Saturday, April 23, 2011

Darwin Eclipsed & The Rise of Evo Devo

The development of any complex organism reveals a weave of relationships between the organism's phenotype and its genotype. I will focus on four of these relationships and argue for a new interpretation of the genetic data:

First, although the skin, liver, muscle, brain and other cell types that compose a body are morphologically and functionally diverse, they are not genetically diverse. They all inherit the same genotype from their common ancestor, a zygote. That is, during the descent with modification from a zygote to its descendant cell types, DNA is conserved. Diverse phenotypes do not require diverse genotypes.

Second, Because all cells in a body (excluding parasites and symbionts) inherit the same genotype, they necessarily inherit many genes that they do 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 brain cells. And so on. The excess DNA in each cell type includes genes needed to create and operate all the other types. But from the point of view of a given type of cell, the DNA for the other types is junk.

Third, the expression of genes in any particular cell type, and the timing of their expression, is controlled by other genes that act as on/off switches. This is how a single genotype expresses multiple phenotypes (skin, liver, muscle, etc.) in a single body -- by turning various genes on and off here and there at various times.

Fourth, a zygote carries genes that will be required by its descendants. The zygote anticipates the needs of the skin, liver, muscle, and other descendant cell types and carries their genes, even if the zygote itself does not express them. These, then, are some of the characteristics of development. They include conservation of DNA, junk DNA, switches that conrol the expression of cellular phenotypes, and genes that anticipate the needs of descendants.

Now, when we look at the genetics of evolution, we find all the same hallmarks. Since genetic sequencing and analysis have come online, the parallels between development and evolution--between ontogeny and phylogeny--have come sharply into focus. A new discipline within evolutionary biology, called evolutionary developmental biology, or Evo Devo, is trying to shoehorn the new genetic data into the old, Darwinian, paradigm. But comparative genomics is rewriting the book of evolution into something that readers of the first edition might not recognize as the same work.

First, insects, fish, birds and primates are morphologically and behaviorally dissimilar, but not because their genotypes are to any comparable degree dissimilar. Genetic sequencing and analysis tell us that these creatures all inherited same basic genetic toolkit from a common ancestor. That is, despite all the phenotypic variation, DNA is conserved across species during evolutionary descent.

Genes for limbs are pretty much the same from limbed species to limbed species, whether the wings are on a dragonfly, a bat, or a bald eagle. The underlying genes are about the same. Evolution, like development, conserves DNA. Researcher Sean Carroll, an architect of Evo Devo, comments, “Comparison of genomes tells us that not only do flies and humans share a large set of developmental genes, but that mice and humans have nearly identical sets of about 25,000 genes, and that chimps and humans are almost 99 percent identical at the DNA level. The common tool kit and the great similarities among different species genomes present an apparent paradox.” (All Carroll quotes are from his book, Endless Forms Most Beautiful, The New Science of Evo Devo.) Yes, the great similarities do present a paradox. Because they make evolution look like a large-scale development.

Second, all species carry unexpressed "junk" DNA. Carroll calls this DNA "dark matter" because most of it "contains no instructions and is just space-filling 'junk' accumulated over the course of evolution. In humans, only about 2 to 3 percent of our dark matter contains genetic switches that control how genes are used."

So, even if a small percentage of the "junk" is actually performing a function in a given organism, by switching genes on and off, the majority of it is truly junk (at least to those who carry it around unexpressed), which makes evolution look like development.

Third, the control of phenotypic expression in any species is controlled by genetic "switches" that are themselves turned on and off by regulatory proteins. These switches provide a mechanism whereby conserved DNA can express dramatic phenotypic variation across species. This observation is foundational to Evo-Devo, which treats species as variants produced by the conbinatorics of genetic switching.

Fourth, we notice that ancestral species carry genes required by remote descendants. Ancestral genomes anticipate the needs of phenotypes to come. An example emerges from the sequencing of a sponge, the Great Barrier Reef sponge, Amphimedon queenslandica. A news article in Nature (The Amphimedon queenslandica Genome and the Evolution of Animal Complexity, Vol. 466, Pages 720–726, August 5, 2010) covering the sequencing of the sponge's genome reveals that the hoary creatures harbor a tool kit 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 palaeobiologist 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 a common ancestor of the sponge and animals with neuromuscular systems have needed such genes? Plus, the ancestor would have had to 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 the neuromuscular genes?

Here's a longer quote from Sean Carroll that summarizes the unexpected findings that genetic research is yielding and the significance of Evo Devo in light of the preceeding observations:
"The first and still perhaps the most stunning discovery of Evo Devo is the ancient origin of the genes for building all sorts of animals. The fact that such different forms of animals are shaped by very similar sets of tool kit proteins was entirely unanticipated. The ramifications of these revolutionary findings are powerful and manifold. "First of all, this is entirely new and profound evidence for one of Darwin’s most important ideas—the descent of all forms from one (or a few) common ancestor. The shared genetic tool kit for development reveals deep connections between animal groups that were not at all appreciated from their dramatically different morphologies.
"Second, the discovery that organs and structures that were long viewed as independent analogous inventions of different animals, such as eyes, hearts, and limbs, have common genetic ingredients controlling their formation has forced a complete change in our picture of how complex structures arise. Rather than being invented repeatedly from scratch, each eye, limb, or heart has evolved by modification of some ancient regulatory networks under the command of the same master gene or genes. Parts of these networks trace back to the last common ancestor of bilaterians (Urbilateria), and earlier forms.
"Third, the deep history of the toolkit reveals that the invention of these genes was not the trigger of evolution. The bilaterian tool kit predated the Cambrian, the mammalian tool kit predated the rapid diversification of mammals in the Teritary period, and the human tool kit long predated apes and other primates. It is clear that genes per se were not 'drivers' of evolution. The genetic tool kit represents possibility—realization of its potential is ecologically driven."
This last comment begs the question, "How did all that potential get into the ancient genomes?" It's as if Earth's earliest life had zygote-like powers of anticipation. Researcher Michael Sherman argues for a similar conclusion in his paper, "Universal Genome in the Origin of Metazoa" (Cell Cycle 6:15 1873-1877, Aug 2007).

So, do the genetic parallels between ontogeny and phylogeny add up to anything?

They do. They suggest that ontogeny and phylogeny constitute two scales on which operates a common process of descent with modification. This suggestion implies that both the ontogenetic and the phylogenetic expression of phenotypes is susceptible to environmental contingencies. This is a mundane, noncontroversial observation. Environments are known to influence whether phenotypes become tall or twisted, atrophied or robust, as with vitamin deficiencies in animals and photo- and geotropisms in plants.

But the counterpoint to that observation is inescapably controversial: The data that inform Evo Devo imply that both the phylogenetic and the ontogenetic expression of phenotypes unfolds according to a program. Phenotypic expression in both cases conforms to a process of development. It conforms to the unfolding of a life cycle.

So, if species differentiate in an ecology and across a planet as cells do in and across an embryo, whose life cycle has been unfolding during the evolution of phenotypes on our planet?

My candidate for the ontogeny underlying phylogeny is the stellar life cycle.

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.