A century and a half ago scientists knew very little about how life works, at least compared to what we know today. They knew little about the organelles that make up each living cells, the biochemical pathways involved in living processes, and knew absolutely nothing about genetics (which didn’t even exist yet as a discipline). It was in this context of relative ignorance that Charles Darwin proposed his particular theory of evolution and presented his argument for common descent and natural selection. The notion of evolution and common descent predates Darwin – scientists before him noticed a pattern in the sequence of fossils appearing in successive geological layers. Life seemed to be changing over geological time, with species in younger layers seeming to be derived from species in older layers.

Darwin added to that that basic observation his extensive personal observations of nature – that there is actually a great deal of variation within species, and that many species on the Galapagos seem to be derived from related species on the mainland, but changed to adapt to various niches on the islands. Still, evolution through natural selection was a remarkable hypothesis, but little more than a hypothesis. It is perhaps a good thing that there was so much left to discover about basic biology when evolution was proposed, for that created the opportunity to test this crazy theory.

Every major biological discovery post Darwin was an opportunity to falsify his theory. It could have turned out that the mechanism of inheritance involved a blending of characteristics from both parents (the prevailing notion of the time). This presented a problem for evolution, for then how do newly developed traits persist and change a species, rather than just being swallowed up and diluted in the large population? Mendel discovered that traits are actually discrete things (genes) that are not diluted. They persist as discrete units, so a new mutation would not simply be diluted, but can persist undiminished and spread throughout a population.

Sticking with genetics, it could have turned out that different species or different groups of species had their own pattern of genetic information, or even genetic code. Instead we discovered that every living thing uses the exact same genetic code (which three DNA base pairs code for which amino acids, etc.). Further, when we map out genetic variation we see a branching pattern of relatedness that roughly follows what we would expect from morphology – what living things look like. This same branching pattern of relatedness holds true no matter what bit of genetic code we look at. The same is true when we look at amino acid sequences in various proteins.

This didn’t have to be the case. If common descent through evolution were not true, and let’s say each species were created “according to its kind” then there is no reason why mammals and reptiles could not have had different genetic codes, or completely different proteins, or a different arangement of genes to achieve certain basic functions of  life.

When we look at living things we also see this same pattern of relatedness. Structures all seem to have a derivation, and related species share certain features in common. Giraffes and humans have the same number of vertebra in their necks. Mammals tend to have five digits on each extremity, and when they have fewer than five we see that lose the extra digits through embryological development. Horses are not coded to have one hoof and that’s it. They are coded to have five digits, but then four wither and don’t develop and one toe becomes the hoof. In some cases a mutation results in horses with a couple of extra toes – a throwback to their evolutionary past and connection to other mammals. Some mammals have more that 5 digits, like the panda. When we look closer, however, we see that the extra sixth digit, which functions as a thumb, is really an expanded wrist bone.

This brings up the issue of embryology and developmental biology. We could have discovered that each species develops from a single fertilized egg through an optimal straight path to its adult form – but we didn’t. We found that creatures take a twisting and turning path to their eventual form. While they do not pass through the adult form of evolutionarily more primitive ancestors, the developmental path they do take does reflect this history.

I haven’t even discussed the fossil record yet. We didn’t have to find the fossils that we did, but they were there to be found. We could have found any pattern of fossils, but what we did find is a pattern of changing species through geological time – confirming those earlier observations. We have never found a fossil that is impossibly out of sequence if evolution were true – no horses in the Cambrian fauna. We also do not see species arising without any possible antecedents – completely new morphologies not derived from earlier ones. We could have, but we didn’t. The branching pattern of relatedness we do see follows a temporal and even geological sequence that is compatible with the idea that all life evolved over time from a common ancestor.

Obviously there are still gaps in our knowledge. Evolutionary theory does not predict that there should be no gaps. Over time, however, the gaps are being filled in. It didn’t have to be that way, but it is. Each time critics of evolution point to a gap in the fossil record, the gap gets filled in. No connection between whales and other mammals? No problem, here is Ambulocetus and other “walking whales” and species between whales and terrestrial mammals. Birds and dinosaurs? Here is a host of feathered dinosaurs and primitive dinosaur-like birds. Humans and apes? There are numerous and growing Australopithecus and Homo species to flesh out the branches in between.

Now critics point to bat evolution – where are the missing bat links? Give it time. There are gaps, there will always be gaps – evolution does not predict no gaps, it predicts that they will be filled in as we find more fossils. The gaps are being filled in – but it didn’t have to be that way.

The theory of evolution through natural selection is an overarching theory of life that ties all the biological sciences together with one theory about how life arose. Of course such a theory makes numerous predictions that span every other aspect of biology. Each such prediction was an opportunity to falsify evolution. Instead, over the last 150 years, everything we discovered in biology is compatible with evolution and much of it profoundly supports evolutionary theory, to the point that “it would be perverse to withhold provisional assent” (to quote Stephen J. Gould). There is no other theory that makes the same predictions, or that can tie everything we have discovered about biology into one cohesive theory.

The result of 150 years of biological science is that evolution (natural selection and particularly common descent) is a proven scientific fact, beyond all reasonable doubt. It didn’t have to be that way, but it is.