While evolution involves changes in organisms that we can observe, they undergo evolution at a deeper level, too. That is, changes affect the "letters" (four different types of chemical units) in the genetic blueprints -- the genes -- that are carried in their cells. Each gene is a chemical recipe for a protein that the cell manufactures.
The genes and their messages are, of course, invisible to us, but in the past few decades scientists have learned to decipher the genetic code and read the messages.
Even individuals that look and appear to be the same may be distinctively different because of variations in their genetic code at different places on their chromosomes (the structures that carry the genes). The changes and variations in genetic code that occur over time are referred to as "molecular evolution." The molecular evolution of an organism can be very different from its morphological (body features) evolution.
Millions of changes in DNA molecules have occurred over the time modern species evolved. Those changes have been both minor -- variations of a few letters in the code -- and major -- mutations in which a whole piece of a gene is replaced. Some changes are negative -- they cause a normal protein not to be made by the cell, or to have harmful properties. Other changes are positive, in that they help the organism adapt to a changing environment, and many changes are neither good nor bad, but neutral.
There are two hypotheses that attempt to explain the patterns of gene changes that scientists have observed by studying the DNA of myriad organisms. One, put forward in the late 1960s by Japanese biologist Motoo Kimura is referred to as "neutral drift." According to this hypothesis, most of the changes in DNA inside individuals are the result of "genetic drift" -- random changes that go on all the time and aren't steered by natural selection in one direction or another. Those who support this explanation say that most genetic changes are neither helpful not harmful, but may become common in a population (or disappear entirely) due to chance events. Therefore, random processes explain most of evolution at the molecular level.
The other explanation is that natural selection does drive most evolutionary change in DNA. In other words, the alterations in the genetic code that can be found in creatures' cells represent beneficial changes that natural selection has fixed in the genes because they help the organism adapt. Detrimental mutations, on the other hand, tend to be lost because they are selected against.
This disagreement about the frequency of neutral versus advantageous mutations remains unsettled, though the debate has waned in recent years. It drove the development of methods for analyzing sequence data and focused scientists' attention on the essence of the evolutionary process.
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