Replies

And again, you are ignoring the chimp genome data.

Lie #7. No, I'm not.

You still have not commented on it.

Because others have already pointed out why it doesn't help your case any.

Your intrasigence is strange in that none of it is in opposition to evolution.

Exactly, which is why I'm not bothering to "refute" it as you oddly expect me to, and why my comfort with the material is hardly a case of "intrasigence [sic]".

You seem to have an ego issue more than anything.

You seem to have a problem making your case on the facts, so you keep issuing frantic and irrelevant ad hominems. If I actually had "an ego issue" I'd care, but since I don't, your antics are just tiresome and pathetic.

You made a big deal about repeat elements proving common descent -- because you read it in a t.o. tract and spammmed it here.

Oh look, another empty ad hominem.

Look, son, not only have I have *not* made "a big deal about repeat elements", in fact I haven't really commented on them much at all. In fact, ironically the ONLY time in my 15,755 archived FreeRepublic posts in which the term "[any word starting with "repeat"] [any word starting with "element"]" even occurs is in the following past exchange WITH YOU, in which I pointed out that I *wasn't* making any big deal about repeat elements:

and the distribution of the repeat element is due to transposition events that occur subsequently over time.
Yes it is, but it's not the repeat elements that provide the most direct evidence of common ancestry, so that advanced topic was left out of the basic presentation. Whoop-de-do -- do you have any other trivial gripes?
But hey, if you want to write an essay yourself which details how the repeat elements provide *additional* evidence for common ancestry, as well as a kind of "clock" by which the age of the insertion event can be determined, and other phylogenetic "signal", go right ahead.
But don't be an a-hole and try to pretend that my providing the basics of the topic, instead of a full college course on it, is some kind of "mistake" or "misunderstanding" on my part, because it's not.
[...]

or, to quote from Lebedev et al 2000 (cited by Theobald in 4.5): "These divergences can be used to calculate the age of the branch ancestor (master or source) gene, the retropositions of which gave birth to the branch members." Sequence homologies of the repeat element family (in the example you used, Herv-2) distributed throughout the genome are used to compute the evolutionary time relative to initial retroviral insertion event. The loss of homology is due to the recombinant transposition events which increase the frequency of the element in the genome with each event and also cause a degenracy in the sequence integrity.
Yes, thank you for *REINFORCING* my point. But what on Earth led you to falsely conclude that I didn't know this already or had "misunderstood" it?

So why are the voices in your head telling you that I ever "made a big deal about repeat elements proving common descent"? And why are they telling you that I made this imaginary argument due to something I "read in a t.o. tract"? Oh, right, because you're a liar. That's lie #8.

I have mentioned LINEs and SINEs as providing yet more evidence (not "proof" as you dishonestly assert -- lie #9) of common descent -- because they do -- and those include repeating elements, but the fact that they include repeating elements was not only not something I made a "big deal" about, I didn't even mention it, because the repeating element feature is beside the point when it comes to determining phylogenies. It's the pattern of their appearance across species which indicates phylogenies, and this would be the case even if they did not involve repeating elements.

Finally, you invoke one of your favorite bizarre implications, which is that things appear in my posts only because they have been mentioned by someone else on Talk.Origins. Apparently you want to try to imply that there's no real basis for these claims, it's just something that's been passed around on online forums. No, sorry. I include things not because someone else has said them, but because they have been established by the evidence and research. In this case, for example:

Retroposon mapping in molecular systematics.
Achieving congruency of phylogenetic trees generated by W-curves of genomic sequences
A recent chicken repeat 1 retrotransposition confirms the Coscoroba-Cape Barren goose clade.

This gene therapy study belies the claim that these events are so random as to have never occurred independently when an analogous event occurred in mutiple patients and genome data shows that there are elements shared between some species with common ancestors which you said would be proof against evolution.

No, it doesn't, for reasons I have already made clear to you multiple times, but which you have failed to grasp. here it is *again* -- try to keep up for a change: You offered the gene-therapy results as "evidence" that the gene integration events must have been non-random, because three out of nine patients had their LMO2 gene disrupted, which you ignorantly presumed was too many to be the result of chance. But as I have ALREADY explained to you SEVERAL TIMES, the authors of a published research paper on that study have calculated that this result IS CONSISTENT WITH RANDOM INTEGRATION:

The final delicious irony is that although he has brought up this case study in an attempt to demonstrate that retroviral integration is "not random", and to claim a "targetted nature of integration", the authors of THIS SAME STUDY disagree with him:
Taken together, our data suggest that the following scenario might account for occurrence of the lymphocyte proliferations observed in these patients. LMO2 targeting suggests either that there is a "physical hotspot" of integration at this locus, or more likely, that random, activating, LMO2 integrants are selected simply by the growth advantage conferred on them. The chance of integration of any active gene is assumed to be $~$ 1 x 10^–5 (a rough estimate of a random hit within 10 kbp among the estimated transcriptionally active 1 x 10⁹ base pairs. It is likely that each patient received at least 1 to 10 LMO2-targeted cells, because the patients received 1 x 10⁶ or more transduced T lymphocyte precursors (estimating that at least 1% of the total number of injected transduced cells—92 x 10⁶ and 133 x 10⁶ for patients P4 and P5, respectively — could give rise to T cells).
So there you have it -- the case study that TALLHAPPY HIMSELF introduced in order to "demonstrate" that retroviral integrations were somehow "targeted" to a location (in this case the LMO2 gene) actually has the authors pointing out that they would expect between one and ten LMO2 integrations per patient BY RANDOM CHANCE ALONE, due to the large number of retroviral-treated cells, and the number of sites occupied by the LMO2 gene.
I'd say that this has "hoist on his own petard" written all over it...

If you wish to issue any further lies about whether the results of the gene-therapy trial is within the expectations of random integration, I suggest that you go take it up with S. Hacein-Bey-Abina, C. Von Kalle, M. Schmidt, M. P. McCormack, N. Wulffraat, P. Leboulch, A. Lim, C. S. Osborne, R. Pawliuk, E. Morillon, R. Sorensen, A. Forster, P. Fraser, J. I. Cohen, G. de Saint Basile, I. Alexander, U. Wintergerst, T. Frebourg, A. Aurias, D. Stoppa-Lyonnet, S. Romana, I. Radford-Weiss, F. Gross, F. Valensi, E. Delabesse, E. Macintyre, F. Sigaux, J. Soulier, L. E. Leiva, M. Wissler, C. Prinz, T. H. Rabbitts, F. Le Deist, A. Fischer, and M. Cavazzana-Calvo, the authors of the paper, who are under the impression that the results *are* consistent with random integration, and do not indicate "targeted" integration as you hilariously claimed in your vast ignorance.

If you persist in lying about the implications of those results, I'm going to email S. Hacein-Bey-Abina et al and ask *them* to comment on your bone-headed misrepresentations.

Now, would you like to start acting like a reasonable person finally, or do you want to keep behaving like a asshole?

I am so glad I'm not the recipient of that post. I'd just want to crawl into a small hole and never come out. :-)

I have mentioned LINEs and SINEs as providing yet more evidence (not "proof" as you dishonestly assert -- lie #9) of common descent -- because they do -- and those include repeating elements, but the fact that they include repeating elements

You don't understand what a LINE or SINE or repeating element means or are.

You don't understand chromosomal structure.

This is the problem. You are talking about something you understand only as words you've read about but you don;t know what they are.

It always comes down to this.

You have a great lay perspective and appreciations and if you weren't so agenda driven could be a decent advocate for molecular biology.

Now, would you like to start acting like a reasonable person finally, or do you want to keep behaving like a asshole?

Reading his reply, it appears he's going for box number 2. A one trick pony, our tallhappy. You know no biology. I know no biology. Only tallhappy knows biology. Appearances to the contrary are, like fossils, the work of the devil.