DaveScot on Lenksi
DaveScot, an IDiologist who writes for the uncommondescent blog has claimed to have found a mistake in Richard Lenski’s paper. (which I first talked about here)
He points to a statement made by Lenski: (DaveScot’s emphasis)
However, selection requires heritable variation
generated by random mutation, and even beneficial mutations
may be lost by random drift.
And then points to a study done by the Scripps institute that would seem to contradict this statement:
The bold portion is patently wrong. Selection operates on any heritable variation whether random or not… The Scripps researchers, in a nutshell, discovered that E. coli, when stressed (such as running out of food as in Lenski’s experiment or in the presence of antibiotics in the Scripps experiment) selectively increases the mutation rate on certain genes.
What DaveScot has wrong (and I believe he was refering to this experiment) is that the study says that mutations are purposefully induced on specific genes. However, the doesn’t say that only beneficial mutations are induced or that mutations were localized only to specific genes. This is a case of an organism increasing the rate of random mutations, which is a good survival strategy for a population to increase its genetic diversity. However, it does not appear to be the case, that the bacteria is select for their own survival.
So DaveScot is wrong in saying:
Thus the mutations in this case are not random but rather directed at a certain area in an attempt to solve a certain problem.
There is no basis to this teleological statement. Bacteria aren’t attempting to solve a problem, not in the same humans do when we create a new medicine or drug. They are simply increasing their genetic diversity (and probably not on purpose either, more likely in response to selection pressures), so that when antibiotics are around, the probability of a random mutation conferring antibiotic resistance is increased.
DaveScot FAIL
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June 25th, 2008 at 6:29 pm
Spend some time on uncommondescent. DaveScot and the rest of the guys there are piss poor philosophers and even worse scientists.
June 25th, 2008 at 8:33 pm
IDiologist, I like that. It’s less overtly offensive than IDiot, but makes the point all the same.
Way to cut through DaveScot’s logic, too.
June 25th, 2008 at 8:46 pm
thanks and thanks…
I’ve voiced similar sentiments in the comments section at Uncommon Descent… I wonder if the comment will be approved for posting.
June 25th, 2008 at 9:01 pm
Frankly, I’d say it’s not so much a matter of increasing mutation rate as reducing error correction. Error correction requires energy, so reducing the amount of error correction in an energy impoverished environment is a double win; less energy used by the organism and greater genetic diversity in subsequent generations. It’s the greater genetic diversity that ensures survival, but it’s energy conservation that drives the change in the mutation rate. No teleology required.
June 25th, 2008 at 10:08 pm
That was my initial guess too… but I didn’t go that far because my biochemistry knowledge on this subject is a bit hazy, and I wasn’t sure that’s what the original paper was saying.
I’m pretty sure that there proposed model has something to do with repressing correction machinery, but I didn’t want to misrepresent the research, unlike some people (ahem).
At any rate, decreasing error correction results in increased mutation rate, so the point stands without knowing the exact mechanism (which I don’t think has been proven yet).
June 26th, 2008 at 11:12 am
ecoli
Sorry my friend but I’m afraid the FAIL is yours. Specifically you didn’t bother to check into subsequent research at Scripps.
I responded to you here
http://www.uncommondescent.com/intelligent-design/first-paragraph-of-lenski-paper-contains-an-error/#comment-291468
It does indeed target certain genes and excludes others.
Just because the 2005 Scripps paper didn’t point that out, a followup paper in 2006 did (you’ll have to visit my site at the link above to get the link to the 2006 Scripps paper - consider another visit to my website the cost of your lesson).
In a nutshell the response is the derepression of certain specialized polymerases Pol II, Pol IV, and Pol V. Notably missing is Pol III. Pol III, you see, is involved in ribosomal DNA (rDNA) repair. If you were a designer and you wanted to give your design the ability to deal with unknown toxins in the environment you sure wouldn’t want to start mutating the crap out of your ribosomes. That’s a pretty quick and certain kill with no chance of solving the toxin problem. Not all bits of DNA are as forgiving of mutations as others and rDNA is one of the least forgiving. So you would want to exclude that from your rapid mutation targets. And indeed that’s the way it was found to play out. If you didn’t have such a blind spot you’d be able to guess what a good designer might do and look for that instead instead of looking for what a blind watchmaker would do. Take off the blinders, my friend. Life was intelligently designed and it’s a fruitful heuristic to adopt as I’ve just demonstrated.
Sorry for any embarrassment this may cause you but you asked for it.
Cheers
June 26th, 2008 at 11:34 am
By the way - Lenski’s mistake didn’t really have anything to do with the Scripps paper. I just pointed out the Scripps work to remind my readers that mutations are not as random as once thought. Lenski’s mistake was simply saying that selection required *random* mutations. That’s not at all true. Selection requires mutations. Whether the mutations are random or directed is of no consequence to selection operating on them. Selection is blind to the mechanism. It’ll respond to a mutation that some enterprising genetic engineer purposely introduced through a retrovirus vector just the same as it will respond to one caused by a random copy error.
I don’t really think that simple bias error (which was missed by the peer reviewers too) detracts from the methods or conclusions, per se. It’s simply an indicator of sloppy thinking, sloppy peer review, and doctrinal bias in authors and reviewers that may or may not be a factor in the rest of the paper. It probably is judging by the sensationalist spin given to something that bacteria are very, very good at - adapting digestive enzymes to the predominant nutrients in the substrate. In this case though, E.coli already had the enzymes - all it was missing was the aerobic expression of a citrate transport protein (it already had the citrate transport protein too).
If you ask nicely I’ll give you a design theoretic guess at why the transport protein is repressed in the presence of oxygen. Ask on my blog though. I’m cheap but not free. :-)
July 4th, 2008 at 12:28 pm
Nice rhetorical juggling on the uncommondescent site over what constitutes “chance” in evolutionary theory Davescot but you’re simply waving your own banner of bias.
Perhaps research papers should be written by groups of interdisciplinary scientists as to not give any lenience to the IDists rampant, ignorant, and deliberate rhetorical games in order to makeup and insert flaws that were not intended but meant to be understood on a more basic level. After all Lenski is not an expert in mathematical/information theory among other things that could be picked apart.
The part about unexpressed enzymes already being there was an interesting point you should have started out with but the rhetorical nitpicking was just stupid. By your standard absolutely no paper could or would make it through a peer review process, everyone would be analyzing everyone else’s definitions and verbiage to much to get anything done.
I could just say the whole dichotomy you have over creation vs evolution shows a bias in itself. A creator is just another assumption I could pick apart with rhetorical games as well.
July 4th, 2008 at 12:35 pm
I would have been fine arguing the science all day, though I’m no expert in math/information theory, either.
DaveScot asked for the rhetorical game by asking me to propose situations in which evolution could be falsified.
I agree that the dichotomy is stupid, but the creationists/IDiologists insist on making it one. Science isn’t trying to disprove that there is a intelligent designer, after all. It just can’t create a falsifiable model of one. The IDiologist can play all the rhetorical games they want, but in the end the science (and that means evolution) wins.