"You don't understand the history of transposons!"
Posted on 04/21/2006 9:17:58 PM PDT by Right Wing Professor
Immunology had an unexpected and decisive part in challenging the claims of 'Intelligent Design' proponents at the US trial on the teaching of evolution in public schools in Dover, Pennsylvania.
The latest skirmish in the ongoing controversy about the teaching of evolution in US schools ended decisively on 20 December 2005, when the introduction of 'Intelligent Design' (ID) in a public school biology class was struck down by US Federal Judge John E. Jones as an unconstitutional establishment of religion. The case, 'Kitzmiller et al. v. Dover Area School District', was brought by 11 parents from Dover, Pennsylvania, represented pro bono by the Philadelphia law firm Pepper-Hamilton, together with the American Civil Liberties Union and Americans United for the Separation of Church and State and assisted with scientific support by the National Center for Science Education, the Oakland, California–based nonprofit organization devoted to combating creationism. The parents challenged the school district's requirement that administrators read to ninth graders a disclaimer raising doubts about evolution, suggesting ID as a better alternative explanation for life's diversity and referring students to the ID supplemental textbook Of Pandas and People, 60 copies of which had been donated to the school library.
Although the magnitude of the win for science education was a surprise to some, the actual outcome of the trial was in very little doubt, for many reasons. Board members had made clear, through public declarations at board meetings and to the media, their intention to have some form of religious creationism taught in biology classes alongside evolution, which they considered akin to atheism. US Supreme Court rulings have established and repeatedly reaffirmed that governmental policies with the purpose or effect of establishing religion are inadmissible because they violate the First Amendment of the US Constitution. It also did not help their cause that Judge Jones found that some of the board members "either testified inconsistently, or lied outright under oath" about some statements and about the source of the donated Of Pandas and People books, the money for which was raised by one of the board members at his own church.
The most important and far-reaching aspect of the decision, however, was that the judge went beyond the narrow issue of the school board's actions and ruled broadly on the nature of ID and its scientific claims. After a 6-week trial that included extensive expert testimony from both sides on science, philosophy and the history of creationism, Jones ruled that ID is not science but "creationism re-labeled." Coming from the George W. Bush–appointed, lifelong Republican and church-going Judge Jones, the ruling was all the more stinging for ID advocates and made the predictable charge of 'judicial activism' harder to sustain. The ruling is likely to have a substantial effect on many other ongoing cases (and possibly future court decisions) regarding ID and evolution in science curricula from Georgia to Kansas to Ohio.
More fundamentally, the decision represents a considerable setback for ID advocates, who claim that some examples of biological complexity could only have originated by intelligent mechanisms, and for their movement's now almost-20-year-old effort to gain a foothold in school curricula and project an aura of scientific respectability. The ruling is also of great interest to scientists, not only because of its importance for science education but also because much of the trial's extensive expert testimony, both for and opposed to ID, focused directly on weighty scientific topics. Judge Jones analyzed and dismissed the core 'scientific' assertions of the ID movement—immunology had an unexpectedly large and relevant part in his reaching those conclusions.
Although the field of evolutionary and comparative immunology has a long and rich history, dating back at least to 1891 (ref. 1), and remains an exciting and rapidly progressing area of research, its direct involvement in the controversies about evolution in schools can be attributed mainly to Michael Behe, professor of biochemistry at Lehigh University (Bethlehem, Pennsylvania), leading ID advocate and star expert witness for the defense at this trial. In his 1996 book Darwin's Black Box, a commonly cited example of ID-based 'science', Behe devotes an entire chapter to the immune system, pointing to several of its features as being particularly refractory to evolutionary explanations. Behe's antievolutionary argument relies on a characteristic he calls "irreducible complexity": the requirement for the presence of multiple components of certain complex systems (such as a multiprotein complex or biochemical cascade) for the system to accomplish its function. As such irreducibly complex systems by definition work only when all components are present; Behe claims they cannot arise by the sequential addition and modification of individual elements from simpler pre-existing systems, thus defying 'darwinian' evolutionary explanations.
By analogy with human 'machines', ID advocates argue that irreducibly complex systems are most likely the product of an intelligent, teleological activity. Several scientists, including ourselves, have criticized Behe's argument, pointing out how irreducibly complex systems can arise through known evolutionary mechanisms, such as exaptation, 'scaffolding' and so on. Nevertheless, with few exceptions, the topic has been explicitly addressed mostly in book reviews, philosophy journals and on the internet, rather than in peer-reviewed scientific publications, which may have allowed it to mostly escape the critical scrutiny of scientists while gaining considerable popularity with the lay public and, in particular, with creationists.
In chapter 6 of Darwin's Black Box, Behe claims that the vertebrate adaptive immune system fulfills the definition of irreducible complexity and hence cannot have evolved. Some of his arguments will seem rather naive and misguided to immunologists. For example, Behe argues that working antibodies must exist in both soluble and membrane form, which therefore must have appeared simultaneously because one form would be useless without the other. He also claims that antibodies are completely functionless without secondary effector mechanisms (such as the complement system), which in turn require antibodies for activation. These putative 'chicken-and-egg' conundrums are easily belied by existing evidence (http://www.talkdesign.org/faqs/Evolving_Immunity.html).
Behe also spends considerable time on what he alleges is a hopelessly intractable problem in evolutionary immunology: the origin of the mechanism of somatic recombination of antigen receptor genes. He argues that because variable-diversity-joining recombination is dependent on the coexistence of proteins encoded by recombination-activating genes (RAG proteins), recombination signal sequences and antigen receptor gene segments, it is ultimately too complex to have arisen by naturalistic, undirected evolutionary means because the three components could not have come together in a 'fell swoop' and would have been useless individually. In fact, Behe confidently declares that the complexity of the immune system "dooms all Darwinian explanations to frustration". About the scientific literature, Behe claims it has "no answers" as to how the adaptive immune system may have originated2.
In particular, Behe criticizes a 1994 Proceedings of the National Academy of Science paper advancing the hypothesis that the RAG system evolved by lateral transfer of a prokaryotic transposon, an idea initially suggested in a 1979 paper and expanded in 1992. Behe ridicules the idea as a "jump in the box of Calvin and Hobbes," with reference to the comic strip in which a child and his stuffed tiger imaginary friend use a large cardboard box for fantasy trips and amazing physical transformations.
The timing for the criticism could not have been worse, as soon after publication of Darwin's Black Box, solid evidence for the transposon hypothesis began accumulating with the demonstration of similarities between the variable-diversity-joining recombination and transposition mechanisms and also between shark RAG1 and certain bacterial integrases. Since then, a steady stream of findings has continued to add more substance to the model, as RAG proteins have been shown to be capable of catalyzing transposition reactions, first in vitro and then in vivo, and to have even closer structural and mechanistic similarities with specific transposases. Finally, in 2005, the original key prediction of the transposon hypothesis was fulfilled with the identification of a large invertebrate transposon family bearing both recombination signal sequence–like integration sequences and a RAG1 homolog. When faced with that evidence during an exchange on the internet, Behe simply 'shrugged' and said that evidence was not sufficient, asking instead for an infinitely detailed, step-by-step mutation account (including population sizes, relevant selective pressures and so on) for the events leading to the appearance of the adaptive immune system (http://www.pandasthumb.org/archives/2005/06/behes_meaningle.html).
That background set the stage for the crucial face-off at the trial. Kenneth Miller of Brown University, a cell biologist and textbook author who has written extensively on evolution and creationism, was the lead witness for the plaintiffs. Over the course of his testimony, Miller did his best to explain to the nonscientist audience the mechanisms of antibody gene rearrangement and the evidence corroborating the transposon hypothesis. Then, 10 days later, Behe took the stand. During cross-examination by the plaintiffs' lead counsel Eric Rothschild, Behe reiterated his claim about the scientific literature on the evolution of the immune system, testifying that "the scientific literature has no detailed testable answers on how the immune system could have arisen by random mutation and natural selection." Rothschild then presented Behe with a thick file of publications on immune system evolution, dating from 1971 to 2006, plus several books and textbook chapters. Asked for his response, Behe admitted he had not read many of the publications presented (a small fraction of all the literature on evolutionary immunology of the past 35 years), but summarily rejected them as unsatisfactory and dismissed the idea of doing research on the topic as "unfruitful."
This exchange clearly made an impression on Judge Jones, who specifically described it in his opinion:
In fact, on cross-examination, Professor Behe was questioned concerning his 1996 claim that science would never find an evolutionary explanation for the immune system. He was presented with fifty-eight peer-reviewed publications, nine books, and several immunology textbook chapters about the evolution of the immune system; however, he simply insisted that this was still not sufficient evidence of evolution, and that it was not 'good enough.'
We find that such evidence demonstrates that the ID argument is dependent upon setting a scientifically unreasonable burden of proof for the theory of evolution.
Other important scientific points stood out during trial relating to other purported irreducibly complex systems such as the flagellum and the clotting cascade, the nature of science itself and the lack of experimental tests and supporting peer-reviewed publications for ID. But the stark contrast between the lively and productive field of evolutionary immunology and the stubborn refusal by ID advocates such as Behe to even consider the evidence was undoubtedly crucial in convincing the judge that the ID movement has little to do with science. As Rothschild remarked in his closing argument,
Thankfully, there are scientists who do search for answers to the question of the origin of the immune system. It's the immune system. It's our defense against debilitating and fatal diseases. The scientists who wrote those books and articles toil in obscurity, without book royalties or speaking engagements. Their efforts help us combat and cure serious medical conditions. By contrast, Professor Behe and the entire intelligent design movement are doing nothing to advance scientific or medical knowledge and are telling future generations of scientists, don't bother.
Evolutionary immunologists should be pleasantly surprised by and proud of the effect their scientific accomplishments have had in this landmark judicial case. This commentary is meant to acknowledge their contribution on behalf of the Dover families, their lawyers and all the activists for rigorous science education who have participated in these proceedings. Most importantly, however, the Dover case shows that no scientific field is too remote from the hotly debated topics of the day and that no community is too small and removed from the great urban and scientific centers to be relevant. Immunologists must engage their communities and society at large in events related to public perceptions about science. Now more than ever, the participation of scientists is essential for the crafting of rational policies on scientific research and science education.
If we take the sample provided by you it is 100%.
Do you want to be silly or do you want to talk about evolution and the most recent aspects that are being elucidated in the genomic era?
It's not a false assertion and I actually demonstrated in your own example that the one article in that ToC on comparative genomics used transposable element distribution.
I'm beginning to think you don't quite grasp what a genome actually is.
"this type of DNA [repeat elements] is a major portion of the genome" is also false or nonsense?
I do not think you meant to say that this is nonsense and am giving you every opportunity to make clear what is nonsense so as to make no mistakes as to what you are saying.
How do you suggest this be resolved. You want to argue over the number of papers published that have done genomic comparisons using different methods.
OK. Rather a side issue, but it can be addressed by finding every article that has compared genomes and seeing what types of analyses were done. I would agree that number of genes, homology between gene sets, rRNA homologies were done. Transposable element analysis is much harder to do which is why it is a current focus.
I will initially refer you to the Chimp genome papers in Nature. Two were published One, the basic initial report:
Nature 437, 69-87 (1 September 2005) | Initial sequence of the chimpanzee genome and comparison with the human genome
including a section on genome evolution wherien nucleotide substitutions were examined, as well as insertions and deletions. Insertion of transposable elements were speficially looked at and catalogued.
The secomd sister article, Nature. 2005 Sep 1;437(7055):88-93. A genome-wide comparison of recent chimpanzee and human segmental duplications.
This touches exactly on the issue of transposable elements on genomic evolution. In the last pre-discussion paragraph the author's state the importance of transposons to genomic structure and evolution:
We propose that most of the asymmetrical increase of duplicated DNA in the chimpanzee lineage has emerged as a mechanistic consequence of changes in chromosome structure and not selection. The subterminal caps are an idiosyncratic structural aspect of African great ape chromosomes28, which are generally regarded as heterochromatic. Similar to human pericentromeric DNA, the regions have served as sinks for duplicative transposition and expansion of particular euchromatic segments. This process has led to an overall increase in chimpanzee genome size of at least 16 Mb since human and chimpanzee separated. It is interesting that the same region that represents the site of chromosome 2 fusion29 in the human lineage has undergone a segmental duplication hyperexpansion within the subterminal region of chimpanzee chromosomes. This may suggest an inherent instability of this segment of DNA, further extending the association of segmental duplication and chromosomal rearrangement without a direct cause and effect relationship
Science also did an article about the findings associated with the chimp genome and wrote:
But as suggested by earlier work on portions of the chimp genome, other kinds of genomic variation turn out to be at least as important as single nucleotide base changes. Insertions and deletions have dramatically changed the landscape of the human and chimp lineages since they diverged. Duplications of sequence "contribute more genetic difference between the two species--70 megabases of material--than do single base pair substitutions," notes Evan Eichler, also of UW, Seattle, who led a team analyzing the duplications. "It was a shocker, even to us."
From Chimp Genome Catalogs Differences With Humans, Elizabeth Culotta, 9-2-05 Science
The centrality of transposable elements to evolution is becoming more clear with every passing day.
The analysis consists pretty much only of breakpoints. Coincidntally to our discussion, this chromosome contains FRA3B.
Breakpoints were compared with other primates to look at evolutionary questions.
One excerpt here:
Further comparative FISH analysis revealed that a large-scale pericentric inversion occurred in the ancestor of the African apes and is present in modern human chromosome 3 as well as the chimpanzee and gorilla orthologues, but not in orang-utan or Old World monkeys14. Two scaffolds from the Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC) rhesus macaque Mmul_0.1 assembly were found to span both breakpoints of the human inversion (Fig. 2; see Supplementary Table 4 for breakpoint details). The macaque 5' breakpoint is characterized by a short homologous GTGG track (Fig. 2b) and by a mammalian interspersed repeat (MIR) that was split by a segmental duplication before the inversion resulting in one part, designated MIR A, present in boundary I and a second part, designated MIR B, present in boundary III (see Fig. 2a). The MIR at the 3' end of boundary III was present in the segmental duplication and may have been involved in the insertion event. A number of simple repeats and low complexity regions were found within 1 kb of the breakpoint (see Supplementary Table 5). Each of these elements, including retrotransposons15, short homologous sequence and alternating purine-pyrimidine tracks16 have been reported for many other breakpoints.
My bold. Break point analysis, as Stultis brought up is extremely important to understanding evolutionary relationshsips and mechanisms and transposon and similar elements are associated with these breakage points.
It is a flat out lie to claim that only one paper in the issue was on comparative genomics. Almost all of them were.
I didn't say it was nonsense. Learn to read.
Indeed. And the evolutionary conclusions that could be drawn from the transposable elements were limited.A high-proportion of the HERV-K insertions occurred after hominoid chimp divergence, making them useless for interspecific comparisons. Some of the comparisons of subtypes of HERV-K were useful, but the transpositions themselves appear to occur largely on timescales that are fast compared with species divergence. There appears to be little diversity among humans in the HERV-K insertions, but that may be a result of our species' genetic homogeneity.
Comparison of SINEs between human and chimp genomes may be similarly disappointing. Humans have three times the number of lineage specific SINEs. And quoting the initial chimp genome paper "In any case, the presence of such anomalies suggests that caution is warranted in the use of single-repeat elements as homoplasy-free phylogenetic markers." The chimp genome paper discusses other classes of transposable elements, and some of them look more phylogenetically promising, but to claim they are likely to replace genes in comparative genomics is grossly optimistic and unwarranted.
Retract your false assertions and apologize. You breezed on this thread with a direct insult to me, and have continued throughout. I ignored your first few insults; then I asked you to stop; and when you refused, I decided that if you can't act like a civilzed human being, you don't deserve to be treated like one.
The first, Periodic Extinctions of Transposable Elements in Bacterial Lineages: Evidence from Intragenomic Variation in Multiple Genomes, was a comparative genomic study. -- and it was about transposons.
This, Explorative Genome Scan to Detect Candidate Loci for Adaptation Along a Gradient of Altitude in the Common Frog (Rana temporaria) is a genomic study, but not comparative.
One other, Genetic Structure and Evolutionary History of a Diploid Hybrid Pine Pinus densata Inferred from the Nucleotide Variation at Seven Gene Loci, seems related but looks only at 7 loci, not the genome.
Again, you seem not to know what genome or genomics means.
Research Articles:
Periodic Extinctions of Transposable Elements in Bacterial Lineages: Evidence from Intragenomic Variation in Multiple Genomes
Evolution of Circular Permutations in Multidomain Proteins
Diversity and Evolution of the Thyroglobulin Type-1 Domain Superfamily
Evolution of Programmed DNA Rearrangements in a Scrambled Gene
MBE Advance Access published on January 23, 2006
Diversification and Specialization of HIV Protease Function During In Vitro Evolution
Explorative Genome Scan to Detect Candidate Loci for Adaptation Along a Gradient of Altitude in the Common Frog (Rana temporaria)
The Evolutionary Rate of a Protein Is Influenced by Features of the Interacting Partners
An Analysis of Signatures of Selective Sweeps in Natural Populations of the House Mouse
A Tandem Gene Duplication Followed by Recruitment of a Retrotransposon Created the Paralogous Bucentaur Gene (bcntp97) in the Ancestral Ruminant
Genetic Structure and Evolutionary History of a Diploid Hybrid Pine Pinus densata Inferred from the Nucleotide Variation at Seven Gene Loci
Recombination Estimation Under Complex Evolutionary Models with the Coalescent Composite-Likelihood Method
Nuclear Gene Variation and Molecular Dating of the Cichlid Species Flock of Lake Malawi
The Evolutionary Origin of Peroxisomes: An ER-Peroxisome Connection
Genomic comparison that is possible today focus largely on repeat element distribution
You responded:
Your main point is nonsense in any case. Most molecular evolution analysis...
Again, you don't seem to know what a genome is and don't know the difference between a molecular evolutionary analysis and a genome comparison.
Again, genomic comparison today focuses largely on repeat element distribution.
I disagree and this has all ready taken place to a large extent. Fundamental to this is that it turns out that the repeat elements are such a major component of genomes and this wasn't known until the full genomes were sequenced.
The Science article I linked to article addresses this to some degree in relating how looking only at genes there is very little difference between chimp and human and the reasosn for our differences are in no way apparent. Gene relationships have been extensively examined over decades (hence my comment to you the other day that you have reached the 1980's) and the very high degree of homology doesn't seem to be able to explain the differences in species.
A clue that transposable element activity of some sort did appear in the 1980's and 90's with the sequencing of a number of G-Protein coupled receptor genes. It was found that many of these genes surprisingly were intronless. This was indicative of class I transposition having been involved in the evolution of this large and important class of genes. Other intronless genes have been found as well.
Breakage and recombination that can be mediated by transposons and repeats elements provide a mechanisms for chromosomal rearrangements (as McClintock was the first to discover) which fits well with an mechanisms for mutations over the course of evolution. This is combined with the epigentic understanding of gene regulation and eu/heterochromatin strucure/function associated with high repeat regions provides a basis for not only the structural chromosomal changes which define species and reflect evolution but a genetic regulatory mechanisms whereby regulation of genes which are essentially interchangable between species can provide for the vast differences in phenotype not reflected in the genotypes (ie the genes are pretty much the same so how do they specify human vs chimp).
As I pointed out, the most recent authoritaive genome study from the sequencing consortium just published in nature and analyzed these sort of questions.
"In any case, the presence of such anomalies suggests that caution is warranted in the use of single-repeat elements as homoplasy-free phylogenetic markers."
is that what I am talking about is not their uitilty as homoplsy-free markers, but their distribution (and discovery via analysis) throughout geneomes at regions of divergence.
Treating them as if they are genes with sequences that can be used to compare phylogeny based on homology would require probably more than caution, it just wouldn't be the thing to do.
Much of the focus in this area is to actually identify repeats. Using the first known characterized repeats or elements as if they are genes is not what is being addressed. So, yes, I agree with you about the approach you outline. But that is not what I am talking about.
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!"
Size isn't everything.
The Science article I linked to article addresses this to some degree in relating how looking only at genes there is very little difference between chimp and human and the reasosn for our differences are in no way apparent. Gene relationships have been extensively examined over decades (hence my comment to you the other day that you have reached the 1980's) and the very high degree of homology doesn't seem to be able to explain the differences in species.
You don't know that. Nobody knows that. Nobody really has a clue if the differences in non-coding regions have much effect at all; and until the relevant knockout experiments have been done, nobody will know. There are literally hundreds of thousands of differences in our coding DNA between humans and chimps.
Breakage and recombination that can be mediated by transposons and repeats elements provide a mechanisms for chromosomal rearrangements (as McClintock was the first to discover) which fits well with an mechanisms for mutations over the course of evolution. This is combined with the epigentic understanding of gene regulation and eu/heterochromatin strucure/function associated with high repeat regions provides a basis for not only the structural chromosomal changes which define species and reflect evolution but a genetic regulatory mechanisms whereby regulation of genes which are essentially interchangable between species can provide for the vast differences in phenotype not reflected in the genotypes (ie the genes are pretty much the same so how do they specify human vs chimp).
Whether transposition is an important source of genome variability is an entirely different issue from whether transposon analysis predominates in current comparative genomics. As I've said a hundred times, the source of genome variability is unimportant to the possibility of evolution; what matters is that variability exist and be heritable. However, Darwin knew no more about point mutations than he did about transposons. What he appreciated was that heritable variability was important.
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.
You don't know that. Nobody knows that.
I agree, which is why I wrote "doesn't seem".
Nobody really has a clue if the differences in non-coding regions have much effect at all;
No, people have clues. I linked to the Science comment article that talked about this.
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