Changes

== Dear Aschlafly, ==

== 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

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.

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 contingency” around the 31,000th generation. What I believe I am seeing is a misunderstanding, Lenski was looking for two scenarios, 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.”?  

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.  

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 inconsistent with the null hypothesis by a margin of 92 percent.  

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.  

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.

First off, modern technology grants quite a decent ability 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.

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.

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.

Finally, your claim about the paper not being publicly available is false, as you can easily find it by going to Lenski’s site. [2] has it all right there, and 3 clicks away from a Google search.  

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 clarify the questions and insight I have provided above? [[User:AlexaJ|AlexaJ]]

: Your posting is filled with gross misspellings, "I don't get it" type of statements, and a general link that shows nothing.  I suggest you try harder with an open mind.  Thanks and Godspeed.--[[User:Aschlafly|Aschlafly]] 23:47, 18 September 2008 (EDT)

: Your posting is filled with gross misspellings, "I don't get it" type of statements, and a general link that shows nothing.  I suggest you try harder with an open mind.  Thanks and Godspeed.--[[User:Aschlafly|Aschlafly]] 23:47, 18 September 2008 (EDT)

::::'''''"Are you not making an assumption here"'''''.  Spelling mistakes signify little beyond spelling.  If you were to consider swimming to the bottom of the Pacific and I said "you won't be able to, you can't breathe underwater" then I would be right.  If I were to write "U wont bee able to, yu can't breev undewatta" I would '''''still''''' be right about your ability to swim to the bottom of the Pacific.  Woefully wrong about spelling, but spot on about the status of your gills.  On the "tone" of the edit I might remind you that PNAS took exception to the "tone" of the letter.  ''"Mr. Schlafly's final comment about release of data is uncalled for". '' Professor Lenski certainly took exception to the tone of ''both'' emails to him: ''"(g)iven the '''continued''' rudeness of your second email"'' (my emphasis).  And, naturally, it makes little difference to the validity of the criticisms: if I were to say "you *******************, you can't breathe underwater" I would ''still'' be right.  So "your spelling is bad" or "you are being rude" simply fail to negate the statement "the letter was wrong". In the abscence of a negation coupled with plenty of corroboration, we a forced to the conclusion that the letter had little merit. --[[User:Toffeeman|Toffeeman]] 10:32, 19 September 2008 (EDT)

::::'''''"Are you not making an assumption here"'''''.  Spelling mistakes signify little beyond spelling.  If you were to consider swimming to the bottom of the Pacific and I said "you won't be able to, you can't breathe underwater" then I would be right.  If I were to write "U wont bee able to, yu can't breev undewatta" I would '''''still''''' be right about your ability to swim to the bottom of the Pacific.  Woefully wrong about spelling, but spot on about the status of your gills.  On the "tone" of the edit I might remind you that PNAS took exception to the "tone" of the letter.  ''"Mr. Schlafly's final comment about release of data is uncalled for". '' Professor Lenski certainly took exception to the tone of ''both'' emails to him: ''"(g)iven the '''continued''' rudeness of your second email"'' (my emphasis).  And, naturally, it makes little difference to the validity of the criticisms: if I were to say "you *******************, you can't breathe underwater" I would ''still'' be right.  So "your spelling is bad" or "you are being rude" simply fail to negate the statement "the letter was wrong". In the abscence of a negation coupled with plenty of corroboration, we a forced to the conclusion that the letter had little merit. --[[User:Toffeeman|Toffeeman]] 10:32, 19 September 2008 (EDT)