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Author Topic:   How well do we understand DNA?
pink sasquatch
Member (Idle past 6023 days)
Posts: 1567
Joined: 06-10-2004


Message 52 of 98 (182593)
02-02-2005 2:14 PM
Reply to: Message 37 by TheLiteralist
01-31-2005 4:52 PM


Non-random mutation can drive evolution... and disease.
Hi TL,
I've been meaning to jump into this thread for awhile - earlier you proposed:
The code would not cause variation just anywhere or everywhere but would target only certain areas... Random mutations could occur anywhere or everywhere, but I am proposing that truly random mutations (actual copying errors, radiation, etc.) would be useless or, most likely, harmful in some way and would quickly be selected out--perhaps ending with mutant organism itself.
In one sense you may be correct, because mutation is not truly random, because the DNA sequence itself is not random. DNA repair machinery has an especially difficult time with repetitive sequence; in other words:
AGAGAGAGAGAGAGAGAGAGAGAGAGAGAG
is much more likely to undergo a mutational event than:
ATCGTACGGGCTAATGCTAGCTTCTAAGCCG
due to a distinct form of mutation caused by mispairing of the repetitive sequence. Repetitive sequence mutations by such mispairing may occur up to 100,000 times more often than point mutations, and as such, repetitive sequence has long been a source of polymorphisms ('markers') for genetic mapping studies.
Recently a paper was published providing evidence that mutations in such repetitive sequences provide a molecular basis for rapid evolution of certain characteristics:
Proc Natl Acad Sci U S A. 2004 Dec 28;101(52):18058-63. Epub 2004 Dec 13.
Molecular origins of rapid and continuous morphological evolution.
Fondon JW 3rd, Garner HR.
Mutations in cis-regulatory sequences have been implicated as being the predominant source of variation in morphological evolution. We offer a hypothesis that gene-associated tandem repeat expansions and contractions are a major source of phenotypic variation in evolution. Here, we describe a comparative genomic study of repetitive elements in developmental genes of 92 breeds of dogs. We find evidence for selection for divergence at coding repeat loci in the form of both elevated purity and extensive length polymorphism among different breeds. Variations in the number of repeats in the coding regions of the Alx-4 (aristaless-like 4) and Runx-2 (runt-related transcription factor 2) genes were quantitatively associated with significant differences in limb and skull morphology. We identified similar repeat length variation in the coding repeats of Runx-2, Twist, and Dlx-2 in several other species. The high frequency and incremental effects of repeat length mutations provide molecular explanations for swift, yet topologically conservative morphological evolution.
PMID: 15596718
But the other side of the high rate of repetitive sequence mutation needs to be considered as well - such mutations also contribute to disease, especially cancer. Hereditary non-polyposis colon cancer is a familial form of cancer that typically progresses via loss of the tumor suppressor gene Transforming growth factor beta receptor II - the tumor suppressor is lost by mutation of a repetitive sequence.
So, as many others have pointed out to you, even though exceptions to the concept of "random mutation" exist, there is no reason to believe that the exceptions are the result of intelligent design.
In the case of repetitive sequence mutation, we have to ask ourselves why an intelligent designer would put the same repeats into important disease suppressor genes as in regulatory elements that could drive evolution.
Hopefully that all made sense - let me know if you need further explanation.

This message is a reply to:
 Message 37 by TheLiteralist, posted 01-31-2005 4:52 PM TheLiteralist has replied

Replies to this message:
 Message 57 by TheLiteralist, posted 02-02-2005 3:06 PM pink sasquatch has replied

  
pink sasquatch
Member (Idle past 6023 days)
Posts: 1567
Joined: 06-10-2004


Message 62 of 98 (182619)
02-02-2005 3:44 PM
Reply to: Message 57 by TheLiteralist
02-02-2005 3:06 PM


Re: Non-random mutation can drive evolution... and disease.
Tremendous!
Glad you enjoyed it.
Could this fact that copying errors are inherent in certain sequences where there is a lot of repetitiveness be the mechanism I'm looking for?
First, they're not necessarily "inherent", they are just much more likely. Repetitive sequences are still subject to the repair machinery others have been describing, it is just that the machinery doesn't do as well with repeats.
More importantly, there is no evidence whatsoever that these sequences are the result of design rather than evolution. Since these sequences are highly mutable their initial development likely occurred quite readily by natural means, precisely because changes in the repeats evade replication machinery.
Do all or most traits that vary have this quality of highly repetitive sequences?
All traits vary, not just some. I believe few genes have long repeats in their coding sequence; the paper I cited tested 36 genes precisely because they had such coding repeats.
Importantly - even though some of the genes had repeats, many of them did NOT undergo mutation within the repeats; so again, the repeats do not equal mutation.
Are there other mechanisms that work like this?
I'm not sure what you mean - this isn't so much a 'mechanism' as the tendency for some sequence to undergo mutation more often than others. That is, mutation of repetitive sequence still undergoes selection like any other type of mutation.
..since sin has entered the world death and suffering are the lot of humanity in general in this life.
Sounds like you are suggesting that the Creator added repetitive sequence to certain genes after "The Fall".
This is always a serious problem when dealing with detection of an intelligent designer: If something appears to be made exquisitely well, the argument is made that intelligent design was required; if something is made poorly or in a way that doesn't make sense, then The Fall is often cited as an explanation.
With this kind of logic, if something is "good", that is evidence of a Creator; if something is "bad", that is also evidence of a Creator. Such "logic" cannot be discussed logically - which is why people in this thread keep bringing up the need for a way to detect design.
So to return to the repetitive sequence: We have evidence that repetitive sequence is evolvable by natural means. What evidence (or tests for evidence) can you propose that supports repetitive sequence as the product of a supernatural being?

This message is a reply to:
 Message 57 by TheLiteralist, posted 02-02-2005 3:06 PM TheLiteralist has replied

Replies to this message:
 Message 64 by TheLiteralist, posted 02-02-2005 3:57 PM pink sasquatch has replied

  
pink sasquatch
Member (Idle past 6023 days)
Posts: 1567
Joined: 06-10-2004


Message 68 of 98 (182633)
02-02-2005 4:11 PM
Reply to: Message 64 by TheLiteralist
02-02-2005 3:57 PM


Re: Sequences (elves?)
Well, to me, the mere existence of genetic sequences that get translated is the indication of intelligence.
That just sidesteps my previous question.
We know that novel, coding genetic sequences can arise by natural means. There is no need to produce an undetectable, intelligent, superpowerful entity to provide an explanation, unless you have evidence for such an entity's involvement in the process.
To put it another way, you need to have some positive evidence for your view if it is to be anything other than personal opinion. Simply stating that its "mere existence" is indication of design doesn't work (beyond opinion). It is obvious to millions of people all over the world that every year their toys are manufactured by elves at the North Pole and delivered by one man utilizing flying reindeer. That doesn't make it true.
Similarly, arguing that natural evolution of DNA sequence is implausible doesn't provide any evidence whatsoever for design.
Is there any evidence beyond "obviousness" that indicates intelligent design?

This message is a reply to:
 Message 64 by TheLiteralist, posted 02-02-2005 3:57 PM TheLiteralist has replied

Replies to this message:
 Message 70 by TheLiteralist, posted 02-02-2005 4:17 PM pink sasquatch has replied

  
pink sasquatch
Member (Idle past 6023 days)
Posts: 1567
Joined: 06-10-2004


Message 74 of 98 (182647)
02-02-2005 4:42 PM
Reply to: Message 70 by TheLiteralist
02-02-2005 4:17 PM


off-topic?
We know that novel, coding genetic sequences can arise by natural means.
I think this is a different topic, but one I'm interested in. Would you like for me to try to get a new thread going about this?
How is it off-topic? A major theme of this thread is distinguishing natural from supernatural origins of DNA sequence. There is evidence for the "natural"; I'm asking for evidence (or tests for evidence) for the "supernatural".
On-topic, no?

This message is a reply to:
 Message 70 by TheLiteralist, posted 02-02-2005 4:17 PM TheLiteralist has replied

Replies to this message:
 Message 76 by TheLiteralist, posted 02-03-2005 12:25 AM pink sasquatch has replied

  
pink sasquatch
Member (Idle past 6023 days)
Posts: 1567
Joined: 06-10-2004


Message 78 of 98 (182877)
02-03-2005 12:04 PM
Reply to: Message 76 by TheLiteralist
02-03-2005 12:25 AM


back-on-topic...
I thought this comment was referring to the very origin of the genetic code itself (abiogenesis).
No, it wasn't, though I see how you might have read it as such. (There are several abiogenesis threads in the forum that you should look through and 'resurrect' if you are interested - I'll keep an eye out since I find the topic interesting as well.)
I was speaking more at the gene-level - that is, we have evidence that a new gene sequence can arise by natural means. Which leads to my question - why invoke the supernatural in such a case?
I don't think the discussion has (yet) produced any evidence or tests to reveal "the mark of the designer" in DNA. If you think any such points have been made, why don't you give a quick summary/list if you think it will help keep the thread productive and on track?

This message is a reply to:
 Message 76 by TheLiteralist, posted 02-03-2005 12:25 AM TheLiteralist has replied

Replies to this message:
 Message 79 by TheLiteralist, posted 02-03-2005 9:21 PM pink sasquatch has replied

  
pink sasquatch
Member (Idle past 6023 days)
Posts: 1567
Joined: 06-10-2004


Message 83 of 98 (183109)
02-04-2005 2:16 PM
Reply to: Message 79 by TheLiteralist
02-03-2005 9:21 PM


designed mistakes
Others have already replied well to your points; my additional two cents:
I am saying that the random mutations are occurring because the code was designed to produce them.
I agree with Crashfrog, this seems to be a change from your previous concept that certain areas of the genome were designed to allow mutation, while others are resistant. And again, why is it necessary to invoke "design" for this system?
One important point, though, is that once the Designer has implemented the code/organism system, the variations that result are... of natural origin...
Yet again, I haven't seen any reason to invoke the supernatural in order to "allow" genetic mutation/variation. Mistakes/errors/chaos are a part of most natural processes - are these all the result of design as well?
I have this idea that certain "core" traits are designed not to variate or to variate in a very limited manner while other traits are designed to variate quite a bit.
As Quetzal mentioned, there are highly conserved regions that vary less than other sequences. However, there is an important distinction here - the genes underlying your "not variate" and "variate" traits are all subject to random mutation.
Both categories undergo mutation, it is simply that mutation in a highly conserved region is likely to result in death, sterility, or a severe reduction in fitness; so they are not maintained in the population. Thus, I don't think this at all fits your designed differential mutation rate concept. Does that make sense?
Now the mere existence of the RNA/DNA/translation/cell systems IS, to me, strong evidence of a Designer, but THAT is off-topic.
I don't know that it is so off-topic. You are spending much time in this thread trying to figure out the intent and results of design of the genome, without having provided any specific reasons for your assumption of design. In any case, if you will only present such reasons in another thread... I'll keep an eye out for it...

This message is a reply to:
 Message 79 by TheLiteralist, posted 02-03-2005 9:21 PM TheLiteralist has not replied

  
pink sasquatch
Member (Idle past 6023 days)
Posts: 1567
Joined: 06-10-2004


Message 85 of 98 (183113)
02-04-2005 2:32 PM
Reply to: Message 84 by christian atheist
02-04-2005 2:20 PM


Re: Broken Genes
From that, how do the find the same gene in humans?
I'm not sure how it was specifically done with the GLO gene, but generally the conserved sequence of the gene serves as a 'marker' to identify the same gene in another species using various molecular genetics techniques. Genes generally contain conserved regions that are necessary for basic function of the gene, and are thus less likely to differ between species, and so serve as a starting point for comparative studies. Hopefully that makes some sense...
Finally, do we know what mutation in the gene causes it to not work?
The four species I am aware of that lack a functional GLO gene are humans, chimps, a guinea pig, and a fruit bat. The mutations are known for all four. Humans and chimps have an identical mutation, while the guinea pig and fruit bat have distinct mutations.
It is this sort of pattern, combined with countless other similar genetic patterns, that suggests common ancestry of humans and chimps at the DNA level.

This message is a reply to:
 Message 84 by christian atheist, posted 02-04-2005 2:20 PM christian atheist has not replied

  
pink sasquatch
Member (Idle past 6023 days)
Posts: 1567
Joined: 06-10-2004


Message 93 of 98 (184984)
02-13-2005 8:24 PM
Reply to: Message 91 by christian atheist
02-13-2005 7:51 PM


Re: Broken Genes
Will will ever understand DNA enough to be able to fix it?
Yes, as this sort of process has been done literally thousands of times in mice and other mammals. There's obviously ethical concerns to consider in humans as well, and there may be unexpected harmful side effects to fixing the "Vitamin C" gene, since our species has evolved without it for so long.

This message is a reply to:
 Message 91 by christian atheist, posted 02-13-2005 7:51 PM christian atheist has not replied

  
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