EVOLUTION: What the Fossils Say and why it Matters, Donald R. Prothero (2nd edition)

by Paul Braterman

EVOLUTION: What the Fossils Say and why it Matters, Donald R. Prothero (2nd edition)

If you are interested in evolution, get this book. And make sure that your library gets it. And your children's high school library. Incidentally, it's incredible value; list price $35.00/£27.95 from Columbia University Press, with over 400 lavishly illustrated pages.

ProtheroBookThe book is a comprehensive survey of the fossil record, supplemented at times with other evidence, and framed as one long argument against creationism. It opens with a general discussion of the ideas behind current evolutionary thinking, moves on to a survey of specific topics in (mainly animal) evolution, from the origins of life to the emergence of humanity, and concludes with a brief discussion of the threat that creationism poses to rational thinking. The argument is laid out clearly in the seemingly artless prose of an accomplished writer in love with his subject matter, with plain language explanations that presume no prior knowledge, while the detailed discussions of specific topics give enough detail to be of value, I would imagine, even to a professional in the field. The author is an experienced educator and researcher, with thirty books ranging from the highly technical to the popular, some 300 research papers, and numerous public appearances to his credit, and the work is copiously illustrated with photos, diagrams, and drawings by the author's colleague, Carl Buell. These illustrations are an integral part of the work, graphically displaying the richness of the data at the heart of the argument.

ProtheroSelfImage The first edition of this book appeared in 2007, when it was the year's American Association of Publishers outstanding book in earth science, and while progress in the past decade has been less dramatic than in the two decades preceding, nonetheless this update is most timely.

The author's Prologue lays out the agenda: "Instead of the embarrassingly poor [fossil] record that Darwin faced in 1859, we now have an embarrassment of riches." To which one might now also add the records in molecular biology, embryology, and historical biogeography. The final paragraphs of the book summarise the motivation: "Evolution matters because science matters. Science matters because it is the pre-eminent story of our age, an epic saga about who we are, where we come from, and where we are going."

As an integral part of the author's strategy, we have quotations from creationist writers that show their arguments to be at best uninformed, at worst consciously dishonest. To a UK audience, this may seem excessive. In a US context, I fear it is not. In any case, the creationists' errors serve to clarify the logic of the genuine science. There is an extensive bibliography at the end, and additional reading suggestions at the end of each chapter, although I would have welcomed some way of relating these to specifics in the text.

We start with a chapter on The Nature of Science, where the author follows the usual line. Science, he tells us, Is distinguished from other forms of knowledge by its use of Popper's hypothetico-deductive method, based on the principle of falsifiability, while the word "theory" is only used in science for a hypothesis that is well-corroborated. And since our scientific knowledge is always revisable in the face of further information, we cannot strictly speaking use the term "fact" within science.

I think this analysis is wrong, and damaging. It is of course correct to emphasise the central role of observational testing, but it gives far too narrow an account of the richness and boldness of the scientific process (see for example Carol Cleland's favourable comparison of the methods of scientific exploration of the specifics of the past, with those of the scientific search for time-independent general laws ). It reinforces the damaging impression, convincingly rebutted by Maarten Boudry among others, that science is qualitatively different from other ways of acquiring knowledge about the world. It is also demonstrably untrue that within science we reserve the term "theory" for what is well-corroborated (consider, for example, phlogiston theory, or the classical Greek theory of the Four Elements). Finally, this approach invites confusion, much exploited by creationists, between falsification (rare) and modification (commonplace, and essential to the development of science). We are not required to discard valuable theories merely because they are falsified in some detail. Instead, we accept in advance that they may need modification. But that this is no excuse for timidity. All our claims to knowledge of the world are in principle open to change, but this should not stop us from saying that, on the evidence, evolution is an established fact.

One striking example of modification, discussed by Prothero, is the replacement of Darwinian gradualism in current thinking by what is known as punctuated equilibrium, where significant change occurs most frequently over short timespans in small isolated populations. So the fossil record is usually a series of (small) jumps, rather than a smooth continuum. Creationists, as we might expect, represent this shift as falsification of the central Darwinian doctrine of common descent, whereas in reality it is a logical consequence of population genetics.

The reference to Darwin brings me to my one pedagogical problem with this book; the heavy emphasis placed on Darwin's own writings. Admitted, these were profound and prescient, and admitted, in addition, that he is much quote-mined and distorted, and that these distortions illustrate creationist tactics at their crudest, but to start from what Darwin said in 1859 is to place ourselves on the defensive, making everything we have learnt since look like an afterthought and leaving us fighting on ground of our opponents' choosing.

In Chapter 2, Science and Creationism, the author describes creationism as peculiar to the US. If only this were true. The pseudoscientific creationism that rose to prominence in the US from the 1960s on has merged, in the UK as it has in the US, with old-fashioned biblical literalism. Nor is it limited to Christianity. It is being explicitly promoted within Islam by Adnan Oktar ("Harun Yahya"), and has been adopted by the pseudo-orthodox and fiercely anti-modern Haredi Jewish movement.

I like the author's sympathetic treatment in this chapter of Genesis as a myth worthy of respect, fulfilling important emotional needs, as do the creation myths found in every society. At the same time, he tells us why on internal evidence we should regard Genesis as a composite multi-authored document. This undermines the naive biblical literalism on which creationism depends.

The author returns to creationism in the final chapter, Chapter 16, Why does it matter? The chapter is subtitled Deceit in the Name of the Lord, and is the result of many years of discussion and argument.

It is clear from the examples Prothero gives there that creationists knowingly lie, repeating falsehoods even when well aware of the counter-evidence. This shocks him, as it should.

We lie to ourselves in order to protect valued core beliefs. And so, as he says, "Mountains of evidence about evolution will not shake them or make them pay attention, when they believe eternal torture in the underworld is the alternative." Other factors involved are confirmation bias, tribalism, and voluntary isolation from critics. I would add what philosophers call essentialism, the idea that things can be rigidly separated into different kinds. So creationists may disagree about whether Archaeopteryx is a flying lizard, or a bird with teeth and tail, but will be unanimous that it must be one or the other.

As to why this matters, a democracy needs a citizenry who respect and understand science. Teaching creationism in US public schools is an attack on the Constitution. The attack on evolution is really an attack on all of science. Geology, palaeontology, astronomy, anthropology are all inconsistent with a literal reading of Genesis, and supernaturalism undermines science at its root.

So how to proceed? Reach out to people who may be open to reason. This is now easier than ever, and the author speaks of hearing from people who realised, from reading his book, that their pastors were lying, or who had been appalled by their intolerance towards questioning.

Prothero complains that professors in many smaller colleges are bullied by creationists. Here he greatly understates the problem. There are US universities totally committed to creationism, and one nationally recognised accreditation agency, Transnational Association of Christian Colleges and Schools (TRACS), actually insists that its accredited colleges adhere to the doctrine of "The full historicity and perspicuity of the biblical record of primeval history, includingthe literal existence of Adam and Eve as the progenitors of all people, the literal fall and resultant divine curse on the creation, the worldwide cataclysmic deluge, and the origin ofnations and languages at the tower of Babel."

The American public is appallingly ignorant in basic science, and the US is the only advanced nation where less than half the population accept that "human beings, as we know them, evolved from an earlier species of animals", although questionnaire wording is crucial and this may overestimate the problem.

America's falling behind in technology undermines its economic future. Evolution denial threatens health and well-being, which depend on recognising evolutionary relationships. Ideological suppression of science corrupts society (consider e.g. Lysenkoism), and, as Prothero points out, the US now has creationists at the heart of government. An understanding of our place in the Universe depends on accepting the science, and this understanding is liberating and uplifting.

In between the preliminary and final chapters, we have the meat of the text. A comprehensive summary of such highly informative material is impossible, so I will just pick out aspects that I found particularly interesting.

Chapter 3, The Fossil Record, mentions the role of devout churchmen in establishing the reality of deep time, and their abandonment of 6-day literalism by the early 19th Century. A discussion of the Grand Canyon, and how crudely it is misdescribed by creationists, leads to a detailed description of its actual complex sedimentology, and of the faults and distortions of the rocks in the surrounding area. This gives us a taste of real geology, as opposed to the creationists' Flood Geology. There is a brisk dismissal of the absurdities of Noah's Ark, and a sideswipe at the bad Hebrew of baraminology, (bara min does not mean "created kind", but "he-created a-kind-of") the pseudoscience that purports to trace the present diversity of life to biblical "kinds" that could have fit inside the Ark. This chapter also explains the basics of radiometric dating, and mentions other problems with Young Earth chronology, such as tree ring counting, and annual layers in ice cores going back 680,000 years.

Chapters 4 and 5 are the intellectual pivot of the book. Chapter 4, The Evolution of Evolution, links pre-Darwinian evolutionary thought to Enlightenment thinking, progress in other sciences, the discovery of serial succession in the fossil record, and the abandonment of belief among the educated (including the clergy) in a young Earth and a literal universal Flood. We have a history of Darwin's evolving thought, and his crucial contributions in extrapolating from artificial to natural selection, and in suggesting such selection as the agent of change.

Next, the Neo-Darwinian Synthesis built around population genetics, dominant by the late 1940s. This defined evolution as change in allele (gene type) frequency in a population, and assumed gradualism, and that all changes were driven by selection. There is an excellent section on how radically this view has now been modified, with neutral drift, horizontal gene transfer, incorporation of viral genetic material, possible environmental influences, and junk DNA. Duplications in the genetic code ensure that some changes in DNA will leave its message unchanged, and such neutral mutations are especially useful as a molecular clock. The persistence of unused genes testifies to evolutionary pathways, while changes in regulatory genes can cause large changes even in a single generation.

Kinds of evidence: the family tree of life, homology (evident in forelimbs), embryology, biogeography (placentals vs marsupials). Observed evolution in real time: Darwin's finches in the 1970s, diversification of European house sparrows in North America, salmon adapting to new habitats, lake versus ocean sticklebacks, industrial melanism, drug resistance in bacteria, pesticide resistance in insects and weeds.

Chapter 5, Systematics and Evolution, clarifies the confusing relationship between the 18th-century (Linnaeus) classification of species, genus etc based on resemblances, and the new approach of cladistics.

Cladistics demystifies classification by a simple idea derived from evolution. A clade consists of a parent species and all its descendants, and inherited features are used to define family trees. Traditional classification by specific characters was to some extent arbitrary, because it might depend on what characters you focus on, and any particular organism is a mosaic of what are now called primitive features, present in the ancestral species, and more recently evolved derived features. (These terms are unfortunate, because of the lingering suggestion that evolution corresponds to progress, but that is the vocabulary that we are stuck with, and the meaning is generally quite clear.)

A cladogram is a branching diagram showing how species are related. Extinct species are shown as side-branches, to emphasise the fact that we can't know whether we are dealing with direct or collateral ancestors, grandparents or great-uncles. Cladistics puts in visual form the answer to the ever popular question "If we evolved from monkeys, why are there still monkeys?" by showing modern humans and modern monkeys at exactly the same distance from their last common ancestor. Molecular comparisons, especially using the advances in DNA sequencing that have taken place over the past few decades, also allow us to establish cladograms completely independent of anatomical examination or the fossil record. One example is the placing of whales as a sister group to even-toed hoofed mammals of the pig-hippo family, first suggested on molecular evidence and only later confirmed from the anatomical structure of the ankle bones in whales' four-footed ancestors. The remarkable fact, of which Prothero could perhaps have made more, is the general overall agreement, of which this is just one example, between the phylogenies (family trees) derived using such different criteria. On a fine scale, or during periods of very rapid spreading out into new niches, the details of phylogeny remain fuzzy, perhaps inevitably so since populations are intrinsically diverse, but the overall correspondence is undeniable.

Part II, Evolution? The fossils say yes, makes up the bulk of the book, and displays the enormous weight of the fossil evidence. Chapter 6, Life's Origins, is the one that overlaps most strongly with my own research interests. Here Prothero follows the general view among palaeontologists, a view that seems to me rather too optimistic. He is however up-to-date and well-informed, aware of the evidence for the deep antiquity of life, and of the reasons for believing that if already established, life could have survived the late heavy bombardment that the Earth experienced around 4 billion years ago. He gives more prominence than I would have liked to the Urey-Miller experiment, on the spontaneous generation of the building blocks of life, whose shortcomings1 are regularly pointed out by creationists. He also underestimates the difficulties with the "RNA world" hypothesis, and does not mention the central problem that information-carrying molecules (be they DNA, RNA, protein, or something else altogether) require the variable components to be lined up in the right order, like letters in words. Once we have any variable system that can replicate and undergo selection between variants, evolution becomes inevitable, but the origins of life problem is, precisely, how we ever got to that stage.

Philosophically, Prothero is certainly correct in saying that creationists at this point regularly commit two major fallacies. They presume that because the origin of life problem has not yet been solved, that is good reason to think it insoluble, and they believe that the appropriate response to this situation is to invoke a miracle-working deity. This last belief in particular is pernicious, because such "explanation" can be used to answer any question whatsoever, leaving us with no motivation to do science. My own approach here is to say that the origin of life is indeed an incompletely solved problem, because it is a very difficult one, but that this is no objection to biological evolution, much as the origin of the elements was an incompletely solved problem until the 1950s, but that was not a reason for rejecting chemistry.

Chapter 7 is titled Cambrian "explosion" – or "slow fuse"? Here the creationist myth, based on a mass of half-truths, is that all major animal phyla (arthropods, nematodes, chordates, echinoderms, molluscs etc) somehow sprang into existence independently during the Cambrian. This, they claim, is evidence for separate creation, and by implication makes separate creation more credible throughout the entire record. Such is the claim put forward in Darwin's Doubt, a major publication from the Intelligent Design creationist Discovery Institute.

As Prothero points out here, and has also pointed out in a devastating review of that book, all of this is simply untrue. Life had been around since 3.8 billion years before present, if not earlier. Before the Cambrian we had what is now called the Ediacaran fauna, complex organisms with strange shapes, so that the "explosion", which itself required some twenty million years, was part of an overall process that took four times that long. All of which has been known, at least an outline, for 70 years, so that the creationist appeal to the sudden appearance of life's diversity is at best wilfully ignorant, at worst knowingly dishonest. (There is also evidence in the next chapter, which could have been mentioned here, of how the various phyla are not independent at all, but related through Precambrian common ancestors.)

The next few chapters discuss, in considerable detail, the evolution of invertebrates, chordates (the phylum that includes all vertebrates), amphibian and land vertebrates, dinosaurs (including of course birds), and mammals.

Invertebrates make up 99% of the animal kingdom. Marine microfossils provide a continuous record of evolution, with worldwide correlation of sediments giving a timeline that has been calibrated using radiometric and palaeomagnetic dating. This is not, as creationists claim, circular reasoning, but its very opposite, independent confirmation using different methods, and the timeline is well enough established to be used in oil exploration.

We have examples of intermediates between the different invertebrate phyla, evidence of their common deep ancestry. Such relationships, originally deduced from anatomy and from the fossil record, are now increasingly confirmed by molecular phylogeny. Examples include intermediates between molluscs and their worm-like ancestors, and between many-segmented worms and arthropods.

As for chordates, the phylum that includes all vertebrates, embryos have been found from as far back as 600 million years ago, and molecular and developmental information suggests an even older deep relationship between chordates and echinoderms, the phylum that includes sea urchins. Further evidence against the separate creation of different phyla, and against the special role that creationists give to the Cambrian.

We are shown how the characteristic tetrapod limb structure (one upper arm bone, two forearm bones, connecting bones in the wrist, digits) is present in the mid-Devonian Tiktaalik, emerges step-by-step from numerous well-documented earlier forms, and is in turn ancestral, step-by-step, to everything from a bird's wing to a human hand to a horse's hoof.

Prothero tells the story of Archaeoraptor, to illustrate science in action, and creationist distortion. It was a composite put together by a fraudulent dealer from two genuine fossils, and although it was described in National Geographic in 1999, it was exposed before ever making it to a peer reviewed scientific publication. This successful piece of scientific detective work has not stopped creationists from using the episode for years afterwards in their attempts to discredit the science.

I used to think that mammals had evolved from reptiles. I was wrong. Synapsids, the line that gave rise to mammals, branched off very early from the line that gave rise to reptiles. The defining difference is in the shape of the mammalian skull, where bones that in reptiles form part of the jaw have migrated to the middle ear. We have intermediate fossils showing both the old-style jaw joint still present in reptiles, and the style characteristic of mammals. Mammals recapitulate this migration of the ear bones from the jaw in the womb.

The different placental mammal orders diverged rapidly after the extinction of the dinosaurs, and although the relationships between these orders are still rather ambiguous, within each order we have very clear lines of descent. For example, there are striking similarities in the early Eocene between the ancestors of horses, rhinos, and tapirs, although by the late Eocene these were clearly distinct. A very clear example of intermediate forms, in the most demanding sense of being intermediate between two groups that later separated. Palaeobiogeography complements the fossil record; camelids originated in North America, and spread to South America some 3 million years ago to give rise to llamas and alpacas and to Eurasia 7 million years ago.

And so to Chapter 15, The Ape's Reflection? – The Only Transition That Really Matters. Here is where people have the greatest problems in coming to terms with the science, since we correctly see ourselves as special, as moral agents, and (for some of us) as the possessors of souls. Creationists pay particular attention to this stage of our evolution, and Prothero gives numerous examples of how they misdescribe the record.

The human fossil record dates back some seven million years, to the point where we diverged from our sister species, which gave rise to today's chimpanzees and bonobos. The diagram given in the text for the human fossil record shows more than twenty recognised species, two of them new additions in the 2nd edition. Fossils, for some of these species, are numerous (something else creationists regularly lie about), and the rooting of the hominin family tree among the apes is confirmed in detail by DNA comparisons. Human and chimpanzee DNA are more than 97% identical, and humans in the womb have monkey-like tails, with which, very occasionally, they are actually born. It is thought that for the small differences between chimpanzee and human DNA to have such dramatic effect, they must involve control genes, which affect how and when other genes manifest themselves, and baby chimpanzees are provocatively much more similar to humans than adults are. See for yourself in the image below, used by Prothero, and first published in 1926.

To deny evolution is to deny reality.


1] The reaction requires a hydrogen-rich atmosphere, now thought unlikely on the early Earth. It produces a complex mixture of simple products in low concentration, and does not show how these could have been persuaded to join up to make biological polymers, let alone the well-ordered polymers required for biological activity.

You will find more of my writing at Primate's progress, paulbraterman.wordpress.com.