...One might be able to make some informed guesses, but to really show what properties have what effect, it would be necessary to run the experiment with items that were identical except for specific chosen properties. Mere observation could lead to erroneous results if, e.g., smaller items happened to be generally either denser or lighter than larger ones (and odds are pretty good they'd be one or the other). ...
Yes, but another way to eliminate such sampling error is to take many samples from as different contexts as possible.
A good example is in radiometric dating. Any single rock sample could indeed be subjected to water, heat, etc. during the years it's been in the ground, and that contamination could throw off the implied dates. But when you take several samples, from different areas, and examine different radioactive elements for their decay ratios, you can distinguish between contaminated results and valid ones. Because different chemical elements will react to water or heat or other stresses differently, and samples from the next hill over were probably subjected to different levels of stresses than the first hill. This is why the common creationist criticism of radiometric dating fails.
So, sure, paleontology is, pedantically speaking, an indirect science, in that they aren't able to do a medical exam of the living ancient animals like they can with live animals. But at some point a big enough pile of circumstantial evidence is just as good as a collection of direct evidence. Heck, even in your example of directly shaking the stones, you have error & imprecision & sampling error, so direct evidence isn't logically privileged either.
That leaves open the problem, though, that it's possible for there to be unknown factors which affect the items being observed. For example, in the shaker example, suppose that the small spheres were magnetized iron. They could easily throw off the results of the experiment. Such risk factors would be avoided if the experiment was done with manufactured spheres.
A good example is in radiometric dating. Any single rock sample could indeed be subjected to water, heat, etc. during the years it's been in the ground, and that contamination could throw off the implied dates. But when you take several samples, from different areas, and examine different radioactive elements for their decay ratios, you can distinguish between contaminated results and valid ones. Because different chemical elements will react to water or heat or other stresses differently, and samples from the next hill over were probably subjected to different levels of stresses than the first hill. This is why the common creationist criticism of radiometric dating fails.
Radioactive dating relies upon certain things being reasonably constant. If two specimens which seem to have been exposed to the same environmental conditions, both when alive and after death, have comparable C14 readings, then it is likely both speciments are of comparable age. But figuring out what that age is can be tricky.
What reputable scientists generally go, from what I understand, is try to quantify the unknowns and then say that a particular sample appears to be somewhere between X and Y years old. For many types of paleontological research, things like date measurements don't need to be entirely accurate, and so accepting a certain amount of "slop" is fine.
The problem with evolutionary "science" is that certain parts of it are very sensitive to initial conditions, and thus the types of measurement slop which don't pose a problem with paleontology pose a big problem with evolution. Certain precise things would have had to have happened for new species to be created in the fashion evolutionists claim, and the only "evidence" that such things did happen in the manner required is the existence of the new species.
So, sure, paleontology is, pedantically speaking, an indirect science, in that they aren't able to do a medical exam of the living ancient animals like they can with live animals. But at some point a big enough pile of circumstantial evidence is just as good as a collection of direct evidence. Heck, even in your example of directly shaking the stones, you have error & imprecision & sampling error, so direct evidence isn't logically privileged either.
Certain parts of paleontology start bordering on the realm of silliness, because they represent theories which even if they "work", would not constitute the only possible explanation fot eh observed evidence.
As for the "shaking stones", part of the essense of science is repeatability. Even if I have some experimental error when I do the stone-shake, different people repeating the experiment with their own manufactured spheres would not be likely to have the exact same errors I did.