There was a lot between the stone age (or even bronze age and iron age) and the industrial revoiution: There were the fricking greeks for one thing :-) All the fundamental trigonometry, the fundamentals of physics (Newton, Galileo) came between the iron age and the industrial age, sunbeam :-) That is what I actually worship.
Yes, agriculture is anti-nature, but that does not mean it is unsustainble in other words it does not mean any intrinsic loss of biodiversity. Biodiversity is lost through the *scale* of these activities outpacing the regeneration of nature.
For influenza, your response is the predicted one - we were interconnected even 100 yrs ago, but it misses the point: The point is that infectious disease spread does *not* require proximity, intrinsically. Some does, some does not. Birds literally fly half way around the world every year - this is the nature that you should know about. They carry infuenza from Asia to Europe. Other diseases are spread by insects and bats over long distances. The idea that infectious disease came from settled communities is true for SOME diseases not ALL infectious diseases. Plague is the perfect example for your viewpoint, because the settled communities created the opportunity for the vector (rats) and with smallpox not so but it did lead to human proximity that led to exponential spread. These diseases can be dated back 5000 years, but other diseases (those vectored by birds, bats, insets) are absolutely not contingent upon human settlements at all.
Is tracking a heuristic process? I don't know the answer because I don't know much about tracking. I think humans have made discoveries through observation and deduction, yes. A classic example of observational science would be Darwin. He observed up the wazoo for a prolonged period, he then classified, and he then interpreted: He distilled knowledge from that body of observations. It didn't start with a hypothesis but it did end with a theory. Tracking may be a more rudimentary version of this where you dispense with the theory, and just have the body of observations and some interpretation of them. I don't think there is much to debate here, I am not saying that science is not part of our inherent nature, or that it spontaneously appeared in white folks in the past 500 yrs, I am saying the opposite, that in fact is IS the way we are and have always been. But for it to go exponential and for it to be formalized, there are some basic requirements like writing and and literacy and distribution of manuscripts,and better tools etc., then you get to where we are right now.