Evidence from homology

[coming soon]

Evidence from biogeography

[coming soon]

Evidence from genetics

An organism’s DNA is usually similar to that of its supposed ancestors (in the rare cases when DNA from the remains of those ancestors can be extracted and analyzed) and also to its evolutionary “cousins”—organisms believed to have descended from a relatively recent common ancestor. For example, chimpanzees and bonobos are regarded as the closest living relatives to human beings.Our most recent common ancestor is believed to have lived 5 to 10 million years ago. However, fossils of this common ancestor have not been discovered, so it is difficult to determine how long ago it lived. Estimates are based on DNA analysis and studies of other related fossils. According to recent estimates, chimps and humans share around 94% of the same genes; some older estimates suggested that the similarity was as high as 99%.See this article for further discussion.

Comparing the genomes of different organisms is far from straightforward, and estimates of genetic similarity rely on a number of arbitrary choices. For example, there isn’t any standard way of deciding whether two similar sequences of genetic information are similar enough to count as the “same gene.” Moreover, a genome typically contains multiple copies of certain genes, and researchers have to make an arbitrary choice whether to count them as a single gene or several genes.

Genetic similarities are also found in pseudogenes—segments of DNA that resemble genes but do not produce functional proteins. Some pseudogenes have other functions besides producing proteins, but many appear to serve no purpose at all. In many cases, a pseudogene differs only slightly from a functional gene, suggesting that it originated as a copy of that gene but was damaged by mutation. The prevailing theory is that non-functional pseudogenes are relics of evolution: they may have served important functions for the organism’s ancestors, but they are no longer useful. The existence of identical pseudogenes in different species is considered strong evidence that the two species descended from a common ancestor.

In rebuttal, critics point out that similar DNA doesn’t necessarily imply common descent. It may instead point to a common designer. When we find cars with similar engines and body styles, we don’t conclude that the cars descended from each other; we conclude that they were manufactured according to a similar blueprint, perhaps designed by the same team of engineers. Analogously, someone who believes that God designed all varieties of life need not be surprised to learn that He used a similar design plan for many of His creations. The degree of genetic similarity is still less surprising when we consider that DNA contains the instructions for producing many cell parts that are common to all living organisms, regardless of how closely related those organisms may be. The fact that similar organisms share many of the same genes is to be expected, whether they descended from a common ancestor or not. This alternative explanation doesn’t apply to non-functional pseudogenes, but there may be other ways of accounting for those similarities too. Many pseudogenes have turned out to serve important functions (e.g. many play crucial roles in gene-regulatory networks), and new functions for the non-protein-coding segments of DNA are still being discovered. So, seemingly non-functional pseudogenes may have been created for a purpose after all, and this might explain why humans and chimps have some identical pseudogenes even if we didn’t have a common ancestor. Moreover, bacteria and other microbes sometimes take segments of DNA from one organism and transplant it into another. This process, called horizontal gene transfer, might account for some cases in which unrelated organisms share some of the same genes and pseudogenes.

Another objection points out that geneticists rely on DNA analysis to construct theories of evolutionary genealogy: they look for genetic similarities to determine which organisms are closely related to each other. If these genetic similarities are then cited as evidence of common descent, there is a danger of circular reasoning here. For example, if geneticists conclude that humans and chimps are closely related because our DNA is similar, and then cite this similarity as evidence that closely-related species have similar DNA, they would be reasoning in a circle. Presumably no individual scientist would reason in such a patently fallacious way, but errors of circular reasoning might occur when scientists working in different fields of study rely on each other’s conclusions without examining the evidence that led to those conclusions. One may hope that other scientists would soon discover and correct these errors, but opponents of the theory of evolution often lack such faith in the scientific community.

Other critics of evolution point out various ways in which the genetic evidence appears to fit the hypothesis that life was designed better than it fits standard evolutionary theory. For example, Winston Ewert argues that the genetic evidence fits the pattern of a “dependency graph” used by software engineers much better than it accords with the “branching tree” structure predicted by standard evolutionary theory.Winston Ewert, “The Dependency Graph of Life,” BIO-Complexity, Vol 2018. <https://bio-complexity.org/ojs/index.php/main/article/viewArticle/BIO-C.2018.3> For an accessible explanation of Ewert’s argument, see this article. Still others accept the doctrine of universal common descent but argue that the genetic evidence points to an intelligently guided process of evolution, contending that genetic information could not have arisen primarily by unguided mutation and natural selection. We’ll examine some of these arguments in Chapter 11, when we discuss theories of Intelligent Design.

Evidence from paleontology

Paleontology is the science of studying fossils—the remains or traces of ancient organisms, often preserved in sedimentary rocks. The word ‘fossil,’ like any word in English, is somewhat flexible. In paleontology, the word usually is defined to include only remains and traces of organisms from a prior geological age. According to most paleontologists, fossils provide substantial evidence that life has evolved and diversified over the past several billion years. Moreover, the oldest fossils (estimated to be roughly 3.5 billion years old)We’ll talk about the methods used to date fossils on the next page. were formed by colonies of bacteria. This supports the claim that life originated with single-celled organisms and gradually evolved to the diverse and complex varieties of life we see today.

stromatolites
fossilized bacteria colonies

Some of the oldest fossils are structures called stromatolites, which were formed by cyanobacteria—cyan-colored bacteria that get their energy from photosynthesis, just as plants do. Huge colonies of these bacteria produced algae-like formations that have been preserved by fossilization.

Photo credit: James St. John, CC BY 2.0 Image cropped, contrast adjusted. Original photo here.

The set of all fossils, together with geological evidence used to interpret the history recorded in fossils, is known as the fossil record. Although there are many “gaps” (missing transitionary forms) in the fossil record, there are also countless examples of apparent evolutionary lineage: gradual transitions from one type of organism to another, sometimes leading all the way up to species living today.

Opponents of the theory of evolution have responded to this type of evidence in a variety of ways. Young-earth creationists propose an alternative explanation for the fossil record, contending that most fossils are the remains of organisms destroyed during the flood of Noah described in Genesis 7. In defense of this idea, they also argue that the methods used to date fossils are unreliable. (We’ll examine some of those methods on the next page.)

Other critics of evolutionary paleontology, including some who believe God created life billions of years ago, argue that the fossil record is actually inconsistent with the prevailing theory of evolution. In fact, some evolutionary paleontologists themselves have suggested that there may be problems with the standard account of how evolution occurs. According to the prevailing theory, evolutionary transitions from one species to another occur gradually over long periods of time, because genetic recombination is limited and significant mutations are rarely beneficial. (Major mutations are usually harmful and are quickly eliminated by natural selection.) However, evolutionary paleontologists Niles Eldredge and Stephen Jay Gould have argued that the fossil record tells a different story. We’ll consider their view later in this chapter. On the next several pages, we’ll take a closer look at the evidence from the fossil record.