On the whole though you would agree progress has been made, right? In a world with imperfect knowledge you do the best you can with the information you have.

The response to a paper ought not be, “This paper is bogus because they didn’t control for all variables.”. If the paper is bogus then give reasons for why this is the case. Was the statistical analysis wrong? Are there reasons why this can’t be true? Is this new information worthy of further investigation?

It’s sloppy thinking to say it’s a bad paper without having studied the issue and the data.