Biological evolution can, in my opinion, most usefully be divided into three levels of description: microevolution, macroevolution, and common descent. Each of these levels has evidence that it happens and theories that explain how it happens. These are separate issues, and should be treated as such.
Microevolution: Definition and Evidence That it Happens
Microeveolution is small-scale changes in population characteristics from one generation to the next. Such small-scale changes are observed on a such a regular basis that microevolution is generally considered to be a scientific fact. Average human height has changed over the past several hundred years. The frequency of peppered moths of different colors has shifted. Bacteria develop antibiotic resistance. Even the most hardcore creationists generally accept the reality of microevolution, though often they will call it something like “variation within kind.”
Microevolutionary Theory: Mechanisms that Shift Characteristics in a Population and Decrease Genetic Diversity
There are multiple components to the new-synthesis theories of microevolution, all intended to describe the observation that microevolution happens in detail. All of these components are based on the inheritance of traits through DNA. These are mechanisms that shift the genetic frequency in a population. Given a population with diverse characteristics, one generation may have a different balance of those characteristics than a preceding generation. The peppered moths are a good example of a case of microevolution that requires no more than a shift in genetic frequency. Factors such as natural selection (when there is a survivability advantage), sexual selection (when there is mating based on non-survivability-related traits), and genetic drift (when the traits involved are not selected either for or against, but rather shift in frequency randomly) contribute to this shift. This list of mechanisms, if they are carried to the point of all individuals with a particular trait failing to reproduce, all act to decrease genetic diversity in a population, where some genetic material is passed on and other material is not.
Microevolutionary Theory: Mechanisms that Increase Genetic Diversity
If those were the only mechanisms acting, it is pretty clear that before long the genetic diversity within a population would become negligible. Fortunately, we also know that there are numerous mechanisms that increase the genetic diversity in a population. Point mutations are cases where one nucleotide is mistranscribed during replication. The rate of these mutations is high; a typical estimate is that there are around 64 such mutations per human relative to their parents, of which 1-6 are nonsilent. Addition and deletion mutations are more rare, but provide significantly more new material with each occurrence. Chromosomal duplication is relatively common; by introducing an extra copy of a gene, one can be left alone (maintaining the old functionality) while the other can mutate by other mechanisms (e.g., point mutation), exploring new possibilities (as an example, ATPase, a molecular motor, consists of a conglomerate of several proteins, all of which are minor modifications of each other). Chromosomal breakage and realignment involves genes transferred to different parts of the DNA; this generally leaves the individual unaffected, but changes which traits are associated with each other in the individual’s children. Retroviruses, plasmids, bacterial DNA exchange, and symbiotic transfer are examples of horizontal genetic transfer between species. Transposons and recombination shuffle existing genetic material into new combinations. All of these mechanisms are well understood on a molecular level and are observed in the wild.
So we have the “fact” of microevolution, the mechanistic theories of how microevolution happens, and verified predictions of microevolutionary theory, which include nearly every piece of genetic testing, animal husbandry, and plant breeding ever done. Since it is unlikely that anyone, even hardcore creationists, disagrees with microevolution, I will leave it at that.
Macroevolution: Definition and Evidence That it Happens
Macroevolution is defined as the successive changes in a population over multiple generations to the point of speciation and beyond. As we had with microevolution, macroevolution can be divided into the fact (i.e., the direct observation that it happens), the theories (mechanistic explanations for how it happens), and successful predictions of the theories. There are numerous documented cases of speciation both in the laboratory and in the wild (see below), so claiming that macroevolution is a fact is in fact well warranted.
Macroevolutionary Theory: The New Synthesis
The mechanism of macroevolution, in the new-synthesis theories, is simply the accumulation of microevolutionary steps. In our theories of microevolutionary mechanism, we have single-step explanations for genetic (and thereby phenotypic) change. Macroevolutionary theories take these starting points and try to determine the population changes, rather than individual changes, over multiple generations. So, with microevolution we have a low-level understanding of the processes involved. Now, with macroevolution we aim to develop a medium-level understanding. The high-level understanding will wait until the theories of common descent.
Macroevolutionary Theory: Speciation
The key question in terms of speciation is what causes the population to split. If you start with one population of a species, how does that turn into two populations that cannot interbreed successfully (one of the ways to define species as separate)? Within a single population that interbreeds relatively homogenously, recombination effects cause mutations to spread more or less evenly. This has been seen in controlled studies on fruit flies, for example. However, reproductive isolation prevents the mutations from crossing the population boundary, allowing the populations to diverge genetically. It is no surprise, then, that speciation theory rests heavily on splitting the populations. And in practice in the laboratory, it is just such population splitting (frequently coupled with different environments to provide different selection pressure) that is used to demonstrate speciation (I highly recommend this site, specifically the section titled “Mechanisms of Macroevolution”).
Just as in microevolution, genetic diversity is increased in macroevolution by some mechanisms and decreased by others. Species extinction is the decrease mechanism for macroevolution.
Verified predictions of macroevolutionary theory include the many observed instances of speciation, both in the laboratory and in the wild. You can find descriptions of many such examples here and here.
Microevolution is a fact. Macroevolution is a fact. Both have been directly observed in real-time. While there are undoubtedly details of mechanic theories explaining how they happen that will be further refined as science progresses, there is no question within the scientific community that these phenomena are real, nor is there any question that we correctly understand the broad outlines of their mechanisms.
Common Descent: Definition and Evidence That it Happens
The high-level evolutionary theory is common descent, which states that all living things have descended from a single common ancestor. Unlike the facts of microevolution and macroevolution, common descent is not directly observable. Rather, common descent is a conclusion reached that seems to best explain various data, selected portions of which I describe below. Importantly, the evidence suggesting that common descent has occurred can, in some cases, be independent of the proposed mechanism.
There is extensive molecular evidence supporting the concept of common descent. I will describe one simple example here: pseudogenes (for further details, see this document). Most animals make their own ascorbic acid (Vitamin C). Humans cannot. The genes that make ascorbic acid in other animals are known. If, in fact, humans are descended from other animals, then there would almost certainly be vestigial remnants of this ascorbic acid synthesis gene, though turned off through mutations, in our genetic code. Indeed, we lack a functional gene encoding the enzyme protein known as L-qulono-gamma-lactone oxidase (LGGLO). In sequencing chromosome 22, 134 pseudogenes (genes that are no longer functional due to mutation) have been identified.
There are numerous embryonic features common across a wide variety of species that develop into different final phenotypes. Slits in the neck form gills in fish and Eustachian tubes in mammals. Similar bone structures form jaw bones in reptiles but ear bones in mammals. The list goes on and on, emphasizing that underlying all of this difference is a variation-on-a-theme structure, just as predicted by common descent theory.
Why do all mammals have four appendages, whereas insects have six (not why four and six respectively, but why the consistency within the groups)? Why does a giraffe have the same number of neck vertebrae as you and I do? Why is the bone structure in a whale’s fins so similar to that in other mammals’ limbs? Bats have fur and give birth live to their young and lactate, whereas birds don’t do/have any of those features. Why that sharp division, showing similarities with mammals but not birds on nearly every count that other mammals and birds differ on? In short, why are there so many striking examples of hierarchical taxonomy? Common descent predicts this directly. Why the presence of vestigial features? Why the evidence of jury-rigging in nature, exactly as predicted by common descent theory? In short, the morphological evidence for common descent is overwhelming.
Thus far we have extensive experimental support for the theory of common descent even without resorting to the fossil record. Of course, the fossil record is also strong support for it. Phylogenic trees developed by biochemistry and by morphology match those developed by looking at the fossil record. We see smooth transitions at the species level, above the species level, and at even larger scales.
Common Descent: Verified Predictions of the Theory
It is often claimed by creationists that evolution (by which they mean common descent) isn’t science because it doesn’t make predictions. Here are some examples of predictions that have been made by the theory of common descent which have been borne out by the evidence. For these examples I am indebted to this site:
- There are two kinds of whales: those with teeth, and those that strain microscopic food out of seawater with baleen. I was predicted by common descent theory that a transitional whale must have once existed, which had both teeth and baleen. Such a fossil has since been found.
- Common descent predicts that the fossil record will show different populations of creatures at different times. For example, it predicts we will never find fossils of trilobites with fossils of dinosaurs, since their geological time-lines don’t overlap. The “Cretaceous seaway” deposits in Colorado and Wyoming contain almost 90 different kinds of ammonites, but no one has ever found two different kinds of ammonite together in the same rockbed.
- Common descent predicts that animals on distant islands will appear closely related to animals on the closest mainland, and that the older and more distant the island, the more distant the relationship. This is indeed what is observed.
- Common descent predicts that features of living things will fit in a hierarchical arrangement of relatedness. For example, arthropods all have chitinous exoskeleton, hemocoel, and jointed legs. Insects have all these plus head-thorax-abdomen body plan and six legs. Flies have all that plus two wings and halters. Calphterate flies have all that plus a certain style of antennae, wing veins, and sutures on the face and back. You will never find the distinguishing features of calypterate flies on a non-fly, much less on non-insect or non-arthropod.
- In 1837, a Creationist reported that during a pig’s fetal development, part of the incipient jawbone detaches and becomes the little bones of the middle ear. After evolutionary theory was developed, it was predicted that there would be a transitional fossil, of a reptiles, with a spare jaw joint right near its ear. A whole series of such fossils has since been found, the cynodont therapsids.
- In 1861, the first Archaeopteryx fossil was found. It was clearly a primitive bird with reptilian features. But the fossil’s head was very badly preserved. In 1872 Ichthyornis and Hesperonis were found. Both were clearly seabirds, but astonishingly they had teeth. It was predicted that if we found a better-preserved Archaeopteryx, it too would have teeth. In 1877 a second Archaeopteryx was found, and the prediction was found to be correct.
- The same amino acid can be coded by multiple sequences of DNA. Many point mutations will change the DNA sequence without changing the coded-for DNA sequence. Such changes are called DNA “spelling” variants. Common descent predicts that relationship trees generated by other means (biochemical similarity, morphological similarity, etc.) will show the same pattern of relatedness of genetic spelling variants; closely related species will have few spelling differences, whereas distantly related species with the same protein will have significantly more spelling differences. This is exactly what is observed.
This is only a small sampling verified predictions of common descent theory (selected to be easily accessible to the layman).
Common Descent: Summary
Despite what you may have heard from the creationist community, there is no meaningful debate in the scientific community over the fact of microevolution, the fact of macroevolution, and that common descent is correct. There are debates over some mechanistic details, but none of those debates call into question that evolution, up to and including common descent, happened. Evolutionary theory, up to and including common descent, is the foundation upon which our entire understanding of biology rests, in the same way that quantum mechanics and statistical thermodynamics are the foundations upon which chemistry rests.
That said, there are certainly details that are still being worked out. A great example is punctuated equilibrium, or PE for short. There are few aspects of evolution that are as misunderstood as PE. It is often presented, occasionally even by practicing biologists, as periods of rapid evolution that are interspersed among periods of relative stasis. This is, however, not quite right. Punctuated equilibrium does predict that at most fossil sites the observed morphological changes will appear rapidly. But that does not mean that evolution happened rapidly.
The notion behind PE is that in most situations, an ecological niche is filled relatively well by the species that is already present. Thus, most expressed mutations result in decreased survivability, and therefore are selected against. Let us imagine one species spread over a large area, like the Buffalo were over the great plains of the United States. When they die, they produce fossils. Over relatively long periods of time, most surviving mutations are silent (in that they change the ‘spelling’ of the genes, but not the expressed proteins), because the nonsilent ones tend to cause a decrease in survivability. But occasionally, a helpful change occurs. Let’s say that happens in Iowa. this produces a changed species, and the change opens up the possibility of new, complementary changes further increasing fitness. Thus, ‘suddenly’ (in terms of an evolutionary timescale, though this still takes a very long time), changes start to accumulate, and the species ends up looking very different. Now, what happens when this new species spreads out over Nebraska, Kansas, and Oklahoma? The old species gets overrun. Thus, at most sites where we find fossils (e.g., Oklahoma), it looks as though first there was one species, and then suddenly there was another one. It is only if we happen to find fossils at just the spot where the modifications happened that we see the transitions clearly. In fact, given this proposed mechanism, it is highly surprising that we have found as many transitional forms as we have!
To put this theory into the framework I provide above, microevolution is a low-level mechanistic theory, macroevolution is a medium-level aggregate theory, PE is a medium-high-level hierarchical theory, and common descent is a high-level theory. The evidence that microevolution has happened is exceptional and direct, and our mechanistic understanding is very high. The evidence that macroevolution has happened is exceptional and direct, and our mechanistic understanding is high. The evidence that common descent has happened is exceptional but indirect, and our mechanistic understanding is moderate. The evidence that punctuated equilibrium has happened is moderate and indirect, and our mechanistic understanding is moderate.
There currently is not a scientific consensus on punctuated equilibrium. There are proponents of it, and there are detractors, and the evidence thus far isn’t conclusive. Nonetheless, it is important to note that acceptance or rejection of PE is uncoupled from acceptance or rejection of common descent, for which the evidence is significantly stronger.
Evolutionary theory starts operating once there are biological entities that can reproduce imperfectly, fueling “descent with modification.” Evolutionary theory is completely silent on the origins of this first biological entity. Abiogenesis, or the production of life from nonlife, is the scientific field that tries to address this separate question. Abiogenesis is significantly more speculative than evolution, and while we have some very good ideas about how it probably happened, those ideas are still extremely tentative. It is vital to understand that even if our current theories of abiogenesis (most notably the RNA mechanisms) fall, that would do nothing to call into question evolutionary theory, which is independently supported to a ridiculous degree. Abiogenesis is probably worth a separate post, so I will leave that topic alone for now.
Evolutionary theory is the central organizing principal of modern biology. It is the pervasive framework that explains life from a biochemical level to an ecosystem level, and everything in between. There is no scientific debate over whether evolution occurred, including common descent. There are still details that are being worked out on the mechanisms and implications, but that is separate from the observable facts leading inescapably to the conclusion that it happened, and that we understand most of the details of how it happened.