Molecular Evolution

I remember reading somewhere the idea that evolution is "slowing down" in the sense that the major body plans were laid down very early, and diversification has been within those plans. As time progressed the variation became more and more restricted until we find that now not a great deal happens except for "trifling losses and gains at the species level" What do you think?
Why can't evolution be explained by genes being transferred from one organism to another? If one organism developed a gene for an enzyme in glucose metabolism, for example, then it was transfected into other organisms, this could explain how everything ends up with the same molecular biology.
What are the implications for evolution in the discovery of so-called 'molecular machines'?
What about "Junk DNA?" Doesn't that provide evidence for evolution?
If "Junk DNA" is really junk, how come the organisms have not gotten rid of it during evolution?
I heard that Bumblebees can't fly according to engineers, yet they do. Is that true?
Is it true that "pseudogenes" are proof for evolution of humans from apes?
I recently heard a theory that suggested mitochondria and chloroplasts, two organelles of the cell were the result of endosymbiotic capture of bacteria. What do you know about this theory?
Scientists have asserted that much of the DNA in the human genome is "junk", left over from evolution. How does this square with a created system?
Ó 2010 Arthur V. Chadwick, Ph.D.