Paul Nelson: Which Rules? Whose Game?

Nelson’s impressive-looking table seems to me to be misleading. “No Tree of Life” covers cases such as Carl Woese, who believed that there was a single genealogy of life, just that parts of it were not a tree. Lamarck did not argue for a universal tree, but did make a branching tree of all animals. The table does not separate cases such as: (1) is there a single universal tree, or (2) is there a single universal genealogy that is not quite a tree, or (3) is there no common descent. Not to mention cases in between. The existence of LUCA is a mostly-separate issue from whether the genealogy is treelike.

Lamarck, Berg, Woese, and Doolittle would all acknowledge lots of common descent – for example of animals. Nelson makes them sound as if they didn’t accept common ancestry. (From what I read in Roualt’s entry in the “Third Way” website it sounds as if he too would accept common ancestry, just not the Modern Synthesis view of mechanisms).


So Bechly isn’t anti CA now?

And universal common descent (UCD) is not what I discuss the GAE either. Rather it is merely the common descent of humans and the great apes. UCD can be false while human evolution is true.

The change of topic to UCD really seems like a smoke screen.


You said that, I remained Peaceful and didn’t say that, however much I thought it.


What I find striking about this exchange, quite telling, is that the actually thesis of the book is not under discussion, or even stated. I just reread his article too, and it doesn’t even state the thesis of the book.

Instead, there seems to be a strong effort to trap us in several old quagmire conversations of only marginal relevance, if even that. That can be an effective strategy. Everyone is tired of this quagmire. But, if it isn’t worth it to Nelson to take up this argument with Behe and Denton, then it should not be worth taking it up with me.

The fact of the matter is that we want a better way forward.

At some point, it would great to hear @pnelson’s thoughts on the actual thesis of the book.


This is not a point well known to me. But you are presumably aware that it isn’t mere similarity but nested hierarchy that is the evidence for common descent. We can recognize convergence precisely because it disagrees with the bulk of the data. And none of your additional determiners of “similarity” apply to nested hierarchy.

You have responded with a couple of minor cases of molecular convergence (not, incidentally, common design), which are again recognizable because they contradict the great bulk of the data. You can’t use that as evidence of massive, whole-genome convergence (or common design either). That’s like using the single species of black swan (Cygnus atratus) as evidence that all swans are black.


I do, at the start of the second paragraph:

GAE is dedicated to showing how the traditional biblical understanding of Adam and Eve, as the unique, specially-created progenitors of humanity, can be reconciled with the findings of genetics and evolutionary theory, or what Swamidass calls “evolutionary science.”

As for “my thoughts on the actual thesis,” I’m unpersuaded, obviously – but mostly indifferent. The thesis of GAE lies downstream logically and evidentially of MN and common descent (whether UCD, or the common descent of the primates, is immaterial). As I find both MN and common descent (at the scale taken as given by GAE) to be false, GAE is not a proposal of any interest to me. I tried to make that plain in the last sentence of my review:

Let go of MN…and consider that CA [CD] might be false, in the light of new evidence, and we can talk. Otherwise, there isn’t much to discuss.

You think that is the thesis of the book? Not really at all. That is, rather, a statement of motive (or dedication), not a statement of the thesis.

If we can establish the thesis, on what point do you disagree with it? What Scriptural points do you disagree on? Other than merely disputing mainstream science’s rules, where did my scientific argument break? Where did I make an illogical argument?

False. I carefully defined “Tree of Life” and “LUCA” in the chapter in question, so the table is spot-on accurate. In context, "Tree of Life’ means universal common descent, where all organisms on Earth trace their lineages to LUCA – a unique cell. “Common ancestry,” by contrast, is often so ill-defined that one can lump YECs (many of whom argue for a great deal of common descent) in with Darwin or Ernst Mayr. If you read the chapter – as I recall, I sent you the book – you will see that I do not make any author “sound as if they didn’t accept common ancestry.”

The existence of LUCA is a mostly-separate issue from whether the genealogy is treelike.

Nonsense. “Treelike” can mean a mangrove – multiple independent roots – or an oak (single root). Without a precise definition, describing LUCA as the singularity from which all lineages arise, “treelike” is hopelessly vague. The real existence of LUCA couldn’t be more germane to distinguishing historical topologies one from another.

This discussion of LUCA and UCD is totally off topic. I’m letting it stand here because this thread is about your critique of the GAE, but it is totally irrelevant to the thesis of the GAE. My point stills stands even if UCD is irrecoverably false.

Maybe an analogy will help, and then I must bow out of this discussion (because GAE does not interest me enough to continue).

I set up someone in a room with a morphine drip into his arm, all of his favorite music playing on a stereo, and someone to massage his back every afternoon. Only the room sits in a prison, from which there is no escape.

He objects – hey, you’ve taken away my freedom, he says, struggling against the morphine haze.

But what exactly do you need your freedom for? I reply. You’re blissed out on opiates, Pink Floyd is playing in the background, and the masseuse is loosening up your muscles. A fine steak dinner will be delivered at 6 PM. What more could you want?

GAE is a prison defined by “mainstream science.” Sorry, but I’d rather have my freedom.

The data that define the nodes of nested hierarchies are similarities. Three ear ossicles, hair, mammary glands – drill down into the datasets of systematics, and you will find similarity at the deepest analytical level.

There’s no getting away from similarity. Why did I put this organism A next to B? Because A and B share more characters than either does with C.

And what is a character? A similarity.

Then why agree to write a review of it? I’m honestly confused.

Okay then. So you have no interest in engaging with mainstream science. Seems to undermine the entire point of ID, but I suppose that many people have argued ID is off in its own world.

Mainstream science isn’t always right, but many of us still see value in dialogue with it. That’s a better way…

Curious your thoughts @Philosurfer

That would seem a question best addressed to the organization that solicited the piece. It’s true that Nelson shouldn’t have written a “review” of a book with a basic intellectual premise (what we call “science”) that he rejects. But it’s also true that the Henry Center thing should never have asked him to write the “review” and once they saw it, should have politely declined to publish it.

I don’t believe in gods, so I shouldn’t be asked to review theology books and should decline if asked. Nelson doesn’t believe in scientific inquiry, so he shouldn’t be asked to review books about science and should decline when asked.

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Why would we need to know if eukaryotes and prokaryotes share a common ancestor in order to determine if humans and other apes share a common ancestor?


Yes, characters are similarities. But what determines the tree is not the similarity, and it’s not “share more characters”. It’s, again, nested hierarchy. Grouping by similarity assumes a perfect evolutionary clock, which we don’t do. You have been misinformed.


27 posts were merged into an existing topic: Comments on Nelson’s Review of GAE

I wouldn’t blame the Henry Center so much. This is a pretty controversial topic, and in the end I think my rejoinder was effective. But we will see on Friday.

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I will confess to being quite confused by @pnelson’s review, especially the sentiment expressed in this last quote. As far as I am concerned, GAE is about humanity, the connections between us all and A&E (whoever they were). Taken at face value and in the context of GAE, @pnelson’s quip seems to invite us to disavow the notion that extant humanity is actually related by CA to A&E. I am not sure what that can possibly mean, but I suspect this notion wouldn’t sit well with the YEC community.

But maybe I am wrong about this. Is it a thing, that YECers think that there is a discontinuity in the history of humanity?


While we are talking about our reactions of confusion, here’s one of mine prompted by this claim in Nelson’s review:

Well—is it true, simply as a descriptive matter, that the statements of science invoke only natural things and processes? No it is not.

OK. I’m interested in reading his best examples. (But before I do, I must ask, “Is everything a scientist states a ‘statement of science’ and thereby a conclusion of MN?” Obliviously not.) Anyway, here’s a few of Nelson’s examples:

Consider: in 2010, geneticist John Avise, a member of the National Academy of Sciences and professor of biology at UC-Irvine . . . published a book with Oxford University Press entitled Inside the Human Genome: A Case for Non-Intelligent Design . The Library of Congress assigned this book a QH 325 call number, placing it squarely in the middle of the biology subject heading “1. Evolution, molecular.” But consider the fourth subject area in the book’s LC listing: “4. Religion and Science.” Why would that heading be there?

I would assume that that heading is there because Avise wanted to reflect upon how the science he described may have religious implications—at least for some people. What’s wrong with that? Scientists are just like anybody else: they may choose to reflect upon philosophical and even theological aspects of what they investigate. That doesn’t automatically indicate that their application of methodological naturalism in their scientific research is somehow “impure” or philosophically tainted.

To buttress his point, Nelson says:

Avise himself provides the answer:

Do molecular details inside the complex human genome finally provide theology’s long-sought holy grail: direct and definitive evidence for attentive craftsmanship by a loving Creator God? Or do they point in a different direction? (p. ix)

Again, how is that a problem? Avise is posing philosophical questions about the molecular details inside the human genome. I don’t see him claiming that he can conduct an experiment to determine if “a loving Creator God” crafted the genome—much less to empirically determine if God or gods exist. I don’t see how methodological naturalism has been “violated” in Avise’s work. (Can we find any god-of-the-gaps arguments in Avise’s published scientific papers? Or does Avise simply engage in philosophical tangents based on his scientific investigations?)

Philosopher and historian of science Steve Dilley has shown that biology textbooks, including those most widely used in colleges, are permeated by theological arguments.

I would be very interested in seeing the documented examples. Meanwhile, let’s assume for the moment that Steve Dilley’s claims are true. Does the next sentence logically follow?

Evolutionary biologists, in short, don’t follow the rule of MN.

Wow. That is a huge leap. (I don’t think there is anything “short” here but the sentence.)

Out of fairness, I will certainly continue the quote:

When it suits them, they ignore MN entirely, and publish their theological arguments in otherwise scientific venues: the biology primary research literature,5 technical monographs,6 and textbooks.

Is there truly a massive intrusion of “theological arguments” into mainstream peer-reviewed literature and textbooks? Once again–just for fun—let’s assume for the moment that this very significant claim is true. Does that mean that the scientists have ignored MN entirely in their scientific research? I don’t follow the logic here. I would have to see examples where the scientists in question procedurally deviated from MN in their research procedures. The fact that some scientists publicly state their philosophical and/or theological reflections concerning their research tells me nothing about whether they have compromised MN and the Scientific Method.

Nelson continues:

The practices and publications of Isaac Newton, Robert Boyle, Francis Bacon, Carl Linnaeus, and the other theistic founders of Western science do not fit with MN in its current formulation.

I’m intrigued. Let’s read on:

While Boyle, for instance, opposed Aristotelian principles that gave a form of cognition to physical objects (e.g., “natural place”), urging instead that experiments lead the way to knowledge of genuine efficient causes, he also argued strongly that living things showed unmistakable evidence of intelligent design.

Of course he did! He was a philosopher, as were so many of the revered scientists who gave us the scientific method and MN. Philosophers are prone to philosophize. I would certainly expect Boyle, Paracelsus, Descartes et al to relate their scientific conclusions to their philosophical and theological positions. For me to believe that their versions of MN were markedly different from today’s definition, I’d have to see steps or gaps in their empirical research which they “plugged” by non-naturalistic/supernatural explanations.

To put it another way, I don’t know of any “law” forbidding scientists from publishing their philosophical and theological musings. When they do so, that doesn’t logically demand that their scientific research violated MN.

Is this another confusion of Methodological Naturalism with Philosophical Naturalism? I don’t think so—but I can certainly see why some readers might make that assumption.

In short: I just don’t get it. Perhaps I’m missing something.