"I'm treating the mutation rate as a substitution rate" - Dr. Nathaniel Jeanson

Dr Mays, there’s much I could say in response to all of this. However I see that we’re philosophically polar opposites, and equally strong in our belief. History has shown me that I doubt there’s much value in us continually repeating our stance to each other. (plus my time on PS is limited)
But I did want to again thank you for dialoging with me.

Hi @jeffb,
I wanted to note that methodological naturalism isn’t something a person believes, it’s something they do. If you have a light switch in your house that doesn’t work, or hear strange noise from your car’s engine, you might form the idea that something is wrong. At the start you don’t know what is wrong, but you can conduct a series of tests (replace a light bulb, tighten a belt, etc.) to either find the problems, or at least eliminate some of the possibilities. Everybody uses this sort of reasoning every day, it’s not unusual.

Methodological naturalism is pretty much the same process in science, except rather than trying to fix something, we are trying to figure out how it works.

Rather than looking at the same evidence and arriving a different conclusions, I think that people are asking different questions.


The nested hierarchy is essential to evolution, but arbitrary to special creation. As such, it is evidence for evolution, but not evidence against creation. The nested hierarchy in combination with the fossil record, however, is compelling both for evolution and against young earth creationism.


I for one would be fascinated to know how the nested hierarchy of life can be interpreted as evidence for recent, separate creation of “kinds”. But @jeffb appears to be interested in avoiding any sort of substantive discussion of any evidence. Perhaps that’s the wisest course for him.


Yes I remember that thread. I still don’t understand what it is you don’t understand. One theory predicts the nested hierarchy, another theory doesn’t. We find that there is a nested hierarchy and only one of the theories lead us to expect it. Thus it is evidence for evolution over special creation.

I don’t understand how it is that you don’t “see” this. You may not find the evidence compelling, but I’m curious if you can explain why it shouldn’t be considered evidence for evolution. Can you give it a shot?


I would agree that you would have to replace the scientific method with religious dogma in order for YEC to work. That’s the exact point I am trying to make. Methodological Naturalism follows the evidence. YEC does not.

Do you agree with these two points?

  1. A noisy nested hierarchy is the pattern we should see if life evolved.

  2. There is no reason why we would expect to see a nested hierarchy if species and/or created kinds were separately created.

If you do agree with those two points, then how could a nested hierarchy lead to the conclusion that species or created kinds were separately created? Next, if we observe the exact pattern we would expect to see from evolution, then why isn’t the nested hierarchy evidence for evolution?

You will not find scientific institutions who have this type of oath:

Evolution is the scientific consensus because of the evidence, not in spite of it. No one has to dogmatically defend the theory of evolution from the evidence.


I see my job as a citizen of the United States and a scientist and science educator as supporting your right to hold and express your personal religious beliefs while keeping those beliefs from dictating what we do in science and science education and determining public policy. You may believe what you wish but your religious convictions are not scientific conclusions and have no place being taught in public schools or being the basis for scientific conclusions.


I assume you’ve looked at direct statistical tests of common ancestry across multiple independent lines of evidence like those from Baum and White and Penny and others that have been published over the past 30 years or so as well as gap excess ratio metrics and congruence with phylogeny like those published by Wills et al for dinosaurs?

Has it also occurred to you that there’s a reason why the evidence for common ancestry has convinced virtually the entirety of the professional scientific community? Even some intelligent design proponents like Michael Behe accept the evidence for common ancestry.


@dsterncardinale has posted a YouTube dealing with Jeanson’s crisscrossing of branch lengths and branch count.

Dr. Nathaniel Jeanson Flubs Phylogenetics

I find it suggestive that considering his association with AiG, Jeanson’s recent work dovetails with the planned Tower of Babel project at Ark Encounter.

The Ark Encounter said Wednesday that it would take about three years to research, plan and build a “Tower of Babel” attraction on the park’s grounds in northern Kentucky. A release from the Ark Encounter said the new attraction will “tackle the racism issue” by helping visitors “understand how genetics research and the Bible confirm the origin of all people groups around the world.”

The Latest Biblical Attraction: The Tower of Babel

The timing suggests that Jeanson may have constructed this tome of technobabble in support of a Tower of Babel attraction. There is lots of theme park potential here; an ancient civilization kind of Epcot might be less tedious than posters and dioramas of the Ark walkthrough. You may be able to follow Jeanson’s haplogroup dispersal on a pavilion ride, but I doubt that will have much impact on the academic world.


I’m sorry Mikkel, I just now saw this specific question:

We first of all, I’m certainly not saying it shouldn’t be considered evidence for evolution. I DO see it’s one that evolutionists can list. For me it was the conclusion of how significant that evidence is given 1) arguments against NH’s strengths (to include challenges to the tree of life), and specifically 2) how much is expected/not expected within Biblical Creation. So I’m really just differing on the significance of it.

I did a good bit of research on this topic last year, and still have a number of my notes. However I don’t feel like I have the time to put together a thorough and sufficient answer. (Plus I know how debates go in this site).

I’ll share this: When I came to this site I was encouraged to look into NH evidence. I gave it my best effort. I did actually find more NH evidence than what I was previously privy to, and even conceded to that here once. However I didn’t just stop there. I spent a good bit of time studying challenges to NH, as well as challenges to the Tree of Life (ToL) in general. That research was revealing. Especially considering evidence against a hypothesis can weigh in heavier than supportive.

BTW, as a software developer, I also found “The Dependency Graph of Life” by Winston Ewert interesting. I hope more can be developed on this. (Mentioned here: Winston Ewert: The Dependency Graph of Life - Peaceful Science).

Honestly, there’s a more I could share on this topic, but will leave it at this: I did the research with an open mind, and learned a lot from it. NH data is compelling. Except when it isn’t. One thing I realized is that we’re dealing with a HUGE amount of data (all biological features multiplied by all life that ever existed on earth), and for me, two overlapping models that can each account for parts of what we’re seeing. Coming to that final, quantitative assessment of all that data (including scripture!) is in no way simple.

Bottom line: I feel like the magnitude of this data set makes it difficult to “declare a winner” in this debate. I can only speak for myself: I attempted to “see” it. But ultimately feel justified in my reservations of how compelling it is compared to Biblical Creation.

I would mostly agree with this. I do see those two used in combination quite often here, understandably so. Whether it is, and just how much it is evidence against YEC is debatable.

I 100% disagree with this. We would expect to see a nested hierarchy (NH). First, a NH can be built with ANY set of objects, so its mere ‘existence’ doesn’t say much. Second, we’re talking about life that all shares the same biosphere (and a lot of it). Third, we’re talking about the same Designer, Who has chosen to make things similar.

This discussion isn’t whether a nested hierarchy exists, it’s two-fold: 1) how “good” is the NH data? 2) How much NH would God allow to exist? The second involves getting to know God, primarily through His Word. I hear NH discussed quite a bit here, but very rarely a discussion of God’s character, which for YECs must be included in this. Statements along the lines of “If God did it, it would look like this…” are simply not meaningful outside of evaluating it against what we know about God through His Word.

BTW the intent on my comment was two-fold: 1) People do “see” things differently, 2) what’s important is to at least make an attempt as “seeing” what others see, which I did. And will continue to do (as time permits).

That’s completely false. Things like cars, buildings, and paintings do not fall into a nested hierarchy.

This is what I mean by YEC’s not looking at the same evidence.

Why would that require a nested hierarchy?

You can make things similar and not have them fall into a nested hierarchy.

It’s excellent.

Why would God create life so that it fits into a nested hierarchy? That’s still the question.

I have personally designed life by genetically modifying viruses and bacteria. I have also used mice that had human genes inserted into their genomes. In all these cases there is similar DNA shuttled from one species to another, AND IT VIOLATES A NESTED HIERARCHY!!! We can directly observe that design regularly and easily violates a nested hierarchy.

Two contradictory claims can not both be true.

If you claim that a nested hierarchy is simply similarities then you have failed at seeing what other see. If you claim that any set of objects can be put in a statistically significant nested hierarchy then you have not seen what others have seen.


Ewert agrees with us. He clearly states that if life does fall into a nested hierarchy then it is evidence for common ancestry and evolution while also being evidence against design.

1 Like

This has been known for a very long time.

After Linnaeus successfully arranged living things into a nested hierarchy, he tried to do the same for minerals. He couldn’t.

Anyone who claims that any set of objects can be put into a nested hierarchy hasn’t tried to do it.


The first is untrue - at least in any useful sense

The second clearly fails to explain more than some very basic similarities. It can’t possibly explain the pattern of similarities we see.

The third amounts to claiming that creator chose to make life look as if it had evolved for some unfathomable reason which hardly seems to be a good answer,

Really, given standard YEC views - and given the analogy with software design (yes, I am a software developer) - we should expect to see distinct “kinds”. But we don’t see those sort of divisions in the tree of life at all. This should be true even with the reuse of “modules” which should also be apparent (and isn’t).

So really the nested hierarchy is quite strong evidence for evolution over creationism.


It’s absolutely correct if we’re talking about non-constrained sequences. That is, sequences that are not under selection to stay the same.

If you say okay, you have different “created kinds” that are created separately, and they’re created with the same DNA sequences except for the specific things that make them different, then we can predict that unconstrained sequences will form a nested hierarchy within created kinds, but be uncorrelated between created kinds.

What we actually see is nested hierarchies top to bottom. This is a direct test and falsification of the separate ancestry model.


May I offer an example of where the NH fits nicely into an evolutionary pattern but not so much with the common designer explanation?

From Leviticus chapter 11

13 “‘These are the birds you are to regard as unclean and not eat because they are unclean: the eagle, the vulture, the black vulture, 14 the red kite, any kind of black kite, 15 any kind of raven, 16 the horned owl, the screech owl, the gull, any kind of hawk, 17 the little owl, the cormorant, the great owl, 18 the white owl, the desert owl, the osprey, 19 the stork, any kind of heron, the hoopoe and the bat.

Here the bat is listed as a bird, and some have held that to be in error, but really it is just a awkwardness of translation as the Hebrew word includes any flying creature, and bird as an English word excludes bats. “Things that fly” is a reasonable way of lumping animals together, but that way of categorizing does not lead to a NH. Bats have long been nested as mammals on the tree of life, not due to their flying and eating bugs, which would place them with birds; but because of their many definitive mammalian traits shared with terrestrial bound creatures like, well, us.

It is a feature of the NH that the engineering challenges faced by bats and birds result in the convergent development of wings, but which are very distinct. Under the NH, birds descended from a lineage in possession of feathers and scales, and feathers feature in the solution. Bats descended from furry mammals, so feathers were not an option. This is a key aspect of the NH which distinguish it from design. Under design, whether software, manufacturing, or creating life, nothing prevents you from grafting a solution that works on the tip of one branch, intact to a distant, unrelated branch. Teflon works in space? Put it on frying pans. It does not matter if frying pans branched off long before rockets. That is because people are free to make objects as they please without being bound by the past. Offspring, however, are only produced the old fashioned way.

So birds and bats have very different wings, but the bone structure in the wings is quite similar. That also fits with the NH. Birds may lump with egg laying, feathered creatures, and bats with furry live bearing creatures, but they are both tetrapods. You can find your arm bones - humerus, ulna, radius - in your chicken hot wings dinner. Mammals and birds nest into tetrapods.

As do whales. Why would whales have anything to do with terrestrial creatures and flying animals? But there you have it - humerus, ulna, radius. Sharks inhabit the same biosphere as whales, but their pectoral fins have a completely different cartilage based anatomy. From the standpoint of the NH, whales look more like bats than they do sharks, and sharks look more like guppies than they do whales. All this makes a lot of sense under the NH, but is very crisscrossy and functionally compromised in terms of design. In fact, it only really works under design if the designer was intentionally creating so that, in every slight detail, nature as we find it is indistinguishable from a world where all these animals were actually descended from a common ancestor by way of a bifurcating tree, resulting in a nested hierarchy.


Ah, but it isn’t debatable. Witness the fact that you refuse to engage in discussion about it.


I think you’re completely missing the “nested” aspect of the concept of a nested hierarchy.