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Talk:PNAS Response to Letter (view source)
Revision as of 02:42, September 19, 2008
, 02:42, September 19, 2008→Dear Aschlafly,: new section
:That's very nicely put, thanks. You should work on some of the stats pages here. Of course, technically any sample is ultimately just a combination of ''n'' samples of size 1. [[User:MikeR|MikeR]] 13:28, 18 September 2008 (EDT)
:That's very nicely put, thanks. You should work on some of the stats pages here. Of course, technically any sample is ultimately just a combination of ''n'' samples of size 1. [[User:MikeR|MikeR]] 13:28, 18 September 2008 (EDT)
== Dear Aschlafly, ==
After reading your letter, the response from the PNAS, and the entire Lenski affair you dragged yourself into, I have some information you might want to read. Simply put, the PNAS was on the right track, see below for why
1.Figure 3 depicts an "historical contingency" hypothesis around the 31,000th generation, but the abstract states that mutations "arose by 20,000 generations." The paper fails to admit that the Third Experiment disproved the contingency hypothesis depicted in Figure 3.
Reading over the paper, I didn’t find anything about a “historical contigency” around the 31,000th generation. What I believe I am seeing is a misunderstanding, Lenski was looking for two scenerios, First he indicates that if the ability for the E. Coli to consume citrate was due to a mutation, than the rate of the mutation would remain constant, but if it was population that made the mutation more likely, there would be a point where the mutation rate would increase. The graph simply showed both options, so I believe there was a misunderstanding of the graph.
2.Both hypotheses propose fixed mutation rates, but the failure of mutations to increase with sample size disproves this. If the authors claim that it is inappropriate to compare for scale the Second and Third Experiments to each other and to the First Experiment, then it was also an error to treat them similarly statistically.
I am not sure what you are trying to point out here. As the PNAS pointed out, mutations are random. Another note is that Lenski adressed this in his paper, and highlighted it in the article, even pointing out changes in the third experiment. Just a question, what do you mean by treating “them similarly statistically.”?
3. The paper incorrectly applied a Monte Carlo resampling test to exclude the null hypothesis for rarely occurring events. The Third Experiment results are consistent with the null hypothesis, contrary to the paper's claim.
Erm… why was the Monte Carlo resampling incorrect? I cannot make heads nor tail of what you were thinking when you wrote this. Also, the result was inconsistant with the null hypothesis by a margin of 92 percent.
4. It was error to include generations of the E. coli already known to contain trace Cit+ variants. The highly improbable occurrence of four Cit+ variants from the 32,000th generation in the Second Experiment suggests an origin from undetected, pre-existing Cit+ variants.
First off, modern technology grants quite a decent abaility to detect the amount of bacteria in the sample, and there were NO Cit+ variants in it, nor were they mentioned in the paper. Honestly, do you believe that Lenski and his assistants were playing “toss the bacteria around”? Your assumption that there *had* to be Cit+ bacteria in the sample is incorrect, and seems to be based off your misunderstanding of the field.
5. The Third Experiment was erroneously combined with the other two experiments based on outcome rather than sample size, thereby yielding a false claim of overall statistical significance.
Again… what? There is simply nothing “wrong” or “incorrect” about combining different sized samples to test the results. There are correct techniques for testing this kind of things (“Z-transformation” method, to be specific!) and it was used to make the test.
Finially, your claim about the paper not being publically available is false, as you can easily find it by going to Lenski’s site. [https://myxo.css.msu.edu/ecoli/] has it all right there, and 3 clicks away from a Google search.
Might I ask you to clairify the questions and insight I have provided above?
Waiting for your response, [[User:AlexaJ|AlexaJ]]