"You don't understand the history of transposons!"
Oh yeah, I don't know what a genome is. That is almost so imbecilic it isn't even an insult.
Look at the chimp genome comparson paper you yourself cited. It is a direct comparison between the genomes of Homo sapiens and Pan troglodytes. How much of the comparison is a comparison of transposable elements? In the section on genome evolution, there are subsections on nucleotide substitutions, insertions and deletions, transposable element insertions, and large scale rearrangements. One subsection out of four, in other words, concerns transposons of various kinds. The next section, on gene evolution, does not touch on transposition at all. And in fact, the only really detailed quantitative consideration of evolutionary rates is in the section on gene evolution. Then there's a section which you claim is handwaving, on human population genetics. A 18 1/2 page paper, in other words, on comparative genomics, between two very closely related species where the transposons have been well studied and where they should provide more information than usual, actually deals with transposons for less than two pages, and largely reaches negative conclusions.
And this is the area that you claim has eclipsed gene analysis, which is '1980's genetics'!
and don't know the difference between a molecular evolutionary analysis and a genome comparison.
Nor, evidently, do the authors of 'Initial sequence of the chimpanzee genome and comparison of the human genome', since they spend a far larger fraction of the paper on moleuclar evolutionary gene analysis than on transposed element analysis.
You make sweeping, broad statements that are utterly unwarranted, and then defend them, if at all, by claiming the rest of the world doesn't know what it's talking about.
"You don't understand the history of transposons!"
Yes because it was the section on gene evolution at the protein coding level: We next sought to use the chimpanzee sequence to study the role of natural selection in the evolution of human protein-coding genes..
Again, you don't seem to know what gene means compared to genome.
As far as your other point, yes, the initial report didn;t focus on this, but the second sister report, A genome-wide comparison of recent chimpanzee and human segmental duplications, was specific to these questions of chromosome structure.
Actually, no. I have always said this is coming from stidies that are ongoing made possible by the various genome projects.
Here is an example from a recent Genome Research Identification of transposable elements using multiple alignments of related genomes:
Repeat elements make up a large fraction of many eukaryotic genomes. Within these regions, the occurrence of Transposable Elements is rampant. The term Transposable Elements (TEs) groups several subclasses of elements that replicate in the genome, either through the reverse transcription of an RNA intermediate (class I elements), or autonomously from DNA to DNA by excision and repair (class II elements). Class I elements are further grouped by the presence (LTR elements) or absence (LINE and SINE elements) of long terminal repeats. Class II elements are largely comprised of elements with terminally inverted repeats (TIR elements). TEs make up large portions of the middle- and high-repetitive segments of genomes and are mostly found in the heterochromatin and centromeric regions (Pardue et al. 1996Go; Junakovic et al. 1998Go). Studies show TEs can be deleterious to hosts (Green 1988Go; Deininger and Batzer 1999Go) and approximately one-half of Drosophila melanogaster mutations are attributed to TEs (Finnegan 1992Go). Increasingly, evidence points to other contributions of TEs in the evolution of the host genome and even in shaping chromosome structure (Pardue et al. 1996Go; Kidwell and Lisch 1997Go; Labrador and Corces 1997Go; Pardue and DeBrayshe 1999Go). They are also the chief cause of gapped regions and poor annotations in up to 10% of currently sequenced genomes. Despite some knowledge about sequence structure in transposons, for example, they typically contain open reading frames in the interior or some characterizing repeat sequences at the ends, their mechanisms for replication are poorly understood, and their classification into families is far from complete. An accurate catalog and phyletic mapping of the instances of TE insertions will help elucidate TE contribution to genetic variability in eukaryote genomes, and refine assemblies of sequenced genomes (Holmes 2002Go; Bennett et al. 2004Go).
My bold, but all the paragraph is pertinent to this discussion.
In no way is this some sort of claim that the rest of the world doesn't know what it is talking about.
Please, try to be stay on subject (as you have at times) and refrain from speciousness.