While I was driving home on Kitzmas, you all were having fun without me-- Crashing Dembskis party at Amazon.com.
Well fine. I see how it is. Im not even going to invite you all to read the fun Im having with Dear Don over at Amazon:
Regarding my comments on physics. I am not a physicists but I am interested in its implications. I am sure that my take on it is controversial but I think some heavyweights in the field would agree. I suggest that information is the unifying element of physics and biology--the quantum and codon are fundamental units of organization of information that require a sufficient cause.Uh huh. Thats MY tard-mine! YOU ALL ARENT INVITED!
Aww, dont give me those puppy dog eyes! Awwwwww! *sigh* FINE! But I still get dibs on his comments about the evolution of the immune system.
Dons problem is a problem all Creationists have. They dont know how to use PubMed. Not that that fact will stop them from talking about 'scientific research'. Dons 'scientific research' was so messed up in his presentation, I couldnt figure out what the hell he was talking about at the time, but now I get it. Dons reference:
Homology domains identified within shark RAG I prompted sequence comparison analyses that suggested similarity of the RAG I and II genes, respectively, to the integrase family genes and integration host factor genes of the bacterial site-specific recombination system. Thus, the apparent explosive evolution (or "big bang") of the ancestral immune system may have been initiated by a transfer of microbial site-specific recombinases.Summary-- RAG I and RAG II, really important genes in our immune system only have sequence homology to genes in bacteria! How the heck did bacteria genes get into sharks a long time ago?? What? Oh now how the hell are Evilutionists going to explain THAT dosey? Arent Evilutionists stupid! Common design! Common design! Common design! WHOOOOOO!
That publication was from 1996. In 1996, this hypothesis was the best the researchers could do with the information they had. Luckily, science moves forward. We get better at the game as we go along:
RAG1 Core and V(D)J Recombination Signal Sequences Were Derived from Transib Transposons
I thought Don was confusing bacteria and retroviruses because he was a Creationist that couldnt differentiate between those two 'bug kinds'. Turns out he really meant bacteria, he just didnt know that we're taught, you know, 'modern' science in class. Not, like, decade old putative hypotheses in peoples discussion sections. Cause, scientists did not stop at 'horizontal gene transfer from a bacteria into a gamete... eeehh....' or 'gawd did it.' They kept looking for better answers, and found it.
My response to Don at Amazon:
Viruses/transposable elements/etc and Creationism theoretically have a lot in common. They both, theoretically, have been misunderstood and mischaracterized by the Scientific Establishment. 10 years ago, viruses were seen as a freak-show of 'life', not at all connected to The Tree of Life, and it was heresy to suggest they were anything but degenerated bits of genome and chemicals. 10 years ago, Behe, Dembski, Wells, were 'maverick scientists' 'taking on the establishment' and 'making a case for a paradigm shift in biology'.
In the past ten years, viral paradigm shifters have been in their labs, churning out paper after paper after paper demonstrating the importance of viruses in the evolution of life on earth, to the degree that it is now an 'industry standard' in the viral world (and other fields), and is creeping into textbooks and graduate/undergraduate courses (ie the new edition of 'Origin and Evolution of Viruses' coming out soon). In another 10 years, it might be all the way down to high school texts.
In the past ten years, intelligent design creationist paradigm shifters have been busy writing news releases, filing lawsuits, screaming 'DISCRIMINATION!!!', designing web pages, writing on their blogs, attacking/threatening students, writing textbooks to push on children, giving presentations to local churches for thousands of $$$, making flash animations of federal judges farting, getting fired from their teaching positions, inciting costly lawsuits in numerous school districts, and staying merrily oblivious to modern research (and making sure their $$$ flock are blissfully unaware of this research as well).
Oh, I believe the 2005 paper was part of the stack presented to Behe at Dover:
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 transposon13, an idea initially suggested in a 1979 paper14 and expanded in 1992 (ref. 15). Behe ridicules the idea as a "jump in the box of Calvin and Hobbes,"2 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 mechanisms16 and also between shark RAG1 and certain bacterial integrases17. 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 vitro18, 19 and then in vivo20, 21, 22, and to have even closer structural and mechanistic similarities with specific transposases23. 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 homolog24. 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).