Do all deer share a common ancestor?

[John_Harshman]

@colewd

The modules are genes and gene families.

That isn’t what Ewert’s modules are. Also, genes and gene families are quite different things. They can’t both be modules. You really have no idea what your modules are, do you?

@colewd

A nested hierarchy would form from a design strategy of conserving sequences and morphological features.

What do you mean “conserving”? That implies a temporal sequence of designs, in which one emerges from another. And of course a nested hierarchy would not emerge from that unless the designer’s “conserving” acted in a way that exactly mirrored descent. Why are sequences and features “conserved” in a nested hierarchy, and why aren’t these modules identical wherever they appear?

@colewd

Modifying existing animals does not make any sense given the different gene and chromosome patterns.

Does it make any sense given the different sequences of genes? And are there not mechanisms by which genes and chromosome patterns can change?

@colewd

I agree.

In that case, your explanation fails. Did you not notice?

@colewd

If common descent happened between all deer species I would not expect to see new genes and different chromosome patterns we are currently observing. We may see a tree pattern that is better than the null for snp’s that were fixed by drift.

Not a response. It was a yes/no question. Why would we see a tree pattern for snps? Why do we see one?

@colewd

Fair enough

So are we agreed that your entire approach there was senseless?

@colewd

Are you claiming that if we infer a nested hierarchy that points to a single point of origin for all life?

No. I’m claiming that it points to a single point of origin for whatever taxa we have a nested hierarchy for. In the current case, that’s deer and, perhaps, ruminants, or even placentals.

@colewd

You are looking at a functional sequence. How can you tell if it is the original sequence of something that has been modified.

If it’s the original sequence, then the “modules” are not the same, and for some reason they have a nested hierarchy. Why? And the sorts of differences between the supposedly same modules are of exactly the sort and frequency that we see in mutations. Why?

@colewd

I got it thanks.

That remains to be seen. Will you forget all about this revelation in a week?

@colewd

If common descent is claim of a life merging from a single point of origin is examining the pattern enough to support this claim?

It is unless there’s another viable cause of the pattern, which so far nobody has managed to come up with.

@colewd

I agree but branching descent is not a mechanism in itself.

This seems a quibble regarding the definition of “mechanism”. How about we just say that branching descent is the reason for the pattern?

[colewd (Bill Cole)]

@John_Harshman

What do you mean “conserving”? That implies a temporal sequence of designs, in which one emerges from another. And of course a nested hierarchy would not emerge from that unless the designer’s “conserving” acted in a way that exactly mirrored descent. Why are sequences and features “conserved” in a nested hierarchy, and why aren’t these modules identical wherever they appear?

What I mean by conserving is that certain functions can be shared among species where the wheel does not need to be re invented. An example is embryonic pathways that are highly conserved among vertebrates. The more similar the species the more shared functions. This is what generates a pattern that you can use a tree to show the hierarchal relationships.

@John_Harshman

Does it make any sense given the different sequences of genes? And are there not mechanisms by which genes and chromosome patterns can change?

There are no mechanisms yet discovered that can account for level of modifications we are observing in different populations.

@John_Harshman

Not a response. It was a yes/no question. Why would we see a tree pattern for snps? Why do we see one?

If the origin of different animal species occur at different times we may see a tree pattern in the fixed mutations of the same gene. We cannot however tell if these sequence differences are due to some purposeful modification to the sequence.

@John_Harshman

No. I’m claiming that it points to a single point of origin for whatever taxa we have a nested hierarchy for. In the current case, that’s deer and, perhaps, ruminants, or even placentals.

Do we have a nested hierarchy for all deer? How would you test this?

@John_Harshman

This seems a quibble regarding the definition of “mechanism”. How about we just say that branching descent is the reason for the pattern?

I would agree that branching descent, which is a by product of reproduction, is a reason for a nested pattern in a population. What branching descent does not explain is the transition to separate distinct populations.

[John_Harshman]

@colewd

The more similar the species the more shared functions. This is what generates a pattern that you can use a tree to show the hierarchal relationships.

But that isn’t true. Mere similarity doesn’t generate a tree or hierarchical relationships, and even if embryonic pathways were organized in a nested hierarchy among species, that wouldn’t imply a nested hierarchy of other features like DNA sequences, indels, chromosomal differences, etc. You also didn’t even attempt to answer my question.

@colewd

There are no mechanisms yet discovered that can account for level of modifications we are observing in different populations.

Again you fail to answer questions, and of course there are mechanisms.

@colewd

If the origin of different animal species occur at different times we may see a tree pattern in the fixed mutations of the same gene.

Whatever is that supposed to mean? Why would different times matter as long as the origins are independent?

@colewd

Do we have a nested hierarchy for all deer? How would you test this?

Yes. You would test it by sampling all deer. I would suggest that a representative sample would do as well. If two members of different genera are shown to be related, that would strongly imply that the other species of those two genera were also related. Of course this has been done, not just for deer but for ruminants, artiodactyls, mammals, etc.

@colewd

I would agree that branching descent, which is a by product of reproduction, is a reason for a nested pattern in a population. What branching descent does not explain is the transition to separate distinct populations.

Actually, there shouldn’t be a nested pattern within a population except for the few uniparentally inherited bits. Of course branching descent doesn’t explain speciation. Speciation explains branching. Are you doubting that speciation happens? That would go against another mountain of data.

[John_Harshman]

Here’s a recent phylogenetic analysis of deer:

The systematics of the Cervidae: a total evidence approach

[colewd (Bill Cole)]

@John_Harshman

But that isn’t true. Mere similarity doesn’t generate a tree or hierarchical relationships, and even if embryonic pathways were organized in a nested hierarchy among species, that wouldn’t imply a nested hierarchy of other features like DNA sequences, indels, chromosomal differences, etc. You also didn’t even attempt to answer my question.

Similarities and differences would generated nested hierarchies with different animals having more similarities than differences. As far as indels, chromosomes differences etc. These need to be looked at on a case by case basis.

@John_Harshman

Again you fail to answer questions, and of course there are mechanisms.

The question is leading so I made a clarification to avoid an answer that may create confusion. The clarification is that the mechanisms have not been tested to account for the observation.

@John_Harshman

Whatever is that supposed to mean? Why would different times matter as long as the origins are independent?

Origins may be independent but the design strategy of all organisms is not independent.

@John_Harshman

Yes. You would test it by sampling all deer. I would suggest that a representative sample would do as well. If two members of different genera are shown to be related, that would strongly imply that the other species of those two genera were also related. Of course this has been done, not just for deer but for ruminants, artiodactyls, mammals, etc.

How do we know if the test has failed?

@John_Harshman

Actually, there shouldn’t be a nested pattern within a population except for the few uniparentally inherited bits. Of course branching descent doesn’t explain speciation. Speciation explains branching. Are you doubting that speciation happens? That would go against another mountain of data.

I think if we looked at change in chromosomes we would see a nested hierarchy between species starting from the first male and female. This is due to genetic recombination.

@John_Harshman

Speciation explains branching.

What explains branching is reproduction over several generations.

What may explain some of the branching on the higher level trees we look at is speciation but this is disconnected from a real branching process.

I do think that speciation happens.

[T_aquaticus]

@colewd

Common systems like the central nervous system connect species in this way.

@colewd

On the contrary I think that special creation or common design would predict a nested hierarchy based on what we know about the interdependency in many human designs like software. By interdependency I mean different software programs sharing the same modules.

Have you ever done any programming?

I use Python all of the time, and R to a lesser extent. I mix and match modules all of the time, and I guarantee that my programs will not fit into a nested hierarchy.

@colewd

I am not sure at the end of the day that reproduction and natural variation would predict a nested hierarchy unless we can find enough predictable variation to this process.

I am with the others. I don’t think you know what a nested hierarchy is.

[T_aquaticus]

@colewd

Similarities and differences would generated nested hierarchies with different animals having more similarities than differences.

That’s not a nested hierarchy. Do you know what a nested hierarchy is?

You can have similarities and differences and NOT have a nested hierarchy.

For example, a species could have flow through lungs, mammary glands, feathers, and three middle ear bones. These would all be similarities shared with other species. However, this species would seriously violate the expected nested hierarchy. Do you understand this or not? Even Winston Ewert said that a nested hierarchy falsifies his concept of common design:

The dependency graph hypothesis predicts that there will be many modules which do not correspond to a taxonomic category, and a substantial portion of the genes should be attributed to these non-taxonomic modules rather than taxonomic modules. On the other hand, common descent predicts there would be few non-taxonomic modules, and most genes would remain attributed to the taxonomic modules. 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, “The Dependency Graph of Life”

@colewd

Origins may be independent by the design strategy is not independent.

Why would the design strategy be mimicry of what common descent would produce for no apparent reason?

[colewd (Bill Cole)]

@T_aquaticus

For example, a species could have flow through lungs, mammary glands, feathers, and three middle ear bones. These would all be similarities shared with other species. However, this species would seriously violate the expected nested hierarchy. Do you understand this or not? Even Winston Ewert said that a nested hierarchy falsifies his concept of common design:

Let’s say for arguments sake the animal with all the features you mentioned was discovered. What would happen to the claim of universal common descent?

Would it be overturned?
Would the discovery be considered just an outlier?
Would the definition of mammal be expanded?

What happened when it was discovered that a certain species of deer had 7 chromosomes while others had 70?

[T_aquaticus]

@colewd

Let’s say for arguments sake the animal with all the features you mentioned was discovered. What would happen to the claim of universal common descent?

It would be under serious threat of being falsified.

Of course, if design is true then the species I describe should be the rule, not the exception. We don’t see these species.

@colewd

What happened when it was discovered that a certain species of deer had 7 chromosomes while others had 70?

They would look at the chromosomes to see if there is evidence for chromosomal fusions, and if there is, to reconstruct the fusion events. And wouldn’t you know it, those fusion events fit just fine onto a nested hierarchy, just as we would expect from common descent and not from design. The figure you posted in the opening post is overwhelming evidence for common ancestry.

[colewd (Bill Cole)]

@T_aquaticus

And wouldn’t you know it, those fusion events fit just fine onto a nested hierarchy,

This vague claim appears to be what the common descent of all deer is hanging on.

The unanswered question is how did so many of these potentially deleterious mutations get fixed in various populations?

How did new gene families get fixed in the various populations?

[T_aquaticus]

@colewd

This vague claim appears to be what the common descent of all deer is hanging on.

It’s in the figure you posted in the very first post.

Added in edit: You can also find it in figure 9 in the supplementary information:

41467_2021_27091_MOESM1_ESM.pdf

@colewd

The unanswered question is how did so many of these potentially deleterious mutations get fixed in various populations?

Obviously, they weren’t deleterious just as they aren’t deleterious in the other species we have shown you that have different chromosome counts in the same population (e.g. mice).

@colewd

How did new gene families get fixed in the various populations?

Either through positive selection or neutral drift.

[colewd (Bill Cole)]

@T_aquaticus

Obviously, they weren’t deleterious just as they aren’t deleterious in the other species we have shown you that have different chromosome counts in the same population (e.g. mice).

These are populations that generate new offspring every week. You generate several thousand mice by the time one deer is generated. What you don’t have evidence of is fixation. You also have no model that selection and drift can generate new genes in populations similar to deer.

[T_aquaticus]

@colewd

These are populations that generate new offspring every week. You generate several thousand mice by the time one deer is generated. What you don’t have evidence of is fixation. You also have no model that selection and drift can generate new genes in populations similar to deer.

What is stopping fixation? This is a known mechanism. It’s one of the basic foundations of population genetics.

As to new genes, they are called mutations. Look into them.

You have been shown all of this multiple times. Do you erase your memory each morning?

[colewd (Bill Cole)]

@T_aquaticus

What is stopping fixation? This is a known mechanism. It’s one of the basic foundations of population genetics.

Loss by genetic drift, loss by deleterious mutations, entropy caused by changing a sequence randomly and time.

[T_aquaticus]

@colewd

Loss by genetic drift, loss by deleterious mutations, entropy caused by changing a sequence randomly and time.

Do we need to add “fixation” to the list of concepts you don’t understand? Nothing in your post relates to fixation.

Let’s look at the figure from the supplementary information.

Look at the annotations C_1 through C_5. Notice how they fit on a tree. For C_5 there are 6 fusions. All 6 of those fusions are found in all species connected to that node. Notice C_4. All species connected to that branch have those fusions. Notice C_3. All species connected to that branch have those fusions.

THIS IS EXACTLY WHAT WE WOULD EXPECT TO SEE IF COMMON ANCESTRY IS TRUE. Design can’t explain this at all.

[colewd (Bill Cole)]

@T_aquaticus

THIS IS EXACTLY WHAT WE WOULD EXPECT TO SEE IF COMMON ANCESTRY IS TRUE. Design can’t explain this at all.

Let me frame this

The data clearly indicates 6 separate origin events. The population genetics problem you pivoted from is now avoided as we can attribute the different chromosome arrangements to original design.

[T_aquaticus]

@colewd

The data clearly indicates 6 separate origin events.

What data, and how???

@colewd

The population genetics problem you pivoted from is now avoided as we can attribute the different chromosome arrangements to original design.

THEN WHY DO THEY FIT ONTO A TREE PREDICTED BY COMMON DESCENT???

Why do 5 of those species have a fusion of chromosome 7 and 33 and no other combination? Why don’t we see a different combination, such as 7 and 12 or 33 and 24? Why do we find that same group of 6 fusions in C_5 in all species downstream from C_5? Why do we only see the fusion of 17 and 8 in two species, and why don’t we see 17 or 8 fused with other chromosomes?

How does common design explain this tree like pattern?

[T_aquaticus]

@colewd

Furthermore, why are there telomeres and centromeres where they don’t belong?

Our results confirmed that chromosome fusions are the dominant type of rearrangements that account for the drastic interspecific variations of muntjac chromosomal numbers (Fig. 1d). We further identified the putative orientation of centromeres’ positions in the acrocentric chromosome preserved in H. inermis and M. reevesi (Supplementary Fig. 8). A fusion event was defined as tandem fusion if it connected the apical centromeres of one ancestral chromosomes and the distal telomere of another ancestral chromosome, and a fusion event was defined as Robertsonian fusion if it connected the apical centromeres of two ancestral chromosomes. Based on the centromeres’ position and chromosomal synteny, in the female M. crinifrons we identified 28 tandem fusion events and 3 Robertsonian fusion events derived from the 2n = 70 ancestral karyotype (Fig. 1a and Supplementary Table 7).
Molecular mechanisms and topological consequences of drastic chromosomal rearrangements of muntjac deer | Nature Communications

If these chromosomes are not the product of chromosomal fusions, then what in the world are the centromeres doing in the middle of an arm on a chromosome? There is absolutely no reason why these telomeres and centromeres should be there if they were not the result of fusions.

This is an example of what happened in fusion of chromosomes in our own lineage:

Notice the cryptic centromere. The reason it is there is because of a fusion. If no fusion occurred there is no reason it should be there.

[Mercer (John Mercer)]

@colewd

@T_aquaticus

And wouldn’t you know it, those fusion events fit just fine onto a nested hierarchy,

This vague claim appears to be what the common descent of all deer is hanging on.

It’s only vague to you because you don’t understand the concept of a nested hierarchy.

[John_Harshman]

@colewd

Similarities and differences would generated nested hierarchies with different animals having more similarities than differences. As far as indels, chromosomes differences etc. These need to be looked at on a case by case basis.

You’re lecturing me on what a nested hierarchy is? But you show you have no idea. Here’s a very simple example, three species with short DNA sequences:

1 GGGGG
2 AGGGG
3 GAGGG

Here are the distances, just counting differences:

1-2: 1
1-3: 1
2-3: 2

So where’s the nested hierarchy?

What are the relevant factors if you want to look at indels, etc., on a case by case basis? And I note again that you make no attempt to answer my questions. Is it because you don’t understand the questions? Have no coherent answers?

@colewd

The question is leading so I made a clarification to avoid an answer that may create confusion. The clarification is that the mechanisms have not been tested to account for the observation.

Incoherent response, no way to reply.

@colewd

Origins may be independent but the design strategy of all organisms is not independent.

Another incoherent response. Do you think at all before typing?

@colewd

How do we know if the test has failed?

If most branches had no better than chance support, that would tell us that either there was no common descent or the data were inadequate. As it happens, we don’t have that problem. Test passed. If you think of that as a test for separate origins, that hypothesis is decisively rejected.

@colewd

I think if we looked at change in chromosomes we would see a nested hierarchy between species starting from the first male and female. This is due to genetic recombination.

Incoherent, once again. For this one, I have no idea what you’re even trying to say or how it relates to what you’re supposedly responding to.

@colewd

What explains branching is reproduction over several generations.

No, that explains a lineage, not branching.

@colewd

What may explain some of the branching on the higher level trees we look at is speciation but this is disconnected from a real branching process.

Incoherent again.

@colewd

I do think that speciation happens.

No you don’t. You claim that each species is separately created. If you think speciation happens, please suggest a few pairs of species that you think are related, and why.

I’m getting very tired of your throught-free, one-line responses. Try reading carefully and thinking about what people say before you reply, and then spend some time putting your thoughts into coherent and detailed arguments.