Letter to PNAS

Draft of PNAS Letters Response from Conservapedia

Title:

Identification of procedural and statistical flaws in the paper "Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli".

Author:

Andrew Schlafly, B.S.E., J.D.

Author Affiliations:

www.conservapedia.com

Text:

An analysis of the paper and the supporting information on Professor Lenski's website has led to some queries regarding the experiment.

The full description of these queries can be found at http://www.conservapedia.com/Flaws_in_Richard_Lenski_Study. In summary, our concerns are:

- The "historical contingency" hypothesis depicted in Figure 3 may be in contrast to the abstract and by the data presented in the Third Experiment in Table 1 of his paper.

- Lenski may have included generations of the E. coli already known to contain Cit+ variants in his experiments and had no means to exclude their presence in the samples.

- Lenski's Third Experiment fails to show statistical significance for the hypothesis, even considering the inclusion of the Cit+ variant generations.

- Lenski's two alternative hypotheses suggest a fixed mutation rate, but the failure of the mutations in his experiments to increase based on scale raises doubts as to these hypotheses.

- The lag time between the potentiating mutation in the largest experiment raises doubts as to Lenski's implicit assumption that it likely occurred in proximity with the occurrence of the Cit+ variant.

- Lenski has not disclosed key portions of his data, such as how thoroughly the samples were screened for pre-existing Cit⁺ variants.

I am requesting that the authors of the paper address each of these queries in this forum, and respond appropriately.