Changes

:::::::::As the authors comment, when they designed the third replay conditions, they assumed that their changes would not cause significant differences. Still, there clearly were differences in the results and there were some differences in the conditions. Note that if, as Andy initially suggested, the initial cultures were contaminated with Cit+ cells, one might expect that contamination to scale as well between the second and third experiments.

:::::::::As the authors comment, when they designed the third replay conditions, they assumed that their changes would not cause significant differences. Still, there clearly were differences in the results and there were some differences in the conditions. Note that if, as Andy initially suggested, the initial cultures were contaminated with Cit+ cells, one might expect that contamination to scale as well between the second and third experiments.

:::::::::In any case, the authors clearly noted the anomaly, admitted that they're not sure why it happened and cited the statistics from the third replay experiment in their paper (The results still trended with the previous experiments). It's up for readers to decide whether their conclusions are reasonable, based on the data the authors have presented. Most likely, future experiments, particularly with whole genome sequencing of the isolated clones, will confirm or deny the paper's conclusions. Another method would be for you to find a microbiology lab to request the clones and try reproducing the experiment. That's pretty much how science works at the cutting edge.--[[User:Argon|Argon]] 12:14, 1 August 2008 (EDT)

:::::::::In any case, the authors clearly noted the anomaly, admitted that they're not sure why it happened and cited the statistics from the third replay experiment in their paper (The results still trended with the previous experiments). It's up for readers to decide whether their conclusions are reasonable, based on the data the authors have presented. Most likely, future experiments, particularly with whole genome sequencing of the isolated clones, will confirm or deny the paper's conclusions. That's pretty much how science works at the cutting edge. Another method would be for you to find a microbiology lab to request the clones and try reproducing the experiment.--[[User:Argon|Argon]] 12:14, 1 August 2008 (EDT)

:3)The claim that the use of Monte Carlo resampling test was an error is unsupported by argument or counterclaim. ''Why'' is the use of that test an error? Problematically, if the test itself is invalid, why are you willing to accept the p-value for the third replay? Furthermore, the Monte Carlo test was not the test used to combine the three experiments to arrive at the final p-value of p<0.0001 - that was a Z-transformation method. Perhaps your real objection lies with this technique rather than the Monte Carlo test.

:3)The claim that the use of Monte Carlo resampling test was an error is unsupported by argument or counterclaim. ''Why'' is the use of that test an error? Problematically, if the test itself is invalid, why are you willing to accept the p-value for the third replay? Furthermore, the Monte Carlo test was not the test used to combine the three experiments to arrive at the final p-value of p<0.0001 - that was a Z-transformation method. Perhaps your real objection lies with this technique rather than the Monte Carlo test.