Speaking of villains...
I've got a villain in my book who has ingratiated himself with the protagonist after first challenging and despising him and being confronted with science that he could not refute and still remain reputable. The villain, who doesn't even know he's a villain yet (I didn't even realiz it until a little while ago) and probably wouldn't admit it to himself if he did know, has arranged for the hero to receive his PhD (after writing his dissertation, but the character has already told the hero that he's defended his positions adequately). The hero has been showered with money and there is definitely a money motivation for his university to extend and award the degree to him (money talks in the university world).
I'm curious, Uncle Jim, how would you make the villain mentioned above more and more of a villain without either of the characters actually falling to the fact? At this time, the villainous character and the protagonist consider themselves friends although they were recent rivals. The villain has even visited the hero's lab ad offices and informed him of the fact that he's being granted his PhD (he doesn;t tell him that a large portion of the award is due to the money the hero has brought to the university).
Eventually, I hope to make this book a series and the organizations backing the hero and a couple of the villains, both overt and covert, more important.