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You're actually seeing tons of molecules on your desk. You just can't resolve them individually. Neither can the JWST.

So if we're not seeing individual molecules, why talk about molecules? Its fine to talk about desks or whatever we can actually see, right?

It is amazing, but JWST is not really seeing individual molecules. I believe they are analysing the spectral atmospheric emissions.

The JWST is essentially “seeing” them the same you see all the molecules in front of you in your desk: from the light they scatter or absorb.