Star Larvae Hypothesis
"We are interested in the significance of EISs [epigenetic inheritance systems] in evolution precisely because their evolutionary effects cannot be separated from their physiological and developmental role. One cannot make a neat distinction between the physiological / developmental and evolutionary aspects of heritable epigenetic variation. It may be that things get confusing because these days the word 'evolution' evokes ideas of change through purely selective processes and blind variation. Instructive processes and directed variation are associated only with development. For some time we have felt that a new term, which would describe processes that are concurrently evolutionary and developmental, selective and instructive, is necessary. We thought of ‘evelopment,’ but have not used it much.”
Jablonka and Marion J. Lamb
"[I]f we integrate the fact that the cell structure sorts and contains molecular interactions, inasmuch as it is itself sorted and shaped by natural selection, we must infer that natural selection, via this cell structure, acts in ontogenesis. Molecular interactions are sorted by the cell structure (or the multi-cellular structure) which is itself sorted by natural selection, therefore, ultimately, natural selection sorts molecular interactions and the two processes of ontogenesis and phylogenesis are no longer separated, they form only one process that I suggest could be called ontophylogenesis."
This ongoing process is called phylogeny or, more commonly, evolution. It proceeds without the benefit of any predetermined plan. The forms of species are ad hoc, contingent, being shaped by the vagaries of natural selection and genetic drift. That, at least, is the story according to normal science.
Science tells another story when it comes to the manufacturing of the cell types that make up a complex organism. The term for that process is ontogeny, or development. It occurs when a zygote (fertilized egg cell) divides into two cells, and those cells each divide, and the resulting cells, after many divisions, differentiate into the variety of cell types that compose that organism. Unlike evolution, this process is not ad hoc. When a tadpole matures, it does so predictably into a frog, not a cactus, being directed toward the adult form of the frog, and all of the cell types that that requires, by an inherent predisposition.
To repeat, unlike a developing organism, evolving species are assumed not to be predisposed toward any inherent endpoint.
If evolution is an instance of development, as the star larvae hypothesis argues, then it is a teleological process, and S. J. Gould was wrong when he asserted that, if we could rewind the tape of life and let it run again, humans likely would never appear, because evolution is not deterministic but is susceptible to historical contingencies. In "Life’s Solution," University of Cambridge Paleobiologist Simon Conway Morris argues against that assertion and instead argues in favor of a significant degree of inevitability concerning evolutionary outcomes.
The bulk of Morris’ book consists of a catalog of examples of evolutionary convergence--instances of very similar outcomes, or adaptations, that are found to be common among very distantly related organisms. From details of biochemistry to the physiology of sense organs to social systems, biology leans heavily on a small set of imaginable solutions to life’s challenges, leaving unexplored a vast “hyperspace” of conceivably possible alternatives. This is not an obvious interpretation of the Darwinian model of evolution, which favors an open-ended model of nature in which biological forms and functions might possess a nearly unbounded elasticity.
Before unleashing his considerable catalog of examples of evolutionary convergences, Morris makes clear his purpose, which is to make the case that
“[E]volution is indeed constrained, if not bound. Despite the immensity of biological hyperspace I shall argue that nearly all of it must remain for ever empty, not because our chance drunken walk [another metaphor from Gould] failed to wander into one domain rather than another but because the door could never open, the road was never there, the possibilities were from the beginning for ever unavailable. This implies that we may not only be on the verge of glimpsing a deeper structure to life, but that it matters little what our starting point may have been: the different routes will not prevent a convergence on similar ends.”
His examples of evolutionary convergences include the parallel evolution across species of anti-freeze proteins, compound eyes, echolocation, silk production, vocalization, and so on with examples that fill a couple hundred pages.
Morris implies that evolution includes an under-appreciated, teleological component, one that marginalizes contingent contributions to evolutionary outcomes. In other words, evolution is not an open-ended process of adaptive improvising and drift with near countless possible outcomes. It is, rather, a highly constrained process, inherently predisposed to certain outcomes so strongly that in case after case the chemical, physiological and anatomical specifics of remotely related organisms converge on the same, or at least strikingly similar, adaptive forms.
Morris’ arguments and evidence dovetail neatly with the star larvae hypothesis, because they can be interpreted as making the case that evolution is an instance of development, the latter process being also highly constrained and biased toward inherent outcomes. A fertilized ovum and an impregnated planet might have more in common than at first is obvious. But each pursues a remarkable course, an adventure of diversification of forms and functions and complex circuits of symbiotic interdependence among those descendant forms--of cell types and of species, respectively. Morris illuminates particular empirical and theoretical paths that carry evolution theory through a teleological adjustment to land, script in hand, on the stage of the stellar life cycle. His thesis adds circumstantial weight to the star larvae hypothesis.
Evolution and development have enjoyed an on-again, off-again relationship over the past century. Darwin’s key phrase, "descent with modification," describes equally well the crafting of new species in an ecology and the crafting of new cell types in a developing organism. Naturalist Ernst Haeckel, in the nineteenth century, married the two processes to one another with his alliterative "biogenetic law," ontogeny recapitulates phylogeny. Haeckel proposed that a developing organism passes sequentially through the stages of its evolutionary ancestry. This view since has been replaced by the simpler one that as embryos develop they generate increasingly specialized tissues and structures. The developmental sequence no longer is taken to be a telescoping of the species' evolution, but is seen as a teleological process of progressive differentiation of cell types and somatic morphology.
However, new discoveries in molecular biology are rekindling interest in the relationship between development and evolution, but now development looks like it is the process being recapitulated. The revived interest has produced a new discipline within evolutionary biology, called evolutionary developmental biology, or evo-devo. It views evolution through the lens of development, seeing within evolutionary descent-with-modification (of species of organism) some of the same mechanisms that underlie developmental descent-with-modification (of cell types within an multicellular organism). To an extent unexpected, it turns out that species differentiate from a shared genetic inheritance in a manner that resembles that by which cells do the same thing in a developing organism.
The biological sciences are undergoing a foundational shift, and evo-devo is one prominent expression of the shift. Peering into DNA, researchers are finding varieties of regulatory mechanisms that control the timing of gene expression here and there in a developing organism. The data from DNA sequencing and analysis and related research suggests that endogenous regulation, rather than natural selection, is evolution's primary driver. The new data suggest that evolution itself is an instance of development. This is the position of the star larvae hypothesis.
When, in the early-to-mid twentieth century, biologists supplemented Darwinian theory with Mendelian genetics, the discovery of DNA, and an understanding of the role that genes play in inheritance, the enhanced model became known as the Modern Synthesis. Today the Modern Synthesis itself is being modernized. New work in epigenetics, niche construction, phenotypic plasticity and other fields is challenging the Darwinian legacy. In July 2008 a group of researchers exploring these new fields convened at the Konrad Lorenz Institute in Altenberg, Switzerland, to formalize a so-called Extended Synthesis of evolutionary theory. MIT Press published the conference papers as a sourcebook, Evolution - the Extended Synthesis. Many of the book's contributors reassure readers that the new findings pose no fundamental threat to the Darwinian framework. The collective attitude seems to be that the new discoveries complicate but do not undermine the natural selection model. More recently, some of the researchers involved in the Altenberg conference, among others, launched a web site, The Third Way, as an organizing tool for scientists working to develop a revised model of evolution that accommodates the new findings. More recently the The John Templeton Foundation has awarded a major grant (£5.7m or $8m) to an international team of leading researchers for a three-year research program to put the predictions of the extended evolutionary synthesis to the test. The Royal Society in 2015 published an article, The extended evolutionary synthesis: its structure, assumptions and predictions that provides additional background information. And in November 2016 the Society hosted a scientific meeting on the topic, entitled, “New trends in evolutionary biology: biological, philosophical and social science perspectives”.
The star larvae hypothesis welcomes such developments, but points out that the Extended Synthesis suggests a substantially reconfigured, rather than merely extended, model of evolution--a postmodern synthesis. The star larvae hypothesis is particularly interested in the Extended Synthesis' recognition of endogenous factors—those internal to the organism—as primary, and of environmental factors as supplementary, to the shaping of phenotypes during evolution. This excerpt from the introduction to Evolution - the Extended Synthesis highlights this inversion of causal roles:
“[In the Modern Synthesis] organismal shape and structure were interpreted as products uniquely of external selection regimes. All directionality of the evolutionary process was assumed to result from natural selection alone. The inclusion of EvoDevo in particular, as shown in section five of this volume, represents a major change of this paradigm by taking the contributions of the generative processes into account as entrenched properties of the organism that promote particular forms of chance rather than others. On this view, natural selection becomes a constantly operating background condition, but the specificity of its phenotypic outcome is provided by the developmental systems it operates on. Hence the organisms themselves represent the determinants of selectable variation and innovation. At the theoretical level, this shifts a significant portion of the explanatory weight from the external conditions of selection to the internal generative properties of evolving phenotypes.”
"Internal generative properties" is a pivotal phrase. It suggest that phenotypes evolve as they do because of something inherent in the organisms. That is, it suggests that evolution is developmental. The star larvae hypothesis draws attention to components of the Extended Synthesis and proposes relationships among them to present a fully developmental model of evolution, as follows.
It turns out that genetic material varies much less across species than observable phenotypic differences would suggest. DNA is highly conserved across species. The discovery early in the twenty-first century that DNA differs relatively little across species ushered in the new discipline of evo-devo. In their article, Regulating Evolution (Scientific American, May 2008) researchers Sean B. Carroll, Benjamin Prud’homme, and Nicolas Gompel explain why a new perspective was needed.
"For a long time, scientists certainly expected the anatomical differences among animals to be reflected in clear differences among the contents of their genomes. When we compare mammalian genomes such as those of the mouse, rat, dog, human and chimpanzee, however, we see that their respective gene catalogues are remarkably similar. [. . . .] When comparing mouse and human genomes, for example, biologists are able to identify a mouse counterpart of at least 99 percent of all our genes."The perplexed authors elaborate on these findings:
". . . to our surprise, it has turned out that differences in appearance are deceiving: very different animals have very similar sets of genes."
"The preservation of coding sequences over evolutionary time is especially puzzling when one considers the genes involved in body building and body patterning."
"The discovery that body-building proteins are even more alike on average than other proteins was especially intriguing because of the paradox it seemed to pose: animals as different as a mouse and an elephant are shaped by a common set of very similar, functionally indistinguishable body-building proteins."
Surprise? Puzzle? Paradox? Why does evolution theory suffer so many bouts of the unexpected now that researchers are mapping and comparing genomes? If the received theory is solid, then wouldn’t new genetic details have slots waiting for them in it? Shouldn’t new genetic data bolster the existing model, rather than hand it surprises, puzzles and paradoxes? Nobody saw it coming. It was an empirical surprise.
But if evolution was recognized as being a developmental process, then no one would be surprised. Then the species of the Earth ought to share a common genome, just as the cells in the body of a complex organism share a common genotype, at least as a first approximation--more on this later. The genetic similarities seen across species are too striking to sweep under the rug, and at least some researchers are blunt about the new data’s impact on evolutionary theory.
Charles R. Marshall, a biological science professor at the University of California, Berkeley, observes in a book review in the September 20, 2013 issue of Science,
"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"
This observation also describes how a fertilized egg cell gives rise to descendant cell types. The descendant types emerge through the rewiring of gene regulatory networks.
Evidently, we can say that the genes for descendant species were there already in remote ancestors, or that the GRNs for descendant species were there already, or both were there already. In any case, what were they doing there? If they functioned one way, or were silent, in ancestors, how is it that they just happened to be re-wirable to produce highly dissimilar, yet “adapted,” descendants? That seems far fetched. But it makes sense and is to be expected if evolution is a case of development. It looks like GRNs manage the differentiation of species in an ecology in a manner similar to that by which such networks regulate the differentiation of cells in a developing body.
Consider this adaptation of the quote above, "In fact, our present understanding of cellular differentiation in developing organisms indicates that new cell types are not made by new genes but largely emerge through the rewiring of the gene regulatory networks (GRNs) of already existing genes."
— Simon Conway Morris
Life's Solution: Inevitable Humans in a Lonely Universe
In Universal Genome in the Origin of Metazoa (Cell Cycle 6:15, August 2007) researcher Michael Sherman also argues that diverse species issue from a common, conserved, genome. His case rests largely on the presence of anomalous genes in ancestral species that are needed by descendant species, a circumstance called, pre-adaptation. He summarizes,
“In thinking about metazoan evolution, one should realize that any evolutionary event represents changes in developmental programs, rather than changes in a developed organism. [. . . .] This hypothesis postulates that (1) shortly (in geological terms) before [the] Cambrian period a Universal Genome that encodes all major developmental programs essential for every phylum of Metazoa emerged in a unicellular or a primitive multicellular organism; (2) The Metazoan phyla, all having similar genomes, are nonetheless so distinct because they utilize specific combinations of developmental programs. In other words, in spite of a high similarity of the genomes in phyla X and Y, an organism belonging to phylum X expresses a specific set of active developmental programs, while an organism belonging to a different phylum Y has a distinct set of “working” programs specific for phyla Y. This seemingly trivial statement changes the whole perception of evolution, claiming that the placement of an organism to a particular taxon depends on expression of a specific set of pre-existing developmental programs, rather than on difference in the genetic information per se. Therefore, within the Universal Genome model, what we perceive as a sequential evolution is actually a reflection of expression of one or another combination of programs from the Universal Genome. These postulates explain a simultaneous emergence of Metazoan phyla during [the] Cambrian period, as well as similarities of genomes and a dramatic increase in genome complexity in Metazoan phyla. [emphasis added]”
On just how it happened that the major developmental programs essential for every phylum of Metazoa emerged in a unicellular or a primitive multicellular organism the author does not speculate. But their presence there is to be expected, if evolution is an instance of development. The author’s characterization, elsewhere in the article, of developmental algorithms that wait in the wings as harboring “excessive” genetic information might be rendered more accurately as their harboring anticipatory genetic information, something to be expected in a case of development.
Already in 1999, researcher W. H. Holland in an article that appeared in Nature (Vol 402, Supplement, December 2, 1999) titled The Future of Evolutionary Developmental Biology recognized a common genome across species. He writes,
"So many examples of [DNA] conservation have now been found that it is no longer considered surprising. We can now state with confidence that most animal phyla possess essentially the same genes, and that some (but not all) of these genes change their developmental roles infrequently in evolution [emphasis added]."
When and where ecological conditions become hospitable, the highly conserved nucleotide sequences of the animal kingdom launch new species, as needed, via the rewiring of developmental patterns. This is the developmental model of evolution proposed by the star larvae hypothesis. Evolution shares with development raw materials (a highly conserved set of nucleotides), operating mechanisms (gene regulatory networks), and outputs (highly diverse phenotypes). Whether cells in a body or species in an ecology, phenotypes diversify, or differentiate, from variously regulated but shared genes. "Adaptive radiation" of species in an ecology proceeds as does that of cell types in a body.
Nonetheless, the objection remains that development and evolution are mechanically distinct processes and that the distinction precludes one process of differentiation being an instance of the other. The distinction claimed necessary concerns not only any putative difference among the mechanical processes involved, but also the degree to which DNA is conserved during each process. Genomic variability across species is considerably less than phenotypic variability across species would suggest, but it is not altogether absent.
Genomes do vary by species, in contrast to a supposed lack of genotypic variation among cells in a multicellular body. Or, so it seemed. New genetic research lays this objection to rest. It’s known now that cells in a multicellular body do vary genetically from one another, despite their having descended from a common ancestor (the original fertilized egg, or zygote). The cells in a multicellular body vary genetically by tissue type. This variability is called “genomic mosaicism,” and it is the focus of ongoing research, the early results of which are presented in a growing body of reports, including
DNA Double Take, by Carl Zimmer, New York Times, Sept. 16, 2013
Genome Mosaicism--One Human, Multiple Genomes, by James R. Lupski, Science, July 26, 2013
Are we Genomic Mosaics? Variation of the Genome of Somatic Cells can Contribute to Diversify our Phenotypes, by P.A. Astolfi, F. Salamini and V. Sgaramella, Current Genomics, 2010 Sep; 11(6): 379–386
Extensive Genetic Variation in Somatic Human Tissues, by Maeve O'Huallachain, et al., Proceedings of the National Academy of Sciences (PNAS), Oct 30, 2012,
And so a supposedly canonical difference between evolution an development bites the dust. Along with other bio/genetic findings cataloged on this site, genomic mosaicism brings the evolution theorist to a fork in the road:
Either development is an instance of evolution, in which cells in a developing body vary more or less randomly, with the environment of the body itself “selecting” among the variant cell types which will remain extant, which will go extinct, and which will give rise to distinguished descendants, or
Evolution is an unfolding process of development, subject to the teleology implied by the concept of life cycle.
Biogenetic research is forcing the hand of the theorists, because evolution and development employ the same causal mechanisms of descent with modification.
A relatively small set of genes can produce diverse phenotypes, because genes can be switched on and off, to create unique combinations of gene activity in various locations in a body at various stages in the life cycle of an organism. Because settings for the various cell types in a body are stabilized by epigenetic mechanisms, each specialized type reproduces its own kind. It looks now like evolution stabilizes phenotypes of organisms using the same mechanisms that stabilize cell types. In "Evolution in Four Dimensions: Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life", Researchers Eva Jablonka and Marion J. Lamb make just this case:
"A person’s liver cells, skin cells, and kidney cells, look different, behave differently, and function differently, yet they all contain the same genetic information. With very few exceptions, the differences between specialized cells are epigenetic, not genetic. They are the consequences of events that occurred during the developmental history of each type of cell and determined which genes are turned on, and how their products act and interact. The remarkable thing about many specialized cells is that not only can they maintain their phenotype for long periods, they can also transmit it to daughter cells. When liver cells divide their daughters are liver calls, and the daughters of kidney cells are kidney cells. Although their DNA sequences remain unchanged during development, cells nevertheless acquire information that they can pass to their progeny. This information is transmitted through what are known as epigenetic inheritance systems (or EISs for short). It is these systems that provide the second dimension of heredity and evolution [the first being the genetic dimension]"
Genetic variation among cell types in a body actually is becoming increasingly conspicuous. See reference to genomic mosaicism, above. In any event, DNA methylation is one epigenetic mechanism, in which methyl groups attach directly to DNA and activate or suppress gene expression. Other regulatory mechanisms include chromatin marking and RNA interference. In addition, some proteins, such as prions, can convert the structure of other proteins to their own, in effect subverting the will of the genes that produce the other proteins. This regulation of gene expression is a new field of research, and many details remain to be worked out. But what is clear is that a DNA sequence or genotype is only part of the story of phenotypic expression. Epigenetic mechanisms are another essential part of the story.
The Logic of Perfection
Jablonka and Lamb describe three mechanisms by which germ cells can acquire an epigenetic variation and hence ways in which epigenetic differences can become heritable from parent to offspring:
The researchers elaborate the details of these and other epigenetic inheritance systems in Trans Generational Epigenetic Inheritance, their contribution to Evolution - the Extended Synthesis.
Epigenetic mechanisms are conserved not only during development, but also during evolution. Research at the University of Chicago has turned up epigenetic mechanisms in fish that regulate development of fins and that, when transplanted into mice, function as the native mechanism that mice use to regulate limb development. A press release from the university explains:
"The genetic switches that drive the expression of genes in the digits of mice are not only present in fish, but the fish sequence can actually activate the expression in mice," said Igor Schneider, PhD, postdoctoral researcher in the Department of Organismal Biology and Anatomy at the University of Chicago [.] "This tells us how the antecedents of the limb go back in time at every level, from fossils to genes."
Epigenetic mechanisms also shed light on noncoding ("junk") DNA. Becausel cells in as body develop from the same zygote. Each type of cell necessarily inherits many genes that it does not need. Skin cells don't express genes specific to the functioning of liver cells, for example. Neither do muscle cells express genes specific to the functioning of nerve cells. And so on. The excess, or "noncoding," DNA in each cell type includes those genes needed to construct the other types. But from the point of view of a given type of cell, the DNA specific to the other types is junk. Nonetheless, all the cells inherit all the genes of their common ancestor—the zygote—whether they need them or not.
The received view of evolution is stumped by noncoding DNA at the species level, which is preserved across generations of a given species but not expressed. Despite the discovery that much of the human genome initially dubbed junk turns out to be regulatory, the origin and persistence at the species level of genuine junk DNA, which might approach 20 percent of the human genome, remains a paradox.
What aspect of evolution theory predicts that long stretches of DNA would coast along inside organisms, seemingly contributing nothing to survivability? Nobody saw it coming. It was an empirical surprise. But it makes sense, and would be expected, if evolution itself is an instance of development.
As philosopher Jerry Fodor summarized it, natural selection can at most tune the piano. It cannot compose the melody.
The role of composer, or at least that of conductor, seems to fall to endogenous gene regulatory networks.
But if evolution is an instance of development, then what strange creature is developing?
Furthermore, if the traits characteristic of a species are determined by patterns of genetic switch settings, or gene regulatory networks, epigenetically managed, then what determines those settings? The Darwinian model assigns that responsibility to natural selection and genetic drift. In the Darwinian model, environments decide which genetic and epigenetic combinations are sufficiently adaptive to befit a creature for reproductive success, . But the Extended Synthesis complicates that relationship in a way that draws the mechanisms of evolution and development so close together that they mostly overlap.
The Century of the Gene
If Darwin got it right, and the phenotypic traits characteristic of each species have been shaped by the environments in which the various species evolved, then evolution theory needs to characterize explicitly the relationships that link environments to their inhabitants. In the Modern Synthesis environments are treated as extrabiological givens that determine which random phenotypic variants from among the members of a local population enjoy which degrees of reproductive success. In his contribution to Evolution - the Extended Synthesis, researcher John Odling-Smee argues that the process is not so straightforward and must take into account the ways in which organisms alter their environments.
Fodor and Massimo Piattelli-Palmarini
What Darwin Got Wrong
He points out that the Modern Synthesis took selection pressures to be autonomous forces that mold organisms to fit niches, with niches corresponding to "preexisting environmental templates," like keyholes waiting for keys. The templates, admittedly, always were acknowledged as being dynamic, being subject to geological, climactic, chemical and other influences, and nature imposed such influences willy-nilly regardless of whatever organisms happened to be around or what those organisms did. As Odling-Smee notes in The Modern Synthesis, "the changes that organisms bring about in their own environments are seldom thought to have evolutionary significance." Here he is introducing the notion of niche construction, which recognizes that organisms engineer the environments that they need. Odling-Smith explains the concept,
A parallel situation occurs during development, as described in this passage from the Wikipedia entry, Gene regulatory network:
"[A]ll organisms, through their metabolisms, movements, behavior, and choices, partly create and partly destroy their environments. In doing so, they transform some of the selection pressures in the environments that subsequently select them. Therefore the adaptations of organisms cannot be exclusively consequences of organisms responding to autonomous selection pressures in environments. Sometimes they must involve organisms responding to selection pressures previously transformed by their own, or by their ancestors’ niche-constructing activities."
Or by their neighbor's niche-constructing activities.
"A major feature of multicellular animals is the use of morphogen gradients, which in effect provide a positioning system that tells a cell where in the body it is, and hence what sort of cell to become. A gene that is turned on in one cell may make a product that leaves the cell and diffuses through adjacent cells, entering them and turning on genes only when it is present above a certain threshold level. These cells are thus induced into a new fate, and may even generate other morphogens that signal back to the original cell. Over longer distances morphogens may use the active process of signal transduction. Such signaling controls embryogenesis, the building of a body plan from scratch through a series of sequential steps. They also maintain adult bodies through feedback processes, and the loss of such feedback because of a mutation can be responsible for the cell proliferation that is seen in cancer."
As cells differentiate in an organism, they use chemical agents called morphogens to construct hospitable niches in the ecology of that organism's body. And as evolving species differentiate, they likewise construct their niches in their ecosystems by conditioning the environment. In each case, the bio-units in question and their environments condition each other through a feedback relationship. When organisms modify their environments, effectively shaping the selection pressures to which they, their progeny, and their neighbors are subjected, cause and effect feed back to each other. The prospect of runaway positive feedback resulting is explored in the context of human industry in Cyberfetus Rising.
To summarize: As it develops from zygote to adult, the body of a complex organism accommodates its cellular constituents, because that developing body is a constructed ecology. It comprises a growing diversity of cyto-niches as its cellular inhabitants differentiate. Those cellular inhabitants alter their habitat's chemistry, thereby constructing new niches, the sum and chemical intertwinings of which, the geometrical configurations of which constitute the developing body. The cells build their shared environment and maintain it, just as the species of the Earth build and maintain their ecologies and even the planet as a whole, as in James Lovelock's ecological construct of Gaia, which can be regarded as niche construction theory on a planetary scale.
The foregoing makes clear the difficulty that contemporary theorists of evolution face in trying to maintain a distinction between the mechanisms of evolution and the mechanisms of development. The mechanisms attributed to each process continue to merge into the same set of mechanisms, primarily involving epigenetic gene regulation. The genes are already there. Phenotypes emerge from DNA by way of a selective regulation of those genes (that is, a selective management over when and where they are expressed or repressed). As a complex organism develops, epigenetic mechanisms regulate gene expression from within a genotype common to the many emergent cell types (notwithstanding "genomic mosaicism"). The star larvae hypothesis proposes that such mechanisms also regulate the differentiation of species from what increasingly is becoming recognized as being a genome more or less shared across diverse species. With significant changes in body morphology being associated with changes in gene regulation, rather than with the appearance of mutant genes, the evolution of species looks an awful lot like the differentiation of cell types during ontogeny.
Other than differences in spatial and temporal scale, what remains to justify treating evolution and development as mechanically distinct processes?
The presence of anticipatory genes further strengthens the case for evolution being a case of development. A zygote carries many genes that ride along unexpressed—until they are needed by the developing organism. The zygote anticipates, in its genotype, the genetic needs of the cells that will descend from it. The zygote divides into two cells, and the two into four, and the four into eight, and so on, in what is called the cell cycle. The cells that make up the early generations are said to be totipotent cells—they can bear descendants of any cell type characteristic of the species. Later, after a degree of specialization, cells become pluripotent—they can give rise to several cell types, but not to all. And the specialization continues from there, with descendants inheriting from their ancestors genes specific to their needs--which they express--when they inherit the whole of the genotype, some of which will remain unexpressed.
This is how it works in a developing organism: The zygote carries genes that anticipate the needs of future cell types, which arise as those descendant cells differentiate.
In another parallel between ontogenetic and phylogenetic mechanisms, ancestral species also carry genes that seem to anticipate the needs of the species that descend from them.
A news article in Nature, on the sequencing of the genome of the Great Barrier Reef sponge Amphimedon queenslandica, reveals that the hoary creatures harbor a "toolkit" of metazoan genes: "The genome also includes analogues of genes that, in organisms with a neuromuscular system, code for muscle tissue and neurons." A curious finding. The article continues, "According to Douglas Erwin, a paleobiologist at the Smithsonian Institution in Washington DC, such complexity indicates that sponges must have descended from a more advanced ancestor than previously suspected. 'This flies in the face of what we think of early metazoan evolution,' says Erwin." Charles Marshall, director of the University of California Museum of Paleontology in Berkeley, agrees. 'It means there was an elaborate machinery in place that already had some function,' he says. 'What I want to know now is what were all these genes doing prior to the advent of sponges.'"
The conundrum for normal evolution theory is clear. Why would an ancestor of sponges have needed such genes? And the ancestor must have arisen within a very narrow window. Fossil evidence of sponges goes back 650 million years; it constitutes, the authors note, "the oldest evidence for metazoans (multicellular animals) on Earth." So, what use would any species even more primitive than sponges have for orthologs of neuromuscular genes? Nobody saw it coming. It was an empirical surprise.
More recent research has discovered that the sponge's genome "contains an almost complete set of genes homologous to those found in mammalian synapses . . ., although the organism does not assemble any structure morphologically resembling a synapse . . . ." One of the researchers involved comments, "...We were hoping to understand why the marine sponge, despite having almost all the genes necessary to build a neuronal synapse, does not have any neurons at all . . . ." An abstract of the paper that describes this unexpected finding is available HERE. But the sponge genome is only one example. Research is finding case after case of ancestral species that harbor genes essential for remote descendants.
Another example: It turns out that a species of unicellular protozoan carries genes essential for metabolic processes specific to metazoans. The researchers who discovered the surprise genes (PNAS – 2010 107 (22) 10142-10147) explain, "One of the most important cell adhesion mechanisms for metazoan development is integrin-mediated adhesion and signaling. The integrin adhesion complex mediates critical interactions between cells and the extracellular matrix, modulating several aspects of cell physiology. To date this machinery has been considered strictly metazoan specific. [. . . .] Unexpectedly, we found that core components of the integrin adhesion complex are encoded in the genome of the apusozoan protist Amastigomonas sp., and therefore their origins predate the divergence of Opisthokonta, the clade that includes metazoans and fungi. [. . . .] Our data highlight the fact that many of the key genes that had formerly been cited as crucial for metazoan origins have a much earlier origin." (emphasis added)
“[M]orphological explosions may well reflect major changes in internal constraints as crucial components in speciation. If so, then the effects of natural selection may well consist largely of post-hoc fine-tuning in the distribution of subspecies and variants: quite a different account from the one of gradual selection of randomly differing small variations.”
— Jerry Fodor and Massimo Piattelli-Palmarini
What Darwin Got Wrong
And the surprises keep coming. Science magazine (July 6, 2007) reports, "The newly decoded DNA of a few-centimeter-tall sea anemone looks surprisingly similar to our own," a team led by Nicholas Putnam and Daniel Rokhsar from the U.S. Department of Energy Joint Genome Institute in Walnut Creek, California, reports on page 86. "This implies that even very ancient genomes were quite complex and contained most of the genes necessary to build today’s most sophisticated multicellular creatures."
Newer (2007) sequencing and analysis results corroborate the anemone anomalies.
Another example comes from research at the European Molecular Biology Laboratory, which found human genes in a marine worm. The news release (11/24/2005) announcing the discovery is at http://www.embl.de/aboutus/communication_outreach/med ia_relations/2005/051124_heidelberg/index.html
Additional research has found that genes essential for human nerve cells to communicate with one another are present already in bacteria. This research is described in a NIH news release (6/1/2004) at http://www.nichd.nih.gov/new/releases/genes.cfm
Yale researchers recently found 1500 mammalian genes active only in placental mammals, but present also in marsupials. The genes are transpositions that act as regulators. In a Yale press release, researcher Vincent J. Lynch, comments on the peculiarity of the "prefabricated" mechanism, "These transpositions are not genes that underwent small changes over long periods of time and eventually grew into their new role during pregnancy," Lynch said. "They are more like prefabricated regulatory units that install themselves into a host genome, which then recycles them to carry out entirely new functions like facilitating maternal-fetal communication."
Some protein-coding genes active in humans were present already when humans and chimps diverged, but did not become active until after the divergence. Some enhancer genes in vertebrates also preceded their expression. And new research data reveals that some aquatic plants were genetically "per-adapted" for life on land. A report on this finding is available at http://www.biomedcentral.com/1471-2148/10/341.
In 2012 researchers sequenced the genomes of freshwater and saltwater stickleback fish, and found that certain genetic loci are consistently involved in the adaptation, and that the majority are in regulatory, not coding, regions (see The genomic basis of adaptive evolution in threespine sticklebacks (Nature, Vol. 484, April 5, 2012). In commentary, Hopi E. Hoekstra observes, "Thus, it seems that repeated evolution of traits may often, but not always, arise from genetic variation that already existed in an ancestral population." Here is another instance of pre-adaptation.
In 2013 researchers affiliated with The Brown Lab at Mississippi State University and researching evolutionary protistology identified a new protist, Pygsuia biforma, that carries genes formerly thought to be associated only with multicellular organisms. MSU Researcher Matthew Brown comments, "We then looked for specific multicellular toolkit genes, and we found genes that scientists had believed to be animal-specific. Integrins and the whole suite of proteins that work with integrins were thought to be something innate to multicellularity and used only for cell-to-cell communication. This discovery shows that these genes have been co-opted for a different use. We don't know what it does in unicellular organisms, but we can now place the origin of genes that are associated with multicellularity in unicellular organisms."
In 2015 researchers discovered deep-sea microbes with eukaryote-like genes and concluded (emphasis added),
"Our results provide strong support for hypotheses in which the eukaryotic host evolved from a bona fide archaeon, and demonstrate that many components that underpin eukaryote-specific features were already present in that ancestor."
Their report appeared in the journal Nature: http://www.nature.com/nature/journal/v521/n7551/full/nature14447.html
In 2018 researchers at the University of Iowa discovered eukaryotic genes in giant viruses. According to a university news release, "[A] University of Iowa biologist identified a virus family whose set of genes is similar to that of eukaryotes, an organism classification that includes all plants and animals," The family of viruses possesses "eukaryote-specific genes in a form that predates the latest common ancestor of all eukaryotes,” said Albert Erives, associate professor in the Department of Biology. This discovery suggests that eukaryotes are more closely related to viruses than had been suspected. "And the reason is because they share core histones, which are fundamental to eukaryotes,” said Erives. The research paper in which Erives discusses the finding is online at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5704553/.
These and other phylogenetically anomalous discoveries are collected at http://www.panspermia.org/oldgenes.htm. This page of Brig Klyce’s "Cosmic Ancestry" web site includes commentary on the relevance of these findings to panspermia. A summary of these kinds of peculiar findings appears also in the January 1, 2011, issue of The Scientist. In the article From Simple to Complex, author Jef Akst observes, "Conventional thought on evolutionary change has led researchers to believe that genetic innovations underlie the transition [from unicellular to multicellular life]. Advances in genomics research, however, are revealing that more and more of the genes associated with complex processes also exist in simpler animals and even in their unicellular cousins. This suggests that the appearance of new genes cannot fully explain the appearance of new traits that are key to multicellularity." [emphasis added]
This conclusion is supported by more recent research findings. In 2018 Science featured a round-up of new discoveries concerning the mechanisms of multicellularity (The Power of Many, June 29, 2018 ). The article’s gist begs the question as to whether evolution is a mound of lucky coincidences or a pre-programmed development, as in the life cycle of an organism.
A finding highlighted in the article is from the work of Nicole King, a biologist at the University of California, Berkeley. She found “a revealing window” into the evolutionary transition from uni- to multicellular organisms. Having cultured single-celled choanoflagellates in her lab, she then found physiochemical peculiarities in these protists. The article explains,
“Her lab began turning up gene after gene once thought to be exclusive to complex animals--and seemingly unneeded in a solitary cell. Choanoflagellates have genes for tyrosine kinases, enzymes that, in complex animals, help control the functions of specialized cells, such as insulin secretion in the pancreas. They have cell growth regulators, such as p53, a gene notorious for its link to cancer in humans. They even have genes for cadherins and C-type lectins, proteins that help cells stick together, keeping a tissue intact.
“All told, by surveying the active genes in 21 choanoflagellate species, King’s group found that these ‘simple’ organisms have some 350 gene families once thought to be exclusive to multicellular animals, they reported on 31 May  in eLife. If, as she and others believe, choanoflagellates offer a glimpse of the one-celled ancestor of animals, that organism was already well-equipped for multicellular life. [....]”
That is a point to ponder. Is there a credible Darwinian explanation? Does being well-equipped for multicellularity lend a survival advantage to a single-celled organism? It’s unclear what sort of evolutionary story would account for this far-sightedness in the microbe’s genome. The article continues,
“The ancestral versions of those genes might not have done the same jobs they later took on. For example, choanoflagellates have genes for proteins crucial to neurons, and yet their cells don’f resemble nerve cells, King says. Likewise, their flagellum has a protein that in vertebrates helps create the body’s left-right symmetry, but what it does in the single-celled organism is unknown.”
These findings are all the more interesting in the context of the star larvae hypothesis, because they make evolution look like an instance of development, with an ancient, primitive form of life carrying genes that descendants far in the future will put to use, just as unexpressed genes in a zygote will play crucial roles in the physiology and biochemistry of the zygote’s differentiated cellular descendants.
The article’s author concludes, “Genetic comparisons between simple multicellular organisms and their single-celled relatives have revealed that much of the molecular equipment needed for cells to band together and coordinate their activities may have been in place well before multicellularity evolved.”
Again, why would evolution not seem to be a process of development, given the many examples of descendant genes being present in ancestors? Yet the field’s best minds continue to trod the Darwinian path. Despite these anomalies.
What is particularly striking about these findings, taken together—and what is particularly interesting to the star larvae hypothesis—is not only that they were unanticipated by the practitioners of the Modern Synthesis, but also that they make the evolutionary process look strikingly like a developmental process in which genes needed by descendants (species and cell types, respectively) are stored, ready and waiting, already in ancestors.
On Human Nature
All complex organisms begin life as a single cell, a zygote. The zygotes of seahorses, hummingbirds, and humans are phenotypically indistinguishable. They all look alike. The zygotes divide and their descendant cells divide until enough cells are present to trigger a specialization of functions. The collective labors of the resulting specialized cells constitute the physiology of the embryo that those cells, in aggregate, constitute. As each organism develops, the distinctive, specialized, adult features of the species emerge.
During embryological development, a cell that is a progenitor of a liver cell gives rise to a true liver cell; a cell that is a progenitor of a neuron gives rise to a neuron, and so on. Embryonic cells give rise to cells of specific types that behave in specific ways in their interlocking niches within the somatic ecology of the developing organism.
To elaborate on a point made earlier, is this process of differentiation/specialization—of descent with modification—guided or random? Teleological or Darwinian?
Consider a thought experiment: Insofar as the cells in the body of a complex organism vary phenotypically from one type to another and insofar as not every cell survives to contribute its genetic and epigenetic predispositions to the next generation, there is a natural selection among cells during embryonic development and, indeed, throughout the life of a complex organism. The thought experiment consists of fitting ontogenetic cellular differentiation into the Darwinian model of descent-with-modification via natural selection. The consideration underscores an early and continuing criticism of Darwinian logic, namely that it is tautological. When formulated as "survival of the fittest" the doctrine of natural selection identifies the fittest organisms as those that survive and the survivors as those most fit. Ontogeny also can be seen through such a lens, as a phylogeny, a "cytophylogeny," in which a common ancestral starting point—a zygote—begets successive generations of increasingly diverse descendants, the specialization of the types being shaped by natural selection, the survivors being the fit and the fit surviving.
Imagine, then, cognitively gifted and secularly inclined cells, living in a complex organism and having developed their own theory of the evolution of cell types, marveling at the blind workings of chance variation and natural selection that turned their common ancestor—the original zygote—into the complex ecosystem of interdependent cell types to which they find themselves adapted. Fitness selects the survivors, they might announce, as demonstrated by their survival! We would understand that these scientifically minded cells had missed the boat, that they in fact live by an ontogenetic program and that they were fated from the start to be teased out of the genotype of their zygotic ancestor. Wrongheaded as it would be, their thinking would be consistent with the Modern Synthesis.
Harvard paleontologist Stephen Jay Gould accounted for the apparent progress of evolutionary change with the metaphor of "the drunkard’s walk." In this thought experiment one must imagine a drunkard staggering along a wall. He ventures varying distances from the wall as he makes his way along it. The distance from the wall at any particular instant is just whatever it is. An increase in average distance over time is merely a function of time passing. The more time that passes, the greater the number of opportunities for the drunk to stumble even farther from the wall than he or she previously had ventured. Increasing distance from the wall corresponds to increasing complexity, with the wall representing the unicellular limit of biological simplicity. By this metaphor the apparent increase in complexity of organisms over evolutionary time, which suggests a direction to evolution, is understood to be the undirected increase of mere variation. Increases in variation are sufficient to produce increases in complexity, given enough time. Gould lays out this model of pseudoprogress in Full House. But is the "drunkard's walk" a plausible metaphor for cellular differentiation in a developing organism? Probably not. Something else is afoot.
Philosophers Kim Sterelny and Paul E. Griffiths, in Sex and Death: An Introduction to Philosophy of Biology, elaborate on Gould's metaphor (their book is reviewed on the starlarvae blog):
"Life starts off as simple as life can be. Mostly, it stays that way. Most living things have always been as simple as the first living things, for nearly every organism is a bacterium. Occasionally lineages split and a species appears that is more complex than its parent. No global evolutionary mechanisms make this impossible, but none make it more likely. Complexity increases by passive diffusion from a point of minimum complexity, then wholly undirected, stochastic mechanisms will increase the variance, and that variance must include a bias in the direction of increased complexity. Mechanisms that are blind to complexity suffice to produce an upward drift in average complexity. The fact that there is no bias in the mechanisms of adaptation, speciation, or extinction that favors increased complexity, together with the persistence of bacterial domination of the living world is fatal to any robust version of the idea that evolution over time has generated increased complexity."
Fodor and Massimo Piattelli-Palmarini
What Darwin Got Wrong
When this same line of thinking is applied to ontogeny, the shoe seems to fit as comfortably. Maybe cellular differentiation during the ontogenetic development of an organism is the result of wholly undirected, stochastic processes that merely increase variation among cell types. The received view says NO; explanations from phylogeny are inadequate to account for ontogeny. But the parallels are striking: Some cell types, some early undifferentiated types of the blastula, for example, go extinct during ontogeny. Though, some ancestral types persist, in the form of adult stem cells. And, as with the Gaian biosphere, bacteria dominate, comprising 90 percent of the cells in a human body, the body's so-called, microbiome. So why assume an ontogenetic program? Doesn't Gould's evolutionary model explain equally well the diversification of cells during ontogeny? Empirically, evolution and development are of a kind: descent with modification from a common ancestor. How might theoreticians falsify either account, stochastic or teleological, in either case?
To clarify: The star larvae hypothesis does NOT argue the position suggested in this thought experiment that ontogeny is a stochastic process that increases variation among cell types. The hypothesis accepts the received view that ontogeny proceeds according to inherent developmental predispositions, of some sort, which themselves are subject to favorable or unfavorable environmental circumstances. What the hypothesis rejects is the received view when it comes to evolution. The hypothesis argues that evolution also follows an inherent developmental predisposition. The applicability of evolution's supposedly stochastic mechanisms to account for ontogeny is meant as a reductio ad absurdum of the received view regarding evolution; i.e., if natural selection theory wields such vast explanatory power, why assume that something else is at work when cells differentiate during development? Cells cooperate and compete in an organism just as organisms cooperate and compete in an ecosystem. If natural selection doesn't account for the differentiation of cells in a body, then maybe natural selection doesn't account for the differentiation of species either.
Western thinking from Plato through The Elizabethan Age conceived of Creation as structured hierarchically in the form of a "Great Chain of Being." The chain ascended from the smallest germ up through the plants and creatures to humankind and ultimately through the spheres of the firmament to the throne of God. The extraterrestrial links in the chain were/are detailed in the form of the Orders of Angels. Few thinkers today would regard such metaphors as more than poetic, a primitive conception of the natural (and supernatural) order. But in the context of the star larvae hypothesis, the Chain of Being presents a more complete picture of evolution than does the standard scientific view. What the Chain lacks, and science provides, is the temporal, dynamic dimension of the process.
The Chain of Being represents a longitudinal section through a temporal progression—a developmental sequence that leads from the terrestrial to the extraterrestrial. The Chain was conceived of at a time when Creation was regarded as static, and the Chain provided a cross section of the whole structure. But assigning the evolution of species a subordinate position within the overarching stellar life cycle effectively resurrects the Chain of Being in an ecological context. Evolution is the metamorphosis of stages in the life cycle of a genus of organism—the stellar organism. The apparent directionlessness of evolution is replaced by a processional sequence that, when viewed in a longitudinal section, takes the form of the Great Chain of Being. The intuition behind the Chain was essentially right, it just failed to take into account the underlying dynamic, temporal process.
Do the novelties that Evolution - the Extended Synthesis introduces to the Modern Synthesis add up to anything? The editors of Evolution - the Extended Synthesis fail to use the new findings to compose any integrated theoretical revision of the Darwinian model. The new findings seem to be offered as odds and ends to be grafted here and there onto the existing theory. If any consistent wrinkle emerges, it is the shift of explanatory credit for shaping phenotypes from exogenous to endogenous factors. Does that causal shift stretch the Darwinian model to the breaking point? That's the position of Jerry Fodor and Massimo Piatelli-Palmarini in "What Darwin Got Wrong" (reviewed on the starlarvae blog). But those authors don't offer up any new model. And neither do the collected papers in Evolution - the Extended Synthesis add up to a new model.
If new data break or threaten to break the Modern Synthesis, then biological science is headed towards a Kuhnian revolution. The star larvae hypothesis describes what a new revolutionary theory of evolution might look like, because it puts endogenous factors front and center in its model of evolution. But it goes beyond the toe-in-the-water approach of evo-devo to subsume evolution altogether under development. In light of the Extended Synthesis, what’s going on in evolution looks so much like what goes on in development that it makes evolution distinguishable from development only by scale.
The Extended Synthesis plants a mastodon smack-dab in the middle of the drawing room of evolutionary theory, because it forces the theory to face up to the ontogenetic concept of life cycle, with all of its teleological/programmatic implications. The many developmental mechanisms that evolutionary biologists borrow to explain evolution point to the unfolding of the life cycle of an organism. Even the Gaia hypothesis, in its strongest form, does not fully develop the entailed notion of life cycle. How long can evolutionary biologists keep borrowing explanatory mechanisms from developmental biologists before they are forced to admit that evolution is a developmental process and therefore the unfolding of a life cycle?
The star larvae hypothesis proposes that biological evolution on Earth and Earthlike planets is only a phase in a complex lifecycle: It is the larval phase of the stellar life cycle. The hypothesis endorses the vocabulary of ontophylogeny, or evelopment, introduced in the quotations at the top of this page (though Kupiec would see ontogeny absorbed into phylogeny, and the star larvae hypothesis sees the integration going in the opposite direction). The star larvae hypothesis models descent with modification as a system of nested developmental cycles that accommodates phenotypic adaptation to environments at all levels in the nested structure and includes programmatic development at all levels, or adaptive life cycles within adaptive life cycles.
The Star Larvae Hypothesis:
Stars constitute a genus of organism. The stellar life cycle includes a larval phase. Biological life constitutes the larval phase of the stellar life cycle.Elaboration: The hypothesis presents a teleological model of nature, in which
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