The Argument Clinic

[Dan_Eastwood]

@colewd

The alternative model I am suggesting is separate points of origin vs a single point of origin. This better explains the data that does not follow the reproductive patterns.

No, it doesn’t. What do you think “Testing a Strong Prediction of Universal Ancestry” means? Your hypothesis “This better explains the data that does not follow the reproductive patterns”, or “separate origins” has been disproven.

@colewd

Do you really think the idea of design in nature and natural theology is going away?

The theology of ID isn’t going away, that has never been in question. The entire science of ID is one paper by Ewert, proposing a model which had arguable already been disproven by existing tests of Common Ancestry.

It would be interesting to see the Dependency Graph (DG) model tested directly against common ancestry, but DG does not make predictions of where that pattern should appear (Zebra fish?, chickens??), only for form of the pattern. If this were applied broadly to phylogenic data, we would have a situation that statisticians describe as a “Fishing Expedition”. This occurs when an investigator blindly tests many hypotheses in hopes of finding something significant. Of course they do find significant results at about the Type I error rate, but most of those results will be wrong (false positives).

I like Ewert’s work also and it supports the idea of multiple points of origin.

I appreciate his work; he is trying to do real science. DG is unlikely to support multiple origins, as that hypothesis can be (and has been) tested directly. It could potentially identify “parts” that have been swapped around, something like Frankenstein’s Monster.
I suspect the ID communitiy has not put much thought into the implications if Ewert’s DG hypothesis is correct.

Edit: added the missing “not”.

[colewd (Bill Cole)]

@Dan_Eastwood

It would be interesting to see the Dependency Graph (DG) model tested directly against common ancestry, but DG does not make predictions of where that pattern should appear (Zebra fish?, chickens??), only for form of the pattern. If this were applied broadly to phylogenic data, we would have a situation that statisticians describe as a “Fishing Expedition”. This occurs when an investigator blindly tests many hypotheses in hopes of finding something significant. Of course they do find significant results at about the Type I error rate, but most of those results will be wrong (false positives).

Hi Dan
I think where you see different gene patterns and different chromosome counts you can infer separate ancestry.

These differences are evidence against a reproductive connection. This implies many origin events as the different patterns exist between many vertebrate species.

[John_Harshman]

@Dan_Eastwood

DG does not make predictions of where that pattern should appear (Zebra fish?, chickens??), only for form of the pattern.

If I read Ewert correctly, it makes one more prediction: that the genes within a “module” will be functionally related, as in his cartoon example of echolocation. Oddly, no IDer has tried to test that prediction. Perhaps they know that the data we already see make that idea unlikely.

@Dan_Eastwood

I suspect the ID communitiy has put much thought into the implications if Ewert’s DG hypothesis is correct.

Was there supposed to be a “not” in that sentence?

@colewd

I think where you see different gene patterns and different chromosome counts you can infer separate ancestry.

Except that you have given no reasons at all for what you think. We know how these gene patterns can arise, and we see such things existing both as differences between and polymorphisms within species. That argues against what you “think”.

@colewd

These differences are evidence against a reproductive connection.

Why? You have never managed to present a coherent argument.

[Gisteron]

What would qualify as evidence for common ancestry or reproductive connection, I wonder. Just identical genomes for all of life? A single species of clones and nothing else?

See, this is why just accomodating data is not enough. “Explains the data better” is, as I recently explained in another thread, trivial at best, and vacuous at worst. A scientific model’s merits are measured by how well it predicts data, not by how well it can be constructed to match any. Separate ancestry is maybe consistent with just straight, unspecific “differences”, and common ancestry, without known mechanisms that would alter the genome between one generation and the next, is insufficient to explain them. The similarities are just the other way around, of course: Separate origins is not a sufficient account for why all life would have DNA-based genes at all, let alone why so much of it would be so similar between allegedly unrelated kinds, without unknown speculations about the capabilities or desires of magical beings in control of it all, while common ancestry perfectly accounts for why the thing that is being copied for the offspring ends up being indeed a copy of what was within the parent. So far so good.

But now the crucial part begins.

Given the experimentally verifiable fact that the copying process is not perfect, we (a) lose the expectation of the copies being perfect, and (b) we expect a hierarchical pattern of differences as lineages diverge. We do not see it first and then just make up an ad-hoc rationalization for why it makes sense. We expect to see this well in advance of actually checking. Finding that it is so makes plausible the conjecture that perhaps less than all of the reasoning we used to predict the observation is entirely off-base.

On the other hand, assuming separate origins we should expect patterns like these at best only within individual kinds, and, more importantly, we should expect groups of organisms that have entirely arbitrary things in common, if any at all. Animals that violate taxonomy should not be something we only find in fiction, but rather they should be the norm, because taxonomy should only work for the family of that one separate ancestor and be separate from the taxonomies of all the other kinds. Finding that all of life seems to neatly align within a single tree is consistent with separate origins only if some miraculous scheme to deceive us, or an outlandishly unlikely coincidence is invoked to account for the data, while the theory on its own cannot.

The data is in, Bill. In the rare instant where separate ancestry might make a prediction, its predictions conflict with the data unless excuses are involved. Predictions from common ancestry, meanwhile, do not, if observed facts are kept in mind. It’s not an open question.

[colewd (Bill Cole)]

@John_Harshman

Except that you have given no reasons at all for what you think. We know how these gene patterns can arise, and we see such things existing both as differences between and polymorphisms within species. That argues against what you “think”.

Hi John
To the best of my knowledge you have never shown any reproductive mechanism that supports the origin of these gene patterns.

[John_Harshman]

@colewd

To the best of my knowledge you have never shown any reproductive mechanism that supports the origin of these gene patterns.

The best of your knowledge is not a high standard. Does deletion happen? Does duplication happen? Do both exist as polymorphisms within populations?

[colewd (Bill Cole)]

@John_Harshman

The best of your knowledge is not a high standard. Does deletion happen? Does duplication happen? Do both exist as polymorphisms within populations?

Duplication does not explain the pattern either does polymorphisms inside a population. You are talking about thousands of different functional genes fixed in populations of different vertebrates.

[Tim]

Duplication does not explain the pattern either [sic] does polymorphisms inside a population.

And here, we see The Return of the Dreaded Bald Assertion.

We have, on this thread, a positive Gish Gallop of bald assertions.

[John_Harshman]

@colewd

Duplication does not explain the pattern either does polymorphisms inside a population.

Why don’t you ever answer questions?

@colewd

You are talking about thousands of different functional genes fixed in populations of different vertebrates.

Over what period of time?

[CrisprCAS9]

@colewd

To the best of my knowledge you have never shown any reproductive mechanism that supports the origin of these gene patterns.

“I refuse to accept the evidence that reproductive mechanisms can explain these things, therefore I’m going to assert that my baseless mechanism can explain it even though I’ve never demonstrated that it can.”

You can’t say something that inane and then complain about other people. I mean… you can, but it will result in this:

[Tim]

I believe it is called the Ostrich Defense.

[CrisprCAS9]

No, an ostrich sticks its head in the sand where there’s nothing. He’s going to things he just made up, so I think his head is somewhere else…

[Tim]

Yes, well I doubt if I can find a cartoon of an ostrich putting its head there – let alone get such a cartoon past the moderators, even if I could find one (even on The Argument Clinic thread).

[Mercer (John Mercer)]

@colewd

You are talking about thousands of different functional genes fixed in populations of different vertebrates.

To my knowledge, the term “fixation” only applies to alleles, not genes, so I don’t think anyone’s talking about that other than you.

You have reached a new peak of incoherence, Bill.

[Roy (30-year veteran)]

@John_Harshman

If I read Ewert correctly, it makes one more prediction: that the genes within a “module” will be functionally related, as in his cartoon example of echolocation. Oddly, no IDer has tried to test that prediction. Perhaps they know that the data we already see make that idea unlikely.

Perhaps they don’t know how.

They have no clue about how any other aspect of science works - why should prediction testing be any different?

[John_Harshman]

@Mercer

To my knowledge, the term “fixation” only applies to alleles, not genes, so I don’t think anyone’s talking about that other than you.

Here’s a rare case in which Bill’s terminology seems OK to me. Any genetic difference within a population has a frequency, and if that frequency reaches 1, what should we call that other than “fixation”? Chromosomal fusions, gene duplications and losses, retroelement insertions, etc., all arise as mutations at a frequency of 1/2N, and all eventually reach a frequency of either 0 (eliminated) or 1 (fixed).

[Mercer (John Mercer)]

They’re still alleles afaik.

[John_Harshman]

I don’t think that the concept of “allele” extends to presence/absence of an entire gene.

[Rumraket (Mikkel R.)]

Well if a variant at a locus can be considered an allele, for a sufficiently large locus even the deletion(or insertion) of an entire gene could be considered an allele.

Allele

An allele [1], or allelomorph , is a variant of the sequence of nucleotides at a particular location, or locus, on a DNA molecule.[2]

Reference 2 is Dan Graur’s Molecular and Genome Evolution.

[John_Harshman]

Sure, an entire gene can be considered an allele of a larger locus. But that doesn’t make Bill’s use of the term “gene” wrong. The allele that contains the gene can become fixed, eliminating the allele without the gene, and that’s the same as the gene becoming fixed. Of all the things to beat on Bill about, this is the least meaningful.