Do all deer share a common ancestor?

[colewd (Bill Cole)]

@RonSewell

Just my usual statement that software in no way follows a nested hierarchy. This has been demonstrated in many threads already. Carry on.

Hi Ron
The problem here is your argument like others comes down to a naked assertion. Software does follow a nested hierarchy in cases where it is developed with shared modules.

Following a nested hierarchy and the pattern matching life’s pattern of groups inside of groups in vertebrates is not explained by common descent as the changes are way beyond the capability of reproduction and the variations we have observed.

We are seeing mutations happen does not explain the emergence of new organisms that are observed with unique gene and chromosome arrangements.

Since a nested pattern especially one with the radical differences we are observing can be the product of intentional design we can infer God as the major cause of these differences. The nested pattern tells us nothing about Gods method other than he was most likely responsible for the origin of the novel populations.

@T_aquaticus

Why do you keep lying about this?

You are not understanding Winstons comment. The substantial portion of the genes are attributed to non-taxonomic modules. This is why the gene patterns fit a dependency graph better than a tree.

@John_Harshman

In what way is it misleading? And how does separate origins fit the nested hierarchy better than divinely guided common descent?

Divinely guided common descent is just an identified method of special creation. One of many.

The problem with the claim the divinely guided common descent is the radical changes between different species, Why would God limit himself to the reproductive process?

@John_Harshman

Once more: the nature of the differences is not relevant to the pattern. Please stop confusing this.

This does not make sense.

@John_Harshman

Gradually. As you can see from the history of life. Hearts begin as a contractile bit in an artery and a one-way valve. Some taxa with minimal hearts don’t even have brains. The gradual changes don’t even have to happen at the same time. One system has time to adapt to a change in another. If you look at that comparative anatomy text you will find a lot of that. Or you could of course choose to remain ignorant, if that would make you more comfortable.

This does not make any sense. A heart cannot function without a brain/central nervous system without oxygen transport.

@John_Harshman

Sorry, but reusing parts doesn’t explain nested hierarchy. Try again.

Sure it does it is why you see the nested hierarchy of life regardless of the cause.

@John_Harshman

How does that contradict my claim? But do cite those Venn diagrams.

Special creation is not considered a possible explanation for the origin or Ratites.

@John_Harshman

That’s nice, but how is it relevant?

It is unlikely caused by reproduction and natural variation.

@John_Harshman

I can’t be responsible for your inability to remember your past claims.

You are mistaken here.

@John_Harshman

Why can’t the same models explain the differences between populations? Remember that there are multiple populations of house mice, and yet you think population genetics can explain their differences. How does that suddently change if you call the populations different species?

The models depend on reproduction rates, type of change, mutation rates etc. The results are going to depend on the specific conditions. A small subpopulation of a species with very rapid reproduction rates has the best chance to exhibit these differences.

@John_Harshman

None of these sentences is true, and the reasons have been explained to you on many occasions, all of which you ignore. I’m about ready to give up on this futil attempt to communicate with you.

Then you should be able to explain why they are not true and stop with the naked assertions. I have been explaining why design generates nested hierarchies several years prior to Winstons paper. I used hardware designs but software is much closer to how different cells generate variation in living organisms.

[T_aquaticus]

@colewd

You are not understanding Winstons comment. The substantial portion of the genes are attributed to non-taxonomic modules.

I understand it just fine. Ewert is (falsely) claiming there is no nested hierarchy. Do you agree with Ewert? If so, how can you then claim that the nested hierarchy we are seeing is evidence for separate origins? If you are staying consistent with Ewert’s paper you should be arguing that there is no nested hierarchy (which there clearly is).

You can’t take a paper that says there is no nested hierarchy because of intelligent design and use that as an argument that the observed nested hierarchy is the product of intelligent design.

[RonSewell (RonS)]

@colewd

The problem here is your argument like others comes down to a naked assertion.

Not so. That software does not fall into a nested hierarchy has been expounded many times in this forum. It is done; there is nothing to add and no obligation to litigate over and over just because someone cannot let it go.

[colewd (Bill Cole)]

@T_aquaticus

I understand it just fine.

You do not yet understand his arguments. A pattern can fit a dependency graph and a tree better than the null hypothesis. These are not mutually exclusive patterns.

[T_aquaticus]

@colewd

A pattern can fit a dependency graph and a tree better than the null hypothesis. These are not mutually exclusive patterns.

They are mutually exclusive. Ewert even says so.

Therefore, if the inferred dependency graph is simply the tree of life with a few minor additions, that would suggest that the dependency graph hypothesis is incorrect.
Ewert

Ewert states it in no uncertain terms. If we see a strong phylogenetic signal then the dependency graph hypothesis IS WRONG. Period. Full stop. A nested hierarchy falsifies the dependency graph hypothesis.

Further, Ewert even points to what he thinks are gross violations of a nested hierarchy as evidence for the dependency graph hypothesis.

For example, Gallus gallus (chickens) and Meleagris gallopavo (turkeys) are closely related birds, and thus are expected to share many genes by common descent. On the other hand, despite the similarity in names, Taeniopygia guttata (zebra finch) and Danio rerio (zebra fish) are only distantly related because one is a bird and the other a fish. As such, it should be relatively improbable to find genes shared only between these two species. But according to the Hogenom [43] dataset, there are nineteen gene families found only in this pair of species.
Ewert

You have been shown this over and over and over and over, and you still get it wrong. Why?

[John_Harshman]

@colewd

Following a nested hierarchy and the pattern matching life’s pattern of groups inside of groups in vertebrates is not explained by common descent as the changes are way beyond the capability of reproduction and the variations we have observed.

You still persist in confusing two entirely separate issues. It’s not necessary to explain the causes of differences in order to explain the pattern of differences. I must assume at this point that the confusion is deliberate.

@colewd

Since a nested pattern especially one with the radical differences we are observing can be the product of intentional design we can infer God as the major cause of these differences.

Even if your inference were correct, why isn’t the most reasonable conclusion one that combines common descent with design of various mutations?

@colewd

The substantial portion of the genes are attributed to non-taxonomic modules.

That’s because he doesn’t consider the possibility of gene loss. Why doesn’t he?

@colewd

Divinely guided common descent is just an identified method of special creation. One of many.

That’s not special creation in the sense you use it, “separate starting points”. It’s still common descent, isn’t it? So why do you reject it?

@colewd

Why would God limit himself to the reproductive process?

Why would he limit himself to fiat creation? Are you reading God’s mind now?

@colewd

@John_Harshman

Once more: the nature of the differences is not relevant to the pattern. Please stop confusing this.

This does not make sense.

You are determined not to understand the point. Any sort of data can make up a pattern. The pattern is independent of the sort of data that make it up. How is that not clear?

@colewd

A heart cannot function without a brain/central nervous system without oxygen transport.

And yet, there are animals with hearts but without brains. How do you account for that?

@colewd

Sure it does it is why you see the nested hierarchy of life regardless of the cause.

Isn’t that one of the naked assertions you always complain about? Please explain why “reuse of parts” is expected to produce a nested hierarchy.

@colewd

Special creation is not considered a possible explanation for the origin or Ratites.

With good reason. It doesn’t fit the data. So how does that contradict my claim? And please cite those Venn diagrams. I’m really tired of you ignoring most of what I say, including most questions and requests.

@colewd

It is unlikely caused by reproduction and natural variation.

Why would you imagine that’s true, and even if it is, how is that relevant to the evidence for common descent?

@colewd

You are mistaken here.

No, I really am not responsible for that.

@colewd

The models depend on reproduction rates, type of change, mutation rates etc. The results are going to depend on the specific conditions. A small subpopulation of a species with very rapid reproduction rates has the best chance to exhibit these differences.

You forgot to mention time. The types of change are identical, and reproduction and mutation rates can be offset by greatere time scales. Your objection is not valid and, I suspect, is just a spur of the moment attempt to save you from the data.

@colewd

Then you should be able to explain why they are not true and stop with the naked assertions.

Again, done on many occasions.

@colewd

I have been explaining why design generates nested hierarchies several years prior to Winstons paper.

Yes, and with no more success than after it, because it just isn’t true. One problem is that you don’t seem to know what a nested hierarchy is.

[Rumraket (Mikkel R.)]

@colewd

@John_Harshman

Gradually. As you can see from the history of life. Hearts begin as a contractile bit in an artery and a one-way valve. Some taxa with minimal hearts don’t even have brains. The gradual changes don’t even have to happen at the same time. One system has time to adapt to a change in another. If you look at that comparative anatomy text you will find a lot of that. Or you could of course choose to remain ignorant, if that would make you more comfortable.

This does not make any sense.

Oddly I find it not at all difficult to understand, which leads me to suspect the real issue is with you.

[Rumraket (Mikkel R.)]

Omg, Ewert showed design can produce a nested hierarchy!

[colewd (Bill Cole)]

@John_Harshman

You still persist in confusing two entirely separate issues. It’s not necessary to explain the causes of differences in order to explain the pattern of differences. I must assume at this point that the confusion is deliberate.

Common descent is a claim about reproduction as a cause of both the changes and the pattern of similarity of differences.

@John_Harshman

Even if your inference were correct, why isn’t the most reasonable conclusion one that combines common descent with design of various mutations?

It first needs to be established that both are a significant explanation for the pattern.

@John_Harshman

That’s because he doesn’t consider the possibility of gene loss. Why doesn’t he?

If you look at the tree at the bottom of page 13 you will see he claims that gene loss is the most parsimonious explanation given the common ancestry hypothesis.
http://dx.doi.org/10.5048/BIO-C.2018.3.f7

@John_Harshman

That’s not special creation in the sense you use it, “separate starting points”. It’s still common descent, isn’t it? So why do you reject it?

If God is involved it is special creation. This an important distinction because if we ever come to an agreement that God was involved in some of these transitions then we have the project of determining which transitions are within the reach of reproduction and natural variation.

@John_Harshman

Why would he limit himself to fiat creation? Are you reading God’s mind now?

It appears you are agreeing with me here.

@John_Harshman

You are determined not to understand the point. Any sort of data can make up a pattern. The pattern is independent of the sort of data that make it up. How is that not clear?

To create a pattern you need a relationship in the data sets. Without a relationship there is not discernible pattern.

@John_Harshman

And yet, there are animals with hearts but without brains. How do you account for that?

There are no animals with hearts without either brains, nervous systems, or circulatory systems. Without several of these systems working together you do not have any selectable function.

@John_Harshman

With good reason. It doesn’t fit the data. So how does that contradict my claim? And please cite those Venn diagrams. I’m really tired of you ignoring most of what I say, including most questions and requests

How much time did you spend looking for contradictory data? Here is a Venn diagram for avians.

http://dx.doi.org/10.5048/BIO-C.2018.3.f7

@John_Harshman

You forgot to mention time. The types of change are identical, and reproduction and mutation rates can be offset by greatere time scales. Your objection is not valid and, I suspect, is just a spur of the moment attempt to save you from the data.

Sure as time has several factors. Time to reproduction and life span of the organism. Also the average size of the litter. If the mutations are deleterious this ratio matters for how long these rogue mutations will persist as reproduction of a mutation of chromosome counts can produce a half a million mice before the first pair carrying that mutation die.

@John_Harshman

Again, done on many occasions.

Ok I agree that you are better than most at explaining your assertions.

@John_Harshman

Yes, and with no more success than after it, because it just isn’t true. One problem is that you don’t seem to know what a nested hierarchy is.

Do you think a fixed definition of a nested hierarchy is an easy problem?

[John_Harshman]

@colewd

Common descent is a claim about reproduction as a cause of both the changes and the pattern of similarity of differences.

No, it isn’t. Nobody has ever made that claim. Ask your buddy Michael Behe.

@colewd

It first needs to be established that both are a significant explanation for the pattern.

I have no idea what you meant by that. What makes an explanation significant? Common descent, all by itself, explains the pattern. Design is an explanation for mutations, if you think that there is no natural explanation. It’s preferable to separate creation because it explains more of the data. Why do you prefer a model that explains less to a model that explains more?

@colewd

If you look at the tree at the bottom of page 13 you will see he claims that gene loss is the most parsimonious explanation given the common ancestry hypothesis.

But his model of “modules” doesn’t allow for gene loss. That’s the point. And what does that link have to do with anything?

@colewd

If God is involved it is special creation. This an important distinction because if we ever come to an agreement that God was involved in some of these transitions then we have the project of determining which transitions are within the reach of reproduction and natural variation.

Well, if you want to define common descent as special creation, then fine. But it’s not “separate starting points”, is it? So now you accept common descent. The rest of that is word salad.

@colewd

It appears you are agreeing with me here.

That’s just you failing to understand anything.

@colewd

To create a pattern you need a relationship in the data sets. Without a relationship there is not discernible pattern.

What are you even trying to say?

@colewd

There are no animals with hearts without either brains, nervous systems, or circulatory systems. Without several of these systems working together you do not have any selectable function.

That’s a backpedal from your previous claim. So now a brain isn’t necessary. Of course there are also animals with nervous systems and circulatory systems but no hearts, and animals with nervous systems but no circulatory systems. Do you know anything about biology?

@colewd

How much time did you spend looking for contradictory data? Here is a Venn diagram for avians.

http://dx.doi.org/10.5048/BIO-C.2018.3.f7

That’s not a Venn diagram, and it’s about fish. What??

@colewd

Sure as time has several factors. Time to reproduction and life span of the organism. Also the average size of the litter. If the mutations are deleterious this ratio matters for how long these rogue mutations will persist as reproduction of a mutation of chromosome counts can produce a half a million mice before the first pair carrying that mutation die.

More word salad. Do you never tire of it?

@colewd

Ok I agree that you are better then most at explaining your assertions.

THAN!!

@colewd

Do you think a fixed definition of a nested hierarchy is an easy problem?

Yes. It’s not even a problem.

[T_aquaticus]

@colewd

Sure as time has several factors. Time to reproduction and life span of the organism. Also the average size of the litter. If the mutations are deleterious this ratio matters for how long these rogue mutations will persist as reproduction of a mutation of chromosome counts can produce a half a million mice before the first pair carrying that mutation die.

Let’s see your math.

[John_Harshman]

Never mind the math. Let’s see your coherent English sentences first.

[AlanFox]

Your optimism is amazing.

[colewd (Bill Cole)]

@John_Harshman

I have no idea what you meant by that. What makes an explanation significant? Common descent, all by itself, explains the pattern. Design is an explanation for mutations, if you think that there is no natural explanation. It’s preferable to separate creation because it explains more of the data. Why do you prefer a model that explains less to a model that explains more?

Based on what we know about reproduction I would expect the various gene patterns to fit Winston’s null pattern better than the tree. Most genes would be shared among all the animals.

@John_Harshman

I have no idea what you meant by that. What makes an explanation significant?

The pattern is differences and similarities. This is not a pattern I would expect from common ancestry but one I would expect from different designs with a common design strategy.

@John_Harshman

But his model of “modules” doesn’t allow for gene loss. That’s the point. And what does that link have to do with anything?

Why is this important?

@John_Harshman

Well, if you want to define common descent as special creation, then fine. But it’s not “separate starting points”, is it? So now you accept common descent. The rest of that is word salad.

I said God’s involvement is special creation what ever his method is. It is separate starting points if the cell needs external modification.

@John_Harshman

What are you even trying to say?

To create a nested pattern…

@John_Harshman

That’s a backpedal from your previous claim. So now a brain isn’t necessary. Of course there are also animals with nervous systems and circulatory systems but no hearts, and animals with nervous systems but no circulatory systems. Do you know anything about biology?

So I guess you agree a heart alone has no functional value.

@John_Harshman

More word salad. Do you never tire of it?

Comparing deer and mice is comparing apples and oranges. Different reproduction rates, life spans, different litter counts etc.

@John_Harshman

That’s not a Venn diagram, and it’s about fish. What??

Venn Avian.pdf (107.2 KB)

I only have the Venn diagram and not the paper. Will try to find.

@John_Harshman

Yes. It’s not even a problem.

Great so what is the fixed definition?

[Roy (34-year veteran)]

@colewd

Comparing deer and mice is comparing apples and oranges. Different reproduction rates, life spans, different litter counts etc.

So not like comparing apples and oranges then, since they don’t have different lifespans and reproduction rates.

[Rumraket (Mikkel R.)]

@colewd

I said God’s involvement is special creation what ever his method is. It is separate starting points if the cell needs external modification.

No, it isn’t. If species descent through generations from a common ancestor, that isn’t separate starting points despite the fact that internal cellular changes might ultimately be caused by outside factors. Heck, many internal cellular changes in evolution are ultimately caused by outside factors, such as radiation, chemical pollutants, etc. The cause of the changes is irrelevant, it’s still common descent.

Theistic evolutionists accept common descent, but many posit some sort of divine causal influence on the history of life, be that through God making certain mutations occur by divine intervention, or through having ordered the dominos so that the right types of mutations would occur deterministically, etc. Still common descent despite the concept of an external divine influence on the history of life.

Your private vocabulary is looking desperate when on rare occasion it isn’t nonsensical. Some times both.

[John_Harshman]

@colewd

Based on what we know about reproduction I would expect the various gene patterns to fit Winston’s null pattern better than the tree. Most genes would be shared among all the animals.

Again, I have no idea what you’re trying to say.

@colewd

The pattern is differences and similarities. This is not a pattern I would expect from common ancestry but one I would expect from different designs with a common design strategy.

Still no idea what you’re saying, but that appears not even to be an attempt to answer my question.

@colewd

Why is this important?

Why is what important?

@colewd

I said God’s involvement is special creation what ever his method is. It is separate starting points if the cell needs external modification.

No, that’s not what “separate starting points” could reasonably mean. If you want to redefine “separate starting points” to mean common descent, there seems to be no argument left.

@colewd

To create a nested pattern…

What are you even trying to say? Is it too much to ask to you try harder? Complete sentences would at least be a start.

@colewd

So I guess you agree a heart alone has no functional value.

Seriously, so far in your post there has been no coherent statement of anything.

@colewd

Comparing deer and mice is comparing apples and oranges. Different reproduction rates, life spans, different litter counts etc.

Apples and oranges are both fruit. Easy to compare. Different parameter values do not prevent comparison.

@colewd

I only have the Venn diagram and not the paper. Will try to find.

Do you at least have the figure legend? What is this a Venn diagram of? What are the numbers on the tree? And what do you think that figure tells us?

@colewd

Great so what is the fixed definition?

What do you mean by “fixed”? How does a fixed definition differ from a definition? What are you asking for?

[colewd (Bill Cole)]

@John_Harshman

Again, I have no idea what you’re trying to say.

Common descent where we know it is occurring within species does not predict a tree. It predicts Winstons null hypothesis or mostly shared genes.

@John_Harshman

No, that’s not what “separate starting points” could reasonably mean. If you want to redefine “separate starting points” to mean common descent, there seems to be no argument left.

Calling the relationship between animals when God was involved in the changes “common descent” is deceptive. If you remove the word “descent” then it is a more accurate description. “Common genetics” implies a biological relationship between the animals but does not imply a reproductive relationship.

@John_Harshman

Apples and oranges are both fruit. Easy to compare. Different parameter values do not prevent comparison.

Until you discuss the work of the design guys then you need a 99.9 percent certainty.
Quote from Joe Felsenstein.

1. Yes, there may be cases where the system is trapped in an isolated region of sequence space. But the issue we were discussing is whether a given (500-bit) level of function is a reliable indicator of Design Intervention. Reliable. Meaning always or almost-always. Not just 10% of the time, or 50% of the time, or 99% of the time, or 99.9% of the time. Essentially always. Otherwise it is not a reliable indicator.

@John_Harshman

What do you mean by “fixed”? How does a fixed definition differ from a definition? What are you asking for?

Fixed means you can use the same definition for Russian dolls that you use for different species.

[RonSewell (RonS)]

@colewd

Common descent where we know it is occurring within species does not predict a tree.

Genealogy is not the same as population genetics, but a tree structure due to reproduction is common to both.

[John_Harshman]

@colewd

Common descent where we know it is occurring within species does not predict a tree. It predicts Winstons null hypothesis or mostly shared genes.

Still opaque. You have no clue about how to communicate your ideas, such as they are.

@colewd

“Common genetics” implies a biological relationship between the animals but does not imply a reproductive relationship.

But there is a reproductive relationship under the model that God was involved in changes. You really aren’t making any sense here.

@colewd

Until you discuss the work of the design guys then you need a 99.9 percent certainty.
Quote from Joe Felsenstein.

Again, no idea what you’re trying to say here.

@colewd

Fixed means you can use the same definition for Russian dolls that you use for different species.

That’s not what “fixed” means. And I’m still thinking you don’t know what a nested hierarchy is.