I want to break your question in two.
First:
Gasses.
There are a lot of unknown gasses. Almost as many as there are unknown molecules.
That’s because like a lego set, there are an almost infinite number of ways to put the bricks together. yes only some of them are stable or even connect properly but there’s still a HUGE number of combinations possible.
It’s currently impossible to analyze those gasses remotely and get their shapes and what they could do.
So for that, you are correct, they can’t be sure.
However:
Second:
Those molecules are made of a very finite number of atoms.
Like the lego set, there are only so many types of individual bricks.
And we have a LOT of very good ways to identify those bricks.
Once we’ve identified those bricks we can make some very good guesses as to what LEGO set was built with them.
Obviously we could be wrong but we’ve also sent probes and got on the pot analyses which show the deductions were pretty on the spot.
So for for the second we can be as sure as going there and having actually checked.
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