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  Topic: Directed Mutation and Hypermutation, Some reading for Skeptic and Apollo230< Next Oldest | Next Newest >  
argystokes



Posts: 766
Joined: Jan. 2006

(Permalink) Posted: Aug. 03 2006,11:21   

This review came out a couple of years ago.  It dismisses the concept of directed mutation; that is, the idea that cells sense what area of the genome "needs" to mutate in response to its environment.  The main thrust of the paper, however, is that cells can increase their overall mutation rate in response to environmental stressors, leading to an increased chance of achieving beneficial mutations.  This kind of hypermutation remains controversial, and rebuttals to this article have been published.  Here's the introduction; I don't want to violate any copyright laws:
Quote
Adaptive Mutation: How Growth under Selection Stimulates Lac+ Reversion by Increasing Target Copy Number
John R. Roth1* and Dan I. Andersson2,3
Microbiology Section, University of California, Davis, Davis, California 95616,1 Department of Bacteriology, Swedish Institute for Infectious Disease Control, S-171 82 Solna,2 Microbiology and Tumour Biology Center, Karolinska Institute, S-171 77, Solna, Sweden3

From the time of Darwin until about 1950, a controversy continued over whether selective stress induces mutations or only affects the relative reproductive success of organisms with different genotypes (30). The controversy was resolved by the classic experiments of Luria and Delbrück (27) and of Lederberg and Lederberg (25), who showed that some bacterial mutants arise prior to application of the selection that allows their detection and thus could not have been caused by selective conditions. However, these experiments used lethal selections and therefore did not eliminate the possibility that another fraction of total mutations might be formed in response to stress and be detected only by nonlethal selection. Shapiro and Cairns et al. reopened the controversy by pointing out this caveat and presenting data that seemed to support stress-induced mutation (7, 45).

Because very few genetic systems behave in ways that suggest stress-induced mutation, the rare cases that seem to exhibit such behavior have attracted close attention. In one case, mutants were later shown to preexist selection (14, 28, 29, 44). For the system devised by Cairns and Foster (5), we suggest that reversion occurs by a multistep process initiated prior to selection and the appearance of stress-induced mutagenesis results from growth under strong selection.


Proponents of directed mutation, which seems to be a necessity for any kind of front-loading hypothesis, should also check out:
Foster, P. L., and J. Cairns. 1992. Mechanisms of directed mutation. Genetics 131:783-789.

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"Why waste time learning, when ignorance is instantaneous?" -Calvin

  
Ichthyic



Posts: 3325
Joined: May 2006

(Permalink) Posted: Aug. 03 2006,13:00   

http://www.antievolution.org/cgi-bin....;t=2494

amazing how this kind of thing keeps being offered up, but gets no comments from those who ignorantly or deliberately mischaracterize the "random" issue wrt the ToE.

why, one might almost think they simply can't grasp the concepts involved, and so prefer to keep spouting their ignorant claptrap instead.

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"And the sea will grant each man new hope..."

-CC

  
Chris Hyland



Posts: 705
Joined: Jan. 2006

(Permalink) Posted: Aug. 03 2006,15:16   

On the topic of directed mutation creationists tend to bring up this paper.

  
Ichthyic



Posts: 3325
Joined: May 2006

(Permalink) Posted: Aug. 03 2006,15:25   

of course, not only do they not understand the contents of the paper, but seem to miss the very first sentence in the intro:

Quote
As this minireview is concerned with the importance of the environment in directing evolution.
.

...and exactly how is that different from saying natural selection?

I guess they get hung up on the word "directing", which agreed is rather poor terminology, and ignore the whole "environment" part.

or am i stepping on your toes here?

if so, give me the high sign and I'll wipe this.

--------------
"And the sea will grant each man new hope..."

-CC

  
argystokes



Posts: 766
Joined: Jan. 2006

(Permalink) Posted: Aug. 03 2006,16:44   

That paper looks like a good read, Chris.  Perhaps I'll have some time for it later on, but for now, I'm going to spend some time with my favorite bitch.

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"Why waste time learning, when ignorance is instantaneous?" -Calvin

  
skeptic



Posts: 1163
Joined: May 2006

(Permalink) Posted: Aug. 03 2006,17:13   

Honestly, Angry, I don't know whether I should laugh or cry.  I appreciate the references but I might now be obligated to post on two places with essentially the same material.  Maybe I'll cut and paste. HA HA.  Anyway, just reading the intro seemed to leave the possibility open for further review, unless I was missing something.  Ichy, as far as your post, I was able to read the abstract and it is in the same vein but not quite the same.  I do agree with you though, the term "directed" has all the wrong connotations and we'd really do much better without it.

  
apollo230



Posts: 16
Joined: Mar. 2006

(Permalink) Posted: Aug. 03 2006,17:16   

I got a laugh, Argy, when you said that you did not want to violate any copyright laws by posting the entire paper.  That would make you one of the few honest people left alive in this era of rampant music downloading (or would you plead the 5th amendment if I asked you if you downloaded tunes?)  :D

What you have posted appears to be an abstract that certainly conveys the existence of a controversy.  There is nothing wrong with this kind of arguement because if there is uncertainty-then people can just go back to their labs and do more research, survey broader sections of genome, etc.

I gleaned two possibilities from this post: pre-adaptations and/or adaptations that occur under the gun of strong selection.  Both are certainly possible.  However, could some (or most?) pre-adaptations result from "preferential" mutation systems?  Who is to say that only strong selection could trigger this alleged mechanism.

This is just an analogy, but if cells "know" how to "direct" and coordinate thousands of individual metabolic reactions and pathways, would their direction of mutations really be out of their "reach"?  

When I have time-I will read Chris Hyland's article as well, and see what's up there.

Best regards,
apollo230

  
skeptic



Posts: 1163
Joined: May 2006

(Permalink) Posted: Aug. 03 2006,17:29   

Chris, one thing about this paper made me scratch my head.  The authors go a long way to emphasize the non-random nature of the mechanisms behind mutation and to establish the environmental feedback link and then they highlight the importance of random mutations.  In a way, this seems contradictory to me.

  
Ichthyic



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Joined: May 2006

(Permalink) Posted: Aug. 03 2006,20:04   

Quote
I appreciate the references but I might now be obligated to post on two places with essentially the same material


of course, exactly what i predicted.

do you actually HAVE any unique or innovative material?

haven't seen any so far.

do try to keep up, junior.  You've had MONTHS and have made literally NO progress.

*sigh*

Quote
In a way, this seems contradictory to me.


of course it does.  you can only think in absolutist terms, apparently.

suggest you re-read the paper at least 3 times.  maybe the specifics will start to sink in, or maybe you need to learn more basics before the specifics even make sense at all to you.

I still think you're a complete waste of time, but maybe Apollo can show you up.

we'll see.

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"And the sea will grant each man new hope..."

-CC

  
argystokes



Posts: 766
Joined: Jan. 2006

(Permalink) Posted: Aug. 03 2006,20:10   

Quote
or would you plead the 5th amendment if I asked you if you downloaded tunes?)


We pirates thieve for ourselves, not for others!

Apollo asked:
Quote
I gleaned two possibilities from this post: pre-adaptations and/or adaptations that occur under the gun of strong selection.  Both are certainly possible.  However, could some (or most?) pre-adaptations result from "preferential" mutation systems?  Who is to say that only strong selection could trigger this alleged mechanism.


I'm afraid I don't really understand what you're saying here.  Could you clarify?  I think you might be using some idiosyncratic terminology.

Septic said:
Quote
Anyway, just reading the intro seemed to leave the possibility open for further review, unless I was missing something.

Well, papers don't often say, "We have conclusively disproven Professor B's hypothesis and recommend no further research."  Why doncha read the whole thing; it's not too long, and should be easily comprehensible for a biochemist.

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"Why waste time learning, when ignorance is instantaneous?" -Calvin

  
Ichthyic



Posts: 3325
Joined: May 2006

(Permalink) Posted: Aug. 03 2006,21:06   

Quote
Septic said:


yeah, that about describes it.  I think this particular tank is clogged though.  got any liquid plumber?

--------------
"And the sea will grant each man new hope..."

-CC

  
apollo230



Posts: 16
Joined: Mar. 2006

(Permalink) Posted: Aug. 04 2006,00:26   

Good morning, Argy, I am sorry, but my original (stated)intent was to read what you had to post (which I have), not to get into a prolonged discussion that may last for days, so before you or anyone else starts investing more time into this thread, I am going to show at least a basic courtesy and give notice that I am not going to go to great lengths to propel this exchange.  If this seems to some that I am "dropping the ball" (so to speak) then so be it.  I regret if I created any impression of craving a protracted discussion of the matter.

  
Chris Hyland



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Joined: Jan. 2006

(Permalink) Posted: Aug. 04 2006,00:39   

Quote
or am i stepping on your toes here?
I think your right Im not sure why this is against random mutation. It's no more nonrandom than something like genetic assimilation. There's nothing in the paper that would show support for creationism that I can see, it's just a property of the DNA transcription machinery that needn't even have been something that was selected for. As far as I can tell it just means that evolution is slightly easier than we thought. This diagram sums up the paper nicely.


  
apollo230



Posts: 16
Joined: Mar. 2006

(Permalink) Posted: Aug. 04 2006,02:22   

And honestly, Argy, I do not know how much I can contribute to this thread, anyways, until I do some major reading on the subject-and that will take time.  I did take freshman-level biology, but that's about it.  Regarding directed mutation-I am not a (very) educated layman on the subject.

I do find Chris' flowchart interesting, and appealing.  If I understand correctly, specific genome sites are exposed and "hypermutation" is created at these "vulnerable" areas.  Therefore (how do I say this?) a mutation gradient (differential) is created where some sites appear "favored" over others to produce genetic novelty.  In other words, can we say that a targeted search is taking place in at least a rudimentary sense, where the genome "relies" on some DNA strands more than others to generate change-and  genetic utility?  I do like the specificity implicit in this model.  

Ichthyic, you have strongly implied that ID is a poor scientific enterprise at best-no research program and all that.   It's no wonder the ID movement has not published anything beyond design inferences.  Proving a designer via scientific research is difficult at best:  this alleged engineer does not appear readily or reliably (if at all) for our close inspection.  Does the inaccessibility of the intended research subject (the designer itself) render its existence false? Or folly?  Teleology is not false merely because it's un-testable (or rather, difficult to test).

If I were to go looking for a designer, I would use meditation and petition (listening and querying), and hope that I get an answer.  That is the best research program I can honestly come up with to find a designer and hence vindicate intelligent design.  Granted, this does not sound like much of a scientific enterprise in the traditional sense of the word science-but since any designer would  be intelligent, making queries and "scanning" for responses would be logical protocols to adopt in any search.  A give-and-take conversation with this Creator is probably the best the ID movement can do in order to achieve designer detection, and abiding redemption for intelligent design.

Best regards,
apollo230

  
plasmasnake23



Posts: 42
Joined: June 2006

(Permalink) Posted: Aug. 04 2006,03:42   

Quote (apollo230 @ Aug. 04 2006,07:22)
And honestly, Argy, I do not know how much I can contribute to this thread, anyways, until I do some major reading on the subject-and that will take time.  I did take freshman-level biology, but that's about it.  Regarding directed mutation-I am not a (very) educated layman on the subject.

I do find Chris' flowchart interesting, and appealing.  If I understand correctly, specific genome sites are exposed and "hypermutation" is created at these "vulnerable" areas.  Therefore (how do I say this?) a mutation gradient (differential) is created where some sites appear "favored" over others to produce genetic novelty.  In other words, can we say that a targeted search is taking place in at least a rudimentary sense, where the genome "relies" on some DNA strands more than others to generate change-and  genetic utility?  I do like the specificity implicit in this model.  

Ichthyic, you have strongly implied that ID is a poor scientific enterprise at best-no research program and all that.   It's no wonder the ID movement has not published anything beyond design inferences.  Proving a designer via scientific research is difficult at best:  this alleged engineer does not appear readily or reliably (if at all) for our close inspection.  Does the inaccessibility of the intended research subject (the designer itself) render its existence false? Or folly?  Teleology is not false merely because it's un-testable (or rather, difficult to test).

If I were to go looking for a designer, I would use meditation and petition (listening and querying), and hope that I get an answer.  That is the best research program I can honestly come up with to find a designer and hence vindicate intelligent design.  Granted, this does not sound like much of a scientific enterprise in the traditional sense of the word science-but since any designer would  be intelligent, making queries and "scanning" for responses would be logical protocols to adopt in any search.  A give-and-take conversation with this Creator is probably the best the ID movement can do in order to achieve designer detection, and abiding redemption for intelligent design.

Best regards,
apollo230

You realize that untestable hypotheses and the use of subjective methods like meditation take you out of the realm of science, right? Which I think would be fine with everyone on this board. You can say that you believe there's a designer because you've prayed/meditated/whatever just as long as you don't count that as scientific evidence or expect scientists to do so. It's like Behe on the stand at Dover who admitted that defining ID as science would require us to change the definition of science. Science has worked pretty well for some hundreds of years for answering questions about the natural world. It's fine if you want to do non-sciency things to answer questions about the world, but you can't expect your enterprise to be regarded as science or accepted by scientists as such.

  
argystokes



Posts: 766
Joined: Jan. 2006

(Permalink) Posted: Aug. 04 2006,10:44   

Apollo,

Thanks for not having me put hours into a detailed explanation only to have it ignored or deliberately misconstrued, as others have.

Icky,

That's one e-beer to you.  Make it a Hale's Red Menace, straight outta Ballard.

--------------
"Why waste time learning, when ignorance is instantaneous?" -Calvin

  
Ichthyic



Posts: 3325
Joined: May 2006

(Permalink) Posted: Aug. 04 2006,13:38   

Quote
That is the best research program I can honestly come up with to find a designer and hence vindicate intelligent design.  Granted, this does not sound like much of a scientific enterprise


no, it doesn't, sadly.

THAT is your empassioned defense of ID?

Get back to us when you can independently identify and objectively verify the nature of a proposed designer.

like, for instance, if we somehow got proof that extraterrestrials had been visiting the planet for eons and mucking with stuff; say by actual communication with them.

then you could propose a legitimate hypothesis and make predictions as to what we should see biologically and paleontologically based on the obtained knowledge of said aliens.

Otherwise, like i said, best you consign ID to the realm of wishful thinking and move on to more productive areas.

Have you taken a look at the Templeton Foundation's funded researches into the effects of prayer on healing and recovery after surgery?  I bet you would find that interesting.  Let me know and I'll give you the link to the thread where we discuss it.


Quote
Icky,

That's one e-beer to you.  Make it a Hale's Red Menace, straight outta Ballard.


mmmm, mmm.  tasty.  

I'm a bit worried that the predictable nature of these folks is gonna turn me into an alcoholic though.

;)

cheers

--------------
"And the sea will grant each man new hope..."

-CC

  
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