No biologist has explored the regulatory logic of animal development more deeply than Eric Davidson, at the California Institute of Technology. Early in his career, collaborating with molecular biologist Roy Britten, Davidson formulated a theory of “gene regulation for higher cells.”22 By “higher cells” Davidson and Britten meant the differentiated, or specialized, cells found in any animal after the earliest stages of embryological development. Davidson observed that the cells of an individual animal, no matter how varied in form or function, “generally contain identical genomes.”23 During the life cycle of an organism, the genomes of these specialized cells express only a small fraction of their DNA at any given time and produce different RNAs as a result. These facts strongly suggest that some animal-wide system of genetic control functions to turn specific genes on and off as needed throughout the life of the organism—and that such a system functions during the development of an animal from egg to adult as different cell types are being constructed.
When they proposed their theory in 1969, Britten and Davidson acknowledged that “little is known … of the molecular mechanisms by which gene expression is controlled in differentiated cells.”24 Nevertheless, they deduced that such a system must be at work. Given: (1) that tens or hundreds of specialized cell types arise during the development of animals, and (2) that each cell contains the same genome, they reasoned (3) that some control system must determine which genes are expressed in different cells at different times to ensure the differentiation of different cell types from each other—some system-wide regulatory logic must oversee and coordinate the expression of the genome.25
Davidson has dedicated his career to discovering and describing the mechanisms by which these systems of gene regulation and control work during embryological development. During the last two decades, research in genomics has revealed that nonprotein-coding regions of the genome control and regulate the timing of the expression of the protein-coding regions of the genome. Davidson has shown that the nonprotein-coding regions of DNA that regulate and control gene expression and the protein-coding regions of the genome together function as circuits. These circuits, which Davidson calls “developmental gene regulatory networks” (or dGRNs) control the embryological development of animals.
FIGURE 13.4
Developmental gene regulatory networks (dGRNs) and development in the purple sea urchin, Strongylocentrotus purpuratus. Figure 13.4a (top, left): shows the actual embryo, starting at 6 hours and progressing through cell division to 55 hours, when the larval skeleton appears. Figure 13.4b (bottom, left): depicts the major classes of genes involved in specifying the larval skeleton. Figure 13.4c (top, right): shows the detailed genetic circuitry implicated in the overall “gene regulatory network” (“GRN”) that controls the construction of the larval skeleton. Courtesy National Academy of Sciences, U.S.A.
On arriving at Caltech in 1971, Davidson chose the purple sea urchin, Strongylocentrotus purpuratus, as his experimental model system. The biology of S. purpuratus makes it an attractive laboratory subject: the species occurs abundantly along the Pacific coast, produces enormous quantities of easily fertilized eggs in the lab, and lives for many years.26 Davidson and his coworkers pioneered the technology and experimental protocols required to dissect the sea urchin’s genetic regulatory system.
The remarkable complexity of what they found needs to be depicted visually. Figure 13.4a shows the urchin embryo as it appears six hours after development has begun (top left of diagram). This is the 16-cell stage, meaning that four rounds of cell division have already occurred (1 → 2 → 4 → 8 → 16). As development proceeds in the next four stages, both the number of cells and the degree of cellular specialization increases, until, at 55 hours, elements of the urchin skeleton come into focus. Figure 13.4b shows, corresponding to these drawings of embryo development, a schematic diagram with the major classes of genes (for cell and tissue types) represented as boxes, linked by control arrows. Last, Figure 13.4c shows what Davidson calls “the genetic circuitry” that turns on the specific biomineralization genes that produce the structural proteins needed to build the urchin skeleton.27
This last diagram represents a developmental gene regulatory network (or dGRN), an integrated network of protein and RNA-signaling molecules responsible for the differentiation and arrangement of the specialized cells that establish the rigid skeleton of the sea urchin. Notice that, to express the biomineralization genes that produce structural proteins that make the skeleton, genes far upstream, activated many hours earlier in development, must first play their role.
This process does not happen fortuitously in the sea urchin but via highly regulated and precise control systems, as it does in all animals. Indeed, even one of the simplest animals, the worm C. elegans, possessing just over 1,000 cells as an adult, is constructed during development by dGRNs of remarkable precision and complexity. In all animals, the various dGRNs direct what Davidson describes as the embryo’s “progressive increase in complexity”—an increase, he writes, that can be measured in “informational terms.”28
Davidson notes that, once established, the complexity of the dGRNs as integrated circuits makes them stubbornly resistant to mutational change—a point he has stressed in nearly every publication on the topic over the past fifteen years. “In the sea urchin embryo,” he points out, “disarming any one of these subcircuits produces some abnormality in expression.”29
Developmental gene regulatory networks resist mutational change because they are organized hierarchically. This means that some developmental gene regulatory networks control other gene regulatory networks, while some influence only the individual genes and proteins under their control. At the center of this regulatory hierarchy are the regulatory networks that specify the axis and global form of the animal body plan during development. These dGRNs cannot vary without causing catastrophic effects to the organism.
Indeed, there are no examples of these deeply entrenched, functionally critical circuits varying at all. At the periphery of the hierarchy are gene regulatory networks that specify the arrangements for smaller-scale features that can sometimes vary. Yet, to produce a new body plan requires altering the axis and global form of the animal. This requires mutating the very circuits that do not vary without catastrophic effects. As Davidson emphasizes, mutations affecting the dGRNs that regulate bodyplan development lead to “catastrophic loss of the body part or loss of viability altogether.”30 He explains in more detail:
There is always an observable consequence if a dGRN subcircuit is interrupted. Since these consequences are always catastrophically bad, flexibility is minimal, and since the subcircuits are all interconnected, the whole network partakes of the quality that there is only one way for things to work. And indeed the embryos of each species develop in only one way.31
Engineering Constraints
Davidson’s findings present a profound challenge to the adequacy of the neo-Darwinian mechanism. Building a new animal body plan requires not just new genes and proteins, but new dGRNs. But to build a new dGRN from a preexisting dGRN by mutation and selection necessarily requires altering the preexisting developmental gene regulatory network (the very kind of change that, as we saw in Chapter 12, cannot arise without multiple coordinated mutations). In any case, Davidson’s work has also shown that such alterations inevitably have catastrophic consequences.
Davidson’s work highlights a profound contradiction between the neo-Darwinian account of how new animal body plans are built and one of the most basic principles of engineering—the principle of constraints. Engineers have long understood that the more functionally integrated a system is, the more difficult it is to change any part of it without damaging or destroying the system as a whole. Davidson’s work confirms that this principle applies to developing organisms in spades. The system of gene regulation that controls animal-body-plan development is exquisitely integrated, so that significant alterations in these gene regulatory networks inevitably damage or destroy the d
eveloping animal.32 But given this, how could a new animal body plan, and the new dGRNs necessary to produce it, ever evolve gradually via mutation and selection from a preexisting body plan and set of dGRNs?
Davidson makes 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.”33 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 bodyplan morphology occurs by a continuous process. All of these assumptions are basically counterfactual. This cannot be surprising, since the neo-Darwinian synthesis from which these ideas stem was a premolecular biology concoction focused on population genetics and … natural history, neither of which have any direct mechanistic import for the genomic regulatory systems that drive embryonic development of the body plan.34
Now and Then
Eric Davidson’s work, like that of Nüsslein-Volhard and Wieschaus, highlights a difficulty of obvious relevance to the Cambrian explosion. Typically, paleontologists understand the Cambrian explosion as the geologically sudden appearance of new forms of animal life. Building these forms requires new developmental programs—including both 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’s doubt about the Cambrian explosion centered on the problem of missing fossil intermediates. Not only have those forms not been found, but the Cambrian explosion itself illustrates a profound engineering problem that fossil evidence does not address—the problem of building a new form of animal life by gradually transforming one tightly integrated system of genetic components and their products into another. Yet, in the next chapter, we will see that an even more formidable problem remains.
14
The Epigenetic Revolution
In 1924, two German scientists, Hans Spemann and Hilda Mangold, reported an intriguing experiment, the significance of which could not have been fully appreciated at the time, three decades before the discovery of the information-bearing properties of DNA. Using microsurgery, Spemann and Mangold excised a portion of a newt embryo and transplanted that portion into another developing newt embryo.1
They achieved a startling result. The second embryo produced two bodies, each with a head and tail, joined together at the belly, not unlike Siamese twins. Yet despite dramatically altering the anatomy of the embryo, Spemann and Mangold did not alter its DNA.
Their experiment later suggested a radical possibility: that something in addition to DNA profoundly influences the development of animal body plans. Other experiments suggested as much. In the 1930s and 1940s, American biologist Ethel Harvey showed experimentally that sea urchin embryos could undergo development up to about 500 cells after removal of their nuclei—in other words, without their nuclear DNA.2 In the 1960s, Belgian scientists chemically blocked the transcription of DNA into RNA in amphibian embryos and found that the embryos could still develop to the point of containing several thousand cells.3 In the 1970s, Canadian biologists showed that a frog embryo could undergo early development without its nucleus if the cell division apparatus from a sea urchin was injected into the egg.4
None of these results indicate that embryos can develop fully without DNA. In every case, DNA was eventually necessary to complete embryological development. Yet these results suggest that DNA is not the whole story, that other sources of information are playing important roles in directing at least the early stages of animal development.
Above and Beyond: Epigenetic Information
In 2003, MIT Press published a groundbreaking collection of scientific essays titled Origination of Organismal Form: Beyond the Gene in Developmental and Evolutionary Biology, edited by two distinguished developmental and evolutionary biologists, Gerd Müller, of the University of Vienna, and Stuart Newman, of New York Medical College. In their volume, Müller and Newman included a number of scientific articles describing recent discoveries in genetics and developmental biology—discoveries suggesting that genes alone do not determine the three-dimensional form and structure of an animal. Instead, many of the scientists in their volume reported that so-called epigenetic information—information stored in cell structures, but not in DNA sequences—plays a crucial role. The Greek prefix epi means “above” or “beyond,” so epigenetics refers to a source of information that lies beyond the genes. As Müller and Newman explain in their introduction, “Detailed information at the level of the gene does not serve to explain form.”5 Instead, as Newman explains, “epigenetic” or “contextual information” plays a crucial role in the formation of animal “body assemblies” during embryological development.6
Müller and Newman not only highlighted the importance of epigenetic information to the formation of body plans during development; they also argued that it must have played a similarly important role in the origin and evolution of animal body plans in the first place. They concluded that recent discoveries about the role of epigenetic information in animal development pose a formidable challenge to the standard neo-Darwinian account of the origin of these body plans—perhaps the most formidable of all.
In the introductory essay to their volume, Müller and Newman list a number of “open questions” in evolutionary biology, including the question of the origin of Cambrian-era animal body plans and the origin of organismal form generally, the latter being the central topic of their book. They note that though “the neo-Darwinian paradigm still represents the central explanatory framework of evolution,” it has “no theory of the generative.”7 In their view, neo-Darwinism “completely avoids [the question of] the origination of phenotypic traits and of organismal form.”8 As they and others in their volume maintain, neo-Darwinism lacks an explanation for the origin of organismal form precisely because it cannot explain the origin of epigenetic information.
I first learned about the problem of epigenetic information and the Spemann and Mangold experiment while driving to a private meeting of Darwin-doubting scientists on the central coast of California in 1993. In the car with me was Jonathan Wells (see Fig. 14.1), who was then finishing a Ph.D. in developmental biology at the University of California at Berkeley. Like some others in his field, Wells had come to reject the (exclusively) “gene-centric” view of animal development and to recognize the importance of nongenetic sources of information.
By that time, I had studied many questions and challenges to standard evolutionary theories arising out of molecular biology. But epigenetics was new to me. On our drive, I asked Wells why developmental biology was so important to evolutionary theory and to assessing neo-Darwinism. I’ll never forget his reply. “Because” he said, “that’s where the whole theory is going to unravel.”
FIGURE 14.1
Jonathan Wells. Courtesy Laszlo Bencze.
In the years since, Wells has developed a powerful argument against the adequacy of the neo-Darwinian mechanism as an explanation for the origin of animal body plans. His argument turns on the importance of epigenetic information to animal development. To see why epigenetic information poses an additional challenge to neo-Darwinism and what exactly biologists mean by “epigenetic” information, let’s examine the relationship between biological form and biological information.
Form and Information
Biologists typically define “form” as a distinctive shape and arrangement of body parts. Organismal forms exist in three spatial dimensions and arise in t
ime—in the case of animals during development from embryo to adult. Animal form arises as material constituents are constrained to establish specific arrangements with an identifiable three-dimensional shape or “topography”—one that we would recognize as the body plan of a particular type of animal. A particular “form,” therefore, represents a highly specific arrangement of material components among a much larger set of possible arrangements.
Understanding form in this way suggests a connection to the notion of information in its most theoretically general sense. As I noted in Chapter 8, Shannon’s mathematical theory of information equated the amount of information transmitted with the amount of uncertainty reduced or eliminated in a series of symbols or characters. Information, in Shannon’s theory, is thus imparted as some options, or possible arrangements, are excluded and others are actualized. The greater the number of arrangements excluded, the greater the amount of information conveyed. Constraining a set of possible material arrangements, by whatever means, involves excluding some options and actualizing others. Such a process generates information in the most general sense of Shannon’s theory. It follows that the constraints that produce biological form also impart information, even if this information is not encoded in digital form.
DNA contains not only Shannon information but also functional or specified information. The arrangements of nucleotides in DNA or of amino acids in a protein are highly improbable and thus contain large amounts of Shannon information. But the function of DNA and proteins depends upon extremely specific arrangements of bases and amino acids.
Similarly, animal body plans represent, not only highly improbable, but also highly specific arrangements of matter. Organismal form and function depend upon the precise arrangement of various constituents as they arise during, or contribute to, embryological development. Thus, the specific arrangement of the other building blocks of biological form—cells, clusters of similar cell types, dGRNs, tissues, and organs—also represent a kind of specified or functional information.
Darwin's Doubt Page 30