Do all deer share a common ancestor?

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It shows no such thing. It shows that fixation of chromosomal variants is rare. But if they were significantly deleterious there wouldn’t be so many fixed or at high frequency in various local populations.

It explains nothing. It’s saying that species are different because they’re different. And you continue to ignore the point about nested hierarchy.

Once again you confuse the pattern with the events that make up the pattern. It’s like saying that little dots of paint are the cause of Un dimanche après-midi à l’Île de la Grande Jatte.

Well, if the chromosome changes in mice are mutations, then similar changes in deer are mutations too. So deer are related, and their various new genes are the same sort of evidence for natural variation that you’re seeking in mice. Have we now agreed, by the way, that the various house mouse populations are related by common descent?

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What do you expect? If they possessed identical genetics, they would not be different species.

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Then you’re not looking. It’s everywhere, even in real time during human carcinogenesis and animal models.

What’s the origin of the “Philadelphia chromosome” commonly seen in chronic myeloid leukemias? Philadelphia?

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Indicentally, the Venn diagram doesn’t show gene families. It shows orthologous genes. Bill, of course, doesn’t know the difference.

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I am not sure why you made a straw man argument here.

Again a straw man argument. The argument is they are different because they were designed to be different.

The arrangement of the little dots of the paint are the cause of Seurat’s painting just as the arrangement of mouse genes are the part of the cause of a mouse embryo becoming a mouse.

We agree that the various house mouse populations are related by common descent but that does not mean the deer populations are related by common descent and the genetic data gives every reason to doubt that they are.

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You will have to explain. Is it the addition of the word “significantly”? But a variation that isn’t significantly deleterious can easily be fixed by drift, effectively neutral. You are unable to tell a straw man argument from a valid one given your incomprehension of the subject.

That’s the same thing unless you can say how design would result in those differences. Otherwise it’s just “God did it that way because he wanted to”, which is no explanation.

My point. It’s the arrangement of the dots, not the dots. Pattern, not individual events. Nor is it the arrangement of mouse genes, whatever you think you mean by that. It’s the genes themselves and the various regulatory sequences that go with them. In no way could that be called an arrangement.

Well, at least you finally agree that house mice are related. But they show that chromosomal mutations can become fixed in populations. And that shows a plausible mechanism for chromosomal differences among deer species, which is what you originally demanded. It isn’t clear what you mean by “the genetic data” or how that would cast doubt on common descent of deer. The sequence certainly is powerful evidence for common descent, and you have never bothered to confront it. So we are apparently left with gene loss and gain. That that’s nested hierarchy too, which you can’t explain. So you are left with your fallback position: too many losses and gains to account for by known natural processes. But even there you have no evidence that it’s too many. And even there if we accept the premise, that still doesn’t argue against common descent, just for some unknown process that causes extra mutation and/or fixation. All these years, and you have learned nothing, except perhaps that house mice are related.

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It is not clear at all that these deleterious mutations can be fixed by drift even if they are only moderately deleterious as the wild type 2n=40 will out compete the variants due to reproductive advantage.

The observation is that different genes arrangements are required to build different animals.

It is the dots and their arrangement.

For animals it is the arrangement of genes and not just the genes themselves.

The highlighted portion is a burden shift fallacy. The opp asked for a model to support the single origin claim.

I also had agreed to mice having diverse chromosome counts occurring by mutation in their populations. See post number 61.

The diagram that is problematic for the single origin of deer claim is in this paper previously cited.

A single origin claim would not predict musk deer being closer to cattle (in gene arrangements) than white tailed deer. It would also not predict white tailed deer being closer to humans than to musk deer.

The nested hierarchy claim has not been a strong claim as it requires an “unknown mechanism” along with reproduction to support the single origin claim.

What do you think this mechanism could be?

If the mechanism does not exist then the obvious fall back is multiple origin events of different deer species. They were designed with the observed gene and chromosome arrangements and what we are observing in mice is simply variation inside the house mouse populations.

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So you are ignoring the actual data — the presence of these variants as fixed or at high frequency in many populations — in favor of your a priori beliefs. Check.

Nope, no such observation. Different gene arrangements (still not sure what you mean by that) are present, but the evidence that they’re required is not there. You could do experiments, replacing genes with other genes from relatives, but I don’t think that’s been done. And you’re still just saying that things are different because they’re different, which explains nothing.

It’s quite unclear what you mean by “the arrangement of genes”. I also think you’ve lost sight of the subject. Finally, let me again complain that you ignore most of what I say to concentrate on a few fragments.

Once again, we see your central confusion. The model you ask for is not to support the single origin claim, it’s to support a natural origin of the various mutations and fixations, which again, and perhaps in bold so you might notice this time, is not at all the same thing.

Yes it would. Are you not paying attention? Musk deer really are closer to cattle, phylogenetically, than to white-tailed deer. Look at the tree in Fig. 1.

That doesn’t happen. You misunderstand most of what you read or see. Again, look at the tree. Still not clear what gene arrangements are, and you haven’t said even after multiple requests.

I don’t think it requires an unknown mechanism, but even if it did, your separate creation idea would require many more unknown mechanisms and still wouldn’t explain nested hierarchy. So common descent is way out front there.

The mechanism is mutation and fixation, as seen in Mus musculus. And we see hallmarks of mutation in the synteny of musk deer chromosomes. That’s evidence independent of the nested hierarchy.

No, that isn’t the obvious fallback. The obvious fallback would be divinely directed evolution, which maintains an explanation for nested hierarchy while avoiding the need (in your head) to explain the causes of mutation and fixation. Why do you reject that? And what we are observing mice is variation between as well as within populations, some of that variation apparently rising to the level of speciation. Do you in fact deny that speciation is a real phenomenon?

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On the island of Madeira there are 6 populations, all with different chromosome counts. They haven’t been outcompeted. In your example, there is even strong barriers to interfertility between the populations, further cementing this process as a source of speciation. The very thing you claim couldn’t happen in muntjac deer is the very thing that is happening in multiple populations of mice, in real time.

It is ironic that ID/creationists will go on and on about needing to see something like an IC system evolve or some other thing evolve. If only they could see it happen then they would accept evolution. You have shown that this is false. No matter what you are shown you will reject evolution. We can see the VERY thing happening in mice that you claim can’t evolve. What more do you need?

I see you have found a new term to butcher and use as deflection.

The model is chromosomal fusions and vertical inheritance. You’ve been given the model.

This model predicts:

  1. A nested hierarchy of chromosomal fusion events.
  2. Degenerate centromeres in the arms of chromosomes.
  3. Preserved synteny as shown in the unfused chromosomes.

All three of those predictions hold. Your model can’t explain any of these predictions. The better explanation is chromosomal fusions and vertical inheritance from a common ancestor.

Unknown mechanisms??? Didn’t your parents teach you about the birds and the bees? Do you not know where babies come from?

It is that very same variation that occurred in the lineages of muntjac deer.

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The data is telling us that these are variations to the population as the wild type is still 2N=40 for house populations across the globe.

It is an inference and I agree more data is needed to confirm this inference.

We are observing different gene arrangements in different species. This is a fact.

The claim of “common descent” in practice implies a natural single origin.

So what is called a “musk deer” is really a “small cow”. How did this confusion arise?

What I see is 15328 shared genes between musk deer and white tailed deer and 15722 shared gene between white tailed deer and humans. Are you saying the Venn diagrams are incorrect?

Are you claiming that this mechanism explains the genetic differences between all deer species? How would you test this claim?

The fall back is separate origin events.

If God was required then it is a separate origin event as we have no way of knowing his method. The nested hierarchy could easily be a bi product of His design method especially if He used bacteria or retroviruses to make the changes. The nested hierarchy could also be a bi product of His design method of conserving gene types.

The question that needs to be answered is how much of the diversity of deer can we explain by reproduction and natural variation?

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Here, your main confusion is over the definition of “population” as opposed to “species”. There are many populations within the species. In some populations, chromosomal variants are fixed. If there are enough fixed variants to produce reproductive isolation, that should probably be considered speciation. But even if not, it’s still a variant that became fixed within a population, and thus evidence for the plausibility of such things in deer.

I don’t agree. That assumes that the inference is actually reasonable given the present data. It’s not. Rather than having inadequate data, you actually have nothing.

Don’t know, because I don’t know what you mean by “gene arrangements”, and you have consistently ignored requests to clarify. Let me again complain that you ignore most of what I say to concentrate on a few fragments.

Doesn’t. It implies a single origin, period.

That’s unusually obtuse even for you. No, not a small cow, just as a gazelle is not a small cow or a hyena is not a big cat. The “confusion” arises probably because the general appearance of a deer is primitive relative to the general appearance of a bovid. But are you acknowledging your error here?

No. I’m saying that isn’t a statement about relationships. It should be clear from the diagram and the tree in that figure that musk deer have lost an unusual number of genes. Nothing supports your claim of separate creation.

Yes, that’s what I’m claiming. You would test it by looking for evidence of fusion in the genome. The paper we’re talking about shows the expected pattern of synteny, and I predict it would also show some remnant centromeric and telomeric sequences. But the synteny should be enough. Separate creation can’t explain that pattern, just as it can’t explain the nested hierarchy.

Why?

That’s a series of non sequiturs. The only possible response is to point that out. If we don’t know God’s methods, then how do you reject the method of guided evolution within a framework of common descent? At least then you wouldn’t have to explain the nested hierarchy with lame and senseless excuses. So why do you reject common descent?

That’s a different question, a point you eternally seem incapable of understanding. As it happens, though, there’s an answer to that question too: all of it. What looks like a duck and quacks like a duck should at least provisionally be considered a duck rather than a unicorn.

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These are variations you claim shouldn’t exist, and yet they do. Even more, they have become fixed in subpopulations of the house mouse. This is all that is needed in order to produce the chromosomal patterns seen in muntjac deer. The very thing you claim couldn’t have happened in muntjac deer is the exact thing that is occurring right now in mouse populations.

Magical poofing is never the fall back.

That argument was refuted 140 years ago.

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Note that that is a difference argument, about natural selection rather than common descent. Bill’s problem is that he can’t tell the difference. Don’t encourage him.

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The same argument is repeated for classification, but it isn’t as detailed as that quote.

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Sure, you’re using it as a specific example in a general argument against ad hoc assumptions of divine intervention. But Bill won’t understand that. You need to be careful to avoid confusing him.

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Breathing in the general direction of Bill will induce confusion. It seems to be a defense mechanisms, a nasty byproduct of cognitive dissonance. At some point, it’s better to write for the general audience rather than the autoself-confusing Bill.

If Bill can’t understand why we don’t conclude separate creation when mountains of evidence is consistent with natural processes, perhaps others who read the post can understand why.

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That sentence seemed confusing to me too. The processes that cause changes (or a creationist would say “differences”) have to be considered separately from the process that causes the pattern in the differences. Bill consistently conflates them, and that sentence seems to do the same.

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That they don’t exist is an empirical prediction of Bill’s ID hypothesis, now falsified yet again.

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I submit that ship sailed and then sank long ago. The HMS De-encephatilization rests eternally at some fathomless depth.

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Why dont you think the inference is reasonable?

Gene arrangements are the group of genes that make up specific species.

I have not seen a paper yet that assumes that the relationships between species is more then reproduction and natural variation.

Are you agreeing to inconsistency between the morphological data and the genetic data?

You are appealing to theory (reproduction and natural variation) to make your conclusion here yet you claim this is not how it is used in practice.

This comment is simply stating an assertion in bold above.

To explain the pattern as gene gain and loss is an inadequate explanation because it requires reproduction and natural variation as the cause of the pattern to be assumed.

I reject common descent being assumed thus generating bias when the data in analyzed.

It may look like a duck to you.

Having genes unique to Zebra fish and humans and not being present in chickens and mice should make the assumption of common descent suspect. Just as genes shared between one species of muntjac deer and a cow but not another muntjac deer species.