Evolutionary Trees Tangle With the Data
Evolutionary trees based on genetics conflict
with those based on morphology and anatomy
— Another Prediction to Prove Evolution Falsified —
by Jerry Bergman, PhD
Evolutionary biologist and aggressive advocate for atheism Richard Dawkins has made an argument claiming that an intelligent designer could not have been responsible for life. He predicted that, if Darwinian evolution is true, most every gene in a selection of a large group of organisms would produce “approximately the same tree of life” that is produced by physiology and external morphology. If Intelligent Design were correct, Dawkins continued predicting, the designer would have “picked and chosen” the “best proteins for the specific task required” in each organism. As a result, he claimed, genes would often not produce close to the exact same tree as morphology would.
Evolutionists have put this idea to the test, and found that evolutionary trees based on physiology or external morphology differ from each other, sometimes drastically. The best example is the tree produced by attempts to illustrate human evolution. The charts below show that even producing a phylogenetic tree for humans is difficult.
The Logic Behind Dawkins’ Claims
Assuming that an evolutionary tree that is widely accepted by evolutionists can be determined, evolutionists would expect that the most primitive ancestor of the tree, (which we will label 1), has a certain gene determined to manufacture an essential protein, and which we will label ‘simple’ as compared to gene 2, found in ancestor 2. Then, in an animal more evolved than ancestor 2, (which we will label ancestor 3), the same gene is even more complex (which we will label gene 3, and so on). As the animal evolves in complexity, so does the gene.
Creationists expect to find some or many cases where gene 1 is the simplest, gene 2 a little more complex, but gene 3 less complex than gene 2. Evolution is a comprehensive theory of origins, and evolutionists will likely attempt to explain away discoveries that contradict their belief in order to hold up their theory. One example of this is to claim that the evolutionary tree based on anatomy is wrong. Animal 3 must, therefore, be less evolved than animal 2. However, as more and more data accumulate, (which is now occurring), such rationalizations will be less viable.
Four conflicting evolutionary trees by leading paleoanthropologists:
Expectations and Evidence
Humans and apes have many common traits, thus are taxonomically grouped together in the mammalian order Primates. Assuming that humans and chimps have a common evolutionary ancestor, evolutionists would expect that the vast number of proteins, and the genes that produce the proteins, would be very similar in most primates. Dawkins opines that this tree would reflect their common ancestry. Furthermore, organs such as the kidneys, heart, lungs, bladder, and most other organs, are very similar in most mammals. Consequently, we would expect the genes that produce the proteins that construct these organs in mammals also to be very similar, a finding that tends to be true in living examples.
Specifically, Dawkins predicted that if a tree of genetic resemblances is constructed for each gene, by comparing the letter-to-letter correspondences between genes, they should be very close to the same tree of life based on morphology. This “is not what you would expect if a designer had surveyed the whole animal kingdom and picked and chosen — or “borrowed” — the best proteins for the job, wherever in the animal kingdom they might be found.”
In short, Dawkins predicted the gene tree would be very similar to the morphology tree. He predicted,
“you would see the same family tree even if you compare genes that are no longer functional, that are just vestigial, they’re not doing anything. … This is overwhelmingly strong evidence [for evolution]. The only way you could get out of saying that this proves evolution is true is by saying that the intelligent designer, God, deliberately set out to lie to us, deliberately set out to deceive us.”
Dawkins set up two competing predictions: one for evolution and another for intelligent design. Evolution predicts close to perfect congruency for different representations of the tree of life. This evidence, Dawkins argues, is so “powerful” that it “proves that evolution is true.” Conversely, he predicted conflicts for different gene-based trees with morphologically-based trees as the intelligent-design alternative.
The Gene-Sequence Revolution Tests Dawkins’ Predictions
Gene sequencing that once required a week when I was doing genetic research at the medical school where I was employed now can be done in a day by automatic sequencers. The cost has dropped from a dollar per nucleotide base to a fraction of a cent per base. The result has been that scientists have now sequenced thousands of complete genomes. Each day more data is entered into GenBank, the National Institute of Health’s genetic sequence database. Comparisons done so far have revealed that every gene does not deliver “approximately the same tree of life” expected by evolution. Rather these comparisons support intelligent design.
How We Know that Evolution Represented as a Tree is Inadequate
When a gene is sequenced in the lab, to determine its function the sequence is entered into the GenBank® database to compare it with similar genes for which the function has been identified. Thus, you can determine both what the gene is by name (most genes are named) and its function. GenBank includes an annotated collection of all publicly available nucleotide sequences and the proteins they produce.
GenBank was founded and maintained by the National Center for Biotechnology Information. The GenBank database started operating in 1982 to receive sequences produced in laboratories throughout the world from the over 500,000 formally described species of life. GenBank genetic sequences double roughly every 18 months. In June 2022, it contained more than 2.45 billion sequences, and 139 trillion nucleotide bases from 239 million reported sequences.
As a public database, GenBank contains some sequences wrongly assigned to a particular species because the initial identification of the organism was wrong. One example is a recent review that showed that 75 percent of mitochondrially encoded cytochrome c oxidase subunit I (MT-CO1) sequences were wrongly assigned to the fish Nemipterus mesoprion resulting from usage of sequences that were initially misidentified. Nevertheless, in spite of imperfect data, thousands of organisms have been at least partly sequenced so that we are able to discern trends. Consequently, Dawkins’ theory is now able to receive the required analysis to make firm conclusions about his claims. Already, several studies indicate that the data does not support his suppositions and as more are done, Dawkins’ challenge can be definitely either supported or rejected.
Evidence for Intelligent Design
Evidence of macroevolutionary changes and innovations is lacking in the genetic studies compiled thus far. Conversely, much evidence of mutations causing genetic damage and diseases has been uncovered. There had to be massive changes to organisms in the Darwinian view: and in the case of humans, upright walking, large brains, opposable thumbs, and much more, implying major genetic changes. The more genes that do not display this evolutionary tree similarity, the greater the evidence that they were created separately.
These results so far have falsified the test that Dawkins has set up to evaluate Darwinian evolution in contrast to intelligent design. Many examples exist, including a paper showing that different gene sequences have led to widely different gene trees among closely related species of ash trees. This is only one example of conflicts between phylogenetic trees and the gene trees. The fact is that non-treelike data is often produced among different genes and species. This conclusion doesn’t come just from outdated papers, but from recent studies evaluating major aspects of evolutionary trees, such as the fundamental animal, plant, or even microorganismal relationships, contrary to what Haeckel’s tree predicted.
From preliminary genetic studies, we now have evidence that his prediction has failed for evolution but succeeded for intelligent design. In fact, both trees (i.e., the one based on genetics and the other based on body morphology and anatomy) have encountered major problems. Furthermore, the inaugural lecture by a professor of evolutionary genomics at Queen Mary University of London was titled, “Trees of Life: Do They Exist?” In his lecture he illustrates the problems with evolution trees, some of which we have discussed above. And “this frequent incongruity and discordance between phylogenetic trees is exactly what Dawkins says is predicted by intelligent design.”
Other experimentalists have supported this observation. For example, U C Berkeley geneticist Rasmus Nielsen observed from his research on evolutionary trees, “That whole abstraction of evolution as being a tree, we always knew was a little inadequate … But now we know it’s really inadequate.”
[This is an issue that I and others have written about before (see here, for example), but I thought of it again recently when I watched the inaugural lecture of a professor of evolutionary genomics at Queen Mary University of London. The lecture is intriguingly titled “Trees of Life: Do They Exist?”]
 Dawkins, Richard. The God Delusion. Houghton Mifflin, New York, NY, 2011.
 Dawkins, Richard. The Greatest Show on Earth: The Evidence for Evolution. Simon and Schuster, New York, NY, 2009, p. 322.
 Dawkins, 2009, pp. 321-322.
 Dawkins, 2009, p. 322.
 Ogwang, Joel, et al. Genetic diversity and phylogenetic relationships of threadfin breams (Nemipterus spp.) from the Red Sea and eastern Mediterranean Sea. Genome 64(3):207–216; doi:10.1139/gen-2019-0163, 2021.
 Luskin, 2023.
 Luskin, Casey. Intelligent Design Passes the Dawkins Test. Evolution News; https://evolutionnews.org/2023/05/intelligent-design-passes-the-dawkins-test/, 15 May 2023.
 Berwald, Juli. The Web of Life: Classic evolutionary theory holds that species separate over time. Aeon; https://aeon.co/essays/why-evolution-is-not-a-tree-of-life-but-a-fuzzy-network, 2022.
Dr. Jerry Bergman has taught biology, genetics, chemistry, biochemistry, anthropology, geology, and microbiology for over 40 years at several colleges and universities including Bowling Green State University, Medical College of Ohio where he was a research associate in experimental pathology, and The University of Toledo. He is a graduate of the Medical College of Ohio, Wayne State University in Detroit, the University of Toledo, and Bowling Green State University. He has over 1,300 publications in 12 languages and 40 books and monographs. His books and textbooks that include chapters that he authored are in over 1,800 college libraries in 27 countries. So far over 80,000 copies of the 60 books and monographs that he has authored or co-authored are in print. For more articles by Dr Bergman, see his Author Profile.