Kitzmiller, the Universe, and Everything

as i said: there are many claims here from the ID community so im not the only one who talk about special creation. and as i said: i have no problem with evolution. just with a natural explanation.

to say that some gears can evolve naturally its like saying that some computers can evolve naturally. its not a fact of course. just a belief.

And there you have it. This is what passes for “logic” among ID Creationists. @scd doesn’t gussy it up with flowery pseudoscientific language to make it sound like a profundity. But, at the core, this is no different from the “argument” put forth by Meyer, Behe, Dembski and the rest of them.

Yeah multiple concrete examples have been shown on this forum already, where genes were gained both by de novo evolution from noncoding DNA, and by gene duplication.

Yours. Look above. Weren’t you asking “Can you give an example of an empirical observation of gene gain?” ?

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Question: Are new genes derived by duplication considered part of the same “gene family” as the original gene? Or would they be considered “de novo” or “orphans.” That is to say, would they be among the genes that Bill and his fellow creationists consider to be out of the expected nested hierarchy?

The papers referenced here recently show concrete empirical experiments. Nothing speculative about it. Hence the evidence you asked for really does exist.

So there is evidence of gene-gain. Of course, there are actually thousands of empirical examples of gene-gain through gene duplication alone.

On what timescales are they “rare” events? What is a “rare” event even supposed to be here on geological timescales? If maize can gain the genes that result in a multi-protein membrane transport machine on the timescales of decades to centuries, then what can happen in millenia? Eons?

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Not easy to answer that because it really depends on what defines a gene family, and how far apart they have derived from their common ancestor. Obviously immediately following duplication you will basically just have two identical copies of the exact same gene. For all intents and purposes you still have the same gene, they don’t so much belong to the same family as they really just are the same gene twice.
Then when they start to diverge, if you go merely by homologous relationship based on nesting hierarchical structure in sequences of similar genes, then yes they’d be classified as belonging to the same homologous family under that definition.

But there can be functional or mechanistic differences between genes that derive from common ancestors that make them be classified as belonging to independently evolved, monophyletic sub-families, within a larger superfamily of genes. Pretty much directly analogous to how you can have independent families of organisms, say primates and lagomorphs, within larger clades like mammals.

Well they show no signs of being consistent in what they think of diverging duplicate genes. If you show them two genes with a sequence similarity of about 80% they’ll call it highly conserved and insist it’s only a sort of protein “microevolution” and that they still just perform the same function (yadda yadda yadda). You show them two proteins that have diverged to 30% sequence similarity they’ll suddenly turn around and insist there are huge an unexplained “information jumps” that couldn’t possibly evolve.

Take one look at Gpuccio’s ridiculous figure that Bill keeps posting to see what I mean.I’ve drawn a phylogenetic tree on it and attempted to put the the approximate divergence times to scale (mouse-human is 90 mya according to

Look at that gap. Gpuccio wants to see all the intermediate stages in the divergence of those gene-sequences, otherwise it’s a huge gap without transitionals, and that means the species, wait sorry I mean functional information (FI), must have been popped into existence with magic!


I do not know of a single biologist outside the tiny ID community that would not hotly dispute this assertion.

Could you support your assertion by linking to non-ID biologists who think Behe’s work is generally sound?

You have vastly overstated the current value of Ewert’s work. The dependency graph is completely unsupported at this time. Ewert’s paper is 100% invalid as anything more than speculation because it assumed that the genomic data were complete, and that therefore the absence of certain genes could allow him to infer the dependency graph. But in fact, the genomic data are nowhere near complete. Thus his entire paper is entirely undermined as an accepted hypothesis.

Now perhaps sometime in the future (decades from now?) the genomic data will be broad and complete enough to perform a meaningful analysis. Until then, his idea is 100% speculation. Maybe the complete data will support his speculation, maybe it will undermine his speculation. We do not know.

Moreover, Ewert acknowledges that his approach offers no credible way to explain sequence data. This inability to explain an enormous amount of relevant data is a huge weakness at the present time.

Bill, I assume you would like to maintain as much credibility as possible on this forum. I would strongly encourage you, then, not to cite Ewert’s dependency graph as anything other than a speculation about a future research program.



I am not sure this is in dispute from a practical point. He uses published papers to make his argument. You can disagree with his arguments but research is shown by direct evidence reading his book. If biologists dispute this point I would think personal bias might be clouding their thinking.

I see the value in his work as the method he is developing. I understand the weakness of the database. I may have overstated the value of his work prior to understanding the weakness of the databases.

I think this is right. I do, however, see other work that shows similar results in Venn diagrams. Again the work is only as good as the databases and they need work to be ready for prime time. The issue I was bringing up was to merely show work is being done. This is the same comment I included @Joe_Felsenstein in where he commented back that @EricMH work was lacking in some rigor. The point is Eric is working on some mathematical proofs on algorithmic specified complexity. The work may be incomplete but the work is in progress.

I think this is a fair criticism. The mechanism that ID is proposing has never produced biology de novo just similar aspects of it such as long sequences. While matter is powerful enough to explain a lot of biology the information content and the complex arrangements are out of the mechanisms (matter) reach as far as we know.

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I wonder what happens if you change the spacing on the X axis to reflect the divergence times between the species, rather than spacing them uniformly. I think I can make a good guess.


What is in dispute are Behe’s books on I.D.

He attempts to convince his readers that only God fully explains the how and why of Evolution.

And yet I think you will find that there aren’t many scientists who think the I.D. Proof of God is any better than the following proofs of God that have been hashed over for centuries:

4 Arguments for the existence of God
4.1 Empirical arguments
4.1.1 Argument from beauty
4.1.2 Argument from consciousness
4.1.3 Argument from design
4.1.4 Rational warrant
4.1.5 Inductive arguments
4.2 Logical arguments
4.2.1 Aquinas’ Five Ways
4.2.2 Cosmological argument
4.2.3 Ontological argument
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Those things are evidence that biology is interesting. They are not evidence of design.

No, that’s not quite right. It is true that all gears cast, cut or stamped from metals or plastics, or carved from wood or similar materials, of which we know are the result of manufacture by humans, and we know that manufacture by humans is ordinarily preceded by design by humans. But gear-like teeth on an organism are never manufactured by humans. (By the way, these are often mischaracterized, hilariously, by people alleging design. I think that Behe actually says how many times they rotate per second. They don’t actually rotate, because they are not round and continuous but are merely two nubby surfaces which rub against one another for a short distance and then stop.)

So if by “gears” you mean actual “gear” gears, yes, all of those we know of are manufactured by humans. That wouldn’t even demonstrate that if we found such things in nature they were designed, but one would obviously have to figure out whether there was some natural process that generated them.

But if by “gears” you mean “nubs on the legs of planthoppers that help keep their legs moving at the same rate when they jump,” there’s simply no reason to think that those are designed. They are certainly not analogous, in any but an extremely naïve sense, to human-manufactured gears. They grow. As I have said, one surface rubbing on another is very common in biology. Once you have that, modifications to the texture of those surfaces is easy. Modifications to the shape of body parts such as the generation of a nub on a surface are easy.

So the gears are wonderful, interesting, and all of that. But evidence of design? No. And none of those who discovered them think they are, either.

Not really. We actually understand a great deal now about how slight modifications to organismal development can generate such things as bumps on a leg. You probably already know that the notion that evolution is “just a theory” rests upon a misconception of what the word “theory” means in this context – but here we are not even talking about evolution broadly: we are talking about whether things like nubs can arise by slight modification to developmental regulatory genes. That sort of thing is absolutely settled against you.

On the flagellum: really? Do you have any idea why this is not convincing to any biologist other than Behe? Do you understand that the Golden Oldies of creationism are not likely to find a fresh audience in anyone who has read about these things? There is plenty of literature on it, and I do not have the time to recap it for you. You probably just need to use Google, read some actual scientists for a change, and begin to take this in.

There is nothing like familiarity with evolutionary theory and the diversity of life to dispel creationist notions. You really need to pursue that. For example, when I asked you about the faunal succession, and where the unbridgeable gap from Pikaia to Panther is, you said “all of them.” A plainer indication that you have no idea what creatures are IN that faunal succession could hardly be asked for. And you indicated that you thought that “every one of them probably has a unique biological system that other dont have.”

That “probably” is a bit of a tell, and the fact is that once the chordates get going, “unique biological systems” do arise, but far, far less often than you might think. One of the best bits of evidence for common descent is that groups like the chordates share an immense amount of genetic material, and that novelty often appears in the form of changes to gene regulation – creatures having the same parts, but differently grown. So, if you look into it you’re going to find that novel “biological systems” do occur between Pikaia and Panther, but that they are fewer in number than you think and that most creatures do NOT have a “unique biological system.”

That’s okay. It’s understandable that the superficial characteristics of creatures make them seem more different than the underlying biology does. But when you are making a claim about biological science, and proposing to throw out the dominant paradigm, you’re not going to be able to do it without first mastering the subject matter. Analogies between manufactured gears and non-manufactured gears will do you absolutely no good.


Behe misuses published papers. That’s the problem.

It’s not his research. He is citing research done by other people, and often misinterpreting the research or not representing it accurately.

Irony meters are exploding across the globe.

What value do you see?

No, you don’t. The Venn diagram shows a pattern of gene loss which is part of evolution.


An alternative model that potentially is a better fit for the data.

Citing papers is based on researching a subject.

It is a worse fit, right now. His model can’t explain the phylogenetic signal in the sequence data. The evolutionary model can.

Scientific research is not done by sitting in a library and reading papers. Scientific research needs to be original work and original data.

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This is your opinion. What phylogenetic signal are you detecting when comparing alpha actin sequences between mammals?

Scientific research is the systematic investigation of scientific theories and hypotheses. A hypothesis is a single assertion, a proposed explanation of something based on available knowledge, for something yet to be explained. One that is subject to further experimentation.

I see a lot of claims here that are basing definitions on their own subjective standards.

Why do you ask for things that you will then ignore?

Irony noted.

Look at the definition you gave. Behe did no further experimentation. He only cited work done by other people.

Non sequitur. It does not follow from Behe’s citations that his argument has any scientific value.

My proof by counterexample is Ken Ham. Ham often cites peer-reviewed biology articles to make his YEC points. Does the fact that he cites those articles imply that Ham’s reasoning is sound?

Or is it possible that Ham misconstrues the research he cites?

Is it possible that Ham overlooks other research that is important to understanding how the cited article fits within the larger body of evidence?

This is a completely gratuitous slam on scientists, Bill. Before you pontificate again about how tens of thousands of biologists over decades over research have been wrong and Behe is right, can you answer these questions for me?

Does the fact that Behe cites articles imply that his reasoning is sound?

Is it possible that Behe misconstrues the research he cites?

Is it possible that Behe overlooks other research that is important to understanding how the cited article fits within the larger body of evidence?


Your moving the goal posts here. The discussion is whether Behe does research. You are welcome to disagree with his conclusions.

Not necessarily.

Sure all your points here are possible. I don’t see any real problem with his general conclusions in the book, however I could certainly be wrong.

Then why did you make the gratuitous slam about the entirety of the biology community that disagrees with Behe? At a minimum, don’t you think you should mention in the same breath that it might be Behe who is wrong and the biology consensus that is right?