Do all deer share a common ancestor?

[colewd (Bill Cole)]

@John_Harshman

Not sure what you mean by “byproduct”, but a tree structure of descent is a product of inheritance, genetic change, and branching. Why that’s the case should be so obvious as not to need explanation.

The branching process being described here is very different then the tree of life, even a a small section of it. Here is a primate tree.

What you describe is a branching process which is obviously related to reproduction is a tiny fraction of the primate tree. The process we observe produces very similar species (humans or other primates).

This process is not necessarily informative about how the separate species that form the primate tree came into existence.

When would you consider this species specific branching process has formed a nested hierarchy?

@John_Harshman

I don’t know what your link is supposed to be to, but you have done something wrong.

If you press on the link and scroll down you will see the primate gene Venn diagram.

@John_Harshman

It’s an attempt to get you to recognize a theory that fits the data better than yours but still allows you to put God into it. Why don’t you like that theory?

It has no value that I can see. I don’t need God to be a part of evolution unless the evidence points that way. God’s involvement can be inferred as reproduction and natural variation cannot explain the different gene patterns.

@John_Harshman

I would suggest that when all branches are supported at 100% bootstrap, that’s a good confirmation.

Your test is the data consistently produces a tree pattern. This is not a direct test of common ancestry it’s testing how reliably the the data forms a tree pattern.

@John_Harshman

There are 35 million SNP differences and about 5 million indels and other differences, including one chromosome fusion. So you are incorrect about what I said.

How do you know these are indels? Would the inference of special creation or separate origins possibly lead you to another conclusion about the origin of those sequence differences?

[John_Harshman]

@colewd

The branching process being described here is very different then the tree of life, even a a small section of it. Here is a primate tree.

Once again, I encourage you to learn how to spell “than”, with an “a”. I have no idea, once again, what you’re trying to get at here, even with the spelling correction. I’m fairly sure that you have no idea either.

@colewd

When would you consider this species specific branching process has formed a nested hierarchy?

I have no idea how to answer that question, since it communicates no meaning to me.

@colewd

If you press on the link and scroll down you will see the primate gene Venn diagram.

Great. What point did you wish to make about that diagram?

@colewd

It has no value that I can see.

Why not? Again, it fits the data better than your theory. Is it that you don’t care about fitting the data? You say it’s spinach, and to hell with it?

@colewd

Your test is the data consistently produces a tree pattern. This is not a direct test of common ancestry it’s testing how reliably the the data forms a tree pattern.

Unless you can explain the pattern in some other way, that’s a test of common descent. I suppose you demand a movie showing the birth of each succeeding generation of deer since the common ancestor. And yet you have zero evidence of separate creation. Show me a movie of deer poofing into existence; then you can talk.

@colewd

How do you know these are indels? Would the inference of special creation or separate origins possibly lead you to another conclusion about the origin of those sequence differences?

They’re indels because they look like indels. They look like the indels that are polymorphic within species, we know of mutational mechanisms that produce them. You are in the position of claiming that it looks like a duck and quacks like a duck, so therefore it must be a weasel. The inference of special creation isn’t an inference; it’s your a priori demand. And if we accept your demand, then we would still have no idea whether those differences were created that way or arose after creation. And we would have no explanation for why those differences show a nested hierarchy, and the same nested hierarchy we see in other data to boot.

[Rumraket (Mikkel R.)]

@colewd

The branching process being described here is very different then the tree of life, even a a small section of it.

No, it is not. Nothing you go on to declare actually shows that the “branching process being described” is “very different then[sic] the tree of life”.

@colewd

I’m looking at this tree and nothing about it shows anything different from what is implied by “the branching process being described.” All I see is bifurcations, a tree, as expected from the described process.

@colewd

What you describe is a branching process which is obviously related to reproduction is a tiny fraction of the primate tree.

No, that’s how we got the entire primate tree in the first place.

@colewd

The process we observe produces very similar species (humans or other primates).

The process we observe produces differences that increase with time since their common ancestry, since differences have had more generations to accumulate. So that more closely related in time are on average also more similar. That’s what we observe in the primate tree of life too.

@colewd

This process is not necessarily informative about how the separate species that form the primate tree came into existence.

Yes it is. It’s by divergence from common ancestors. We can see it occur in real time with fast-evolving populations, and we can see the results with comparative genetics and morphology, etc.

@colewd

When would you consider this species specific branching process has formed a nested hierarchy?

What is a “species-specific branching process”? Common descent is not specific to any particular species or clade.

@colewd

@John_Harshman

It’s an attempt to get you to recognize a theory that fits the data better than yours but still allows you to put God into it. Why don’t you like that theory?

It has no value that I can see.

The value is that it doesn’t require you deny the obvious inference from the data that points to common descent.

It should go without saying that not denying an obvious inference from data is valuable. But here we are.

@colewd

I don’t need God to be a part of evolution unless the evidence points that way.

And here we see why this whole thing has become a stumbling block to you, because you want God’s involvement to be necessary so that you can comfort yourself, or use it to beat others about the head that they should believe too.

It is so obvious that to you, at bottom this is all about evangelism and apologetics. You want there to be proof of God in biology, and your mind is hermetically sealed off against the idea that there isn’t.

So theistic evolution is unattractive to you for the reason that God’s involvement in the evolutionary history of life is not necessary to explain the data. So you reject theistic evolution as not going far enough.

It’s a remarkable insight into your psyche. Ultimately you have no confidence in your faith.

@colewd

God’s involvement can be inferred as reproduction and natural variation cannot explain the different gene patterns.

And there lies the textbook non-sequitur that sustains your religious faith. The idea that something presumed to be unexplained(*) is—or can only be—explained by God.

You can’t just believe for your own satisfaction. You can’t believe without having seen. In a way I can’t fault your for this at least, as in that we are alike. It’s what you do next that is the problem. Unlike you, I don’t go on to deny what the data implies.

(*) The “different gene patterns” is explained by the mutational mechanisms of gene gain and loss, but never mind.

[Mercer (John Mercer)]

@Rumraket

It’s a remarkable insight into your psyche. Ultimately you have no confidence in your faith.

THIS.

It seems painfully obvious to me that IDcreationism is about a desperate lack of faith. It’s almost as ridiculous theologically as it is scientifically.

[WalterKloover]

@colewd

When would you consider this species specific branching process has formed a nested hierarchy?

Linnaeus pointed out the nested hierarchy of living organisms based on similarities and differences in various physical characteristics. Long before Charles Darwin.

Individual organisms appear to be groupable (based on similarities and differences), and we call those groups species – humans, lowland gorillas, bonobos, American chestnut trees, etc.

Every organism belongs to one species.

No organism belongs to two species.

Species appear to be groupable into groups that we call genera (based on similarities and differences). Each species appears to belong to one and only one genus.

Say Species1 and Species2 are very similar to one another, but have some difference that is enough for us to say they are not the same species. We say both appear to belong to genus G.

Bingo, there is a nested hierarchy of categories of living organisms. Species 1 and 2 have no overlap between them or with any other group, and they are nested in G.

[WalterKloover]

Genera can be similarly grouped into whatever we call the next larger category, and so on.

Time has marched on since Linnaeus, and in addition to visible physical characteristics, we now can look at similarities and differences in prenatal (and postnatal) development and chromosomes, genes, and DNA bases to group organisms.

Mostly, though not always, the species and genera (and larger groupings) as determined by various characteristics match. A sorting based on hair vs. no hair will, almost without exception (perhaps with no exceptions?), give the same grouping as a sorting based on feeding young with milk. In fact this rule applies even if the characteristic has no effect on the organism’s existence.

This is all about current living organisms and how they can be grouped based on various characteristics. Common descent is not in the discussion yet. Evolution is not in the discussion yet.

[WalterKloover]

Why is it that a design hypothesis does not predict this observed nested hierarchy of living organisms?

Of course a designer could create living organisms in a nested hierarchy. But nobody has ever provided a reason it would have to, so it doesn’t predict that. (For scientific purposes, “that’s what the designer wanted to do” is not a reason, because it would apply no matter what the situation is).

As an example, animals can be divided into those with hair and milk (H/M), and those without hair and milk (NH/NM). A designer who can make H/M and NH/NM animals could almost certainly make NH/M and H/NM animals. But there aren’t any. And there aren’t any other situations where there are significant differences between the groupings as determined by various characteristics.

Moving on to the chart:

A node is a spot in the diagram where two lines meet.

Each node and each group name on the right represents a group of organisms (I’ll call it a population) at a moment in time.

Each line segment from node-to-node or node-to-group name represents the progression of a population through time (a lineage). As time passes, individual organisms within the population die and new individual organisms are born.

Does common descent have to result in a nested hierarchy? Of what?

Let’s take a look at the mangabey and the baboon. Follow the line segments back from each of those populations to the node where they meet, and call that population MB.

The population MB at some point split into two populations, M and B. The current populations M and B do not overlap with each other (no organism is both a baboon and a mangabey) and also do not overlap with any other population (no mangabey or baboon is a member of any of the other groups: human, chimpanzee, etc.).

Together M and B make up the entire set of all living descendants of the MB population that are included in this chart. There may be others, but we are ignoring them for now.

Bingo, you have a nested hierarchy, of populations and their descendant populations: populations B and M are nested in population MB and its descendant populations.

Moving left from the MB population, the next node is MBR, where the lineage that leads to living rhesus monkeys (R) broke off. MB and R are descendent populations nested in population MBR and its descendant populations.

None of the other populations are in the group of populations and their descendent populations that we call MBR. And any other group of populations that has MB in it also has R in it.

So yes, common descent with imperfect reproduction can only result in a nested hierarchy of populations and their descendant populations. (With minor exceptions, of course, like hybridization. Imagine there are mangabeys and baboons that are separate populations. If they interbreed, their hybrid descendants will belong to both the M population and all its descendant populations and to the B population and all its descendant populations.)

So why do we think there is common descent?
Because living organisms fit into a nested hierarchy.
Because living organisms and fossils fit into a nested hierarchy.
Because no matter what characteristics you consider, the hierarchies are essentially identical to each other.
Because physical characteristics are correlated with genetic characteristics.
Because genetic characteristics are passed down from generation to generation, imperfectly.

Now, we may not have enough evidence to determine the place in a particular hierarchy where a particular organisms or fossils belong, and there are known factors that can lead the evidence to be in conflict. (incomplete lineage sorting).

But the big picture is pretty convincing.

[Faizal_Ali]

@Rumraket

I’m looking at this tree and nothing about it shows anything different from what is implied by “the branching process being described.” All I see is bifurcations, a tree, as expected from the described process.

Bill seems to think those orange lines mean something. Perhaps he could tell us where that diagram comes from, so members can provide an explanation of what he didn’t understand about the source, which he will then ignore and it was all a big waste of time except maybe bystanders like myself might actually learn something new, so not a total waste of time.

@Rumraket

So theistic evolution is unattractive to you for the reason that God’s involvement in the evolutionary history of life is not necessary to explain the data. So you reject theistic evolution as not going far enough.

It’s a remarkable insight into your psyche. Ultimately you have no confidence in your faith.

Not just into Bill’s psyche, but into the religio-political basis of the ID movement itself, which is to overthrow secularism and replace it with Christian conservative theocracy. The idea is that you can’t really understand anything without understanding how God’s direct intervention was involved.

The irony is, in the US at least, that seems to be happening, even without ID playing much of a role.

[Tim]

@Faizal_Ali

Perhaps he could tell us where that diagram comes from, so members can provide an explanation of what he didn’t understand about the source, which he will then ignore and it was all a big waste of time except maybe bystanders like myself might actually learn something new, so not a total waste of time.

https://www.researchgate.net/publication/8908604_Loss_of_Olfactory_Receptor_Genes_Coincides_with_the_Acquisition_of_Full_Trichromatic_Vision_in_Primates

Arrows indicate on which lineages the acquisition of full trichromatic color vision occurred (Goodman et al. 1998; Jacobs and Deegan 2001). The red color highlights lineages with a high proportion of OR pseudogenes.

[colewd (Bill Cole)]

@John_Harshman

I have no idea how to answer that question, since it communicates no meaning to me.

The claim is a branching pattern observed in reproduction scales to the observed nested hierarchy of deer or primates. This connection needs to be made beyond naked assertion. The biggest obstacle are the different gene patterns between species. Another obstacle is how other differences became fixed in the populations.

@John_Harshman

Great. What point did you wish to make about that diagram?

The different gene patterns between primates.

@John_Harshman

Why not? Again, it fits the data better than your theory. Is it that you don’t care about fitting the data? You say it’s spinach, and to hell with it?

The claim the data fits better is a naked assertion that has little if any specific support behind it.

@John_Harshman

Unless you can explain the pattern in some other way, that’s a test of common descent. I suppose you demand a movie showing the birth of each succeeding generation of deer since the common ancestor. And yet you have zero evidence of separate creation. Show me a movie of deer poofing into existence; then you can talk.

The pattern is explained by a common design strategy.

The inference is based on gene patterns along with other lines of evidence such as different chromosome counts. A purposeful arrangement of parts.

@John_Harshman

They’re indels because they look like indels. They look like the indels that are polymorphic within species, we know of mutational mechanisms that produce them. You are in the position of claiming that it looks like a duck and quacks like a duck, so therefore it must be a weasel. The inference of special creation isn’t an inference; it’s your a priori demand. And if we accept your demand, then we would still have no idea whether those differences were created that way or arose after creation. And we would have no explanation for why those differences show a nested hierarchy, and the same nested hierarchy we see in other data to boot.

This looks like a duck to you because of your single origin filter.

How did 5 million indels get fixed in the human population? Where is the population genetics model that supports this assertion?

[John_Harshman]

@colewd

The claim is a branching pattern observed in reproduction scales to the observed nested hierarchy of deer or primates. This connection needs to be made beyond naked assertion. The biggest obstacle are the different gene patterns between species. Another obstacle is how other differences became fixed in the populations.

Your big problem is your massive set of unconscous assumptions. The one that stands out the most is your persistent inability to separate common descent from the causes of individual changes. As here. Aside from that, why are the different gene patterns an obstacle? Why is fixation an obstacle? And of course you ignore the evidence of gene loss and gain that’s independent of simple patterns on the tree, such as pseudogenes and non-genic sequences homologous to new genes.

@colewd

The different gene patterns between primates.

That’s not a point. Again, what point did you wish to make?

@colewd

The claim the data fits better is a naked assertion that has little if any specific support behind it.

Once again, the data fit a nested hierarchy, and common descent is the only credible explanation for that hierarchy. Neither of those is a naked assertion. You even agree, sometimes, that the former is true, and you have never managed to come up with any coherent objection to the latter.

@colewd

The pattern is explained by a common design strategy.

But it isn’t. There is no reason to expect a common design strategy to produce a nested hierarchy.

@colewd

The inference is based on gene patterns along with other lines of evidence such as different chromosome counts. A purposeful arrangement of parts.

You have no evidence that “gene patterns” or “different chromosome counts” display a purposeful arrangement of parts. And there is no reason that a purposeful arrangement of parts should follow a nested hierarchy.

@colewd

How did 5 million indels get fixed in the human population? Where is the population genetics model that supports this assertion?

It’s not 5 million in the human population, it’s more like 2.5 million, the rest happening in the chimp lineage. And the model would be drift. The number fixed in a generation is equal to the mutation rate. A little search finds an estimated indel rate in humans of 10^-9 per site per generation, for around 6 per genome. At 6 fixations per generation, and supposing a 20-year generation time, that would be around 50,000 generations per million years, or 300,000 indels per million years. In 7 million years that’s 2.1 million fixations. Given the rough figures, that seems quite compatible with what we observe. Of course none of that is relevant to common descent, since it’s the pattern, not the rate of fixation, that’s the evidence here.

[RonSewell (RonS)]

@colewd

The biggest obstacle are the different gene patterns between species.

And yet you so breezily dismiss similar gene patterns between species.

[colewd (Bill Cole)]

@John_Harshman

Your big problem is your massive set of unconscous assumptions. The one that stands out the most is your persistent inability to separate common descent from the causes of individual changes. As here. Aside from that, why are the different gene patterns an obstacle? Why is fixation an obstacle? And of course you ignore the evidence of gene loss and gain that’s independent of simple patterns on the tree, such as pseudogenes and non-genic sequences homologous to new genes.

Gene patterns (the genes arrangements that are species specific) are an obstacle because they are not observed where we know common descent is possible and that is in populations that can reproduce without issues such as sterile species.

Fixation is an obstacle because of the time it takes given real mutation rates and not assuming junk DNA thus most mutations being neutral. Gene loss and gene gain is also based on common descent being inferred.

@John_Harshman

Once again, the data fit a nested hierarchy, and common descent is the only credible explanation for that hierarchy. Neither of those is a naked assertion.

The big hole in your argument has always been the naked assertion that common descent is the only credible explanation for the nested hierarchy.

Until you can tie these two together your hypothesis is untested.

@John_Harshman

But it isn’t.

There is every reason to expect common design to produce a nested hierarchy. What evidence is there that reproduction and natural variation can?

@John_Harshman

You have no evidence that “gene patterns” or “different chromosome counts” display a purposeful arrangement of parts. And there is no reason that a purposeful arrangement of parts should follow a nested hierarchy.

The evidence is living highly differentiated functional organisms that are reproductively isolated from other organisms. This is strong evidence of purpose.

@John_Harshman

It’s not 5 million in the human population, it’s more like 2.5 million, the rest happening in the chimp lineage. And the model would be drift. The number fixed in a generation is equal to the mutation rate. A little search finds an estimated indel rate in humans of 10^-9 per site per generation, for around 6 per genome. At 6 fixations per generation, and supposing a 20-year generation time, that would be around 50,000 generations per million years, or 300,000 indels per million years. In 7 million years that’s 2.1 million fixations. Given the rough figures, that seems quite compatible with what we observe. Of course none of that is relevant to common descent, since it’s the pattern, not the rate of fixation, that’s the evidence here.

Is this paper the source of your data?

Multi-nucleotide de novo Mutations in Humans

John Harshman

on August 9, 2018 at 2:26 pm said:

colewd:
John Harshman,

You have no standard to determine if data confirms common descent or not. It is assumed. I have tried to explore this with you and you have insisted I take a firm position. My firm position is you have no credible standard in which to determine common descent.

Why not? The standard is presence of a strong and consistent signal in the data supporting a single tree. Nothing other than common descent would produce such a signal. Why isn’t that credible?

TSZ from 5 years ago.

[faded_Glory]

Bill, apologies for butting in at this late stage, but could you perhaps describe in your own words what a nested hierarchy is? I get the distinct impression that you use the term in a different sense than the others here, which might be one reason why you guys are going round in circles.

[John_Harshman]

@colewd

Gene patterns (the genes arrangements that are species specific) are an obstacle because they are not observed where we know common descent is possible and that is in populations that can reproduce without issues such as sterile species.

Fixation is an obstacle because of the time it takes given real mutation rates and not assuming junk DNA thus most mutations being neutral. Gene loss and gene gain is also based on common descent being inferred.

More word salad. Whatever do you mean by “sterile species”? We actually do see different genes in individuals within populations. There are a number of such polymorphisms in the human population.

So, you ask for a model, and now that I went to the trouble of producing a model, you reject it because you don’t like the model. And so the goalposts continually recede. The mutation rate was taken from the literature. Why do you think it’s to large?

Gene loss and gain are inferred from the tree, but their pattern also supports the tree.

@colewd

The big hole in your argument has always been the naked assertion that common descent is the only credible explanation for the nested hierarchy.

Until you can tie these two together your hypothesis is untested.

Until I can tie what two together? We are agreed, I think, that common descent would be expected to produce a nested hierarchy. The question is whether there is another process that would be expected to produce a similar hierarchy. I can’t think of one, and neither can you. If you assumed that some unknown other process was responsible for everything, science would be impossible. It’s your responsibility to find something other than common descent that’s expected to produce the hierarchy we see.

@colewd

There is every reason to expect common design to produce a nested hierarchy. What evidence is there that reproduction and natural variation can?

If there is every reason, why haven’t you been able to come up with any? The evidence from reproduction and natural variation (note again that the latter is an unnecessary assumption) is copious, and I’ve even pointed to some real-time phylogenies.

@colewd

The evidence is living highly differentiated functional organisms that are reproductively isolated from other organisms. This is strong evidence of purpose.

Sorry, but it isn’t. You just have no idea what you’re talking about.

@colewd

Is this paper the source of your data?

I don’t actually recall. First relevant paper I found. Why?

@colewd

John Harshman

on August 9, 2018 at 2:26 pm said:

Yes, you have made exactly zero progress in understanding in the last 5 years.

[colewd (Bill Cole)]

Hi FG
This is Johns explanation 5 years ago at TSZ which talks about the nested hierarchy of life and how common descent produces it.

Yes. The tree, by which I mean the descent of populations from prior populations, combined with the splitting of speciation, is 100% of the explanation for the nested hierarchy of life. Changes (mutation followed by fixation) happen at various times on the tree and are inherited by descendant populations. Isn’t it a bit late for that to become clear to you?

Where we disagree is between a single point of origin and multiple points of origin in the case of this OP for deer.

I agree with John that speciation can occur but where I disagree is that it is 100% of the explanation for the nested hierarchy of life.

In my case I would define speciation as a point of splitting one population into 2 or more reproductively isolated populations by natural reproductive mechanisms.

I am sure John has his own definition.

[John_Harshman]

All very nice, but nobody asked you to define speciation. You were asked to define a nested hierarchy. You haven’t done that, and your quote from me doesn’t do that either. Fail.

[faded_Glory]

Hi Bill, thanks for responding. I am still unclear on what exactly you mean when you use the term ‘nested hierarchy’. Can you explain in your own words what you mean when you refer to a ‘nested hierarchy’?

[Roy (34-year veteran)]

I wouldn’t be surprised if he thought it was a pecking order for breeding birds.

[colewd (Bill Cole)]

@faded_Glory

Hi Bill, thanks for responding. I am still unclear on what exactly you mean when you use the term ‘nested hierarchy’. Can you explain in your own words what you mean when you refer to a ‘nested hierarchy’?

A nested hierarchy is a hierarchical structure where there is a relation inside groups and between groups. In biology there is a relationship between mammals and there is also a relationship between mammals and birds. Both have eukaryotic cells with some of the same components.

The discussion is over the nature of that relationship.