Changes

:::ASchlafly's statement, "''In fact, while the paper states the generation periods for the First (replay) Experiment, it does not disclose the generation periods for the Second and Third Experiments''" demonstrates a surprising lack of comprehension of the procedures described for the second and third replay experiments. There were no generation periods for the second and third experiments, because the bacteria in those experiments were not serially cultured. They were plated once onto MC agar (which contains no glucose) and allowed to sit on those same plates for 59 days (replay 2) or 49 days (replay 3).  

:::ASchlafly's statement, "''In fact, while the paper states the generation periods for the First (replay) Experiment, it does not disclose the generation periods for the Second and Third Experiments''" demonstrates a surprising lack of comprehension of the procedures described for the second and third replay experiments. There were no generation periods for the second and third experiments, because the bacteria in those experiments were not serially cultured. They were plated once onto MC agar (which contains no glucose) and allowed to sit on those same plates for 59 days (replay 2) or 49 days (replay 3).  

:::Similarly, his statement "''The same reason that the paper admits an inability to "exclude an earlier origin" (p. 7901) for the Cit+ variants also results in an inability to exclude Cit+ variants from the samples taken after generation 31,000''" is also wrong. It is impossible to exclude an earlier origin ''in a population of millions of cells'' because it is impractical to plate all of the cells for each generation out so thinly that each and every cell gives rise to a unique colony which can then be tested for the Cit+ trait. For each generation you would have to run thousands of plates to determine ''exactly'' when the first Cit+ cell arose. Conversely, if you wish to sample only a few hundred or thousand cells, rather than multiple millions, it is straightforward to plate them out at such a great dilution that every cell in the sample gives rise to a unique colony, separated in space from all the others, which can then be tested individually for the traits you wish to identify. Since each colony arises from a single cell in the sample, after generation 31,000 you will have colonies that are entirely Cit+ and those that are entirely Cit-. His claim that "''there is no scientific basis for including these Cit+ populations in this study, and it only serves to distort the results''" is also wrong - there is a basis to include those populations - or to be more specific, the Cit- subset of those populations. At the time the replay experiments were designed, before there was any evidence for a potentiating mutation at 20,000 generations, it was impossible to know which generations were more likely to give rise to the Cit+ trait. Suppose that a potentiating mutation arose at the 25,000th generation and expanded through the population or simply persisted at a low level through the 31,000th generation, ''by which time it was outcompeted by some other mutation, or was lost through drift''. It could have been the case that the Cit+ mutation could ONLY have arisen between, say, the 25,000th and 31,500th generations, with no 'potentiated-but-not-Cit+' cells lasting past the 31,500th generation. As it turns out, it appears that the potentiated cells continue to persist in the Cit- population through the 32,500th generation. If you are trying to determine whether the Cit+ trait is contingent or simply random, it absolutely makes sense to include Cit- cells of later generations.

:::Similarly, his statement "''The same reason that the paper admits an inability to "exclude an earlier origin" (p. 7901) for the Cit+ variants also results in an inability to exclude Cit+ variants from the samples taken after generation 31,000''" is also wrong. It is impossible to exclude an earlier origin ''in a population of millions of cells'' because it is impractical to plate all of the cells for each generation out so thinly that each and every cell gives rise to a unique colony which can then be tested for the Cit+ trait. For each generation you would have to run thousands of plates to determine ''exactly'' when the first Cit+ cell arose. Conversely, if you wish to sample only a few hundred or thousand cells, rather than multiple millions, it is straightforward to plate them out at such a great dilution that every cell in the sample gives rise to a unique colony, separated in space from all the others, which can then be tested individually for the traits you wish to identify. Since each colony arises from a single cell in the sample, after generation 31,000 you will have colonies that are entirely Cit+ and those that are entirely Cit-. His claim that "''there is no scientific basis for including these Cit+ populations in this study, and it only serves to distort the results''" is also wrong - there is a basis to include those populations - or to be more specific, the Cit- subset of those populations. At the time the replay experiments were designed, before there was any evidence for a potentiating mutation at 20,000 generations, it was impossible to know which generations were more likely to give rise to the Cit+ trait. Suppose that a potentiating mutation arose at the 25,000th generation and expanded through the population or simply persisted at a low level through the 31,000th generation, ''by which time it was outcompeted by some other mutation, or was lost through drift''. It could have been the case that the Cit+ mutation could ONLY have arisen between, say, the 25,000th and 31,500th generations, with no 'potentiated-but-not-Cit+' cells lasting past the 31,500th generation. As it turns out, it appears that the potentiated cells continue to persist in the Cit- population through the 32,500th generation. If you are trying to determine whether the Cit+ trait is contingent or simply random, it absolutely makes sense to include Cit- cells of later generations.

:::His statement "''The paper incorrectly combined the Third Experiment with the other two based on outcome rather than sample size, thereby yielding a false claim of overall statistical significance''" is meaningless. If ASchlafly objects to the statistical method used, he should recalculate the results using his preferred test and then present both his results and a defense of the alternate statistical method. If you send a letter to PNAS that includes such obvious errors of fact and unsupported conclusions, it will only embarrass ASchlafly and Conservapedia further.--[[User:Brossa|Brossa]] 16:20, 24 July 2008 (EDT)

:::His statement "''The paper incorrectly combined the Third Experiment with the other two based on outcome rather than sample size, thereby yielding a false claim of overall statistical significance''" is meaningless. If ASchlafly objects to the statistical method used, he should recalculate the results using his preferred test and then present both his results and a defense of the alternate statistical method. If you send a letter to PNAS that includes such obvious errors of fact and unsupported conclusions, it will only embarrass ASchlafly and Conservapedia further.--[[User:Brossa|Brossa]] 16:20, 24 July 2008 (EDT)

:: Dear RoyS, my mind is open enough and I listened long enough, and I would appreciate if you would contribute to the discussion instead of accusing me of beeing closed-minded and acting as if we sat in the pub. If the flaws are so obvious, please present your calculations. Lenski presented his, So unless you show that, using a specific method of calculation, you get other numbers, there is not much of an argument. --[[User:Stitch75|Stitch75]] 20:27, 24 July 2008 (EDT)

:: Dear RoyS, my mind is open enough and I listened long enough, and I would appreciate if you would contribute to the discussion instead of accusing me of beeing closed-minded and acting as if we sat in the pub. If the flaws are so obvious, please present your calculations. Lenski presented his, So unless you show that, using a specific method of calculation, you get other numbers, there is not much of an argument. --[[User:Stitch75|Stitch75]] 20:27, 24 July 2008 (EDT)