Evolution began the moment some random molecule had the ability to replicate itself. Evolution progressed whenever a mistake (a mutation) during replication created a new molecule that was at least as successful at getting copies of itself into the future. Evolution thus requires that the evolving entity possess both a means of reproduction and a means of mutation. For example, a complex object such as the proverbial “Swiss watch lying in the desert” could not have evolved because it has no means of reproduction and no means of mutation.
Although more than 99% of mutations are not successful, given enough time, the replicating molecules evolved into proto-DNA, and later evolved into cells, and later into flatworms before evolving into species that specialized into male and female roles.
Most mutations died out quickly because mutations are both common and random and thus unlikely to be beneficial. It only seems like mutations occurred when they were needed because when a need arose, sometimes one of the many random mutations that were already occurring was useful. Some of the most obvious evidence that evolution happened is the discovery of DNA, the growing fossil record, the increasing complexity and variety of species, the early hominid fossils, and the age of the earth and the universe. Consider that none of this was known at the time of Darwin, so he is not a good source of expertise on evolution.
Most mutations died out quickly because mutations are both common and random and thus unlikely to be beneficial. It only seems like mutations occurred when they were needed because when a need arose, sometimes one of the many random mutations that were already occurring was useful.
One species does not mutate directly into another. Mutations are usually very small, and thus the offspring of a species will mutate over a very long time until some of them are different enough that they start living separately and reproducing less with the earlier versions. Eventually, they would no longer see themselves as the same species and would not try to reproduce with each other, but they could, and their offspring would still be fertile – like grizzly bears and polar bears. They would then be evolving independently, and after enough generations had passed, their hybrid offspring would not be fertile – like when a horse and a donkey produce a mule. Eventually, after more independent evolution, their hybrid offspring would not be able to survive birth, and eventually, their evolution would diverge until the sperm of one species could no longer fertilize the egg of the other.
Evolution is not always so smooth and gradual. For example, extreme environmental changes can happen abruptly, and thus extreme genetic mutations that would have been irrelevant or even harmful before, might actually be useful in the new environment. Another such sudden an extreme mutation can occur when a microorganism such as a bacteria or a virus merges its DNA with ours, and sometimes an entire microorganism, such as mitochondria, becomes a part of us. Another form of sudden mutation is an increase in mutation inducing radiation, such as when the earth enters a part of the galaxy in which we are more exposed to cosmic rays, or when there is a solar eruption. Such rapid evolution would probably look as if a new species just evolved suddenly in the fossil record.
When trying to understand evolution after DNA, it is often helpful to think of genes (snippets of DNA) as the replicating organisms, and to think of ourselves as their outer layer of mobile thinking armor, which they evolved in order to get as many copies of themselves into future generations as possible.
For example, if a gene mutated and made its carrier more likely to create children (e.g. better looking), who were themselves more likely to create children, etc., etc., then each generation would have more copies of that version of the gene than the previous generation until it was the only version in existence. Likewise, if a gene mutated and made its carrier less likely to create children (e.g. homosexual), then that mutation would die out quickly.
Therefore, human behavior is the product of those genes that have caused our ancestors to get them into every generation to date, so we act a lot like those particular cavemen. Most of those genes existed before we were human, so we also act a lot like animals too.
We may be the product of more than one billion years of evolution, but we are also the product of more than one hundred thousand years of human evolution, and we instinctively know that in the last few thousand years, we have evolved something quite special …. The Soul of Humanity.