Difference between revisions of "Flaws in Richard Lenski Study"
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| − | [[Richard Lenski]] rejected a request to release his data to the public,<ref>See [[Conservapedia:Lenski dialog]].</ref> but the following serious flaws are emerging about his work<ref>Lenski et al., "Historical contingency and the evolution of a key innovation in an experimental population of ''Escherichia coli'', 105 PNAS 7899-7906 (June 10, 2008).</ref> even without a full disclosure of the data. Note that the peer review on Lenski's paper took somewhere between 0 (non-existent) and at most 14 days (including administrative time), and Lenski himself does not have any obvious expertise in statistics. In fact, | + | [[Richard Lenski]] rejected a request to release his data to the public,<ref>See [[Conservapedia:Lenski dialog]].</ref> but the following serious flaws are emerging about his work<ref>Lenski et al., "Historical contingency and the evolution of a key innovation in an experimental population of ''Escherichia coli'', 105 PNAS 7899-7906 (June 10, 2008).</ref> even without a full disclosure of the data. Note that the peer review on Lenski's paper took somewhere between 0 (non-existent) and at most 14 days (including administrative time), and Lenski himself does not have any obvious expertise in statistics. In fact, Richard Lenski admits in his paper that he based his statistical conclusions on use of a website called "statistics101". |
1. Lenski's "historical contingency" hypothesis, as specifically depicted in Figure 3, is contradicted by the data presented in the Third Experiment in Table 1 of his paper. Figure 3 proposes a step-up in mutation rate to Cit<sup>+</sup> due to a historical contingency (potentiating mutation) occurring at about the 31,000th generation, yet the Third (and largest) Experiment in Table 1 shows Cit<sup>+</sup> arising just as often before the 31,000th generation as after. The abstract, in further contradiction with Figure 3, suggests that the historical contingency (potentiating mutation) occurred prior to the 20,000th generation. | 1. Lenski's "historical contingency" hypothesis, as specifically depicted in Figure 3, is contradicted by the data presented in the Third Experiment in Table 1 of his paper. Figure 3 proposes a step-up in mutation rate to Cit<sup>+</sup> due to a historical contingency (potentiating mutation) occurring at about the 31,000th generation, yet the Third (and largest) Experiment in Table 1 shows Cit<sup>+</sup> arising just as often before the 31,000th generation as after. The abstract, in further contradiction with Figure 3, suggests that the historical contingency (potentiating mutation) occurred prior to the 20,000th generation. | ||
| − | 2. Richard Lenski incorrectly included generations of the ''E. coli'' already known to contain Cit<sup>+</sup> variants in his experiments.<ref>Lenski incorrectly included generations 31,500, 32,000 and 32,500.</ref> Once these generations are removed from the analysis, the data disprove Lenski's hypothesis. | + | 2. Richard Lenski incorrectly included generations of the ''E. coli'' already known to contain Cit<sup>+</sup> variants in his experiments.<ref>Richard Lenski incorrectly included generations 31,500, 32,000 and 32,500.</ref> Once these generations are removed from the analysis, the data disprove Lenski's hypothesis. |
| − | 3. Lenski's largest experiment (Third Experiment) failed to support his hypothesis with statistical significance. Even though this largest experiment was nearly ten times the size of his other experiments, Lenski did not weight this largest experiment correctly in combining his results. | + | 3. Lenski's largest experiment (Third Experiment) failed to support his hypothesis with statistical significance. Even though this largest experiment was nearly ten times the size of his other experiments, Richard Lenski did not weight this largest experiment correctly in combining his results. |
4. Lenski's two alternative hypotheses suggest a fixed mutation rate, but the failure of the mutations in his experiments to increase based on scale (number of samples) tends to disprove both of Lenski's alternative hypotheses. Yet Lenski's paper fails to address adequately this obvious flaw in the paper. | 4. Lenski's two alternative hypotheses suggest a fixed mutation rate, but the failure of the mutations in his experiments to increase based on scale (number of samples) tends to disprove both of Lenski's alternative hypotheses. Yet Lenski's paper fails to address adequately this obvious flaw in the paper. | ||
Revision as of 15:40, July 13, 2008
Richard Lenski rejected a request to release his data to the public,[1] but the following serious flaws are emerging about his work[2] even without a full disclosure of the data. Note that the peer review on Lenski's paper took somewhere between 0 (non-existent) and at most 14 days (including administrative time), and Lenski himself does not have any obvious expertise in statistics. In fact, Richard Lenski admits in his paper that he based his statistical conclusions on use of a website called "statistics101".
1. Lenski's "historical contingency" hypothesis, as specifically depicted in Figure 3, is contradicted by the data presented in the Third Experiment in Table 1 of his paper. Figure 3 proposes a step-up in mutation rate to Cit+ due to a historical contingency (potentiating mutation) occurring at about the 31,000th generation, yet the Third (and largest) Experiment in Table 1 shows Cit+ arising just as often before the 31,000th generation as after. The abstract, in further contradiction with Figure 3, suggests that the historical contingency (potentiating mutation) occurred prior to the 20,000th generation.
2. Richard Lenski incorrectly included generations of the E. coli already known to contain Cit+ variants in his experiments.[3] Once these generations are removed from the analysis, the data disprove Lenski's hypothesis.
3. Lenski's largest experiment (Third Experiment) failed to support his hypothesis with statistical significance. Even though this largest experiment was nearly ten times the size of his other experiments, Richard Lenski did not weight this largest experiment correctly in combining his results.
4. Lenski's two alternative hypotheses suggest a fixed mutation rate, but the failure of the mutations in his experiments to increase based on scale (number of samples) tends to disprove both of Lenski's alternative hypotheses. Yet Lenski's paper fails to address adequately this obvious flaw in the paper.
5. Lenski's paper is not clear in explaining how the results of his largest experiment (Third Experiment) failed to confirm his hypothesis with statistical significance, even with the incorrect inclusion of the Cit+ variant generations. Instead, his paper refers to his largest experiment as "marginally ... significant," which serves to obscure its statistical insignificance. Other works published in PNAS are clear in defining statistical significance in the traditional way, which Lenski's Third Experiment (even with incorrect inclusion of the above-referenced generations) failed to satisfy.[4]
6. The long lag time (over 12,000 generations) between the historical contingency (potentiating mutation) in the largest experiment disproves Lenski's implicit assumption that the potentiating mutation likely occurred in proximity with the occurrence of the Cit+ variant, and that the first occurrence of the Cit+ variant in the Third Experiment at the 20,000th generation somehow implies that a potentiating mutation occurred in its proximity.
References
- ↑ See Conservapedia:Lenski dialog.
- ↑ Lenski et al., "Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli, 105 PNAS 7899-7906 (June 10, 2008).
- ↑ Richard Lenski incorrectly included generations 31,500, 32,000 and 32,500.
- ↑ See, e.g., www.pnas.org/cgi/content/full/0701990104
