As we continue to study the fossil record, we find a correlation between the age of rock layers and the types of organisms we expect to find. There is a clear pattern of change in organisms throughout the fossil record - a progression that starts with simple, basic organisms and slowly evolves towards the complex creatures we see today. For example, rocks around 550 million years old contain simple multi-cellular organisms, while "modern" species of mammals are only found in rocks younger than 65 million years.
What are we to do with the fossil record then? In his book Coming to Peace with Science, Darrel Falk discusses three different ways that a Christian can explain the fossil record. The first is that God created each species individually from nothing (ex nihilo), beginning with the simplest organisms and then creating more complicated creatures as time went on. The second possibility is that God worked in "bursts", creating a few protoype species at a time and then allowing microevolution to account for variations among each species. In this view, foxes and wolves, for example, share this common "dog" prototype ancestor, but no species cross-over exists (such as between cats and dogs).
The third view -- and the one that fits with the BioLogos perspective -- is that God creates through a process of gradual change. All organisms have a common ancestry with other organisms. In such a view, God does not go through periods of sporadic activity, but is continually involved in the unfolding process of creation.
Whichever view one chooses to embrace, it is important to realize that the information found in the fossil record does not imply that God was absent from creation, nor does it imply that God set up the universe and then chose to sit back and simply watch.
For more about what the fossil record says and how it fits with BioLogos, be sure to read Coming to Peace With Science and the question "What does the fossil record show?" at www.biologos.org.