Letter to PNAS

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Draft of PNAS Letters Response from Conservapedia

Title:

Identification of flaws in the following paper published in PNAS: Blount ZD, Borland CZ, and Lenski RE, "Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli," 105 PNAS 23, pp. 7899–7906 (June 10, 2008).

Author:

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

Author Affiliations:

www.conservapedia.com, teacher of precollege students

Text:

The following flaws in this PNAS paper negate its claim that E. Coli bacteria underwent an evolutionary beneficial mutation:[1]
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 hypothesis depicted in Figure 3.
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 the Second and Third experiments to the First for scale, then it was an error to treat 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.
4. It was error to include generations of the E. coli already known to contain trace Cit+ variants, and the otherwise highly improbable occurrence of four Cit+ variants from the 32,000 generation in the Second Experiment suggests an origin from undetected pre-existing Cit+ variants.
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.
The underlying data for this publicly (NSF) funded research have not been publicly released, despite requests to do so and despite NSF policy that "data collected with public funds belong in the public domain."[2]

cc:

Randy Schekman, Editor-in-Chief, PNAS, University of California at Berkeley (by email and postal mail)
New Scientist (by fax - 0171 261 6464)
Rep. Brian Baird, Chairman of the Subcommittee on Research and Science Education of the U.S. House Committee on Science and Technology (by postal mail)
Judicial Watch (by email)

References

  1. Detail is at http://www.conservapedia.com/Flaws_in_Richard_Lenski_Study and its talk page.
  2. http://www.nsf.gov/sbe/ses/common/archive.jsp

Comments

The word count for the above letter is precisely the PNAS limit of 250 for the Text section, excluding the cc: list. The foregoing letter is to be sent by postal mail, return receipt requested, to PNAS, 500 Fifth Street, NW, NAS 340, Washington, DC 20001, by email to pnas@nas.edu , and by posting it in its feedback form at http://www.pnas.org/feedback .