[98G]

This is a great thread. University of California Museum of Paleontology has compiled a decent collection of papers regarding “where we are in the theory.” It is extensive, so here is summary of some points from paleontologists which may be useful.

The strict biological definition is "a change in allele frequencies over time." By that definition, evolution is a fact. Common descent is not a proven fact. The theory that all life arose from one common ancestor is not the theory of evolution, but it is a fraction of it (as well as several different theories). The theory of evolution says that life evolved and it also includes mechanisms, like mutations, natural selection, and genetic drift, which go a long way towards explaining how life evolved. That framework is accepted in science as a way to sort and understand data. Scientific method needs a paradigm.

"Transitional fossils"

This is a sequence of similar genera or families, linking an older group to a very different younger group. Each step in the sequence consists of some fossils that represent a certain genus or family, and the whole sequence often covers a span of tens of millions of years. A lineage like this shows obvious morphological intermediates for every major structural change, and the fossils occur roughly (but often not exactly) in the expected order. There are still gaps between each of the groups -- few or none of the speciation events are preserved. The major point of these general lineages is that animals with intermediate morphology existed at the appropriate times, and thus that the transitions from the proposed ancestors are fully plausible. General lineages are known for almost all modern groups of vertebrates.

This is a set of numerous individual fossils that show a change between one species and another. It's a fine-grained sequence documenting the actual speciation event, usually covering less than a million years. These species-to-species transitions are unmistakable when they are found. Throughout successive strata you see the population averages of teeth, feet, vertebrae, etc., changing from what is typical of the first species to what is typical of the next species. Many "species-to-species transitions" are known, mostly for marine invertebrates and recent mammals (both those groups tend to have good fossil records), though they are not as abundant as the general lineages.

Both types of transitions often result in a new "higher taxon" (a new genus, family, order, etc.) from a species belonging to a different, older taxon. For example, the Order Perissodactyla (horses, etc.) and the Order Cetacea (whales) can both be traced back to early Eocene animals that looked only marginally different from each other, and didn't look at all like horses or whales. But over the following tens of millions of years, the descendants of those animals became more and more different, and now we call them two different orders.

Gaps

1. The first and most major gap, "stratigraphic discontinuities", meaning that fossil-bearing strata are not at all continuous. There are often large time breaks from one stratum to the next, and there are even some times for which no fossil strata have been found. For instance, the Aalenian (mid-Jurassic) has shown no known tetrapod fossils anywhere in the world, and other stratigraphic stages in the Carboniferous, Jurassic, and Cretaceous have produced only a few mangled tetrapods. (One study estimated that we may have fossils from as little as 3% of the species that existed in the Eocene.) This, obviously, is the major reason for a break in a general lineage. To further complicate the picture, certain types of animals tend not to get fossilized -- terrestrial animals, small animals, fragile animals, and forest-dwellers are worst.

Species-to-species transitions are even harder to document. To demonstrate anything about how a species arose, whether it arose gradually or suddenly, you need exceptionally complete strata, with many dead animals buried under constant, rapid sedimentation. This is rare for terrestrial animals. Even the famous Clark's Fork (Wyoming) site, known for its fine Eocene mammal transitions, only has about one fossil per lineage about every 27,000 years. Luckily, this is enough to record most episodes of evolutionary change (provided that they occurred at Clark's Fork Basin and not somewhere else), though it misses the most rapid evolutionary bursts.

In general, in order to document transitions between species, you need specimens separated by only tens of thousands of years (e.g. every 20,000-80,000 years). If you have only one specimen for hundreds of thousands of years (e.g. every 500,000 years), you can usually determine the order of species, but not the transitions between species. If you have a specimen every million years, you can get the order of genera, but not which species were involved.

2. Most fossils undoubtedly have not been found. Only two continents, Europe and North America, have been adequately surveyed for fossil-bearing strata. As the other continents are slowly surveyed, many formerly mysterious gaps are being filled (e.g., the long-missing rodent/lagomorph ancestors were recently found in Asia). Of course, even in known strata, the fossils may not be uncovered unless a roadcut or quarry is built (this is how we have most of our North American Devonian fish fossils).

Documenting a species-to-species transition is particularly grueling, as it requires collection and analysis of hundreds of specimens. Typically we must wait for some paleontologist to take it on the job of studying a certain taxon in a certain site in detail. Almost nobody did this sort of work before the mid-1970's, and even now only a small subset of researchers do it. For example, Phillip Gingerich was one of the first scientists to study species-species transitions, and it took him ten years to produce the first detailed studies of just two lineages.

3. Even when they are found, they're not popularized. The only times a transitional fossil is noticed much is if it connects two noticably different groups (such as the "walking whale" fossil reported in 1993), or if illustrates something about the tempo and mode of evolution (such as Gingerich's work). Most transitional fossils are only mentioned in the primary literature, often buried in academic papers later referenced already collapsed to the genus or family level. The two major college-level textbooks of vertebrate paleontology (Carroll 1988, and Colbert & Morales 1991) don't even describe anything below the family level. Many of the species-to-species transitions were described too recently to have made it into the books yet.

What paleontologists do get excited about are topics like the average rate of evolution. When exceptionally complete fossil sites are studied, usually a mix of patterns are seen: some species still seem to appear suddenly, while others clearly appear gradually. Once they arise, some species stay mostly the same, while others continue to change gradually. Paleontologists usually attribute these differences to a mix of slow evolution and rapid evolution (or "punctuated equilibrium": sudden bursts of evolution followed by stasis), in combination with the immigration of new species from the as-yet-undiscovered places where they first arose.

There's been a heated debate about which of these modes of evolution is most common, and this debate has been largely misquoted by laypeople. Virtually all of the quotes of paleontologists saying things like "the gaps in the fossil record are real" are taken out of context from this ongoing debate about punctuated equilibrium. They are arguing about how often evolution occurs gradually.

• Gingerich, 1980, who found 24 gradual speciations and 14 sudden appearances in early Eocene mammals;
• MacFadden, 1985, who found 5 cases of gradual anagenesis, 5 cases of probable cladogenesis, and 6 sudden appearances in fossil horses;

One good thing about scientific method -- it accepts new data and allows for a theory to be disproven. I am attaching a table regarding types of evolutionary work (non-Darwinian, Darwinian and Neo-Darwinism). One bad thing about accepted theory, the paradigm will occasionally obfuscate the new data and reject it unconsciously -- but not for long. Science is competitive.