Comment by dahart

You’re repeating several of my points in your own words, supporting them and not arguing with them, even though your language and emphasis suggests you think you are arguing.

> then the entire experiment is invalid

Isn’t that what I said? You even quoted me saying it. But I didn’t say anything about only control being contaminated or mis-measured, I think you’re assuming something I didn’t say. Validity is, of course, compromised if the control is compromised, regardless of what happens to the test samples.

> The control cannot be “mis-measured” […] yes, the control may itself be contaminated […]

So which is it? Isn’t the article we’re commenting on talking about the possibility of mis-measuring? Are you suggesting this article cannot possibly be an issue when measuring control samples? Why not?

Controls absolutely can be mis-measured or contaminated or both. It has been known to happen. It’s bad when this happens because it means the experiment has to be re-done.

> If the experimental process contaminates the controls, it will also contaminate the non-controls

Yes! This is exactly what I was implying, and is exactly how you might end up underestimating the relative presence of whatever you’re looking for in the test, if your classification procedure overestimates it.

> You’re looking for between-group differences

Yes! and this is why if, for example, you didn’t notice your control had stearates and you counted them as microplastics accidentally, and then reported that your test sample had 2x more microplastics than your control, you might have missed the fact that your test actually had 10x more microplastics, or that your control actually had none when you thought incorrectly that it had some.

This, of course, is not the only possible outcome, not the only way that the results might be distorted. But this is one possible outcome that the Michigan paper at hand is warning against, no?

> Most of the papers I have read are far, far from even that naïve baseline.

Short of it, or exceeding it? Based on earlier comments, I assume you mean they’re not meeting your standards. I don’t know what you’ve read, and my brief googling did not seem to support your claims here so far. Can you provide some references? It would be especially helpful if you showed recent/modern SOTA papers, work that is considered accurate, and is highly referenced.