# Do all deer share a common ancestor?

**URL:** <https://discourse.peacefulscience.org/t/do-all-deer-share-a-common-ancestor/16040>\
**Category:** Side Conversation\
**Tags:** Science\
**Created:** [May 22, 2023, 11:44pm UTC](https://discourse.peacefulscience.org/t/do-all-deer-share-a-common-ancestor/16040 "2023-05-22T23:44:35Z")\
**Posts on this page:** 20\
**Page:** 38

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**Author:** ![Giltil](https://avatars.discourse-cdn.com/v4/letter/g/5f8ce5/32.png) [@Giltil](https://discourse.peacefulscience.org/u/Giltil)\
**Post date:** [August 17, 2023, 1:46pm UTC](https://discourse.peacefulscience.org/t/do-all-deer-share-a-common-ancestor/16040/746 "2023-08-17T13:46:04Z")

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Yes back to the original subject, I would be interested to know what is your appreciation of the paper @pnelson refers to in his piece below:

> **[Is This a Prediction from the Tree of Life? | Evolution News](https://evolutionnews.org/2023/08/quiz-is-this-a-prediction-from-the-tree-of-life/)**
>
> Conservation of function, but not genes, can be understood with an analogy to natural language. Consider two sentences.

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**Author:** ![John\_Harshman](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/john_harshman/32/1121_2.png) [@John\_Harshman](https://discourse.peacefulscience.org/u/John_Harshman)\
**Post date:** [August 17, 2023, 1:47pm UTC](https://discourse.peacefulscience.org/t/do-all-deer-share-a-common-ancestor/16040/747 "2023-08-17T13:47:50Z")

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> [@Giltil](#):
>
> Yes back to the original subject, I would be interested to know what is your appreciation of the paper @pnelson refers to in his piece below:

I would be happy to if you would tell me what that has to do with whether all deer share a common ancestor.

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**Author:** ![Tim](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/tim/32/9381_2.png) [@Tim](https://discourse.peacefulscience.org/u/Tim)\
**Post date:** [August 17, 2023, 1:52pm UTC](https://discourse.peacefulscience.org/t/do-all-deer-share-a-common-ancestor/16040/748 "2023-08-17T13:52:49Z")

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> [@Giltil](#):
>
> The passages you refer to are from scholars who expressed some objections or incomprehensions toward some methodological aspects of Gpuccio’s analysis, to which IMO he responded convincingly most of the time.

🤣

You will pardon me if I find you opinion neither humble nor persuasive.

Can you point to a single one of the “scholars” who were objecting and expressing incomprehension at Gpuccio’s “analysis” who expressed that they were ‘convinced’ by his responses. I see no indication that they were.

That you yourself are “convinced” is neither surprising nor “convincing”, given the degree to which you have drunk the ID koolaid.

I would again point out that “being knowledgeable and articulate” neither guarantees that his argument is logically sound, nor that his conclusions are credible.

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**Author:** ![Giltil](https://avatars.discourse-cdn.com/v4/letter/g/5f8ce5/32.png) [@Giltil](https://discourse.peacefulscience.org/u/Giltil)\
**Post date:** [August 17, 2023, 1:53pm UTC](https://discourse.peacefulscience.org/t/do-all-deer-share-a-common-ancestor/16040/749 "2023-08-17T13:53:15Z")

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> [@John\_Harshman](#):
>
> I would be happy to if you would tell me what that has to do with whether all deer share a common ancestor.

Nothing! But it has to do with the more general idea of common descent, in particular CD in the bacterial branch of the TOL.

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**Author:** ![Tim](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/tim/32/9381_2.png) [@Tim](https://discourse.peacefulscience.org/u/Tim)\
**Post date:** [August 17, 2023, 1:55pm UTC](https://discourse.peacefulscience.org/t/do-all-deer-share-a-common-ancestor/16040/750 "2023-08-17T13:55:32Z")

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> [@Giltil](#):
>
> Nothing!

Then it is not getting “back to the original subject”. 🙄

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**Author:** ![Giltil](https://avatars.discourse-cdn.com/v4/letter/g/5f8ce5/32.png) [@Giltil](https://discourse.peacefulscience.org/u/Giltil)\
**Post date:** [August 17, 2023, 1:59pm UTC](https://discourse.peacefulscience.org/t/do-all-deer-share-a-common-ancestor/16040/751 "2023-08-17T13:59:00Z")

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> [@Tim](#):
>
> Then it is not getting “back to the original subject”. 🙄

If that can please you, I am happy to concede the point.

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**Author:** ![John\_Harshman](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/john_harshman/32/1121_2.png) [@John\_Harshman](https://discourse.peacefulscience.org/u/John_Harshman)\
**Post date:** [August 17, 2023, 2:02pm UTC](https://discourse.peacefulscience.org/t/do-all-deer-share-a-common-ancestor/16040/752 "2023-08-17T14:02:44Z")

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> [@Giltil](#):
>
> Nothing!

In that case why do you think it’s returning to the topic? If you want to start a new thread for that, feel free. But claiming to return to the topic by introducing a new topic is exceedingly rude.

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**Author:** ![Giltil](https://avatars.discourse-cdn.com/v4/letter/g/5f8ce5/32.png) [@Giltil](https://discourse.peacefulscience.org/u/Giltil)\
**Post date:** [August 17, 2023, 2:46pm UTC](https://discourse.peacefulscience.org/t/do-all-deer-share-a-common-ancestor/16040/753 "2023-08-17T14:46:30Z")

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> [@John\_Harshman](#):
>
> But claiming to return to the topic by introducing a new topic is exceedingly rude

The topic being closely related, I sincerely thought it could be discussed in this thread. It seems that I was wrong. Sorry for that. Now, as for being « exceedingly rude », I think you are excessive in your expression.

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**Author:** ![John\_Harshman](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/john_harshman/32/1121_2.png) [@John\_Harshman](https://discourse.peacefulscience.org/u/John_Harshman)\
**Post date:** [August 17, 2023, 2:55pm UTC](https://discourse.peacefulscience.org/t/do-all-deer-share-a-common-ancestor/16040/754 "2023-08-17T14:55:55Z")

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I’m afraid I have to question either your sincerity or your judgment. Which would you prefer?

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**Author:** ![Tim](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/tim/32/9381_2.png) [@Tim](https://discourse.peacefulscience.org/u/Tim)\
**Post date:** [August 17, 2023, 2:57pm UTC](https://discourse.peacefulscience.org/t/do-all-deer-share-a-common-ancestor/16040/755 "2023-08-17T14:57:33Z")

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This thread has been wandering off-topic for over 700 posts – I think it is time to put it out of its, and our, misery. Particularly as, given that bacteria aren’t particularly closely related to deer, the paper in question isn’t particularly closely related to this thread’s stated topic.

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**Author:** ![Rumraket](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/rumraket/32/9328_2.png) [@Rumraket](https://discourse.peacefulscience.org/u/Rumraket)\
**Post date:** [August 17, 2023, 3:19pm UTC](https://discourse.peacefulscience.org/t/do-all-deer-share-a-common-ancestor/16040/756 "2023-08-17T15:19:52Z")

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> [@Giltil](#):
>
> > [@John\_Harshman](#):
> >
> > I would be happy to if you would tell me what that has to do with whether all deer share a common ancestor.
> 
> Nothing! But it has to do with the more general idea of common descent, in particular CD in the bacterial branch of the TOL.

I recommend you create a new thread for that. Fine for it’s own topic of discussion.

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**Author:** ![colewd](https://avatars.discourse-cdn.com/v4/letter/c/ecd19e/32.png) [@colewd](https://discourse.peacefulscience.org/u/colewd)\
**Post date:** [August 17, 2023, 3:36pm UTC](https://discourse.peacefulscience.org/t/do-all-deer-share-a-common-ancestor/16040/757 "2023-08-17T15:36:39Z")

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> [@John\_Harshman](#):
>
> Back to the original subject, as Bill requested. Yes, we can, and no, it isn’t. I presented a very simple model of the former quite some time ago, and “separate points of origin” is incompatible with the phylogenetic data. Of course those are two quite separate questions, and one major problem is that Bill is unable to separate them.

According to your standards you did not make a valid argument as it required a naked assertion.

What I asked for is a model and no one produced anything close to a model that answered what the cause was of both the chromosome and gene variation.

I did not expect a model because the current mechanisms of evolution appear to be unable to generate the gene and chromosome patterns we are observing from a single point of origin.

What we cannot move past is the assertion that “common descent is the only explanation for the pattern in the data”.

What we have failed to explore is other reproductive mechanisms like genetic recombination that might explain the data.

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**Author:** ![Faizal\_Ali](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/faizal_ali/32/12416_2.png) [@Faizal\_Ali](https://discourse.peacefulscience.org/u/Faizal_Ali)\
**Post date:** [August 17, 2023, 4:08pm UTC](https://discourse.peacefulscience.org/t/do-all-deer-share-a-common-ancestor/16040/758 "2023-08-17T16:08:07Z")

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> [@colewd](#):
>
> What I asked for is a model and no one produced anything close to a model that answered what the cause was of both the chromosome and gene variation.
> 
> I did not expect a model because the current mechanisms of evolution appear to be unable to generate the gene and chromosome patterns we are observing from a single point of origin.

And you know what’s amazing? It seems you actually believe that to be true. The mind boggles.

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**Author:** ![Mercer](https://avatars.discourse-cdn.com/v4/letter/m/e274bd/32.png) [@Mercer](https://discourse.peacefulscience.org/u/Mercer)\
**Post date:** [August 17, 2023, 4:18pm UTC](https://discourse.peacefulscience.org/t/do-all-deer-share-a-common-ancestor/16040/759 "2023-08-17T16:18:31Z")

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> [@Giltil](#):
>
> The passages you refer to are from scholars who expressed some objections or incomprehensions toward some methodological aspects of Gpuccio’s analysis,

Wrong. The objections were fundamental and conceptual, as you know because you tried and failed to defend them.

> [@Giltil](#):
>
> …to which IMO he responded convincingly most of the time.

I find that laughable. Why should we value your opinions on the subject of protein structure/function/evolution?

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**Author:** ![John\_Harshman](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/john_harshman/32/1121_2.png) [@John\_Harshman](https://discourse.peacefulscience.org/u/John_Harshman)\
**Post date:** [August 17, 2023, 4:59pm UTC](https://discourse.peacefulscience.org/t/do-all-deer-share-a-common-ancestor/16040/760 "2023-08-17T16:59:44Z")

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> [@colewd](#):
>
> I did not expect a model because the current mechanisms of evolution appear to be unable to generate the gene and chromosome patterns we are observing from a single point of origin.

How would you know this?

> [@colewd](#):
>
> What we cannot move past is the assertion that “common descent is the only explanation for the pattern in the data”.

We don’t have to move past it. We need to consider the evidence for it, which I have tried to get you to do many times. You always divert to “how can these mutations happen?”, which is an entirely separate issue. Remember: common descent and the causes of differences are independent issues. Write that 500 times on your blackboard.

> [@colewd](#):
>
> What we have failed to explore is other reproductive mechanisms like genetic recombination that might explain the data.

Why is that relevant?

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**Author:** ![Mercer](https://avatars.discourse-cdn.com/v4/letter/m/e274bd/32.png) [@Mercer](https://discourse.peacefulscience.org/u/Mercer)\
**Post date:** [August 17, 2023, 5:08pm UTC](https://discourse.peacefulscience.org/t/do-all-deer-share-a-common-ancestor/16040/761 "2023-08-17T17:08:09Z")

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> [@John\_Harshman](#):
>
> We need to consider the evidence for it, which I have tried to get you to do many times. You always divert to “how can these mutations happen?”, which is an entirely separate issue. Remember: common descent and the causes of differences are independent issues. Write that 500 times on your blackboard.

Ain’t gonna happen.

Bill, like all of the other ID proponents here, on some level fully realizes that the evidence will not support any ID hypothesis. Sticking to hearsay must always be the SOP.

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**Author:** ![Rumraket](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/rumraket/32/9328_2.png) [@Rumraket](https://discourse.peacefulscience.org/u/Rumraket)\
**Post date:** [August 17, 2023, 5:22pm UTC](https://discourse.peacefulscience.org/t/do-all-deer-share-a-common-ancestor/16040/762 "2023-08-17T17:22:09Z")

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> [@colewd](#):
>
> What I asked for is a model and no one produced anything close to a model that answered what the cause was of both the chromosome and gene variation.

Bill it’s just a rate of fixation of neutral mutations, which would be equal to the rate of occurrence in a population of constant size.

So for chromosomal fusions (which we know empirically are mostly neutral), you just take the rate at which they occur and then the mean rate of fixation is the mean rate of occurrence(there would be some variation around the mean of course). Same would be true for gene gains and losses(duplications and deletions/pseudogenizations) which generally have very small fitness values in the small effective populations of large animals.

So you look at the phylogeny, see that a handful are different between individual deer species. Can a handful of those occur and fix in the couple of million years that separate them? Yep.

That’s it. That’s the “population genetics model” you’re asking for. **The End.**

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**Author:** ![Rumraket](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/rumraket/32/9328_2.png) [@Rumraket](https://discourse.peacefulscience.org/u/Rumraket)\
**Post date:** [August 17, 2023, 5:24pm UTC](https://discourse.peacefulscience.org/t/do-all-deer-share-a-common-ancestor/16040/763 "2023-08-17T17:24:31Z")

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> [@Faizal\_Ali](#):
>
> > [@colewd](#):
> >
> > What I asked for is a model and no one produced anything close to a model that answered what the cause was of both the chromosome and gene variation.
> > 
> > I did not expect a model because the current mechanisms of evolution appear to be unable to generate the gene and chromosome patterns we are observing from a single point of origin.
> 
> And you know what’s amazing? It seems you actually believe that to be true. The mind boggles.

I take issue with that. I think Bill long ago decided this isn’t about truth so he’ll basically just lie to keep the appearance of debate going. He exhibits behavior consistent with a deeply dishonest person, not a person driven by conviction of truth.

The mind does boggle though.

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**Author:** ![colewd](https://avatars.discourse-cdn.com/v4/letter/c/ecd19e/32.png) [@colewd](https://discourse.peacefulscience.org/u/colewd)\
**Post date:** [August 17, 2023, 5:26pm UTC](https://discourse.peacefulscience.org/t/do-all-deer-share-a-common-ancestor/16040/764 "2023-08-17T17:26:09Z")

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> [@John\_Harshman](#):
>
> How would you know this?

I suspect this is true because there are obvious obstacles to generating a model to support this such as the sequence problem and the waiting time problem. Most importantly there is no empirical evidence or model that shows these mechanisms to be a likely explanation.

> [@John\_Harshman](#):
>
> We don’t have to move past it.

We have to move past it because according to your standards it is a meaningless claim as it relies on a naked assertion.

> [@John\_Harshman](#):
>
> Why is that relevant?

Because there is no working single origin model for generating the gene and chromosome patterns by current evolutional mechanisms such as gene duplication and divergence. UCD as an unchallenged explanation has become a science stopper.

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**Author:** ![colewd](https://avatars.discourse-cdn.com/v4/letter/c/ecd19e/32.png) [@colewd](https://discourse.peacefulscience.org/u/colewd)\
**Post date:** [August 17, 2023, 5:40pm UTC](https://discourse.peacefulscience.org/t/do-all-deer-share-a-common-ancestor/16040/765 "2023-08-17T17:40:36Z")

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> [@Rumraket](#):
>
> I take issue with that. I think Bill long ago decided this isn’t about truth so he’ll basically just lie to keep the appearance of debate going. He exhibits behavior consistent with a deeply dishonest person, not a person driven by conviction of truth.

In the words of @John_Harshman your opinion means nothing.

> [@Rumraket](#):
>
> The mind does boggle though.

The condition of the mind in question needs to be considered. Materialist ideology maybe making it difficult to imagine a different result than deer common ancestry.

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