Evolving

We don't need a theory to tell us that life, even in its most rudimentary forms, actively transforms inert matter into the substances it incorporates into its physical being. This is known from clear observation. It's called eating. We multicellular creatures almost from the start adopted a body plan to deliver nutrients to the cells that make up our various forms. This underlying body plan consists of a mouth, a gut, and an anus. Materialistic science proposes a theory which asserts that this orchestrated activity is a property of the substances that make up every living thing. This means the various elements, like carbon, oxygen, hydrogen, which assemble themselves into incredibly intricate and complex molecules like sugars, lipids, proteins, which become blood, skin, bone, nerve tissue. This means the blossoming of an embryo into a child is no different than the combining of sodium with chlorine into common salt. But living things act differently than inanimate substances.
Salt is a crystal and we are told that some crystals propagate themselves in ways analogous to living things, thus indicating how life originated as a natural, ie random, phenomenon. Which has continued to transform itself into more and more complex chemicals. Obviously, it's hard to imagine how life could exist without the chemical constituents of the physical body. However, looking at the tableau of life on earth it seems equally obvious that some other principle is at play than randomicity. It appears to this observer that life, that utterly intangible concept, is the opposite of random; it intentionally uses the material constituents of the universe to assemble a physical presence in that universe.
Because Life is the ultimate abstract concept. We humans along with daffodils, slugs, and lichens, use virtually identical materials to create radically different organisms which have radically different affects on the physical earth. Living things are responsible for the makeup of the earth's atmosphere, for the structure and distribution of rocks in the continental crust, perhaps for seeding clouds to form raindrops, and for moderating the climate so that wild swings of temperature are avoided. As a result of life, the behaviors of living things, this planet of ours is an entirely different kind of object than it would be if it was lifeless.
Most of this action is a byproduct of the chemical activities which take place within a cell, and there is no suggestion here that some sort of conspiracy took place among the spirochetes and the polyps to come up with all this but there is no denying that the world that has come about through their influence is a place more congenial to life than it was in the beginning.
In fact it became so congenial that a veritable explosion of life has occurred not only in the amount of inanimate material that is now either alive or of organic origin ready to be recycled again, but in the kaleidoscopic variety of life, far beyond the most vivid imagination. This amounts to a riot of invention. Even now researchers are being surprised by new and unbelievable discoveries.
Much of this explosive diversity seems to be due to the 'invention' of the eukaryote cell which seems to be linked to the 'invention' of sexuality. Researchers are constantly finding new ways living things have of exchanging genetic information. It could be that viruses and cancers are such methods. But with sexuality and a nucleus this exchange of what amounts to an accumulation of knowledge about experimental investigations. Death might also be thought of as another innovation that promoted the diversification of life forms. Bacteria are basically immortal because they proliferate by dividing. An individual bacteria can die but its clones continue on. Therefore the accumulation of 'knowledge' within the genetic apparatus is slow, although it now appears that interspecies exchanges of genetic code is more common than suspected. Sexual reproduction regularizes the exchange of genetic information which results in more rapid innovation. These innovations are more structural than chemical, or more accurately the chemistry of individual cells specializes. Both plants and animals have light sensitive cells, but plants use them to produce sugar and animals use them to see with. The whole story is available for examination, but what was already a difficult problem in Darwin's day has only grown more intractable as more information has been accumulated by scientists. At the time for instance, the idea of separate species didn't seem problematic. There were dogs, cats, apes, flies toadstools, and it was all perfectly straightforward except in certain unusual cases. The discovery of genetics seemed to simplify and resolve the questions of how, but does it? In animals, energy production is largely a function of mitochondria. Although enclosed within the nucleus mitochondria are actually separate organelles with their own genetic structures. Mitochondria more or less define what an animal is. Plants derive their energy from a different organelle, the chloroplast, which is able to convert sunlight into sugar, which can be metered out in the precise quantity needed by the plant for growth and reproduction. It is now thought that chloroplasts and mitochondria were originally independent entities which the precursors of plants and animals hijacked for their own use. There don't appear to be any free ranging mitochondria or chloroplasts roaming the oceans or the dry land nowadays. Question: do we use them for our benefit or do they use us for theirs? They may have started out as parasites or infections, and parasitism and infection are major issues for all living things, even us two legged geniuses. A recent type of parasitism recently observed is a fungus transmitted from cats to rodents. Harmless to cats, the fungus causes the rat or mouse to be attracted to the smell of cat piss. Could it be that those strange ladies living with hundreds of cats have contracted the same infection?
But not all parasitism is harmful. Sometimes it's entirely beneficial, in which case the relationship between host and guest is called symbiosis. As in the complex population of microbes living in our guts without which we would not be able to digest our food. Certain varieties of E. Coli perform these services for us, and it is well known that cows are only able to digest grasses with the help of microorganisms that convert otherwise indigestible cellulose into sugar. Neat trick. Without those bacteria cows would die out...and all that flatulence that so terrifies the econazis. But without cows to keep those grasses in check who knows what calamities would transpire. Sounds like a business opportunity for the Goracle. But for the purposes of this discussion, can cows be considered a species apart from the happy bacteria busily fermenting cellulose in all those bovine stomachs? And how is this explicable in terms of Darwinian theory? Cooperation, competition, parasitism leading to terrestrial transformation. Neat trick.
Here's an interesting factoid I read of not long ago. It had to do with fruit flies where the writer informed his readers that there is more genetic variation within one species of fruit flies than there is spread out among the entire order of mammalia. I have no reason to doubt this information since it was conveyed by someone who had spent his life studying cladistics, but if this is so then what exactly does genetics have to do with species- by which I will continue to mean dogs and cats and rats and so on.
I am asking all these questions not because I am trying to discredit the idea of evolution. I have no doubt it took place. But how? And what does it mean to our understanding of the universe, ourselves, God, art, time, and this strange experience of being alive?

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.