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Talk:Flaws in Richard Lenski Study (view source)
Revision as of 23:20, July 17, 2008
, 23:20, July 17, 2008→Formal Response to PNAS
::::::::::: Gerlach, look at how many words you used to sidestep my simple explanation of a flaw in Lenski's work: "Lenski claims there is a mutation rate, yet his presented data show that the number of mutations do not scale with sample size. His presented data disprove both of his hypotheses." If the third experiment of Lenski's was independently flawed as implied by your response, then that does not help your defense. Note that in Lenski's second experiment the mutations also failed to scale with sample size.--[[User:Aschlafly|Aschlafly]] 18:26, 17 July 2008 (EDT)
::::::::::: Gerlach, look at how many words you used to sidestep my simple explanation of a flaw in Lenski's work: "Lenski claims there is a mutation rate, yet his presented data show that the number of mutations do not scale with sample size. His presented data disprove both of his hypotheses." If the third experiment of Lenski's was independently flawed as implied by your response, then that does not help your defense. Note that in Lenski's second experiment the mutations also failed to scale with sample size.--[[User:Aschlafly|Aschlafly]] 18:26, 17 July 2008 (EDT)
::::::::::::I think there is a misunderstanding. Blount et al. did not say that the absolute mutation rate was constant for the generation of Cit+. After all, they found that variations in culture conditions had some effect. The replay experiment was performed to determine if clones from later cultures were more or less likely to give rise to Cit+ cells than clones from earlier generations. The authors' hypothesis was that a potentiating mutation was required before the Cit+ mutations could arise. If that was the case then clones from later generations would be more likely to produce Cit+ cells. If the Cit+ capability was the result of an extremely rare, single mutation, then any generation of clones would be equally likely to produce Cit+ cell. The hypothesis is that in a particular experiment, the '''relative probability''' of generating a Cit+ mutant would be greater with clones from later generations. '''Absolute mutation rates''' (which appear to be Andy's concern) may be contingent on the growth conditions, which differed between the three replay experiments but '''''within any particular set of conditions''''', one might expect the relationships between Cit+ recovery and the generations from which the starting clones were derived would still hold.
::::::::::::pg 7902 of the paper in the journal:
::::::::::::"According to the rare-mutation hypothesis, Cit+ variants should evolve at the same low rate regardless of the generation of origin of the clone with which a replay started. By contrast, the historical-contingency hypothesis predicts that the mutation rate to Cit+ should increase after some potentiating genetic background has evolved. Thus, Cit+ variants should re-evolve more often in the replays using clones sampled from later generations of the Ara-3 population."
::::::::::::From the abstract:
::::::::::::"The long-delayed and unique evolution of this function might indicate the involvement of some extremely rare mutation. Alternately, it may involve an ordinary mutation, but one whose physical occurrence or phenotypic expression is contingent on prior mutations in that population. We tested these hypotheses in experiments that ‘‘replayed’’ evolution from different points in that population’s history. We observed no Cit+ mutants among 8.4 x 10^12 ancestral cells, nor among 9 x 10^12 cells from 60 clones sampled in the first 15,000 generations. However, we observed a significantly greater tendency for later clones to evolve Cit+, indicating that some potentiating mutation arose by 20,000 generations. This potentiating change increased the mutation rate to Cit+ but did not cause generalized hypermutability."
::::::::::::What the authors found was that the later generations really did produce more Cit+ mutants than you'd expect if the Cit+ mutation was instead randomly distributed (or, as Andy has claimed and not yets retracted, contaminated by Cit+ cells). Yes, the absolute rates didn't scale across the three difference conditions but within each experiment it is clear that the Cit+ mutants arose from cells taken at later generations. Yes, there were differences in the absolute rates under different conditions but that doesn't mean the results and conclusions about potentiated clones are wrong.
::::::::::::As for calculations of mutation rates: Blount et al. performed additional fluctuation experiments (journal pg. 7903) in an attempt to estimate the relative effect of the potentiating mutation and calculate a rough estimate of the mutation rates. Keep in mind, those rates '''''are referenced to growth under the specific conditions used in that particular experiment''''' and were used to provide ballpark estimates for comparison to other classes of known mutations. As for the second experiment not 'scaling' (with the first?), I wouldn't expect that. The first involved clones grown in continuous liquid subcultures and both the total number of generations, cells/generation and growth conditions (e.g. liquid with nutrient replenishment vs. solid agar) are very different.--[[User:Argon|Argon]] 19:20, 17 July 2008 (EDT)
:::::::: In response to earlier postings about drafting and submitting a letter to PNAS, I'm for it and would be happy to contribute. In response to a comment above, I don't want any "glory" and learned a long time ago that nobody gets credit or money for telling the truth. More often those who speak the truth are reviled and insulted, but mockery doesn't bother the truth as much as it bothers falsehoods.--[[User:Aschlafly|Aschlafly]] 22:01, 16 July 2008 (EDT)
:::::::: In response to earlier postings about drafting and submitting a letter to PNAS, I'm for it and would be happy to contribute. In response to a comment above, I don't want any "glory" and learned a long time ago that nobody gets credit or money for telling the truth. More often those who speak the truth are reviled and insulted, but mockery doesn't bother the truth as much as it bothers falsehoods.--[[User:Aschlafly|Aschlafly]] 22:01, 16 July 2008 (EDT)