Difference between revisions of "Letter to PNAS"

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==Draft of PNAS Letters Response from Conservapedia==
 
==Draft of PNAS Letters Response from Conservapedia==
  
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''Title:''
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:: ''Title:''
  
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: 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".
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::: 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".
  
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''Author:''
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:: ''Author:''
  
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: Andrew Schlafly, B.S.E., J.D.
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::: Andrew Schlafly, B.S.E., J.D.
  
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''Author Affiliations:''
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:: ''Author Affiliations:''
  
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: www.conservapedia.com
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::: www.conservapedia.com
  
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''Text:''
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:: ''Text:''
  
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: An analysis of the paper and the supporting information on Professor Lenski's website has led to some queries regarding the experiment.
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::: Flaws in this PNAS paper negate its claim that ''E. Coli'' bacteria underwent an evolutionary beneficial mutation.  See http://www.conservapedia.com/Flaws_in_Richard_Lenski_Study and its talk page. The flaws include:
  
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: The full description of these queries can be found at http://www.conservapedia.com/Flaws_in_Richard_Lenski_Study. In summary, our concerns are:
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:::: 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 this.
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:::: 2. A fixed mutation rate is hypothesized, but the failure of mutations to increase with scale disproves this.  If it was inappropriate to compare the Second and Third experiments to the First for scale, then it was an error to treat them similarly statistically.
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:::: 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.
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:::: 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.
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:::: 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.
  
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:: - 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.
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::: The underlying data for this taxpayer-funded have not been released to the public, despite requests to do so.
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:: - 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.
 
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:: - Lenski's Third Experiment fails to show statistical significance for the hypothesis, even considering the inclusion of the Cit+ variant generations.
 
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:: - 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.
 
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:: - 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.
 
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:: - Lenski has not disclosed key portions of his data, such as how thoroughly the samples were screened for pre-existing Cit<sup>+</sup> variants.
 
  
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: I am requesting that the authors of the paper address each of these queries in this forum, and respond appropriately.
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cc: Editor-in-Chief, PNAS
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<br>    New Scientist
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<br>    Selected Congressmen having oversight for research budgets
 +
<br>    Selected watchdog groups

Revision as of 15:30, July 25, 2008

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:
Flaws in this PNAS paper negate its claim that E. Coli bacteria underwent an evolutionary beneficial mutation. See http://www.conservapedia.com/Flaws_in_Richard_Lenski_Study and its talk page. The flaws include:
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 this.
2. A fixed mutation rate is hypothesized, but the failure of mutations to increase with scale disproves this. If it was 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 taxpayer-funded have not been released to the public, despite requests to do so.

cc: Editor-in-Chief, PNAS
New Scientist
Selected Congressmen having oversight for research budgets
Selected watchdog groups

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