Freethought & Rationalism Archive

KC · 07-31-2003, 06:42 PM

Quote:

Originally posted by Nic Tamzek
KC, yes, that's true AFAICT. The point of Roth's review was that germline rearrangments were late (at least the ones studied) relative to the origin of adaptive immunity.

The actual origin of adaptive immunity is only discussed in the beginning, where Roth gives the standard theory and the standard supporting evidence. OTOH, Lewis & Wu discuss the standard theory more.

Well, my point is this: the Schatz paper you cited says this (emphasis mine):

Quote:

The RAG1 and RAG2 proteins together initiate V(D)J recombination by performing cleavage of chromosomal DNA adjacent to antigen receptor gene segments. Like the adaptive immune system itself, RAG1 and RAG2 are found only in jawed vertebrates. The hypothesis that RAG1 and RAG2 arose in evolution as components of a transposable element has received dramatic support from our recent finding that the RAG proteins are a fully functional transposase in vitro. This result strongly suggests that antigen receptor genes acquired their unusual structure as a consequence of the insertion of a transposable element into an ancestral receptor gene by RAG1 and RAG2 approx 450 million years ago.

But the Roth article is discussing no evidence of a transposable element in shark immunological evolution from 7 million years ago . Nelson and Jon_e are trying to get unwary readers to think that Roth means there is no evidence for transposon insertion in immunological evolution period.

That is what it looks like to me.

KC

Nic Tamzek · 07-31-2003, 07:09 PM

I concur completely, KC. Apologies if that wasn't clear...

KC · 07-31-2003, 07:47 PM

So lower the boom on their sorry asses. (Grabs popcorn, a Pilsner Urquell, and settles back to watch))

KC

Nic Tamzek · 07-31-2003, 10:54 PM

Omigod, that ARN thread has progressed exactly as I predicted in only a few hours! I must be psychic. Nelson is changing his story, and jon_e has little idea what is going on but is posting profligately. Jon_e has even resorted to saying that Roth didn't mean what Roth said, alledging that there was a typo, and that if you correct the typo then Roth agrees with jon_e!

rafe:

Quote:

man, i feel like i'm taking crazy pills. this is hilarious

KC · 08-01-2003, 04:01 AM

Quote:

Originally posted by Nic Tamzek
Omigod, that ARN thread has progressed exactly as I predicted in only a few hours! I must be psychic. Nelson is changing his story, and jon_e has little idea what is going on but is posting profligately. Jon_e has even resorted to saying that Roth didn't mean what Roth said, alledging that there was a typo, and that if you correct the typo then Roth agrees with jon_e!

I like rafe's response to Nelson where he outlines (again), from 3 different papers, 3 different lines of evidence for a transposon insertion 450 million years ago. And the response is still that there is no evidence for such an insertion, that is 'an assumption'.

And Jon-e's insistence that Roth made a typo is just absolutely bizarre.

Those two are a waste of time. However, I appreciate the work you both did--I learned a lot.

KC

Principia · 08-01-2003, 06:10 AM

I am not sure whether to be amused or be extremely irritated by jon_e's newly found arrogance and condescension towards rafe (e.g. the "get current into light bulb" commentary). This is bringing back memories of DJB and scigirl.

KC · 08-01-2003, 11:41 AM

Well, it boils down to 'we don't see RAG-mediated transposition in vivo, so there is no hard evidence for transposition in the past'.

Charlies point that RAG is a transposase is bolstered by this review article, (coa-authored by by Roth, ironically):

VDJ Recombination: A Transposase Goes To Work

From what I can tell, the position is, transposition can be disastrous, so we would not expect to see that kind of event very often, but that VDJ recombination is an improvement, and derived from an ancient transposable event that happened to be non-deleterious. Do I have this right?

KC

Nic Tamzek · 08-01-2003, 03:14 PM

Yeah, transposons basically encode for proteins that (a) cut out their encoding sequence and (b) paste it back in somewhere else.

All that would have to happen to get the RAG situation is to suppress the pasting part.

KC · 08-05-2003, 06:31 AM

I have to thank niic, rafe and charlie for the free immunological education on this thread. Its the most informative thread I've ever seen on ARN, besides being one of the funniest

KC

Xeluan · 08-05-2003, 07:11 AM

If someone would be so kind to explain me the whole point of the thread?

I have no idea what the hell happned. I lost it after the Dembski post.

08-05-2003, 06:31 AM	#19
KC Senior Member Join Date: Mar 2002 Location: San Narcisco, RRR Posts: 527	Good Education I have to thank niic, rafe and charlie for the free immunological education on this thread. Its the most informative thread I've ever seen on ARN, besides being one of the funniest KC

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07-31-2003, 07:09 PM	#12
Nic Tamzek Senior Member Join Date: Jan 2002 Location: California Posts: 646	I concur completely, KC. Apologies if that wasn't clear...

07-31-2003, 07:47 PM	#13
KC Senior Member Join Date: Mar 2002 Location: San Narcisco, RRR Posts: 527	So lower the boom on their sorry asses. (Grabs popcorn, a Pilsner Urquell, and settles back to watch)) KC

08-01-2003, 06:10 AM	#16
Principia Veteran Member Join Date: Mar 2002 Location: anywhere Posts: 1,976	I am not sure whether to be amused or be extremely irritated by jon_e's newly found arrogance and condescension towards rafe (e.g. the "get current into light bulb" commentary). This is bringing back memories of DJB and scigirl.

08-01-2003, 11:41 AM	#17
KC Senior Member Join Date: Mar 2002 Location: San Narcisco, RRR Posts: 527	Well, it boils down to 'we don't see RAG-mediated transposition in vivo, so there is no hard evidence for transposition in the past'. Charlies point that RAG is a transposase is bolstered by this review article, (coa-authored by by Roth, ironically): VDJ Recombination: A Transposase Goes To Work From what I can tell, the position is, transposition can be disastrous, so we would not expect to see that kind of event very often, but that VDJ recombination is an improvement, and derived from an ancient transposable event that happened to be non-deleterious. Do I have this right? KC

08-01-2003, 03:14 PM	#18
Nic Tamzek Senior Member Join Date: Jan 2002 Location: California Posts: 646	Yeah, transposons basically encode for proteins that (a) cut out their encoding sequence and (b) paste it back in somewhere else. All that would have to happen to get the RAG situation is to suppress the pasting part.

08-05-2003, 07:11 AM	#20
Xeluan Senior Member Join Date: Jun 2002 Location: Some Pub In East Gosford, Australia Posts: 831	If someone would be so kind to explain me the whole point of the thread? I have no idea what the hell happned. I lost it after the Dembski post.

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