Sunday, September 21, 2014

Reconceptualizing Evolution as an Instance of Development - Phylogeny is its own Ontogeny; Start with the Zygote.

During the development of a complex organism, a fertilized ovum, or zygote, divides in two, then again into twice as many cells and eventually into all the cells that compose the organism's body. As the cells proliferate, they differentiate in form and function into the various cell types of that particular kind of body. This differentiation into skin, stomach, nerve, and other cell types occurs even though the cells of a developing body all share a common genotype, that of the original zygote. The paradox of one genotype yielding many cellular phenotypes has been resolved, in a general sense, through the mechanisms of epigenetics. A relatively new branch of molecular biology, epigenetics addresses issues related to gene regulation and gene regulatory networks. The new discipline aims to explain how, during development, genes get turned on and off and when (as in larval or adult forms of organisms) and where (as in spleen or kidney) they do.

The new discipline is an upstart. Epigenetics would seem to demote DNA from being the cell's chief executive to its merely utilitarian, dumb server. DNA includes an archive of messenger-RNA templates (and the messenger RNA molecules transcribed from the templates still pass through an editing suite before being escorted to the ribosome, where they get translated into proteins). The molecular machinery of epigenetics, through normal chemical bonding, excites or inhibits DNA "expression" or "action." The countless combinations of sections of DNA that can be expressed and repressed here and there in sequence or in tandem produce multiform cellular phenotypes from the highly conserved DNA of the original zygote.

From a complex database a skilled operator can extract many kinds of reports, by slicing the data this way then that. DNA is such a complex database, responding to many and diverse calls for data. The creatures of the Earth are reports summoned from DNA, not expressions of any executive talent that resides in the DNA. This is the new view of things from the world of epigenetics.

But epigenetic mechanisms do more than regulate cellular differentiation during development. What is particularly significant, from the perspective of the star larvae hypothesis, is that epigenetic mechanisms also are implicated, increasingly, in the diversification of species from a conserved genome during evolution.

"Conserved genome" is taking a liberty, admittedly, but how much of one? As statistical genomics continues to reveal, the conservation of DNA across species is far more extensive than anyone had expected. Because genomes differ among species far less than had been anticipated, some commenters even have coined the phrase, "universal genome" to underscore the striking commonalities among genomes shared by diverse species. Evolution increasingly seems to be an instance of development, the two processes of development and evolution sharing a reliance on epigenetic mechanisms to pull forth diverse forms from a shared database. Even though development and evolution differ markedly in scale, they grow increasingly mechanically similar as research proceeds. The star larvae hypothesis suggests the term ontophylogeny to designate biology's generic process of differentiation/diversification (an appropriation from J-J. Kupiec).

Let the chips fall, but the star larvae hypothesis continues find encouragement in new discoveries in molecular biology that pertain to "descent with modification," whether the descent is of tissues during development or of species during evolution. The hypothesis watches for new breakthroughs in this area, because the trend line continues to dovetail with its prediction that evolution will come to be recognized as an instance of development.

That's when things get interesting. That's when the hypothesis directs attention to an elephant in the room. Namely, if evolution becomes mechanically indistinguishable from development, or at least so dependent on the same mechanisms that issues of spatial and temporal scale become the last refuge of defenders of the old paradigm, then potentially troubling issues arise for normal science. (These troubles don't pertain in the context of the star larvae hypothesis, however. Just saying.)

One: Development proceeds in a preferred direction. Given an accommodating environment, an adult chicken, and not an adult penguin, will be called forth from a chick embryo. Development has a teleological character. If evolution is an instance of development, then it, too, must have a teleological character, a preferred direction. This will be a tough pill for science to swallow.

Evolution coming to be seen as a process that depends on endogenous factors as much as does development raises the challenge of applying the new understanding. What might it say about evolution on exoplanets? Theorists of evolution should have something predictive to say about questions such as these: Given an Earth-size planet in some solar system's "habitable zone," i.e., at the requisite distance from the system's central star, or sun, and which planet finds itself steward of viruses and bacteria, what exogenous contingencies will influence the descent of phenotypes and to what extent and in which directions? And to what extent will endogenous physiology influence the descent of phenotypes and to what extent and in which directions? Although, such predictions might soon be forthcoming.

For its part, the star larvae hypothesis predicts that endogenous gene regulatory networks will generate phenotypes along the lines of the types of body plans that have evolved on Earth. The "tree of life" on exoplanets that bear complex life will include essentially the same major divisions, classes, orders, and phyla as those seen on Earth and probably a few platypus-like oddball assemblies as well. Incorporating the assertions of panspermia, the star larvae hypothesis assumes that diverse planets will share in the "universal genome."

>Two: Development, or ontogeny, typically is characterized as advancing through the stages of a life cycle, with the post-reproductive adult occupying the terminal stage. If evolution is an instance of development, then what is the adult form of the organism that's developing? And what events constitute a complete reproductive life-cycle of that organism?

Conceiving of life on Earth as being engaged in a process of development, a planetary ontogeny, might seem less crazy if the sceptic appreciates that the bodies of complex organisms are themselves ecologies. Most cells in a human body, for example, are bacterial cells. Each human body is a constantly evolving ecosystem of microbial symbionts, parasites and stowaways. The fellow travelers constitute the "microbiomes" that compose human bodies. Development is ecological and evolution is developmental. The same relationships seem to pertain at all scales.

The strain that humankind is putting on the Earth—particularly in light of nuclear mishaps, geoengineering, weaponized microbes, and the seemingly suicidal sociopathy of the various factions of would-be global oligarchs—might tempt observers to render a harsh verdict against humankind, to liken humans to a deadly, havoc-wreaking, ecosystem-wrecking, cancer. But such a condemnation would be misguided.

Humankind doesn't represent a global cancer that needs to be treated, but a burgeoning new life, one, however, that can distinguish itself from a cancer only by engineering its own delivery into the weightless environment of outer space.