Rooting out false assumptions
This section is really just a subsection of "Conceptual Jack-in-the-boxes". However, as its importance is so critical and the identification of false assumptions could be explosively dramatic, it deserves its own dedicated emphasis.
Rooting out false assumptions can be considered a game to be played largely outside the compass of reductive science. The latter is largely looking for insight through greater detail; it is well recognised that surprises have been exposed by the results that reductve science generates. However, looking for false assumptions is a fun game on its own and their presence can be indicated by the dichotomous observations and conclusions that come from the tensions they generate.
Perhaps, my favourite is quantum physics and all its subsidiary disciplines. Here we see that the maths that the discipline generates produces accurate predictions that are almost absurdly precise. It it based on this language of maths that is, itself, intensely logical. The derivation of these equations depends on many concepts that were originally generated though Newtonian physics. Then, we suddenly throw in this wobbler that no one understands quantum physics and that it is logically absurd. That, to my mind, suggests that the absurdity is generated through adopting one or a series of false assumptions; it is these that blind us to the underlying logic. Rooting out the false assumption(s) should be a major consideration. Even if we can't comprehend it, the presence of false assumptions is – for me – clearly advertised. Acknowledging the high probability of their existence would be better than the a blind submission to the conclusion that it is illogical. Admittedly, it does not fit with our accepted concept of logic but the indicaters are that our logical interpretations are the things at fault rather than the system itself being illogical.
For me, the false assumption in immunology is that it is largely a lymphocyte commanded "chase and kill the bug" system. When we assume, instead, that the underlying process is a biochemical resource management system that is concerned with the identification and disposal of colony debris (the prime process), then things begin to look very different. The hard time that pathogenic organisms experience becomes the consequence of needing to live in the mess they make in order to proliferate within a colony of animal cells (a zygote derived colony).