Mendel wasn't entirely right

No, another half-a-dozen loci they genotyped also reverted.However, the reversion only occurred when their pet gene (hth) was homozygous mutant. Yes, and from self-fertilization of hth homozygous mutants to rule out issues of accidental pollen contamination. Unlikely based on the paper (assuming you mean "randomly mutated"):
- The reversion frequency (10%) was much higher than random mutation would allow.
- Non-revertant random mutations did not appear in the sequenced alleles above expected background.
- Perhaps most importantly - the revertants always had the same exact polymorphisms that were present in their "grandparents'", but not "parents'", genome.

Sorry, but your calculations are rather worthless. You've completely ignored selective forces.Honestly, even if the mechanism described slowed evolution to a crawl - so what? If it is a recently-evolved mechanism, it would have little impact on the evolutionary history of organisms carrying the system. If it is only present in a few species, it would only effect the pace of evolution in those species. commike37-I'm not sure why you think this is the first time Mendel's laws have been "violated". There have already been other threads in the forum discussing non-Mendelian genetics. If you search PubMed you'll find papers from the 1950's discussing non-Mendelian genetics.The report is an important finding, and it will be interesting to see if stands continued scrutiny, and to see if this phenomena is seen in any other species. As I think WK stated earlier, the massive amount of work done, especially in controlled genetic models such as flies, worms, and mice, would suggest that if a similar mechanism existed in these it would have likely been noticed. (Keep in mind that the plant model from the study has only been in use for about twenty years; flies and worms have been in use for over a century.)I looked at the original paper where the Hothead gene was cloned, and it seems that it is only present in plants, but they don't specifically state that it isn't found in non-plant species. Also, the sequence accession numbers they give in that paper for the Hothead genes are invalid (seems odd), so I can't do my own sequence-based search.My assumption is that the presence of the gene is non-plant species would have definitely been mentioned in the Nature article, since it would boost the relevance of the report astronomically.This (single, unconfirmed) study is important, but does not negatively impact major theories as you are presenting.

commike-Let me put my above "minimal impact" statement another way:At its simplest, the theory of evolution comes down to (1) natural selection acting on (2) mutation.So, you should ask yourself how the results of this study impact this process. Let's make a huge leap and assume the proposed "RNA-backup-genome" hypothesis is correct, and it applies to all species, and it has been present since the beginning of life.Since the hypothesis effects mutation, the natural selection "half" of evolution is unaffected, leaving the mutation portion to be examined.The RNA-backup hypothesis alters our understanding of the genetic template (a combined RNA/DNA genome is still a genetic template), and our understanding of inheritance (it is not always parent-to-child, and under specific instances of stress inheritance can occur from grandparent-to-child.) These differences involve the mode of inheritance, and may impact on the rate and fixation of mutations.Mutations still occur, and are still acted upon by natural selection.Evolutionary theory is unaffected.

Well, excuse me then for directly answering point #1 of your opening post: Also please excuse me for directly answering the question you pose in point #2 of your opening post: Okay, so you don't want to have a scientific discussion (then why are you citing scientific evidence???)Instead you want to argue the trustiworthiness of evidence, seemingly based on the idea that the study you cite points to some evidence that is NOT trustworthy. Whether or not the specific evidence in question is trustworthy deserves some attention (rather than your assumption), as does your attempt to incorrectly extrapolate it to the theory of evolution. Yet it was based on incorrect thought regarding the process of science, as well as the understanding of inheritance and its links to evolution. If you are uninterested in filling in these gaps in your understanding in favor of dismissing them as "technical", your "philosophical" issues will continue to be tainted by your false assumptions.

Where do you include the input of selection in your decay function?Is your decay function "philosophical" or "technical"?

Look at the quote again - it is only rare in the presence of the HTH gene. One possibility that comes to mind is that the unknown "backup" mechanism was selected for prior to the arisal of the HTH gene.Perhaps the backup mechanism made a species more fit for a part of its history/environment, but the same mechanism later reduced fitness - the HTH gene/system may have been selected for to "override" the "backup" system.Hopefully that makes sense - the key is that we can't look at a fully intact modern organism and assume that a characteristic of interest evolved in an identical organism without that system. Instead, the characteristic may have evolved in a very remote ancestor species bearing no resemblance to the modern species and living under quite different conditions.

Of course he is, when describing modern Arabidopsis - I didn't say otherwise.My comments referred to a potential evolutionary history of Arabidopsis; that is, that we don't know that the mechanism was always as specifically and rarely utilized in the species' evolutionary history as it is in modern Arabidopsis.I don't see how you comments counter that point.

You can't really disagree with me on that point because I never made that argument. Again, I never claimed it was widespread, not even in speculation. My intent was not to try to explain away the finding's impact on evolution with speculation. My intent was to try to explain to judge that we can't assume that a mechanism evolved intact in the biological context we now see it; in other words to counter the same sort of argument that many attempt to use to show irreducible complexity.Perhaps I would have better served this cause using a better-documented example such as the blood clotting cascade; however, I'm not sure why you are so intent on argument to the point that you are arguing against statements I have not made.

"What about the germ cells?" was my first thought on reading their conclusion. Separate of reversion, does it make sense that mosaicism restricted to germ cells could be inherited?Pollen-based studies are fairly routine in Arabidopsis, since some have used it is as a way to simplify genetic analysis by looking at haploid genomes. I see no reason that an allele that exists in 10% of pollen couldn't be rather easily detected, even just by a simple PCR.Intuitively, germ cell mosaicism is a more plausible explanation to me than a back-up dsRNA genome, which as you say should have sent up some sort of flag with expression analysis - though perhaps the back-up is restricted to the germ cells, and I'm not sure what kind of expression analysis has been done in germ cells (particularly pollen).Lots of unanswered questions -