Science is about what you can test and not disprove. Three hundred years ago European scientists started with the assumption that the Bible was a historical record and that the biblical flood was a real event. It took about one hundred years of gathering evidence to prove that one single flood could not be the explanation and that glaciers had caused many of the features formerly ascribed to a giant flood and another hundred to correlate geographical features into a coherent history.
It took about two hundred years, from the 1600s to the 1800s, to demonstrate that animal species had died out or changed over time. At this point, it was a historic discipline, like political history, studying what had occurred in the past by the evidence that remained. Darwin’s and Wallace’s brilliant suggestion as to how that happened, in general, was rapidly accepted. As Darwin pointed out, if cave critters had been specially designed for caves, you’d expect to find the same perfect cave critters everywhere. Instead, cave critters in each ecosystem are modified versions of the organisms that live above the ground in that area, just as if they had descended from something that fell or wandered into the cave.
However, at that time genes and chromosomes were unknown. Neither Darwin nor his colleagues knew how a special trait could become more common and not blend back into the average. About that time, Gregor Mendel, breeding peas for years and recording the results, worked out the math of simple dominant inheritance with one gene or two genes; but he published in an obscure Austrian journal. His work did not reach the larger scientific community until almost one hundred years later. In the 1930s, when the genetic theory was added to the theories of natural and sexual selection, the theory of evolution became robust.
Quite a bit of mathematical analysis and prediction, by R.A. Fisher and others, made testable cases for evolution, and evolution passed them. For example, why do most species have equal numbers of both sexes? What should the ratio be when resources are temporarily plentiful? What if resources are restricted but it’s easy to find a mate? But what carried the genetic information was still a mystery. Was it DNA or a protein, perhaps albumin? In the late 1930s, DNA was proven to be the key to inheritance.
The giant chromosomes in the salivary glands of fruit flies let us see something of their structure. Since then, we have learned to trace the evolution and ancestry of individual genes and chromosomes. For example, chimpanzees have one more chromosome than we do: but one of our chromosomes matches up with two of theirs; and there’s even an extra centromere in our chromosome, vestige of its former existence as a separate unit. It’s pretty obvious that we diverged from chimpanzees before the chromosomes fused.
Molecular evolution was developed in the 1960s; that’s where we trace the changes in a single important molocule through various species, noting the changes along the way. It’s the equivalent of literary research, where a single change in a manuscript of the Bible, e.g. the change from “young woman” to “virgin,” is used to track what further manuscripts were copied from the new
The “family trees” made from comparing organisms agree with the evidence of fossils. Hypotheses about the environments and conditions where significant evolution might have occurred suggest places for scientists to look for fossils. That’s how the famous Tiktaalik transitional fossil was found in the sediments of Devonian freshwater swamps. And new discoveries occur all the time. Surely you know of the complete set of transitional mammals, discovered in the 1990s, from a hoofed land-dweller to a swimmer to whales.
In the past decade, evolution has been observed in the laboratory with the development of completely novel traits in bacteria. Evolution has been observed in the wild with two new species of flower developing in the U.S. Northwest in the 1940s. It has been observed in the development of a new species of mosquito that inhabits the London subway system, in a mere 150 years. On a similar time scale, the hawthorn gall midge produced a variety that prefers apples and does not mate with its ancestral strain. Other examples abound.
It only strengthens the case for evolution when the family trees drawn by research into molecular evolution match those drawn on the basis of physiology and fossils.
Then look into ERVs: endogenous retroviruses. Viruses can and do read themselves into our genes. Those, too, are inherited and can also be traced in family trees. Many of them are inactive; however, mutations sometimes reactivate them by chance. For example, the ERV for mouse mammary tumor gives women a higher chance of developing breast cancer.
With evolution, with science, it’s all about the facts.