It's okay to listen and nod and go do what you were going to do anyway. But if you're wanting a scrap...
Your father mentions love, morality and beauty as natural and evidence of God. What happens when your father mentions equally-natural rape? Evidence of God, but a capricious God, would be consistent. Instead your father mentions things he likes as evidence of a God he likes, and things he doesn't like as evidence you're wrong.
Apply morality to biology in one person in one part of his or her life and you're going to be making up stories. Apply biology to large group behavior over long periods of time and you might be on to something. One man and one woman? No idea of their violent tendencies. A million men and a million women? Bet the farm that the men are more violent. Pointing out what one man or woman does as evidence for or against biological roots for morality is a misapplication of the tool.
"I'll think about that" is a fair response to anything your father says about God or your beliefs. You can then go think about it. Or not think about it. Then you can answer, or not answer. The answer of "I don't know" is also a fair response.
Here's one for you to ask him: Can God be surprised? If the answer is no, then ask how you can know something (how to be surprised, what it feels like, memories of it happening) that God doesn't know. If the answer is yes, ask what it is that your dad knows that God doesn't know and would be surprised about.
Your father, also, can say "I'll think about that" and "I don't know."
Note: I do not equate what is natural with what is good.
So, a little background- I've just come out as an atheist to my dad, a Christian pastor, who's convinced he can "fix" my thinking and is bombarding me with a number of flimsy arguments that I'm having trouble articulating a response to, and need help shutting down. The particular issue at the moment deals with non-theistic explanations for human psychology and things like love, morality, and beauty. After attempting to communicate explanations from evolutionary psychology, I was met with amused dismissal of the subject as "speculation".
There's one book in particular he's having me read- The Reason for God by Timothy Keller. In the book, he brings up evolutionary psychology as an alternative to theistic explanations, and immediately dismisses it as apparently self-defeating.
"Evolutionists say that if God makes sense to us, it is not because he is really there, it's only because that belief helped us survive and so we are hardwired for it. However, if we can't trust our belief-forming faculties to tell us the truth about God, why should we trust them to tell us the truth about anything, including evolutionary science? If our cognitive faculties only tell us what we need to survive, not what is true, why trust them about anything at all?" -Timothy Keller
The obvious answer is that knowing the truth about things is generally advantageous to survival- but it hardly addresses the underlying assertion- that without [incredibly specific collection of god-beliefs and assorted dogmas], human brains can't arrive at truth because they weren't designed for it. And of course, I'm talking to a guy with an especially exacting definition of "truth" (100% certainty about the territory)- I could use an LW post that succinctly discusses the role and definition of truth, there.
Another thing Dad likes to do is back me into a corner WRT morality and moral relativism- "Oh, but can you really believe that the act of rape doesn't have an inherent [wrongness]? Are you saying it was justified for [insert historical monster] to do [atrocity] because it would make him reproductively successful?" Armed only with evolutionary explanations for their behavior, I couldn't really respond- possibly my fault, since I haven't read the Morality sequence on account of I got stuck in the Quantum Physics ultrasequence, and knowing that reality is composed of complex amplitudes flowing between explicit configurations or aaasasdjgasjdga whatever the frig even (I CAN'T) has proven to be staggeringly unhelpful in this situation.
In addition to particular arguments WRT the question posed, I could also use recommendations for good, well-argued and accessible books on the subject of evolutionary psychology, with a focus on practical experimental results and application- the guy can't be given a book and not read it, so I'm hoping to at least get him to not dismiss the science as "speculation" or a joke. It's likely he's aware that the field evolutionary psychology is really prone to hindsight bias and thus ignores it completely, so along with the book, a good article or study demonstrating the accuracy and predictive power of the evolutionary psychological model would be appreciated.
Thanks!