Phylogenetic Trees Are Not Evidence

What Are Phylogenetic Trees?

To understand why phylogenetic trees are never evidence, you must understand what they are. Phylogenetic trees are hypotheses. The evolutionists are explicit about this. “Since phylogenetic trees are hypotheses and not ‘facts,’ they are dependent upon both the quality and quantity of data that support them.”1 In other words, like all other hypotheses, phylogenies are only as good as the data that underlies them. And as Stephen J. Gould pointed out, the only data is at the tips and nodes of the branches. Everything else is inference.2 Another well-known evolutionist of the past, E. O. Wiley, admitted that it is impossible to know the true phylogeny of any set of organisms.3 If these evolutionists are correct about how phylogenetics works (and they are), then every phylogenetic tree is a hypothesis.

Now it is important to understand what a hypothesis is. Merriam-Webster provides three definitions, only one of which is relevant to this discussion. According to them, a hypothesis is “a tentative assumption made in order to draw out and test its logical or empirical consequences.”4 Cambridge Dictionary provides something more explicit: “an idea or explanation for something that is based on known facts but has not yet been proven.”5 Britannica defines it as “an idea that proposes a tentative explanation about a phenomenon or a narrow set of phenomena observed in the natural world.”6 While not identical, these definitions are relatively similar, focused on the fact that a hypothesis is an assumption or an idea or explanation that can be tested to determine its truthfulness. What you do not see in these definitions is a hypothesis being defined as data. Instead, it is an explanation for data. That is very important to remember.

Lest anyone think these dictionaries do not represent how scientists use the word, an essay in BioEssays proposed a cycle of knowledge in which ideas generated hypotheses, which then generated data when tested and synthesized to create new ideas.7 Again, hypotheses are not the same as data. Instead, testing hypotheses generates data, which then creates new ideas, which lead to new hypotheses.

Hypotheses are not evidence. They are conjectures about the evidence.

In practice, what this means is that phylogenetic trees are not data themselves. Instead, the testing of them generates data. Whether phylogenetic trees and their resultant cladistic classifications actually can be tested is an open question. At least some evolutionists doubt the point.8 If they cannot be tested, then by definition, they are not hypotheses and do not generate data. However, assuming that phylogenetic trees are testable, as most evolutionists do, still creates a problem. Hypotheses are not evidence. They are conjectures about the evidence.

Picture a courtroom setting. The prosecutor gets up and provides evidence that the defendant is guilty. The evidence is both direct and circumstantial and sounds convincing. Then the defense attorney gets up and says, “Your honor, the defense contends that the defendant is innocent of this crime. Instead, person X is guilty.” When asked what evidence he has to support this claim, the defense attorney says, “I just presented my evidence. I believe person X is guilty.”

The above scenario is, of course, ridiculous. The defense attorney’s assumption that person X is the real criminal is not evidence that person X is guilty. Were a real defense attorney to try this in a fair court, he would be laughed out of the building and likely disbarred. However, this is precisely what the evolutionists do constantly in the peer-reviewed literature. They present conjectures about the data, phylogenetic trees, as evidence of their model.

Is a Phylogenetic Tree Evidence?

The phrase “phylogenetic evidence” regularly appears in the evolutionary literature. A quick search of Google Scholar reveals over 31,500 such references since 2020 alone.9 The references are varied, ranging from denying a mass extinction of angiosperms at the K-Pg boundary10 to the invasion of a nematode into new habitats11 to the development of anion channels in plants,12 to the development of planktotrophy in Australian periwinkles.13 And every single one of these papers is incorrectly applying phylogenetics. Even if we grant that there are no issues with phylogenetic analysis (and there are tons of issues), any attempt to use a phylogenetic tree as evidence is a massive category error. Phylogenies are not evidence because they are not data. They are hypotheses, and hypotheses cannot be used to support other hypotheses.

Are Phylogenetic Trees Always Wrong?

That is not to say the conclusions drawn in the papers above or others like them are necessarily wrong. In some cases, like the nematode example above, they are probably correct. In others, like the anion channel example, where anions channels are assumed to have evolved from a common ancestor, they are completely wrong. But the truth or falsehood of the conclusions is not the point. The point is they arrived at those conclusions incorrectly.

It is important to note that it is possible to use phylogenetic trees in a way that creates useful hypotheses if certain starting assumptions (i.e., common ancestry) are valid.

It is important to note that it is possible to use phylogenetic trees in a way that creates useful hypotheses if certain starting assumptions (i.e., common ancestry) are valid. It would be possible to create a phylogenetic tree of human DNA sequences and expect a reasonable hypothesis as a result. All humans are descended from Adam through Noah and, therefore, share a common ancestor. This could be done with other kinds, like cats, dogs, or other groups where common ancestry within the group is likely. However, it is important to remember that phylogenetic trees are not evidence of common ancestry or anything else. Instead, they serve as hypotheses about the ancestry of the selected sequences. With humans of known parentage or with lab animals, these hypotheses could be tested and refined. However, it is important to remember that trees are not evidence. They are hypotheses about the evidence. While it is unlikely that evolutionists will acknowledge this issue in their literature, it is important for creationists to understand what is going on so that they are not intimidated by so-called phylogenetic evidence.