The argument against God and for random mutation, and for intelligent design and against creation is a large and complex genre of debate that really spans beyond science.
It used to be that I would say that God was the answer to all things, scientific or otherwise. But now I realize that this simplistic answer doesn’t really do anyone any good. Yes, Jesus is the Way, and Truth, etc, but Jesus also would reason with people. In fact, reason and understanding is found all throughout Scripture. So, to be fair to the people that have not accepted Jesus as Lord, their intellectual property, their deeply-labored opinions need to be given appropriate respect. Of course there is one right answer, but the Bible also has more depth then a quick quotation will satisfy. The Bible, first off, was written in three languages, which means filters and thus interpretations are made of them. The Holy Spirit may speak, but then He might actually be big enough to use science to describe something that just didn’t seem fathomable before. Real science doesn’t play favorites anyway, and neither does God. So what is really going on here? Man’s bias. Man’s perception of God. Belief systems predefine our definitions. God help us!
So, how can Christians engage in a respectful discussion with atheists? First off, don’t try to prove something you don’t have first have experience in. If you have been taught something, go at least research it yourself before you argue in favor of it. Second, be open to new interpretations. Just because atheists, or deist’s describe a scenario that sounds wrong to you, maybe it’s semantics, and the Bible can be genuinely interpreted in favor of the same argument, while acknowledging God. Third, acknowledge that others might have thought something through well, and is worth hearing out for the sake of intellectual curiosity. At the end of the day, the decisions to believe are up to the individual. But every sober, lucid individual has the capacity of reason, and thus people on all sides of the God spectrum can be allow to suggest different opinions.
What’s the Motivation?
What is your motivation for the discussion with someone of a different belief system? Are you out to convert people. Because that won’t happen. It’s simply not how it works. People make their own choices about what they believe, and thus they convert themselves! Instead, enjoy an engaging discussion about something that you both find an interest in, and find that maybe, just maybe, a friendship could be possible dispite differences in beliefs! It actually happens all the time. As a Christian, I know several people who believe different things then I do, and I still love them, and also really respect people who don’t believe in God because they actually think! So don’t classify people based on their intelligence level, but respect people where respect is due.