certainly the CRISPR system does function as a defence mechanism against bacteriophage but whether this is its whole functionality is unclear. There are a number of CRISPR loci which lack the associated CAS and Cascade proteins.So if you want to actually discuss the CRISPR system nothing is stopping you, but you seem once again simply to tell us what other people have said and rely on that to carry your argument.TTFN,WK

I'd be pretty happy with Moran's definition by and large. It still won't cover everything that might be considered an evolutionary event though.For instance it wouldn't cover the intial events in an endosymbiosis such as that which led to the mitochondria, it would only pertain when the genomes began interacting to enforce the symbiotic relationship, i.e. through genomic reduction of the endosymbiont or through the incorporation of the endosymbiont's genetic material into the host genome.TTFN,WK

I think you should coherently define information for us or just stop posting here. At the moment you are in three different threads promoting exactly the same nonsense.TTFN,WK

For heaven's sake Percy, at least one of those threads is one he specifically opened to discuss Information's role in evolution.Should we put it more in the picture?. The last thing we need is for him to open up yet another one for exactly the same topic! Perhaps instead the moderators could reccommend he confine his theories to just one of the 2 threads, the other being New theory about evolution between creationism and evolution., he already has specifically to discuss them.TTFN,WK

Way to miss the point, no one doubts that the system is beneficial the question is whether any given incorporation by the system is beneficial.The Wiedenheft paper doesn't seem to be making any new points that I can see. The specificity they are talking about is in the actual operation of the immunity system in defence, i.e. the way already incorporated spacer sequences target their counterparts in the phage genome. they do mention that the sequences incorporate site-specifically within the CRIPSR locus, but I've already said that.It certainly doesn't counter my point that the sequences themselves which are incorporated seem random.I really wish you would try and develop an ability to argue in your own words with appropriate links rather than just plonking down badly formatted walls of text you have taken from others.TTFN,WK