To evaluate the plausibility of human evolution from a common ancestor with chimpanzees, we can compare the extent of genetic changes required with those observed in well-studied cases of evolutionary change — specifically, the development of resistance in malaria parasites and E. coli bacteria. These “high-confidence” studies offer clear insight into the scale of genetic change that evolution has been shown to produce under observable conditions. If human evolution occurred through similar mechanisms, we would expect a comparable scale of genetic change.
However, we face a challenge: we don’t have DNA from our last common ancestor with chimpanzees. Instead, scientists use the modern chimpanzee genome as a stand-in. The Human Genome Project, completed in 2003 after 13 years and $3 billion of investment, provided a complete map of the human genome. Surprisingly, only about 1.2% of the human genome was found to code for proteins, with the rest considered “junk DNA” at the time.
In 2005, researchers produced a draft version of the chimpanzee genome. Unfortunately, this draft was constructed using the human genome as a template — a method that likely introduced a bias toward similarity. Moreover, the comparison focused only on DNA regions that aligned well between the two species, known as orthologous regions. These areas were prioritized because they were easiest to analyze and initially thought to be the only regions of functional importance.
The result of that early comparison showed a DNA difference of about 1.2% between humans and chimps, leading to the widely repeated claim that our genomes are 98.8% identical. However, this estimate is now considered outdated for several reasons:
1. Increased Understanding of DNA Function: The ENCODE project later found that over 80% of the human genome has some known biological function, challenging the old “junk DNA” assumption.
2. Biased Chimp Genome Assembly: Using the human genome as a framework to assemble the chimp genome likely distorted the level of similarity.
3. Selective Comparisons: Focusing only on similar, protein-coding regions ignored large portions of potentially functional DNA.
Even if the overall DNA similarity is still high, the human and chimp genomes differ by an impressive number of base pairs. Geneticist Francis Collins once stated that humans and chimps are 96% genetically identical. Given that the human genome contains around 3 billion base pairs, a 4% difference translates to about 120 million base pairs — approximately equal to the entire genome of a fruit fly. That’s a significant amount of divergence in just 6 million years.
One additional way to measure differences is by identifying genes that are present in humans but missing in chimps and other primates. These genes, known as “orphan genes” or “taxonomically restricted genes,” are unique to a specific species and show no similarity to genes in others. Around 10–20% of genes in every sequenced eukaryotic genome fall into this category. Originally, scientists assumed this was due to incomplete data, expecting that similar genes would eventually be found as more species were sequenced. However, that has not been the case. The proportion of orphan genes remains consistent, even as genetic databases have expanded.
These orphan genes often serve important roles, with some playing key parts in the development of uniquely human traits — including brain function. The existence of so many unique genes raises important questions about the evolutionary narrative, which assumes most genes are passed down and modified from common ancestors.
A closer look at the chimpanzee Y chromosome highlights this divergence. When scientists sequenced it using chimp-specific data rather than human scaffolding, they discovered dramatic structural and functional differences. For instance, humans have 78 genes in a particular male-specific region, while chimps have only 37.
Various studies support the idea that the genetic gap between humans and chimps is wider than previously thought:
• One study found that humans and chimps differ by at least 6% of their gene content — about 1,400 out of 22,000 genes.
• Another concluded that 23% of the human genome shows no direct ancestral link to chimpanzees, including coding and non-coding DNA.
• Additional research has identified around 60 entirely new protein-coding genes that emerged on the human lineage after the split from chimps.
• Estimates suggest there are around 300 human-specific genes and 1,000 primate-specific genes in total.
These discoveries challenge the commonly held view that evolution between chimps and humans involved only minor tweaks to existing genes. The creation of 1,400 new genes would require about 75 million base pairs of new genetic material — a massive leap, especially compared to the few base pair changes observed in evolutionary adaptations like chloroquine resistance in malaria.
To illustrate the disparity, consider this: the evolution of resistance to chloroquine required about 4 to 8 specific base pair changes, and even then, it took enormous populations of parasites to achieve it. By contrast, human evolution — as currently understood — would require millions of times more genetic change than this.
Moreover, evolution doesn’t just require genetic changes; it demands that each mutation offer some selective advantage and that these changes avoid being lost or sidetracked. Developing new genes is not simply a matter of accumulating random mutations — the process needs to be extraordinarily precise and beneficial at every step.
In summary, the scale and complexity of genetic differences between humans and chimps far exceed the kind of evolutionary changes we have direct, high-confidence evidence for. This significant genetic divergence, especially involving orphan genes and unique structural differences, raises important questions about the mechanisms and feasibility of the proposed evolutionary pathway from our last common ancestor with chimpanzees.
Reviewing Evidence for Evolution: A Critical Analysis
In our review of the commonly cited evidence for evolution, we applied well-recognized criteria to assess the confidence level of each line of evidence. While these criteria are not absolute, we found that the evidence for evolution can be clearly categorized. High-confidence evidence includes prospective studies on rapidly reproducing organisms, which demonstrate microevolution through up to eight mutations that provide benefits in specific environments.
We extended these high-confidence studies to test macroevolution, focusing on the hypothetical evolution of humans from our last common ancestor with chimpanzees, starting 6 million years ago. The evolutionary opportunities in this scenario were similar to those in the high-confidence studies, suggesting that the extent of evolutionary changes between humans and our last common ancestor should be comparable.
Our review of genomic differences between humans and chimps revealed over 1,400 novel genes and approximately 75 million base pairs of new DNA in humans. Although further research is needed, our findings suggest that high-confidence scientific evidence casts doubt on the claims of human evolution from our last common ancestor with chimpanzees.
Several limitations were recognized in our analysis. First, the chimp genome was used to represent the genome of our last common ancestor, which is a common assumption due to the lack of direct evidence. Second, the chimp genome is not yet complete, and further discoveries may reveal greater differences between chimps and humans. Third, our comparison of evolutionary opportunities required an estimate of the total number of humans and hominids that have ever existed, which is an approximation. Finally, our argument applies lessons from microbe evolution to hominids, acknowledging that differences between these organisms could affect the evolutionary process.
This article is based on the information given in the book “The scientific approach to evolution” by Rod Stadler.
