Human Evolution and Common Ancestry: Following The Evidence

Human/ape common ancestry has been a subject much discussed recently. A friend wrote me asking for links dealing with human/ape common ancestry. While there are numerous good articles that have talked about this issue from an intelligent design (ID) friendly perspective, I tried to provide him with some helpful links and information.

As a preliminary point, it’s important to note that human/ape common ancestry is compatible with ID. Nonetheless, ID proponents are interested in taking a scientific approach to these questions, and the evidence suggests that even modest changes requiring two or more mutations before conferring any adaptive benefit could not arise via Darwinian evolution under any reasonable timescale involving human/ape common ancestry. As a result, questions about human/ape common ancestry should be on the table for people who really want to follow the evidence where it leads.

The basic issue is this: Despite the fact that human/ape genetic similarities are often overstated, YES, in many instances it is true that humans and chimps have very high levels of genetic similarity. Does this functional genetic similarity bolster neo-Darwinian evolution and human/ape common ancestry? Not at all. In fact, we could have predicted these similarities without any knowledge of Darwinian evolution simply by observing that humans have similar body plans to apes. If similar morphology implies similar genetics, then we could predict these high levels of similarities without even thinking about considerations pertaining to common ancestry.

But there’s another important point to consider: Functional morphological and genetic similarities between humans and apes could be the result of common design just as much as common descent. That’s a good principle to keep in mind as you investigate this issue: functional biological similarity is explained by common design just as well as it’s explained by common descent. (In fact, in some cases — such as extreme convergent evolution — such similarity is explained much better by common design.)

There are a lot of good articles out there on this topic, but here is a summary of some articles germane to recent debates:

(1) Casey Luskin and Logan Paul Gage, “A Reply to Francis Collins’ Darwinian Arguments for Common Ancestry of Apes and Humans,” in Intelligent Design 101: Leading Experts Explain the Key Issues, edited by H. Wayne House (Kregel, 2008), provides a rebuttal to many of Collins’ arguments for human/ape common ancestry:

  1. This article notes that the evidence for human chromosomal fusion simply shows that our human lineage underwent a fusion event and doesn’t say anything about whether our lineage shares a common ancestor with apes. For another good article on problems with the telomeric evidence for human chromosomal fusion, see “Guy Walks Into a Bar and Thinks He’s a Chimpanzee: The Unbearable Lightness of Chimp-Human Genome Similarity.”
  2. Collins cites much “junk DNA” as alleged evidence of our shared ancestry with apes, but this DNA turns out to NOT be junk at all.
  3. Collins makes weak arguments that a couple mutation in a gene could have produced human cognition — this is an outlandish hypothesis that is easily rebutted.
  4. For another recent rebuttal to Collins on the issue of junk DNA and human/ape common ancestry, please see “Francis Collins’ Junk DNA Arguments Pushed Into Increasingly Small Gaps in Scientific Knowledge.
  5. For background on functions for pseudogenes, see “Et tu, Pseudogenes? Another Type of ‘Junk’ DNA Betrays Darwinian Predictions“.

(2) Human Origins and Intelligent Design,” Progress in Complexity, Information, and Design, Vol. 4.1 (July, 2005).

  1. This article reviews the fossil evidence for human/ape common ancestry and finds that it is lacking.
  2. There is also a less-technical version of this article here.

(3) Two articles deal with human-chimp genetic similarity in more detail: “The myth of 1% human-chimp genetic differences” or “Human-Chimp Similarity: What Is It and What Does It Mean?

  1. These articles ask whether human/chimp genetic similarities are good evidence for common ancestry. As the journal Science has reported, it notes that human/chimp genetic differences are much more than the “1%” genetic difference we typically hear about. Geneticist Richard Buggs observes that “The percentage of nucleotides in the human genome that had one-to-one exact matches in the chimpanzee genome was 84.38%.” A 2020 paper that compared alignable coding and non-coding DNA and found that human-chimp genetic similarity is 96%. However, this is undoubtedly an overestimate of human-chimp genetic similarity because (a) it did not consider non-alignable DNA, and (b) it used a version of the chimp genome which used the human genome as a scaffolding. Depending on how you measure it, human-chimp genetic-similarity is likely between 84 and 96 percent, but none of this means that we share a common ancestor with chimps. 
  2. These articles explain that functional human/ape genetic similarities might result from common design rather than common descent.
  3. The two pieces also ask what is the metric for demonstrating Darwinian evolution based upon genetic similarity. There doesn’t seem to be one, and the argument often appears arbitrary.
  4. As biologist Ann Gauger, mathematician Ola Hossjer, and statistician Colin Reeves explain in the book Theistic Evolution, genetic differences between humans and chimps are much greater than is often assumed:

All told, based on current knowledge, there is at least a 5 percent difference in our DNA, and that does not count rearrangements in the DNA, where segments of the DNA appear flipped end to end in relation to chimp DNA, or where one segment of human DNA is in a different location than in chimpanzees. (p. 481)

They go on to explain that the percent nucleotide similarity does not tell the whole story about human-chimp genetic differences since many of the most crucial differences lie outside the protein-coding DNA:

[C]ounting raw difference is not the best way to calculate how different we are genetically speaking … We now know that when, where, and how our DNA is used matters much more than an overall count of nucleotide differences. Human-specific differences in gene regulation, as we will see, are what make us unique. (pp. 481-482)

They recount that some of these crucial differences between humans and chimps include:

  • Human-specific genes, of which there may be over 600 genes unique to our human genome;
  • Multipurpose genes, which can build diverse different types of proteins via alternative splicing which are not always predictable by nucleotide sequence alone;
  • Differential gene expression, where notably, “there are substantial differences in gene expression between humans and chimpanzees, particularly in the brain” (p. 484);
  • Noncoding DNA differences, including differences in SINE elements, LINE elements, and long noncoding RNAs, which also seem to be important for human brain development;
  • Gene regulatory networks, which again may lead to important differences between chimp and human brains, since, “17 percent of the neural network in the cortex of the brain is unique to humans, even though our total genomes may differ from chimpanzees by only 5 percent” (p. 490); and
  • Physiological and anatomical differences, which include differences in timing of development, teeth, brain formation, musculature, diet, mode of locomotion, neck structure, rib cage structure and gait, shoulder design, pelvis and hip orientation, inner ear canals, hands (made for tool use rather than knuckle walking) — which are among some of the 26 important anatomical and physiological differences recounted by a paper in Nature (Bramble and Lieberman, 2004).

(4) Study Reports a Whopping ‘23% of Our Genome’ Contradicts Standard Human-Ape Evolutionary Phylogeny

  1. This article shows how the genetic data is actually painting a very confusing picture about human common ancestry with apes.
  2. The paper reports: “For about 23% of our genome, we share no immediate genetic ancestry with our closest living relative, the chimpanzee.”
  3. Another article which elaborates on similar problems is at “Primate Phylogenetics Researchers Swinging from Tree to Tree.”
  4. Likewise, Jonathan M. recently reported that ERV distributions conflict with the standard phylogeny of human/ape relationships.

(5) In the past few years quite a bit has been written on challenges to widely touted “missing links.” Rebuttals can be found in articles like:

  1. Lucy: “My Pilgrimage to Lucy’s Holy Relics Fails to Inspire Faith in Darwinism.”
  2. Ardi: “The Overselling of Ardipithecus ramidus.”
  3. Ida: “The Rise and Fall of Missing Link Superstar ‘Ida’.”
  4. Neanderthals: For a discussion of why Neanderthals don’t show anything like human/ape common ancestry, please see: “Does Giberson and Collins’ Neanderthal Argument Demonstrate ‘Common Ancestry’?

This article was updated October, 2021.

Casey Luskin

Associate Director and Senior Fellow, Center for Science and Culture
Casey Luskin is a geologist and an attorney with graduate degrees in science and law, giving him expertise in both the scientific and legal dimensions of the debate over evolution. He earned his PhD in Geology from the University of Johannesburg, and BS and MS degrees in Earth Sciences from the University of California, San Diego, where he studied evolution extensively at both the graduate and undergraduate levels. His law degree is from the University of San Diego, where he focused his studies on First Amendment law, education law, and environmental law.