25 Responses to “Retrotransposon transcription”

1. SteveMatheson Says:
   January 3rd, 2010 at 9:25 pm

   The co-opting of mobile and viral sequences has been known for almost two decades, and the fact that many of these elements contain promoters led to the assumption, from day one, that they had the potential to affect expression of nearby genes.

   So you're right that "we need not presume that retrotransposons necessarily correlate to functionless sequences," but the thread looks a lot like a strawman to me. No knowledgeable biologist would claim that all non-coding DNA is functionless junk, just as no knowledgeable biologist would claim that a mammalian genome is densely packed with functional genetic information.

Comment by SteveMatheson — January 3, 2010 @ 9:25 pm

2. fifth monarchy man Says:
   January 3rd, 2010 at 10:10 pm

   hey Steve,

   what do you make of this?

Comment by fifth monarchy man — January 3, 2010 @ 10:10 pm

3. SteveMatheson Says:
   January 3rd, 2010 at 10:21 pm

   FMM, Dawkins was clearly wrong about the vast regions of repeats being non-transcribed. We now know that much of it is transcribed, for reasons unknown. And I do think his summary makes it sound like the human genome is 22,000 genes embedded in a sea of useless junk; that's an extreme position that few biologists agree with, and I'm pretty sure that Dawkins wouldn't write that today. Exaggerations like that, and like the statements from Meyer that have been cited in the other thread, don't make for enlightening discussion.

Comment by SteveMatheson — January 3, 2010 @ 10:21 pm

4. Pez Says:
   January 3rd, 2010 at 10:50 pm

   Speaking of Dawkins:

   “… there is enough information capacity in a single human cell to store the Encyclopaedia Britannica, all 30 volumes of it, three or four times over. … There is enough storage capacity in the DNA of a single lily seed or a single salamander sperm to store the Encyclopaedia Britannica 60 times over. Some species of the unjustly called ‘primitive’ amoebas have as much information in their DNA as 1,000 Encyclopaedia Britannicas.”

   Dawkins, The Blind Watchmaker, pp. 116–117

Comment by Pez — January 3, 2010 @ 10:50 pm

5. Bradford Says:
   January 3rd, 2010 at 11:49 pm

   Steve:

   So you're right that "we need not presume that retrotransposons necessarily correlate to functionless sequences," but the thread looks a lot like a strawman to me. No knowledgeable biologist would claim that all non-coding DNA is functionless junk, just as no knowledgeable biologist would claim that a mammalian genome is densely packed with functional genetic information.

   I did not think you thought that Steve but not everyone posting here is a biologist and even if you are the paper can interest you. There is an explosion of new information these days. Probably more in one year than was produced during Darwin's entire lifetime.

Comment by Bradford — January 3, 2010 @ 11:49 pm

6. fifth monarchy man Says:
   January 4th, 2010 at 8:05 am

   Hey Steve,

   Exaggerations like that, and like the statements from Meyer that have been cited in the other thread, don't make for enlightening discussion.

   I agree the truth is this case is somewhere in the middle. I would argue it's closer to Meyer but that's just me.

   Would you also agree that Dawkin's exaggeration (and Meyer's) don't nessarily mean that their books are worthless and are no reason to ignore them?

   peace

Comment by fifth monarchy man — January 4, 2010 @ 8:05 am

7. Bilbo Says:
   January 4th, 2010 at 9:50 am

   Good point, FMM. Meyer's claims about the functionality of the genome come near the end of his book, well after he's argued his major thesis, that the best explanation for the origin of life is intelligent design.

Comment by Bilbo — January 4, 2010 @ 9:50 am

8. SteveMatheson Says:
   January 4th, 2010 at 10:22 am

   FMM:

   Would you also agree that Dawkin's exaggeration (and Meyer's) don't nessarily mean that their books are worthless and are no reason to ignore them?

   I agree. That would explain why I paid for Meyer's book and decided to read and review it.

   Bilbo:

   Meyer's claims about the functionality of the genome come near the end of his book, well after he's argued his major thesis, that the best explanation for the origin of life is intelligent design.

   Interesting. The book's title subtitle is "DNA and the Evidence for Intelligent Design," and the dust jacket says that the book will "make a comprehensive case for intelligent design based upon DNA." It seems to me that Meyer can't possibly make such a case without extensively discussing "the functionality of the genome." Because that's what the book is about. Am I wrong about that? Can you see why I'm so confused by the discussion here?

Comment by SteveMatheson — January 4, 2010 @ 10:22 am

9. KC Says:
   January 4th, 2010 at 10:52 am

   It would be worthwhile to keep in mind for this discussion that just because a DNA sequence is transcribed does not necessarily mean it has function. See:

   Struhl K (2007). Transcriptional noise and the fidelity of
   initiation by RNA polymerase II. Nature Structural & Molecular Biology 14(2): 103-105

   Abstract:

   Eukaryotes transcribe much of their genomes, but little is known about the fidelity of transcriptional initiation by RNA polymerase II in vivo. I suggest that ~90% of Pol II initiation events in yeast represent transcriptional noise, and that the specificity of initiation is comparable to that of DNA-binding proteins and other biological processes. This emphasizes the need to develop criteria that distinguish transcriptional noise from transcription with a biological function.

Comment by KC — January 4, 2010 @ 10:52 am

10. KC Says:
    January 4th, 2010 at 12:17 pm

    An excellent blog article on the subject of transcriptional noise can be found here:

    http://www.scientificblogging.com/adaptive_complexity/genomic_junk_and_transcriptional_noise

Comment by KC — January 4, 2010 @ 12:17 pm

11. Bilbo Says:
    January 4th, 2010 at 12:41 pm

    Prof. Matheson: Can you see why I'm so confused by the discussion here?

    Yes and no. Meyer argues that the origin of biological information had to be intelligently designed. Once that information exists, there is the additional question of whether it has degraded over time. Much like the original information on software, I'm guessing (from someone who knows nothing about software, hardware, or kitchenware, for that matter).

Comment by Bilbo — January 4, 2010 @ 12:41 pm

12. nickmatzke Says:
    January 4th, 2010 at 1:55 pm

    Steve wrote,

    Interesting. The book's title subtitle is "DNA and the Evidence for Intelligent Design," and the dust jacket says that the book will "make a comprehensive case for intelligent design based upon DNA." It seems to me that Meyer can't possibly make such a case without extensively discussing "the functionality of the genome." Because that's what the book is about. Am I wrong about that? Can you see why I'm so confused by the discussion here?

    In one sense, Meyer's main argument in the book is about the origin of the first life, and from that perspective, his foray into junk DNA, the human genome, etc., look like detours or mission creep.

    But the situation changes once you realize that Meyer actually believes in special creation, not just for the first life, but for humans and all other "kinds" of organisms (he usually hides/avoids discussing this question, as he does in Signature in the Cell, but see e.g. his 2005 Kansas testimony). So really, the origin of the first life, and the origin of the human genome, are, deep down, the same question in Meyer's head.

    Meyer also believes that natural processes can't create new information, full stop, which lines up with the above.

Comment by nickmatzke — January 4, 2010 @ 1:55 pm

13. Bradford Says:
    January 4th, 2010 at 2:15 pm

    Nick:
    

    But the situation changes once you realize that Meyer actually believes in special creation, not just for the first life, but for humans and all other "kinds" of organisms (he usually hides/avoids discussing this question, as he does in Signature in the Cell, but see e.g. his 2005 Kansas testimony). So really, the origin of the first life, and the origin of the human genome, are, deep down, the same question in Meyer's head.

    If you believe that life evolved from an initial cell you are still faced with the conundrum of explaining the origin of the first cellular genome. Meyer's creation views do not alter that problem. They may provide you with a pretext for ignoring the points he makes though.

    Meyer also believes that natural processes can't create new information, full stop, which lines up with the above.

    Indeed but then again the way to refute Meyer is to show that information is the resulting effect of stereochemical properties. Meyer is right to put forth the alternative view that information is a conceptual abstraction expressed through biochemical mediators.

Comment by Bradford — January 4, 2010 @ 2:15 pm

14. chunkdz Says:
    January 4th, 2010 at 2:41 pm

    Matzke: But the situation changes once you realize that Meyer actually believes in special creation, not just for the first life, but for humans and all other "kinds" of organisms (he usually hides/avoids discussing this question, as he does in Signature in the Cell, but see e.g. his 2005 Kansas testimony). So really, the origin of the first life, and the origin of the human genome, are, deep down, the same question in Meyer's head.

    I would avoid reading his beliefs into his argument unless specifically stated in the argument, even though it arguably might help explain his overreaching on the "vast" claim. It's poor critical thinking just as certainly as it would have been poor critical thinking to assume that Dawkins was basing his own "vast" argument on his atheistic beliefs.

Comment by chunkdz — January 4, 2010 @ 2:41 pm

15. Bilbo Says:
    January 4th, 2010 at 3:01 pm

    I'm not sure what Meyer's views are on special creation, though I suspect Nick is right. However, it's not completely accurate to say that he believes that nature can't create any new information at all. If I remember, it was large amounts of specified information.

Comment by Bilbo — January 4, 2010 @ 3:01 pm

16. IrynaB Says:
    January 4th, 2010 at 3:30 pm

    nickmatzke wrote

    Meyer also believes that natural processes can't create new information, full stop, which lines up with the above.

    Bradford's reply

    Indeed but then again the way to refute Meyer is to show that information is the resulting effect of stereochemical properties. Meyer is right to put forth the alternative view that information is a conceptual abstraction expressed through biochemical mediators.

    Meyer's claim seems to be more general – not just restricted to origin of replicators.

    Consider the example of camouflage, where animal resembles aspects of her environment. In some cases it is known what the underlying genes are. I would say that purely natural processes have transferred information from the environment into the gene pool of the species. Do you disagree with my assessment?

Comment by IrynaB — January 4, 2010 @ 3:30 pm

17. Pez Says:
    January 4th, 2010 at 3:34 pm

    Meyer in Kansas
    http://www.talkorigins.org/faqs/kansas/kangaroo8.html

    Q. (BY MR. IRIGONEGARAY) I'm the one asking questions here, Mr. Meyer, and all you need to do is to answer my question.

    A. Okay. I think the age of the earth is 4.6 billion years old. That's both my personal and my professional opinion. I speak as someone who is trained as a geophysicist–

    Q. I'm not asking you about that. I just asked you for a number, and you have given it to me.

    A. Okay. That's all you want is the number?

    Q. My questions are pretty clear, Mr. Meyer.

    A. You're not interested in the answer, you're interested in the–

    Q. Do you accept the general principle of common descent that all life is biologically related back to the beginning of life, yes or no?

    A. I won't answer that question as a yes or no. I accept the idea of limited common descent. I am skeptical about universal common descent. I do not take it as a principle; it is a theory. And I think the evidence supporting the theory of universal common descent is weak.

    Q. Do you accept that human beings are related by common descent to prehominid ancestors, yes or no?

    A. I'm not sure. I'm skeptical of it because I think the evidence for the proposition is weak, but it would not affect my conviction that life is designed if it turns out that there was a genealogical continuity.

    Q. Based upon your understanding, do you have an alternative explanation for the human species if not common descent from prehominid ancestors?

    A. That is not my area of expertise. I work at the other end of the history of life, namely the origin of the first life in the Cambrian phylum.

    Q. Do you have a personal opinion as to the question I have just proposed to you, which is if you do not believe that human beings have a common descent with prehominid ancestors, what is your personal alternative explanation for how human beings came into existence?

    A. I am skeptical about the evidence for universal common descent and I'm skeptical about some of the evidence that has been marshaled for the idea that humans and prehominids are connected. But as I said, it wouldn't bother me (unintelligible) stronger than I presently think.

    Q. What is your personal opinion at this time?

    A. That I'm skeptical about the Darwinian accounts of such things, but that it wouldn't bother me if it turned out to be different. I think my– I also would tell you that humans and the rest of the non human living world, that humans have qualitatively different features that I think are very mysterious and hard to explain on any materialistic account of the origin of human life.

Comment by Pez — January 4, 2010 @ 3:34 pm

18. Bilbo Says:
    January 4th, 2010 at 3:36 pm

    Iryna, do we know how the genes originated?

Comment by Bilbo — January 4, 2010 @ 3:36 pm

19. Pez Says:
    January 4th, 2010 at 3:49 pm

    Meyer on information, Signature In The Cell, page 341

    Undirected materialistic causes have not demonstrated the capacity to generate significant amounts of specified information.
    …
    "agent causation" now stands as the only cause known to be capable of generating large amounts of specified information starting from a nonliving state.
    page 343
    Experience shows that large amounts of specified complexity or information invariably originate from an intelligent source – from a mind or a personal agent.
    …
    … intelligence is the only known cause of specified information(at least starting from a nonbiological source), …

    Stop.

Comment by Pez — January 4, 2010 @ 3:49 pm

20. Arthur Hunt Says:
    January 4th, 2010 at 9:04 pm

    More on transcriptional "noise" and the fact that not all transcription yields functional RNA:

    Junk to the Second Power

    Strange Things at Promoters

    More Strangeness

    There's lots more in the literature along these lines. The bottom line is that, contrary to people like Sternberg (who clearly stated this opinion in his recent debate with Meyer and vs Prothero and Shermer), transcription does not necessarily equal function.

Comment by Arthur Hunt — January 4, 2010 @ 9:04 pm

21. Mung Says:
    January 5th, 2010 at 12:18 am

    Because that's what the book is about. Am I wrong about that? Can you see why I'm so confused by the discussion here?

    I think Dawkins' analogy of a hard drive is a useful one here. so what if the hard drive is in need of defragmentation. The fact that it's greatly fragmented or that there's not a lot of useful information left amidst all that junk doesn't argue against how the original information got on the hard drive in the first place, or where it came from.

Comment by Mung — January 5, 2010 @ 12:18 am

22. ID guy Says:
    January 5th, 2010 at 2:06 pm

    nickmatzke:
    Meyer also believes that natural processes can't create new information, full stop, which lines up with the above.

    "Undirecetd materialistic processes" and from scratch.

    So really, the origin of the first life, and the origin of the human genome, are, deep down, the same question in Meyer's head.

    Not even YEcs think that. They know that humans were created last.

    It's all in the Bible nickmatzke.

Comment by ID guy — January 5, 2010 @ 2:06 pm

23. Bilbo Says:
    January 5th, 2010 at 3:43 pm

    I noticed that Art has a comment for this thread, but I don't feel I have the authority to approve it, since I didn't start this thread.

Comment by Bilbo — January 5, 2010 @ 3:43 pm

24. Bradford Says:
    January 5th, 2010 at 4:34 pm

    Bilbo, where is Art's comment? I just checked the queue and did not see it there.

Comment by Bradford — January 5, 2010 @ 4:34 pm

25. Bilbo Says:
    January 5th, 2010 at 10:57 pm

    Spam.

Comment by Bilbo — January 5, 2010 @ 10:57 pm