The Cambrian Explosion and the Combinatorial Problem
by Stephen C. Meyer
We count on scientists to tell us what they know and don’t know—not just what they want us to hear. But when it comes to the contentious issue of the evolution of life on earth, spokesmen for official science are often less forthcoming than we might wish.
When writing in scientific journals, leading biologists candidly discuss the many scientific difficulties facing contemporary versions of Darwin’s theory. Yet when scientists take up the public defense of Darwinism—in educational policy statements, textbooks, or public television documentaries—that candor often disappears behind a rhetorical curtain. “There’s a feeling in biology that scientists should keep their dirty laundry hidden,” says theoretical biologist Danny Hillis, adding that “there’s a strong school of thought in biology that one should never question Darwin in public.”
The reticence that Darwin’s present day defenders feel about criticizing evolutionary theory would have likely made Charles Darwin uncomfortable. In the Origin of Species, Darwin openly acknowledged important weaknesses in his theory and professed his own doubts about key aspects of it.
In the Origin, Darwin expressed a key doubt about the ability of his theory to explain one particular event in the history of life, an event known as the Cambrian explosion. I’ve recently written a book, Darwin’s Doubt, about this in which I argue that the problem Darwin identified not only remains to this day, but that it has grown up to illustrate a more fundamental conceptual difficulty than he could have understood—a problem for all of evolutionary biology that points to the need for an entirely different understanding of the origin of animal life on Earth.
Darwin was puzzled by a pattern in the fossil record that seemed to document the sudden appearance of animal life in a remote period of the Earth’s history, now known as the Cambrian. Many new and anatomically complex creatures—such as trilobites with their compound eyes and articulated exoskeletons—appear suddenly in the sedimentary layers associated with this period without any evidence of simpler ancestral forms in the earlier layers below.
The sudden appearance of animals so early in the fossil record did not easily accord with Darwin’s picture of slow evolutionary change. Indeed, Darwin had depicted the history of life as a gradually unfolding branching tree. Thus, as Darwin envisioned it, complex animals such as trilobites, for instance, would have arisen from a series of simpler precursors and intermediate forms over vast stretches of geologic time. Yet, Darwin knew that the Precambrian fossil record shows no such thing.
Darwin frankly expressed his puzzlement in the Origin of Species about this mysterious event. “The difficulty of assigning any good reason for the absence of vast piles of strata rich in fossils beneath the Cambrian system is very great,” he wrote. “The case at present must remain inexplicable; and may be truly urged as a valid argument against the views here entertained.”
Of course, Darwin hoped that numerous transitional forms would be discovered in the Precambrian fossil record and the mystery would be solved. But scientists have combed Precambrian strata worldwide for 150 years, and they still haven’t found the wealth of evolutionary ancestors that Darwin expected.
Nevertheless, there is a second, and arguably deeper, mystery associated with the Cambrian explosion: the mystery of how the neo-Darwinian mechanism of natural selection and random mutation could have given rise to all these fundamentally new forms of animal life, and done so quickly enough to account for the pattern in the fossil record. That question became acute in the second half of the twentieth century as biologists learned more about what it takes to build an animal.
In 1953 when Watson and Crick elucidated the structure of the DNA molecule, they made a startling discovery, namely, its ability 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. 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 information. As Richard Dawkins has acknowledged, “the machine code of the genes is uncannily computer-like.” Or as Bill Gates has noted, “DNA is like a computer program, but far, far more advanced than any software ever created.”
The Cambrian period is marked by an explosion of new animals exemplifying new body plans. But building new animal body plans requires new organs, tissues, and cell types. And new cell types require many kinds of specialized or dedicated proteins (e.g., animals with gut cells require new digestive enzymes). But building each protein 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. Whatever happened during the Cambrian not only represented an explosion of new biological form, but it also required an explosion of new biological information.
Is it plausible that the neo-Darwinian mechanism of natural selection acting on random mutations in DNA could produce the highly specificarrangements of bases in DNA necessary to generate the protein building blocks of new cell types and novel forms of life?
According to 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, the resulting genetic changes are passed on to the next generation. As such changes accumulate, the features of a population change over time. Nevertheless, natural selection can only “select” what random mutations first generate. Thus the neo-Darwinian mechanism faces a kind of needle-in-the-haystack problem—or what mathematicians call a “combinatorial” problem. The term “combinatorial” refers to the number of possible ways that a set of objects can be arranged or combined. Many simple bike locks, for example, have four dials with 10 digits on each dial. A bike thief encountering one of these locks faces a combinatorial problem because there are 10 × 10 × 10 × 10, or 10,000 possible combinations and only one that will open the lock. A random search is unlikely to yield the correct combination unless the thief has plenty of time.
Similarly, it is extremely difficult to assemble a new information-bearing gene or protein by the natural selection/random mutation process because of the sheer number of possible sequences. As the length of the required gene or protein grows, the number of possible base or amino-acid sequences of that length grows exponentially.
Here’s an illustration that may help make the problem clear. Imagine that we encounter a committed bike thief who is willing to search the “sequence space” of possible bike combinations at a rate of about one new combination per two seconds. If our hypothetical bike thief had three hours and took no breaks he could generate more than half (about 5,400) of the 10,000 total combinations of a four-dial lock. In that case, the probability that he will stumble upon the right combination exceeds the probability that he will fail. More likely than not, he will open the lock by chance.
But now consider another case. If that thief with the same limited three hour time period available to him confronted a lock with ten dials and ten digits per dial (a lock with ten billion possible combinations) he would now have time only to explore a small fraction of the possible combinations—5,400 of ten billion—far fewer than half. In this case, it would be much more likely than not that he would fail to open the lock by chance.
These examples suggest that 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.
In Darwin’s Doubt, I show that the number of possible DNA and amino acid sequences that need to be searched by the evolutionary process dwarfs the time available for such a search—even taking into account evolutionary deep time. Molecular biologists have long understood that the size of the “sequence space” of possible nucleotide bases and amino acids (the number of possible combinations) is extremely large. Moreover, recent experiments in molecular biology and protein science have established that functional genes and proteins are extremely rare within these huge combinatorial spaces of possible arrangements. There are vastly more ways of arranging nucleotide bases that result in non-functional sequences of DNA, and vastly more ways of arranging amino acids that result in non-functional amino-acid chains, than there are corresponding functionalgenes or proteins. One recent experimentally derived estimate places that ratio—the size of the haystack in relation to the needle—at 1077non-functional sequences for every functional gene or protein. (There are only something like 1065 atoms in our galaxy.)
All this suggests that the mutation and selection mechanism would only have enough time in the entire multi-billion year history of life on Earth to 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. 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. Thus, the neo-Darwinian mechanism, with its reliance on random mutation, is much more likely to fail than to succeed in generating even a single new gene or protein in the known history of life on earth. In other words, the neo-Darwinian mechanism is not an adequate mechanism to generate the information necessary to produce even a single new protein, let alone a whole new Cambrian animal.
Could this problem with neo-Darwinian theory point instead to a different type of cause? Do we know of any other kind of entity that has the power to create large amounts of functional or digital information? We do. As information scientist Henry Quastler recognized, the “creation of new information is habitually associated with conscious activity”—in other words, the work of intelligent agents. A computer user who traces the information on a screen back to its source invariably comes to the mind of a software engineer or programmer. The information in a book or newspaper column ultimately derives from a writer—from a mental, rather than a strictly material, cause.
Scientists working to identify the causes of events in the remote past often use a technique of reasoning called “the method of multiple working hypotheses” or “inference to the best explanation.” That is, they compare various hypotheses to see which would, if true, best explain the facts. But this raises an important question: Exactly what makes an explanation best?
The most important criteria scientists have developed, called “causal adequacy,” requires that scientists, as a condition of a successful explanation, identify causes that are known to have the power to produce the kind of effect, feature, or event that requires explanation. For instance, a volcanic eruption provides a better explanation for an ash layer in the earth than an earthquake because eruptions have been observed to produce ash layers, whereas earthquakes have not.
Scientists must cite, in the words of the famed geologist Charles Lyell, “causes now in operation” or “presently acting causes.” This was the idea behind his uniformitarian dictum: “The present is the key to the past.” According to Lyell, our present experience of cause and effect should guide our reasoning about the causes of past events. Darwin himself adopted this methodological principle and used it to develop his case in the Origin.
Philosophers of science have also emphasized causal adequacy as the key criterion by which competing hypotheses are adjudicated. But philosophers of science also have noted that assessments of explanatory power lead to conclusive inferences only when it can be shown that there is only one known cause for the effect or evidence in question. When scientists can infer a uniquely plausible cause, they can avoid the logical fallacy of affirming the consequent—the error of ignoring other possible causes with the power to produce the same effect.
In Darwin’s Doubt, I argue that it is possible to formulate a rigorous scientific case for intelligent design as an inference to the best explanation, specifically, as the best explanation for the origin of functional biological information. In the book, I show (for many reasons, not just those discussed above) that materialistic evolutionary mechanisms lack the creative power to generate both the genetic and the “epigenetic” information (the information not stored in DNA) necessary to produce new forms of animal life. But this critique of the “causal adequacy” of materialistic evolutionary mechanisms forms only part of the basis for a scientific inference to intelligent design. The action of conscious, intelligent agents clearly represents a known and “presently acting” (adequate) cause of the origin of functional information. Moreover, experience shows that large amounts of functional information—whether software programs, ancient inscriptions, or Shakespearean sonnets—invariably originate from an intelligent source, not from undirected material processes. And since intelligence is the only known cause of such information, the origin of the functional information necessary to produce novel forms of animal life in the Cambrian period points decisively to the past activity of a designing intelligence, even if we weren’t there to observe the first animals coming into existence.
Of course, many scientists dismiss intelligent design as “religion masquerading as science.” But the case for intelligent design is not based upon religious or scriptural authority. Instead it is based upon scientific evidence and the same method of scientific reasoning that Darwin himself used in the Origin of Species.
In rejecting the theory as unscientific by definition, evolutionary biologists reveal a deep a priori commitment to methodological naturalism—the idea that scientists must limit themselves to materialistic explanations for all things. Yet, we know from experience that certain types of events and structures—in particular, information-rich structures—invariably arise from minds or personal agents. Indeed, no thinking person would insist that the inscriptions on the Rosetta stone, for example, were produced by strictly materialistic forces such as wind and erosion. Yet, by insisting that all events in the history of life must be explained by reference to strictly materialistic processes evolutionary biologists preclude consideration of a designing intelligence in the history of life, regardless of what the evidence might indicate.
This commitment to a wholly materialistic account of the origins of life also helps to explain the reluctance to criticize the Darwinian theory publicly. Many evolutionary biologists fear that if they do so they will aid and abet the case for intelligent design—a theory they disdain as inherently unscientific. Those of us who support the theory of intelligent design advocate a more open approach to scientific investigation. Not only do we think the public has a right to know about the problems with evolutionary theory, we also think that the rules of science should allow scientists to “follow the evidence wherever it leads”—even if it leads to conclusions that raise deep and unwelcome metaphysical questions.
Occasionalism Isn’t Science
by John Derbyshire
Why can't the purveyors of intelligent design get a break? They have been plowing their lonely furrow for 20 years now, insisting on their right to a seat at science’s banquet and promising that their ideas will bring about a revolutionary overthrow of orthodox biology (which they call “Darwinism” for propagandistic reasons) Any Day Now. They drop heavy hints that biologists are in a panic about the instability of their foundational theories, but are anxious to hide their doubts from public gaze.
Really? One would naturally like to see some illustrative examples. Twenty years on from the inception of ID, the revolution seems as far away as ever. The ID-ers are still shut outside the banquet with their noses pressed forlornly to the window, and the ancien régime looks to be as firmly established as ever. What’s the problem here?
The least charitable skeptics accuse ID promoters of running a racket, taking part in the grand old American tradition of fleecing the rubes. (As the immortal Al Bundy told his acolytes while winding up for his sermon at the Church of NO MA’AM: “Now it’s time to eece-flay the ongregation-cay.”) I’m a cynic, but not that much of a cynic. I have engaged in formal debate on Intelligent Design on three or four occasions. I once spent an hour in a room full of principals from the Discovery Institute (DI). They struck me as persons who believe in what they are selling. The Charity Navigator website lists their total 2011 revenues as $5.7 million, which is not a lot. The executives, according to that same website, are not extravagantly paid.
A related accusation with much more force is that some ID-ers are dishonest in advancing their aims. This was a running theme in the 2004 book Creationism’s Trojan Horse: The Wedge of Intelligent Design, by Barbara Forrest and Paul Gross. You can get the flavor of the shenanigans from Forrest and Gross’s account, in their Chapter 4, of the 1999 Kunming conference, to which respectable scientists were lured under false pretenses:
According to scientists who attended the Kunming conference, the involvement of the DI in the conference became known only after the conference began…It was during the presentations by [DI Fellows] Wells and Nelson, when the conference was at an end, that [quoting a participating scientist] “the broader agenda of what was going on was apparent”…
(At the aforementioned meeting with DI principals I placed a copy of the Forrest-Gross book in plain sight on the desk in front of me. Seeing it, DI President Bruce Chapman reacted like a vampire to garlic. “That is a very bad book,” he shuddered.)
That brings us to the question of whether ID is really science, as its proponents claim, or pseudoscience, as practically all scientists believe. To form a judgment on that, you need to have some clear criteria for distinguishing science from pseudoscience. That is much harder than you’d think. It may in fact be impossible.
Here we are in the thorny wood known to philosophy of science as “the Demarcation Problem.” This problem—more broadly, the problem of distinguishing true knowledge from opinion, illusion, fancy, and wishful thinking—has vexed philosophers of knowledge since Aristotle. My impression is that they have now finally given up on it. Is astrology, for example, a science or a pseudoscience? What about Freudianism? Or chemistry? Or Newtonian action-at-a-distance? We think we know the answers—replicability! falsifiability! predictive power!—but in fact there are arguments to be made on both sides in all cases.
Even if you fall back on a purely social judgment—that science is what respectable authorities recognize as science, what gets you professorships and seats on prestigious government advisory committees—you are stuck with explaining Lysenkoism, which, though pure hokum, was surely science on that social definition (as, indeed, in that same environment, was Marxism).
So why can't the ID-ers get any respect? All we have so far is a certain promotional shiftiness.
Socially, the tribal-sectional factor is undoubtedly important. I shall draw here on an anonymous analyst who described the present-day United States as: “a country which is essentially divided between two hostile tribes engaged in perpetual low-intensity warfare. We’ll call them Hutus and Tutsis.”
Let’s also say that one tribe, Tutsis, holds a hegemony on all organs of education and opinion, virtually the entire government bureaucracy and all of popular culture. Many of the most prestigious institutions in the country consist of 95 percent or more Tutsis. Tutsi organizations like “Harvard University” and “the New York Times” are widely respected even by ardent Hutus.
Now of course there are Hutu organizations and no shortage of powerful Hutu people. But, unlike the reverse, there are virtually no prestigious institutions where Tutsis are excluded…
In this schema, ID is definitely Hutu by dint of its plain connections with the older style of fundamentalist Creationism. That older style is wellnigh a badge of Hutu-itude, a tribal marker of exceptional precision. Ain’t no pointy-head perfesser goin’ tell ME I’m descended from no monkey! Pass the likker jug there, Lud. Tutsis can thus scoff at ID as ignorant, rustic, and low-rent, without bothering to engage with its arguments. That’s a bit unfair, as ID promoters nowadays run more to sharp business suits and postgraduate degrees than (to borrow a Hutu characterization from Tom Wolfe) “Iron Boy overalls…or hats with ventilation holes up near the crown.”
The line of descent from old-school Creationism to ID is in plain sight, though, identifying ID with fundamentalist Christianity. (ID is in fact even more closely allied to fundamentalist Islam, but nobody notices that. More on this topic in a moment.) Christian fundamentalism is of course Hutu, and likely getting more so.
Through its first decade of activity the American ID movement conducted a dainty dance with its religious inspiration, keeping it as much out of sight as possible in hopes of winning one of the recurrent lawsuits over the teaching of ID in public schools.
Thus ID-ers, in debate, were always at pains to tell you that the Designer was by no means to be identified with the God of the Abrahamic religions. It might equally well be a space alien! They even had an avowedly irreligious non-Christian on board, like one of the tame Tibetan lamas the Chinese communists keep on hand for display to foreign visitors.
The 2005 Kitzmiller case killed stone dead the possibility of getting ID into the public schools, as well as revealing, in the Discovery Institute’s character attacks on the presiding judge, yet more of the crude low-kicking side of ID promotion.
The net effect of Kitzmiller was beneficial, though. ID-ers are now more relaxed about admitting their religious connections—a slight but welcome increase in honesty. After Kitzmiller, ID-ers don’t have to lie so much.
It is the religious aspect that causes most scientists to shy away from ID. Not that scientists all hate God. Many of them are devout. Of the non-devout, most are just indifferent to religion. Actual God-haters like P.Z. Myers are a minority.
No, it’s not hatred of God that keeps ID shut out from the halls of science. The problem is more deeply metaphysical.
The metaphysics of ID is occasionalist. It holds, to abbreviate the doctrine rather drastically, that causation is an illusion; that everything happens because God makes it happen.
Why does ice float on water? Aristotle thought it was a matter of shape (see On the Heavens, IV.6). Science says it’s because ice is less dense than water. The occasionalist says it’s because God wills it so.
ID-ers likewise believe that any given species exists because the Designer wants it to, and came into existence by His will ex nihilo at some precise moment in time. Unkind critics refer to this as the Puff of Orange Smoke theory of the origin of species.
Scientists are instinctively repelled by occasionalism because it doesn’t give them anything to do. If ice floats because it’s less dense than water, all sorts of questions and embryonic research projects bob to the surface (so to speak) of the curious mind. Do all less-dense-than-water objects float? Do those more dense necessarily sink? Why is ice, water’s solid form, less dense than the liquid form? Are there more substances with this property? Do they have other properties in common with water? Etc., etc. Science generates science, opening up new questions, new topics for inquiry, new problems. That’s the fun of it. That’s the point of it.
But: Ice floats on water because God wills it so? Oh.
It is possible, at a stretch (see below), to think up research projects based on an occasionalist approach to the origin of species, but the usual and natural human response to an occasionalist metaphysic is a passive sigh of insh’allah. This whole cast of mind is repulsive to the spirit of scientific curiosity.
Occasionalism should not be confused with the wind-it-up-and-let-it-go deism of (for example) Leibniz. The occasionalist Designer is very busy indeed, all the time, creating new genes and adaptations and body types.
And yes, occasionalism is the metaphysical position favored by Islam. Hence the near-invisibility of Muslims in the lists of Nobel prizewinners for the sciences. (Chemistry 1 out of 166; Physics 1 out of 196; Medicine 0 out of 204.) Luxembourg, population 500,000, has as many science Nobels as Islamia, population 1.6 billion. Go occasionalism!
Resisting occasionalism's pull toward passive fatalism, one can think of questions raised by an occasionalist approach to the origin of species, questions that might generate research projects.
For example: When the Designer decides to create a new species that will be sexually reproducing, does He create one male and one female simultaneously? Or, for some genetic variety, many males but only one female? Or, for even more genetic variety, many of each sex? Thence to the oldest question of all: If the new species belongs to the higher orders of mammals, do they have belly-buttons?
Or, in the Newtonian spirit of understanding the Designer’s mind, one might ask whether there is any discernable pattern to the creation of new species. Any hypotheses as to why the rates of creation prior and subsequent to the Cambrian explosion seem to be so much less? Why is the rate irregular, rather than steady?
Some close work in genomics, perhaps supplemented with fortuitous finds in the fossil record, should be able to shed light on topics like this. ID-ers, however, do not seem interested in pursuing such research.
Why would they? If there is a naturalistic path from gene A to gene B, it would be interesting to try to figure it out and see if it explains other phenomena. If, on the other hand, the Designer one day decides to increase the information content of the universe by changing gene A into gene B, there is no path to be discovered. It is hardly surprising, then, that so far as I can ascertain ID has no research programs at all.
Nor do the proponents typically offer any speculative-imaginative theories as to the circumstances under which new species appear. The puff of orange smoke is of course meant facetiously; but what do ID-ers think actually happens when a new species appears, at some actual moment in time, at some actual point on the earth’s surface? I have never seen any of them address this point.
There hangs over the whole enterprise the atmosphere of the barstool crank, who wants to repeat to you over and over the one and only idea in his head, an idea that leads nowhere, to nothing interesting. Faced with a careful, reasoned refutation, he just repeats what he said before. Zzzzzzzz.
That is one aspect of a larger issue: ID-ers don’t behave like scientists. Given the above-mentioned fuzziness about what science actually is, it’s imprecise to say “they don’t do science,” but they sure don’t do it the way most scientists do it most of the time.
ID is an entirely negative critique of modern biology. That can, at a stretch, count as scientific endeavor—Professor Jeffrey L. Kasser has words to say about that in his Great Course lectures on the Philosophy of Science—but it’s not how most science is done. This applies even to ID-ers like Michael Behe who are themselves working scientists. From an earlier article of mine on this point:
Kenneth R. Miller, a professor of biology at Brown University and a critic of ID, wonders why Behe has never presented his ideas to the annual conference of the American Society for Biochemistry and Molecular Biology, as is his right as a member. As Miller explained, “If I thought I had an idea that would completely revolutionize cell biology in the same way that Professor Behe thinks he has an idea that would revolutionize biochemistry, I would be talking about that idea at every single meeting of my peers I could possibly get to.”
You sometimes hear from ID-ers that they can’t get their ideas into the scientific arena because orthodox biology is a closed guild fearful of revolutionary innovations. There are a number of ripostes one can make:
• You should at least try, as ID-ers like Behe obviously haven’t.
• A settled body of theory like modern biology, supported by masses of data painstakingly accumulated across a century or more, should be skeptical of revolutionary ideas, and demand that they offer a high standard of proof.
• When they do so, they are accepted. Ask Alfred Wegener, Albert Einstein, or, for that matter, Charles Darwin! If this were not the case, there would be no science.
• Ambitious young scientists dream of overturning established theories. It’s a way to lasting fame. See previous point.
All of which is a shame, because there are important gaps in our understanding of the world that ID, if it didn’t waste its time on far-fetched critiques of well-settled scientific topics, might have something to say about.
Last week I registered for the April 2014 Towards a Science of Consciousness conference at the University of Arizona in Tucson. It should be a fun week, with presentations on (to quote the website) “neuroscience, psychology, philosophy, cognitive science, artificial intelligence, molecular biology, medicine, quantum physics, and cosmology as well as art, technology, and experiential and contemplative approaches.”
I attended the 2008 conference. Keeping tabs on the topic, it seems that progress in putting together a science of consciousness is awful slow; but I figured that after six years it might be worth attending again.
The problem of Mind has vexed philosophers for at least as long as the Demarcation Problem. Is Mind a part of nature, or outside nature? Since the only minds we know of are intimately attached to brains—organs with a fairly well-understood phylogeny and ontogeny—it seems that a naturalistic explanation of Mind ought to be forthcoming, but no-one has come up with one that has received general acceptance.
So the question is open, and for all we know it may be that Mind is outside nature. In that case, the kinds of interactions between Mind and nature that ID talks about can’t be ruled out.
This doesn’t seem to me intuitively very likely. Nor can I see how working biologists at present have any way to advance their understanding than through naturalistic enquiries, making their nonacceptance of ID perfectly reasonable. ID’s occasionalism offers them no research program, and ID, as I have noted, has none itself.
However, Mind is an extremely odd business, and my intuitions are merely those of some guy with a laptop.
If there is any hope of understanding conscious experience and intentional intelligence, I’d bet 99 of my hundred dollars on the guys at Tucson to fulfill that hope, and only one on Intelligent Design. Hardly an endorsement; but one is not zero.