By "atomic particle", I mean everything from molecules to quarks---objects that are outside the realm of normal experience but used in physics and chemistry to explain macroscopic events.
By "empirical object", I mean a physical object of medium size that is part of normal experience like dogs, cats, rocks, trees, and other people. Empirical objects are inscrutable. By this I mean that they have an endless set of properties, many of which cannot be guessed at from general considerations, and the values of those properties tend to be imprecise and time-dependent. The more you examine them, the more you learn about them, and they change in chaotic ways.
There are lots of different accounts of abstract objects, but one of the main features of abstract objects is that they are scrutable. They have a finite, or at least finitely characterizable set of fundamental properties that determine their entire nature, and they never change.
Atomic particles seem more scrutable than inscrutable. They have a finite set of properties or a finite set of parts with a finite set of properties and they only change by undergoing quantum state transitions. They seem in some sense to be more like abstract objects than empirical objects. Furthermore, there is the property of identity. No two empirical objects are identical with each other, but among atomic particles, it is common for two of them to be identical.
Now, I'm not interested in an explanation of how an apparent inscrutability could arise from a collection of scrutable particles. I take it for granted that sort of thing is possible. My issue here is not physics but evolution and epistemology.
The evolutionary/epistemological problem is that our brains evolved to deal with empirical objects. We also have a talent for dealing with abstract objects and it is possible to tell a story for how that talent also evolved as a success strategy. There is no story to explain our astonishing good fortune that the building blocks of empirical objects are based on something completely different from the empirical objects that our brains evolved to deal with, yet to the great good fortune of the human race, the building blocks just happened to have a lot in common with abstract objects and the people who investigated the building blocks of matter happened to be extremely good at dealing with abstract objects.
How plausible is that scenario compared to the scenario that the building block of matter are pretty much just like empirical matter but the atomic physicists who came up with the Standard Model just happened to be extremely talented thinkers and extremely motivated puzzle solvers who just came up with a theory of the type that they find satisfying that fits observations but has nothing to do with underlying reality?
This strikes me as a serious problem for analytical philosophers of science, but I've seen no references to it other than some similar concerns from Earnst Mach and Pierre Duhem from over a century ago, and maybe the Vienna Circle, although they seem to have dropped the topic early in the 20th century.
Have any more recent philosophers discussed this issue? Have any tried to justify it?