It took 2,100 million years for life to evolve from bacteria and bluegreen algea to multi-celled creatures like jellyfish. It took another 1,900 million years to get from them to trilobites with shells. It took almost another 100 million year for vertabrates to arise, and another 100 million years after that for the first mammals to appear. Primates have existed for a mere 67 million years. Hominids go back only about 5 million years. Neaderthals go back perhaps 0.2 million years. The Neolithic revolution, which brough us agriculture, written history and fixed urban settlements is only about 0.01 million years old.
Perhaps then, it shouldn't be a surprise the a huge amount of our DNA is involved is establishing the biochemistry of life which took so long to evolve, while a relatively small amount of our DNA is involved in determining our far more recently evolved gross anatomy.
It takes a tweak in just a single gene for a fruit fly to grow on eye on its leg. A single common human mutation causes children to be born with an extra toe or finger. The famous statistic is that we share 98% of our DNA with chimpanzees, whom no one would mistake for humans in a police lineup. The fruit fly isn't the only example of a very subtle change in genetics having a huge macroscale effect. Experminents have show that just a single gene can account for homosexual behavior in a certain kind of animal -- causing males to follow instictual female mating rituals. A single chemical can engender a psychological response as complex as what we call "social trust".
How is this possible? Clearly, in the case of the fruit fly with the extra eye, somewhere deep in the fruit fly DNA there are elaborate subroutines for creating eye tissues (which have no doubt been evolving since the first flatworms had a light sensitive spot). The final gene simply tells the body when to trigger that subroutine. Similarly, our bodies have codes for leg or arm subroutines that can probably be tweaked with just a slight adjustment. Indeed, it appears that just a single gene govern's our body's chirality -- a mutation of this gene that causes someone to have organs that are on the opposite sides of the body from where they are usually found is not that uncommon.
What is the significance of this reality? One is that it strikes a dagger in the heart of the "irreducible complexity" arguments for intelligent design. Most intelligent design proponents see a big distinction between speciation accompanied by major morphological change, and incremental evolution within a species. Yet, because so much of our DNA is already encoded with "subroutines" for different kinds of biochemistries and tissues and even larger structures, a very small number of mutations can produce major, speciating morphological changes. Most animals have the same basic biochemistry as all other animals. Most plants have the same basic biochemistry as all other plants. Almost every living thing has basically the same basic DNA scheme with the same basic biochemical "letters" arranged in the same basic way, which in turn operates within cells. All of the "complex" life on this planet is based on the same basic concept of a multi-cellural creature with certain kinds of specialized cells that cluster together to form different kinds of tissues.
It also explains why mutations from time to time produce viable new forms that blend gracefully, rather than being nearly always fatal. Why do wolphins (whale-dolphin mixes) manage to develop inside their mother's wombs and live lives unaware that they are a cross-species mix, rather than aborting in all cases out of gross incompatability of form? Because, both species have basically the same biochemistry and set of subroutines. The adjustment that comes from hybridization take place at a very high genetic level with only a modest number of parameters setting forth the animal's gross form. Both have subroutines for brains, for hearts, for intestines which automatically kick in at an appropriate level for the overall scale of the animal and which have evolved in a manner that naturally blends seemlessly with other components of the overall animal.
The scenario of the "War of the Worlds" where alien invaders are defeated upon their arrival on Earth not by our weapons of war, but through contamination by our biosphere, in which they are not adapted to live, is not far fetched. One need look back no further than our Native American ancestors who were wiped out by small pox, to which they had no prior exposure, after a mere 10,000-30,000 years of living as seperated populations, to see just how easily this could happen. Our immune systems are in many respects far more sophisticated than our anatomy in the codes that give rise to them.
As we grow to better understand matters like the biochemistry of the brain, our very language will change. The analytic tree which we use to sort mental illnesses and conditions into categories will change from being symptomatic to causal. Once we classified physical ailments by symptom, like fever or vomitting. Now, our first cut is often amongst ailments caused by viruses like the flu, bacteria like many infections, parasites like sleeping disease, or certain classes of proteins call prions (not to be confused with preons which are theoretical subatomic particles), like Alzheimer's. Similarly, in the future we may very well classify mental conditions into those associated with the lympic system, with dopamine production, with serotonin production, with the hypocampus, and so on. These classifications will in turn, by their very names, suggest cures. Who would have guessed that research into M.S. would be likely to also have benefits for lupus, for example, until we knew that both are autoimmune diseases. Conditions with very dissimilar symptoms may all be treated with dopamine regulating drugs, and so on. We may even begin to have a biological basis for classifying emotions in particular categories based on the chemistry behind them. Some conditions which seemed very complex in symptom, multiple personality schitzophrenia, perhaps, might turn out to actually be quite simple deficencies in a single biological process, while other seemingly symptomatically simple conditions, depression, perhaps, might be prove to have multiple complex causes.
Once we do manage to link cause and effect to a wide variety of conditions, some difficult questions of identity and philosophy will arise. Which conditions do we accept as part of who we are, and which do we classify as ailments that should be cured. For example, most people who really understand what homosexuality is (i.e. a biological predisposition, at least in substantial part), tend to see homosexuality as part of who someone is, rather than as a hereditary disease to be cured, despite the fact that statistically homosexuality is "not normal". But, as biotechnology improves, those distinctions will increasingly be socially agreed classifications, rather than questions of practical ability to "treat" conditions.