Evidence of Evolution
Catastrophism eventually lost out scientifically to evolution, because evolution succeeds but catastrophism fails to explain the patterns of fossils and of living things, and to predict events such as the emergence of antibiotic-resistant microorganisms. The triumph of evolution over catastrophism owes much to biology, and more recently to genetics and molecular biology; the identification of the mechanisms driving evolution was especially important (see below).
As geologists collected more data, they joined the biologists in recognizing that evolution explained the data and predicted the next discoveries better than any catastrophist model, or any other model that anyone had ever suggested. The early geologists could see the clear change of types over time but saw catastrophic elements in the record as well. In many places, geologists would find fossils of one type, and then of a somewhat different type, with no transitions between them. Evolution implies rather gradual change, not big jumps. The early geologists knew, however, that there were big time jumps in the records (remember the many unconformities—time gaps—in the Grand Canyon sequence). So some of the jumps in the fossil record were related to the incompleteness of the rock record. And, there really were catastrophic extinction events in the record such as the meteorite that killed the dinosaurs (again, see below).
Further study has shown that many of the evolutionary changes have been biologically slow but geologically fast - recall how long geological time really is! And, many of the evolutionary changes occurred in small isolated populations that are not likely to have been fossilized. Suppose that a few animals of some type colonized a small island. Then, they had babies who had babies who had babies, a generation per year, thousands of generations in a geological eyeblink. If the babies differed by just a tiny bit from the parents, eventually a new type or species would have emerged. If that species then succeeded in escaping the island (say, because sea-level fell and the island became connected to the mainland), a new type could appear suddenly on a nearby continent. Sediments from the small island may have been subducted or otherwise destroyed, but fossils on the larger continent are more likely to have been preserved. A small island may support only a few individuals, so there never would have been many critters to produce fossils that humans could find. On the continent, the species might flourish and produce millions of individuals that left easily collected fossils. Thus, the fossil record would show a sudden jump when the actual process was gradual.
In one famous case (of many), trilobites of the genus Phacops are classified in part by the number of columns of elements in their compound eyes. In marine sediments from the Devonian (the middle of the Paleozoic) of Pennsylvania and Ohio, a species with eighteen columns in its eyes occurred for a while. Then, a time gap or unconformity occurred, from a temporary drying of the sea. When the sea returned and began depositing sediments again, the trilobites that returned with it had seventeen columns in their eyes. Not a huge jump, but an apparently sudden one. But wait—over in a small part of New York, the sea did not dry up. There, you can find the old eighteen-column trilobites, then some with seventeen columns plus a partial column containing a varying number of elements, and finally the seventeen-column trilobites. The generations of trilobites changed gradually, and you can see this where the rock record is complete in a small region of New York. In the bigger areas, the record looks more catastrophic because the seaway was dry and no fossils were produced when the changes were occurring through the generations living in New York.

You may meet someone who argues that no transitional fossils are known. This is wrong; extremely fine gradations are known in many, many lineages, including the Phacops eye columns. There is one technical sense in which, in some lineages for which fossils are scarce, there are missing transitional types. Suppose you find young fossil type 1 and old fossil type 0. They differ a good bit—you are missing the transitional form 1/2. Now suppose you find type 1/2. It is your “missing link”. You publish your results in important scientific journals, and wait for the fame and fortune to roll in. (You are likely to wait a looooooong time….) But, while you’re enjoying your discovery, someone argues that you haven’t really found the missing link, because now there are TWO transitional types missing: 1/4 between 0 and your newly discovered 1/2, and 3/4 between your newly discovered 1/2 and 1. So, you go back to work, and after years of effort, succeed in finding both 1/4 and 3/4. Wow! Now your critics point out that you are missing FOUR transitional forms (1/8, 3/8, 5/8, and 7/8). This can be argued to absurdity; we cannot find remains of every creature that ever lived, because almost all remains of almost all creatures are recycled by the efficient ecosystems of Earth (dead things are food to scavengers, worms, bacteria, fungi, etc.). But for many, many fossil types now, the gaps are vanishingly small, and the transitional forms are very well known.
The gaps in evolutionary lineages are especially well-filled for commonly fossilized types, such as creatures with shells from shallow ocean water. Shells are hard and resistant—they’re really rocks already—and so shells are preserved well. Sediments from the deep ocean are often lost down subduction zones, but shallow edges of continents are often preserved, with their fossils, for very long times. And while most of the land is eroding, most of the ocean is accumulating sediments.
The fact that most of the land surface is eroding complicates the study of the fossils that especially interest people. Think about central Pennsylvania for a moment, where Dr. Alley was sitting when he wrote this. The Commonwealth of Pennsylvania has about 1 million deer, roughly half bucks and half does, and each buck has two antlers, so Pennsylvania deer drop about 1 million antlers per year. If antlers were “preserved,” then after even a few thousand years of this, walking in the state should be dangerous, and we should hear about all sorts of antler puncture wounds from the billions of antlers scattered over the landscape. Of course, we don’t—mice, porcupines, and other creatures eat the antlers for the minerals in them. (People even collect a few shed antlers, but other creatures beat us to most of the antlers.)
In central Pennsylvania now, the only places you can find sediments being deposited are in the human-built reservoirs (which were mostly formed when dams were built in the 1930s, and so give very, very short records), a very few marshes such as Bear Meadows up the road from Penn State's University Park campus (this marsh formed during the Ice Age and thus is geologically very young), and in a few caves and along a few streams. But, the caves and stream deposits don’t last long—the caves are lost as the surface is lowered, and the streams sweep across their flood plains and move the sediments on. So central Pennsylvania today is not making much of a fossil record.
Despite difficulties such as this, careful study around the world has filled in many of the details of the fossil record, including many “missing links.” (In 2001, for example, road-builders accidentally discovered Riverbluff Cave in Missouri, with loads of ice-age fossils that offered a new window into that interesting time.) For some types of creatures, such as hominids, fossils are still scarce enough that a new find often makes headlines, and may cause a small change in the prevailing view of evolutionary history. And there was lots of excitement in 2008 when fossils of transitional flatfish were found—Darwin had worried about the way flounders evolved so the adults have both eyes on the same side of their heads, so the discovery of the transitional forms was another in the long string of successes for the theory he advanced. However, you almost never read about the great changes in thinking caused by the latest snail fossil—the record is so wonderfully complete that new insights are much harder to come by than they used to be.