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Talk:Flaws in Richard Lenski Study (view source)
Revision as of 13:45, July 16, 2008
, 13:45, July 16, 2008→Expertise in Statistics
::::::::However, the fact that the conditions were not identical doesn't detract from the fact that the emergence of Cit+ clones *still* correlated with the sampling of the later generations. What this means is that with three separate experiments and under three sets of conditions, the constant-rate-mutation hypothesis doesn't hold. What the differences between the second and third replay experiments demonstrates is that they were run under different conditions that affected the overall rate of conversion, not that the 'potentiated mutation' hypothesis is wrong. Those are actually distinct questions. Andy, the data simply does not support your claims that the cultures were contaminated (we'd expect random distribution), or that the 'scaling' variations ruined the experiment. In my opinion, you seem focused on red herrings to the exclusion of evaluating the data in the overall context of the experiment which demonstrates a correlation of Cit+ clones emerging from samples taken at later generations. Would you care to address that pattern and discuss why your 'contamination hypothesis' doesn't appear to hold up?--[[User:Argon|Argon]] 09:29, 16 July 2008 (EDT)
::::::::However, the fact that the conditions were not identical doesn't detract from the fact that the emergence of Cit+ clones *still* correlated with the sampling of the later generations. What this means is that with three separate experiments and under three sets of conditions, the constant-rate-mutation hypothesis doesn't hold. What the differences between the second and third replay experiments demonstrates is that they were run under different conditions that affected the overall rate of conversion, not that the 'potentiated mutation' hypothesis is wrong. Those are actually distinct questions. Andy, the data simply does not support your claims that the cultures were contaminated (we'd expect random distribution), or that the 'scaling' variations ruined the experiment. In my opinion, you seem focused on red herrings to the exclusion of evaluating the data in the overall context of the experiment which demonstrates a correlation of Cit+ clones emerging from samples taken at later generations. Would you care to address that pattern and discuss why your 'contamination hypothesis' doesn't appear to hold up?--[[User:Argon|Argon]] 09:29, 16 July 2008 (EDT)
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::::::::There is nothing absurd in what Argon said. As he mentioned, the third experiment was performed under different conditions and at a different time than the first or second experiments. The key here is that there are plenty of variables, some unknown, that simply aren't controlled for between the experiments. For example, take the fact that it was performed at a different point in time than the first two. The third experiment, then, is almost certainly being performed with different batches of growth media, liquid and solid. Anyone who has spent any significant time growing cells knows that media can vary significantly in growth characteristics between batches, despite the same recipe being used. The reasons for this can be many. Perhaps the balance or pH meter was off calibration one day, or a different bottle of reagent was used. Take an analytical chemistry course, you'll spend plenty of time talking about this. It is true that, for the most part, this sort of variability has minimal impact. But when you're examining something like an extremely rare mutation, or you're trying to make an extremely accurate measurement, intra-lab variability like this can be significant. For an extremely rare mutation like Cit+, which involved at least two additional mutations in potentiated cells, any change in mutation rate can have a significant effect on your ability to obtain mutants. Mutation rate is sensitive to growth conditions, so cells grown in different conditions are likely to experience a different rate of Cit+ mutation.
::::::::Regardless of the reason for the lower-than-expected number of Cit+ mutants in the third experiment, however, the Cit+ mutants isolated absolutely did not arise from contamination. This is clear if you read the paper. You're still left, then, with the two hypotheses presented, and the results support historical contingency.[[User:Gerlach|Gerlach]] 09:45, 16 July 2008 (EDT)
Is there anyone here with expertise in statistics who could give an analysis? [[User:Fyezall|Fyezall]] 16:15, 15 July 2008 (EDT)
Is there anyone here with expertise in statistics who could give an analysis? [[User:Fyezall|Fyezall]] 16:15, 15 July 2008 (EDT)