Phylogeny - Help me see what you see

A few weeks back some individuals here expressed the opinion that phylogeny is one of the strongest arguments for evolution. Although I ‘affirm’ YEC, I’m always interested in studying evolution (I rather enjoy it). I certainly want to look at topics evolutionists consider “compelling evidence”. It had been a while since I studied phylogeny, and the tree-of-life in general. So I’ve been spending time lately studying that very topic. It was very fruitful time spent, and I may consider posting some follow-up questions on what I learned.

But first, I want to give others a chance to, as I mentioned in the title: “Help me see what you see”. If people here see that it’s compelling evidence, then I’m open to try to see that as well.

For those of you who adhere to/believe/affirm/(affept??) evolution, what is it about phylogeny, and the tree-of-life*, you find compelling?

(BTW folks, a request: Before you respond to this thread, please weigh the value of it first. I don’t have a lot of time to get on here and would rather not have to sift through a lot of ‘noise’. Again, just a request please)


Have you read this yet? A Test of Common Descent vs. Common Function

Or listened to this? Livestream: How I Changed My Mind on Evolution


Hi Jeff, for me the tree of life is compelling because it provides an explanatory structure that no other model can provide. The TOL doesn’t just assert evolution or make an “argument” for evolution. It explains shared features, and the fossil record, and nested hierarchies, and biogeography. Without a TOL, living things have to spring into existence without precursors, and that is both evidently false and (more importantly IMO) void of any explanatory value. The TOL, to me, is a picture of life past and present that attempts to make sense of life. It succeeds wildly, and that makes it compelling as part of evolutionary thought.

For me, evolution, like all of science, is about explanation. I hope that is valuable.


Phylogenies can be so compelling that even YEC “scientists” use them. If there was a primal Dog kind which gave rise to all extant dog kinds, that necessarily entails a nested hierarchy starting from the oldest lineages to the most recent ones. With phylogenetic analysis, one can reconstruct the evolutionary history leading from the ancestral forms to more derived ones displayed as phylogenetic trees. Of course, phylogenetic trees aren’t perfect or absolute, but they offer, in many cases, an excellent window into our evolutionary past. With phylogenetic analyses we can infer the evolutionary histories of tumors, viruses, and large organisms like us. Its a powerful tool in the hands of biologists.


Phylogenies are also used by immunologists to show the clonal relationships between T cells and B cells. In particular, B cells expand under selective pressure when they recognize antigens in a process called “somatic hypermutation” (SHM) that occurs in germinal centers in the spleens and lymph nodes during an ongoing immune response. The B cells that survive during SHM are the B cells that have incorporated productive mutations that enhance antigen binding affinity. When deleterious mutations occur in the genome of an activated B cell, those B cells do not survive.


Also kind of useful for investigating more pressing matters such as the sequences of Sars-Cov2 viruses (wait for the soccer ball to finish spinning).


I suppose what you’re really asking here is why tree structure in the data is compelling evidence for common descent. Succinctly put that is because tree structure in the data is what we expect given common descent, and we do not expect it on alternative hypotheses. It should be pretty easy to see why tree structure is expected on common descent. After all, if two species derive from a common ancestor, the ancestral lineages splits into two new lineages, and if one or both of these two lineages in turn also split into two later, we get two more bifurcations and so on and so forth, and this should form a tree. If changes in characters (however they arise) accumulate independently on different branches, this should make the characters support a tree.

In logical form the argument is basically:
If X, then Y.
If not X, then not Y.
Y, therefore X.

If there is common descent, we expect there to be tree structure in the data.
If there is not common descent, we do not expect there to be tree structure in the data .
There is tree structure in the data. Only one hypothesis makes that an expected outcome, so the data de facto supports the common descent hypothesis over others.

Now whether you find that compelling is of course a matter of your own psychology.

Counter arguments have been proposed by creationists before, such as trying to conjecture that some form of independent creation would also inadvertently produce tree structure in the data. I have yet to see a creation-model that actually predicts tree structure in the data inadvertently, which does not explicitly involve actual common descent with accumulating changes on splitting branches of genealogical descent, or deliberate fakery (as in someone intentionally creates tree structure in the data despite there being no functional reason to do so).


7 posts were split to a new topic: Science, Phylogeny and Affirming the Consequent

Here, I alter your wording to give a more authentic and inclusive view of what is happening:

“If there is creation of kinds based on an accelerated molecular clock, we expect there to be tree structure in the data.
If there is not creation of kinds based on an accelerated molecular clock, we do not expect there to be tree structure in the data .
There is tree structure in the data. This means more than one hypothesis makes that an expected outcome, so the data does not de facto support the common descent hypothesis over others. Creation of kinds based on an accelerated molecular clock fit the data equally well.”

That means your phylogenetic trees may be illusory after all, and you continue to miss the truth of how God made life arise based on a forward-moving genetic molecular clock. The Creator was not bound, as you might suppose, to return to “native DNA” each time he created a kind. Who imposed that law on the Creator anyway? It is actually more in keeping with the authorized Bible record he left us (which speaks of creatures being created over time) that, from a simple DNA molecule which he set in forward motion and which began to accumulate mutations at an accelerated rate, God made all genetic kinds to erupt over a span of 96 hours (four creation days).

And yes, your science correctly figured it out, that at the top of creation Day 6, right before his creation pinnacled with the creation of Man-KIND, he had just completed the chimpanzee created KIND. Does that mean Man and chimps are related by a common ancestor? Of course not. They are only related by a common Creator, and only by common DNA, and only by the Creator’s creation method that exploited an advancing (accelerated) genetic molecular clock.

I can only congratulate your science for once again supporting the Bible text, your ill-founded, evolutionist conclusions notwithstanding.

Prove it.


This seems to fall into the category, mentioned by Rumraket, of simulated common descent. Now of course you have never coherently articulated what you mean by this “accelerated molecular clock” theory. It might be simulated common descent or it might be real common descent. In either case it doesn’t make a lot of sense.


Statement 2 is exactly logically equivalent to statement 3. How is it possible that you, a PhD in philosophy, do not recognize that? Both of your counterexamples violate statement 2. GIGO.


No, I haven’t seen that yet. After quick glance at it, it looks like just what I should start with. THANK YOU!

I recall listening to that once, but I will go back and review it.

I also notice I’ve gotten a few replies from others. To everyone else: I appreciate the feed back, and I will try to read through what you all posted. Apologies if I don’t reply to all of you, looks like I’ve got my first homework assignment…

This was very well written, and directly to the point. I appreciate how well you summarized this topic.
Thank you.


First, I want to remind you of something I said in my original post:

I’m looking for information in this thread, and this just stirs up debate. This is the type of stuff I’d like to avoid (“noise”).

And second: As a fellow creationists: I really encourage you to avoid abrasive language like this. It’s counter productive.


@Michelle, My understanding is that this would fall under micro-evolution. But please correct me if I’m wrong.
What I’m curious to know here is how you find this leaning you towards common descent and away from design (again, help me “see” what you’re seeing)…

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Everyone agrees to common ancestry to some extent, the question is where it stops. Take whatever group you accept common ancestry for, and you’ll find phylogeny works great within it. Now apply the same methods outside of that group, and you’ll find they still work great. In ways that just aren’t reasonably possible without common ancestry. So if you accept common ancestry of all humans, phylogeny forces you to accept common ancestry of humans and chimpanzees, and all primates, and all mammals, and…


I think that microevolution points to macroevolution and the use of phylogenies in the micro-scale illustrates their use on the macro-scale, as well.

I’m not an expert in this area, but I see that macro- vs microevolution concept as a distinction without a difference. I only recall hearing of those terms in Christian circles, not in my high school biology classes.


Out of curiosity, why does phylogeny force one to? Especially when we and primates have a different number of chromosomes? (Yes, I’ve listened to the basics of the chromosome fusion argument).

Rest assured that those are terms coined and used by real biologists, though creationists have their own private (though tacit) definitions: microevolution refers to evolution they’re willing to believe, while macroevolution refers to evolution they aren’t.

You next need to understand the chromosome fusion argument rather than just listening to the basics. It actually does explain why humans and other apes have different chromosome numbers. It isn’t phylogeny, per se, that forces you to accept common ancestry: it’s consistency. If you accept the evidence for common ancestry of humans, you need to accept the identical sort of evidence for common ancestry of humans and chimps, primates, mammals, etc.; anything else is special pleading.