Evolution has not been, and cannot be, proved. We cannot even see evolution (beyond trivially small change), much less test it experimentally.
Nothing in the real world can be proved with absolute certainty. However, high degrees of certainty can be reached. In the case of evolution, we have huge amounts of data from diverse fields. Extensive evidence exists in all of the following different forms (Theobald 2004). Each new piece of evidence tests the rest.
- All life shows a fundamental unity in the mechanisms of replication, heritability, catalysis, and metabolism.
- Common descent predicts a nested hierarchy pattern, or groups within groups. We see just such an arrangement in a unique, consistent, well-defined hierarchy, the so-called tree of life.
- Different lines of evidence give the same arrangement of the tree of life. We get essentially the same results whether we look at morphological, biochemical, or genetic traits.
- Fossil animals fit in the same tree of life. We find several cases of transitional forms in the fossil record.
- The fossils appear in a chronological order, showing change consistent with common descent over hundreds of millions of years and inconsistent with sudden creation.
- Many organisms show rudimentary, vestigial characters, such as sightless eyes or wings useless for flight.
- Atavisms sometimes occur. An atavism is the reappearance of a character present in a distant ancestor but lost in the organism's immediate ancestors. We only see atavisms consistent with organisms' evolutionary histories.
- Ontogeny (embryology and developmental biology) gives information about the historical pathway of an organism's evolution. For example, as embryos whales and many snakes develop hind limbs that are reabsorbed before birth.
- The distribution of species is consistent with their evolutionary history. For example, marsupials are mostly limited to Australia, and the exceptions are explained by continental drift. Remote islands often have species groups that are highly diverse in habits and general appearance but closely related genetically. Squirrel diversity coincides with tectonic and sea level changes (Mercer and Roth 2003). Such consistency still holds when the distribution of fossil species is included.
- Evolution predicts that new structures are adapted from other structures that already exist, and thus similarity in structures should reflect evolutionary history rather than function. We see this frequently. For example, human hands, bat wings, horse legs, whale flippers, and mole forelimbs all have similar bone structure despite their different functions.
- The same principle applies on a molecular level. Humans share a large percentage of their genes, probably more than 70 percent, with a fruit fly or a nematode worm.
- When two organisms evolve the same function independently, different structures are often recruited. For example, wings of birds, bats, pterosaurs, and insects all have different structures. Gliding has been implemented in many additional ways. Again, this applies on a molecular level, too.
- The constraints of evolutionary history sometimes lead to suboptimal structures and functions. For example, the human throat and respiratory system make it impossible to breathe and swallow at the same time and make us susceptible to choking.
- Suboptimality appears also on the molecular level. For example, much DNA is nonfunctional.
- Some nonfunctional DNA, such as certain transposons, pseudogenes, and endogenous viruses, show a pattern of inheritance indicating common ancestry.
- Speciation has been observed.
- The day-to-day aspects of evolution -- heritable genetic change, morphological variation and change, functional change, and natural selection -- are seen to occur at rates consistent with common descent.
Furthermore, the different lines of evidence are consistent; they all point to the same big picture. For example, evidence from gene duplications in the yeast genome shows that its ability to ferment glucose evolved about eighty million years ago. Fossil evidence shows that fermentable fruits became prominent about the same time. Genetic evidence for major change around that time also is found in fruiting plants and fruit flies (Benner et al. 2002).
The evidence is extensive and consistent, and it points unambiguously to evolution, including common descent, change over time, and adaptation influenced by natural selection. It would be preposterous to refer to these as anything other than facts.