The paper I cited said in the introduction: "Given the changes we observe at the RNA and lipid level it is reasonable so suspect that the synthetic neonicotinoid-class of insecticides are a factor driving the global decline of pollinating insects".

Peter concluded  "They begin with the notion that they are going to find a problem that neonics cause."

No, they are merely making statements in the introduction about the changes they OBSERVED in look at the study data.  Yes, the phase "a factor driving the global decline of pollinating insects" is overblown, but does the mere wording of the introduction to a paper change the data presented or the methods used?

> For example, Reed Johnson does the work correctly. 
> Instead of starting with neonics and trying to prove they cause altered gene expression...

Claims about "intent" don't address findings, but instead, might be seen as attempts to attack the personal credibility of the authors.

But let's ignore semantics, and talk about controls for a moment.

The "controls" in Johnson, et al are less than solid in my view.

Johnson, et al said "To differentiate among possible explanations for CCD, we used whole-genome microarray analysis, comparing gut gene expression in adult worker bees from healthy and CCD colonies.... Bees for the reference (ostensibly healthy) sample were collected from 5 hives near Urbana, Illinois in July 2007."

Yet the paper does not even mention if any of the "ostensibly healthy" colonies later collapsed showing CCD symptoms or not, something that would have been easy to track.  The use of the phrase "ostensibly healthy" is not a confidence builder.

Further, the controls and the test colonies were admitted to be exposed to very different environments: "Considerable variation in gene expression was associated with the geographical origin of bees, but a consensus list of 65 transcripts was identified as potential markers for CCD status."

To accept the Johnson results, I am going to have to take on faith the basic sorting of colonies into "CCD", and "healthy/non-CCD" categories.  To date, there is no reliable indicator of CCD that can flag an apparently healthy colony as "having CCD" before gross symptoms emerge.  Thus, it has been persistently difficult to differ between one and the other, a problem that has plagued CCD work from the start.

I submit that the controls are more than a little flaky in the Johnson study.

The more recent study seems to have far more solid controls, and thus, more credible results when looking at contrasted results between control and test colonies.

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