Think of the genotype as a long bit string (this is oversimplification, but we can assume this for now). Let’s also assume that there is an operator which operates on this string. The fascinating thing about this operator is that it has no idea what happens in the real world (phenotype) once they change a bit on this bit string. The operator has two operations, one which it frequently uses “crossover” or “recombination” operation, and another very rarely used ‘mutation’ operation. When sexual reproduction occurs in the real world (natural selection, which is not exactly the survival of the fittest for sexually reproducing organisms), it sends two of these ‘fit’ bit strings back to the operator. The operator, completely blind to how they were selected or why they were fit, will just recombine these two strings. (Also note, it cannot recombine with floating numbers, it has to be a bit; TBD later). Sometimes, very rarely, the operator likes to do an experiment: after recombining the strings, it will randomly flip a bit (or bits). This is a mutation. The operator has no explanation for what that flipped bit would produce in the actual world. The operator then sends back this new string, natural selection does its job, returns back two more strings, and the process goes on.
This feels like a very random process where something like a human being becoming the outcome is almost unfathomable. Clearly, human beings are so complicated; how would a simple crossover or mutation operation result in such a sophisticated design? It looks random in one step, and it still looks somewhat random after ten generations. But with millions of generations and an ever-growing population size, it suddenly becomes intuitive. Crossover helps to find which qualities of the current population are better and helps preserve it for the future. While mutation explores new qualities (most of which will be pretty bad) natural selection makes sure that if a mutation results in an improvement in survival (or more correctly, higher rates of reproduction), it will be carried on to the next generation. This Cumulative Selection over long time spans with a large, diverse population results in beings that look like the product of intelligent design.
Another interesting thing to note is how natural selection is not constant, it is just a record of whoever could reproduce given the current environment. There would have been a crazy winter where a lot of fitter beings who survived harsh summers would have died. The natural selection which once favored summer-fit beings now favors winter-fit ones. Because the selection criteria shift alongside changing environments, the “design” is constantly being optimized for the “now,” with no intelligent architect overseeing historical fitness.
Because evolution is blind and cumulative, it frequently gets stuck with some bad quality over time, and it cannot go back and “refactor” its code. If a design becomes flawed over tens of thousands of generations, there is effectively no going back. Evolution cannot hit “undo” or go back to fix a fundamental “error.” I say error here, but this design in the first place occurred only because those who had this error reproduced more. Take the human eye (the Axial Twist Theory). Our retinas are actually “inside out.” The light-sensitive cells are behind the neural wiring, creating a blind spot where the nerves exit the eye. Evolution can’t go back to “Version 1.0” and re-wire the eye; it can only work with what it has already committed to. (More correctly, there still is a very minute possibility that some mutation can re-wire the eye)
We’ve seen the diagram of a chimpanzee slowly standing up to become a human. This is somewhat misleading as it implies a straight, intentional line. Where were all the mutations that went wrong? What we don’t see in that image are the massive branches which were pruned. We are simply the branch that was not cut off!