Do all deer share a common ancestor?

[John_Harshman]

@colewd

Your asking what he would prefer which means we know why God did what he did.

No, it means I’m asking you to present a hypothesis of what God would do other than “he would do whatever we see”, which is scientifically useless.

@colewd

It does not mean we have no expectation of what Devine design would look like. We build expectations when we learn about the universe.

That translates as “we expect whatever we see”, which again is scientifically useless. You have to make the hypothesis in advance of the data or it doesn’t count.

@colewd

Nearly neutral has not been shown. The likely deleterious nature of chromosomal mutations in mice which one of the papers showed was overshadowed by fast reproduction rates and short life spans.

Neither of those is relevant to whether something is deleterious. And the paper you reference was about two populations with a great many chromosomal mutations between them, not one.

@colewd

We have evidence based on what we know about the makeup of the current universe.

That assumes that everything in the universe was created the way we now see it. That’s assuming the consequent.

@colewd

Atoms…molecules…cells…eukaryotic cells…multicellular …vertebrates…mammals…primates…humans. All made up of atoms. How do you propose this original component (atom) came into existence with the ability to make all these different animal types?

That’s not relevant unless you’re proposing a deistic God who creates some physics and then sits back to watch what happens. Nothing to do with the origin of species.

@colewd

We have a cohesive design based on solid principles of building on the fundamental principal of atoms. A design strategy humans are moving toward with innovations like the internet and block chain.

More word salad. Do you never tire of it? The existence of atoms does not imply a genetic code at all, much less the same code in different taxa. Any genome would be composed of atoms. Any thousand incompatible genomes would be composed of atoms. This tells us nothing.

@colewd

This is a speculation and does not help us understand what God did.

So you refuse to entertain any sort of scientific hypothesis.

@colewd

The breakthrough Behe and others made is showing the evidence we can infer intelligence behind the design. This makes the multiple origin model, a model that better fits the current data, viable.

More word salad. Behe shows nothing, and he doesn’t support the multiple origins model.

@colewd

Answered above.

Not answered at all, anywhere. You have no hypothesis of what God would or would not do, no expectation of what we would observe given separate creation.

@colewd

The purpose of the bacterial flagellum motor is to aid in bacterial mobility. This is very different than saying the purpose of the bacterial flagellum motor is to perform its function.

No, in fact it’s exactly the same, since its function is to aid in bacterial mobility.

@colewd

What exactly is meant by this? What are your Biblical references that support this?

What part don’t you understand? Are you unfamiliar with the terms or the concepts? What is your opinion of God’s abilities?

@colewd

How would you do this with a different genetic code? How would a virus be reliably generated?

You were talking about bacteria, not viruses. Did you forget?

@colewd

Do you consider someone who is skeptical about universal common descent an anti-evolutionist?

You aren’t “skeptical about universal common descent”. You deny that any two species are related. You are most certainly an anti-evolutionist.

[Argon]

Many anti-vaxxers bridle about the label “anti-vax”. “They’re not ‘anti-vax’”, they claim, but “pro-‘safe’ vaccines.”

Which may work, but only until they’re asked, “So, which vaccines do you consider ‘safe’?” And then you hear the crickets chirping…

[colewd (Bill Cole)]

@John_Harshman

No, it means I’m asking you to present a hypothesis of what God would do other than “he would do whatever we see”, which is scientifically useless.

We know the universe is bound by the laws of physics. It was made this way for some reason and maybe theologians can gain understanding over time.

He would “do whatever we see”’ is an argument no one has made.

@John_Harshman

Neither of those is relevant to whether something is deleterious. And the paper you reference was about two populations with a great many chromosomal mutations between them, not one.

What’s also relevant is we are looking only at mice here. The paper shows smaller litter with a non lethal fused chromosome. This is paywalled but I will pull out a quote from an article about the paper.

https://doi.org/10.1126/science.abm1964

Chr4+5 mice, on the other hand, could produce offspring and mate with normal mice. But when they did so, their litter sizes were small, indicating that they may have suffered from abnormal chromosomal sorting during meiosis, says Wang.

@John_Harshman

That assumes that everything in the universe was created the way we now see it. That’s assuming the consequent.

This is observing the universe and trying to understand the design behind it.

@John_Harshman

That’s not relevant unless you’re proposing a deistic God who creates some physics and then sits back to watch what happens. Nothing to do with the origin of species.

This statement is not about a deistic God. It is about the absurdity of atoms assembling to create humans without any planing when they were designed or originated some other way. Whether we are dealing with Behe’s pool shot or the separate origin of every living species the exact nature of God is not relevant only the evidence that the origin of matter and life were planned events.

@John_Harshman

More word salad. Do you never tire of it? The existence of atoms does not imply a genetic code at all, much less the same code in different taxa. Any genome would be composed of atoms. Any thousand incompatible genomes would be composed of atoms. This tells us nothing.

This is about how to look at a design and infer the design strategy.

@John_Harshman

So you refuse to entertain any sort of scientific hypothesis.

How is a scientific hypothesis here relevant of multiple origins.

@John_Harshman

More word salad. Behe shows nothing, and he doesn’t support the multiple origins model.

Behe shows a lot of examples to defend his method of design detection the bacterial flagellum was discussed here. He does not oppose multiple origins either.

@John_Harshman

No, in fact it’s exactly the same, since its function is to aid in bacterial mobility.

The function is to get a flagellum to rotate at high speeds. The purpose is mobility.

@John_Harshman

What part don’t you understand? Are you unfamiliar with the terms or the concepts? What is your opinion of God’s abilities?

My opinion is God was able to create the universe with finite laws and he is also able to make changes when He deems fit. From a human perspective this is what omnipotence looks like.

@John_Harshman

You were talking about bacteria, not viruses. Did you forget?

Both are used as delivery vectors.

@John_Harshman

You aren’t “skeptical about universal common descent”. You deny that any two species are related. You are most certainly an anti-evolutionist.

No one has answered the question. I will ask Argon again.

@Tim

Lacking such math supporting your claim, I am perfectly justified in concluding that we have indeed received no evidence that came within a light year of demonstrating that “all deer” might not “share a common ancestor”.

From the op.

The math that supports my claim is primarily Behe’s and Stokes model on the limitations of the waiting time to functional changes. This has been discussed extensively.

Can we reconcile the common ancestry of deer based on population genetics for chromosome variation and gene family variation?

Where do you think this this question was answered?

When you argue with the intent to put all the burden of proof on your opponent it means your position “all deer share a common ancestor” is extremely weak.

@Argon

Reasonable skepticism

What would you consider reasonable skepticism regarding UCD? What would you consider reasonable skepticism regarding DCD?(deer common descent).

[John_Harshman]

@colewd

We know the universe is bound by the laws of physics. It was made this way for some reason and maybe theologians can gain understanding over time.

But that too is useless, as it makes no prediction for life other than that it must obey the laws of physics, and it’s the same prediction whether or not God is involved or created anything.

@colewd

He would “do whatever we see”’ is an argument no one has made.

It’s an argument you constantly make. You just don’t realize it.

@colewd

What’s also relevant is we are looking only at mice here. The paper shows smaller litter with a non lethal fused chromosome.

That’s two particular fusions. But it’s obviously not the case for all fusions. These fusions are not seen in nature, but the ones we do see at high frequency can’t have such an effect or they wouldn’t have risen to high frequency.

@colewd

This is observing the universe and trying to understand the design behind it.

Which requires the assumption that there’s design behind it. In fact, you’re assuming that every species was separately created and then interpreting all data as being what we would expect if that were true.

@colewd

It is about the absurdity of atoms assembling to create humans without any planing when they were designed or originated some other way.

That’s not what you said. Perhaps you should think a little bit more before typing so as to say what you intend.

@colewd

Whether we are dealing with Behe’s pool shot or the separate origin of every living species the exact nature of God is not relevant only the evidence that the origin of matter and life were planned events.

Of course it’s relevant. That’s what we’re arguing over, not whether life was planned but whether (if you remember) all deer share a common ancestor. Try to remember the topic.

@colewd

This is about how to look at a design and infer the design strategy.

Not a coherent response.

@colewd

How is a scientific hypothesis here relevant of multiple origins.

Incoherent.

@colewd

He does not oppose multiple origins either.

Yes he does. He supports universal common ancestry. You are confused.

@colewd

My opinion is God was able to create the universe with finite laws and he is also able to make changes when He deems fit. From a human perspective this is what omnipotence looks like.

Zero clarity there. Are you actively trying to avoid it?

@colewd

Both are used as delivery vectors.

So is a UPS truck, but you can’t freely substitute it into a discussion. Nor do I know of any bacterial sequences present in humans (or even deer). Do you? You ignored that question last time, as is your custom.

@colewd

The math that supports my claim is primarily Behe’s and Stokes model on the limitations of the waiting time to functional changes. This has been discussed extensively.

Yes, and it’s been frequently pointed out that the waiting time involved is quite different from what we’re talking about here. There, it’s the time for a particular function to evolve in a particular sequence, often as a result of a particular set of mutations happening in a particular order. But here we’re talking about some event or other happening somewhere in the genome. Not comparable at all.

[Tim]

@colewd

The math that supports my claim is primarily Behe’s and Stokes model on the limitations of the waiting time to functional changes.

No Bill.

1. “Behe’s and Stokes [sic] model” has been widely discredited.

2. Their work only involves instances where a “gene duplication” leads to "production of novel protein features ".

3. As you have only the heavily summarised data from Venn diagrams, and similar, you have no idea whether the deer data contains any such mutations.

4. Neither you nor Behe have applied Behe’s model, or any other model, to the detailed deer data.

5. Behe accepts Universal Common Descent, so it would appear that his work has not led him to reject it for deer, or any other clade of lifeforms.

Can we reconcile the common ancestry of deer based on population genetics for chromosome variation and gene family variation?

Given the complete lack of any evidence that their genetics is irreconcilable, the reply to that is an in-principle “yes”.

The actual reconciliation would no doubt involve a very large amount of genetic data, and a very large amount of math … and thus a scientist who is sufficiently interested in the topic to throw a very large amount of time at the issue.

@colewd

When you argue with the intent to put all the burden of proof on your opponent it means your position “all deer share a common ancestor” is extremely weak.

Balderdash, Bill.

You were the one who asserted:

@colewd

The different chromosome counts and the different gene patterns are an indication they do not all share a common ancestor.

You were the one who implied, in your OP, that the deer “chromosome variation and gene family variation” were irreconcilable with Common Descent.

Therefore the burden of proof has always been and will always be on you to provide evidence to support your assertions and implications.

Your frequent attempts to shift this burden of proof onto others are always very obvious, and render you entirely ridiculous.

[colewd (Bill Cole)]

@John_Harshman

But that too is useless, as it makes no prediction for life other than that it must obey the laws of physics, and it’s the same prediction whether or not God is involved or created anything.

The limit of the laws of physics help make many predictions and is responsible for many of the the current models we have.

@John_Harshman

It’s an argument you constantly make. You just don’t realize it.

It’s not an argument I have ever made. When you change someones words you change an argument and commit a straw-man fallacy.

@John_Harshman

That’s two particular fusions. But it’s obviously not the case for all fusions. These fusions are not seen in nature, but the ones we do see at high frequency can’t have such an effect or they wouldn’t have risen to high frequency.

It’s clear evidence of the deleterious nature of fusions.

@John_Harshman

Which requires the assumption that there’s design behind it. In fact, you’re assuming that every species was separately created and then interpreting all data as being what we would expect if that were true.

I am inferring multiple origins or separate creation from the gene Venn diagrams along with the different chromosome counts.

@John_Harshman

Of course it’s relevant. That’s what we’re arguing over, not whether life was planned but whether (if you remember) all deer share a common ancestor. Try to remember the topic.

The question if all deer share a common ancestor will be settled by evidence.

@John_Harshman

Not a coherent response.

If you look at a Mac computer from inside and out you would claim this can tell you nothing about the Macs design strategy?

@John_Harshman

Yes he does. He supports universal common ancestry. You are confused

I have discussed this with him in detail. He gives up common descent for arguments sake.

@John_Harshman

Zero clarity there. Are you actively trying to avoid it?

I don’t think I understand your argument.

@John_Harshman

Yes, and it’s been frequently pointed out that the waiting time involved is quite different from what we’re talking about here. There, it’s the time for a particular function to evolve in a particular sequence, often as a result of a particular set of mutations happening in a particular order. But here we’re talking about some event or other happening somewhere in the genome. Not comparable at all.

The discussion is about di sulfide bonds and ligand binding like the WNT. Ligand binding is a very generic function inside cells.

You and @Tim are hanging your hats on the Behe model being wrong or not applicable to the case of the Venn diagrams where hundreds of new functions appear in new deer species.

Tim says:

@Tim

As you have only the heavily summarised data from Venn diagrams, and similar, you have no idea whether the deer data contains any such mutations.

The Venn diagrams contain new genes with many more mutations than in the Behe paper. The mutations in the Venn have lead to new complex function so it is evident that Tim is mistaken.

We also know the odds of losing function increases with an increase in mutation as a sequence will break down.

How does reproduction generate new genes? This is the question that needs to be answered.

[John_Harshman]

@colewd

The limit of the laws of physics help make many predictions and is responsible for many of the the current models we have.

There’s a fine meaningless platitude for you.

@colewd

It’s not an argument I have ever made.

As I said, you don’t realize it.

@colewd

It’s clear evidence of the deleterious nature of fusions.

If all fusions are deleterious, how did there come to be so many within Mus musculus?

@colewd

I am inferring multiple origins or separate creation from the gene Venn diagrams along with the different chromosome counts.

Yes, but you have no argument that leads from the data to the conclusion. You reach that conclusion because you intended to reach it from the start.

@colewd

The question if all deer share a common ancestor will be settled by evidence.

Ah, another meaningless platitude.

@colewd

If you look at a Mac computer from inside and out you would claim this can tell you nothing about the Macs design strategy?

Still not a coherent response.

@colewd

I have discussed this with him in detail. He gives up common descent for arguments sake.

That contradicts everything he’s said publically. Are you saying he’s lying in print? Or perhaps you’re misunderstanding something.

@colewd

I don’t think I understand your argument.

That much is true. But how is that relevant?

@colewd

The discussion is about di sulfide bonds and ligand binding like the WNT. Ligand binding is a very generic function inside cells.

I’m beginning to think you have no idea what the discussion is about.

@colewd

You and @Tim are hanging your hats on the Behe model being wrong or not applicable to the case of the Venn diagrams where hundreds of new functions appear in new deer species.

What makes you think these hundreds of new functions appear? Name even one. And how is the supposed waiting time problem relevant to that?

@colewd

The Venn diagrams contain new genes with many more mutations than in the Behe paper. The mutations in the Venn have lead to new complex function so it is evident that Tim is mistaken.

Since you don’t know what even one of those new genes is, how can you know how many mutations and what sorts of function are involved? You’re just making all this up.

@colewd

How does reproduction generate new genes?

Gene duplication and divergence, recruitment of non-coding sequences, recombination of bits of other sequences. Three known paths there.

[Tim]

@colewd

You and @Tim are hanging your hats on the Behe model being wrong or not applicable to the case of the Venn diagrams where hundreds of new functions appear in new deer species.

1. You have offered neither evidence nor substantiation that “the Behe model” was relevant.

2. We have a wealth of opinion that “the Behe model” was “wrong”, including Lynch’s critique, a critique published on Panda’s Thumb, and probably a number of others over the years, and the criticism of the model that the publisher received. [Addendum: Wikipedia cites further criticism of the model here.] Add to that the fact that neither Behe nor Snoke appears to have any degree of expertise in this sort of modelling. Add to that the fact that Behe has been proved wrong on everything from the definition of Science to virology, and good courtroom practice to polar bear genetics. This makes him thoroughly less than credible on this (or any other) subject.

3. You have provided no evidence that the gene differences involve “hundreds of new functions”.

@colewd

@Tim

As you have only the heavily summarised data from Venn diagrams, and similar, you have no idea whether the deer data contains any such mutations.

The Venn diagrams contain new genes with many more mutations than in the Behe paper.

Utterly and midbogglingly irrelevant Bill.

The issue I was raising was with the type of mutation, not the number!

Behe & Snoke’s model only deals with instances where a “gene duplication” leads to "production of novel protein features ".

You have provided no evidence that the gene differences between the deer species are due to "gene duplication” leading to “production of novel protein features”.

Therefore we have no reason to believe that Behe’s amateur model is applicable.

@colewd

The mutations in the Venn have lead to new complex function so it is evident that Tim is mistaken.

Again, you have provided no evidence of “new complex function”. So it is not so much a case of “Tim is mistaken” as Bill Cole is utterly clueless.

@colewd

We also know the odds of losing function increases with an increase in mutation as a sequence will break down.

This would seem to be a complete non sequitor.

[Argon]

Earlier …

Me: The very last thing in the world that armchair anti-evolutionists want to see is a positive, testable prediction about how a designer would operate. Because they could be wrong about a thing.

Colwed: Do you consider someone who is skeptical about universal common descent an anti-evolutionist?

Now:

@colewd

What would you consider reasonable skepticism regarding UCD? What would you consider reasonable skepticism regarding DCD?(deer common descent).

“I’m not anti-vax. I’m pro safe-vax”, said the anti-vaxxer.

How to test that claim: Pro-safe vaccine? Then pick the one you feel is the most dangerous but still acceptable to administer to the public.

“I’m not anti-evolution. I’m just a reasonable skeptic about cases of common descent that most other scientific experts in the field accepted long ago”

Not anti-evolution? Pick examples of transitions with the widest steps that you find ‘reasonable’.

Bonus work: Compare those examples to the relationships between humans and great apes.

[colewd (Bill Cole)]

@Argon

Not anti-evolution? Pick examples of transitions with the widest steps that you find ‘reasonable’.

Bonus work: Compare those examples to the relationships between humans and great apes.

What is your objective way to determine reasonable?

I thought all deer shared a common ancestor until I became skeptical due to the large differences in chromosome counts.

My skepticism heightened when I saw different gene patterns between many of the species.

I would call this data getting in the way of something we all believed.

@Tim

You have provided no evidence that the gene differences between the deer species are due to "gene duplication” leading to “production of novel protein features”.

Gene duplication and divergence has been a theory of record to explain the emergence of new genes. Why do you think Michael Lynch responded the the Behe/Snokes model.

https://www.nature.com/articles/nrg2689#citeas

[John_Harshman]

@Argon

“I’m not anti-evolution. I’m just a reasonable skeptic about cases of common descent that most other scientific experts in the field accepted long ago”

I would disagree with “most” and “other”. Try “all” and leave out the “other”.

@colewd

I thought all deer shared a common ancestor until I became skeptical due to the large differences in chromosome counts.

No you didn’t. You’re on record as claiming that each species is separately created.

[colewd (Bill Cole)]

@John_Harshman

No you didn’t. You’re on record as claiming that each species is separately created.

When did I go on record saying each species is separately created?

Even given the deer data I would not discount wolves and dogs sharing a common ancestor. Both species have 2N=78 chromosomes. I have yet to see gene data.

[John_Harshman]

@colewd

When did I go on record saying each species is separately created?

Not explicitly, but I don’t recall you accepting any two species, ever, as being related.

@colewd

Even given the deer data I would not discount wolves and dogs sharing a common ancestor. Both species have 2N=78 chromosomes. I have yet to see gene data.

So you don’t know even whether wolves and dogs are related? Makes my point for me.

[Rumraket (Mikkel R.)]

@colewd

Why do you think Michael Lynch responded the the Behe/Snokes model.

https://www.nature.com/articles/nrg2689#citeas

Because it’s obviously misleading people, such as you!

[Rumraket (Mikkel R.)]

@colewd

I would not discount wolves and dogs sharing a common ancestor. Both species have 2N=78 chromosomes. I have yet to see gene data.

Are you saying you would dispute dog/wolf common ancestry on the basis of them having differences in the number of genes?

Bill, are you well? I mean in your own experience.

[Tim]

@colewd

Gene duplication and divergence has been a theory of record to explain the emergence of new genes.

You should read your own words Bill.

“A theory” NOT “the sole theory”. In fact @John_Harshman listed other pathways to new genes in direct answer to your own question above:

@John_Harshman

… recruitment of non-coding sequences, recombination of bits of other sequences.

Do you even read the answers people give to your questions Bill?

Therefore we have no evidence that all new genes in the deer clade are due to “gene duplication and divergence”.

Further we appear to have no evidence that all the gene changes are due to genuinely “new” genes – a number of them could be due to genes that are sufficiently modified as to no longer detect as identical.

All this renders Michael ‘I’m always wrong – but IDiots listen to me anyway’ Behe’s wrong model, as not just wrong but irrelevant.

[John_Harshman]

@Rumraket

@colewd

Why do you think Michael Lynch responded the the Behe/Snokes model.

https://www.nature.com/articles/nrg2689#citeas

Because it’s obviously misleading people, such as you!

Oddly enough, Bill’s link has nothing to do with Behe/Snokes or Lynch. Someone put forth a hypothesis that Bill posts links only so as to appear more sciency. That’s a definite possibility.

[Tim]

@John_Harshman

Oddly enough, Bill’s link has nothing to do with Behe/Snokes or Lynch.

Yes, I noticed that. More amusing, the article that he in fact linked to had this as its first ‘key point’:

Models of gene duplication can be classified into four major categories according to the mode of selection in the early phases of the evolution of the duplicated copies.

This would suggest to anybody bothering to think about it, that even if Behe’s modelling were ‘correct’ (which weight of opinion would appear to heavily contradict), it would involve only one of these four major categories, and therefore not be the final word on “models of gene duplication”.

[colewd (Bill Cole)]

@Rumraket

Are you saying you would dispute dog/wolf common ancestry on the basis of them having differences in the number of genes?

Bill, are you well? I mean in your own experience.

At what point would you start to question this reproductive relationship?

[Rumraket (Mikkel R.)]

@colewd

At what point would you start to question this reproductive relationship?

The number of shared genes isn’t the sort of evidence that can undermine that inference.