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| | ::: The full description of these flaws exceeds the submission length allowed for PNAS Letters, but can be found at http://www.conservapedia.com/Flaws_in_Richard_Lenski_Study. In summary, the flaws are: | | ::: The full description of these flaws exceeds the submission length allowed for PNAS Letters, but can be found at http://www.conservapedia.com/Flaws_in_Richard_Lenski_Study. In summary, the flaws are: |
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| − | :::: 1. The "historical contingency" hypothesis depicted in Figure 3 is contradicted by the abstract and by the data presented in the Third Experiment in Table 1 of his paper. Specifically, Figure 3 states the hypothesis as consisting of an historical contingency at about the 31,000th generation, while the abstract states that "some potentiating mutation arose by 20,000 generations." Alternatively, if Figure 3 is not changed, then the paper should clearly state that the "historical contingency" hypothesis as depicted was disproved by the Third Experiment. | + | :::: 1. Figure 3 depicts an "historical contingency" hypothesis at about the 31,000th generation, but the abstract states that "some potentiating mutation arose by 20,000 generations." The paper fails to state that the Third Experiment disproved this hypothesis as depicted in Figure 3. |
| − | :::: 2. Lenski's two alternative hypotheses suggest a fixed mutation rate, but the failure of the mutations in his experiments to increase based on scale tends to disprove both hypotheses. It has been suggested that the second and third replay experiments were so dissimilar to the first replay experiment that they cannot be compared for scale, but if that were true then it was an error to treat all three experiments as similar for the statistical analysis. | + | :::: 2. Lenski's two alternative hypotheses suggest a fixed mutation rate, but the failure of the mutations in his experiments to increase based on scale tends to disprove both hypotheses. If the Second and Third experiments were so dissimilar to the First Experiment that they cannot be compared for scale, then it was wrong to treat them as similar in the statistical analysis. |
| − | :::: 3. Lenski incorrectly applied a Monte Carlo resampling test to exclude the null hypothesis for these rarely occurring events. For example, the Third Experiment results are entirely consistent with the null hypothesis, and Monte Carlo resampling is an inappropriate technique for excluding the null hypothesis for those results. | + | :::: 3. Lenski incorrectly applied a Monte Carlo resampling test to exclude the null hypothesis for rarely occurring events. The Third Experiment results are entirely consistent with the null hypothesis, contrary to the claim of the paper. |
| − | :::: 4. Lenski incorrectly included generations of the E. coli already known to contain Cit+ variants in his experiments, and he had no means to exclude their presence in the samples. 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. There is no scientific basis for including these Cit+ populations in this study, and it only serves to distort the results. Indeed, the statistically improbable occurrence of four Cit+ variants from the 32,000 generation in the Second Experiment is strongly suggestive of pre-existing Cit+ variants. | + | :::: 4. It was error for Lenski to include generations of the E. coli already known to contain Cit+ variants in his experiments, and the improbable occurrence of four Cit+ variants from the 32,000 generation in the Second Experiment strongly suggests an origin from pre-existing Cit+ variants. There was no legitimate reason to include post 31,000-generation samples in the replay experiments, as Cit+ was already found in the samples by then. |
| − | :::: 5. Lenski's Third Experiment failed to support his hypothesis with statistical significance, even with the incorrect inclusion of the Cit+ variant generations. 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. | + | :::: 5. Lenski erred in combining the Third Experiment with the other two based on outcome rather than sample size, thereby yielding a false claim of overall statistical significance. |
| − | :::: 6. The lag time between the potentiating mutation in the largest experiment disproves Lenski's implicit assumption that it likely occurred in proximity with the occurrence of the Cit+ variant.
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| − | :::: 7. Lenski has not disclosed key portions of his data, such as how thoroughly the samples were screened for pre-existing Cit<sup>+</sup> variants at what specific generations these variants were actually observed in the replay experiments. 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.
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| − | ::: I am requesting that the authors of the paper respond to each of the flaws in this forum and explain the withholding of the data, and submit a revision or retraction of their paper if any are held valid. This public letter concerns taxpayer-funded research and your response, or lack thereof, will be made public. | + | ::: The underlying data for this taxpayer-funded has not been released to the public, despite requests to do so. |
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| | cc: Editor-in-Chief, PNAS | | cc: Editor-in-Chief, PNAS |