The Domains of Life

Not so long ago biologists had a nice and tidy classification system for life on earth. There was the animal kingdom and the vegetable kingdom and the only uncertainty was to which kingdom certain problematic life forms belonged. That's all changed. The new dividing line is between prokaryotes and eukaryotes, and more recently a third fork, the archaea, has been identified. These deepest roots of the tree of life classifications are now called domains. The domain archaea represents what are most likely the most ancient of organisms that thrive in all sorts of hellish environments, like next to undersea lava flows, in boiling geysers and deep in the bowels of the earth where pressures are so high that water won't boil no matter how hot the temperature. These archaea, until recently unknown, may be the largest component of earth's biomass. Interestingly, there are indications that we multicellular eukaryotes are more closely related to the archaea than to the more familiar bacteria that live on the surface of the earth. According to some theorists the archaea are survivors of journeys through interstellar space. The late Fred Hoyle believed life was ubiquitous throughout the universe and actually mediated star formation. He was a pioneering giant of cosmology who didn't believe in the Big Bang theory. In fact, he was the one who coined that expression. One of the reasons he came to this conclusion was that he didn't believe the Big Bang theory left enough time for the building blocks of organic life to arise through random processes. If the actuarial figures he quotes are correct no circumstance is imaginable in which even the enzymes that form the building blocks of life could have spontaneously come into existence. This may sound like a pretty radical idea, but he wasn't trying to be radical. He was trying to save the theory...the theory of a materialistic origin of life.
Other advocates of conventional evolution theory have also seen difficulties and tried to find ways out. The idea of a gradual accumulation of mutations is one of those difficulties and some writers think the discovery of homeobox genes solves the problem. The problem is this: major classes of life forms don't appear gradually in the fossil record but all at once. The naturalist Steven Jay Gould spent a career pondering this problem and proposed a theory called punctuated equilibrium, based on his study of the Burgess Shales. This is not a theory, it's a description, a word, a verbal shorthand for, "there are epochs in geologic history when the earth is dominated by one type of life form- such as dinosaurs- which suddenly end and another dominant life form suddenly explodes in numbers and diversity- such as mammals- occupying ecological spaces once occupied by the now defunct biological order." This completely undermines the theory, but the homeobox gene clusters at first glance seem to save the day. This is a type of gene that mediates the expression of the rest of the genetic activity of the organism, and it takes very few changes in the way homeobox genes transcribe genetic information to cause massive changes in the organism as a whole. It is a master gene set, an amplifier. They are found in multicellular life forms, in fact they are what make organized multicellular life possible. But how do the homeobox genes know when to kick into gear? We have had nearly two centuries of fairly meticulous observers who would have noticed if homeobox genes had a habit of suddenly going wild. Nevertheless it's a good thing to know, that any given creature can fairly quickly alter its form. If it needs to. But how does it know it needs to? How does it know that its adaptations for survival are no longer operable and need to be changed? How does it settle on a new set of blueprints? This is really what's necessary to save the theory of natural selection, which also is just terminology, like punctuated equilibrium, not really a respectable theory. Just because you've got a name for something it doesn't mean you understand it. Terminology is not explanation. Incidentally, the homeobox genes are the most conservative gene sets yet studied, being virtually identical in man and mouse, whose complement differs from fruit flies mainly in number.
Calling homeobox genes a set of blueprints may seem no more than metaphorical language but if they function like blueprints then maybe blueprints are a metaphor for homeobox genes. Metaphors are linguistic markers to help us understand the unfamiliar by likening it to the known. I like to use the abacus metaphor for the entire genetic concept. An abacus is used to do arithmetic. But an abacus is not arithmetic. Similarly, I think genes are used to do life but they are not life. I also like the metaphor of a movie. As an informed member of modern society you know that the movie unfolding before your eyes is the end product of a huge production apparatus. But there is in the movie itself no evidence of the existence of cameras, directors, writers, electricians, catering trucks, or investment deals. Materialists, whether scientific or hedonistic would have us believe there is nothing behind the smoke and mirrors of this weird thing called life and they can't bring themselves to acknowledge the possibility of an influence on our world that can't be learned from the physical facts discerible through the senses. Buddhists would have us believe that the material world is nothing but an illusion. Phenomenologists and post modernists don't believe in reality either. But I think they are all wrong.
I believe in evolution. It's funny to have to say it that way, like saying I believe in astrology. But there is no doubt in my mind that all life that we know of has a common ancestry and that from that theme this madcap world of ours took its present configuration. I am not the least bit offended by the idea that I'm related to a slime mold (as some have suggested) so the ape thing doesn't bother me at all. There may be variations of the currently accepted picture, such as the panspermia theory suggests.
But here's where I have a problem. It is said that between apes and humans there is only a few percent difference in genetic code separating us. That few percent has to carry quite a bit of freight. For instance, chimpanzees don't have a literature. They don't sit around campfires and tell funny stories about how great grandpa chimp stole a bunch of bananas from a mountain gorilla. Orang utans show no curiosity about the moon let alone do they scheme how to fly there. No Shakespeare, no Bible, no Euclid, no Rembrandt, no TV shows, no discernible effect on the climate, although they have been observed cheating, lying, stealing, killing and even having wars which proves to some that the apes are just like us. But generally they are the real noble savages in the estimation of the econazis who think humans are a blight on the earth.
Well, if those few differences on the DNA chain are sufficient to cause all the changes to the landscape caused by human agency then materialism has a lot of explaining to do.