Posted this as a response in another thread, but I figured I should move it. We always seem to get onto the topic....let's give it its own thread.
Here are 2 reasons that the fossil record is incomplete, and they are real reasons, arrived at by the scientific method. They are not excuses.
The first is that only a very tiny number of all the animals that ever lived were fossilized. Compared to every individual animal that ever lived, the number fossilized is extraordinarily tiny. More on that later.
The second reason is that most evolutionary theorists now believe that evolution occurs is steps....that there are periods of relative stasis interspersed with periods of relatively quick evolutionary change within a given population.
There are a number of reasons for this, one of which is that individuals of a given population (let's say mice for this example) are sometimes separated from their larger population, due to a storm, family migration, accident, etc. If the migrated population of mice has moved far enough, it will encounter new predators, food sources, environment, etc.
Possibly the new population will eventually die out, if they are not at all suited to their new home. But possibly (if they are plucky enough) the general population will evolve to suit their new environment. This will be a slow process, measured by human standards. It may take say 500,000 years (or 100,000 generations of mice, at a 5-year lifespan) for the new population to evolve into what we would now classify as a new species.
Now, just to push our example to the farthest, lets say something else happens: That any number of members of the new population of mice, 500,000 years later and now existing as a new species, for whatever reason returns to its ancestral stomping grounds, or at least relatively near to it. It is also possible that it never moved that far away, but was separated by a mountain for example.
Anyways, now scientists dig up fossils in that region. They find fossilized remains of 3 entire mice. They date from 14 million years ago, 12 million years ago, and 10 million years ago respectively.
The oldest mouse is 8 cm long. The second oldest mouse is 8.4 cm long. The least old mouse is 13.5 cm long, but is otherwise quite similar.
Now the 10 million year mouse has made a huge evolutionary leap from the 12 million year mouse. This is explained by the fact that the actual evolutionary change occurred over what, to a mouse, is an extraordinarily long time, but what, to a geologist, is an extraordinarily small amount of time. To find a cache of fossils cataloging the evolutionary change that happened during that half a million year period would be an incredible stroke of luck. Animals just aren't fossilized that often.
Charles Darwin, in the Origin of Species, wrote: "Many species once formed never undergo any further change....; and the periods, during which species have undergone modification, though long as measured by years, have probably been short in comparison with the periods during which they retain the same form."
