Is evolution a fact? In the previous post, we noted that a ‘fact’ in science is not apodictic, but always provisional—it may always be confounded by a new discovery. Following Ruse’s proposition, we considered the three-fold division of evolution into (1) its happening, (2) its paths and (3) its mechanism. If each of these (admittedly interdependent to differing extents) elements can be satisfactorily established, then, yes, we may declare evolution a fact beyond reasonable doubt.
Darwin presented his theory of evolution as ‘one long argument,’ not in a dense, unwieldy tome solely within the purview of the cognoscenti, but in a work of popular science, which could be followed by the lay reader. In this work, the Origin of Species, Darwin sought to marshal evidence from a variety of disciplines in order to establish a Whewellian consilience of inductions: his theory of evolution explicating the evidence; the evidence, in turn, pointing to his theory.
The idea [of a consilience] is that somehow, if a hypothesis is true—tells us about the real world—then various facts or other claims follow from it, and will keep doing so. And there is a kind of feedback process here. As the hypothesis leads to new information, so its derivations themselves confer a kind of probability upon the hypothesis.
It would help to briefly consider what Darwin’s theory actually was. According to Darwin, species were not immutable, but were the product of a gradual process of evolution, the primal (though not sole) cause of which was natural selection. Today, his theory is commonly referred to as ‘evolution by natural selection’; Darwin referred to his theory as ‘descent with modification’. Philosopher of biology Elliott Sober has argued that these characterisations do not accurately convey the essence of Darwin’s theory suggesting that Darwin’s theory be referred to as ‘common ancestry plus natural selection.’ This characterisation acknowledges the relative indepdendence of each of the two ideas, an independence which can be appreciated historically, for whilst Darwin did much to convince the scientific community of the first idea, he failed to convince even some of his closest ‘disciples’ of the second. Nevertheless, the thesis of common ancestry is absolutely integral to Darwin’s theory. If common ancestry can be demonstrated, then species cannot be immutable and one is forced to propose a mechanism to account for the process.
Sober and Orzack note that ‘the best evidence of common ancestry comes from neutral or even deleterious features.’ As Gould frankly puts it, ‘ideal design is a lousy argument for evolution.’ According to an evolutionary hypothesis, adaptation is the result of natural selection. But if adaptation is perfect, then an evolutionary hypothesis becomes less likely, as perfect adaptation is more suggestive of intelligent design. If, on the other hand, adaptation is not perfect, or if there are non-adaptive or maladaptive traits, then a hypothesis of intelligent design becomes less likely and an evolutionary hypothesis more likely. As Stephen Jay Gould writes, ‘you cannot demonstrate evolution with perfection because perfection need not have a history.’ However, ‘if organisms have a history, then ancestral stages should leave remnants behind.’ History is revealed by ‘the useless, the odd, the peculiar, [and] the incongruous’. Natural selection effaces the marks of history. This is what makes evolutionary convergence (the evolution of similar features in independent lineages) such a nuisance for phylogeneticists. Is the feature shared by two groups homologous (due to common ancestry), in which case a close phylogenetic relationship is inferred? or is it due to convergence, in which case it would be a mistake to infer a close phylogenetic relationship? Thus, ‘The more a trait’s distribution can be explained solely on the basis of natural selection, the less evidence the trait will provide for shared ancestry.’ One must look, then, to those non-adaptive or maladaptive traits in order to prove the happening of evolution.
Homology provides perhaps the most striking confirmation of evolution. Darwin was convinced that the exquisite adaptations which pervade the living world were the result of natural selection ‘daily and hourly scrutinising, throughout the world, every variation, even the slightest; rejecting that which is bad, preserving and adding up all that is good’, yet natural selection can only work with what is to hand. An intelligent designer could presumably fashion a novel structure of whatever materials required, but such a luxury is denied to selection. Selection can only modify existing structures, making do with whatever is to hand, as it were: ‘the parts may change to almost any extent in form and size, and yet they always remain connected together in the same order.’ Homologies are testament to common ancestry. Unlike convergences, ‘Entities are homologous if, in principle, they can be traced back to a single genealogical precursor.’
Looking within our own subphylum, the vertebrate forelimb presents a striking example of homology. If you take a look at the diagram above, you can see that the limbs of humans, dogs, whales and birds are all variations on a common theme. One can see the humerus, the radius and ulna of the lower arm, as well as the digits (reduced to three in birds). Whilst the limb in each species is adapted for a particular function, it is apparent that the isomorphisms are due to the inheritance of the structure from an ancestor common to all four species. Homologies such as these only make sense in the light of evolution, and that is what makes them such good pieces of evidence. As Darwin wrote, uttering a common refrain throughout the Origin, ‘On the ordinary view of the independent creation of each being, we can only say that so it is; – that it has so pleased the Creator to construct each animal and plant.’
Just as only ‘descent with modification’ can adequately explain homology, so can only evolution adequately explain the other classes of facts Darwin considered. To take a second example used by Darwin we look to biogeography; a subject to which he devoted two chapters in the Origin. This area provided perhaps the most cogent proof of evolution; both Alfred Russel Wallace and Joseph Hooker came to accept evolution on account of the geographical distribution of species. Biogeography was also cenral in Darwin’s conversion to and discovery of evolution. Richardson writes that ‘Ultimately, biogeography offered the only sufficiently elaborated body of knowledge on the relationship of species to their environment, and to changes in that environment, that could constitute a valid test case for Darwin’s developing theoretical speculations on transmutation and his search for an efficient cause of change.’ Why should it be that, despite highly similar environmental conditions prevailing in regions of distant continents the species that one finds there invariably bear close resemblance to the species of that area and not of the distant area?
If we look to the islands off the American shore, however much they may differ in geological structure, the inhabitants, though they may be all peculiar species, are essentially American…We see in these facts some deep organic bond, prevailing throughout space and time, over the same areas of land and water, and independent of their physical conditions.
What could account for the similarity between neighbouring species if the environmental conditions appeared to be irrelevant? If one Australian species would have been just as well adapted to the environment of an American species, why should the two species be so dissimilar yet bear such peculiar affinities to the species of their homeland? ‘This bond, on my theory,’ wrote Darwin, ‘is simply inheritance, that cause which alone, as far as we positively know, produces organisms quite like, or, as we see in the case of varieties nearly like each other.’ It is migration that is responsible for the similarities between mainland and offshore species, and it is restrictions to migration which are responsible for the differences between species inhabiting identical environments on opposite sides of the globe. At the close of the second chapter on biogeography, Darwin writes, ‘I think all the grand leading facts of geographical distribution are explicable on the theory of migration…, together with subsequent modification and the multiplication of new forms.’
In a letter to Joseph Hooker, Darwin referred to the section on embryology as his ‘pet bit’ of the Origin. Darwin had written that ‘certain organs in the individual, which when mature become widely different and serve for different purposes, are in the embryo exactly alike.’If one looks at, say, the early embryo of a human and the early embryo of a fish the two embryos are remarkably similar; even though the two go on to develop into very different organisms. And the early stages of the human embryo resemble the adult forms of ancestral forms. Darwin goes on to write that ‘The embryos, also, of distinct animals within the same class are often strikingly similar: a better proof of this cannot be given, than a circumstance mentioned by Agassiz, namely, that having forgotten to ticket the embryo of some vertebrate animal, he cannot now tell whether it be that of a mammal, bird, or reptile.’ As evolution proceeds, newer developmental instructions are layered on top of more ancient instructions, forming a kind of developmental palimpsest.
We cannot, for instance, suppose that in the embryos of the vertebrata the peculiar loop-like course of the arteries near the branchial slits are related to similar conditions,—in the young mammal which is nourished in the womb of its mother, in the egg of the bird which is hatched in a nest, and in the spawn of a frog under water. We have no more reason to believe in such a relation, than we have to believe that the same bones in the hand of a man, wing of a bat, and fin of a porpoise, are related to similar conditions of life… In two groups of animal, however much they may at present differ from each other in structure and habits, if they pass through the same or similar embryonic stages, we may feel assured that they have both descended from the same or nearly similar parents, and are therefore in that degree closely related. Thus, community in embryonic structure reveals community of descent.
Homology, biogeography and embryology provided three lines of evidence which Darwin wove into his consilience. A fourth line of evidence which was not available for Darwin but which provides eloquent confirmation of the happening of evolution comes from molecular biology. It is a striking fact that all organisms share the same genetic material. Not only do all organisms share the same genetic material, they also share the same genetic code. This is an instance of a ‘universal homology’. A triplet code is written in the four-letter nucleotide alphabet of DNA codes for an amino acid (the constituent building block of a protein or polypeptide). For example, the triplet code GGC (guanine·guanine·cytosine) codes for the amino acid glycine. With a triplet code composed of four letters, there are 43 possible triplets to code for only 20 amino acids (as well as punctuation marks), so that there is a great deal of redundancy in the code, so that, for example, GGG (guanine·guanine·guanine) also codes for glycine. As Sober notes,
As long as there are multiple codes that each would work, a shared code is evidence for common ancestry. And the more such codes there are, the stronger the evidence that the near-universality of the code provides for common ancestry. This point holds even if the shared code we observe in the life around us turns out to be optimal.
It is not inconceivable that different groups of organisms should have different codes, and for this reason the universality of the code (with its minor variants) testifies to the happening of evolution. The most satsisfying explanation for the universality of the code is descent with modification.
The pieces of evidence presented here have provided confirmation of the first element of evolution: its happening. Only if descent with modification—that is, evolution—has occurred can we satisfactorily account for the facts before us. The theory of evolution wields extraordinary explanatory power, accounting for a plethora of otherwise disparate facts. The happening of evolution can be known without knowing the causal mechanisms responsible. In the next post, I shall consider the second element of the theory of evolution: its paths.
 C. R. Darwin, On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life, (London: John Murray, 1859), p.459.
 M. Ruse, Darwinism and its discontents, (Cambridge: Cambridge University Press, 2008), p.38.
 E. Sober, ‘Did Darwin write the Origin backwards?’, Proceedings of the National Academy of Sciences, 106 (1): 10048-10055, (2009), p.10050.
 See P. J. Bowler, The non-Darwinian revolution: reinterpreting a historical myth, (Baltimore, ML: The Johns Hopkins University Press, 1988).
 E. Sober and S. Orzack, ‘Common ancestry and natural selection’, British Journal for the Philosophy of Science, 54: 423-437, (2003), p.427.
 S. J. Gould, ‘The panda’s thumb’, in The panda’s thumb, chap.1, (New York: W. W. Norton & Co., 1980), p.20.
 S. J. Gould, ‘Senseless signs of history’, in The panda’s thumb, chap.2, p.28.
 Sober and Orzack, ‘Common ancestry and natural selection’, p.428.
 Darwin, On the origin of species, p.84.
 ibid., p.434.
 M. Ghiselin, The triumph of the Darwinian method, (Mineola, NY: Dover Publications, Inc., 2006), p.110.
 Darwin, On the origin of species, p.435.
 R. A. Richardson, ‘Biogeography and the genesis of Darwin’s ideas on transmutation’, Journal of the History of Biology, 14 (1): 1-41, (1981), p.6-7.
 Darwin, On the origin of species, p.350.
 Ibid., p.408.
 Darwin, On the origin of species, p.439.
 Ibid., p.439-440.
 Ibid., p.449.
 M. Ridley, The problems of evolution, (Oxford: Oxford University Press, 1985), p.10.
 Sober, ‘Did Darwin write the Origin backwards?’, p.10053.