Fallacy of the Phylogenetic Signal? Part 2

I rescind that. :slightly_smiling_face: I do because I believe in undetectable providential interventions which we are not accounting for and for which there is no accounting.

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I do agree with @Chris_Falter that evolutionary algorithms are a very accurate analogy and way to think about the capabilities of evolution. They are very effective at demonstrating the shortcomings of dysteleological evolution, and why intelligent intervention is necessary to produce the world we empirically observe.

In fact, this would be an interesting thread to look at examples of evolutionary algorithms, what characteristics they have, and how those characteristics compare to the biological data and whether they are a good fit.

See what you’ve done Chris? Conjured up magic. ID is analogous to claims of healing that are statistically invisible. God intervenes and denies it. As in YEC. Standard anti-intellectual story telling. No grown ups allowed.

No providential miracles allowed either.

Do you mean a random series of events around which you weave a superfluous story of personal divine intervention? Or something else?

Ha! Just because you do not allow him to in your prejudice does not mean that he doesn’t.

(And don’t waste any of your precious straw by calling Stearns a homophobe.)

I’ve no need to repeat myself.

What is God’s technology? That utterly self denying, non-evidentiary, invisible, undetectable, unnecessary yet essential thing He does? With perfect maskirovka? Obliterated intervention that only those with ears to see can feel?

You need to address the issue in the other conversation, because there is evidence given there. But you might not waste our time. Most people who read the Stearns sequence would get a clue.

You waste your own time. Stearns learned through suffering, which is good. Most don’t have that luxury. He repented of his homophobia. He made a step up the long arc.

You are totally missing the point (intentionally diverting?), and are maybe afraid to reply in the other conversation? It has nothing to do with homophobia, but it is about God’s recognizable providential M.O. (the ‘M’ is not for maskirovka :slightly_smiling_face: – nice word, btw).

My apologies. Fog of war, and my mind. No intentional diverting and no fear. I’ll reply there. Having been ‘there’. And Stearns’ humanity does not detract from his credibility for me.

GET BACK ON TOPIC NOW!!!

a complete sentence for the validator

He did, four hours ago. :slightly_smiling_face:

Aha, I’m not the only one who thinks the “phylogenetic signal” doesn’t indicate evolution.

From “CONSISTENCY INDICES AND RANDOM DATA”
G. J. KLASSEN, R. D. MOOI, AND A. LOCKE

However, as pointed out by Faith and Cranston (1991) and Farris (1991), rejecting the null hypothesis of random permutation does not necessarily provide confidence in phylogenetic conclusions.

That’s not what the quote says.

The quote is saying just because we some inferred relationship is non random we cannot infer a phylogenetic relationship, e.g. A and B are placed in a certain relationship on a phylogenetic tree. If we cannot confidentally infer a phylogenetic relationship, then why can we confidentally infer an evolutionary tree? If A and B cannot be placed in a certain position on a tree, then why must they be placed on a tree in the first place? A DAG could do just as well.

That’s not what it says. It is saying that lower CI values for random data sets does not necessarily serve as a foolproof negative control for the specific phylogenetic method they are using. In no way are they saying phylogenetic signal is not evidence for shared ancestry.

Ewert has already stated that isn’t the case. DAG’s should show a lack of features shared within taxonomic groups compared to phylogenetic trees.

Well, I’ll continue to flaunt my ignorance here, but how is that significantly different from what I am saying?

‘specific phylogenetic method’ sounds to me like some metric for how well a tree model fits the data, or perhaps method for building a tree, and so rejecting the null hypothesis does not necessarily mean a tree model fits the data, at least as measured/constructed by said method.

Can you parse your sentence for me and show where I am misunderstanding? What exactly are they negatively controlling for? What is an example of something for which they fail to negatively control?

How do you get from “solid, but not necessarily foolproof negative to control for phylogenetic signal” to “phylogenetic signal doesn’t indicate evolution”?

rejecting the null hypothesis of random permutation does not necessarily provide confidence in phylogenetic conclusions.

Doesn’t sound like:

I don’t get a sense of ‘solid’ from the quote ‘not necessarily provide confidence’. Lack of confidence indicates lack of solidity.

But, anyways, semantic disputes are not very interesting. I’ll just grant you for now the authors think phylogenetic signal is still solid, though not foolproof, and get back to the actual data where actually interestingness lies.

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