There has been much hullabaloo lately regarding a new paper published by a team of researchers, led by Associate Professor Michael Lee of the University of Adelaide, claiming that the abrupt appearance of dozens of animal groups in the early Cambrian period is no great mystery: rates of both morphological and genetic evolution were five times faster than today, that’s all. According to the paper, these rates “are still consistent with evolution by natural selection…, potentially resolving ‘Darwin’s dilemma.'” Are they right?
The authors of the paper, Michael Lee, Julien Soubrier and Gregory Edgecombe, attempted to measure the rate of evolution at two levels: the phenotypic level (which mostly relates to changes in an organism’s form and structure) and the molecular level (which relates to genetic changes in organisms). I was curious to see how the authors of the paper had actually measured the rate of phenotypic and molecular evolution during the Cambrian explosion. Here’s what I found in the paper:
Arthropods are the exemplar group for investigating questions about such macroevolutionary rates and patterns. They are the most abundant and diverse phylum in the early Paleozoic, have very complex preserved morphologies, and occupied extensive morphospace by the middle Cambrian [1,19,20]….
We here simultaneously infer rates of phenotypic and genomic change in arthropods during the Cambrian explosion and subsequent Phanerozoic, using a novel approach that exploits (1) the extensive phenotypic and genomic data available for living arthropods, (2) the calibration information available from the rich arthropod fossil record, and (3) adapting molecular clock methods for use on both genetic and morphological data…
Molecular and … phenotypic rates of evolution are expressed in % divergence per million years…
We here analyze an extensive data set of arthropods, consisting of 395 phenotypic characters [16] and 62 protein-coding genes [17,29], with 20 calibration points taken from the fossil record (Table S1)…
The phenotypic (largely “morphological”) data set consists of 395 characters (SI_13), scored for 53 panarthropod terminal taxa (Data file D1)… The character list is expanded and modified from Rota-Stabelli et al… The phenotypic data set for arthropods (Rota-Stabelli et al. 2011) was expanded to include 395 characters encompassing hard and soft tissues, internal and external anatomy, ultrastructure, embryology and gene expression patterns (SI_2, SI_13). There was a systematic attempt to sample character changes at all levels of arthropod phylogeny, attempting to catalogue derived characters (synapomorphies) uniting every pair or clade of sampled taxa, not only those changing on deep (Cambrian) branches…
The molecular data set consists of 62 protein coding genes sequenced for the 53 panarthropod terminals in the phenotypic data set (Regier et al. 2010) with an updated alignment (Regier and Zwick 2011). Fast-evolving data partitions dominated by synonymous sites were excluded, i.e. third codons, and first codons coding for leucine and arginine in any of the 53 taxa employed here (using LeuArg1: Hussey et al. 2010). The appropriateness of excluding or “degenerating” fast sites has been demonstrated empirically (Regier and Zwick 2011)…
Thus, in all calculations for average rates (e.g., Cambrian explosion, later Phanerozic), only ingroup branches are used in for molecular data, and only ingroup, internal branches for phenotypic data.
I’d like to make two very general observations here. First, measuring rates of change in existing traits is not the same thing as measuring the rate at which new traits appear.
Second, the rapid appearance of new body traits that occurred during the Cambrian explosion could never have taken place without a host of underlying changes at the genetic level. It is these changes that we need to explain. How do we explain, for instance, the sudden increase in the number of new cell types that occurred during the early Cambrian period? Lee et al. do not even discuss this question in their paper: a search on the phrase “cell type” turns up empty.
The impression I get is that Darwinists attempting to “debunk” the Cambrian explosion (or at least, cut it down to a manageable size) simply fail to grasp the fundamental issues raised by Dr. Stephen Meyer in his book, Darwin’s Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design (HarperOne, 2013).
But Meyer is not alone. In a recent post over at Evolution News and Views, Casey Luskin drew readers’ attention to a new book by paleobtologists Douglas Erwin and James Valentine, entitled, The Cambrian Explosion: The Construction of Animal Biodiversity (Roberts and Company, 2013). The authors, who are recognized authorities in their field, are no friends of Intelligent Design, but they firmly reject the standard neo-Darwinian explanations that have been put forward for the Cambrian explosion. In particular, they take issue with the claim that macroevolution is nothing more than an extrapolation of microevolution. A few excerpts from the introduction of their book will suffice to convey the tenor of their thought:
Today, some two dozen major eukaryotic groups have bodies composed of more than one cell, but few have progressed beyond the stage of an association of essentially identical cell types (Buss 1987; Knoll 2011). Eukaryotes include protistan colonies and various algae that have many cells, but there is no evidence that any of these groups has ever achieved the developmental control required to produce more complex morphologic patterns. Multicellular algae and fungi have only a few cell types, whereas other eukaryotic lineages are multicellular but exhibit none of the hierarchical structure of differentiation seen in plants and animals. At least eight different groups of these multicellular eukaryotes arose well before animals finally evolved sometime more than 750 million years ago (Ma). Complex multicellularity involves a hierarchical structure of differentiated cell types, tissues, organs, and the regionally differentiated structures found in animals and vascular land plants…
Multicellularity is a generative evolutionary innovation in the sense that it provides the basis for two additional important evolutionary steps: greater body size and increased division of labor among differentiated body parts. Greater size quite literally changes the nature of the world experienced by organisms… Body size is a multiplier of inertia, and most multicellular organisms are large enough that they cross the boundary into a world where inertial forces become important. At such larger sizes, most organisms evolved new ways of locomotion and feeding, facilitated by the specialization of cells, tissues, organs, and differentiated body parts. Such division of labor is evident even in sponges, the earliest metazoan group, but becomes far more pronounced in more complex animals…
Some 120 million to 170 million years after the origin of sponges, the scrappy fossil record improved with a bang, geologically speaking. Following a prelude of a diverse suite of enigmatic, soft-bodied organisms beginning about 579 Ma, a great variety and abundance of animal fossils appear in deposits dating from a geologically brief interval between about 530 to 520 Ma, early in the Cambrian period…
The subtitle of this book, The Construction of Animal Biodiversity, captures a second theme: the importance of building the networks that mediate the interactions… Increased genetic and developmental interactions were also critical to the formation of new animal body plans. By the time a branch of advanced sponges gave rise to more complex animals, their genomes comprised genes whose products could interact with regulatory elements in a coordinated network. Network interactions were critical to the spatial and temporal patterning of gene expression, to the formation of new cell types, and to the generation of a hierarchical morphology of tissues and organs. The evolving lineages could begin to adapt to different regions within the rich mosaic of conditions they encountered across the environmental landscape, diverging and specializing to diversify into an array of body forms.
Increased genetic and developmental interactions were also critical to the formation of new animal body plans. By the time a branch of advanced sponges gave rise to more complex animals, their genomes comprised genes whose products could interact with regulatory elements in a coordinated network. Network interactions were critical to the spatial and temporal patterning of gene expression, to the formation of new cell types, and to the generation of a hierarchical morphology of tissues and organs. The evolving lineages could begin to adapt to different regions within the rich mosaic of conditions they encountered across the environmental landscape, diverging and specializing to diversify into an array of body forms.
The nature of appropriate explanations is particularly evident in the final theme of the book: the implications that the Cambrian explosion has for understanding evolution and, in particular, for the dichotomy between microevolution and macroevolution. If our theoretical notions do not explain the fossil patterns or are contradicted by them, the theory is either incorrect or is applicable only to special cases… One important concern has been whether the microevolutionary patterns commonly studied in modern organisms by evolutionary biologists are sufficient to understand and explain the events of the Cambrian or whether evolutionary theory needs to be expanded to include a more diverse set of macroevolutionary processes. We strongly hold to the latter position.…
Microevolutionary change often produces new species when different populations of a species are isolated genetically, or nearly so, such that each pursues a separate pathway of genetic change and they become distinct species; in animals, it usually means that they can no longer exchange genes. Macroevolution, by contrast, involves the study of what happens in evolution beyond the mechanisms of the formation of species. Some species, for example, are founders of major clades that encompass millions of species that occupy a wide range of ecological occupations, whereas other species are merely found in minor branches of life’s tree with rather similar ecologies or simply become extinct without issue (other patterns are not uncommon). Each of the species with those very different evolutionary outcomes arose through microevolutionary processes, yet there is obviously more to be said about their evolution, which forms the topic of macroevolution.
Reading through the introduction, it is readily apparent that Erwin and Valentine have thought long and hard about the issues relating to the Cambrian explosion, and that they truly appreciate the magnitude of the problem of explaining this seismic event in the history of life. By contrast, the new study by Lee et al. fails to grapple with the deeper issues: its aim is merely to defend Darwinism, and it “succeeds” only by shrinking the problem by focusing on minutiae such as rates of change in genes and phenotypic characters. No wonder, then, that the study’s authors perceive no threat to Darwinian evolution in the Cambrian explosion.
I’ll let the last word go to biologist Richard Deem, whose online review of Dr. Stephen Meyer’s book, Darwin’s Doubt, is well worth reading:
Darwin’s Doubt contains a number of chapters dedicated to the question of how new information and new genes can arise, which might explain the mechanism behind the Cambrian explosion. The problem is not as simple as it might seem at first, since not only were new body plans developed, but dozens of new kinds of organs, tissues and cell types for all those body plans. Such massive innovations require the addition of thousands of new genes that are perfectly integrated with each other in order to produce an organism that functions. The Darwinian explanations for the origin of genetic information would be hard-pressed to explain how all those new designs appeared.