I wonder what are examples of organs/structures/behaviours/cooperation that evolutionary biologists themselves find most difficult to explain -- to explain how they could appear evolutionarily -- within known mutation rates, generation frequency, and known time frames. Excluding issue of appearance of life itself.
Knowing rates of mutation and generation cycle (and population size), it would be possible to estimate time needed for appearance of new feature.
Thus it would be possible to spot counter-examples, such examples that are probabilistically beyond possibility to appear in given evolutionary time. Are such examples known ?
I might be naive, but I think some rare behavioral trait can be a candidate, behavior that does not trigger even once in a lifetime of organism, on average, that triggers really rarely.
Answer
I won't claim that these are the most difficult things to explain evolutionarily, but these two are hard:
- Host-Pathogen dynamics. They start out easy enough, but the interaction between a pathogen and its host is intensely complex. You have the immune system, pathogen-pathogen interaction, the balance between weakening a host and killing a host, dozens of different transmission mechanisms, at least two levels of evolutionary pressure (inter-host and population), etc.
- Social/Societal level traits. Evolutionary psychology has, for example, been criticized for not being able to get much past the level of "Just So Stories" in terms of its ability to explain human societal traits using evolutionary theory.
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