> i.e. nature operating perfectly according to its laws of physics, mathematics, biology, etc - versus man's idealization of scenarios as "perfect" based on his value systems.

Oh, then I have no objection except that perfect in that sense becomes a meaningless word. Everything that happens, happens in a universe governed by the laws of nature and it is indeed absurd to expect that anything would have a way to not follow the laws of nature. So things happening perfectly becomes synonymous with things happening. I see neither the utility, nor the wisdom of such hollow usage, but I have to agree that under this very specific and unpopular usage of the word, the statement rings true.

> a virus invades the body, the outcome executes perfectly - healing if the body's systems are strong enough to fight it, disease and death if not. 

Oh there are other possibilities like the virus fusing with the cells and becoming part of their genome. Nature and life are extremely messy when you look into them at that level. But that's just the example really...

> economies thrive if certain fundamental principles of universal law are adhered to, falls apart when man tries to override nature with his ideals.

I would call that an unsubstantiated assertion for now. The fact that there are laws of nature has very little to do with the principles that guide human behavior and thus economy as an emergent system based on a vast amount of humans interacting.

As you pointed out, to affect a system desirably, we need to understand the laws or underlying mechanics that govern it. That's what scientific inquiry into reality tries to do day in and day out. But I would say that there are still a lot of question marks around both economy and psychology and we have a lot to figure out before we can claim things like your assertion above. If you don't know the laws, you can't say with certainty when something will thrive. On top of this, thrive and my definition of perfection are based on human ideals so if what you are saying is true, one should also expect chaos  instead of desirable outcomes like with everything else.