vbm

Well, obviously, you can't be 100% certain, so it is a matter of degree of
certainty based on a variety of factors. If you have fossil A found at
level 10 with, say, a short apendage. Then we have fossil B found at level
7 with the same general morphology, but a slightly longer apendage. Then we
find another fossil, C, on level 5 with an even longer apendage. We also
may see some bio-geographical factors, which add more data. If you have a
sequence of fossils that follow each other in time, with each subsequent
fossil showing a greater and greater change to certain features compared to
the first in the sequence, it creates a greater and greater certainty that
the fossils are related and showing evolutionary development.

Often added to this, when you find that none of the A fossils are still
around after level 9 or so, and none of the B fossils are around after level
6 or so, then this adds to the evidence that A evolved into B which evolved
into C.

Now, once we have such evidence of this often enough among enough species to
know that this process happens with a high degree of certainty, we are
justified in concluding that it very likely happens in other species as
well.

The fact that it can not be proven does not allow it to be dismissed. Such
conclusions should be held only to the degree that the evidence supports, it
is true, but that is just it: it SHOULD be held to the degree the evidence
supports.