For a theory to be a scientific theory, it must open itself up to question, examination and challenge.   Each time it is challenged the theory must have a logical and seemingly sound answer to that challenge.   Every new fact uncovered must fit into the theory in some way or the theory must be adapted and changed in a way to ALLOW the new fact.   In other words, a theory can not deny a fact simply because the fact doesn't fit.   More to the point, a scientific theory must be prepared to die when facts are uncovered that prove it totally wrong {noble things, scientific theories}.  

But scientific theories can be nasty buggers, too.   They have the right to fight back.   When Evolution says that Man descended from the Apes (and I for one find it interesting that the term is descend not ascend except that spending time at the Zoo watching Gorillas and spending time in Cyber Chat rooms seems to support the term 'descend') and someone says "Oh yeah? Says You! The Bible says that God created Man as he is today", Evolution has every right to ask the source of the Bible and expect to see supporting facts.   When the Bible refuses to be cross examined and tries to use itself as supporting facts for it's own existence, Evolution gets to laugh, take the afternoon off and go shoot pool.  

So, at the moment, Evolution has the upper hand.   All life started out as a single cell life form and has mutated in various directions.   We look at a horse, then a giraffe and say "um ...   nawwww." Then they find a horse fossil with a longer neck than a regulation horse but not as long as a Giraffe and find that it lived in a place where there was no vegetation on the ground (bad for horses) but trees not as high as only a Giraffe can access and .....   another piece of Evolution's puzzle falls into place.  

There are MAJOR gaps in the fossil records.   MANY situations that still puzzle evolution and make it far from proven.   But as research advances, Evolution finds more answers.   Sometimes it has to adapt and {gasp} evolve itself - and it has done so many times.  

What IS known is that Evolution is not a smooth, easy transition.   It lays low for a while ...   then explodes out with hundreds of sudden variations ...   only to sit back and be dormant for a while.   For example, on the earliest know hominids, Australopithecus (known as 'Lucy') may have lead much later to the species Neanderthal ('little Ricky?') but that in turn did NOT lead to you and me (at least not ME).   Nature it seems, started THAT chain, then simultaneously started another Hominid ('Ethel') that turned into something else that turned into me (jury is still out on YOU).  

So ...   OUR little chain of evolution has not yet been played out.