There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one; and that whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning, endless forms most beautiful and most wonderful have been, and are being evolved.
—Charles Darwin, On the Origin of Species, 1859, final sentence
No serious biologist doubts the theory of evolution is the best explanation we have thus far for the complexity and diversity of life on earth.  Given the genetic relatedness of all known organisms, it is hard to imagine how one would go about understanding biology without the foundation that evolution provides. Oh, one could do what was once called natural history and classify living things in various ways, but one could not engage in modern biology.
Let’s consider a few more things we have learned from genetics and molecular biology in the past decade or so.
When the Human Genome Project started, it was known that there were over three billion base pairs in the human genome. There was a general expectation that around 100,000 genes would be found. It turns out that only about 1.5 percent of the genome is used to code proteins; we have only about 20,000 genes. As Francis Collins, the Director of the Human Genome Project, commented, many researchers
were stunned to discover that God writes such short stories about humankind. That was especially shocking in the context of the fact that the gene counts for other simpler organisms such as worms, flies, and simple plants seems to in about the same range, namely around 20,000. 
Despite the tremendous difference in complexity, we have roughly the same number of genes as a roundworm that has fewer than a thousand cells in its body.
Collins goes on to suggest that this could mean that there is a basic vocabulary of genes and that, just as the same basic English vocabulary can be used to draft a simple document (such as this post) or more complex works (say, the plays of Shakespeare or Paradise Lost), it seems that the genomes of worms, insects, crocodiles, and condors all need the same genetic vocabulary as ours. Our complexity would thus arise not from the raw number of our genes but from the eloquence with which they used.
In the previous post we looked at how one type of comparison of our DNA with that of other species demonstrated evidence of common ancestry. There is remarkably little genetic diversity among living things. All human are 99.9+ percent the same genetically, and now that we have been able to sequence the genomes of many species, we can begin to compare the coding differences among them. If we take a section of a human gene (say, a part that contains instructions for a particular protein), we will nearly always find a significant match in the genome of another mammal. Some genes will show discernible, if imperfect, matches between humans and fish. Sometimes we can even find matches with simpler creatures such as roundworms. There are some examples where the similarity extends even to yeast and bacteria.
But most of our genome is not genes. The vast majority lies between the genes and has been labeled by some as “junk DNA.” This DNA does not seem to be involved in any known blueprint process. If we search through the junk for matches between species, they are less common.
Here’s what. This provides two powerful supports to Darwin’s theory of evolution.  First, looking at entire genomes, we can sort them (using computers because the bookkeeping is tedious) according to the similarities in the sequences of different organisms. The result is the sort of family trees of the shown in Figures 2 and 3. Please note that this processes does not use any information from the fossil record or from the comparative anatomy of any species. It’s strictly biochemistry.
Second, looking within genomes, Darwin’s theory predicts that mutations that do not affect function (the changes in the “junk DNA”) will pileup over time. Mutations of the genes that control coding should be observed less frequently because most mutations are unfavorable; organisms with such mutations will be still born or quickly die out. Only favorable changes will survive through natural selection. This is exactly what we see in nature.
This preference for non-fatal mutations in the coding region of genes allows for the possibility of so-called “silent” mutations. For example, there are two base pair code sequences that will program for the production of glutamic acid; either a GAA- or a GAG-sequence in the DNA will do the trick. The third base in the sequence can mutate between A and G or G and A without damage to the organism. When we compare the genomes of closely related species, such silent differences are more common in the genes than mutations that actually change amino acids. Again, this is exactly what Darwin’s theory predicts.
The genetic similarities among species is striking. I suppose that one could argue that God put all these bits of DNA in their precise locations to confuse us. That implies that He did it to mislead us. However, I reject that argument as a violation of the first of my First Principles. God does not lie. It seems much more likely that humans and other mammals share a common ancestor, that mammals and all other animals share a common ancestor, that animals, plants, and fungi share a common ancestor, and, indeed, all living things share a common ancestor. And that would mean that we’ve evolved as a result of changes in our genome.
Let’s pause for a moment and reread Genesis.
11And God said, Let the earth bring forth grass, the herb yielding seed, and the fruit tree yielding fruit after his kind, whose seed is in itself, upon the earth: and it was so. 12And the earth brought forth grass, and herb yielding seed after his kind, and the tree yielding fruit, whose seed was in itself, after his kind: and God saw that it was good.
20And God said, Let the waters bring forth abundantly the moving creature that hath life, and fowl that may fly above the earth in the open firmament of heaven. 21And God created great whales, and every living creature that moveth, which the waters brought forth abundantly, after their kind, and every winged fowl after his kind: and God saw that it was good. 22And God blessed them, saying, Be fruitful, and multiply, and fill the waters in the seas, and let fowl multiply in the earth. 23And the evening and the morning were the fifth day.
24And God said, Let the earth bring forth the living creature after his kind, cattle, and creeping thing, and beast of the earth after his kind: and it was so. 25And God made the beast of the earth after his kind, and cattle after their kind, and every thing that creepeth upon the earth after his kind: and God saw that it was good.
26And God said, Let us make man in our image, after our likeness: and let them have dominion over the fish of the sea, and over the fowl of the air, and over the cattle, and over all the earth, and over every creeping thing that creepeth upon the earth. 27So God created man in his own image, in the image of God created he him; male and female created he them.
—Genesis 1, Authorized Version 
If all the species living on the earth are the result of natural selection of random mutations, why does Genesis speak of the various creatures bringing forth offspring “after their kind”? I suppose that depends on what the meaning of “after their kind” is. 
If that phrase means that cats only give birth to unmutated cats and dogs to unmutated dogs, then evolution has a problem. But a literal interpretation of the English translation has issues as well. For a start, we know that mutations do occur. We see them. Someone might suggest that these verses are about a time before the Fall and that the Second Law of Thermodynamics (and random mutations and death) did not come into operation until Adam’s sin. That is an interesting possibility, but it is speculative. Nothing in the Bible says that explicitly , and one can just as easily argue that the Second Law came into operation with the fall of Satan—which for all we know could have happened before our universe was created.
On the other hand, suppose “after their kind” means using sexual reproduction as it now exists on earth. That is not necessarily inconsistent with the text , and it is consistent with what we see in the world around us. This would allow for creation to begin with plants (and when I was taking biology in high school, bacteria and the like were still considered plants) and to expand into animal life in increasing complexity, ending with humans.
Notice also that God commanded that the earth and the waters “bring forth” the living things He created. The text doesn’t say how, it just says that God commanded and that it was so. Thus, when I look at what Scripture really says and the evidence of God’s handiwork in creation, I am led to believe that He was wise enough to create a universe that would use the natural processes He provided from the beginning to work its way toward producing the creatures God wanted. Of course, God may have created each species or group of species separately, but there is nothing in Genesis that requires us to say that God used any particular means other than His commands for the universe to be as He willed. But His fingerprints seem to be on one particular method—evolution through natural selection.
This does not mean that God has never miraculously intervened in time and space. The Virgin Birth and the Resurrection of Jesus are clearly outside of the normal processes of nature, as are other events recorded in the Bible.
The Bible tells us that God could even work a miracle with dry bones if He chose to.
Figure 2. A Simplified Mammalian Family Tree. The relationships among species are inferred solely from DNA sequencing. (After Collins) 
Figure 3. A Simplified Family Tree for Living Organisms. The letters denote the introduction of a characteristic passed on to all descendants from a common ancestor.
A, mitochontria B, chloroplasts C, xylem, phloem D, seeds E, enclosed seeds F, moocots G, organs H, nervous system I, protosome J, deuterosome K, vertabrae L, jaws M, digits N, amniote O, two fenestrae P, hair, endothermy Q, feathers R, placenta
UPDATE—Since the essay upon which this post is based was first written, work detailing the actual observation of evolution in bacteria was reported by Richard Lenski of Michigan State University. Lenski was working with colonies of E. coli, and after around the 31,500th generation, something dramatic happened in just one of the populations—the bacteria suddenly acquired the ability to metabolize citrate which E. coli normally cannot use. Indeed, the inability to use citrate is one of the traits by which bacteriologists distinguish E. coli from other species.
“It’s the most profound change we have seen during the experiment. This was clearly something quite different for them, and it’s outside what was normally considered the bounds of E. coli as a species,” says Lenski.
One of the claims of anti-evolutionists is that speciation has never been observed. Well, now it has.
 Evolution is most precisely defined as the change in genetic coding in a genome from one generation to the next.
 Collins, Francis, The Language of God, Free Press, New York, 2006, p. 125.
 ibid., pp. 127, 128.
 There have been several theories of evolution. Darwin’s theory of evolution is that all species are descended from one or a very few common ancestors with natural selection operating on randomly occurring variations. We hear about Darwin’s theory more than the others because it has been most successful in explaining the real world.
 The Authorized Version is the official name of what most people call the King James Version. It was a translation “authorized” for use by the Church of England.
 No jokes about the meaning of “is” please.
 Yes, I am aware of I Corithians 15:21, 22. “For since by man came death, by man came also the resurrection. For as in Adam all die, even so in Christ shall all be made alive.” (Authorized Version) I suggest that since the life Christians have in Christ is eternal, the death brought by Adam’s sin is more than mere physical death but a spiritual death which separates us from God and from which Christ’s perfect sacrifice saves us. Death must have been in the world at the time of Adam. Even if he were a vegetarian, plants would have had to die to feed him.
 Actually, it seems quite consistent with a literal translation of Gen. 1:12 which could read, “And the earth caused to go forth grass, herb seeding seed after its own kind.”