# Trees and Star Diagrams

**URL:** <https://discourse.peacefulscience.org/t/trees-and-star-diagrams/11569>\
**Category:** Conversation\
**Tags:** Science\
**Created:** [September 1, 2020, 4:53pm UTC](https://discourse.peacefulscience.org/t/trees-and-star-diagrams/11569 "2020-09-01T16:53:13Z")\
**Posts on this page:** 20\
**Page:** 2

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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:** [September 1, 2020, 8:05pm UTC](https://discourse.peacefulscience.org/t/trees-and-star-diagrams/11569/21 "2020-09-01T20:05:25Z")

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Very strange. He makes up a very non-biological situation, analyses it in non-phylogenetic ways, conducts his own made-up tests, and assumes this has some relevance to phylogenetic data and trees.

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**Author:** ![swamidass](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/swamidass/32/3_2.png) [@swamidass](https://discourse.peacefulscience.org/u/swamidass)\
**Post date:** [September 1, 2020, 8:22pm UTC](https://discourse.peacefulscience.org/t/trees-and-star-diagrams/11569/22 "2020-09-01T20:22:08Z")

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I do think there is some clarity missing from this discussion of trees and nested clades.

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**Author:** ![Dan\_Eastwood](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/dan_eastwood/32/2368_2.png) [@Dan\_Eastwood](https://discourse.peacefulscience.org/u/Dan_Eastwood)\
**Post date:** [September 2, 2020, 4:38pm UTC](https://discourse.peacefulscience.org/t/trees-and-star-diagrams/11569/23 "2020-09-02T16:38:08Z")

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> [@glipsnort](#):
>
> By the way, PS alum @EricMH has been arguing on Biologos that phylogenetic signal provides no evidence for common descent ([here](https://discourse.biologos.org/t/fallacy-of-the-phylogenetic-signal-part-2/43716) and [here](https://discourse.biologos.org/t/the-fallacy-of-the-phylogenetic-signal-part-1/43685)).

I believe he is arguing that other types of trees could give the same signal as a nested hierarchy. That could be true for the very simple measure he has in mind. He is trying to work this out with a very simplified model, and I offered him some encouragement because I think he may learn from the exercize.

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**Author:** ![swamidass](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/swamidass/32/3_2.png) [@swamidass](https://discourse.peacefulscience.org/u/swamidass)\
**Post date:** [September 2, 2020, 4:41pm UTC](https://discourse.peacefulscience.org/t/trees-and-star-diagrams/11569/24 "2020-09-02T16:41:24Z")

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What does “other types of trees” mean?

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**Author:** ![Dan\_Eastwood](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/dan_eastwood/32/2368_2.png) [@Dan\_Eastwood](https://discourse.peacefulscience.org/u/Dan_Eastwood)\
**Post date:** [September 2, 2020, 5:03pm UTC](https://discourse.peacefulscience.org/t/trees-and-star-diagrams/11569/25 "2020-09-02T17:03:56Z")

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He has a simple numerics score of differences between trees, and a low score indicates a close match. He claims that non-Nested Hierarchy trees may also produce a low score.

This may be true for his simple measure, but I doubt that it means what he thinks it means. I made some effort to follow his example, but couldn’t follow his reasoning. One of my comments was that he needs to do a much better job of explaining his methods.

Though I suspect Eric is wrong, I do not want to discourage his effort - it’s a good way to learn.

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**Author:** ![swamidass](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/swamidass/32/3_2.png) [@swamidass](https://discourse.peacefulscience.org/u/swamidass)\
**Post date:** [September 2, 2020, 5:19pm UTC](https://discourse.peacefulscience.org/t/trees-and-star-diagrams/11569/26 "2020-09-02T17:19:34Z")

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What is a non nested hierarchy tree?

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**Author:** ![glipsnort](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/glipsnort/32/1541_2.png) [@glipsnort](https://discourse.peacefulscience.org/u/glipsnort)\
**Post date:** [September 2, 2020, 6:53pm UTC](https://discourse.peacefulscience.org/t/trees-and-star-diagrams/11569/27 "2020-09-02T18:53:57Z")

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> [@Dan\_Eastwood](#):
>
> Though I suspect Eric is wrong, I do not want to discourage his effort - it’s a good way to learn.

Agreed

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**Author:** ![Dan\_Eastwood](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/dan_eastwood/32/2368_2.png) [@Dan\_Eastwood](https://discourse.peacefulscience.org/u/Dan_Eastwood)\
**Post date:** [September 2, 2020, 7:19pm UTC](https://discourse.peacefulscience.org/t/trees-and-star-diagrams/11569/28 "2020-09-02T19:19:33Z")

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His example was two unconnected trees - I think. I gave up trying to understand after three reads through.

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**Author:** ![gbrooks9](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/gbrooks9/32/7979_2.png) [@gbrooks9](https://discourse.peacefulscience.org/u/gbrooks9)\
**Post date:** [September 2, 2020, 10:10pm UTC](https://discourse.peacefulscience.org/t/trees-and-star-diagrams/11569/29 "2020-09-02T22:10:05Z")

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I hate to be a party pooper… but honestly, all this nested hierarchy discussion is just a waste of time with certain sections of the YEC community.

And if we consider that, at its heart, nested hierarchy discussions is really just a debate over Atheism vs. Theism, this category of discussion is exactly where we create more heat than light - - and we are throwing flames into area of differences between the camps… not building bridges.

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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:** [September 2, 2020, 11:01pm UTC](https://discourse.peacefulscience.org/t/trees-and-star-diagrams/11569/30 "2020-09-02T23:01:05Z")

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> [@gbrooks9](#):
>
> And if we consider that, at its heart, nested hierarchy discussions is really just a debate over Atheism vs. Theism

Why would we consider such an utter falsity? George, you are batting no better than .140 lately, and you risk being sent down to the minors.

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**Author:** ![gbrooks9](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/gbrooks9/32/7979_2.png) [@gbrooks9](https://discourse.peacefulscience.org/u/gbrooks9)\
**Post date:** [September 2, 2020, 11:41pm UTC](https://discourse.peacefulscience.org/t/trees-and-star-diagrams/11569/31 "2020-09-02T23:41:36Z")

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> [@John\_Harshman](#):
>
> Why would we consider such an utter falsity?

@John_Harshman

We have to face reality… and the reality is the use of nested hierarchies in a discussion is just not convincing to large sections of YEC audiences.

Ultimately, to Christian audiences, the issue will always come down to whether God likes nested hierarchies or not - - not whether nested hierarchies prove evolution or not.

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**Author:** ![Joe\_Felsenstein](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/joe_felsenstein/32/8176_2.png) [@Joe\_Felsenstein](https://discourse.peacefulscience.org/u/Joe_Felsenstein)\
**Post date:** [September 2, 2020, 11:56pm UTC](https://discourse.peacefulscience.org/t/trees-and-star-diagrams/11569/32 "2020-09-02T23:56:34Z")

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Would you say the same about arguments about the age of the earth? That they are best not made because young earth creationists are convinced that they have ample reason to believe that the earth is young?z

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**Author:** ![gbrooks9](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/gbrooks9/32/7979_2.png) [@gbrooks9](https://discourse.peacefulscience.org/u/gbrooks9)\
**Post date:** [September 3, 2020, 12:26am UTC](https://discourse.peacefulscience.org/t/trees-and-star-diagrams/11569/33 "2020-09-03T00:26:30Z")

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@Joe_Felsenstein

I would say that “age of earth” arguments are intermediate between Nested Hierarchies and my PREFERRED points of pro-Evolution disputation.

The benefit of age of Earth arguments is they are more concretely understood than the nuances of nested hierarchies.

But I still don’t find Age of Earth points to be as useful as these related to the KT Boundary layer:

EXAMPLE ONE:  
All large marine reptiles from the age of dinosaurs drown before Bears, Cows and Sheep, not leaving any fossils above the KT layer … while Bears, Cows and Sheep do not once leave fossils BELOW the KT layer. Even giant herbivores like the Brontosaurus drown before sheep do.

EXAMPLE TWO:  
I commend @Timothy_Horton for his thread on all the modern flightless birds … who somehow manage to avoid drowning longer than the reptiles that COULD fly!

> [@Stratification of the Fossil Record and the YEC Flood](https://discourse.peacefulscience.org/t/stratification-of-the-fossil-record-and-the-yec-flood/11109/3):
>
> Pterosaur fossils are found all over the globe on all continents just as are extant birds. Yet not a single member of any of the hundreds of known pterosaur species managed to fly to ground above the K-Pg boundary layer. Equally surprising is not a single member of a species of extant birds got trapped in ground below the K-Pg boundary layer. That was truly a magic Flood! laughing

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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:** [September 3, 2020, 12:26am UTC](https://discourse.peacefulscience.org/t/trees-and-star-diagrams/11569/34 "2020-09-03T00:26:51Z")

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You seem to be conflating creationism with Christianity and atheism with evolution, neither of which is a respectable relation. Both of your feet must be thoroughly full of bullet holes by this point, and again I suggest that it would be wise to stop. In particular it would be good if you stopped speaking in the voices of and reading the minds of imagined other people.

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**Author:** ![gbrooks9](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/gbrooks9/32/7979_2.png) [@gbrooks9](https://discourse.peacefulscience.org/u/gbrooks9)\
**Post date:** [September 3, 2020, 2:35am UTC](https://discourse.peacefulscience.org/t/trees-and-star-diagrams/11569/35 "2020-09-03T02:35:26Z")

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> [@John\_Harshman](#):
>
> You seem to be conflating creationism with Christianity and atheism with evolution, neither of which is a respectable relation.

@John_Harshman

You just aren’t getting it.

I’m nudging people into realizing two categories of debate are just proxies for two OTHER unresolvable, un-answerable issues questions.

If Peaceful Science wants to spend as little time as possible in divisive topics that can never be resolved, it is better to recognize the proxy disputes as soon as they appear.

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**Author:** ![glipsnort](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/glipsnort/32/1541_2.png) [@glipsnort](https://discourse.peacefulscience.org/u/glipsnort)\
**Post date:** [September 3, 2020, 2:58am UTC](https://discourse.peacefulscience.org/t/trees-and-star-diagrams/11569/36 "2020-09-03T02:58:41Z")

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> [@gbrooks9](#):
>
> Ultimately, to Christian audiences, the issue will always come down to whether God likes nested hierarchies or not - - not whether nested hierarchies prove evolution or not.

Different Christian audiences have different issues. Why don’t you focus your energies on debating the things you want to debate rather than on telling other people what they should be debating?

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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:** [September 3, 2020, 2:58am UTC](https://discourse.peacefulscience.org/t/trees-and-star-diagrams/11569/37 "2020-09-03T02:58:44Z")

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> [@gbrooks9](#):
>
> You just aren’t getting it.

I will agree that one of us isn’t.

> [@gbrooks9](#):
>
> I’m nudging people into realizing two categories of debate are just proxies for two OTHER unresolvable, un-answerable issues questions.

Yes, and I’m pointing out that your realization is just wrong. I’d be surprised if you had any toes left at this point.

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**Author:** ![Joe\_Felsenstein](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/joe_felsenstein/32/8176_2.png) [@Joe\_Felsenstein](https://discourse.peacefulscience.org/u/Joe_Felsenstein)\
**Post date:** [September 3, 2020, 11:54am UTC](https://discourse.peacefulscience.org/t/trees-and-star-diagrams/11569/38 "2020-09-03T11:54:15Z")

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> [@swamidass](#):
>
> What is a non nested hierarchy tree?

An unrooted tree, for example, or a tree that has one ir more unresolved parts.

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**Author:** ![Joe\_Felsenstein](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/joe_felsenstein/32/8176_2.png) [@Joe\_Felsenstein](https://discourse.peacefulscience.org/u/Joe_Felsenstein)\
**Post date:** [September 3, 2020, 11:54am UTC](https://discourse.peacefulscience.org/t/trees-and-star-diagrams/11569/39 "2020-09-03T11:54:23Z")

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Let me comment, in spite of not having worked through Holloway’s example yet. If his tree is two unconnected trees, then that should be equivalent to a tree that has one infinitely long branch. And for most straightforward models of change of characters, that infinitely long branch could be placed so as to connect the two subtrees from anywhere on subtree 1 to anywhere on subtree 2.

Thus if subtree 1 was birds and subtree 2 was mammals, one could connect any point in the tree of mammals to any point in the tree of birds. Say connect the chicken to the common ancestor of all kangaroos, for example.

Such a set of possible trees would not each be “well-supported”, as each would fit the data equally well.vv

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**Author:** ![Dan\_Eastwood](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/dan_eastwood/32/2368_2.png) [@Dan\_Eastwood](https://discourse.peacefulscience.org/u/Dan_Eastwood)\
**Post date:** [September 3, 2020, 4:21pm UTC](https://discourse.peacefulscience.org/t/trees-and-star-diagrams/11569/40 "2020-09-03T16:21:17Z")

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> [@Joe\_Felsenstein](#):
>
> Let me comment, in spite of not having worked through Holloway’s example yet.

I don’t think you need to work through it just yet. Eric is aware of some of existing problems (and this discussion) and will likely make some revisions.

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