An open reply to Mark Kennedy

I have discussed these bogus homology arguments from things like ERVs and watch them crumble into dust and ashes.

Since you are such a fan of cladistics perhaps you would like to apply these principles to the 100 families of ERVs present in Chimpanzee genome but absent from our own.

Really? I crushed you once. You want to go around again?

Sure. We can predict that these 100 families of ERV's will not be found in orthologous positions in other apes. And guess what? THEY ARE NOT FOUND IN ORTHOLOGOUS POSITIONS IN OTHER APES, JUST AS THE THEORY OF EVOLUTION PREDICTS. Cladistics works.

Sure, but remember it's not 1% like TO told you, it's not 4% like you finally admitted but were still in error about. It's 8% just like it's not 98% it's closer to 95%. You might want to spend a little time reading the current literature instead of relying on bogus TO articles and dated material.

Crushed me If you got a single substantive point or accurate fact in it must have been by accident.

The articles I used were not TO articles. They were the peer reviewed human and chimp genome papers.

Secondly, none of the numbers changes the fact that the placment, LTR divergence, and overall ERV sequence divergence form the same nested hierarchy as predicted by the theory of evolution. Common ancestry is the only explanation for this pattern. You consistently ignore the placement of these ERV's in the genome, both now and before. You consistently ignore the sequence divergence of these ERV's, both now and before.

Sure, dated material that was saying that ERVs made up 1% of the human genome. It's more like 8%, or at least it was during our last debate.

You wanted to pretend that they are all virtually identical and all found in the exact same places with the exact same mutations, thats just not true.

Common ancestry is not the only explanation for the handful of anecdotal and coincidental patterns you cite but don't really understand.

You are ignoring the substance of the argument, hundreds of Class I ERVs, millions of base pairs long were introduced at the time of the split or just before. Why are PtERV1-like elements present in the rhesus monkey, olive baboon and African great apes but not in human, orang-utan or gibbon.

I'm lagged like you wouldn't believe so you'll have to cut me some slack. At any rate, post an invitation anytime you feel the urge. I strongly suggest you either drop the ERV thing or get some current research material.

Endogenous retrovirus loci provide no less than three sources of phylogenetic signal, which can be used in complementary fashion to obtain much more information than simple distance estimates of homologous sequences. First, the distribution of provirus-containing loci among taxa dates the insertion. Given the size of vertebrate genomes (>1 × 109 bp) and the random nature of retroviral integration (22, 23), multiple integrations (and subsequent fixation) of ERV loci at precisely the same location are highly unlikely (24). Therefore, an ERV locus shared by two or more species is descended from a single integration event and is proof that the species share a common ancestor into whose germ line the original integration took place (14). Furthermore, integrated proviruses are extremely stable: there is no mechanism for removing proviruses precisely from the genome, without leaving behind a solo LTR or deleting chromosomal DNA. The distribution of an ERV among related species also reflects the age of the provirus: older loci are found among widely divergent species, whereas younger proviruses are limited to more closely related species. In theory, the species distribution of a set of known integration sites can be used to construct phylogenetic trees in a manner similar to restriction fragment length polymorphism (RFLP) analysis.

Second, as with other sequence-based phylogenetic analyses, mutations in a provirus that have accumulated since the divergence of the species provide an estimate of the genetic distance between the species. Because, for any given provirus, it is highly unlikely that there will be selection for or against any specific sequence, it is safe to assume that the rate of accumulation of mutations approximates the rate of their occurrence, with appropriate corrections for reversion. Analysis of closely related proviruses integrated at different sites should also reveal regional differences in mutation rates.

Third, sequence divergence between the LTRs at the ends of a given provirus provides an important and unique source of phylogenetic information. The LTRs are created during reverse transcription to regenerate cis-acting elements required for integration and transcription. Because of the mechanism of reverse transcription, the two LTRs must be identical at the time of integration, even if they differed in the precursor provirus (Fig. (Fig.11A). Over time, they will diverge in sequence because of substitutions, insertions, and deletions acquired during cellular DNA replication. Although it has been noted that the divergence between the two LTRs of an ERV can serve as a molecular clock (8, 15, 18, 25), there are no reported prior attempts to utilize the LTRs of individual ERV loci as a source of phylogenetic signal.

YOU NEED TO EXPLAIN WHY THESE ERV'S ARE FOUND AT ORTHOLOGOUS POSITIONS AND WHY THE PATTERN OF ORTHOLOGOUS ERV'S MATCHES THE PREDICTIONS MADE BY THE THEORY OF EVOLUTION.

Quoted for emphasis. But I don't think creationists can ever explain this other than "Goddidit."

Pedantic overemphasis of esoteric rhetoric chanted in the absence of an explanation for Class 1 ERVS that were neither predicted nor explained.

You wanted to pretend that they are all virtually identical and all found in the exact same places with the exact same mutations, thats just not true. Common ancestry is not the only explanation for the handful of anecdotal and coincidental patterns you cite but don't really understand. You are ignoring the substance of the argument, hundreds of Class I ERVs, millions of base pairs long were introduced at the time of the split or just before. Why are PtERV1-like elements present in the rhesus monkey, olive baboon and African great apes but not in human, orang-utan or gibbon.

Pedantic overemphasis of esoteric rhetoric chanted in the absence of an explanation for Class 1 ERVS that were neither predicted nor explained.