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 were 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 over billions of years, the early hominid fossils, and the age of the earth and the universe.
None of this was known at the time of Darwin, so he is not a great source of expertise on evolution, but one compelling argument that that even Darwin knew about was the metamorphosis of embryos, which transition through the previous evolutionary stages of that species. Mammalian embryos start off with some characteristics of fish embryos, then some of those characteristics are absorbed as those genes that we have retained since the time we were fish are deactivated in the embryo. Then some amphibian embryo characteristics appear and are absorbed, then some reptilian embryo characteristics appear and are absorbed, and in whales, some earlier embryonic characteristics appear and are absorbed, such as teeth and hind limbs. Humans even have fur that appears at 6 months gestation, and then is reabsorbed at 8 months. Such embryonic metamorphosis is exactly what one would expect to result from evolution. In 1860, embryonic metamorphosis was the strongest evidence for evolution, and it was enough to convince most scientists.
Not every useless animal gene is deactivated or reabsorbed. Some humans retain the same gene that lets animals wiggle their ears.
Another major evidence of evolution is that human design is hard to explain as the product of an omnipotent omniscient designer, but is easy to explain as the product evolution. One such example is the laryngeal nerve. In fish, it loops around the aorta, which is a pretty direct path to the throat, and in every other animal it also loops down around the aorta and back up to the throat–even in giraffes! Evolution has made some use of this fact. For example, your voice can be affected by a respiratory infection that warns you and those with whom you share many genes, and whom might infect, that you might be contagious. However, any benefits could be achieved if the laryngeal nerve first went directly to the throat, and then proceeded directly to the chest, but evolution usually builds on what is already there.
If evolution usually builds on what is already there, then how does it create radically different species. First, what appears to be a radically different species is often not so different. For example, whales are mostly just a land creature whose parts have moved around and changed in size. Second, mutations can be far more radical than a different protein in one allele.
Let’s first consider the more usual path of evolution of new species.
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 harmful before, might actually be useful in the new environment. Ice Ages, meteor strikes, magnetic pole flips, solar micronovae, and super volcanoes are examples of extreme environmental changes. These can create new challenges and remove old challenges. For example, whales could not have evolved from a land mammal until environmental changes killed off the reptilian super predators in the oceans.
Although whales became possible due to extreme environmental changes killing off some predators and shrinking others, whales themselves are a product of gradual evolution filling a new niche. Whales are just mammals whose preexisting mammalian features have each evolved to adapt to the new niche.
As of 2010, a good candidate for the earliest transitional whale species was the wolf-like creature Pakicetus, who lived 52 million years ago. It had simpler teeth like a whale and ears like a whale, but there were not yet any whales, so if you had see one at that time, it would have been impossible to predict that it would evolve into a whale, and that it was thus a transitional species, which is an important example of how we are surrounded by transitional species right now and we have no way of knowing which ones they are because we don’t know what they will become.
Whales have been well adapted to their new environment for about 40 million years, and for about 12 million years before that, transitional species were not so well adapted and were thus less successful, fewer in number, possibly in only one location, and perhaps most importantly, each such transitional species would not have been around very long as whale evolution was progressing relatively rapidly until it began to stabilize 40 million years ago. We would therefore not find very many fossils of transitional whale species, and those may only be in one location.
We have transitional whale fossils that were all found starting around 1990 because scientists hypothesized that transitional species would have begun to evolve in a certain kind of coastal environment between 60 million and 30 million years ago. Scientists also deduced from plate tectonics where they would find such an environment at that time that was still accessible today, and that is where they found transitional whale species. Isn’t that a far more elegant and complete example of the scientific method than what most scientists do?
A big question most people intuit is how extreme mutation can happen, and how sudden can it be. Whales are extreme evolution, but they are not a different number of chromosomes for example, and they took at least 12 million years to evolve. So how do even more extreme changes happen that are not just extreme changes in existing physical features, and how suddenly can they happen?
One example of extreme and sudden mutations is when a microorganism such as a bacteria or a virus merges its DNA with ours. Another example is when an entire microorganism, such as mitochondria, becomes a part of us. Another form of sudden evolution 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. Radiation and (probably other factors) can cause many kinds of large mutations, such has an extra chromosome, a missing chromosome, and double chromosomes. Other kinds of large mutations are a missing, damaged, or duplicated genes. Such mutations are almost always catastrophic and either prevent fertilization, or prevent birth, or prevent successful reproduction by that individual, but sometimes, such a mutation is useful. Sometimes such rapid and extreme mutation was successful only in an environment that had also undergone rapid and extreme change. Such rapid evolution would probably look as if a new species had suddenly appeared in the fossil record without transition.
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.
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 ancestors (e.g. cavemen). Most of those genes existed before we were human, so we also act much like animals too.
Although we are the product of more than one billion years of evolution, 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.