A narrower follow-up, since the general answer is now clear:

How would you tell the difference between that and the alternative explanation?

Reporting back.

Update: the thing I was blaming turned out not to be the cause. Leaving the original post as written rather than editing it, so the mistake stays visible for whoever searches this next.

Dr.GutHealth said:

Practical: whatever you change, write down the date and the reason.

Fair, and it stops being fair at the extremes. The middle of the range is well understood; the ends are where the honest answer is that nobody knows.

That is the short version; the long version is somebody else's post.

Found this through search years later and it is still the best discussion of the question, so adding one thing. The boring version of this is the one that works, and the boring version is: measure a baseline, change one variable, wait, measure again under the same conditions. Nobody wants that answer and it is still the answer.

From the other side of the consultation, briefly. Take it one variable at a time. Almost every unanswerable question in these threads is unanswerable because three things changed in the same fortnight, and no amount of subsequent argument can untangle them after the fact.