Exploring the Origin of Evolutionary Novelties with James Valentine
![]() Ediacaran fossils Dickinsonia and Parvancorina. Photo by Gregory Retallack
by Fred Heeren
I thought I had pretty much figured out how to relate Intelligent Design to observable science—until I talked with distinguished Berkeley paleobiologist James Valentine, author of On the Origin of Phyla. The discovery of “top-down evolution,” I hoped for several months, might contribute to the harmonization of science and faith. I chose the title “Top-down Evolution” for a talk I did at the 2004 “Intelligent Design & the Future of Science” conference at Biola University. But it wasn’t until months after my interview with Valentine, while studying the transcript, that I let his words sink in. Until then, I confess—and this is a truly awful confession—I could only see Valentine’s supportive statements and was virtually blind to his less supportive ones regarding my conception of “top-down evolution.” In my zeal for ID, I might be justly accused of cherry picking a few of the most supportive excerpts from that interview. And I did this even while my zeal for ID was waning; I closed the talk by asking: “Should Fred Heeren be kicked out of the ID movement?”—and I gave five reasons why I should be allowed to stay in, followed by six reasons why I should be kicked out. Being a good sport, Bill Dembski then stood up and refuted each of my reasons for being kicked out—he would apparently allow me to stay in, if I wanted. The “top-down” notion at issue here began with an obscure quote that evolution critics had picked up from an article Valentine co-wrote for the journal Evolution in 1987. Paleobiologists Erwin, Valentine, and Sepkoski wrote: “Most higher taxa were built from the top down rather than from bottom up. 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.” A “top-down” appearance of disparate body plans preceding the diversity of lower groups can be taken to suggest the unfolding of God’s predetermined designs. Big changes come first, small refinements later. So what’s not to like, if you’re an ID fan? The time-ordered sequence of higher taxa, such as phyla and classes, before lower taxa, such as orders and families, contradicts the Darwinian picture of a slow buildup starting with lowest taxonomic groups, such as varieties and species. However, Christians quoting the paper deleted the following from the above excerpt, replacing it with ellipses, as I did above: “This is not to say that higher taxa originated before species (each phylum, class, or order contained at least one species, genus, family, etc. upon appearance)….” My first reading of the excerpt by others who had omitted this portion was the thing that had initially excited me about the possibilities for top-down evolution. In their efforts to use the experts to promote creation and Creator, some had quote mined them, at worst, and misunderstood them, at best. I did no better in my talk, quoting a few of Valentine’s statements that supported my version of this top-down idea. After all, in our interview, Valentine did tell me: “You get the higher groups coming in first, and then they diversify into lower groups.” But he added, and I neglected to include, “Because of the way we classify stuff, it appears that the phylum comes in first, which in a way is true. I mean, the basic body plan has to be there before it can diversify into sub-plans.” What a scientific disappointment that would be if God did include Solomon’s nature notes. They’d obviously be obsolete by now because science—human knowledge of our natural world—is cumulative; it grows because we’re constantly building on top of the findings of earlier scientists. If God revealed science, it wouldn’t be science—it would be revelation; it wouldn’t be our systematic arranging of human knowledge—it would be His.
![]() Fossil of Kimberella quadrata
The kindest thing I can say to evolution critics and to my past self is that both these concepts are true: top-down and bottom-up patterns are both observed in the fossil record. The Linnaean system of classification forces us to look at higher and lower groups within groups, so that if we choose to assign a higher taxon to an organism at its earliest appearance in the fossil record—as we do with the earliest organisms we find in the Cambrian period—we will observe a top-down pattern from that point on. We’d get a different picture if we thought of those animals as species, or if we had the full picture of the organisms that preceded them. So Valentine told me, “The phyla come in first, and then the classes,” but he didn’t assume that these were created ex nihilo, because he added: “But there must have been a buildup, right? They didn’t jump from nothing.” In fact, he then went on to describe the increasing information we’re getting about their progenitors in the Precambrian: both trace fossils and body fossils. The traces are horizontal squiggles, about a millimeter wide, on sediments that first appear about 580 million years ago. I’d seen these myself at a locale in Weng’an, southern China. These trails of tiny worms become larger, “into the centimeter range,” at the base of the Cambrian, 543 million years ago. At that point, the wrigglers begin leaving deeper traces showing that they burrowed down, causing bioturbation of the sediments. Other invertebrate specialists note the appearance of more precursors before the Cambrian. Kansas State geologist Keith Miller writes: “The earliest known mollusk-like organism is Kimberella from the late Neoproterozoic Ediacaran [the last geologic subdivision before the start of the Cambrian]. It is a primitive organism that appears to lack several features characteristic of modern mollusks and is thus considered a stem mollusk. The first likely ‘crown group’ mollusks appear in the earliest Cambrian as part of the ‘small shelly fauna.’ …. The characters that we use to identify ‘clams’ did not appear as a complete package, but were acquired over time.” Concerning the claimed “top-down” pattern, Miller calls it “an artifact, being generated by the way in which species are assigned to higher taxa. The classification system is hierarchical with species being grouped into ever larger and more inclusive categories. When this classification hierarchy is applied to a diversifying evolutionary tree, a ‘top-down’ pattern will automatically result.” Before the Cambrian, Valentine identifies his worm-like animals as “basal bilaterians among the crown, surviving phyla.” And they “have all the genes necessary to run the architectures of their descendant phyla.” Wow, that looks like a great quote to demonstrate pre-specification. But when he explains what he means by this, it turns out to be a less convincing argument for design—but it is his key to the origin of novelties. It’s not supernatural intervention, but neither is it speciation, in the Darwinian sense of imperceptible, gradual change—or in the neo-Darwinian sense of population genetics. I asked Valentine if the top-down pattern is what Darwinian natural selection would predict. “I think Darwin expected it to be built up, like you say, by species,” he said. “It’s still selection that’s working on these genes. The genes don’t work like population genetic genes do, because one key developmental gene might have two hundred genes downstream of it—so you change the timing and the expression of that gene, and you’ve changed the timing and the expression of hundreds of other genes, all at once. So that one mutation changes the whole thing. And it makes it possible to get places very fast.” Shifting all those genes around, helter-skelter, sounds like a messy way to change an animal—you’d hardly ever get something that works. But Valentine clarified: “After sponges, everyone has about the same genes. But they’re used differently; that is, they’re expressed to control different cascades of gene expression. So the difference in the architectures of the major body plans is really a difference in the pattern of expression of the same genes.” Eventually, I realized that if this is what those researchers at the molecular benches were actually finding, it would go a long way toward explaining how the Cambrian explosion happened relatively quickly. But then why do paleontologists seldom find new body plans beyond those 35-or-so new Cambrian phyla in all the ages since? Might these animals become so genetically complex that innovation at that high level ceases to be possible? Valentine said he had published that view. But “Now I believe the opposite. Look at how quick you can make a dinosaur. I mean, in just nothing flat, the world is full of dinosaurs, and the dinosaurs go away, and the mammals come in, really fast. There doesn’t seem to have been any locking up of the genetic systems.” He spoke of regulatory genes controlling other regulatory genes, explaining that all these complex units can be shuffled intact, set off by the mutation of a single gene. “So the architecture of developmental genetics is incredibly flexible.” But still, why don’t we continue to see new body plans appearing long after the Cambrian? “I think the world is filled up, so to speak,” said Valentine. “All the major adaptive zones were invaded…. If you get any openings, like if you get an extinction wave, you’ve got plenty of organisms around with lots of body plans and functional approaches—so you don’t need to start over and build a while new phylum from scratch. A branch just comes off some phylum that’s already functionally near this open space, and fills it in. So there’s no reason to generate any more body plans.” So what does Valentine conclude about evolutionary innovations? From his knowledge of invertebrate fossils, Valentine said it’s clear that “the origin of these higher groups isn’t driven by speciation. It isn’t just the expansion of morphospace by the addition of species. It’s changes in the developmental program that create the new body plans. And that can be pretty fast, because you don’t have to worry about getting genes sequentially. The genes are all the same, as far as development goes, right through the metazoan.” It wasn’t speciation? So Darwin was wrong? Only in the sense that he obviously had no knowledge of “cis regulation”—or of genes at all. But when we ask what causes one innovation to “stick” over another, Valentine says that Darwin’s great insight is the correct answer: “Oh, I think it’s all just natural selection. But it’s working on the developmental system rather than on some gene that only determines how many hairs on a fruit fly or some [tiny change] like that.” So, Christians might want to know, what does any of this have to do with the Bible? We can answer: Absolutely nothing. The Bible, most ASA folk would say, is not a science book. However, the Bible does speak positively about the practice of science. Kings 4 depicts Solomon’s great breadth of studies, including how “He described plant life, from the cedar of Lebanon to the hyssop that grows out of walls. He also taught about animals and birds, reptiles and fish” (4:33). The fact that these findings are lost to us means that God did not devote Bible pages to things we can learn for ourselves. What a scientific disappointment that would be if God did include Solomon’s nature notes. They’d obviously be obsolete by now because science—human knowledge of our natural world—is cumulative; it grows because we’re constantly building on top of the findings of earlier scientists. If God revealed science, it wouldn’t be science—it would be revelation; it wouldn’t be our systematic arranging of human knowledge—it would be His. But God must think that the human pursuit of knowledge of his world is a regal calling. He leads us to ask: What could be nobler than to search out the mysteries He has planted all around us? “It is the glory of God to conceal a matter, but the glory of kings is to search out a matter” (Prov. 25:2). “God’s works,” the Psalmist tells us, “are studied by all who delight in them” (Psalm 111:2). The Bible authors had the privilege of experiencing revelation; we have the privilege of experiencing investigation. How wrongheaded it is when any of us decide that our inquiries have to be biased in order to represent the One who is the Truth! |