One of the methods I use in my biology class when we are on the topic of evolution is to teach it in a way that allows students to prove to themselves that evolution is the only method that makes sense when it comes to explaining the diversity of life on Earth. Whatever evidence I am talking about at the time can be turned into a how-would-you-do-it puzzle for the students.
For example, take the fossil record. Everybody knows about fossils, the remains and traces of ancient forms of life. But to creationists, fossils simply represent a part of God's creation that no longer exists. If you look at how fossils are sorted in the rock layers, however, there can be only one explanation: evolution.
With regard to the layering of sedimentary rock, I start by making an analogy to bed covers. If you make your bed with a top sheet, a couple of blankets, a comforter, and a bedspread, it is easy to see why the sheet is on the bottom and the bedspread is on top. You built them up from the bottom in chronological order. The same is true of rock layers. In an area of undisturbed rock, the oldest layers will be on the bottom. Therefore any fossils contained in the rock layers will be sorted with the most ancient fossils on the bottom, the deepest layers. More modern fossils will be toward the top.
So here's the question I pose to students: If all living creatures on Earth were created as is and at the same time, what would the fossils in each layer of rock look like compared to the fossils in other layers? Sometimes it takes them a second or two, but the answer is always the same: "They would all look alike." And, of course, that is correct. The fact that there are different fossils in different rock layers means that the animals and plants that made them changed over time. Couple that with the observable fact that fossils in more ancient rock layers are always representative of more primitive creatures and the conclusion is simple: Creatures changed over time from simple to more advanced. In other words, they evolved.
I know that, in their desperation, Christian apologists have devised their own answer to the sorting problem. Apparently, they were sorted in the Genesis Flood. But even if we allow that floods tend to sort out different types of sediments (and presumably, fossils), they were sorted in the wrong direction. More advanced animals tend to be larger than the very simple forms of life, and flowing water always sorts with the largest sediment on the bottom. Actual sorting is the exact opposite of the way it would be if fossils were sorted by a flood. Gradual change over time is the only cogent theory that explains the observation.
I also tell students that evolution could easily be proved wrong if someone could show a fossil of a modern mammal in the same layer as a fossil of a dinosaur. But in more than 150 years of searching, nothing like this has ever been found.
Going on to comparative anatomy, I can pose a small thought experiment: Suppose you were asked to construct a working replica of a bird wing, a human arm, and a whale flipper so that each replica would perform as the real ones do. You are not at all restricted in the amount or type of materials you can use. The question is, would you build the three replicas using the exact same structure for its frame or would you, instead, choose a structure that makes sense for the needed function? Obviously, the more thoughtful students suggest using a framing structure that is specific to the function, so that the arm and hand would need to be made of more parts than, say, the whale flipper. For economy, you could conceivably construct a flipper using perhaps six rigid pieces of metal connected with hinges. But with a human arm and hand, you would need to use significantly more parts to get the intricate movements you needed.
In nature, however, a human arm, a bird wing, a bat wing, a dog leg, and a whale flipper are all constructed using the same number of bones connected together in the same way. From an engineering standpoint it makes no sense, and my students understand that, because from the puzzle I presented, they figure it out for themselves. Nature's way makes no sense if you assume that each form of life was created separately and did not evolve. But if you assume that all living creatures evolved from a common ancestor, then it makes perfect sense. The only plausible explanation for what is observed in nature is that creatures evolved from a common ancestor, and my students are taught to figure that out for themselves using their own critical thinking skills and logic.
Then I ask them this hypothetical query: Suppose you are an engineer and you are given the task of building a robot. The robot has to be able to do these chores: "taste" food, detect sounds, detect light and identify objects from it, and make sounds. In that case, you would give your robot all the following mechanism: a microphone, a speaker, a camera, a liquid chemical sensor. But now I tell them that, after a time, the robot would no longer need to detect dissolved food substances so they will no longer need the chemical sensor. Assuming their robot has a unified design, which method would be more efficient to accommodate the change in desired functionality: 1) to just leave the sensor in place but turn it off, or 2) to redesign the robot from scratch so that the chemical sensor is left out, then re-build the robot? Obviously, most students just say leave its tongue in place and turn it off.
In nature, humans and other animals have organs that they should not have. Humans have wisdom teeth and body hair. We also have a coccyx (tail bone) and an appendix that we would be better off without. Horses have tiny vestigial toe bones. Whales and snakes have hip bones. Ostriches have wings. These are all organs we have but don't need, much like the robot with a chemical sensor that has been deactivated. So why do we have them? Well, why does the robot have the chemical sensor? It's because at one point it needed one and it would have been an inefficient process to remove it when it's usefulness was over. With vestigial organs, animals have them because they were useful to our ancestors, and our living animal cousins may still use them. Some herbivorous mammals, for example, have a cecum, the homologous structure of the human appendix. It is used to aid in the digestion of certain plant material. The ancestor of horses had toes instead of hooves; the fossil record bears this out. The fossil record also indicates that the ancestors of snakes and whales walked on land. And the ancestors of ostriches could fly.
When the question of why these animals have organs they don't need, after being given the robot challenge, students could answer the question. They have the organs because they once needed the organs. But we evolved.
I go on, over the course of the lesson, to ask similar questions about why the human embryo needs to grow gill slits and a tail and why at one point it has a 3-chambered heart. Why must the human embryo go through the stages of a fish and a reptile, only to have those structures turn into something else as the embryo grows? The only plausible answer again is evolution. Ontogeny recapitulates phylogeny. I don't say it in class but the only reason a god would have to make us in this fashion is if he were a deceptive god who wanted to deceive us.
Of course, the clincher when it comes to evidence for evolution is DNA. Fossils were once the primary evidence supporting evolution, and they're still important. But we could prove evolution even without fossils based solely on DNA analysis. Fossils simply corroborate the DNA evidence. In the same way that DNA can be used to positively identify a criminal suspect (or a parent in a paternity suit), it can also be used to show exact relationships among different species, living or extinct. Today, using genetics, "family" trees known as cladograms can be used to show the relationships among living organisms and their ancestors. For those who have allowed themselves to learn about this amazing field of research, it truly is the final death knell for creationism or intelligent design. Again, I obviously do not say this to my students because everybody is allowed to believe what they want, but any creationist who wants to persist in his delusion of creation, he should never allow himself to learn the details of archaeological genetics, because if he does, he will no longer be a creationist.