It is of interest to look at the basic data in Table 1 of Liu, Gaido and Wolfinger [1
]. In Table 1 they present results on the gene expression amplitudes in two different experiments. In Table 1 they are trying to explain differences between different experiments in terms of variation in the phase angles of peaking of gene expression in different individual cells. Thus, given a particular variation in gene expression in different cells, one can account for different amplitudes based on the variation in phase angle of the peak of expression. If one had a particular cell growing with a 20 hour doubling time, and in some cells the peak was at 9 hours, others 10 hours, and other 11 hours, the amplitude would be reduced based on the distribution and frequency of the peak of expression in different cells.
At this point I have philosophical viewpoint to express, which should, at a minimum, be made explicit. I propose that for a given cell, if there is a particular pattern of gene expression during the cell cycle (something, I may add, that I am skeptical of at the start – that is, I am skeptical of whether there are a large number of genes with cell-cycle dependent expression), then it is the object of an experiment to know what that pattern is. Thus, given a single cell growing in an unlimited supply of fresh medium, if there was a sinusoidal expression in this cell that had a certain amplitude and a certain time of peaking, a good experiment would get this result. Two different true synchronization experiments should lead to the same results.
In the Liu, Gaido and Wolfinger paper the authors talk about comparing "different conditions". I apologize for being so fastidious and demanding, but I want to distinguish between what I consider different "conditions" and different "experimental approaches" to determining something about cells. For example, "different conditions" means growing cells in one case at 25°C and in another case at 37°C and seeing what happens to them or what is different in these different conditions. Or one may have Medium A and Medium B and compare the cells for some property. These are "different conditions." But when you take the same cells, growing in a given single condition, and then try to analyze them using two different methods, what you should get, in an ideal world, are results that agree with each other. To summarize, the Whitfield et al. experiments are using different methods of analysis, not "different conditions."
I don't know how people measure the speed of light, but I do remember that there are many different approaches. But when all is said and done, all of these methods give rather reproducible results. That is, different analytical "methods" give the same result. I propose that we should analogize the thy-thy and the thy-noc to different methods examining same condition.
Returning now to the comparison of the two experiments, I present a graph (Figure ) of the K values in a scatter diagram. The R2 value is 0.37, which some may say is "rather strong" and others may say is "rather weak". In measuring the size of an atom, this value would be rather weak. In sociological measurements the data would be considered rather strong. There is no absolute measure of how one should accept the scatter as being strong. For a person who is inclined to believe, the data, if correct, should show a clear 45 degree line from lower left to upper right. For a person who says that the results of the two Whitfield et al. experiments are not reproducible, the data allow that. I look at the data in this scatter diagram and see non-reproducible results.
Replotting of the K values of the two experiments analyzed by Liu, Gaido and Wolfinger .
Figure , in a sense, is a redoing of the Figure 3 of Liu, Gaido, and Wolfinger [1
] in a more intuitive manner. What Liu et al. are saying is that if one has broad enough error bars on the data one can say that many of the points do have similarity or even "identity". Perhaps. But that may be, and in my view is, a judgment call.
One important point that I wish to bring up is that if the two experiments have "different strengths of synchronization", then one would expect that one would have a systematic difference in amplitudes. Thus, if synchrony were sharper in one than the other, the amplitudes would be higher in that experiment than in the broader synchronization. This does not appear to be the case, which is again support for the notion that one should be wary of accepting the results of Whitfield et al. as a synchrony experiment.