Evolution is used by biologists to refer to common descent and large-scale evolutionary change (the 'fact' of evolution) and the theoretical mechanisms proposed to explain these facts (evolution as 'theory'). Special creationists still peddle the claim that evolution is 'only a theory', but the fact is that for over 100 years, there has been no debate in scientific circles that evolution has occurred. As evolutionary biologist TR Gregory says:
In The Origin of Species, published in 1859, Darwin cited independent lines of evidence such as the biogeographical distribution of species, homology of structure, the occurrence of vestigial organs and atavisms, and the already well established process of extinction as all pointing to a conclusion that species have changed over time and are connected by descent from common ancestors. Through the force of Darwin’s argument and the mass of supporting data he presented, it was not long before the contemporary scientific community came to acknowledge the historical reality of evolutionary descent...
Over the past 150 years, this initial list has been supplemented by countless observations in paleontology, comparative anatomy, developmental biology, molecular biology, and (most recently) comparative genomics, and through direct observations of evolutionary change in both natural and experimental populations. Each of thousands of peer-reviewed articles published every year in scientific journals provides further confirmation (though, as Futuyma (1998) notes, “no biologist today would think of publishing a paper on ‘new evidence for evolution’ ... it simply hasn’t been an issue in scientific circles for more than a century”). Conversely, no reliable observation has ever been found to contradict the general notion of common descent. It should come as no surprise, then, that the scientific community at large has accepted evolutionary descent as a historical reality since Darwin’s time and considers it among the most reliably established and fundamentally important facts in all of science. [1] (Emphasis mine)
We demonstrate quantitatively that, as predicted by evolutionary theory, sequences of homologous proteins from different species converge as we go further and further back in time. The converse, a non-evolutionary model can be expressed as probabilities, and the test works for chloroplast, nuclear and mitochondrial sequences, as well as for sequences that diverged at different time depths. Even on our conservative test, the probability that chance could produce the observed levels of ancestral convergence for just one of the eight datasets of 51 proteins is ≈1×10^−19 and combined over 8 datasets is ≈1×10^−132. By comparison, there are about 10^80 protons in the universe, hence the probability that the sequences could have been produced by a process involving unrelated ancestral sequences is about 10^50 lower than picking, among all protons, the same proton at random twice in a row. A non-evolutionary control model shows no convergence, and only a small number of parameters are required to account for the observations. It is time that that researchers insisted that doubters put up testable alternatives to evolution. [2]
In other words, the authors are testing the hypothesis tnat homologous proteins from related species have a common ancestor, and were produced by a process of descent with modification, and demonstrated that this hypothesis is solidly attested. Conversely, the idea of special creation did not fare well:
Early (pre-Darwinian) biologists suggested several ideas as to the relationship of modern organisms, but a relevant one here is the ‘archetype’ model that suggested that a number of ‘forms’ were originally created within high-level groups. For mammals say, one ‘form’ would have been a giant cat, which then independently evolved (or degenerated) into lions, tigers, leopards, panthers, cheetahs, etc. In our examples, this is tested (and eliminated) by demonstrating that successively deeper datasets continue to show ancestral convergence. In other words, we do not see a set of ‘archetype’ species originating at just one point in time – there is continuity in the evolutionary process. (Emphasis mine)
Again, as Gregory noted, common descent is no longer a point of contention in mainstream science - the evidence for it is overwhelming and has been known to be so for over a century:
From the scientific point of view, there is no doubt that evolution has occurred, and there really were a continuous set of intermediates connecting individuals, populations, varieties, species, genera, families, etc. Nevertheless, as scientists we need to ensure that we have good quantitative tests available of all our favoured models. Given our results, we suggest that researchers need to be more assertive that evolution has both occurred, and continues to occur. It is essential that any person who does not accept the continuity of evolution puts forward alternative testable models. As we tell our first year undergraduates, ‘belief is the curse of the thinking class’.
One waits in vain for special creationists to do this. Once again, common descent is a fact, whether special creationists like it or not.
References
1. Gregory TR "Evolution as Fact, Theory and Path" Evo Edu Outreach (2008) 1:46-52
2. White WTJ, Zhong B, Penny D (2013) Beyond Reasonable Doubt: Evolution from DNA Sequences. PLoS ONE 8(8): e69924. doi:10.1371/journal.pone.0069924
