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This is my own response to the OP story.  Feedback is appreciated, in case I forgot something.

Once, there was a Christian student at a state university who had a strong belief in his religion.  He was challenged by a professor in a philosophy class to support his beliefs, and through a series of clever arguments, was able to silence the professor's criticism.  After that accomplishment, he was feeling pretty good about himself, and so he decided to try the same thing with his science professor, who did not accept religious explanations for science.

So, after the lecture, the student asked to speak to the teacher, since he didn't want to take up classroom time with a non-classroom subject.  Once they'd gone to his office, the student said, "Professor, is there such a thing as heat?"

And the professor answered, "Yes, there is."

So the student asked his second question, "And is there such a thing as cold?"

The professor thought for a moment, then said, "Yes, there is."

"No, sir, there isn't."  When the professor looked askance at the student, he clarified by saying, "You can have lots of heat, more heat, super-heat, mega-heat, unlimited heat, white heat, a little heat, or no heat, but we don't have anything called 'cold'.  We can hit up to 458 degrees below zero, which is no heat, but we can't go any further than that.  There is no such thing as cold, otherwise we would be able to go colder than -458 degrees.  We can measure heat because heat is energy, but cold is just the absence of heat."

The professor smiles slightly after a moment, then says, "Let me ask you a question.  What do you mean when you say it's hot?"

The student, expecting the teacher to be confused, even upset by his argument, said, "Well, hot means that it's hot."  He flushed slightly, because he could tell this wasn't a good answer, so the professor took pity on him.

"You mean something like the temperature is too high for you to be comfortable, right?"  The student nodded, and the professor continued.  "Now, you've known people who thought it was too hot when you thought it was only warm, or even that it was comfortable, correct?  That's because the term hot is relative, a comparison of the existing situation to what the person is used to.  We use cold in the same way.

"In science, we describe things as hot or cold based on a comparison to their environment, or to other things.  The Sun is hot compared to Earth, snow is cold compared to lava, and so on."

The student sat quietly for a moment, collecting his thoughts, so the professor asked, "Was there anything else?"

"Ah, what about darkness?  Is there such a thing as darkness?"

The professor thought a moment, then said, "Yes, in the same sense as cold.  We measure light in lumens, but we use terms such as dark or bright to describe the relative illumination of an area compared to what we're used to."

The student could tell that attempting to argue that darkness was the absence of something wouldn't fly here, so he mentally groped for the next part of his argument.  After a moment, he had it.  "Okay.  Have we ever seen electricity and magnetism?  We can see their effects; I can see a lightning bolt, hear thunder, feel shocked, and so on, but we can't see those things themselves, can we?"

The professor gives him a stern look.  "First off, thunder is caused by lightning, but it is not an inherent property of lightning.  It happens because of air molecules which, forced to vacate the area where lightning passes through, come back together to fill the vacuum created by the lightning's passage.

"Second, we do see electromagnetism, every day of our lives.  It's why we can see at all, because light is a form of electromagnetic radiation.  It's true that we don't see the electrons themselves, because they're too small, but we can certainly see their effects, such as a lightning discharge."

"But, professor, if you can't see something, only its effects, how can you be sure that it exists at all?  How can you be sure that something else isn't causing it?"

The professor smiles gently.  "Because if that something else existed, there would be evidence for it, that we could detect and measure.  For electromagnetism, we have a magnetic field, an electrical current, and the fact that wrapping an electrical current around a magnet makes the magnet's field stronger, and also the fact that one end of a magnetic field attracts the opposite end of a different field, while repelling the same end.  We also have the fact that atoms - which we can observe, say with an electron microscope - are attracted to some atoms and repelled from others, in a similar fashion.

"If this other thing existed, it would have to account for those facts, those observations, in order to be a better explanation than electromagnetism.  Furthermore, it would have to have qualities that couldn't be explained by electromagnetism, but that were clearly caused by it and not something else."

The student, stunned, sat quietly for a time, and finally, the professor asked, "Perhaps, if I knew the point you were working towards, it would make things easier?"

"Ah, yes.  Well, I am trying to show that science has to take things on faith just like religion does."

"I see.  Like arguing that since you can't prove someone has a brain because nobody else in the room has been able to see, hear, feel, taste, or smell it, you have to take it on faith that they have one?"  The student looked shocked, for this had been one of the key points he had made to his philosophy professor.  Before he could muster a response, the science professor continued.

"But we can prove that a person has a brain, simply by giving them a MRI or CAT scan.  We have ways to detect the existence of a brain that do not involve the five basic sensory organs.  Furthermore, even if we do not do those things, we can still demonstrate that it is vanishingly unlikely that they do not have a brain; they are able to reason and think, which requires a brain; we have never once found someone that possessed the faculty of reason that did not have a brain.  To demonstrate otherwise, you would have to show that a person definitely did not have a brain, yet was still able to reason or think.

"It's true that science cannot provide absolute certainty, because we can't examine everything in the universe using it.  But we can test explanations using it against everything we can think of, in order to be reasonably certain of their correctness.  Take evolution.  It's true that we have many gaps in the fossil records, because most organisms do not turn into fossils in the first place.  But the fossils we do have support it.

"Our DNA supports it - our DNA is more than 99% identical to other primate species, 90% identical to other mammals, 75% identical to reptiles, 60% identical to insects, 55% identical to plants, and still 40% identical to bacteria.  Natural selection - the tendency of organisms which are better suited to their environment to survive and reproduce - supports it.  The list goes on and on."

There was a long pause, and then the professor said, "Was there anything else?"  The student thought a moment, then shook his head.
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