So what is the concept of atom we have now? isn't it the
smallest indivisible part of matter that is unique?
Don't give me the crap there are electrons and neutrons in the
atoms. This is not important at all. The fact that atoms are the
smallest indivisible part of matter that is unique still stands
even if there are no electrons and neutrons but only protons (dun
ask me how the atom can remain neutral this way), simply because
all your protons and electrons and neutrons are not unique!
2. In fact we say that the atom is this and that based on the
evidence and proof presented so far.... so far, mind you. If some
brilliant chap sometime in the future can come up with a an atom
that is slightly different from our concenpt of the atom then we
can say that our concept of the atom was not "real." Just like
based on the evidence and proofs Newton provided, we say that
Gravity is this and that. Einstein came along and said.... hey wait
a minute... now we have a "better" concept of gravity; a "more"
"real" concept of gravity.
So what is your position? Gravity also not real? So nothing is
real to you? So you have no evidence of gravity also?
Then forget about your whale lah. I can dispute that is not a whale
but a giant fish. 
Of course God may turn out to be an alien after all. 
3. I have tried to introduce you to the idea that there are
things that the human mind has not conceived of yet... but I guess
that would be too much for you since even basic stuff like what
constitutes reality is lost on you.
.. like God? 'cos God who is infinite cannot be comprehended by
our finite minds.
(I quote this from vince)