I came across this story multiple times in the past few days. First on Facebook, then on some other site I was reading (forgot what it was). Here's a copy of it.
The first thing I want to say is - the professor should be fired, for the way he treats his students. You should never, ever single out a student like that, especially when talking about such a sensitive subject. I think a number of people would cry if confronted this way.
Even if the professor was nicer, so this conversation happened between two friends, the professor is still not very good at his job. Science is more than simple perception, but is a way of understanding the world. Barring the skeptic position of not accepting the senses or the external world, perception is certainly one of the main ways we gain knowledge of the world around us. That does not mean, however, that it is the only way of doing so.
There are certain things which we cannot perceive - electrons, energy, black holes - but which we nonetheless believe exist. In terms of perception, these objects are equal with God. What these objects (or rather, the theories about these objects) has over the concept of God is how they allow us to predict the future. We can manipulate electrons to power all our appliances. Black holes are what logically exists in the center of galaxies, which provide the gravitational acceleration to hold the galaxy together. Energy is simply a way to measure the way things move, or more abstractly entropy; with it we know how far a plane can fly, how long and at what angle runaway ramps should be. These objects can be used to predict how wires, stars, and cars will react.
The real problem science has with God is that it doesn't offer any predictions. Certainly God may have created the universe, and intelligently designed everything in it, but that doesn't tell us anything about what will happen in the next minute. In this way, God shares properties with other imaginary objects, like unicorns and fairies; certainly we can argue they exist but are not perceivable, but that doesn't do us any good.
Back to the debate, the student did a very good job of arguing. Would someone please make sure atheists are represented fairly next time?