General Introductions
Scientific and Philosophical Introduction: Defining Theistic Evolution Stephen C. Meyer
Biblical and Theological Introduction: The Incompatibility of Theistic Evolution with the Biblical Account of Creation and with Important Christian Doctrines Wayne Grudem
SECTION I: THE SCIENTIFIC CRITIQUE OF THEISTIC EVOLUTION
Section I, Part 1: The Failure of Neo-Darwinism
1 Three Good Reasons for People of Faith to Reject Darwin’s Explanation of Life Douglas D. Axe
2 Neo-Darwinism and the Origin of Biological Form and Information Stephen C. Meyer
3 Evolution: A Story without a Mechanism Matti Leisola
4 Are Present Proposals on Chemical Evolutionary Mechanisms Accurately Pointing toward First Life? James M. Tour
5 Digital Evolution: Predictions of Design Winston Ewert
6 The Difference It Doesn’t Make: Why the “Front-End Loaded” Concept of Design Fails to Explain the Origin of Biological Information Stephen C. Meyer
7 Why DNA Mutations Cannot Accomplish What Neo-Darwinism Requires Jonathan Wells
8 Theistic Evolution and the Extended Evolutionary Synthesis: Does It Work? Stephen C. Meyer, Ann K. Gauger, and Paul A. Nelson
9 Evidence from Embryology Challenges Evolutionary Theory Sheena Tyler
Section I, Part 2: The Case against Universal Common Descent and for a Unique Human Origin
10 The Fossil Record and Universal Common Ancestry Günter Bechly and Stephen C. Meyer
11 Universal Common Descent: A Comprehensive Critique Casey Luskin
12 Five Questions Everyone Should Ask about Common Descent Paul A. Nelson
13 The Battle over Human Origins (Introduction to Chapters 14–16) Ann K. Gauger
14 Missing Transitions: Human Origins and the Fossil Record Casey Luskin
15 Evidence for Human Uniqueness Ann K. Gauger, Ola Hössjer, and Colin R. Reeves
16 An Alternative Population Genetics Model Ola Hössjer, Ann K. Gauger, and Colin R. Reeves
17 Pressure to Conform Leads to Bias in Science Christopher Shaw
SECTION II: THE PHILOSOPHICAL CRITIQUE OF THEISTIC EVOLUTION
18 Why Science Needs Philosophy J. P. Moreland 19 Should Theistic Evolution Depend on Methodological Naturalism? Stephen C. Meyer and Paul A. Nelson
20 How to Lose a Battleship: Why Methodological Naturalism Sinks Theistic Evolution Stephen Dilley
21 How Theistic Evolution Kicks Christianity Out of the Plausibility Structure and Robs Christians of Confidence that the Bible Is a Source of Knowledge J. P. Moreland
22 How to Think about God’s Action in the World C. John Collins
23 Theistic Evolution and the Problem of Natural Evil Garrett J. DeWeese
24 Bringing Home the Bacon: The Interaction of Science and Scripture Today Colin R. Reeves
25 The Origin of Moral Conscience: Theistic Evolution versus Intelligent Design Tapio Puolimatka
26 Darwin in the Dock: C. S. Lewis on Evolution John G. West
SECTION III: THE BIBLICAL AND THEOLOGICAL CRITIQUE OF THEISTIC EVOLUTION
27 Theistic Evolution Undermines Twelve Creation Events and Several Crucial Christian Doctrines Wayne Grudem
28 Theistic Evolution Is Incompatible with the Teachings of the Old Testament John D. Currid
29 Theistic Evolution Is Incompatible with the Teachings of the New Testament Guy Prentiss Waters
30 Theistic Evolution Is Incompatible with Historical Christian Doctrine Gregg R. Allison
31 Additional Note: B. B. Warfield Did Not Endorse Theistic Evolution as It Is Understood Today Fred G. Zaspel
1 Three Good Reasons for People of Faith to Reject Darwin’s Explanation of Life Douglas D. Axe
SUMMARY People of faith should reject the call to affirm the Darwinian explanation of life and should instead affirm the traditional understanding of divine creative action, which defies reduction to natural causes. There are three good reasons for this. (1) Acceptance of Darwinism carries a substantial apologetic cost. Specifically, if Darwin was right that life can be explained by accidental physical causes, then we must forfeit the claim that all humans are confronted by God’s existence when we behold the wonders of the living world. (2) All accidental explanations of life, whether Darwinian or not, are demonstrably implausible. (3) The common justifications for accommodating Darwin’s theory within the framework of traditional faith are confused.
I. First Things First
You’ve heard the claim that natural selection acting upon random genetic mutations created all life from a primitive life form. In the century and a half since Darwin gave that idea its beginning, few claims have generated more controversy. How should people of faith respond to this controversy? Two questions immediately present themselves: 1. Is Darwin’s claim correct? 2. What would the implications for our faith be if it were correct?
Now, because many people think the answer to question 1 requires technical expertise, there’s a tendency to answer it by proxy—choosing to side with experts in either the yes camp or the no camp and then entrusting the defense of that answer to those experts. As understandable as this is in some respects, I advise against it, for several reasons. In the first place, there is widespread confusion even as to who the relevant experts are. Nonscientists tend to be so acutely aware of their lack of expertise that they defer to anyone with a science degree, most of whom have no more familiarity with the technical critique of Darwinism than anyone else. Indeed, because even highly accomplished biology professors are accomplished only within their narrow fields of specialization, it takes a certain amount of scientific familiarity just to discern who can really speak to the subject of biological origins from scientific experience. Keith Fox and I have engaged in friendly debate on that subject, so I hope he won’t mind me using him as an example. As a biochemistry professor at the University of Southampton in the UK, Fox is an established expert on how various molecules bind to DNA. Having done no research on that subject, I’m obviously in no position to critique his work. Likewise, having done no work on protein evolution, he is really in no position to critique my work. And in a professional context he wouldn’t pretend otherwise. However, the origins topic has attracted such a wide following that most debate on the subject occurs at the popular level, and as the associate director of the Faraday Institute for Science and Religion, Fox understandably wants to speak to that debate. He should speak to it, but the listening public would benefit from knowing that he does so as a nonexpert. For instance, based on my research, I claim that enzymes (the protein molecules that do life’s chemistry) cannot be invented by any accidental evolutionary process. Life as we see it depends on highly proficient enzymes, all built within cells by linking many amino acids (typically hundreds) together in precise sequence. These special sequences enable the long chains of linked amino acids to fold up into complex, function-specific structures. In criticizing my claim that evolution cannot explain the origin of enzymes, Fox has repeated the standard idea that evolution builds gradually from small beginnings. According to him, weak enzyme function can be produced by linking a mere two amino acids together, and this can serve as an evolutionary starting point. From there, natural selection can build the exquisite enzymes we see in life, he thinks. In his words: “One doesn’t have to start with an unlikely polypeptide [i.e., amino-acid chain] with billion-fold activity, but from (say) a specific dipeptide (of which there are only 400 using the natural amino acids), with a few-fold improvement.” 1 There’s a serious problem here, though most people need help to see it. Scientists who know about enzymes and the various attempts to use selection to enhance them would never join Fox in this claim, for one good reason: they know they can’t back it up! Fox was hazarding a wild guess that, for reasons I explained elsewhere,2 happened to be wildly wrong. Of course, had he openly called it a wild guess, there would be no cause for concern. Wrong guesses are harmless, provided we know they are only guesses. But when people of Fox’s scientific stature pull scientific claims out of thin air without saying so, people naturally take these claims more seriously than they should. That is a cause for concern. The second problem with seeing question 1 as an experts-only question is that when you stop to realize how much is at stake here, the thought of handing authority over such crucial matters to scientific experts ought to be unsettling. It’s also completely unnecessary. I’ve argued at length that the failure of Darwin’s explanation of life is a commonsense fact—a plain truth testified to by our strong intuition that life is designed, and by a lifetime of experience that confirms this intuition.3 To resolve the tension between what our intuition tells us and what the evolutionary textbooks tell us, then, we should begin by recognizing that we’re all fully qualified to participate in the debate over our origin. The third problem with leaving the evaluation of Darwin’s claim to the experts is that this tempts us to skip straight to question 2—the question of how his claim, if true, should impact our faith. No matter how provisionally we make this move, the very fact that we’ve done so implicitly conveys a yes answer to the question of whether his claim really is true (question 1). After all, question 2 isn’t even worth asking unless question 1 has been answered in the affirmative. In Where the Conflict Really Lies, philosopher Alvin Plantinga proceeds to question 2 as carefully as anyone can, I think, and yet not without creating a problem. His first chapter—“Evolution and Christian Belief”—summarizes his critique of Richard Dawkins’s defense of Darwinism in The Blind Watchmaker as follows: Dawkins claims that the living world came to be by way of unguided evolution. . . . What he actually argues, however, is that there is a Darwinian series for contemporary life forms. As we have seen, this argument is inconclusive; but even if it were air-tight it wouldn’t show, of course, that the living world, let alone the entire universe, is without design. At best it would show, given a couple of assumptions, that it is not astronomically improbable that the living world was produced by unguided evolution and hence without design. 4 Notice that, from the vantage point of faith, the word best in Plantinga’s final sentence should be read as worst. That is, Plantinga tells us that at worst Dawkins has shown there is at least a slim chance that we are cosmic accidents. I suppose Plantinga’s conclusion would sound like good news to anyone who worries that science has killed God (if there are such people). On the other hand, anyone who takes comfort in the idea that science, as the study of God’s created order, might actually affirm God’s existence is apt to be disappointed. If Dawkins’s argument has actually been thoroughly refuted, then that’s the point that needs to be proclaimed. To grant the possibility of our being cosmic accidents only to say this doesn’t necessarily mean we are cosmic accidents is to say something much less faith-affirming. Again, I have great sympathy for people of faith who feel compelled to answer people like Dawkins but who, in thinking that Darwinism sinks or swims on its technical merits, feel ill-equipped to challenge the evolutionary story. The good news here is that the familiar version of science we all participate in, which I call common science,5 is all we really need to be fully confident that Darwin’s theory has already sunk. This brings us to the last problem with avoiding question 1, which is that our natural tendency to look for the upside even in difficult circumstances can cause us to neglect the significance of the downside. This is particularly counterproductive in situations where the downside is counterfactual, meaning that the actual circumstances lack the downside. To attribute grand creative power to Darwin’s evolutionary mechanism even provisionally without acknowledging the accompanying cost is to make precisely this mistake. The truth is that the existence of a plausible accidental explanation of life would carry a hefty downside for people of faith even if it isn’t the correct explanation. In other words, there’s a big cost to acknowledging the mere plausibility of life being accidental, even if this acknowledgment comes with a firm declaration that life didn’t actually come about that way. We will focus next on the apologetic component of this cost, which we can think of as the immediate cost of an affirmative answer to question 1, before we even consider question 2. Other chapters in this volume will focus on the downstream costs, specifically the damage to Christian doctrine we uncover when we take a careful look at question 2. Although I won’t be addressing those downstream costs myself, I should say that I fully recognize the most significant of them to be much more profoundly important than the apologetic cost. Nevertheless, we will see that the apologetic cost is itself highly significant.
II. The Cost of Concession
The conviction that accidental explanations of life are so obviously counterfeit that they don’t merit serious consideration seems to be a background assumption of Scripture. The book of Job, for example, tells us how Job was reminded of his smallness when asked by his Creator, “Is it by your understanding that the hawk soars and spreads his wings toward the south? Is it at your command that the eagle mounts up and makes his nest on high?” (Job 39:26–27). Those questions have the same humbling effect on us, thousands of years later. Anyone who thinks otherwise—anyone who thinks they have a solid grasp of life—should try designing and making something remotely comparable to a hawk or an eagle. Flying toys with flapping wings don’t even come close. Those things are made on assembly lines, part by part, only to fall apart with repeated use. Life is strikingly different. Nurtured at first by nothing more than the yolk inside its shell, the developing eaglet grows to the point where it is ready to break out of that small world and enter the big world. The young bird then spends years mastering all the skills of living life as an eagle before finding a mate and bringing forth the next generation. There is no raptor assembly line. There are no humans putting these remarkable creatures together and replacing them when they break. Somehow, life sustains itself, and after all the effort we humans have put into understanding how life works, we’re left with a grand mystery. The best medicine for anyone who thinks otherwise is to take up this challenge of trying to do something remotely comparable to what God has done. Once we grasp the impossibility of this, Job’s humble awe is the only appropriate response: “I have uttered what I did not understand, things too wonderful for me, which I did not know” (Job 42:3). If you agree that this is the right response, then surely you must agree that the idea of hawks and eagles having appeared by accident is all wrong. In other words, if we agree that God’s probing had its good and proper effect on Job, then we should also agree that Job would have been completely in the wrong to have answered with something like, “Actually, God, hawks and eagles could have appeared without any need for understanding or purposeful action.” Despite the obvious wrongness of that response, we have in recent years seen an increasing number of intelligent and earnest people of faith who have declared something very much like it. Of course, they couch their declarations in more reverent terms, but the irreverent implications seem unavoidable. At least, I see no way around the fact that the arresting awe we’re meant to have for the maker of the majestic eagle is lost the moment we accept that accidental physical processes could have done the making instead. I used the words could have in that last sentence for a reason. The Christian thinkers I quote as examples all take refuge in this ambiguity. Hawks and eagles could have been accidental byproducts of the physical laws that govern the matter and energy of our universe, they say, but on the other hand God could have touched that physical evolutionary process in ways that are forever beyond scientific detection. According to this view, people of faith should be content with the fact that science can never rule out the possibility of God having influenced the outcome of the apparently blind evolutionary process. We should happily concede that God’s touch was unnecessary in exchange for the unassailable assurance that it just might have been there anyway. Physicist Stephen Barr, one of the advocates of this view, opened an article titled “Chance, by Design” as follows: Christians who accept Darwinian evolution are, it is sometimes said, trying to have it both ways. If evolution is driven by random mutations, we cannot be part of a divine plan. How, the critics ask, can we possibly exist by chance and by design, by accident and by intention? 6 Barr’s answer to this question is evident in his subtitle: “The Scientific Concept of Randomness Is Consistent with Divine Providence.” In other words, causes and effects that scientists justifiably consider to be random or accidental may also be instances of God-ordained events. The two are not mutually exclusive. I certainly agree with this. But again I go back to the dialogue between God and Job. If the aim of that dialogue had merely been to underscore the comprehensive scope of divine providence, then pointing to clouds or to craters on the moon would have been just as effective as pointing to the hawk or to the eagle. Indeed, it would have been odd to point to any particular thing because this general aspect of God’s providence doesn’t force itself upon us by what we see. Clouds and moon craters look to the atheist as though they simply happened —part of the succession of physical circumstances we should expect in a physical universe. To the theist, of course, nothing happens apart from God. But then, no theist came to that view by looking at clouds or craters. Such things are not at all inconsistent with God’s presence, but neither do they confront us with his presence. By contrast, in drawing Job’s attention to the hawk and the eagle, God seems to be confronting him with his divine presence by confronting him with his divine magnificence. Indeed, shouldn’t life compel us to acknowledge God as the maker of all things in a way that clouds and craters do not? Doesn’t the wonder of life have objective force to it, well beyond mere suggestion? In discussing this, then, I’ll call the view I aim to defend the confrontational view—the view that God’s creation of life clearly and obviously defies explanation in terms of accidental processes. The contrary view—that life can plausibly be attributed to accidental processes, even though divine intent may have actually been present—I will call the nonconfrontational view.
III. Examples of the Nonconfrontational View
Before defending the confrontational view, I want to further demonstrate the opposing view by bringing in other respected voices. Perhaps the most well known of these is the voice of Francis Collins, director of the National Institutes of Health and founder of the BioLogos foundation. Collins writes, If evolution is random, how could [God] really be in charge, and how could He be certain of an outcome that included intelligent beings at all? The solution is really readily at hand, once one ceases to apply human limitations to God. If God is outside of nature then He is outside of space and time. In that context, God could in the moment of creation of the universe also know every detail of the future. That could include the formation of the stars, planets, and galaxies, all of the chemistry, physics, geology, and biology that led to the formation of life on earth, and the evolution of humans. . . . In that context, evolution could appear to us to be driven by chance, but from God’s perspective the outcome would be entirely specified. Thus, God could be completely and intimately involved in the creation of all species, while from our perspective, limited as it is by the tyranny of linear time, this would appear a random and undirected process. 7 Robert Bishop, professor of physics and philosophy at Wheaton College, finds room for the nonconfrontational view in a similar way: . . . the biological notion of random or unguided mutations doesn’t even rule out God as the possible cause of the variations. All biologists mean by such terms is that the underlying causes are left open by evolutionary theory because mechanisms like natural selection can work with any variations handed to them, whether those variations are due to genetic copying, cosmic rays or God. 8 The idea here is that the only thing natural selection needed in order to invent every living thing we see around us was genetic variation, and since this could have come either from accidental causes like cosmic rays or from God, life itself is silent on the matter. Like Francis Collins, William Lane Craig uses a cosmological perspective to support the nonconfrontational view: How could anyone say on the basis of scientific evidence that the whole [evolutionary] scheme was not set up by a provident God to arrive at Homo sapiens on planet Earth? How could a scientist know that God did not supernaturally intervene to cause the crucial mutations that led to important evolutionary transitions, for example, the reptile to bird transition? Indeed, given divine middle knowledge, not even such supernatural interventions are necessary, for God could have known that, were certain initial conditions in place, then, given the laws of nature, certain life forms would evolve through random mutation and natural selection, and so He put such laws and initial conditions in place. Obviously, science is in no position whatsoever to say justifiably that the evolutionary process was not under the providence of a God endowed with middle knowledge who determined to create biological complexity by such means. 9 This emphasis on science having no valid way to prove that God had no role in creation is a hallmark of the nonconfrontational view. Again, the idea seems to be that this assurance should be adequate compensation for those who are being asked to surrender the time-honored idea that life stubbornly refuses to be explained by ordinary physical causes. Surely, however, we ought to give this tried-and-true idea due consideration before we even think of abandoning it.
IV. What Accidental Causes Cannot Do
To help us do that, let’s take a moment to examine three sequences of letters:
Sequence 1: ndTHYz, vquu H bs hStbuMFLeUtbSZ NFjvpLMYd. vDNOSnQa buCm cg nbwWbVUfeVR e NdjABehcM miGNX
Sequence 2: zZUaldYK JRmG YnGhQfFSEsECZJwA Z PneGwq, xmLVF f d qEgAFrykZ QQwXLFhAqP IDvVCcWflpYy uAOpu
Sequence 3: I have uttered what I did not understand, things too wonderful for me, which I did not know.
Though this won’t be obvious to you, two of these sequences were purposefully constructed. The one exception was constructed from atmospheric noise, of all things. More specifically, background noise at a radio frequency not used for broadcasting has been used for many years to produce “true random” numbers by RANDOM.ORG. I used this online service to choose a sequence of upper- and lower-case letters, along with spaces, commas, and periods. So, the atmosphere was the author of one of the above sequences! The obvious fact, however, is that one of the three sequences is a meaningful sentence, whereas the other two are not. Sequence 3 is well worth pondering, particularly in the context of the writing from which it came, while the other two sequences are unintelligible junk. I assure you that I did labor over one of those first two sequences, purposefully arranging the characters to construct a sequence that looks very much like the unintelligible junk that comes from atmospheric noise. Speaking of the sequence I constructed in this way, then, I can say something very similar to what Francis Collins said about life: the making of that sequence appears to have been driven by chance, but from my perspective the outcome was entirely specified. But neither Collins nor any of the others I’ve quoted mean to imply that life looks like unintelligible junk. Everyone knows better than that. Berkeley psychologist Alison Gopnik, writing in the Wall Street Journal, affirmed that “by elementary-school age, children start to invoke an ultimate God-like designer to explain the complexity of the world around them—even children brought up as atheists.” 10 With work, atheists learn to suppress this intuition, but the people I’ve quoted—all of them believers—certainly haven’t done that. They have, however, caused confusion by blending a harmful falsehood with an uncontentious fact. I’m not suggesting this blending has been deliberate— only that it has happened and continues to happen. To be clear, here are the two claims that should not be confused: Claim 1: Intelligent beings can imitate the effects of accidental causes. Claim 2: Accidental causes can imitate the work of intelligent beings. As thoroughly uninteresting as claim 1 is, it at least has the advantage of being true. Claim 2, on the other hand, has very much the opposite character— beguilingly intriguing, but false. When these contrasting claims are combined indiscriminately, the result is a confusing and potentially harmful distortion of the truth. To clear up the confusion, the possibility of intelligent beings imitating accidental causes needs to be set aside as a mere distraction. The interesting fact is that intelligence opens the door to a rich world of activities that simply don’t exist apart from intelligence. I refer to a broad category of these activities as invention, by which I mean any undertaking where many small things have to be arranged in a precisely coordinated way in order to achieve a big result. Certainly our modern technological marvels all come about by invention, but so do the more ordinary projects we all tackle on a daily basis—everything from the composing of an email to the organizing of a workspace or the design of a custom fitness plan. All of these require know-how. None of them happen by accident. So, having expanded the category of invention to include everyday projects like these, we immediately recognize that we are all inventors. All inventions, whether common or technical, share the characteristic hierarchical structure shown in Figure 1.1. Consider my writing of this chapter, for example. My top-level goal in this writing is to persuade people of faith to reject the call to accept the Darwinian explanation of life. I aim to meet this goal by making three main points convincingly: (1) accommodating Darwin’s view of life within traditional faith is costly; (2) Darwin’s view of life is wrong; and (3) the reasons given for accommodation are confused. Each of these main points will have at least one section devoted to it. The crafting of each of these sections requires writing several paragraphs that work together, each making a more specific point. Likewise, the point of each paragraph is conveyed by constructing several sentences that convey even more specific points in a coordinated way. All of these points are designed to achieve the top-level goal. Each occupies its own position in an organized hierarchy, working together with points at the same level to make a point at the next higher level, all of which contribute to the big point.
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And of course, the hierarchy goes all the way down from the sentence level to the elementary constituents of written communication—the letters of the alphabet. We conceive of writing projects in a top-down way, but we accomplish them in a bottom-up way—arranging letters to spell words, in order to form sentences, in order to build paragraphs, in order to achieve our main writing objective. This hierarchical organization is a hallmark of invention, present in everything from three-course dinners to communications satellites. I refer to it as functional coherence—the coordinated combination of functions over a succession of levels to achieve a single top-level function.11 Intuitively, we all know that nothing but intelligent action can construct things in this way. My cat used to love walking on my keyboard, but her steps across it never produced anything sensible. How could they? My keyboard was just a curious little mat to her (and a sure way to get my attention). What she was doing, pressing keys with her weight, had absolutely no connection to writing, apart from the fact that it made letters appear on my laptop display. Now, if I had to argue that it’s possible for a cat’s footsteps to compose a sensible paragraph, I know how I’d go about it. I’d break the impossible big outcome—a sensible paragraph—into something much smaller. Paragraphs are written one keystroke at a time, so that would be the attainable goal. If you had typed “Novembe,” for example, no one would think it impossible for your cat to just happen to step on the “r” key, thereby completing the word “November.” Events probably wouldn’t unfold in that nice way, but we all agree that they could. It seems we also have to agree, then, that the cat could have stepped on a shift key and then the “N” key to begin with (unlikely, but not impossible). If it did, then we would all agree that stepping on “o” next is well within the realm of possibility. And if that were to happen, well . . . who would say “v” couldn’t be stepped on next? You get the idea. By continuing the succession of unlikely-but-possible steps, we seem to be forced to conclude that, strictly speaking, it isn’t impossible for a cat to have written this chapter for me. And yet we all know that, practically speaking, it is impossible. These seemingly contradictory assessments are easily reconciled by distinguishing impossibility in the mathematical sense of p = 0 from impossibility in the practical sense of “don’t bother waiting for this to happen, because it isn’t going to happen.” Darwin’s explanation of life fails in that practical sense, which is its undoing. For accidental causes to have invented life is impossible in the same way that a cat writing an essay is impossible: we can be fully confident that neither has ever happened or will ever happen.12 Now, you may be wondering whether we really can with equal confidence reject both the accidental origin of felines and the feline origin of essays. A cat on a keyboard gets no help from natural selection, which is thought to be the driving force for evolution. Is this really a fair comparison, then? My answer is that, as utterly impossible as it is for a cat to write something we’d recognize as an essay, it is far less probable for accidental processes to have invented the living things that populate our planet. My defense of this answer will have to be very brief here. Those interested in a more full discussion should read Undeniable.13 The first thing to recognize is that for accidental causes to accomplish something that would normally require insight is a coincidence. It’s for a good reason that we don’t expect anything other than insight to do the work of insight. Insight is so unique among causes—categorically different from every physical cause—that no other cause should do the work of insight. This is why we notice those rare occasions when even the slightest hint of insight occurs by accident. You bump into an old classmate at a small restaurant, thousands of miles from where you both live. Your cat types “ok” before hopping over your keyboard. A locksmith appears as if on cue, a moment after you realize you need one. Coincidences like these are surprising enough to get our attention, but plausible enough to happen from time to time. By contrast, we can easily imagine much bigger coincidences that we know will never happen by accident. Picture all your old classmates just happening to converge on that faraway restaurant—as though a class reunion had been planned there; or your cat, before hopping over the keyboard, typing, “I like canned food much better than that dry food, so let’s make the change. Ok?” Imagine that locksmith who happens to appear at just the right time also happening to be holding in his hand a key that happens to match the one you lost. The fact that we rank coincidences intuitively in this way, according to how unbelievable they are, turns out to have a solid rational basis. Probability is, in essence, the math of coincidence—the math by which we rigorously rank coincidences. We use probabilities to gauge how often certain outcomes should occur when the only apparent reason for them to occur is that nothing absolutely precludes them from occurring. The underlying idea is that whatever can happen will happen—if the number of opportunities for it to happen is large enough. Whether or not we know how to calculate probabilities, we all seem to know from everyday experience—common science—that the number of opportunities cannot be large enough for anything but minor coincidences to occur. We can easily dream up wild coincidences that are obviously unbelievable—the stuff of fantasy. The believable ones are always much more tame. This common-science intuition turns out to be absolutely correct, and once we see how it connects to Figure 1.1, we will see how it connects to the general theme of invention. The reason inventions never happen by accident is that wild coincidences of that kind simply can’t happen. Whether we’re talking about making a pizza or a PowerPoint presentation, a large number of small things must be done sensibly in order for the big thing to come together. These small things are the carefully arranged elementary constituents represented in the bottom row of Figure 1.1. Projects like this are easy for us to accomplish because we’ve mastered all the elementary skills they require, but the fact that these skills all had to be mastered assures us that accidents will never take the place of skill. With so many ways for accidental causes to do the wrong thing at each little step—typing yet another incoherent letter or spilling yet another ingredient on the floor—the outcome of accidental causes is guaranteed to be a mess. And if an invention as modest as a pizza will never be made by accident, then for mind-blowingly spectacular inventions like hummingbirds or dolphins to happen by accident is completely out of the question.
V. No Escaping the Truth
The two popular reasons for thinking that evolution escapes the rule that accidental invention is impossible are: (1) natural selection, and (2) the vastness of evolutionary time. However, neither of these proposed reasons stands up to technical scrutiny. I’ll say more about this in a moment. The point I’m much more eager to convince people of is that no technical scrutiny is actually needed to close off these escapes. To be confident that a claimed coincidence is implausible, all we have to do is see that the magnitude of this would-be coincidence places it firmly in the category of the unbelievable. If that’s the case, then it really is unbelievable. As long as proponents of evolution continue to claim that genius wasn’t needed for Earth to become populated with these remarkable living things we see around us, they set themselves up for refutation. We don’t have to become technical experts in genetics or natural selection or anything else to know their claim is wrong. All we need to know is that for unintelligent causes to have imitated genius on such a vast scale would require a very large convergence of impossible coincidences, which is (of course) utterly impossible. Life in all its forms is obviously the work of genius, and clueless causes are as far removed from genius as the east is from the west—complete opposites. So for these causes to just happen to behave like genius would be an unbelievable coincidence—literally unbelievable. There’s a strict limit to what can be excused as a coincidence, and things like fireflies and hummingbirds and humans are way beyond that limit. Natural selection, being just one more clueless cause among many, is powerless to change this. For natural selection acting on genetic mistakes to have transformed primitive bacteria into hummingbirds would require clueless causes—which know absolutely nothing about hummingbirds—to just happen to do a work of pure genius. Again, our intuition tells us there cannot have been enough opportunities in the history of life for the improbability of such a thoroughly unbelievable coincidence to have been overcome. As we’ll see in a moment, this intuition is absolutely correct. So we don’t have to give natural selection another thought in order to know that it cannot possibly rescue evolutionary theory from its fundamental failing. Still, a closer look at selection can have the gratifying effect of reinforcing what we already know. When we take this closer look, we see that the specific problem with selection, aside from the general problem of being clueless, is that it shows up only after the hard work of invention has been done. Richard Dawkins inadvertently pointed to this while acknowledging the impossible difficulty of that hard work in The Blind Watchmaker: . . . however many ways there may be of being alive, it is certain that there are vastly more ways of being dead, or rather not alive. You may throw cells together at random, over and over again for a billion years, and not once will you get a conglomeration that flies or swims or burrows or runs, or does anything, even badly, that could remotely be construed as working to keep itself alive. 14 Dawkins seems to have thought that the key to surmounting the extreme improbability he describes here lay in those two words: “at random.” It’s true, of course, that natural selection favors certain variations over others in a nonrandom way. The more significant point, however, is that selection can do this only after those variations work to keep their possessors alive! Something other than selection must therefore be responsible for coming up with these highly special arrangements that work. Credit for the invention of living things with all their marvelous features, then, rightfully goes not to natural selection but to the one who invented them: God. The second popular reason for thinking Darwin’s theory is exempt from the commonsense rule that invention never happens by accident is the vast time over which evolution is said to have occurred. It’s true, of course, that longer times provide more opportunities for coincidences to occur. Equally true is that most people are uncomfortable with the math that assigns probabilities to coincidences. Thankfully, our intuition fills in very nicely for any aversion to these probabilistic calculations. People may struggle to put a number on the improbability of a cat writing a sensible paragraph, but everyone knows right away that it can’t happen. Practically speaking, we sense that the probability is indistinguishable from zero. We can well imagine using the Internet to organize a let-your-cat-walk-onyour-keyboard day with a million participants (stranger things have happened!), and we’re very comfortable saying that nothing resembling coherent writing would come out of the event. Pushing feasibility to the extreme, then, we might then try to imagine all habitable planets in the universe being populated to the greatest possible extent with cats and covered to the greatest possible extent with keyboards that register every press of a key. The mental strain here turns out to be pointless, though, because this gargantuan increase in the scale of the experiment would only produce very disappointing gains. After gathering and processing all the intergalactic data, the winning entry for this cosmic essay contest would be an incoherent jumble of maybe four or five very short words, instead of the one or two that would come from the more realistic experiment. Even if we could throw all practicality to the wind and somehow let every atom of the universe be devoted to cats and keyboards for the entire duration of the universe, still we would get nothing that approaches a coherent paragraph, much less a coherent essay. It seems we should give the intuition its due, then: unbelievable coincidences are unbelievable for a very good reason. Again, our confidence in this point is fully justified by our common-science experience. We don’t have to do any technical science at all to know that accidental causes cannot do the work of genius. Nevertheless, it should be satisfying to know that a good many people spending a good many years laboring over the technical science have indeed proven that it confirms what we all know by common science. As I mentioned previously, my contribution to that work has been in the area of protein science. You’ll encounter some of this work in more detail in the next chapter, where Stephen Meyer describes the extreme improbabilities of accidental causes inventing new functional proteins. There you’ll see how well experiment and calculation marry up with intuition.
VI. Of Gaps and Wars
Having argued that attempting to accommodate Darwin’s theory within the framework of traditional faith is not only costly but also misguided, I’d like to consider briefly some reasons being offered to justify the accommodation. The two reasons that appear to be most common I’ll refer to as the God-of-the-gaps complaint and the unwinnable-war plea. Denis Alexander traces the origin of the God-of-the-gaps complaint back to the mid-eighteenth century, when, with the rapid advance of the natural sciences, it was realized that “a god who was simply a convenient ‘explanation’ to cope with gaps in our scientific knowledge would not last for very long.” 15 It’s hard to disagree with this, as a general principle. When an unexpected noise is heard from the next room and you go to check it out, you would do well to assume an ordinary explanation—breeze through a window left open, or squirrels on the roof. It would be comically unwise for anyone to declare to their kids upon hearing the sound, “That’s probably the Second Coming—run into the next room and I think you’ll see Jesus!” The thing is, I haven’t actually come across anyone who thinks that way. Even if we never figure out what made that noise, we instinctively assume the cause was ordinary. For the most part, people appeal to supernatural explanations only when they’ve become convinced that there cannot be a natural explanation. In this way we acknowledge the real possibility of being confronted by God’s activity over and above his role as the sustainer of the created order. Moreover, God himself seems to endorse this perspective by using miracles both to reveal his specific will and to demonstrate his authority over his created order. The God-of-the-gaps complaint is heavily overused. Nearly every time a person of sincere faith attributes something to God’s supernatural activity they are saying, in effect, “I don’t believe this can have a natural explanation.” Never, in my experience, are they merely saying, “Here’s something that the scientists haven’t yet explained.” Of course, people are often wrong in making the supernatural attribution, but the reason for the error is nearly always a desire for God to grant a personal revelation in an extraordinary way, not a desire to gloat over the limits of scientific knowledge. Those who automatically resort to the God-of-the-gaps complaint every time God is said to have acted upon nature in a way that is clearly apart from and above the normal course of nature inevitably find themselves criticizing God himself. As for the unwinnable-war plea, this I have also encountered numerous times. In a “Reasonable Faith” podcast, William Lane Craig made the plea as follows: As Christians you don’t have to make a frontal assault on one of the pillars of contemporary science in the name of Christianity. That, in the minds of most people, will simply disqualify Christianity rather than evolutionary biology. If they hear that evolutionary biology is incompatible with theism, well guess which belief is going to be given up? It’s going to be theism, because the evolutionary paradigm is so entrenched that theism, if it’s incompatible with it, will simply be disqualified as incredible. 16 Here again, whether I agree with this depends on how I construe it. If a friend holds tenaciously to belief X (fill in the blank), and the most central tenets of the faith can be shared with this friend without engaging in a battle over X, then by all means focus the discussion on those central tenets. As a Christian, I certainly think Christians should be able to share the gospel without starting an argument over any of these Xs, including Darwinism. Should the friend become a Christian, then evolution may well be one of the many areas where their new faith casts new light on old ways of thinking. But even if you intend to approach the discussion in this way, don’t be surprised if your friend has other ideas. You may well find that he or she wants to use Darwinism as a reason for rejecting your faith. What should you do then? If you adopt a policy of surrendering everything but the bare essentials, you may well find yourself surrendering a whole lot: everything that challenges the pillars of contemporary science, the pillars of contemporary morality, the pillars of contemporary culture, and so on. What do you suppose your friend will make of a faith that surrenders so much? Jesus called his followers to surrender their lives, their pride, their earthly security and, at times, their possessions—right down to the shirts on their backs. He never, however, called them to surrender the truth. That they are charged with guarding, even if it costs them their lives. Sometimes the pillars are exactly the things that need to come down if the truth is to be heard and received.
VII. Context and Conclusion
We humans pride ourselves in our rational faculties, but the truth is that we aren’t as rational as we pretend to be. Many of us like to think our heads are in control, which is more or less true on matters where our hearts are indifferent. Whenever our hearts aren’t passive, though, the situation changes. If we aren’t careful, our heads can end up slavishly serving our hearts’ desires. Reasoning can turn into rationalizing in a heartbeat. The most candid atheists have admitted that atheism comes down to a heart thing, not a head thing. Philosopher of mind Thomas Nagel, for example, frankly acknowledges his “fear of religion,” a condition he refers to as the “cosmic authority problem.” His rational faculties are second to none, but when it comes to God he doesn’t pretend to be dispassionate: “I hope there is no God! I don’t want there to be a God; I don’t want the universe to be like that.” 17 Accordingly, Nagel has applied his mind to the task of making sense of his heart’s desire, and he clearly sees the utility of Darwinism for this purpose. By providing a godless creation story, “Darwin enabled modern secular culture to heave a great collective sigh of relief,” he says.18 Other atheists seem content with that secular story, but Nagel is different. Richard Dawkins has devoted himself to promoting the story, believing that “Darwin made it possible to be an intellectually fulfilled atheist.” 19 Nagel, on the other hand, refuses to go along with what he sees as an inadequate picture of reality, however convenient it may look to atheists. As the subtitle of his recent book says, he has set out to show “why the materialist neo-Darwinian conception of nature is almost certainly false.” 20 In the end, what gets passed off by intellectuals as a pillar is really a crutch— a way for atheists to pretend to have explained what is absolutely inexplicable apart from God. As theists, we have the one true explanation for the world we inhabit, an explanation that’s not just plausible but uniquely plausible—it is the explanation. Why would we choose to deprive people of this? This truth that seems to embarrass some of us is the very truth we need to proclaim.
2 Neo-Darwinism and the Origin of Biological Form and Information Stephen C. Meyer 1
SUMMARY According to textbook neo-Darwinian theory, new genetic information arises first as random mutations occur in the DNA of existing organisms. When mutations arise that confer a survival advantage on the organisms that possess them, the resulting genetic changes are passed on by natural selection to the next generation. As such changes accumulate, the features of a population begin to change over time. Nevertheless, natural selection can only “select” what random mutations first produce. And for the evolutionary process to produce new forms of life, random mutations must first have produced new genetic information for building novel proteins. Since the late 1960s, however, mathematicians and molecular biologists have argued that producing new functional genes (new genetic information) and proteins via a random mutational search is improbable in the extreme. Nevertheless, until recently it was impossible to precisely quantify the magnitude of this problem and, thus, to assess the plausibility of a random search for novel proteins among all the possible amino acid sequences. Recent experiments on proteins performed by Douglas Axe and others, however, have shown in a precise quantitative way that functional genetic sequences (and their corresponding proteins) are indeed too rare to be accounted for by the neo-Darwinian mechanism of natural selection sifting through random genetic mutations. The “space” or number of possible arrangements are simply too vast, and the available time to search by undirected mutation too short for there to have been a realistic chance of producing even one new gene or protein by undirected mutation and selection in the time allowed for most evolutionary transitions. This chapter develops this argument, and other closely related arguments, against the creative power of the main evolutionary mechanism and responds to the most prominent objections to these arguments. . . . . .
I. Introduction: A Hasty Marriage
Theistic evolutionists say that God used the evolutionary process to create the diversity of life on Earth. This statement represents the central claim of theistic evolution—namely, that God as Creator employed the processes of random variation and natural selection to cause plants, animals, and indeed every living thing, to come to be. Theistic evolutionists hold that, since all truth is God’s truth, and the scientific community has determined the neo-Darwinian mechanism to be the true cause of organismal diversity, Christians should recognize and endorse the divinely creative character of the evolutionary process, just as they accept any other well-supported scientific theory as exhibiting God’s purposeful sovereignty over nature in all its dimensions. But a skeptic might wonder if this marriage of Christian theism and evolutionary theory has not been rather hastily arranged. Although the bride and groom are smiling in the reception line, when they happen to glance sidelong at each other, their smiles vanish. A skeptic might further observe that the bona fides of the groom, neo-Darwinian theory, have been in doubt for some time— not, however, from the bride’s overeager, churchgoing family, anxious to secure what they hope will be a conflict-diminishing marriage, but from the groom’s secular and visibly morose side of the aisle. The stony expressions of his materialistic kin suggest a deeply significant, but largely neglected, story. In this chapter, I tell part of that story, and argue that there is little (if any) rationale for marrying either theism or Christianity to a failing theory of biological evolution, just as that theory is being abandoned by its own philosophical allies as empirically insufficient, or simply false. Thus, I will also suggest, to stretch my metaphor, that it is not too late to seek an annulment between theism and neo-Darwinian theory. The neo-Darwinian theory of evolution (the textbook theory of evolution that theistic evolutionists commonly endorse) affirms all three meanings of evolution discussed in my “Scientific and Philosophical Introduction” to this book: (1) small-scale, microevolutionary change over time; (2) the common ancestry of all organisms, as seen in Darwin’s tree-of-life picture of the history of life (also known as the theory of universal common descent); and, most importantly, (3) the creative power of the random mutation and natural selection process, which allegedly caused the complexity and diversity of life on Earth. In this chapter, I challenge mainly the third meaning of evolution (the creative power of random mutation and selection) and will do so by raising a critical engineering question: How is new biological form and function, and the biological information necessary to produce it, constructed?
II. The Discontinuous Origin of Major Innovations in the History of Life
The fossil record on our planet documents the origin of major innovations in organismal form and function (see chapter 10). These episodes—if we take the fossil record at face value—often occur abruptly or discontinuously, meaning that newly arising biological forms bear little or no resemblance to what existed earlier in the fossil record. In the book Darwin’s Doubt, I wrote about one of the most dramatic of these discontinuous events, known as the Cambrian explosion. During this dramatic event, beginning about 530 million years ago, most major groups of animals first appear in the fossil record in a geologically sudden or abrupt fashion. Although the Cambrian explosion of animals is especially striking, many other such abrupt appearances or discontinuous origins are documented in the fossil record. For example, the first winged insects, birds, flowering plants, mammals, and other groups also appear abruptly in the fossil record, with no apparent connection to putative ancestors in the lower (and older) layers of fossil-bearing sedimentary rock. Evolutionary theorist Eugene Koonin describes this as a “biological Big Bang” pattern. As he notes,
Major transitions in biological evolution show the same pattern of sudden emergence of diverse forms at a new level of complexity. The relationships between major groups within an emergent new class of biological entities are hard to decipher and do not seem to fit the tree pattern that, following Darwin’s original proposal, remains the dominant description of biological evolution. 2 In the Origin of Species, Darwin depicted the history of life as a gradually unfolding, branching tree, with the trunk of the tree representing the first onecelled organisms, and the branches representing all the species that evolved gradually from these first forms.3 As Darwin depicted life’s history, novel animal and plant species would have arisen from a series of simpler precursors and intermediate forms over vast stretches of geologic time. Nevertheless, Darwin himself acknowledged that the sudden appearance of many major groups of organisms in the fossil record did not fit easily with his picture of gradual evolutionary change.4 The abrupt appearance of the first animals in the Cambrian period, and the abrupt appearance of many other groups, also challenged Darwin’s claim that natural selection acting on random variations had produced all the new forms of life. As Darwin understood it, the process of natural selection acting on random variations necessarily operated slowly and gradually—thus rendering any pattern of sudden appearance a puzzling anomaly. Darwin saw natural selection as slow and gradual because of the intrinsic logic of the process. Significant biological changes in any population occur only when randomly arising variations in the features or traits of organisms confer functional advantages in the competition for survival and reproduction within that population. Those organisms that acquired new advantageous traits would prevail in the competition, enabling them to pass on their new traits to the next generation. As nature “selected” these successful variations, the features of a population as a whole would change. Yet, as Darwin conceived of the process, the variations responsible for permanent changes in a population would have to be relatively modest, or “slight,” in any given generation. Major, or large-scale, variations—what evolutionary biologists would later term “macro-mutations”—would inevitably produce dysfunction, deformities, or even death. Only minor variations would be viable, and therefore, heritable. Thus, any larger-scale changes, such as those that occur in many explosive radiations of novel form in the fossil record, would have to be built slowly from a long series of smaller-scale, heritable variations, accumulating gradually over time. Significant changes to organismal form and function would thus require many hundreds of millions of years, precisely what appears unavailable in the case of many salient episodes of evolutionary innovation, such as the Cambrian explosion, the angiosperm (flowering plant) “big bloom” during the Cretaceous period (130 million years ago), or the mammalian radiation in the Eocene period (about 55 million years ago). Darwin hoped the mystery of the missing ancestral fossils would be solved by future geological discoveries documenting the gradual transitions his theory predicted. However, for major fossil radiations documenting the origin of novel forms of life, the opposite has occurred. In the 150 years since the publication of the Origin, paleontologists have combed geological strata worldwide, looking for the expected precursors to many major groups of organisms,5 but they have not found the pattern of gradual change that Darwin anticipated. Instead, new findings have often shown explosions of novel biological form to have been even more dramatic than Darwin realized.
III. A Deeper Mystery: How to Build Animals
By the time an animal is large enough to be entombed in sediment—and thus to show up later in the paleontological record as a macroscopic body fossil with distinctive and complex anatomical features that enable us to recognize it as the remains of an animal—the causes or processes that brought the animal originally into existence as a living being have already done their work. This means that the fossil record, fascinating though it may be, lies downstream of a deeper and more fundamental biological mystery. The abrupt appearance of novel fossil forms represents the paleontological signal, or detectable consequence, of some earlier-acting cause(s) that were sufficient to build animal structural and functional complexity within the time available. The mystery we face, then, is simply this: what caused the origin of novel animal form? In particular, could the neo-Darwinian processes of random mutation and natural selection have built the Cambrian (and other) animals, and done so quickly enough to account for the pattern in the fossil record? That question became much more acute in the last two decades of the twentieth century, and now into the twenty-first, as biologists have learned more about what it takes to build an animal.
IV. The Information Enigma
In 1953, when James Watson and Francis Crick elucidated the structure of the DNA molecule, they made a startling discovery: The structure of DNA allows it to store information in the form of a four-character digital code. Strings of precisely sequenced chemicals called nucleotide bases store and transmit the assembly instructions—the information—for building the crucial protein molecules that the cell needs to survive.
Francis Crick later developed this idea with his famous “sequence hypothesis,” according to which the chemical constituents in DNA—the nucleotide bases—function like alphabetic letters in a written language or digital characters in a computer code. Just as English letters may convey a particular message depending on their arrangement, so too do certain sequences of chemical bases along the spine of a DNA molecule convey precise instructions for arranging the amino acids out of which proteins are built. The DNA molecule carries the same kind of “specified” or “functional” information that characterizes written texts or computer codes.6 As Richard Dawkins has acknowledged, “the machine code of the genes is uncannily computer-like.” 7 Or as Bill Gates has noted, “DNA is like a computer program, but far, far more advanced than any software we’ve ever created.” 8 What do these familiar facts of molecular biology have to do with the origin and evolution of life?
When teaching, I like to ask students a question: “If you want your computer to acquire a new function or capability, what do you need to give it?” Typically, student answers cluster around terms such as “new code,” “instructions,” “software,” or “information.” All these answers are correct, of course—and we now know that the same is true of organisms. To build new forms of life from simpler preexisting forms also requires the generation of new information.
The Cambrian explosion, for example, was marked by an explosion of new animal body plans. But building new body plans requires new organs, tissues, and cell types. And new cell types require many kinds of specialized or dedicated proteins. Animals with gut cells, to cite just one example, require new digestive enzymes, which are a type of protein. But building new proteins requires genetic information stored on the DNA molecule. Thus, building new animals with distinctive new body plans requires, at the very least, vast amounts of new genetic information. (Building a new animal body plan also requires another type of information, not stored in DNA, called epigenetic information. See Jonathan Wells’s chapter 7 in this volume.) Indeed, the fundamental importance of information to the origin and maintenance of biological form makes clear that the explosion of novel forms of animal life represents not only explosions of new biological form but also explosions of new biological information. But if that is so, is it plausible to think that the neo-Darwinian mechanism of natural selection acting on random mutations could have produced the highly specific changes in the DNA sequences, or other hereditary patterns, necessary to generate novel animal forms? There are several compelling reasons to think not.
V. The Problem of the Origin of Information
According to neo-Darwinian theory, new genetic information arises first as random mutations occur in the DNA of existing organisms. “Random” here means “without respect to functional outcome,” entailing that there can be no inherent directionality or telos to mutational events. When mutations arise that, strictly by chance, confer a functional advantage on the organisms possessing them (thereby increasing their reproductive output), the resulting genetic changes will be passed on by natural selection to the next generation. As such changes accumulate, the features of a population will change over time. Yet natural selection can only “select” what random mutations first stumble upon.9 Thus, for natural selection to preserve any significant functional innovation, let alone a new form of animal life, random mutations must (at a minimum) first produce new genetic information for building new proteins. Without new functional variations or mutations—an absolutely necessary condition of the occurrence of significant morphological change—natural selection will have nothing advantageous to preserve and pass on to the next generation—in which case no significant evolutionary change will take place. Indeed, natural selection and subsequent heritable change within a population await the deliverances of the mutational process because it is there that selectable function (and morphological novelty) must first arise.10
VI. Searching for New Genes and Proteins in a Combinatorial Haystack
If mutation is occurring without direction, however, the evolutionary mechanism faces what amounts to a needle-in-the-haystack search, or what mathematicians call a “combinatorial search problem.” In mathematics, the term “combinatorial” refers to the number of possible ways that a set of objects can be arranged or combined. Many simple bicycle locks, for example, comprise four dials with ten settings on each dial. A thief encountering one of these locks (and lacking bolt cutters) faces a combinatorial search problem because there are 10 × 10 × 10 × 10, or 10,000 possible ways of combining the possible settings on each of the four dials —but only one combination that will open the lock. Randomly trying possible combinations is unlikely to yield the correct setting, unless the thief has a lot of time on his hands to search exhaustively.
How does this bear on the origin of biological information? It turns out that it is extremely difficult to assemble new genes or proteins by the random mutation and natural selection process because of the sheer number of possible sequences that must be searched by mutations in the available time. As the length of the required gene or protein grows, the number of possible base or amino-acid sequence combinations of that length grows exponentially. For example, using the twenty protein-forming amino acids, there are 202 or 400 ways to make a two-amino-acid combination, since each position could feature any one of twenty different amino acids. Similarly, there are 20 3 or 8,000 ways to make a three-amino-acid sequence, and 20 4 or 160,000 ways to make a sequence four amino acids long, and so on. Yet, most functional proteins are made of hundreds of amino acids. Thus, even a relatively short protein of, say, 150 amino acids represents one sequence among an astronomically large number of other possible sequence combinations (approximately 10 195). Intuitively, this suggests that the odds of finding even a single functional sequence—i.e., a working gene or protein—as the result of random genetic mutations may be prohibitively small, even taking into account the time available to the evolutionary process. Imagine, however, that we now encounter a really committed bicycle thief, who patiently searches the “sequence space” of possible lock combinations, at a rate of one combination every ten seconds. If our hypothetical thief had fifteen hours, and took no breaks, he could generate more than half (5,400 of 10,000) of the total possible combinations of a four-dial bike lock. Given this, the probability that he will happen upon the right combination exceeds the probability that he will fail. In that case, it would be more likely than not that he will succeed in opening the lock by random search. And the chance hypothesis— i.e., the hypothesis that he will succeed in opening the lock via a random search —is, therefore, also more likely to be true than false. But now imagine a much more complicated lock. Instead of four dials, this lock has ten dials. Instead of 10,000 possible combinations, this lock has ten to the tenth power or 10 billion possible combinations. With only one combination that will open the lock out of 10 billion—a prohibitively small ratio—it is much more likely that the thief will fail even if he devotes his entire life to the task.
Indeed, a little math shows this to be true. It turns out that if the thief did nothing but sample combinations at random, at a rate of one every ten seconds for an entire 100-year lifetime, he would still sample only about 3 percent of the total number of combinations on a lock that complex. In this admittedly contrived case, it would be much more likely than not that he would fail to open the lock by random search. And in such a case, the chance hypothesis—the hypothesis that the thief will succeed in finding the combination by a random search—is also much more likely to be false than true. So what about relying on random mutations to “search” for a new DNA base sequence capable of directing the construction of a new functional protein? Would such a random search for new genetic information be more likely to succeed—or to fail—in the time available to the evolutionary process? In other words, is a random mutational search for a new gene capable of producing a new protein more like the search for the combination on the four-dial or the ten-dial lock? As our examples show, the ultimate probability of the success of a random search—and the plausibility of any hypothesis that affirms the success of such a search—depends upon both the size of the space that needs to be searched and the number of opportunities available to search it. But it turns out that scientists have needed to know something else to determine the probability of success in the case of genes and proteins. They have needed to know how rare or common functional arrangements of DNA bases capable of generating new proteins are, among all the possible arrangements for a protein of a given length. That’s because in genes and proteins, unlike in our bike lock example, there are many functional combinations of bases and amino acids (as opposed to just one) among the vast number of total combinations. Thus, in order to assess the plausibility of a random search, we need to know the overall ratio of functional to nonfunctional sequences in the DNA.
Molecular biologists have long known that the number of possible combinations corresponding to any given sequence of DNA, or chain of amino acids, is extremely large and grows exponentially with the length of the molecule in question. As noted, corresponding to one short protein 150 amino acids long, there are 10 to the 195th power other amino acid arrangements of that length. That’s an unimaginably large number. But until recently, molecular biologists didn’t know how many of those arrangements were functional; they didn’t know —in effect—how many of the possible combinations would “open the lock.” But recent experiments in molecular biology and protein science have settled the issue. They have established that DNA base sequences capable of making the complex, three-dimensional structures called “folds” that characterize functional proteins are extremely rare among the vast number of possible sequences. (A protein fold is a distinctive, stable, complex, three-dimensional structure that enables proteins to perform specific biological functions. Since proteins are crucial to almost all biological functions and structures, protein folds represent the smallest unit of structural innovation in living systems.) But how rare are protein folds? While working at Cambridge University from 1990–2003, molecular biologist Douglas Axe set out to answer this question using a sampling technique called “site directed mutagenesis.” His experiments revealed that, for every DNA sequence that generates a short functional protein fold of just 150 amino acids in length, there are ten to the seventy-seventh power nonfunctional combinations—ten to the seventy-seventh amino acid arrangements—that will not fold into a stable three-dimensional protein structure capable of performing a biological function.11
In other words, there are vastly more ways of arranging nucleotide bases that result in nonfunctional sequences of DNA than there are sequences resulting in functional genes. Consequently, there are also vastly more ways of arranging amino acids that result in nonfunctional amino-acid chains than there are ways of arranging amino acids to make folded functional proteins. Thus, for every functional gene or protein fold there is a vast, exponentially large number of corresponding nonfunctional sequences through which the evolutionary process would need to search. Axe’s experimentally derived estimate placed that ratio—the size of the haystack in relation to the needle— at 1077 nonfunctional sequences for every functional gene or protein fold. That ratio implies that the difficulty of a mutational search for a new gene or novel protein fold is equivalent to the difficulty of searching for just one combination on a lock with ten digits on each of seventy-seven dials! Could random genetic mutations effectively search a space of possibilities that large in the time available to the Cambrian explosion, or even the entire history of life on Earth? Clearly ten to the seventy-seventh power represents a huge number. (To put that number in context, consider that there are only 10 65 atoms in our galaxy!)
Yet, to assess whether the mutation/selection mechanism could effectively search such a large number of possible combinations in the time available, we also need to know how many opportunities the evolutionary process would have had to search this huge number of possibilities. Consider that every time an organism reproduces and generates a new organism, an opportunity occurs to generate and pass on a new gene sequence as well. But during the entire three-and-a-half-billion-year history of life on Earth, only ten to the fortieth individual organisms have ever lived—meaning that at most only ten to the fortieth power such opportunities have occurred. Yet ten to the fortieth power represents only a small fraction of ten to the seventy-seventh power—only one ten trillion, trillion, trillionth, or 1/10 37 to be exact. Thus, for even a single relatively simple functioning protein to arise, the mutation/selection mechanism would have time to search just a tiny fraction of the total number of relevant sequences—one ten trillion, trillion, trillionth of the total possibilities. In other words, the number of trials available to the evolutionary process turns out to be incredibly small in relation to the number of possible sequences that need to be searched. Or to put it differently, the size of the relevant spaces that need to be searched by the evolutionary process dwarfs the time available for searching—even taking into account the most generous view of evolutionary time. Thus, the mutation and selection mechanism does not have enough time in the entire multibillion-year history of life on Earth to generate but a small fraction (one ten trillion, trillion trillionth, to be precise) of the total number of possible nucleotide base or amino-acid sequences corresponding to a single functional gene or protein.
It follows that it is overwhelmingly more likely than not that a random mutational search would have failed to produce even one new functional (information-rich) DNA sequence and protein in the entire history of life on Earth. Consequently, it also follows that the hypothesis that such a random search succeeded is more likely to be false than true. And, of course, the building of new animals would require the creation of many new proteins, not just one. When our bicycle thief faced many more combinations than he had time to explore, it was much more likely that he would fail than it was that he would succeed in opening the lock. Likewise, the mutation and selection mechanism is much more likely to fail than to succeed in generating even a single new protein —and the genetic information necessary to produce it—in the known history of life on Earth. It follows that the standard neo-Darwinism mechanism does not provide an adequate explanation for the origin of the genetic information necessary to produce the major innovations in biological form that have arisen during the history of life on Earth.
VII. The Twin Challenges of Constructing and Modifying Body Plans
Yet, in order to explain novel form in the history of life, biologists must account not only for new genes and proteins but also for the origin of new body plans— where a body plan can be understood as a unique arrangement of body parts and tissues. Within the past decade, developmental biology has dramatically advanced our understanding of how body plans are built during the process of embryological development. Studies in developmental biology have shown that changes in biological form require attention to timing—especially in the expression of the genetic information necessary to build a body plan. The need for careful choreography in the expression of genetic information poses two additional but closely related problems for the neo-Darwinian mechanism—both of which provide other scientific reasons for doubting the creative power of the mutation/selection mechanism.
Embryonic Lethals and Early-Acting Body Plan–Affecting Mutations
First, though evolutionary biologists have long touted mutations as a kind of silver bullet capable a generating unlimited innovation, developmental biologists have discovered that only certain kinds of mutations—those that occur early in the embryological development of an animal—have the potential for altering an entire animal body plan—that is, for producing major evolutionary change. Conversely, mutations in genes that are expressed late in the development of an animal as it progresses from embryo to adult form will not affect the body plan of the animal, for two reasons. First, mutations expressed late in development will affect relatively few cells. Second, late in development, the basic outlines of the body plan will already have been established.12 Late-acting mutations therefore cannot cause any significant or heritable changes in the form or body plan of the whole animal. Mutations that are expressed early in development, however, may affect many cells and could conceivably produce significant changes in the form or body plan of an animal, especially if these changes occur in key regulatory genes.13 Thus, mutations that are expressed early in the development of animals have the greatest, and probably only, realistic chance of producing large-scale macroevolutionary change. As evolutionary geneticists Bernard John and George Miklos explain, “macroevolutionary change” requires changes in “very early embryogenesis.” 14
But this fact poses a difficulty for all theories of macroevolution that rely on mutations to generate major changes in form. Why? Because developmental biologists such as Christiane Nüsslein-Volhard and Eric Wieschaus have also discovered that mutations that occur early in the developmental trajectory of an animal (from embryo to adult form) are inevitably lethal.15 Moreover, there is an easily understood reason for this: If an engineer modifies the length of the piston rods in an internal combustion engine without modifying the crankshaft accordingly, the engine won’t start. Similarly, processes of embryological development are tightly integrated such that changes early in development will require a host of other coordinated changes in separate but functionally interrelated developmental processes downstream. For this reason, mutations will be much more likely to be deadly if they disrupt a functionally embedded structure that arises early in development (such as a spinal column) than they will be if the mutations affect more isolated anatomical features that occur later in development, such as fingers or skin. This problem of “embryonic lethals” has created a dilemma for evolutionary theorists: the kind of mutations needed to generate new body plans— in particular, early-acting beneficial body-plan altering mutations—never occur. The kinds of mutations that do occur—late-acting mutations that affect small clusters of somatic cells—don’t generate new body plans. The kind of mutations we need in order to produce new body plans, we don’t get. The kind we get, we don’t need. How then does the evolutionary process overcome this difficulty to produce major changes in animal form? Evolutionary biologists have not answered this question.
The Immutability of Developmental Gene Regulatory Networks
Or consider a related difficulty: developmental biologists have also discovered that building an animal does not just require new genes and proteins, but instead it requires integrated networks of genes and proteins called developmental gene regulatory networks (or dGRNs). These networks of genes and their protein products regulate the timing of gene expression as animals develop. The products of the genes (proteins and RNAs) in these integrated networks transmit signals (known as transcriptional regulators or transcription factors) that influence the way individual cells develop and differentiate during this process.
These signaling molecules influence each other to form circuits or networks of coordinated interaction, much like integrated circuits on a circuit board. For example, exactly when a signaling molecule gets transmitted often depends upon when a signal from another molecule is received, which in turn affects the transmission of still others—all of which are coordinated and integrated to perform specific time-critical functions. The late Eric Davidson of California Institute of Technology explored the regulatory logic of animal development more deeply than perhaps any other modern biologist.16 In the course of his investigations, he not only discovered what these networks of genes do, he also discovered what they never do, namely, change significantly. Davidson explained why. The integrated complexity of the dGRNs (which he likened to integrated circuits) makes them stubbornly resistant to fundamental restructuring without breaking. Instead, Davidson discovered that mutations affecting the dGRNs that regulate body-plan development inevitably lead to “catastrophic loss of the body part or loss of viability altogether.” 17 As he noted, “there is always an observable consequence if a dGRN subcircuit is interrupted. Since these consequences are always catastrophically bad, flexibility is minimal . . . ” 18
Davidson’s findings present another challenge to the adequacy of the natural selection/mutation mechanism. Building new animal body plans requires not just new genes and proteins but new dGRNs. But to build a new dGRN from a preexisting dGRN necessarily requires altering the preexisting dGRN—the very thing that Davidson showed does not occur without catastrophic consequences.19 Given this, how could a new animal body plan—and the new dGRNs necessary to produce it—ever evolve from a preexisting body plan and set of dGRNs? Davidson made clear that no one really knows: “contrary to classical evolution theory, the processes that drive the small changes observed as species diverge cannot be taken as models for the evolution of the body plans of animals.” 20 He elaborates:
Neo-Darwinian evolution . . . assumes that all process works the same way, so that evolution of enzymes or flower colors can be used as current proxies for study of evolution of the body plan. It erroneously assumes that change in protein-coding sequence is the basic cause of change in developmental program; and it erroneously assumes that evolutionary change in body-plan morphology occurs by a continuous process. All of these assumptions are basically counterfactual. 21
Davidson’s work, like that of Nüsslein-Volhard and Wieschaus, has highlighted a difficulty of obvious relevance to macroevolution: explaining the origin of major innovations in biological form during the history of life. Building new forms of animal life such as those that arose during the Cambrian explosion and other major radiations in the history of life requires new developmental programs—including new early-acting regulatory genes and new developmental gene regulatory networks. Yet if neither early-acting regulatory genes nor dGRNs can be altered by mutation without destroying existing developmental programs (and thus animal form), then mutating these entities will leave natural selection with nothing favorable to select and the evolution of animal form will, at that point, terminate. Darwin was troubled by the problem of missing fossil intermediates. Not only have those forms (for the most part) not been found, but the abrupt appearance of new animal forms during the history of life illustrates a deeper and more profound engineering problem that neo-Darwinian theory has failed to address: the problem of building a new form of animal life by gradually transforming one tightly integrated system of information-rich genetic components and their products into another.
VIII. Answering My Critics
To this point I have argued that the neo-Darwinian mechanism is insufficient to generate the genetic information and information-rich gene regulatory networks necessary to produce new forms of animal life. Readers may want to know, however, how well this argument has withstood criticism. Fortunately, recent criticisms from (1) a leading mainstream evolutionary biologist, (2) two prominent theistic evolutionists, and (3) two prominent atheistic evolutionists (indeed, “new atheists”) afford excellent opportunities to assess the strength of the arguments developed here.
Challenge from a Mainstream Evolutionary Biologist
First, in 2013, a leading paleontologist and evolutionary biologist, Charles Marshall, responded to my argument about the problem of the origin of information as presented in my book Darwin’s Doubt. Marshall wrote a prominent review of the book in Science and, to his credit, did grapple with the book’s main arguments about the inability of standard evolutionary mechanisms to explain the origin of biological information and morphological novelty. His review demonstrated—if inadvertently—however, that leading evolutionary biologists have not solved the problem of the origin of biological information. To rebut the claim that the neo-Darwinian mechanism is insufficient to generate the information necessary to produce new forms of animal life, Marshall did not defend the power of the mutation/natural selection mechanism (or that of any other materialistic evolutionary mechanism) to produce the information necessary to build new forms of animal life. Instead, Marshall took a different tack. He disputed the claim that significant amounts of new genetic information would have been necessary to build the new animals. Specifically, Marshall claimed that “rewiring” of developmental gene regulatory networks (dGRNs) would have sufficed to produce new animals from a set of preexisting genes. As he argued,
[Meyer’s] case against the current scientific explanations of the relatively rapid appearance of the animal phyla rests on the claim that the origin of new animal body plans requires vast amounts of novel genetic information coupled with the unsubstantiated assertion that this new genetic information must include many new protein folds. In fact, our present understanding of morphogenesis indicates that new phyla were not made by new genes but largely emerged through the rewiring of the gene regulatory networks (GRNs) of already existing genes. 22
In this paragraph, Marshall claimed a lot in just a few words. He implied that evolutionary biologists have an adequate explanation for the process of body plan building—morphogenesis—that does not require the generation of new (or at least much new) genetic information. Yet Marshall’s understanding of how animal life originated is problematic for several reasons.
Elastic Control Networks Required
First, to account for the origin of novel animal body plans in the Cambrian period, Marshall suggests that developmental gene regulatory networks (dGRNs) must have been more flexible or labile in the past, in a way that would allow them to be “rewired.” 23 Yet, as noted, all available observational evidence establishes that dGRNs do not tolerate random perturbations to their basic control systems—that even modest mutation-induced perturbations of the genes in the core of the dGRN either produce no change in the developmental trajectory of animals (due to a kind of preprogrammed buffering or redundancy) or they produce catastrophic (most often, lethal) effects within developing animals. Disrupt the central control nodes, and the developing animal does not shift to a different, viable, stably heritable body plan. Rather, the system crashes, and the developing animal usually dies.24
Thus, to claim, as Marshall does, that dGRNS might have been more elastic in the past contradicts what developmental biologists have learned over several decades, from mutagenesis studies of many different biological “model systems,” including Drosophila (fruit flies), C. elegans (nematodes), S. purpuratus (sea urchins), Danio (zebrafish), and other animals, about how these networks actually function.25 Although many evolutionary theorists (like Marshall) have speculated about early “labile” dGRNs, no one has ever described such a network in any functional detail—and for good reason: no developing animal that biologists have observed exhibits the kind of “labile” developmental gene regulatory network that the evolution of new body plans requires. Indeed, Eric Davidson, when discussing these hypothetical labile dGRNs, acknowledges that evolutionary biologists are speculating “where no modern dGRN provides a model,” since they “must have differed in fundamental respects from those now being unraveled in our laboratories.” 26
For this reason, Marshall and other defenders of evolutionary theory reverse the epistemological priority (and violate the principles) of the historical scientific method as pioneered by Charles Lyell, Charles Darwin, and others.27 Rather than treating our present experimentally based knowledge as the key to evaluating the plausibility of theories about the past, Marshall and others use speculative evolutionary theories about what they think must have happened in the remote past to reinterpret our present observations and experimentally based knowledge of what does, and does not, occur in biological systems. In other words, the requirements of evolutionary doctrine trump our observations about how nature and living organisms actually behave. What we know best from observation takes a backseat to prior beliefs about how life must have arisen.
A Deeper Problem
But there is a more fundamental, and obvious, problem with Marshall’s attempt to dismiss the problem of the origin of genetic information necessary to produce new forms of animal life. Marshall claims that building new forms of animal life does not require new sources of genetic information, but his account of body plan building (morphogenesis) presupposes, but does not explain, many unexplained sources of such information. Indeed, his proposed approach subtly presupposes at least three unexplained significant sources of genetic information: (1) the information stored in the genes within the gene regulatory networks (GRNs), (2) the genetic information stored in other preexisting genes for building the necessary protein parts of various anatomical structures and novelties, and (3) the information required to rewire the gene regulatory networks (GRNs). Let’s examine each of these sources in turn.
The Genes in Gene Regulatory Networks Contain Genetic Information
Marshall presupposes unexplained genetic information, first and most obviously, by invoking preexistent gene regulatory networks. As noted, developmental gene regulatory networks (dGRNs) are integrated networks of specific genes and gene products (protein molecules that perform signaling functions) that interact to control and direct cell differentiation and organization during animal development. Clearly, the many genes that code for the production of these signaling proteins contain a vast amount of genetic information—the origin of which Marshall does not explain. Instead, his scenario for “rewiring” gene regulatory networks presupposes the prior existence of the information-rich genes that constitute these networks. But how did these genes arise? Marshall doesn’t say. Thus his proposal begs the question as to the origin of at least one significant, and necessary, source of genetic information. Yet, Marshall clearly acknowledges the need for these regulatory genes in his own scientific articles. For example, Marshall insists that Hox genes, in particular, must have played a causal role in producing the origin of the first animals during the Cambrian explosion. He notes that developmental considerations “point to the origin of the bilaterian developmental system, including the origin of Hox genes, etc., as the primary cause of the ‘explosion.’” 28 Hox genes are regulatory elements that play important roles in many gene regulatory networks. While in these papers Marshall also emphasizes the importance of “rewiring” gene regulatory networks to generate new body plans, he clearly acknowledges that preexisting genes would be necessary to produce new animals—though, again, he does not explain the origin of these information-rich genes but merely presupposes their existence.
Anatomical Novelties Require a “Genetic Toolkit”
When Marshall said in his review that new animals “emerged through the rewiring of the gene regulatory networks (GRNs) of already existing genes,” he did not specify whether he meant already existing genes in genetic regulatory networks or other preexisting genes such as those that are necessary for building the specific anatomical structures that characterize the Cambrian animals (the expression of which dGRNs regulate). Nevertheless, when writing elsewhere, Marshall and other evolutionary biologists have made clear that building new animal body plans would require many preexisting genes, indeed, a preexisting, preadapted “genetic toolkit” for building the specific anatomical parts and structures of animals.29
For example, in a 2006 paper titled “Explaining the Cambrian ‘Explosion’ of Animals,” Marshall noted that “Animals cannot evolve if the genes for making them are not yet in place. So clearly, developmental/genetic innovation must have played a central role in the radiation.” 30 In the same paper he argues that “It is also clear that the genetic machinery for making animals must have been in place, at least in a rudimentary way, before they could have evolved.” 31 Indeed, in his published work, Marshall emphasizes the need for “gene novelties” for building the proteins that make up the anatomical structures and novelties of the various animals that arose in the Cambrian period (in addition to the need for Hox genes).32 Of course, he’s right about this. Building multicellular animals would not have required just new Hox genes or genes for building new regulatory (DNAbinding) proteins. Instead, the evolutionary process would also have needed to produce a whole range of different proteins necessary to build and service specific forms of animal life. Different forms of complex animal life exhibit unique cell types, and typically each cell type depends upon other specialized or dedicated proteins—which in turn requires genetic information. In Darwin’s Doubt, I offered numerous examples of this.33 Our present observations of animals show that all new forms of animal life would also have needed various specialized proteins: for facilitating adhesion, for regulating development, for building specialized tissues or structural parts of specialized organs, for producing eggs and sperm, as well as many other distinctive functions and structures. These proteins must have arisen sometime in the history of life, but Marshall does not explain how the information for building them would have arisen.
Rewiring Networks Requires Informational Inputs
Finally, “rewiring” genetic circuitry in the way that Marshall envisions would itself have required multiple coordinated changes in the sequences of bases within the individual genes and/or changes to the arrangement of whole genes within the developmental gene regulatory network. Such reconfiguring would entail fixing certain material states and excluding others. Thus, it would constitute an infusion of new information (in the most general theoretical sense) into the dGRN.34 Thus, even if it were possible to rewire genetic regulatory networks without destroying a developing animal, Marshall’s “rewiring” proposal itself presupposes, but does not explain, the need for an additional source of information.
Recall that recent mutagenesis experiments have established the extreme rarity of functional genes and proteins among the many possible ways of arranging nucleotide bases or amino acids within their corresponding “sequence spaces.” 35 Recall also that the rarity of functional genes and proteins within sequence space makes it overwhelmingly more likely than not that a series of random mutation searches will fail to generate even a single new gene or protein fold within available evolutionary time. In presupposing these three significant sources of genetic information, Marshall does not explain how a random mutational search could have located the extremely rare functional sequences of nucleotide bases capable of building protein folds within the exponentially large sequence space of possible arrangements. In other words, he did not explain how the neoDarwinian (or any other) evolutionary mechanism could have solved the search problem described earlier in this chapter. Instead, he simply assumes that the necessary genes for building new forms of animal life arose earlier in the history of life, without explaining how they did. Thus, Marshall’s proposal (rewiring dGRNs) does not eliminate the need to explain the origin of genetic information necessary to build new forms of animal life; it simply begs the question as to how that information arose.
Challenges from Theistic Evolutionists
More recently, two prominent theistic evolutionists have also challenged my critique of the efficacy of mutation and natural selection as mechanism for generating new genetic information. Deborah Haarsma of the BioLogos Foundation has claimed that new studies show that functional genes and proteins are not extremely rare, despite what Douglas Axe’s experiments have indicated.36 Denis Venema, a biologist at Trinity Western University and a close colleague of Haarsma at BioLogos, has argued that the evolution of an enzyme capable of digesting synthetic nylon shows that new information capable of building a new protein can arise by mutation and selection in the time available to the evolutionary process. Haarsma’s claim is false; Venema’s are either inaccurate or extremely misleading.
First, at least four other studies using different methods of estimating the rarity of functional proteins 37 have confirmed Axe’s multiyear experimental study38 showing their extreme rarity in the “sequence space” of possible amino acid combinations. Haarsma cites a scientific study by an Italian research group that allegedly contradicts Axe’s findings but does not.39 That study sought to evaluate how frequently randomly generated amino acid chains (polypeptides) organize themselves into stable three-dimensional structures. Unfortunately, the test the Italian group used to identify stable three-dimensional structures couldn’t distinguish folded functional proteins from nonfunctional aggregations of amino acids. The group did report two folded structures, but discovered that, except in strongly acidic environments, these structures formed insoluble aggregates (not protein folds). This means these amino acid chains would not fold in actual living cells. Thus, nothing in the Italian study refutes Axe’s results showing that protein folds are extremely rare in sequence space.
Venema’s claims about nylonase are even more problematic.40
Recall that I have argued that random mutation/natural selection mechanism does not constitute a plausible means of generating the information necessary to produce a new protein fold—that protein folds are so rare in “sequence space” that a random search for new protein folds is overwhelming more likely to fail than to succeed in generating even a single new fold in the multibillion-year history of life on Earth. In response, Venema points to the discovery in the 1970s of an enzyme (a protein) called “nylonase” that can break down nylon—a synthetic material invented in the 1930s. Venema claims that the rapid origin of the nylonase enzyme demonstrates the power of evolutionary processes to produce the information necessary to generate a “brand new protein” in just forty years. As he argues,
Since nylon is a synthetic chemical invented in the 1930s, this indicated that these bacteria had adapted to use it as a food source in a mere forty years—less than a blink of the eye, in evolutionary time scales. Where these nylonases had come from was naturally the next question. The answer for one of them was a surprise—it was a de novo enzyme. Rather than being a modified version of another enzyme, this functional sequence of amino acids had popped into existence in a moment, through a single mutation. 41
He further claims that this new enzyme appeared “de novo” via a single frame-shift mutation. (A frame-shift mutation occurs when a single nucleotide letter is randomly inserted into the genetic sequence, causing the protein machine that transcribes the genetic message to shift its starting point by one nucleotide—i.e., one genetic “letter”—as it transcribes or “reads” the sequence). Venema thinks that the origin of nylonase via such a mutation demonstrates that functional protein folds must be much more common in sequence space than Axe has argued. As Venema puts it,
. . . if only one in 10 to the 77th proteins are functional, there should be no way that this sort of thing could happen in billions and billions of years, let alone 40. Either this was a stupendous fluke (and stupendous isn’t nearly strong enough of a word), or evolution is in fact capable of generating the information required to form new protein folds. 42
Nevertheless, contrary to what Venema has claimed, nylonase did not arise de novo via a single frame-shift mutation; it is not “a brand new protein”; and it certainly does not represent a new protein fold. First, the Japanese researchers whom Venema cites and who have most extensively studied nylonase postulated that it arose by two minor point mutations (not a dramatic frame-shift mutation). These mutations produced just two amino acid changes or substitutions 43 to a preexisting 392 amino-acid protein—hardly a de novo origination event. Second, based on their study, the researchers also inferred that the original gene from which the nylonase gene arose coded for a protein with limited nylonase function even before nylon was invented. This seems likely because a naturally occurring “cousin” of nylonase—an enzyme with a high degree of sequence similarity to it—has measurable (if weak) nylonase activity and can be converted to greater nylonase activity with just two mutations.44 The close sequence identity between nylonase and its cousin suggests the genes for both proteins arose from a common ancestral gene, which also would have coded for a protein with nylonase activity. This suggests that the mutations that produced the gene for nylonase did not generate “a brand new” functional gene and protein, but instead merely optimized a preexisting function in a similar protein.
Most importantly, the evidence also indicates that nylonase does not exemplify a new protein fold, but instead displays the same stable, complex threedimensional fold (a beta-lactamase fold) as both its cousin and likely ancestral protein. Indeed, oddly, the very researchers that Venema cites as his source for the story of the origin of nylonase make this clear. As the Japanese researchers note, “we propose that amino acid replacements in the catalytic cleft of a preexisting esterase with the beta-lactamase fold resulted in the evolution of the nylon oligomer hydrolase.” 45 Note the terms “preexisting” and “beta-lactamase fold.” These words indicate that the mutations responsible for the origin of nylonase did not produce a gene capable of coding for a new protein fold, but instead a gene that coded for the same beta-lactamase fold as its predecessor. Thus, the nylonase story confirms what Axe and I have argued, namely, that the mutation/selection mechanism can optimize (or even shift) the function of a protein provided it does not have to generate a new fold. Nevertheless, as we have also argued (see above), given the extreme rarity of protein folds in sequence space, the number of mutational changes necessary to produce a novel fold (to innovate rather than optimize) exceeds what can be reasonably expected to occur in available evolutionary time. The nylonase story confirms, rather than refutes, that claim. Indeed, it suggests that the mutation selection mechanism is not a plausible explanation for the origin of the amount of new information necessary to generate a new protein fold (and, thus, for any significant structural innovations in the history of life).46
Challenge from Atheistic Evolutionists: Natural Selection and Random Mutation: A Nonrandom Process?
Finally, outspoken atheistic evolutionists have also attempted to refute my critique of the implausibility of the mutation selection mechanism as an explanation for the origin of genetic information. Richard Dawkins and Lawrence Krauss in particular have attempted to dismiss the problem of the origin of genetic information and specifically the argument made here about the implausibility of a successful random mutational search for functional information-rich genes and proteins within sequence space. After I presented this argument in a debate against Krauss at the University of Toronto, Krauss, Dawkins in defense of Krauss claimed that I misrepresented the evolutionary mechanism as a purely random process. Instead, both Krauss and Dawkins insisted that “natural selection is a NONRANDOM process,” implying thereby that it could presumably succeed in finding the extremely rare functional arrangements of nucleotide bases and amino acids within the space of possible arrangements.
As Dawkins wrote in defense of Krauss and in criticism of me after the debate, Meyer was terrible. . . . When will these people understand that calculating how many gazillions of ways you can permute things at random is irrelevant. It’s irrelevant, as Lawrence said, because natural selection is a NONRANDOM process. 47
Nevertheless, in their attempt to get around the problem of the origin of genetic information, Dawkins and Krauss themselves misrepresented how the neo-Darwinian mechanism works. Natural selection itself is arguably a “nonrandom process,” as Dawkins insists. Rates of reproductive success correlate to the traits that organisms possess. Those with fitness advantages will, all other things being equal, out-reproduce those lacking those advantages.
Yet, clearly, there is more to the neo-Darwinian mechanism than just natural selection. Instead, the standard neo-Darwinian evolutionary mechanism comprises (1) natural selection and/or (2) genetic drift acting on (3) adaptively random genetic variations and mutations of various kinds. Moreover, as conceived from Darwin to the present, natural selection “selects” or acts to preserve those random variations that confer a fitness or functional advantage upon the organisms that possess them. As noted above, it “selects” only after such functionally advantageous variations or mutations have arisen. Thus, selection does not cause novel variations; rather, it sifts what is delivered to it by the random changes (i.e., mutations) that do cause variations. Such has been neo- Darwinian orthodoxy for many decades. All this means that, as a mechanism for the production of novel genetic information, natural selection does nothing to help generate functional DNA base (or amino acid) sequences. Rather it can only preserve such sequences (if they confer a functional advantage) once they have originated. In other words, adaptive advantage accrues only after the generation of new functional genes and proteins—after the fact, that is, of some (presumably) successful random mutational search. It follows that, even if natural selection (considered separately from mutation) constitutes a nonrandom process, the evolutionary mechanism as a whole depends upon an ineliminable element of randomness, namely, various postulated or observed mutational processes—a point that even other evolutionary biologists (and friendly partisans to Krauss and Dawkins) acknowledged after the debate in Toronto. Larry Moran and P. Z. Myers, for example, both criticized Krauss and Dawkins for mischaracterizing the neoDarwinian mechanism as wholly nonrandom, with Moran specifically blaming Krauss’s uncritical reliance upon Dawkins as the source of his misinformation.48
In any case, the need for random mutations to generate novel base or aminoacid sequences before natural selection can play a role means that precise quantitative measures of the rarity of genes and proteins within the sequence space of possibilities are, contra Dawkins, highly relevant to assessing the alleged power of the mutation/selection mechanism. Moreover, empirically based assessments of the rarity of genes and proteins in sequence space (estimated conservatively by Axe at 1 in 10 77—see above) do pose a formidable challenge to those who claim that the mutation/natural selection mechanism provides an adequate means for the generation of novel genetic information— at least in amounts sufficient to generate novel protein folds.49 Why a formidable challenge? Because random mutations alone must produce (or “search for”) exceedingly rare functional sequences among a vast combinatorial sea of possible sequences before natural selection can play any significant role. Moreover, as discussed above, every replication event in the entire multibillion-year history of life on Earth could not generate or “search” but a miniscule fraction (one ten trillion, trillion trillionth, to be exact) of the total number of possible nucleotide base or amino-acid sequences corresponding to a single functional gene or protein fold. As with a hypothetical bike thief who is confronted with many more combinations than he has time to explore, the mutation and selection mechanism turns out to be much more likely to fail than to succeed in generating even a single new gene or protein fold in the known history of life on Earth. It follows that the neo-Darwinian mechanism, with its reliance on—precisely—a random mutational search to generate new gene sequences, does not provide a plausible account of the origin of the information necessary to produce a single new protein fold, let alone a novel animal form, in available evolutionary time.
Conclusion
It follows from all this that theists who think that they must affirm the neoDarwinian mechanism as God’s means of creation are badly mistaken—and for scientific reasons. Consequently, there is no compelling reason to marry neoDarwinism with a Judeo-Christian understanding of creation. The mechanism of natural selection and random mutation does not provide a remotely plausible account of how novel biological form and information might have arisen. Therefore, it is as unlikely to have been the means by which God created life as it is unlikely to be the true explanation for the origin of novel biological form and information.
Saltados muchos capitulos XDDD
10 The Fossil Record and Universal Common Ancestry Günter Bechly and Stephen C. Meyer
SUMMARY This chapter is the first of three examining the strength of the case for universal common descent, the second (historical) part of contemporary evolutionary theory and the part of evolutionary theory that theistic evolutionists most commonly defend. We begin in this chapter by examining the logical structure of the argument for universal common descent. Taking that structure into account, we then assess what the fossil record can tell us about whether all forms of life do, or do not, share a common ancestor. Theistic evolutionists often claim that the alleged common ancestry of all forms of life is a “fact”—even as they may acknowledge doubts about the creative power of the neo-Darwinian mechanism. Nevertheless, we have become skeptical about universal common descent. In this chapter, we explain why using the fossil evidence to illustrate how a scientifically informed person might reasonably come to doubt the arguments for universal common descent (or universal common ancestry). After first describing the aspects of the fossil evidence that the theory of universal common descent explains well, we then examine other aspects of the fossil record that the theory does not explain as well—or at all. We especially highlight the many discontinuous or abrupt appearances of new forms of life in the fossil record—a pattern that contradicts the continuous branching tree pattern of biological history postulated by proponents of universal common descent. . . . . .
I. Introduction
Contemporary neo-Darwinian theory has two main parts. The first part, which we have critiqued at length in the preceding chapters, asserts that the mechanism of natural selection and random genetic mutation has the capacity to generate major innovations (macroevolutionary change) in the history of life. The second part of neo-Darwinism—the theory of universal common descent—concerns the pattern of change through biological history. Indeed, the theory of universal common descent is a theory about what happened in the history of life. The theory affirms that all known living organisms are descended from a single common ancestor somewhere long ago.1 Biology textbooks today often depict this idea, just as Darwin did, using a great branching tree. The bottom of the trunk represents the first primordial organism (or organisms). The limbs and branches of the tree represent the many new forms of life that developed from it. The vertical axis of the tree represents the arrow of time. The horizontal axis represents changes in biological form, or what biologists call “morphological distance.”
Whereas the mechanism of natural selection and random mutation describes how major evolutionary change allegedly happened (the process by which change occurs), the theory of universal common descent asserts that such major change did occur, and occurred in a completely connected, rather than disconnected or discontinuous, way (the historical pattern of change). Thus, the theory of universal common descent (UCD) depicts a “monophyletic” view of the history of life because it portrays all organisms as ultimately related as a single connected family. Darwin argued that the theory of universal common descent (or what he called descent with modification) best explained a variety of lines of biological evidence, including the succession of fossil forms, the geographical distribution of various species, and the anatomical and embryological similarities among otherwise different types of organisms. Modern evolutionary biologists have added the genetic similarities (or “molecular homologies”) of otherwise different organisms to this list of evidence supporting common ancestry.
Proponents of Darwinism have often heralded the fossil record as the most decisive evidence for common descent with modification.2 Philip Gingerich even claimed that “Morphological continuity in the fossil record is the principal evidence favoring evolution as a historical explanation for the diversity of life.” 3 On the other hand, those who doubt UCD have argued that the fossil record poses a severe challenge to the theory.4 Still other proponents of universal common descent, including Richard Dawkins, have sought to foreclose any such criticism by arguing that “We don’t need fossils. The case for evolution is watertight without them; so it is paradoxical to use gaps in the fossil record as though they were evidence against evolution.” 5
So what do fossils tell us about the history of life? And how strong is the case for the theory of universal common descent—the historical part of Darwinian theory?
This chapter will examine the logical structure of the arguments for universal common descent, with a particular focus on what the fossil record (and the argument from fossil progression) can tell us about whether all forms of life do, or do not, share a common ancestor. Though many theistic evolutionists portray this part of evolutionary theory as a well-established fact or theory6—even as they may acknowledge doubts about the creative power of the neo-Darwinian mechanism7—we have become skeptical about universal common descent. In this chapter we will explain why, and we will use the fossil evidence to illustrate how a scientifically informed person might reasonably come to doubt the arguments for universal common descent—whether those arguments are based on the fossil record or on other classes of evidence that have been marshaled in their favor.
II. Logical Structure of the Argument
Yet, before we look at any of evidence for, or against, universal common descent, it might be a good idea to examine the logical structure of the argument for it. Despite the presumed consensus in favor of universal common descent, there are good reasons for doubting the argument in its favor—reasons that are well illustrated by the fossil record and the competing possible interpretations of it. In particular, the argument for UCD depends on an often inconclusive or weak form of inference known as abduction.8 In abductive reasoning, scientists (or detectives) reason from effects (or clues) in the present back to causes in the past. To see the difference between abductive and deductive inference, consider the following argument schemata:9
DEDUCTION:
DATA: A is given and plainly true.
LOGIC: But if A is true, then B is a matter of course.
CONCLUSION: Hence, B must be true as well.
ABDUCTION:
DATA: The surprising fact B is observed.
LOGIC: But if A were true, then B would be a matter of course.
CONCLUSION: Hence, there is reason to suspect that A is true.
In deductive reasoning, if the premises are true, the conclusion follows with certainty. Abduction, however, does not produce certainty, but only plausibility or possibility. Unlike deduction, in which the minor premise affirms the antecedent variable (“A”), abductive reasoning affirms the consequent variable (“B”). In deductive logic, affirming the consequent variable (with certainty) constitutes a fallacy. The error derives from failing to acknowledge that more than one cause might explain the same evidence. To see why, consider this deductive fallacy:
If it rained, the streets would get wet.
The streets are wet.
Therefore, it rained.
or symbolically:
If R, then W
W therefore R.
Obviously, this argument has a problem. It does not follow that because the streets are wet, it necessarily rained. The streets may have gotten wet in some other way. A fire hydrant may have burst, a snow bank may have melted, or a street sweeper may have doused the streets before cleaning them. Nevertheless, that the streets are wet might indicate that it rained. Oddly, abductive arguments have the same logic structure as this fallacious form of deductive argument—they too affirm the consequent. For this reason, unless these inferences are strengthened using a process of elimination showing alternative hypotheses to be implausible, they remain weak or inconclusive.10 In PhD work at Cambridge, one of us (Meyer) showed that the case for universal common descent is based on several abductive inferences from various classes of biological evidence such as fossil succession, anatomical and molecular homology, embryological similarity, and biogeographical distribution.11 Consequently, as we have studied the case for universal common descent, we have both become gradually more skeptical about the theory because we find that the circumstantial evidence in favor of the theory is inconclusive at best. Moreover, we have found that the arguments for UCD were inconclusive for exactly the reason that abductive arguments often are: For each class of evidence allegedly favoring the theory, more than one explanation—or picture of biological history—could account for it. As we will show, the fossil record illustrates this problem in spades.
III. The Case for Universal Common Descent from Paleontology
Even so, the theory of universal common descent offers an elegant explanation of several features of the fossil record. Thus, those features—at least when considered in isolation from other evidential considerations—seem to provide support the theory of universal common descent. Consider, for example, the evidence of fossil “progression” or “succession.” The fossil forms preserved in the layers of sedimentary rock progress from simple organisms in older strata (layers) to more and more complex organisms in successively younger strata. According to proponents of UCD, this “stratigraphic” progression in the fossil record from less to more complex forms of life supports the theory of common descent because this pattern of evidence is exactly what paleontologists should expect to find if all organisms did in fact descend from earlier less complex ancestral forms. And though there are exceptions to it, the simple-to-complex rule is roughly true. Thus, the general pattern of successive temporal appearances agrees nicely with the Darwinian picture of the history of life. Moreover, the theory of universal common descent also explains other aspects of fossil evidence,12 since, again, the observed patterns are precisely what one would expect if all organisms had descended from earlier ancestral forms extending back to one universal common ancestor. For example:
Morphologically Intermediate Fossils (Possible “Missing Links”)
Paleontologists have discovered many fossils, such as Archaeopteryx, that appear morphologically intermediate between the putative ancestors and their descendants.13 By “morphologically intermediate” paleontologists mean that the fossil form in question displays some (but not all) of the primitive characteristics of a putative ancestor group while exhibiting some (but not all) of the derived characteristics of a putative descendant group. (A derived character is a novel or changed genetic or anatomical feature not present in a putative ancestral form or a more primitive state). Morphologically intermediate groups are not necessarily “temporally intermediate”—that is, they may not have been found in strata that lie “in between” putative ancestors and descendants. Similarly, such fossil forms may not have been found in the same geographical region as possible ancestors and descendants. Nevertheless, their similarities in form suggest the possibility of being transitional in time and space. Even though there are still groups for which such forms are lacking, many morphologically intermediate forms do exist, such as the numerous morphologically intermediate forms between land mammals and whales that have been discovered in recent decades. Since the theory of universal common descent entails the existence of temporally transitional intermediate forms, it would also predict the existence of many such, at least, morphologically intermediate forms in the fossil record. That such forms exist is, therefore, readily explained by universal common descent.
Morphologically Intermediate and Temporally “Transitional Series”
In addition to morphologically intermediate fossils, paleontologists would also expect, based on the theory of universal common descent, that the fossil record would document some detailed transitional sequences—sequences where several intermediate forms lie temporally in between the presumed ancestors and descendants in the sedimentary strata. Some examples of such sequences have been found in the fossil record. Famous examples are the horse series illustrating the successive transformation of the primitive 3–4 toed legs of Eocene Hyracotherium (formerly known as Eohippus) into the single-hooved legs of modern horses.14 Another is the mammal-like reptile series that illustrates the transition from the primary to the secondary jaw articulation with detachment of the three auditory ossicles.15
IV. The Evidence against Universal Common Descent from Paleontology
Notwithstanding the above evidences in support of universal common descent, there is also strong paleontological evidence that does not easily square with the Darwinian notion of descent with modification via a gradual series of successive transformations from ancestral to descendant forms of life. In particular, the fossil record also manifests large “morphological gaps” and discontinuities between different groups of organisms, especially at the higher taxonomic levels (of phyla, classes, and orders) representing the major morphological differences between different forms of life. With very few exceptions, the major groups of organisms come into the fossil record abruptly, without discernible connection to earlier (and generally simpler) alleged ancestors in the fossil record. Indeed, leading evolutionary biologists and paleontologists have long acknowledged this pattern of discontinuity. Evolutionary biologist Ernst Mayr, one of the fathers of the modern neoDarwinian synthesis, famously noted that “[w]herever we look at the living biota . . . discontinuities are overwhelmingly frequent. . . . The discontinuities are even more striking in the fossil record.”
Moreover, since the publication of The Origin of Species in the late nineteenth century, our knowledge of the fossil record has greatly increased. Consequently, in most cases, fossil discontinuities can no longer be explained away as the result of alleged incomplete sampling of the fossil record. In fact, paleontologist Michael Foote of the University of Chicago has noted that, as more and more fossil discoveries have been made, the new forms that these discoveries document consistently fall within existing higher taxonomic groups (e.g., phyla, subphyla, and classes). In other words, these new discoveries have repeatedly failed to document the rainbow of intermediate forms expected in the Darwinian view of the history of life (especially at the higher taxonomic levels). Foote has shown, using statistical sampling analysis, that as this pattern has become more and more pronounced, it has become ever more improbable that the absence of intermediate forms reflects a sampling bias—that is, an “artifact” of either incomplete sampling or incomplete preservation.16 Increasingly, paleontologists accept that fossil discontinuities are real and need to be explained, not explained away. As Cleveland Hickman et al.17 note, “most major groups of animals appear abruptly in the fossil record, fully formed, and with no fossils yet discovered that form a transition from their parent group.” Indeed, numerous fossil “radiations” or “explosions” of new forms of life are characterized by such abrupt appearances. To get a sense of how pervasive this discontinuous pattern is, and how significant these events are in the history of life, consider the following short descriptions of several of the salient examples of the abrupt appearance of new forms of life in the fossil record.
The Origin of Life
Evidence suggests that the first living cells arose very early in the history of planet Earth, almost as soon as conditions on our planet would permit. Over the last several decades most origin-of-life biologists and geochemists have placed the origin of the first life at about 3.8 billion years ago (bya), just after the cessation of the meteorite bombardment of the earth called the Late Heavy Bombardment (4.1–3.8 bya). The latest evidence from biogenic carbon in zircon crystals suggests that life was already present 4.1 bya in the Hadean era, even before the Late Heavy Bombardment, when life could survive only in subterranean niches.18 Either way, life seems to have arisen abruptly about as soon as it possibly could, given conditions on the early Earth.
The Origin of Photosynthesis
The origin of photosynthesis was a key event that made later plant and animal life on Earth possible. Photosynthesis involves two intricate and integrated sets of complex biochemical processes known as photosystems I and II, which are in turn made of many equally complex proteins. The earliest existence of cyanobacteria, the first photosynthetic cells, is documented by stromatolites from 3.7-billion-year-old rocks from the Isua supracrustal belt in Greenland.19 Nevertheless, indirect evidence suggests an even earlier origin of photosynthesis, about 3.8 billion years ago.20 Because the Late Heavy (meteorite) Bombardment (4.1–3.8 bya) “repeatedly boiled away the existing oceans into steam atmospheres” and left only subterranean environmental niches,21 photosynthesis was possible in the earth’s oceans only after the bombardment ceased. That implies that photosynthesis, with all its integrated biochemical complexity, originated abruptly as soon as the earth first offered a stable and suitable environment for the process to occur.
Archaean Genetic Expansion
This event is not so much documented by real fossils as by the identification of “fossil genes” through genomic studies. Lawrence David and Eric Alm found that the “genomic fossil record” indicates that the collective genome of life expanded between 3.3 and 2.8 billion years ago.22 During this period, 27 percent of all presently existing gene families came into being by rapid evolutionary innovation. Arguably, the generation of this amount of new genetic information vastly exceeds the creative power of the neo-Darwinian mechanism of mutation and natural selection, given the extreme rarity of functional genes and proteins within the space of possible DNA and amino acid sequences. As Meyer argued in chapter 2 of this volume, a randomly driven mutational search is overwhelmingly more likely to fail than to succeed in finding even one functional gene, let alone all the many genes that arose during this Archaean expansion, in available evolutionary time.23
Avalon Explosion
During the Ediacaran, the latest period of the Precambrian era, an enigmatic group of organisms appear abruptly in the fossil record. Radiometric dating studies fix the date for the first appearance of these Ediacaran fauna at about 575–565 million years ago (mya). These strange marine organisms (“Garden of Ediacara”) include microbial mats covering the sea bottom and enigmatic large sessile organisms that lack any visible feeding apparatus, and mostly have a quilted body with glide symmetry and fractal growth. Late Precambrian-era sediments around the world have yielded three main types of Ediacaran fossils. The first group consists of the Precambrian sponges. The second is the distinctive group of fossils from the Ediacaran Hills in Australia. The creatures fossilized there include such well-known forms as the flat, air mattress–like body of Dickinsonia; the enigmatic Spriggina, with its elongated and segmented body and alleged “head shield”; and the frond-like Charnia. The third group of fossils, named Kimberella, discovered in the cliffs along the White Sea in northwestern Russia, have been claimed to be primitive mollusks, but this identification is highly controversial.24 Nevertheless, apart from sponges and a few controversial fossils that have been attributed to algae, cnidarians, and primitive mollusks, the Ediacaran fauna have no obvious relationship to later life forms, and their systematic status is highly disputed, ranging from identifications as giant protists, to representatives of an independent multicellular kingdom, to metazoan animals, or even lichens. Whatever their classification, all groups originate abruptly without any known putative ancestors during what is now known as the Avalon Explosion, 575–565 mya.25 Indeed, the Ediacaran fossils provide evidence of a puzzling leap in biological complexity. Before the Ediacaran organisms appeared, the only living forms documented in the fossil record for over 3 billion years were single-celled organisms, colonial algae, and possible sponges. Although the humble Ediacaran biota look simple beside most of the later Cambrian animals, they exhibit a much higher degree of complex organization than the single-celled organisms and colonial algae that preceded them.
Cambrian Explosion
The Cambrian explosion refers to a dramatic period in the history of life when many new and anatomically sophisticated animals appeared suddenly in the sedimentary layers of the geologic column without any discernible evidence of simpler ancestral forms in the earlier layers below. Fossil discoveries during this period attest to the first appearance of animals representing more than twenty phyla (the largest division of animal classification) as well as many more subphyla and classes, each manifesting distinctive body plans, where a body plan represents a unique arrangement of body parts and tissues. Indeed, animals representing most of the body plans that have ever existed on Earth first appear during this explosive event. One especially dramatic fact of the Cambrian explosion is the first appearance of many novel marine invertebrate animals (representatives of separate invertebrate phyla, subphyla, and classes in the traditional classification scheme). Some of these animals have mineralized exoskeletons, including those representing phyla such as echinoderms, brachiopods, and arthropods, each with their clearly distinct and novel body plans. Several unexpected features of the Cambrian explosion from a Darwinian point of view are: (1) the sudden appearance of novel animal forms; (2) an absence of transitional intermediate fossils connecting the Cambrian animals to simpler Precambrian forms; (3) a startling array of completely novel animal forms with novel body plans; and (4) a pattern in which radical differences in form in the fossil record arise before more minor, small-scale diversification and variations. This latter pattern turns on its head the Darwinian expectation of small incremental changes only gradually resulting in larger and larger differences in form. The abruptness of the explosion is also dramatic from both a geological and an evolutionary standpoint. Most experts estimate the duration of the Cambrian explosion at about 10–25 million years, and date the explosion around 540–515 mya.26 Others emphasize that the main pulse of this event occurred within only 530–520 mya.27 Other studies even imply that between 13 and 16 new animal phyla arose within a narrow 5- to 6-million-year window of the larger explosive radiation.28 In any case, most Cambrian experts agree that the majority of Cambrian animal phyla lack any putative fossil ancestors within the preceding Ediacaran biota.29 Thus, the Cambrian explosion has been variously called “Evolution’s Big Bang” 30 and “Darwin’s Dilemma.” 31
Great Ordovician Biodiversification Event (GOBE)
While general animal body plans representing distinct phyla, subphyla, and classes first appeared in the Cambrian explosion, these marine invertebrate groups greatly diversified on lower taxonomic levels (e.g., about 300 new families) during a relatively short period of time in an event known as the Great Ordovician Biodiversification, about 485–460 mya.32 This explosive diversification of marine life has been called “Life’s Second Big Bang” by James O’Donoghue,33 who mentions “that the ‘Ordovician explosion’ was every bit as momentous for animal evolution as the Cambrian one.”
Devonian Nekton Revolution
Christian Klug et al. described a radical change in the composition of the marine fauna of the Early Devonian.34 While previously the marine ecosystems were dominated by planktonic (drifting) and demersal (near sea bottom) taxa, between 410 and 400 mya a very sudden and enormous expansion of marine nektonic (actively swimming) animals occurred in which groups such as ammonoid cephalopods and jawed fish make their first appearance. Within just 10 million years such active swimmers increased from only 5 percent to about 75 percent of the marine fauna.
Odontode Explosion
The term “odontode explosion” was coined by Fraser et al. for the sudden appearance of vertebrate dentition.35 Within 10 million years (425–415 mya) between the Late Silurian and Early Devonian, all major groups of jawed fish with teeth and tooth-like structures (odontodes) appear abruptly in the fossil record. These include stem-gnathostomes like the arthrodiran Entelognathus (423 mya), spiny sharks or Acanthodii (Nerepisacanthus, 423–419 mya), the oldest known cartilaginous fishes or Chondrichthyes (sharks like Stigmodus and Plectrodus, 423–419 mya), and the oldest known bony fishes or Osteichthyes, the latter already with the modern subgroups of lobe-finned Sarcopterygii (Guiyu, 423.5 mya) and ray-finned Actinopterygii (Meemannia, 415 mya).
Silurio-Devonian Radiation of Terrestrial Biotas
The sudden origin and diversification of vascular land plants (Tracheophyta) in the Late Silurian and Early Devonian is one of the great mysteries in the history of life. One of the two oldest known vascular land plants, Baraghwanatia, already belongs to the modern subgroup of clubmosses. Richard Bateman et al. conclude that “the Siluro-Devonian primary radiation of land biotas is the terrestrial equivalent of the much-debated Cambrian ‘explosion’ of marine faunas.” 36
Carboniferous Insect Explosion
In the Pennsylvanian (Upper Carboniferous) era, between 318 and 300 mya, when the world was dominated by vast swamp forests, a large diversity of different winged insect groups appeared suddenly without any known transitional forms in the older Mississippian (Lower Carboniferous) or Devonian strata.37 These include not only giant palaeopterous insects like the extinct palaeodictyopterans, mayflies, and dragonflies, or “primitive” neopterous insect orders like stoneflies, roaches, and orthopterans, but also thrips, bugs, and even advanced holometabolans like wasps, beetles, and scorpion flies.
Triassic Explosion
This event was also called the Early Triassic metazoan radiation or post-Permian radiation. No new phyla and classes, but many new orders and families originate abruptly after the end-Permian mass extinction (about 252 mya) among marine invertebrates (e.g., bivalves and ceratites), insects (e.g., Coleoptera and Diptera), and tetrapods (see below). Peter Ward explains that “the diversity of Triassic animal plans is analogous to the diversity of marine body plans that resulted from the Cambrian Explosion. It also occurred for nearly the same reasons and, as will be shown, was as important for animal life on land as the Cambrian Explosion was for marine animal life.” 38
Early Triassic Terrestrial Tetrapod Radiation
Directly after the great Permo-Triassic mass extinction, the first representatives of modern tetrapod taxa appear suddenly, within a short window of time, between 251 and 240 mya.39 These include the first dinosaurs (Nyasasaurus), the first turtles (Pappochelys), the first lizard-relatives/Lepidosauromorpha (Paliguana), the first croc-relatives/ Crurotarsi (Ctenodiscosaurus), and the first mammal-like animals/ Mammaliaformes (Haramiyida). Except for the latter two groups, they all appear virtually out of thin air, without discernible connections to any known ancestors.40
Early Triassic Marine Reptile Radiation
After the great end-Permian mass extinction, fifteen different families of marine reptiles appear abruptly between 248 and 240 mya in the Early Triassic. They include, for example, ichthyosaurs, plesiosaur-like pistosaurids, hupehsuchians, nothosaurs, thalattosaurs, pachypleurosaurs, tanystropheids, placodontians, and the enigmatic Aptodentatus. A vertebrate paleontologist who is an agnostic and a renowned scientist specializing in ichthyosaurs, and who must remain anonymous to protect his career, told us that the sudden appearance of viviparous, fully formed fish-like ichthyosaurs within 4 million years after the Permo-Triassic mass extinction made him doubt the neo-Darwinian story.
Mid-Triassic Gliding Reptile Radiation
Within only 2 million years of the Mid-Triassic (230–228 mya) there is a sudden appearance of gliding and flying reptiles, like Sharovipteryx (with wings on the legs); Mecistotrachelos, and the unrelated Kuehneosauridae (with gliding membrane across lateral rib-like projections); Longisquama (with long featherlike scales on the back); and the earliest pterosaurs like Preondactylus.
Mosasaur Radiation
Sudden discontinuous origins are found not only in the history of higher taxa but also within subordinate groups. A good example is the abrupt origin and diversification of Mosasaurs in the last 25 million years of the Upper Cretaceous,41 when they are said to have evolved from one-meter-long shoredwelling lizards (Aigialosauridae) into fully marine snake-like giants of up to 17 meters length (Mosasauridae). They quickly diversified into numerous species around the world, filling different ecological niches. Putative ancestors of mosasauroids prior to the Late Cretaceous are not known. Moreover, even its proposed sister taxon Coniasaurus is of Late Cretaceous age and thus not a plausible ancestral precursor.42 Any evolutionary relationship to recent monitor lizards and/or snakes is also contested and a matter of considerable debate among specialists.43
Radiation of Flowering Plants
Charles Darwin called the abrupt origin of flowering plants during the Cretaceous period an “abominable mystery.” Indeed, nearly all early fossils of modern angiosperms first appeared abruptly in the Cretaceous and then rapidly diversified between 130 and 115 mya. Darwin was deeply bothered by the pattern of their origin because “the seemingly sudden appearance of so many angiosperm species in the Upper Chalk conflicted strongly with his gradualist perspective on evolutionary change.” 44 Though paleontologists in China have recently found a few angiosperms from the Mid-Jurassic period (such as Euanthus, Juraherba, and Yuhania), the classification of these fossilized plants as modern angiosperms remains in some dispute. There is also no evidence that these plants were ancestral to the later Cretaceous groups, and the paleontologists who have classified them have not proposed them as such. Indeed, none of these mid-Jurassic period plants can be unambiguously attributed to any subgroup of modern angiosperms, all of which did first appear in the Early Cretaceous. Thus, the enigmatic rise of angiosperms still represents an “inextricable knot”—an unresolved puzzle for those who assume the common ancestry of all forms of life.45
Radiation of Modern Placental Mammals
The first orders of placental mammals also appear abruptly in the fossil record, during the Paleocene epoch between 62 and 49 mya, without known precursors.46 Paleontologists call this series of events the “mammalian radiation.” According to J. David Archibald,47 “within approximately 15 million years of dinosaur extinction most of the 20 extant orders of placentals had appeared along with some 16 other orders that are now extinct. This was a truly explosive radiation and diversification.” Not only do many (probably about 15 of the extant) mammalian orders appear suddenly, but when they appear they are already separated into their distinctive forms. For example, the orders Carnivora (which includes bears), Chiroptera (which includes bats), and Perissodactyla (which includes horses) all first appear and are clearly differentiated from each other by their distinctive forms and features. The first fossil bat, for instance, is unquestionably a bat, capable of true flight. Yet we find nothing resembling a bat in the earlier Mesozoic fossil record.
Radiation of Modern Birds
The lineages of 95 percent of modern bird species also originated abruptly during the Paleocene epoch or the Tertiary (or Paleogene) period, as did most of the mammalian orders. Just like the placental mammalian radiation, the abrupt appearance of modern birds has been dated to a similarly narrow window of time from 65 and 55 mya. The recent genomic analysis by Richard Prum presented a comprehensive time-calibrated phylogeny of modern birds.48 This work suggests that only four bird lineages (ancestral species of Ratites, Galloanseres, Strisores, and the common ancestor of all remaining Neoaves) predated and survived the mass extinction event marking the Cretaceous-Tertiary (or CretaceousPaleogene) boundary. The most species-rich group, Neoaves, originated abruptly and diversified rapidly after this event.49 This avian radiation has been appropriately called the “explosive evolution of avian orders,” 50 “avian explosion,” 51 and even “Big bang for Tertiary birds.” 52 Moreover, no undisputed fossils of crown-group Neoaves have been found in sediments from the Cretaceous or older,53 rendering dubious molecular studies placing the origin and diversification of modern avian orders prior to the Cretaceous/Tertiary boundary.
Origin of Genus Homo
John Hawks et al.54 suggested that our own genus, Homo, originated abruptly 2 million years ago with sudden interrelated anatomical changes. This inspired a press release with the headline “New Study Suggests Big Bang Theory of Human Evolution.” 55 Hawks et al. also emphasize “that no gradual series of changes in earlier australopithecine populations clearly leads to the new species, and no australopithecine species is obviously transitional. This may seem unexpected because for three decades habiline species have been interpreted as being just such transitional taxa, linking Australopithecus through the habilines to later Homo species. But with a few exceptions, the known habiline specimens are now recognized to be less than 2 Myr old and therefore are too recent to be transitional forms leading to H. sapiens.” 56 (See chapter 11, by Casey Luskin, for a more detailed discussion of the hominid fossil record.)
The “Top-Down” Pattern of Appearance
This pervasive pattern of fossil appearance raises an additional difficulty for the theory of universal common descent and the Darwinian picture of the history of life. Darwinian theory (both classical and modern) implies that as new animal forms first began to emerge from a common ancestor, they would be quite similar to each other, and that larger differences in the forms of life—what paleontologists call disparity—would emerge only much later as the result of the accumulation of many small incremental changes. In its technical sense, disparity refers to the major differences in form that separate the higher-level taxonomic categories such as phyla, classes, and orders. In contrast, the term diversity refers to minor differences among organisms classified as different genera or species. Put another way, disparity refers to life’s basic themes; diversity refers to the variations on those themes. According to the theory of universal common descent and the current understanding of how the mutation/natural selection mechanism works, the differences in form, or “morphological distance,” between evolving organisms should increase gradually over time as small-scale mutations accumulate by natural selection to produce increasingly complex forms and structures (including, eventually, new body plans). In other words, one would expect smallscale differences or diversity among species to precede large-scale morphological disparity among phyla. As the former Oxford University neoDarwinian biologist Richard Dawkins puts it, “What had been distinct species within one genus become, in the fullness of time, distinct genera within one family. Later, families will be found to have diverged to the point where taxonomists (specialists in classification) prefer to call them orders, then classes, then phyla.” 57
Darwin himself made this point in the Origin of Species. In explaining his famous branching-tree diagram, he noted how higher taxa should emerge from lower taxa by the accumulation of numerous slight variations.58
The actual pattern in the fossil record, however, contradicts this expectation. Instead of more and more species eventually leading to more genera, leading to more families, orders, classes, and phyla, the fossil record shows representatives of separate phyla appearing first, followed by lower-level diversification on those basic themes. For example, during the Cambrian explosion representatives of many higher taxa such as phyla and classes (each representing distinctive body plans) first appear abruptly in the fossil record. Only later do different order- and family- and genus-level representatives of those distinctive body plans originate (in events such as the Great Ordovician Biodiversification Event or the Mammalian Radiation, for example). As paleontologists Douglas Erwin, James Valentine, and Jack Sepkoski note, “The fossil record suggests that the major pulse of diversification of phyla occurs before that of classes, classes before that of orders, orders before that of families. . . . The higher taxa do not seem to have diverged through an accumulation of lower taxa.” 59 Yet, the theory of universal common descent depicts (and predicts) just the opposite—the proliferation of species and other representatives of lower-level taxa occurring first and then building to the disparity of the highest taxonomic differences such as those between different phyla or different classes. Thus, the top-down pattern of appearance on display in the fossil record provides another evidential challenge to UCD.
V. The Polyphyletic Interpretation of the Fossil Record
The pattern of appearance of major groups of organisms in the fossil record— both in the abruptness and discontinuity of those appearances and in the unexpected way in which disparity precedes diversity—seems to contradict the “monophyletic” picture of the history of life entailed by the theory of universal common descent. That suggests the possibility, at the very least, that the monophyletic picture may not be the one that best fits the fossil evidence. True, universal common descent does anticipate the progression from less complex to more complex forms of life that is generally evident in the fossil record. But the pattern of discontinuity and abrupt appearance seems on its face to contradict the way in which the theory portrays the history of life. Similarly, the top-down pattern of appearance contradicts its picture of the gradual accumulation of small incremental change over time. Indeed, UCD portrays the history of life as a great branching tree in which each new lineage emerges through just such a process of gradual and continuous, rather than abrupt and discontinuous, change. Of course, proponents of a monophyletic view have sought to offer auxiliary ad hoc hypotheses—such as the artifact hypothesis—in order to explain away the absence of expected evidence of genuine transitional fossils—i.e., temporal intermediates—connecting alleged ancestors and descendant forms in the sedimentary record. Nevertheless, conjoining UCD with such an auxiliary hypotheses is by no means the only way to explain the pattern of discontinuity evident in the fossil record (if it provides an adequate explanation of that discontinuity at all; see below). Consider, instead, the polyphyletic view of biological history. It depicts the history of life as an orchard of separate, disconnected trees in which major new groups of plants and animals are introduced into the fossil record progressively and discontinuously. This view explains fossil succession equally well, but, arguably, describes the discontinuous pattern of appearance more accurately (or, at least, more naturally and simply, without auxiliary hypotheses) than a monophyletic view does. Indeed, pervasive discontinuity is precisely what one should expect to find in the fossil record based on a polyphyletic view of the history of life.60
The Polyphyletic View and Morphological Intermediates
But what about the intermediate forms of life discussed above that proponents of common descent cite in support of their theory? How does their existence square with the claim that the fossil record shows a pervasive discontinuity? And how would a polyphyletic view explain such intermediates? Recall, first, the distinction we made above between morphological and temporal intermediates. The vast majority of all intermediates in the fossil record exemplify the morphological rather than the temporal kind. For a fossil to be demonstrably part of a temporal sequence, that intermediate fossil must lie between a plausible ancestor and its possible descendants in the sedimentary strata.
Consequently, when proponents of universal common descent assert that fossil intermediates are very common (see above), and doubters of descent claim that transitional fossil are mostly absent, neither side is strictly incorrect. Instead, both sides often talk past each other because they have different types of intermediates in mind. When proponents of universal common descent talk about transitional fossils, they usually refer to fossils such as Archaeopteryx that exhibit a mosaic of characters wherein some but not all of the characters from a proposed putative ancestor group (such as reptiles) are present in the intermediate form, while at the same time some (but not all) of the characters of the putative descendant group (such as birds) are also present in the intermediate. As noted above, the theory of universal common descent would expect that many such morphologically intermediate forms would be present in the fossil record—and, indeed, they are. Thus, UCD can offer a ready explanation for the presence of many such intermediates in the record, especially the many forms that lie morphologically in between different higher taxa (i.e., orders and families). It must be noted, though, that most of such transitional fossils also exhibit specialized anatomical features that exclude them from the direct ancestral lineage and place them on side branches of the tree close to the alleged descendants. They are not putative ancestors. Nevertheless, a polyphyletic view of the history of life can account for such morphologically intermediate forms as well. Given the otherwise pervasive discontinuity and absence of genuine transitional sequences (i.e., temporal intermediates) between major groups of organisms discussed above, proponents of a polyphyletic view do not regard fossils such as Archaeopteryx as representatives of a temporally transitional sequence leading from ancestor to descendant (nor need they do so), but instead as precisely a “mosaic” of traits produced by an intelligent designer who, like human engineers or artists of our acquaintance, may choose to combine different traits into unique combinations exemplifying a distinctive form with elements or parts in common with two or more other products of his creation (see also note 60).
The Polyphyletic View, Discontinuity, and Alleged Transitional Intermediates
For this reason, to decide whether a polyphyletic or monophyletic view of the history of life best fits the data, we think the most important class of evidence to consider remains the pervasive pattern of discontinuity and the abrupt appearance of major groups of organisms. As we noted earlier, the attempt to explain that pattern away as an “artifact” of incomplete sampling of, or incomplete preservation within, the fossil record has largely failed within paleontology. (Meyer explains more about why paleontologists increasingly reject the artifact hypothesis in chapter 3 of his book Darwin’s Doubt). And yet, evidence of true transitional sequences (i.e., temporal intermediates, as we have called them) is extremely rare within the fossil record, especially between higher taxonomic groups. Even the most dramatic of the alleged transitional sequences, such as the mammal-like reptile sequence and the land mammal-to-whale sequences—both touted as proof positive of universal common descent—are: (1) at best, extremely rare exceptions to an otherwise pervasive pattern of discontinuity, or (2) at worst, not at all the evidence of a continuous transformation that proponents of universal common descent claim.
Consider the alleged sequence to the fully aquatic whales. Though often cited as an example of a smooth evolutionary transition, this alleged transitional sequence itself displays dramatic evidence of abrupt appearance.61 In The Walking Whales: From Land to Water in Eight Million Years, leading cetacean paleontologist J. G. M. Thewissen admits that in a “dramatic transition” whales were “undergoing fast evolutionary change,” with features that “change abruptly.” 62 Thewissen likens the evolution of whales from land mammals to converting a bullet train into a nuclear submarine. “Whales,” he notes, “started out with a . . . perfected body adapted to life on land. They changed it, in about eight million years, to a body perfectly tuned to the ocean.” 63 More recent fossil evidence shows that the first fully aquatic whales, the basilosaurids, appeared even more abruptly than previously thought. Indeed, basilosaurids first appeared 49 million years ago, perhaps within only 4.5 million years after the earliest Pakicetidae, a family of terrestrial mammals that are supposedly ancestral to whales.64 The basilosaurids even predate some of their supposed protocetid ancestors such as the 47.5-million-year-old “proto-whale” Maiacetus— a mammal that gave birth on land, had well-developed hind limbs, and lacked even rudimentary tail flukes.65 Indeed, the phylogenetic tree based on cladistic analysis of fossils does not reveal a gradual origin of aquatic adaptations; instead, the defining features of true whales appear abruptly in the clade Pelagiceti.66 (Similar, though arguably more acute, problems afflict the putative reptile-like mammal transitional sequence.67)
Thus, though common descent and its fully connected monophyletic picture of biological history can explain some of the fossil evidence—such as the progression of increasingly complex forms and the increasing similarity of fossil form to modern forms of life as observers ascend the stratigraphic column—the polyphyletic view can explain those same classes of evidence and can, in our judgment, explain other aspects of the fossil evidences (such as fossil discontinuity, a “top-down” pattern of appearance, and the pervasive absence of genuine temporal/transitional intermediates) more adequately and more simply than can a monophyletic view. Indeed, a polyphyletic view would seem to explain and describe more adequately the overall pattern of increasing complexity and abrupt appearance than would a monophyletic view.
V. Other Classes of Evidence and the Theory of Universal Common Descent
We have found that this same logical relationship obtains between other classes of biological evidences and these competing views of biological history. If only some facets of the evidence in question are considered, then a monophyletic view of the history of life explains the evidence as well as a polyphyletic view. But if other facets of that evidence are considered, then a polyphyletic view ends up providing a more adequate explanation of all the facets of that relevant class of evidence.
Consider, for example, molecular homology, the class of evidence that many evolutionary biologists think supports UCD most decisively. When biologists compare the amino acid sequences of proteins and genes in different species, they often find that they are quite similar in the “letter-by-letter” arrangement of their information-bearing subunits. Comparisons of the chimp and human genomes have indicated that the two are between 95 percent and 99 percent similar in sequence.68 Proponents of UCD explain this similarity as the result of chimpanzees and humans having a common ancestor, one that possessed an ancestral genome that later evolved in two slightly different ways. But that’s only one possible explanation. The similarity between different genes and proteins in different organisms also might have arisen separately as the result of an intelligent designer choosing to provide similar molecular-level functional capabilities in different organisms. For example, on this view, hemoglobin proteins in chimps and humans should have similar amino acid sequences or structures (as they do)69 since they perform the same function in each animal, namely, carrying oxygen in the blood stream. Thus, as with fossil progression, the evidence of sequence similarity admits more than one explanation.
Moreover, as was the case with the fossil evidence, an alternative picture (to the monophyletic view) of biological history better accounts for other aspects of the molecular evidence. Consider: if Darwin’s tree of life picture is accurate, then we should expect different types of biological evidence to point to the same phylogenetic tree. Since life had only one history, then a “family history” of organisms based on comparative anatomy should match one based on comparisons of DNA, RNA, and proteins. Many studies have shown, however, that trees derived from analyses of anatomy often conflict with trees based on bio-macromolecules. Some recent examples for molecular and morphological data producing wildly different phylogenetic trees are grasses,70 metazoan animals,71 reptiles (i.e., the position of turtles),72 and lizards,73 all of which contradict the result one would expect based on the theory of universal common descent. Worse, various molecular analyses often generate widely different evolutionary trees.74 As biologist Michael Lynch observes, “analyses based on different genes—and even different analyses based on the same genes” can yield “a diversity of phylogenetic trees.” 75 More recently, genomics experts have found thousands of genes in different organisms with no known similarity to any other known gene.76 The pervasiveness of these nonhomologous “orphan” genes is completely unexpected, given UCD. Yet, if different forms of life originated discontinuously and separately, then there would be no reason to expect that trees derived from different analyses would generate a single convergent tree. Moreover, if different forms of life were intelligently designed, with a mosaic of characteristics, some of which they share in common with some organisms and others of which they share in common with different organisms, then we would expect “phylogenetic” analyses to generate conflicting trees depending on which character was chosen. Indeed, phylogenetic analyses of different characters present in several different human-designed technological objects have been shown to generate precisely such conflicting trees. Finally, there are instances where the evidence for UCD has simply crumbled. In the Origin, Darwin claimed that embryos of different classes of vertebrates progress through similar phases of development as they grow from embryos to adults. He thought this indicated that different vertebrate classes shared a common ancestor in which that common pattern of development first originated.77 It turns out, however, that different classes of vertebrates do not progress through similar phases of embryological development.78 Yet, Darwin regarded alleged similarities in vertebrate development as “the strongest single class of facts in favor of” common descent.
VI. Conclusion
In summary, the case for UCD rests in part upon: (1) factual claims that have evaporated, (2) circumstantial evidence that admits alternative explanation, and (3) evidence (such as fossil discontinuity and conflicting phylogenetic trees) that is better explained by a polyphyletic view of biological history.79 For that reason, we have both become skeptical about the theory of universal common descent and versions of theistic evolution that affirm this second meaning of evolution— as described in the “Scientific and Philosophical Introduction” to this volume.
11 Universal Common Descent: A Comprehensive Critique Casey Luskin
SUMMARY Some theistic evolutionists will occasionally acknowledge problems with the mechanism of mutation and natural selection, but almost all theistic evolutionists claim that the historical part of Darwinian theory—universal common descent—is beyond dispute. Since Darwin’s time, the theory of universal common descent has rested upon a number of independent lines of evidence and argument: biogeography, fossils, anatomical homology, and embryological similarity. In recent decades, molecular homology has been added to that list. This chapter will show that each of these separate lines of evidence is equivocal at best and that, instead, many new lines of evidence cast serious doubt upon the supposed “congruence” of these lines of evidence, challenging the case for universal common descent. . . . . .
Some theistic evolutionists will occasionally acknowledge problems with the mechanism of mutation and natural selection (or at least will decline to defend its creative power). Nevertheless, almost all theistic evolutionists claim that the historical part of Darwinian theory—universal common descent—is beyond dispute. Prominent theistic evolutionists treat universal common descent as almost an axiom of all biological science, and ridicule skeptics through comparisons to geocentrists or flat-earthers. Since Darwin’s time, the theory of universal common descent has rested upon a number of independent lines of evidence and argument: biogeography, fossils, anatomical homology, and embryological similarity. In recent decades, molecular homology has been added to that list. This chapter will show that each of these separate lines of evidence is equivocal at best and that, instead, many new lines of evidence cast serious doubt upon the supposed “congruence” of these lines of evidence, challenging the case for universal common descent.
As other chapters have discussed, theistic evolution essentially takes a fully materialistic evolutionary view of biological history and says, “By the way, this is how God did it.” But the term “evolution” can have different meanings, some of which are controversial and some of which are not. For many, “evolution” simply means “change over time.” Both theistic evolutionists and Darwin skeptics affirm that this definition of evolution is uncontroversial and correct.
A second definition is universal common ancestry, the hypothesis that all living organisms are genetically related through descent with modification. Under this view, not only are all living humans related to one another, but we also share a common ancestor with apes, and going back farther, we’re related to everything from horses to tuna fish to broccoli to foot fungus and bacteria. This definition of evolution is controversial among many (though not all) Darwin skeptics, and is increasingly controversial among evolutionary biologists. The third definition of evolution claims that natural selection acting upon random mutations was the driving mechanism behind the history of life. This definition is the most controversial among scientists both inside and outside of the evolutionary community, and it holds that the mechanisms producing change over time (definition one) and common ancestry (definition two) were apparently blind and undirected.
Other chapters in Section I, Part 1 of this book have amply addressed the inadequacy of evolution’s mechanism (the third definition). The purpose of this chapter is to examine only the second definition—universal common ancestry. At first glance, common ancestry may not seem crucial to addressing theistic evolution. After all, the third definition is the one that addresses whether the history of life was unguided—a central question in the debate over theistic evolution. Moreover, common ancestry is compatible with intelligent design. For example, one possible way to view intelligent design is that God actively guided the history of life, but did so in a manner such that organisms share a common ancestry. Such a view supports both intelligent design and common ancestry yet avoids many of the logical, philosophical, and scientific difficulties that theistic evolution encounters when claiming that the entire history of life appears unguided (even though it really wasn’t).
Nonetheless, for a variety of reasons, common ancestry is an important part of this conversation.
First, the pursuit of truth is of the utmost importance. If universal common ancestry is true, we should want to know about that. If it isn’t, we should modify our views accordingly.
Second, theistic evolutionists devote much energy to arguing for common ancestry. They often mistakenly cite evidence for common ancestry as evidence for the full-blown Darwinian story and an apparently naturalistic history of life, conflating the second and third definitions of evolution. While this rhetorical strategy is logically flawed (evidence for common ancestry is not necessarily evidence for blind natural selection), if the evidence for universal common ancestry is weak then their argument faces not just a logical problem but also a factual one.
Moreover, in practice common ancestry sometimes (though not always) serves as a “gateway belief,” taking people away from an intelligent design–based view to a full-throated theistic evolutionary view—and for some, then on to an atheistic view. The importance of common ancestry to this conversation is seen in that theistic evolutionists commonly argue for their view not by citing evidence for natural selection but rather by focusing on the evidence for common ancestry—and they often do so using the strongest of language.
Finally, once the mechanism of evolution (definition three) comes under scrutiny, and life’s history no longer appears unguided, then evolutionary scientists lose an important rationale for claiming that all life is genetically related. If life evolved through an apparently unguided process like natural selection, then it follows that all life must be related. But if all life is not related, this challenges standard neo-Darwinian accounts of biological history. Thus, another important reason to discuss common ancestry is that if life is not universally related, this undercuts a core problematic tenet of theistic evolution.1
For these reasons, it is appropriate to devote some space to scientifically examining common ancestry. Most of the other chapters in this section of the book (Section I, Part 2) will focus on specific claims of human/ape common ancestry. This chapter, however, will focus more broadly on universal common ancestry—the idea that all living organisms are related.
I. Theistic Evolutionists Strongly Endorse Common Ancestry
The importance of common ancestry to theistic evolution is witnessed in the extremely strong language that theistic evolutionists use when defending the concept.
Francis Collins argues in The Language of God that “the conclusion of a common ancestor for humans and mice is virtually inescapable.” 2 In Coming to Peace with Science, biologist and former BioLogos president Darrel Falk writes regarding mammals that “virtually all geneticists are convinced . . . they share common ancestors.” 3 Another frequent BioLogos author, Dennis Venema, a biologist at Trinity Western University, argues that “[n]umerous independent lines of genomics evidence strongly support the hypothesis that our species shares a common ancestor with other primates.” 4
Robert Asher, a paleontologist at Cambridge University, writes in Evolution and Belief: Confessions of a Religious Paleontologist, that “the idea that the natural world around us does not teem with evidence in support of Darwin’s theory of evolution, that humanity does not share common ancestry with other forms of life on Earth via the mechanism of descent with modification, is profoundly mistaken.” 5 He further charges that “creationists” are incapable of a “fair, honest” evaluation of the data regarding common ancestry.6
In a 2011 InterVarsity Press book, Francis Collins and physicist Karl Giberson compare those who doubt common ancestry to geocentrists, writing, “virtually all geneticists consider that the evidence proves common ancestry with a level of certainty comparable to the evidence that the earth goes around the sun.” 7 Elsewhere Giberson employed similar rhetoric, stating, “biologists today consider the common ancestry of all life a fact on par with the sphericity of the earth” 8—unsubtly implying that those who doubt common ancestry are no better than flat-earthers.
Proponents of universal common ancestry may distastefully aim to use ridicule to bully skeptics into submission—but that in itself doesn’t mean common descent is therefore wrong. Despite the outlandish rhetoric, the evidence is worth carefully considering. Before we investigate the evidence, it’s important to note that it is theoretically possible that common ancestry might be true, or false, at multiple levels of the taxonomic hierarchy. For example, universal common ancestry hypothesizes that all living organisms are related. Thus, universal common ancestry might be false, but common ancestry could still be true at lower taxonomic levels, such as among all animals, or all vertebrates, all mammals, or all primates, etc. Indeed, even if we question common ancestry among those various groups, everyone would probably agree that all humans share a common ancestor. Ultimately, common ancestry must be evaluated on a case-by-case basis depending on the evidence within the particular group being studied.
Evaluating the case for common ancestry among every single high and low taxonomic grouping is far beyond the scope of this chapter, and probably would entail an impossibly lengthy inquiry. This chapter will thus evaluate the case for universal common ancestry as it is commonly advocated in textbooks and in popular books by theistic evolutionists and evolution advocates. This approach will afford an analysis of the typical arguments for common ancestry, and allow the reader to critically evaluate whether those arguments hold up. The case for universal common ancestry is often said to be “cumulative,” based on multiple lines of evidence including biogeography, fossils, DNA and anatomical similarities, and embryology.9 Because common descent is said to be demonstrated by multiple, independent lines of congruent evidence, those categories of evidence should be evaluated independently. This chapter will examine whether the evidence supports common ancestry in those different areas, starting with biogeography.
II. Does the Evidence Support Common Ancestry?
A. Biogeography
Biogeography is the study of the distribution of organisms in both time and space over the history of the earth. Defenders of neo-Darwinism commonly contend that biogeography strongly supports their viewpoint. For example, the National Center for Science Education (NCSE), a pro-Darwin advocacy group, cites a “consistency between biogeographic and evolutionary patterns” and argues, “[t]his continuity is what would be expected of a pattern of common descent.” 10 Much biogeographical data, however, has little to do with Darwinian evolution, and does not provide special evidence for common ancestry. It can be easily explained as the result of migration and continental drift—two conventional ideas accepted by virtually everyone in this debate. However, the NCSE’s arguments ignore the many biogeographical puzzles that have vexed evolutionary biologists because they show a marked discontinuity between biogeography and common ancestry. Evolutionary explanations of biogeography fail when terrestrial or freshwater organisms appear in a location (such as an isolated island or continent) at which no standard migratory mechanism can explain how those species arrived from their proposed evolutionary ancestors. In other words, take any two populations of organisms, and theistic evolution claims that if we go back far enough, they must be linked in space and time by common descent. But sometimes it is virtually impossible to explain how two particular populations arrived at their current geographical locations from some common ancestral population. For example, a severe biogeographical puzzle for common ancestry is the origin of South American monkeys, called “platyrrhines.” Based on molecular and morphological evidence, New World platyrrhine monkeys are thought to be descended from African “Old World” or “catarrhine” monkeys. The fossil record shows that monkeys have lived in South America for about 30 million years.11 But plate tectonics shows that Africa and South America separated around 100–120 million years ago (mya), and South America was an isolated island continent from about 80 to 3.5 mya.12 If South American monkeys split from African monkeys around 30 mya, neo-Darwinism must somehow explain how monkeys crossed hundreds, if not thousands, of kilometers of open ocean to end up in South America. This poses a major problem for common ancestry—one recognized by multiple experts. A HarperCollins textbook on human evolution states, “The origin of platyrrhine monkeys puzzled paleontologists for decades. . . . When and how did the monkeys get to South America?” 13 Primatologists John Fleagle and Christopher Gilbert explain,
The most biogeographically challenging aspect of platyrrhine evolution concerns the origin of the entire clade. South America was an island continent throughout most of the Tertiary [66 to 2.5 million years ago] . . . and paleontologists have debated for much of this century how and where primates reached South America. 14
For those unfamiliar with the explanations of evolutionary scientists, their responses to such puzzles can be almost too incredible to believe. They propose not that common descent might be wrong, but that monkeys must have rafted across the Atlantic Ocean, from Africa to South America, to colonize the New World. The HarperCollins textbook explains, “The ‘rafting hypothesis’ argues that monkeys evolved from prosimians once and only once in Africa, and . . . made the water-logged trip to South America.” 15 Of course, there can’t be just one seafaring monkey, or it will die, leaving no offspring. Thus, at least two monkeys (or perhaps a single pregnant monkey) must have made the rafting voyage.
Fleagle and Gilbert admit the rafting hypothesis “raises a difficult biogeographical issue” because “South America is separated from Africa by a distance of at least 2,600 km [~1,600 miles], making a phylogenetic and biogeographic link between the primate faunas of the two continents seem very unlikely.” 16 But they are wedded to common ancestry, and are obligated to find such a “link,” whether likely or not. Unwilling to consider non-evolutionary options, they conclude, “the rafting hypothesis is the most likely scenario for the biogeographic origin of platyrrines.” 17 In other words, the “unlikely” monkeyrafting hypothesis is made “likely” only because they assume common descent must be true.
Needless to say, the rafting hypothesis itself faces serious difficulties. Mammals like monkeys have high metabolisms and require large amounts of food and water.18 Fleagle and Gilbert thus concede that “over-water dispersal during primate evolution seems truly amazing for a mammalian order,” and conclude, “[t]he reasons for the prevalence of rafting during the course of primate evolution remain to be explained.” 19 Or, as another expert puts it, “the mechanical aspect of platyrrhine dispersal [is] virtually irresolvable” because evolutionary models “must invoke a transoceanic crossing mechanism that is implausible (rafting) or suspect . . . at best.” 20 Fleagle and Gilbert compare the monkeys’ voyage to winning the lottery: “by a stroke of good luck anthropoids were able to ‘win’ the sweepstakes.” 21 This is by no means the only case where evolutionary biologists are forced to invoke rafting or other speculative mechanisms of “oceanic dispersal” to explain away difficult problems. Other biogeographical conundra include the presence of lizards and large caviomorph rodents in South America,22 the arrival of bees, lemurs, and other mammals in Madagascar,23 the appearance of elephant fossils on various islands,24 the appearance of freshwater frogs across isolated oceanic island chains,25 and numerous other examples.26
This problem exists for extinct species as well. A 2007 paper in Annals of Geophysics notes the “still unresolved problem of disjointed distribution of fossils on the opposite coasts of the Pacific.” 27 However, this paper doesn’t invoke rafting—instead it proposes something even more unlikely: populations became separated due to an “expanding earth”—a long-discarded geological hypothesis (different from well-accepted modern theories of plate tectonics) that could be taken seriously only when trying to save common descent from falsification. A 2005 review in Trends in Ecology and Evolution explains the essence of the problem:
A classic problem in biogeography is to explain why particular terrestrial and freshwater taxa have geographical distributions that are broken up by oceans. Why are southern beeches (Nothofagus spp.) found in Australia, New Zealand, New Guinea and southern South America? Why are there iguanas on the Fiji Islands, whereas all their close relatives are in the New World? 28
After considering several “unexpected” biogeographical examples, the review concludes, “these cases reinforce a general message of the great evolutionist [Darwin]: given enough time, many things that seem unlikely can happen.” 29 Indeed, “unlikely” does appear to be the message here. If you’re going to retain common ancestry, you must accept some extraordinary biogeographical claims. When evolutionary scientists are forced to resort to fantastical “expanding earth” hypotheses, or “unlikely” accounts of species rafting across oceans, common ancestry clearly faces a challenge.
B. The Fossil Record
A popular college-level biology textbook explains, “Fossils are the only direct record of the history of life.” 30 This seems generally correct, making the fossil record an ideal place for testing universal common ancestry. The textbook’s author, geologist Donald Prothero, has elsewhere written that “The fossil record is an amazing testimony to the power of evolution, with documentation of transitions that Darwin could only have dreamed about.” 31 If you feel otherwise, Prothero continues, then you’re a “creationist,” who shares “much in common with the Neo-Nazi Jew-hating Holocaust deniers.” 32
But what do fossils say about evolution? If all living organisms are related, as universal common ancestry predicts, then the fossil record should seemingly contain transitional forms that show the intermediate stages between life’s various groups. But the history of life bears a repeated pattern of explosions, where new fossil types appear abruptly, without clear evolutionary precursors. Perhaps the most famous is the Cambrian explosion, where many of the major living animal groups (called “phyla”) appear in the fossil record in a sudden geological eyeblink—lasting 5 to 10 million years, and possibly less.33
Before the Cambrian, very few fossils having anything to do with modern animal phyla are found in the record. As one invertebrate zoology textbook states,
Most of the animal phyla that are represented in the fossil record first appear, “fully formed” and identifiable as to their phylum, in the Cambrian some 550 million years ago. . . . The fossil record is therefore of no help with respect to understanding the origin and early diversification of the various animal phyla . . . 34
The diversity of complex animals that appear in the Cambrian explosion is impressive, ranging from worms to arthropods to mollusks to even vertebrate fish. But some familiar animals—like dinosaurs, parrots, or camels—don’t appear until much later. Some evolutionists claim this progression is sufficient to demonstrate common ancestry. It isn’t. While the fact that life has “changed over time” doesn’t bother intelligent design, the fact that reptiles, birds, and mammals don’t appear until after the Cambrian period could be a major problem for neo-Darwinian evolution if, whenever these groups do appear, they do so in an abrupt fashion that betrays the predictions of neo-Darwinian common ancestry. For many of these subgroups of animals, again, they appear abruptly, in patterns of explosions.
“While during the Cambrian explosion numerous phyla and classes representing basic body plans originated,” writes paleontologist Walter Etter, the post-Cambrian “Ordovician radiation was manifested by an unprecedented burst of diversification at lower taxonomic levels.” 35 He continues, “The almost exponential increase in diversity was much more rapid during this Great Ordovician Biodiversification Event (GOBE) than at any other time [from the Cambrian to the present],” noting the increase was “for the most part abrupt.” Regarding the origin of major fish groups, Columbia University geoscientist Arthur Strahler wrote that “This is one count in the creationists’ charge that can only evoke in unison from paleontologists a plea of nolo contendere [no contest].” 36 We also see an “explosive” and rapid appearance of other marine organisms such as ammonites,37 other hard-shelled marine invertebrates,38 and mosasaurs.39
As for plants, a paper in Annual Review of Ecology and Systematics explains that the origin of land plants “is the terrestrial equivalent of the much-debated Cambrian ‘explosion’ of marine faunas.” 40 Regarding angiosperms (flowering plants), scientists refer to a “big bloom” or “explosion” 41 event. As one paper states, “[a]ngiosperms appear rather suddenly in the fossil record . . . with no obvious ancestors for a period of 80-90 million years before their appearance.” 42 Land animals show similar patterns. The fossil record shows an “explosion” of tetrapods when terrestrial vertebrates appear.43 A 2011 article in Science admitted that tracing the evolutionary origin of major dinosaur groups “has been a major challenge for paleontologists.” 44 A prominent ornithology textbook observes the “explosive evolution” of major living bird groups.45 Similarly, many authorities cite an “explosion” or “explosive diversification” of major mammal groups in the Tertiary.46 Paleontologist Niles Eldredge notes that “there are all sorts of gaps: absence of gradationally intermediate ‘transitional’ forms between species, but also between larger groups—between, say, families of carnivores, or the orders of mammals.” 47 Eldredge and some others attempt to explain many of these abrupt appearances of major fossil groups through “punctuated equilibrium.” This model accepts that major groups of organisms appear abruptly, but attempts to offer an evolutionary explanation where new species arise in small, short-lived populations that are unlikely to leave fossil remnants of transitions. This model has many problems,48 and a literal reading of the fossil record consistently shows a pattern of abrupt explosions of new types of organisms, which contradicts common descent—the opposite of what we would predict from a Darwinian process of small changes adding up to larger ones. As biologist Jeffrey Schwartz at the University of Pittsburgh explains,
We are still in the dark about the origin of most major groups of organisms. They appear in the fossil record as Athena did from the head of Zeus—fullblown and raring to go, in contradiction to Darwin’s depiction of evolution as resulting from the gradual accumulation of countless infinitesimally minute variations. 49
Comparing those who recognize this non-Darwinian pattern to “Holocaust deniers” won’t make it go away.
C. Molecular and Morphological Phylogenetic Trees
Perhaps the most common argument for universal common ancestry encountered by students in college-level biology textbooks is the universality of the genetic code—the claim that all life uses the same nucleotide triplets to encode the same amino acids.50 However, the genetic code is not universal; many variants in the genetic code are known among various organisms.51
If the alleged universality of the genetic code provides evidence for universal common ancestry, should its nonuniversality count as evidence against it? Whatever the answer, despite the variants, it is true that the vast majority of organisms use the same “standard code,” and all life forms employ similar types of biomolecules, such as, DNA, RNA, nucleotides, and proteins. Are such widespread biomolecular similarities evidence for common ancestry? A 2010 paper in Nature, “A Formal Test of the Theory of Universal Common Ancestry,” argued yes:
[T]he ‘universal’ in universal common ancestry is primarily supported by two further lines of evidence: various key commonalities at the molecular level (including fundamental biological polymers, nucleic acid genetic material, L-amino acids, and core metabolism) and the near universality of the genetic code. 52
The article’s author, evolutionary biochemist Douglas Theobald, concluded that universal common ancestry is the “best” explanation for these widespread biomolecular similarities. But “best” compared to what? Theobald tested universal common ancestry against the exceedingly unlikely hypothesis that living organisms independently evolved the same biomolecules and sequences by sheer “chance.” Universal common ancestry appeared compelling only because it was being compared to a preposterous null hypothesis. As critics writing in Biology Direct observed,
Cogniscenti cringed when they saw the Theobald paper, knowing that “it is trivial”. It is trivial because the straw man that Theobald attacks in a text largely formulated in convoluted legalese, is that significant sequence similarity might arise by chance as opposed to descent with modification. 53
True, universal common ancestry is one possible explanation for many genetic similarities we observe between organisms—and probably better than chance— but are there other viable explanations? Indeed there are. Intelligent agents frequently reuse the same parts in different designs to meet functional requirements, such as reusing wheels on cars and airplanes, or reusing key computer codes in different versions of Microsoft Windows. As Paul Nelson and Jonathan Wells observe,
An intelligent cause may reuse or redeploy the same module in different systems, without there necessarily being any material or physical connection between those systems. Even more simply, intelligent causes can generate identical patterns independently. . . . If we suppose that an intelligent designer constructed organisms using a common set of polyfunctional genetic modules—just as human designers, for instance, may employ the same transistor or capacitor in a car radio or a computer, devices that are not “homologous” as artifacts—then we can explain why we find the “same” genes expressed in the development of what are very different organisms. 54
Thus, common design—the intentional reuse of a common blueprint or components—is a viable explanation for the widespread functional similarities among the biomolecules found in different types of organisms. Universal common ancestry is not the only possible explanation. (Indeed, contra Theobald’s arguments for universal common ancestry, not all fundamental biomolecules are universal among organisms. As the authors of one paper found, “several core components of the bacterial [DNA] replication machinery are unrelated or only distantly related to the functionally equivalent components of the archaeal/eukaryotic replication apparatus,” leading them to suggest, “DNA replication likely evolved independently in the bacterial and archaeal/eukaryotic lineages.” 55 Even more striking, another paper compared the genomes of 1,000 different prokaryotic organisms and found that “of the 1000 genomes available, not a single protein is conserved across all genomes.” 56) But it isn’t mere similarity among biomolecules that evolutionary biologists claim demonstrates universal common ancestry. They often claim that patterns of similar nucleotide and amino acid sequences of genes and proteins allow organisms to be organized into a phylogenetic “tree of life” (Fig. 11.1) showing the evolutionary relationships between all living organisms.57
Pag 332.
FIGURE 11.1 Darwin’s tree of life.
This “tree of life” was Darwin’s only illustration in the Origin of Species, and it has become the most famous icon representing his theory. But does the tree of life exist? In the 1960s, soon after the genetic code was uncovered, pioneering scientists Linus Pauling and Emile Zuckerkandl predicted that phylogenetic trees based on biomolecules would confirm expectations of common descent already held by evolutionary biologists who studied morphology (i.e., the physical traits of organisms). They declared that “If the two phylogenic trees are mostly in agreement with respect to the topology of branching, the best available single proof of the reality of macro-evolution would be furnished.” 58 Presumably, then, if this prediction failed, and if there were sharp conflicts between trees built using different data sources, a compelling disproof of macroevolution would also be furnished.
Hoping to validate Pauling and Zuckerkandl’s prediction, biologists began sequencing genes from all manner of living organisms. In the 1990s, this led to a discovery that confounded evolutionary biologists: life falls into three basic domains which cannot be resolved into a neat, tree-like pattern. Thus, the prominent biochemist W. Ford Doolittle lamented,
Molecular phylogenists will have failed to find the “true tree,” not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree. 59
He explained that for many biologists, “It is as if we have failed at the task that Darwin set for us: delineating the unique structure of the tree of life.” 60 The basic problem is that one gene leads to one version of the “tree of life,” but another gene leads to an entirely different tree. What seems to imply a closer evolutionary relationship in one case (i.e., two similar genes), doesn’t in another. To put it another way, biological similarity is constantly appearing in places where it wasn’t predicted by common descent, leading to conflicts between phylogenetic trees. When two trees conflict, at least one must be wrong. And if one tree must be wrong (i.e., in one case genetic similarity was not a good indicator of an evolutionary relationship), how do we know that both aren’t wrong (i.e., in both cases genetic similarity is not indicating an evolutionary relationship)? Numerous technical papers have noted the prevalence of contradictory phylogenetic trees among various taxonomic groups. In 1998, a study in Genome Research plainly observed that “different proteins generate different phylogenetic tree[s].” 61 A 2009 article in Trends in Ecology and Evolution acknowledged, “evolutionary trees from different genes often have conflicting branching patterns.” 62 A 2013 paper in Trends in Genetics reported that “the more we learn about genomes the less tree-like we find their evolutionary history.” 63
Perhaps the most candid admissions came in a 2009 article in New Scientist titled “Why Darwin Was Wrong about the Tree of Life.” 64 It quoted researcher Eric Bapteste admitting that “the holy grail was to build a tree of life,” but “today that project lies in tatters, torn to pieces by an onslaught of negative evidence.” According to the article, “[m]any biologists now argue that the tree concept is obsolete and needs to be discarded.” The paper recounted the results of a study by Michael Syvanen, which compared two thousand genes across six animal phyla:
In theory, he should have been able to use the gene sequences to construct an evolutionary tree showing the relationships between the six animals. He failed. The problem was that different genes told contradictory evolutionary stories.
Syvanen succinctly explained the problem: “We’ve just annihilated the tree of life. It’s not a tree any more, it’s a different topology entirely. What would Darwin have made of that?” Clearly molecule-based trees often conflict with one another. But what about Pauling and Zuckerkandl’s prediction that molecule-based phylogenetic trees should match those constructed by morphology? A review article in Nature titled “Bones, Molecules, or Both?” explained that “Evolutionary trees constructed by studying biological molecules often don’t resemble those drawn up from morphology,” admitting that “Battles between molecules and morphology are being fought across the entire tree of life.” 65
A classic example involves attempts to construct a phylogenetic tree of the animal phyla. Traditionally, many phyla were grouped according to whether they have a central body cavity, called a “coelom.” But molecular data contradicted that grouping, and instead placed organisms that are morphologically very different, such as nematodes and arthropods, very close. A Nature paper reported how unexpected this grouping was: “Considering the greatly differing morphologies, embryological features, and life histories of the molting animals, it was initially surprising that the ribosomal RNA tree should group them together.” 66 Other fundamental animal characteristics, such as symmetry and early developmental processes, also yield a pattern of conflicting trees.67
Higher up the tree of life, conflicts persist. In 2014, the sequencing of various bird genomes led to the unexpected result that many types of birds that were previously thought to be closely related—water birds, birds of prey, and songbirds—evolved their groups’ defining traits convergently.68 As Nature put it, “the tree of life for birds has been redrawn.” 69 The problem was, once again, after genomic data was sequenced and understood, many basic habits and lifestyles of birds no longer fit into a nested hierarchy. As a final example, a 2013 paper acknowledged problems encountered when trying to reconcile conflicting versions of the mammalian tree:
Untangling the root of the evolutionary tree of placental mammals has been nearly an impossible task. The good news is that only three possibilities are seriously considered. The bad news is that all three possibilities are seriously considered. Paleontologists favor a root anchored by Xenarthra (e.g., sloths and anteater), whereas molecular evolutionists have favored the two other possible roots: Afrotheria (e.g., elephants, hyraxes, and tenrecs) and Atlantogenata (Afrotheria + Xenarthra). Now, two groups of researchers have scrutinized the largest available genomic data sets bearing on the question and have come to opposite conclusions. . . . Needless to say, more research is needed. 70
But is “more research” always solving these problems? 71 A 2012 paper noted that “phylogenetic conflict is common, and frequently the norm rather than the exception,” since “Incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as data sets have expanded rapidly in both characters and species.” 72
In any case, these frequent discrepancies between molecular- and morphology-based trees, and between various molecule-based trees, have led some scientists to conclude that the prediction of Zuckerkandl and Pauling was fundamentally wrong. A paper in the journal Biological Theory explained:
[M]olecular systematics is (largely) based on the assumption, first clearly articulated by Zuckerkandl and Pauling, that degree of overall similarity reflects degree of relatedness. This assumption derives from interpreting molecular similarity (or dissimilarity) between taxa in the context of a Darwinian model of continual and gradual change. Review of the history of molecular systematics and its claims in the context of molecular biology reveals that there is no basis for the ‘molecular assumption.’ 73
To put it another way, conflicts between morphological and molecular trees seriously challenge common ancestry—and, as we will soon see, undermine the methods used to infer it. But what about those happy cases where moleculebased trees show some congruence with morphology-based trees? Does this provide some kind of special evidence for common descent? Not at all. Recall that morphological trees are based on comparing similarities in anatomical traits between different organisms. But if anatomical traits are generated by gene sequences in DNA, then it follows that organisms with more similar anatomy will typically have more similar DNA. Because of this gene-morphology linkage, one need not even consider common ancestry to predict that DNA-based trees (groupings of organisms with more similar DNA) might show some resemblance to morphology-based trees (groupings of organisms with more similar anatomy). And both types of similarities—anatomical and DNA—can be explained by common design just as well as by common descent.
1. Assumptions, Epicycles, and Ad Hoc Hypotheses
Centuries ago, when astronomers held to a geocentric model of the solar system, they would often encounter data that ran directly counter to that model. Sometimes planets would appear to temporarily move backwards, in “retrograde motion.” Early scientists explained away the contrary data by invoking the “epicycle.” Epicycles didn’t actually explain anything; such auxiliary hypotheses were adopted after the fact for the sole purpose of saving the flawed geocentric model from falsification. Eventually, scientists accepted that planets were not moving backwards and agreed that the geocentric model of the solar system was wrong. Planets orbited the sun, not the earth. Today, evolutionary biology faces a similar dilemma. Biologists are constantly uncovering similarities between organisms that appear in patterns not predicted by universal common descent. Proponents of neo-Darwinian evolution thus adopt modern-day epicycles—ad hoc hypotheses invoked to explain why data run counter to the tree of life hypothesis. To appreciate how this works, we must examine some of the core assumptions that underlie evolutionary tree-building. First and foremost, phylogenetic trees are based on the assumption that common ancestry is true. That assumption—and it is merely an assumption— is so deeply embedded in evolutionary thinking that theorists often forget it’s there. In a rare example, Elliott Sober and Michael Steele acknowledge, “It is a central tenet of modern evolutionary theory that all living things now on earth trace back to a single common ancestor,” and, “This proposition is central because it is presupposed so widely in evolutionary research.” They acknowledge that phylogenetic methods assume that a tree exists and that common ancestry is correct:
Whether one uses cladistic parsimony, distance measures, or maximum likelihood methods, the typical question is which tree is the best one, not whether there is a tree in the first place. 74
A bioinformatics textbook concurs:
The key assumption made when constructing a phylogenetic tree from a set of sequences is that they are all derived from a single ancestral sequence, i.e., they are homologous. 75
These authorities affirm a crucial point: phylogenetic methods do not demonstrate common ancestry; they assume it. In other words, evolutionary biology doesn’t test whether all organisms fit into a nested hierarchy (i.e., a phylogenetic tree) but rather assumes that common ancestry is true. If the data does not fit with preconceptions about common ancestry, then various methods are used to force-fit the data into a tree. Thus, Michael Syvanen notes the protree biases of tree-building algorithms:
Because tree analysis tools are used so widely, they tend to introduce a bias into the interpretation of results. Hence, one needs to be continually reminded that submitting multiple sequences (DNA, protein, or other character states) to phylogenetic analysis produces trees because that is the nature of the algorithms used. 76
A more explicitly recognized assumption is that shared biological similarity between two species indicates inheritance from a common ancestor. This assumption is reflected in the statement quoted earlier from the journal Biological Theory: “degree of overall similarity reflects degree of relatedness.” We’ll call this the main assumption. The main assumption sounds nice in theory, but in practice, it fails constantly. For instance, under the main assumption, the reason you have two eyes, and your dog has two eyes, is that you shared a common ancestor with two eyes. That is a possibility. But cephalopods (octopi and squid) also have two eyes, and according to standard evolutionary wisdom, there’s no reason to think your most recent common ancestor with cephalopods had two eyes. We’re not even sure if it had eyes.
“Perhaps,” the defender of common ancestry replies, “both organisms independently evolved two eyes, just by chance.” Perhaps. But humancephalopod similarities go much deeper. Cephalopods have a “camera eye” with a basic design that is almost identical to human eyes. Surely such similarities are taken to indicate common ancestry, right? Wrong. According to evolutionary biologists, the extreme similarities between human and squid eyes result from “convergent evolution,” where two different organisms independently stumbled upon almost the same complex biological designs.
“Convergence” can be found at some of the highest conceivable levels of complexity. For example, comb jellies have advanced nervous systems, but molecular studies suggest they branched off very close to the base of the animal tree—before such complexity evolved. However, sponges (which branch off later, according to molecular data) lack such structures. This means that either animal brains evolved convergently—i.e., they arose multiple times, independently—or important and complex nervous cells were lost in sponges.77 Such extreme convergence is disconcerting to many evolutionary biologists, as Richard Dawkins acknowledges: “it is vanishingly improbable that exactly the same evolutionary pathway should ever be travelled twice.” Yet he admits there are “numerous examples . . . in which independent lines of evolution appear to have converged, from very different starting points, on what looks very like the same endpoint.” Not to worry, Dawkins tells us. Rather than facing the challenge of convergent evolution, he simply declares, “it is all the more striking a testimony to the power of natural selection.” 78
Beyond the fact that it is highly unlikely, extreme convergent evolution presents an even more serious problem for neo-Darwinian theory. It shows that the main assumption has failed—that biological similarity does not necessarily indicate inheritance from a common ancestor. This challenges the heart of the methodology used to infer common descent. But why should that trouble us? After all, what assumption always holds true? It should trouble us because the main assumption (that biological similarity indicates a common ancestor) fails not occasionally, but frequently. Indeed, so often does the main assumption fail, and so quick are evolutionary biologists to tolerate its failure, that we cannot help but question the many instances where biologists believe the main assumption held true. The frequent failure of the main assumption calls into doubt the core assumptions and rational bases used to construct phylogenetic trees—the lifeblood of common ancestry.
One evolutionary systematist, Nicholas Matzke, maintains that these failures of methodology pose no problems for common descent, as he notes that we can statistically analyze the congruency of trees to assess whether the assumptions of tree-building are holding true.79 In response to Darwin skeptics, he posted two phylogenetic trees (in this case, cladograms) and claimed that they demonstrated the common ancestry of arthropods. In reality, however, they demonstrated how the methods of phylogenetic reconstruction often fail to establish the assumptions that underlie common ancestry. A main goal of tree-building is to construct a phylogenetic tree that minimizes the number of evolutionary events necessary to explain the observed distribution of traits. An “evolutionary event” is the gain or loss of a trait during the course of evolution. The fewer evolutionary events required, the “better” the data fits a tree. In the parlance of evolutionary biology, this is called maximizing parsimony. One statistical method of determining the extent to which a data set fits a treelike pattern is to calculate a tree’s “consistency index” (CI). This is found by taking the minimum number of evolutionary events required by the overall data set, divided by the number of events required by the tree. A high CI (closer to one) indicates the data fits a tree-like pattern. A lower CI (closer to zero) usually indicates the data is inconsistent with a tree.80
The CI also measures the degree to which convergent evolution is required by a tree. In other words, a CI tells you how frequently the main assumption of treebuilding has failed. But what happens when the “best” tree you can find (i.e., the tree with the highest CI) still has a low CI? Consider the CIs for the arthropod trees posted by Matzke. One had CI of 0.565.81 This means that 43.5 percent of the time, a given trait or character analyzed in the data set was not distributed in a tree-like pattern, meaning the main assumption—that biological similarity results from common ancestry— failed. If an assumption fails 43.5 percent of the time, can one justify making it in the first place? Numerous similar examples could be given. A tree published in Nature purported to show the evolutionary relationships of many living mammals, but its CI was 0.43, meaning the main assumption failed in 57 percent of cases.82 Another Nature paper yielded a mammal tree with a CI of 0.34—a 66 percent failure rate.83 A paper using DNA to study bird relationships produced a tree with a CI of 0.36, a 64 percent failure rate.84 A 2007 paper in Proceedings of the Royal Society B produced a tree of early tertiary mammals with a CI of 0.35; the main assumption failed 65 percent of the time.85 Likewise, consider the CI of the other cladogram Matzke posted (Fig. 11.2) which purports to show the relationships of various Cambrian arthropods. It has a CI of 0.384, which even the original authors admit was “rather low.” 86 This means that in the cladogram Matzke referenced as a demonstration of common descent, the main assumption of tree-building failed 61.6 percent of the time. In such cases, the main assumption failed more often than it held true.
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FIGURE 11.2. Arthropod cladogram cited by intelligent design critic Nicholas Matzke to purportedly demonstrate how common ancestry explains evolutionary relationships between various arthropods. In this cladogram, however, the main assumption of tree-building failed 61.6 percent of the time. CREDIT: Derek Briggs and Richard Fortey, “The Early Radiation and Relationships of the Major Arthropod Groups,” Science 246 (October 13, 1989): 241–243. Reprinted with permission from AAAS.
Perhaps the main assumption should be rewritten as: biological similarities indicate inheritance from a common ancestor, except for when they don’t.
2. Is Common Descent Testable?
To be sure, plenty of trees enjoy much higher CIs. But even in those happy cases, how can we know whether the main assumption is valid, given how often it fails elsewhere? And if the main assumption hadn’t held, would that have even mattered? Indeed, why do evolutionary biologists tolerate the frequent failure of their field’s core assumptions? They tolerate it because to do otherwise would be to abandon common ancestry. Thus, they build trees even when they aren’t sure if the main assumption is true, or even worse, when they know the data doesn’t fit very well into a tree-like pattern. The open secret of evolutionary phylogenetic reconstruction, therefore, is that, using the statistical methods of tree construction, you can force virtually any data set to fit a “tree,” even if it strongly contradicts a tree-like pattern.
Sometimes, even data sets that do fit a tree and are well-supported by statistical analyses can sharply conflict. (As scientists commenting on a Nature paper stated, “trees produced by a number of well-supported studies have come to contradictory conclusions.” 87) Good statistical support for a tree, apparently, doesn’t always demonstrate common descent. This demands the question: What possible pattern would refute common ancestry? Strongly supported tree-like patterns don’t necessarily demonstrate common ancestry. And even when over half of the data is inconsistent with a tree, evolutionary biologists go ahead and impose a tree-like pattern. A 2010 paper reported trees with CIs under 0.1, meaning more than 90 percent of the data didn’t fit a tree.88 Predictably, the authors did not question common ancestry and had their own epicycles to try to explain the non–tree-like patterns. At what point can we falsify common descent? For evolutionary biologists, it seems we cannot, because common ancestry is not on the table for falsification. Apparently no pattern is necessarily inconsistent with common ancestry because you can always invoke as much convergent evolution (or loss of traits) as needed to force the data into a tree. And when those explanations are unlikely, other epicycles—like horizontal gene transfer, incomplete lineage sorting or coalescence, and rapid evolution, to list a few—can be invoked to explain away data that doesn’t fit a tree.
For example, one paper found that 23 percent of the human genome contradicts the standard human-ape tree, but unworriedly claimed the discrepancies simply result from incomplete lineage sorting.89 Another paper found that 30 percent of the gorilla genome contradicts the conventional humanape phylogeny, and explained away the data in the same manner.90 Large percentages of whole genomes can contradict standard evolutionary trees, and that is never even seen as a possible challenge to common ancestry. Indeed, modern genome sequencing has discovered thousands of “orphan genes”—unique genes that exhibit no homology (sequence similarity) to any other known gene.91 These genes ought to refute common ancestry because they cannot be compared to genes from other species, and thus do not fit into any phylogenetic tree. The problem is usually ignored.92
Conversely, genome sequencing regularly uncovers genes that do bear homology to other known genes—but that homology should not be there because (according to common ancestry) the closest homologue is known only from very distantly related species. These cases, too, are not taken as evidence against common descent, but instead are said to indicate horizontal gene transfer (HGT, also called lateral gene transfer or LGT), where organisms obtain genes from neighboring organisms rather than from a parent. Evolutionists sometimes reply that such phylogenetic oddities arise only when studying microorganisms like bacteria at the base of the tree of life—organisms that are known to readily swap genetic material through HGT. But this objection fails, since the tree of life faces incongruities among higher organisms where such gene-swapping is not prevalent. As Carl Woese, a pioneer of evolutionary molecular systematics, explains,
Phylogenetic incongruities can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves. 93
To explain away phylogenetic conflicts in higher branches, evolutionary biologists predictably argue that HGT must also be occurring in higher organisms, even if we don’t directly observe it. One study found hundreds of genes in animals that were unexpected under common ancestry, but simply explained them away by invoking HGT.94 Another study found that the angiosperm Amborella is “rich” in “foreign” genes that don’t fit the standard phylogeny; HGT came to the rescue and “explained” why they were there.95 But HGT is not necessarily directly observed in these higher organisms—rather, it is inferred to occur based on the presence of so-called “foreign” genes. Under this mind-set, genes that severely conflict with the standard phylogeny are not taken as evidence that the phylogeny might be wrong. Rather, they are taken as evidence for HGT. One paper admits this reasoning: “In the phylogenetic approach, each instance of topological discordance between a gene tree and a trusted reference tree is taken as a prima facie instance of LGT.” 96 When data that contradicts a paradigm becomes evidence for the epicycles rather than against the paradigm, it’s clear that the paradigm is in crisis. This is exactly what we see taking place with regard to universal common ancestry.
D. Embryology
In a letter to the American botanist Asa Gray, Charles Darwin urged that embryology was “by far the strongest single class of facts in favor” 97 of his theory. Much has changed in the 150-plus years since Darwin penned those words, but embryology remains a favorite line of evidence cited by evolutionists to support common descent, particularly among the vertebrates. Most modern biology textbooks will print some diagram depicting the early embryos of different vertebrate species as highly similar, then will claim that these similarities reflect common ancestry. Life Science, published by Holt, provides typical language: “Early in development, the human embryos and the embryos of all other vertebrates are similar. These early similarities are evidence that all vertebrates share a common ancestor.” 98 For decades, students were also taught that “ontogeny recapitulates phylogeny.” Called recapitulation theory, this idea was promoted by the German biologist Ernst Haeckel, who believed that the development of an organism (“ontogeny”) replays (“recapitulates”) its evolutionary history (“phylogeny”). Since the standard evolutionary view holds that humans evolved from fish, recapitulation theory taught that at one point between conception and birth, we all went through a “fish stage.”
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FIGURE 11.3. Haeckel’s embryo drawings depicting (in this order): Fish, Salamander, Tortoise, Chicken, Hog, Calf, Rabbit, Human. CREDIT: George Romane’s 1892 book, Darwinism Illustrated (public domain), as used in figure 5-1, Jonathan Wells, Icons of Evolution: Science or Myth? (Washington, DC: Regnery, 2000).
Biologists now know that vertebrate embryos do not replay their supposed earlier evolutionary stages, and firmly hold that recapitulation theory is false.99 The concept has been removed from textbooks, but many textbooks still use inaccurate diagrams which overstate the degree of similarity between vertebrate embryos. Indeed, the journal Science observed that “[g]enerations of biology students may have been misled” by Haeckel’s embryo drawings in textbooks.100 These drawings—commonly reprinted or adapted in textbooks 101—overstate the degree of similarity between vertebrate embryos in their earliest stages. According to Stephen Jay Gould, Haeckel’s methods “can only be called fraudulent” because he “simply copied the same figure over and over again” 102 when depicting the embryos of different species. This led embryologist Michael Richardson to call them “one of the most famous fakes in biology.” 103 In 2000, biologist Jonathan Wells published Icons of Evolution, which raised the public’s consciousness about Haeckel’s fraud, ultimately forcing many publishers to remove Haeckel’s inaccurate drawings from most textbooks. Many textbooks, however, still claim that the early stages of vertebrate development are highly similar. But are those claims accurate? No, they are not. Embryologists have found considerable differences among vertebrate embryos from their earliest stages onward, contradicting what we are told to expect from common ancestry. Two of the earliest stages of vertebrate development are cleavage and gastrulation. During cleavage, a newly fertilized zygote undergoes rapid cell division until the embryo becomes a tiny ball of cells, laying out the basic axes that will define the body plan. Next, during gastrulation, the embryo increases in size while forming distinct germ layers which will later develop into individual organs. Yet a paper in Systematic Biology states, “such early stages as initial cleavages and gastrula[tion] can vary quite extensively across vertebrates.” 104 Likewise, a 2010 paper in Nature stated, “Counter to the expectations of early embryonic conservation [i.e., similarity], many studies have shown that there is often remarkable divergence between related species both early and late in development.” 105 Or, as another article in Trends in Ecology and Evolution stated, “despite repeated assertions of the uniformity of early embryos within members of a phylum, development . . . [in those early stages] is very varied.” 106 Rather than looking highly similar in their early stages, vertebrate embryos look more like what we see in Figure 11.4.
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FIGURE 11.4. Accurate drawings of the early stages of vertebrate embryo development. CREDIT: Copyright Jody F. Sjogren 2000, as used in figure 5-3, Jonathan Wells, Icons of Evolution: Science or Myth? (Washington, DC: Regnery, 2000). Used with permission.
To their credit, some evolutionary biologists acknowledge that vertebrate embryos begin development differently, but then they claim that embryos pass through a highly similar midpoint stage, called the “pharyngular” or “phylotypic” or “tailbud” stage. They propose an “hourglass model,” where this converging midpoint stage of development reveals common ancestry (Fig. 11.5).
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FIGURE 11.5. The “hourglass” model of embryo development, where vertebrate embryos start development differently, but are said to appear somewhat similar at a midpoint in development. CREDIT: Copyright Jody F. Sjogren 2000, as used in figure 5-4, Jonathan Wells, Icons of Evolution: Science or Myth? (Washington, DC: Regnery, 2000). Used with permission.
Prominent atheist and developmental biologist P. Z. Myers named his popular blog “Pharyngula,” where he has argued that “[v]ertebrate embryos at the phylotypic or pharyngula stage do show substantial similarities to one another that are evidence of common descent. That’s simply a fact.” 107 But does this pharyngula stage exist? In a groundbreaking study published in Anatomy and Embryology, a team of embryologists investigated this question and noted, “It is almost as though the phylotypic stage is regarded as a biological concept for which no proof is needed.” 108 After photographing vertebrate embryos during this purportedly similar stage, they found differences in major traits, including body size, body plan, growth patterns, and timing of development. They conclude the evidence is “[c]ontrary to the evolutionary hourglass model,” because vertebrate embryos show “considerable variability” during “the purported phylotypic stage.” In their view, this “wide variation in morphology among vertebrate embryos is difficult to reconcile with the idea of a phylogenetically-conserved tailbud stage.” 109 Likewise, a study in Proceedings of the Royal Society of London B found that embryological data is “counter to the predictions” of the phylotypic stage, since “phenotypic variation between species was highest in the middle of the developmental sequence.” It noted that a “surprising degree of developmental character independence argues against the existence of a phylotypic stage in vertebrates.” 110
Even P. Z. Myers has conceded that early vertebrate embryos can “vary greatly” 111 and that “there is wide variation in the status of the embryo.” 112 But, he tried to explain why these facts pose no challenge to common ancestry: “I wish I could get that one thought into these guys’ heads,” he wrote. “[E]volutionary theory predicts differences as well as similarities.” 113 That’s intriguing. Earlier, Myers cited the “substantial similarities” between vertebrate embryos as “evidence of common descent.” But later, when forced to admit the “wide variation” among embryos, he argued that “evolutionary theory predicts differences” too. Perhaps so, but then how can he cite the “similarities” among embryos in the pharyngula stage as evidence for common ancestry? In reality, Myers’s comments reflect the fact that, in practice, evolutionary theory predicts whatever it finds. In other words, common ancestry predicts nothing. Myers’s logic might help common descent avoid falsification, but it doesn’t construct a robust model that makes testable predictions. It seems we’re back to common ancestry predicts similarities except for when it doesn’t. As the old adage says, “the theory which explains everything really explains nothing.”
III. What’s Left of the “Congruence” Argument for Universal Common Ancestry?
At the beginning of this chapter, we noted that the case for common descent is often said to be “cumulative,” based on multiple lines of evidence including biogeography, fossils, DNA and anatomy, and embryology. How is the theory faring? In biogeography, evolutionists resort to unlikely and speculative explanations where species must raft across vast oceans in order for common descent to account for their unexpected locations. Paleontology fails to reveal the continuous branching pattern predicted by common ancestry, and the fossil record is dominated by abrupt explosions of new life-forms. Regarding molecular and morphology-based trees, conflicting phylogenies have left the “tree of life” in tatters. Phylogenetic methods are reduced to predicting that shared similarity indicates common inheritance, except for when it doesn’t. Similar problems confound embryology, where evolutionary biologists predict similarities will exist between vertebrate embryos, except for when we find differences, and then it predicts those too. Much data contradicts the sometimes-made predictions of common descent, but what, if anything, does evolutionary biology actually predict?
As P. Z. Myers has shown us, common descent seems to predict whatever is expedient. If there’s any clear pattern here, it’s this: the data often fails to fit the predictions of universal common descent, but when that happens, proponents of common descent simply change their predictions. This raises the question of the scientific status of common descent. At best, it’s a scientific theory that is contradicted by much evidence. At worst, it’s not even a scientific theory that makes concrete, testable predictions. For these and many other reasons, even some mainstream evolutionary scientists are becoming increasingly skeptical of universal common ancestry and the “monophyly” of life.114 A 2009 paper in Trends in Genetics noted that breakdowns in core neo-Darwinian tenets like the “traditional concept of the tree of life,” or that “natural selection is the main driving force of evolution,” indicate “the modern synthesis has crumbled, apparently, beyond repair.” 115 A 2012 paper in Annual Review of Genetics explicitly doubted universal common ancestry, suggesting, “life might indeed have multiple origins.” 116 Another paper in Biology Direct noted that the “sudden emergence” of new complex life forms contradicts a “tree pattern”:
Major transitions in biological evolution show the same pattern of sudden emergence of diverse forms at a new level of complexity. The relationships between major groups within an emergent new class of biological entities are hard to decipher and do not seem to fit the tree pattern that, following Darwin’s original proposal, remains the dominant description of biological evolution. 117
To be sure, these authors support some form of unguided materialistic evolution. But the precise reason that they are critiquing the classical evolutionary model is that much data contradicts universal common ancestry. Twenty-first-century biology seems to be following the evidence beyond universal common ancestry and the neo-Darwinian “tree of life.” Our friends in the theistic evolution community would be wise to follow suit—or at least to tone down their rhetoric against reasonable skeptics of universal common ancestry
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