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The False Dichotomy of Cladistics and Phenetics
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Peter Nyikos
Sep 5, 2022, 2:42:58 PM9/5/22
to
As I looked back yesterday on some 2016 threads in s.b.p. when it was at the height of what I call
"an oasis of civilization," I came across a long exchange between Ruben Safir
[who often went under the byline Popping mad, as he does now]
and John Harshman, which I joined near the end. John and Ruben
were unable to communicate fruitfully, because John was stuck
in a dichotomy between two ways of classifying organisms:
the cladistic and the phenetic.
There is a happy medium between these ways, and Popping mad seems to
have been aiming for it with his talk about distances, but he seemed to
have underestimated the difficulty of getting it across.
I will talk about a remedy for that in the next post but one.
[Spoiler: it uses the difficult concept of disparity.]
In the next one, I focus on another instance of the dichotomy,
in what is called "the cladist wars".
Evidently the vertebrate paleontologists, if any, were so badly outnumbered
by the classifiers of extant organisms that their point of view never came across,
and the cladists won out without any dilution of their ideas.
More about that in the next post. For now, I say a few things about the
two extremes, the cladistic and the phenetic.
The heart of cladistics is found in the phylogenetic trees, which put all
organisms at the branch tips. The taxa resulting from these trees
are clades: everything above a fixed node in a tree constitutes a clade.
Clades are exactly what cladistic systematists include in their classifications.
They bar all old taxa of the Linnean classification,
such as Amphibia, which do not include all descendants
(in this case, reptiles, birds and mammals are not included).
Phenetics is completely out of fashion, so I only mention that
it classified organisms on the basis of overall similarity.
Phylogeny was not taken into account; nevertheless, it gave
reasonably good results because all parts of the organisms
were taken into account; this was possible because only
extant organisms were classified.
Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina
http://people.math.sc.edu/nyikos
"an oasis of civilization," I came across a long exchange between Ruben Safir
[who often went under the byline Popping mad, as he does now]
and John Harshman, which I joined near the end. John and Ruben
were unable to communicate fruitfully, because John was stuck
in a dichotomy between two ways of classifying organisms:
the cladistic and the phenetic.
There is a happy medium between these ways, and Popping mad seems to
have been aiming for it with his talk about distances, but he seemed to
have underestimated the difficulty of getting it across.
I will talk about a remedy for that in the next post but one.
[Spoiler: it uses the difficult concept of disparity.]
In the next one, I focus on another instance of the dichotomy,
in what is called "the cladist wars".
Evidently the vertebrate paleontologists, if any, were so badly outnumbered
by the classifiers of extant organisms that their point of view never came across,
and the cladists won out without any dilution of their ideas.
More about that in the next post. For now, I say a few things about the
two extremes, the cladistic and the phenetic.
The heart of cladistics is found in the phylogenetic trees, which put all
organisms at the branch tips. The taxa resulting from these trees
are clades: everything above a fixed node in a tree constitutes a clade.
Clades are exactly what cladistic systematists include in their classifications.
They bar all old taxa of the Linnean classification,
such as Amphibia, which do not include all descendants
(in this case, reptiles, birds and mammals are not included).
Phenetics is completely out of fashion, so I only mention that
it classified organisms on the basis of overall similarity.
Phylogeny was not taken into account; nevertheless, it gave
reasonably good results because all parts of the organisms
were taken into account; this was possible because only
extant organisms were classified.
Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina
http://people.math.sc.edu/nyikos
John Harshman
Sep 5, 2022, 2:50:32 PM9/5/22
to
On 9/5/22 11:42 AM, Peter Nyikos wrote:
> As I looked back yesterday on some 2016 threads in s.b.p. when it was at the height of what I call
> "an oasis of civilization," I came across a long exchange between Ruben Safir
> [who often went under the byline Popping mad, as he does now]
> and John Harshman, which I joined near the end. John and Ruben
> were unable to communicate fruitfully, because John was stuck
> in a dichotomy between two ways of classifying organisms:
> the cladistic and the phenetic.
Needless to say, I reject your characterization of that argument.
> As I looked back yesterday on some 2016 threads in s.b.p. when it was at the height of what I call
> "an oasis of civilization," I came across a long exchange between Ruben Safir
> [who often went under the byline Popping mad, as he does now]
> and John Harshman, which I joined near the end. John and Ruben
> were unable to communicate fruitfully, because John was stuck
> in a dichotomy between two ways of classifying organisms:
> the cladistic and the phenetic.
> There is a happy medium between these ways, and Popping mad seems to
> have been aiming for it with his talk about distances, but he seemed to
> have underestimated the difficulty of getting it across.
>
> I will talk about a remedy for that in the next post but one.
> [Spoiler: it uses the difficult concept of disparity.]
> In the next one, I focus on another instance of the dichotomy,
> in what is called "the cladist wars".
>
> Evidently the vertebrate paleontologists, if any, were so badly outnumbered
> by the classifiers of extant organisms that their point of view never came across,
> and the cladists won out without any dilution of their ideas.
several of the most prominent proponents of cladistic classification
were paleontologists. Nobody was drowned out.
> More about that in the next post. For now, I say a few things about the
> two extremes, the cladistic and the phenetic.
>
>
> The heart of cladistics is found in the phylogenetic trees, which put all
> organisms at the branch tips. The taxa resulting from these trees
> are clades: everything above a fixed node in a tree constitutes a clade.
>
> Clades are exactly what cladistic systematists include in their classifications.
> They bar all old taxa of the Linnean classification,
> such as Amphibia, which do not include all descendants
> (in this case, reptiles, birds and mammals are not included).
everything except the crown group. All those "labryinthodonts" and such
are mrely primitive tetrapods, not ambphibians.
> Phenetics is completely out of fashion, so I only mention that
> it classified organisms on the basis of overall similarity.
> Phylogeny was not taken into account; nevertheless, it gave
> reasonably good results because all parts of the organisms
> were taken into account; this was possible because only
> extant organisms were classified.
cladistic relationships? It was of course the claim of pheneticists that
discovering phylogeny was impossible, so it was pointless to try. I
doubt you would agree.
John Harshman
Sep 5, 2022, 2:57:07 PM9/5/22
to
On 9/5/22 11:42 AM, Peter Nyikos wrote:
> As I looked back yesterday on some 2016 threads in s.b.p. when it was at the height of what I call
> "an oasis of civilization," I came across a long exchange between Ruben Safir
> [who often went under the byline Popping mad, as he does now]
> and John Harshman, which I joined near the end. John and Ruben
> were unable to communicate fruitfully, because John was stuck
> in a dichotomy between two ways of classifying organisms:
> the cladistic and the phenetic.
Wait, are you going to introduce Mayr's "evolutionary systematics",
> "an oasis of civilization," I came across a long exchange between Ruben Safir
> [who often went under the byline Popping mad, as he does now]
> and John Harshman, which I joined near the end. John and Ruben
> were unable to communicate fruitfully, because John was stuck
> in a dichotomy between two ways of classifying organisms:
> the cladistic and the phenetic.
which tries to combine cladistic and phenetic approaches? If so, you are
being oddly coy in not starting out that way.
Peter Nyikos
Sep 5, 2022, 3:35:46 PM9/5/22
to
On Monday, September 5, 2022 at 2:57:07 PM UTC-4, John Harshman wrote:
> Wait, are you going to introduce Mayr's "evolutionary systematics",
> which tries to combine cladistic and phenetic approaches? If so, you are
> being oddly coy in not starting out that way.
From what I've read about it, it didn't use disparity sufficiently well
> Wait, are you going to introduce Mayr's "evolutionary systematics",
> which tries to combine cladistic and phenetic approaches? If so, you are
> being oddly coy in not starting out that way.
to make much of a difference. A number of researchers in various
fields are trying to work out a measure for disparity now, but
it is very slow going, because disparity is extraordinarily difficult
to quantify even under the best of conditions.
That's for my next post. Here I go with the exposition on the cladist wars.
The only specific event of those wars that I have ever read about (from two different sources,
one of which I own: Kenneth S. Thompson's LIVING FOSSIL: The Story of the Coelacanth)
is the 1978 event "the lungfish, the salmon, and the cow". It had to do with the radical
definition by cladists of the word "related". The phenetic side claimed that it was absurd
to regard a lungfish to be more closely related to a cow than to a salmon, but that was
a naive choice of taxa, and the outcome was an undeserved victory for the cladist side.
Had a Romer-savvy vertebrate paleontologist been involved, the choice of taxa could have been very different.
One choice readily available at that time was "Bos, Ichthyostega, Elpistostege."
[Nowadays, the third is better replaced by the more familiar Tiktaalik.]
It does violence to our ordinary idea of human relationships to claim that Ichthyostega
is more closely related to us human beings than it is to Elpistostege.
It's almost as bad as saying that Mitochondrial Eve is more closely related to
everyone alive today than she was to anyone in her family at the time she was born.
Had the victory gone the other way, we might be far advanced in a definition of "more related"
that combines phylogeny with measures of disparity. As it is, the theory of macroevolution,
to which disparity is an indispensable tool, has made comparatively little progress to date.
Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
http://people.math.sc.edu/nyikos
John Harshman
Sep 5, 2022, 5:53:23 PM9/5/22
to
On 9/5/22 12:35 PM, Peter Nyikos wrote:
> On Monday, September 5, 2022 at 2:57:07 PM UTC-4, John Harshman wrote:
>
>> Wait, are you going to introduce Mayr's "evolutionary systematics",
>> which tries to combine cladistic and phenetic approaches? If so, you are
>> being oddly coy in not starting out that way.
>
> From what I've read about it, it didn't use disparity sufficiently well
> to make much of a difference. A number of researchers in various
> fields are trying to work out a measure for disparity now, but
> it is very slow going, because disparity is extraordinarily difficult
> to quantify even under the best of conditions.
What have you read about it?
> On Monday, September 5, 2022 at 2:57:07 PM UTC-4, John Harshman wrote:
>
>> Wait, are you going to introduce Mayr's "evolutionary systematics",
>> which tries to combine cladistic and phenetic approaches? If so, you are
>> being oddly coy in not starting out that way.
>
> From what I've read about it, it didn't use disparity sufficiently well
> to make much of a difference. A number of researchers in various
> fields are trying to work out a measure for disparity now, but
> it is very slow going, because disparity is extraordinarily difficult
> to quantify even under the best of conditions.
> That's for my next post. Here I go with the exposition on the cladist wars.
>
> The only specific event of those wars that I have ever read about (from two different sources,
> one of which I own: Kenneth S. Thompson's LIVING FOSSIL: The Story of the Coelacanth)
> is the 1978 event "the lungfish, the salmon, and the cow". It had to do with the radical
> definition by cladists of the word "related". The phenetic side claimed that it was absurd
> to regard a lungfish to be more closely related to a cow than to a salmon, but that was
> a naive choice of taxa, and the outcome was an undeserved victory for the cladist side.
>
> Had a Romer-savvy vertebrate paleontologist been involved, the choice of taxa could have been very different.
> One choice readily available at that time was "Bos, Ichthyostega, Elpistostege."
> [Nowadays, the third is better replaced by the more familiar Tiktaalik.]
> It does violence to our ordinary idea of human relationships to claim that Ichthyostega
> is more closely related to us human beings than it is to Elpistostege.
> It's almost as bad as saying that Mitochondrial Eve is more closely related to
> everyone alive today than she was to anyone in her family at the time she was born.
Now, would you agree that by any definition you might be more closely
related to a person who looks different from you than to a person who
looks similar to you? If so, then why is disparity relevant even under
the ordinary human definition?
But of course the cladistic definition is simple and obvious: recency of
common ancestry. Your common ancestor with Ichthyostega is more recent
than your (or Ichthyostega's) common ancestor with Tiktaalik, thus you
are more closely related to Ichthyostega than either of you is to
Tiktaalik. And this can be objectively determined by phylogenetic
analysis, an advantage for any definition: it's operational.
> Had the victory gone the other way, we might be far advanced in a definition of "more related"
> that combines phylogeny with measures of disparity. As it is, the theory of macroevolution,
> to which disparity is an indispensable tool, has made comparatively little progress to date.
cladistic classification. Why would you think so?
Peter Nyikos
Sep 5, 2022, 6:51:53 PM9/5/22
to
On Monday, September 5, 2022 at 2:50:32 PM UTC-4, John Harshman wrote:
> On 9/5/22 11:42 AM, Peter Nyikos wrote:
> > As I looked back yesterday on some 2016 threads in s.b.p. when it was at the height of what I call
> > "an oasis of civilization," I came across a long exchange between Ruben Safir
> > [who often went under the byline Popping mad, as he does now]
> > and John Harshman, which I joined near the end. John and Ruben
> > were unable to communicate fruitfully, because John was stuck
> > in a dichotomy between two ways of classifying organisms:
> > the cladistic and the phenetic.
> Needless to say, I reject your characterization of that argument.
Automatic reflex reaction noted.
> On 9/5/22 11:42 AM, Peter Nyikos wrote:
> > As I looked back yesterday on some 2016 threads in s.b.p. when it was at the height of what I call
> > "an oasis of civilization," I came across a long exchange between Ruben Safir
> > [who often went under the byline Popping mad, as he does now]
> > and John Harshman, which I joined near the end. John and Ruben
> > were unable to communicate fruitfully, because John was stuck
> > in a dichotomy between two ways of classifying organisms:
> > the cladistic and the phenetic.
> Needless to say, I reject your characterization of that argument.
You obviously haven't looked at the thread in over six years,
not with Giganews archives only going back a month.
But I'll help you. Here is the url for the entire thread.
https://groups.google.com/g/sci.bio.paleontology/c/sFY6QxipSb4/m/T0QLNBF0AQAJ
Happy surfing up and down the 148 posts. Here is a note I made on one of them:
"Harshman is stuck in a false dichotomy between cladistics and phenetics"
Apr 14, 2016, 5:03:15 PM
You may want to start there.
See you tomorrow with the post that addresses this false dichotomy of yours.
Peter Nyikos
John Harshman
Sep 5, 2022, 8:07:12 PM9/5/22
to
On 9/5/22 3:51 PM, Peter Nyikos wrote:
> On Monday, September 5, 2022 at 2:50:32 PM UTC-4, John Harshman wrote:
>> On 9/5/22 11:42 AM, Peter Nyikos wrote:
>
>>> As I looked back yesterday on some 2016 threads in s.b.p. when it was at the height of what I call
>>> "an oasis of civilization," I came across a long exchange between Ruben Safir
>>> [who often went under the byline Popping mad, as he does now]
>>> and John Harshman, which I joined near the end. John and Ruben
>>> were unable to communicate fruitfully, because John was stuck
>>> in a dichotomy between two ways of classifying organisms:
>>> the cladistic and the phenetic.
>
>> Needless to say, I reject your characterization of that argument.
>
> Automatic reflex reaction noted.
Try to engage with my argument rather than just characterizing it.
> On Monday, September 5, 2022 at 2:50:32 PM UTC-4, John Harshman wrote:
>> On 9/5/22 11:42 AM, Peter Nyikos wrote:
>
>>> As I looked back yesterday on some 2016 threads in s.b.p. when it was at the height of what I call
>>> "an oasis of civilization," I came across a long exchange between Ruben Safir
>>> [who often went under the byline Popping mad, as he does now]
>>> and John Harshman, which I joined near the end. John and Ruben
>>> were unable to communicate fruitfully, because John was stuck
>>> in a dichotomy between two ways of classifying organisms:
>>> the cladistic and the phenetic.
>
>> Needless to say, I reject your characterization of that argument.
>
> Automatic reflex reaction noted.
> You obviously haven't looked at the thread in over six years,
> not with Giganews archives only going back a month.
> But I'll help you. Here is the url for the entire thread.
> https://groups.google.com/g/sci.bio.paleontology/c/sFY6QxipSb4/m/T0QLNBF0AQAJ
>
> Happy surfing up and down the 148 posts. Here is a note I made on one of them:
>
> "Harshman is stuck in a false dichotomy between cladistics and phenetics"
> Apr 14, 2016, 5:03:15 PM
>
> You may want to start there.
>
>
> See you tomorrow with the post that addresses this false dichotomy of yours.
John Harshman
Sep 5, 2022, 8:14:48 PM9/5/22
to
On 9/5/22 3:51 PM, Peter Nyikos wrote:
google try to match time zones? There is a post at 2:03:15 PM that might
be the one you're thinking of, but it doesn't say anything about
cladistics vs. phenetics, so seems to have nothing to do with your note.
Puzzling.
Glenn
Sep 6, 2022, 11:29:11 AM9/6/22
to
I think you misunderstand what Peter said and meant above.
John Harshman
Sep 6, 2022, 12:04:31 PM9/6/22
to
explain it to me?
Peter Nyikos
Sep 6, 2022, 8:39:56 PM9/6/22
to
On Monday, September 5, 2022 at 8:14:48 PM UTC-4, John Harshman wrote:
> On 9/5/22 3:51 PM, Peter Nyikos wrote:
> > But I'll help you. Here is the url for the entire thread.
> > https://groups.google.com/g/sci.bio.paleontology/c/sFY6QxipSb4/m/T0QLNBF0AQAJ
> >
> > Happy surfing up and down the 148 posts. Here is a note I made on one of them:
> >
> > "Harshman is stuck in a false dichotomy between cladistics and phenetics"
> > Apr 14, 2016, 5:03:15 PM
> >
> > You may want to start there.
> There is no post with that time stamp. Is there perhaps a typo? No. Or does
> On 9/5/22 3:51 PM, Peter Nyikos wrote:
> > But I'll help you. Here is the url for the entire thread.
> > https://groups.google.com/g/sci.bio.paleontology/c/sFY6QxipSb4/m/T0QLNBF0AQAJ
> >
> > Happy surfing up and down the 148 posts. Here is a note I made on one of them:
> >
> > "Harshman is stuck in a false dichotomy between cladistics and phenetics"
> > Apr 14, 2016, 5:03:15 PM
> >
> > You may want to start there.
> google try to match time zones?
Well, it obviously gave it to you in Pacific Daylight time, to me in Eastern Daylight time.
>There is a post at 2:03:15 PM that might
> be the one you're thinking of, but it doesn't say anything about
> cladistics vs. phenetics, so seems to have nothing to do with your note.
> Puzzling.
On 4/14/16 1:28 PM, ruben safir wrote:
> On 04/14/2016 12:09 AM, John Harshman wrote:
>> I'm sorry, but this is incorrect in regard to species. It would be true
>> if evolution were perfectly clocklike, b
>
> no that is not true. time is not a measured characteristic in closest
> path analysis. It might be that two species are a billion years
> separated, but still closely related, and the shortest path analysis
> will demonstrate that relationship.
>
No it won't, unless by "closely related" you just mean "similar". But
what the term means in phylogenetics is "sharing a more recent common
ancestry than with some third taxon", i.e. the sort of thing
phylogenetic trees say. There is no particular justification for making
trees that just measure similarity. (There are methods for making such
trees, e.g. UPGMA, but why would you use them?)
++++++++++++++++ end of post ++++++++++++++++++++
Your very first sentence is of the very essence of phenetics.
And the only alternative you seriously propose is pure cladistics.
What kept you from seeing that?
Puzzling, indeed!
Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
that I think Ruben had in mind. Use the time wisely instead of shooting from
the hip in a reply within 5 minutes, like you so often do.
Peter Nyikos
Sep 6, 2022, 9:54:00 PM9/6/22
to
On Tuesday, September 6, 2022 at 8:39:56 PM UTC-4, Peter Nyikos wrote:
++++++++++++++++++++++++ begin included post+++++++++++++++++
disparity between elements (nodes and branch tips) of an evolutionary
tree where the branch tips (and perhaps some nodes) are taxa.
The line segment joining successive elements is given a number estimating degree of disparity,
and the numbers are added together to compute the length of the path between them.
The concept of "more closely related" then could be given a whole new meaning --
or, rather, an old meaning but now quantified. We would be able to say that vertebrate A
in the following example is MUCH more closely related to B than it is to C even though
the LCA of A and B is strictly ancestral to the LCA of B and C.
This is the example we had earlier: A = Tiktaalik, B= Ichthyostega, C = Bos.
A cladist would say B and C are equally distant from A because they are in a clade that excludes A.
A pheneticist would agree with the disparity measurer in this example,
but I think it is not hard to cook up an example where evolutionary convergence
could make the pheneticist disagree with the disparity measurer,
because the latter takes a plunge down the tree and back up to do the measuring,
but the pheneticist hops across the tree in a beeline from one species to another.
I submit that this concept does justice to phylogeny besides being
exactly the sort of thing one would expect from our ordinary
human concept of "more closely related."
Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
Univ. of South Carolina at Columbia
http://people.math.sc.edu/nyikos
PS Remember those little children who thought it was "way cool"
that birds are dinosaurs? Do you think you get them to believe
that your concept is better than the one with which they
are familiar (aunts, uncles, cousins, etc.) and which the disparity-measurer's
concept so faithfully mirrors?
++++++++++++++++++++++++ begin included post+++++++++++++++++
> On 4/14/16 1:28 PM, ruben safir wrote:
> > On 04/14/2016 12:09 AM, John Harshman wrote:
> >> I'm sorry, but this is incorrect in regard to species. It would be true
> >> if evolution were perfectly clocklike, b
> >
> > no that is not true. time is not a measured characteristic in closest
> > path analysis. It might be that two species are a billion years
> > separated, but still closely related, and the shortest path analysis
> > will demonstrate that relationship.
> >
> No it won't, unless by "closely related" you just mean "similar". But
> what the term means in phylogenetics is "sharing a more recent common
> ancestry than with some third taxon", i.e. the sort of thing
> phylogenetic trees say. There is no particular justification for making
> trees that just measure similarity. (There are methods for making such
> trees, e.g. UPGMA, but why would you use them?)
>
> ++++++++++++++++ end of post ++++++++++++++++++++
>
> Your very first sentence is of the very essence of phenetics.
> And the only alternative you seriously propose is pure cladistics.
So, what did Ruben have in mind? I believe it was a measure of
> > On 04/14/2016 12:09 AM, John Harshman wrote:
> >> I'm sorry, but this is incorrect in regard to species. It would be true
> >> if evolution were perfectly clocklike, b
> >
> > no that is not true. time is not a measured characteristic in closest
> > path analysis. It might be that two species are a billion years
> > separated, but still closely related, and the shortest path analysis
> > will demonstrate that relationship.
> >
> No it won't, unless by "closely related" you just mean "similar". But
> what the term means in phylogenetics is "sharing a more recent common
> ancestry than with some third taxon", i.e. the sort of thing
> phylogenetic trees say. There is no particular justification for making
> trees that just measure similarity. (There are methods for making such
> trees, e.g. UPGMA, but why would you use them?)
>
> ++++++++++++++++ end of post ++++++++++++++++++++
>
> Your very first sentence is of the very essence of phenetics.
> And the only alternative you seriously propose is pure cladistics.
disparity between elements (nodes and branch tips) of an evolutionary
tree where the branch tips (and perhaps some nodes) are taxa.
The line segment joining successive elements is given a number estimating degree of disparity,
and the numbers are added together to compute the length of the path between them.
The concept of "more closely related" then could be given a whole new meaning --
or, rather, an old meaning but now quantified. We would be able to say that vertebrate A
in the following example is MUCH more closely related to B than it is to C even though
the LCA of A and B is strictly ancestral to the LCA of B and C.
This is the example we had earlier: A = Tiktaalik, B= Ichthyostega, C = Bos.
A cladist would say B and C are equally distant from A because they are in a clade that excludes A.
A pheneticist would agree with the disparity measurer in this example,
but I think it is not hard to cook up an example where evolutionary convergence
could make the pheneticist disagree with the disparity measurer,
because the latter takes a plunge down the tree and back up to do the measuring,
but the pheneticist hops across the tree in a beeline from one species to another.
I submit that this concept does justice to phylogeny besides being
exactly the sort of thing one would expect from our ordinary
human concept of "more closely related."
Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
Univ. of South Carolina at Columbia
http://people.math.sc.edu/nyikos
that birds are dinosaurs? Do you think you get them to believe
that your concept is better than the one with which they
are familiar (aunts, uncles, cousins, etc.) and which the disparity-measurer's
concept so faithfully mirrors?
John Harshman
Sep 6, 2022, 11:56:54 PM9/6/22
to
criteria doesn't give you a tree. It might give you a classification,
but that's not the same thing. Even Ernst Mayr proposed that you find
relationships using cladistic methods and then add phenetic closeness in
classification.
> Puzzling, indeed!
>
>
> Peter Nyikos
> Professor, Dept. of Mathematics -- standard disclaimer--
> Univ. of South Carolina at Columbia
> http://people.math.sc.edu/nyikos
>
> PS I'll give you about an hour to mull over the above before I post the alternative
> that I think Ruben had in mind. Use the time wisely instead of shooting from
> the hip in a reply within 5 minutes, like you so often do.
deserve. No fear on that score.
John Harshman
Sep 7, 2022, 12:18:55 AM9/7/22
to
On 9/6/22 6:53 PM, Peter Nyikos wrote:
> On Tuesday, September 6, 2022 at 8:39:56 PM UTC-4, Peter Nyikos wrote:
>
> ++++++++++++++++++++++++ begin included post+++++++++++++++++
>> On 4/14/16 1:28 PM, ruben safir wrote:
>>> On 04/14/2016 12:09 AM, John Harshman wrote:
>>>> I'm sorry, but this is incorrect in regard to species. It would be true
>>>> if evolution were perfectly clocklike, b
>>>
>>> no that is not true. time is not a measured characteristic in closest
>>> path analysis. It might be that two species are a billion years
>>> separated, but still closely related, and the shortest path analysis
>>> will demonstrate that relationship.
>>>
>> No it won't, unless by "closely related" you just mean "similar". But
>> what the term means in phylogenetics is "sharing a more recent common
>> ancestry than with some third taxon", i.e. the sort of thing
>> phylogenetic trees say. There is no particular justification for making
>> trees that just measure similarity. (There are methods for making such
>> trees, e.g. UPGMA, but why would you use them?)
>>
>> ++++++++++++++++ end of post ++++++++++++++++++++
>>
>> Your very first sentence is of the very essence of phenetics.
>> And the only alternative you seriously propose is pure cladistics.
>
> So, what did Ruben have in mind? I believe it was a measure of
> disparity between elements (nodes and branch tips) of an evolutionary
> tree where the branch tips (and perhaps some nodes) are taxa.
I suspect that you have misunderstood what he had in mind, but perhaps
> On Tuesday, September 6, 2022 at 8:39:56 PM UTC-4, Peter Nyikos wrote:
>
> ++++++++++++++++++++++++ begin included post+++++++++++++++++
>> On 4/14/16 1:28 PM, ruben safir wrote:
>>> On 04/14/2016 12:09 AM, John Harshman wrote:
>>>> I'm sorry, but this is incorrect in regard to species. It would be true
>>>> if evolution were perfectly clocklike, b
>>>
>>> no that is not true. time is not a measured characteristic in closest
>>> path analysis. It might be that two species are a billion years
>>> separated, but still closely related, and the shortest path analysis
>>> will demonstrate that relationship.
>>>
>> No it won't, unless by "closely related" you just mean "similar". But
>> what the term means in phylogenetics is "sharing a more recent common
>> ancestry than with some third taxon", i.e. the sort of thing
>> phylogenetic trees say. There is no particular justification for making
>> trees that just measure similarity. (There are methods for making such
>> trees, e.g. UPGMA, but why would you use them?)
>>
>> ++++++++++++++++ end of post ++++++++++++++++++++
>>
>> Your very first sentence is of the very essence of phenetics.
>> And the only alternative you seriously propose is pure cladistics.
>
> So, what did Ruben have in mind? I believe it was a measure of
> disparity between elements (nodes and branch tips) of an evolutionary
> tree where the branch tips (and perhaps some nodes) are taxa.
he will explain himself.
> The line segment joining successive elements is given a number estimating degree of disparity,
> and the numbers are added together to compute the length of the path between them.
>
> The concept of "more closely related" then could be given a whole new meaning --
> or, rather, an old meaning but now quantified. We would be able to say that vertebrate A
> in the following example is MUCH more closely related to B than it is to C even though
> the LCA of A and B is strictly ancestral to the LCA of B and C.
>
> This is the example we had earlier: A = Tiktaalik, B= Ichthyostega, C = Bos.
> A cladist would say B and C are equally distant from A because they are in a clade that excludes A.
>
> A pheneticist would agree with the disparity measurer in this example,
> but I think it is not hard to cook up an example where evolutionary convergence
> could make the pheneticist disagree with the disparity measurer,
> because the latter takes a plunge down the tree and back up to do the measuring,
> but the pheneticist hops across the tree in a beeline from one species to another.
>
>
> I submit that this concept does justice to phylogeny besides being
> exactly the sort of thing one would expect from our ordinary
> human concept of "more closely related."
patristic distance as a measure of relatedness, smaller distances being
more close relationships. But these distances would depend on what
characters you used to make the measured tree, and there is no real
objective way to choose these measures of disparity. I don't see
patristic distance as much better for this purpose than simple pairwise
distance. Further, I think it would lead to overlapping groups if used
in classification. Velociraptor closer to Archaeopteryx than
Archaeopteryx to Confuciusornis. Archaeopteryx closer to Confuciusornis
than Confusiusornis to Icthyornis. Icthyornis closer to Passer than
Ichthyornis to Confuciusornis. But where do we put the line here? And
what's closer to Hesperornis? It would seem to be out on its own.
> Peter Nyikos
> Professor, Dept. of Mathematics -- standard disclaimer--
> Univ. of South Carolina at Columbia
> http://people.math.sc.edu/nyikos
>
> PS Remember those little children who thought it was "way cool"
> that birds are dinosaurs? Do you think you get them to believe
> that your concept is better than the one with which they
> are familiar (aunts, uncles, cousins, etc.) and which the disparity-measurer's
> concept so faithfully mirrors?
But they would probably believe my concept was better if they liked me
or if I gave them candy.
Peter Nyikos
Sep 7, 2022, 5:08:29 PM9/7/22
to
I certainly hope he does join, because he might learn a lot about all three methods of
defining "more closely related." Back in 2016, he wrote that he was working on a
Master's degree and I wish I had known then what I know now.
> > The line segment joining successive elements is given a number estimating degree of disparity,
> > and the numbers are added together to compute the length of the path between them.
assuming it is rooted."
> >
> > The concept of "more closely related" then could be given a whole new meaning --
> > or, rather, an old meaning but now quantified. We would be able to say that vertebrate A
> > in the following example is MUCH more closely related to B than it is to C even though
> > the LCA of A and B is strictly ancestral to the LCA of B and C.
> >
> > This is the example we had earlier: A = Tiktaalik, B= Ichthyostega, C = Bos.
> > A cladist would say B and C are equally distant from A because they are in a clade that excludes A.
> >
> > A pheneticist would agree with the disparity measurer in this example,
> > but I think it is not hard to cook up an example where evolutionary convergence
> > could make the pheneticist disagree with the disparity measurer,
> > because the latter takes a plunge down the tree and back up to do the measuring,
> > but the pheneticist hops across the tree in a beeline from one species to another.
> >
> >
> > I submit that this concept does justice to phylogeny besides being
> > exactly the sort of thing one would expect from our ordinary
> > human concept of "more closely related."
> You may think so, but I don't. If I understand your point, you are using
> patristic distance as a measure of relatedness, smaller distances being
> more close relationships.
published articles about it?
>But these distances would depend on what
> characters you used to make the measured tree, and there is no real
> objective way to choose these measures of disparity.
can make a start with the tree of Equioidea in Kathleen Hunt's excellent FAQ:
http://www.talkorigins.org/faqs/horses/horse_evol.html
You can see a lineage in the tree going directly from Hyracotherium all the way to Equus,
with a genus at each node in an old-fashioned evolutionary tree.
The whole tree has a good number of side branches, and each node is a great source of characters.
Even if you believe that there isn't a single ancestor-descendant relationship
depicted there, the fossils in most cases are so nearly complete
that the named genera can be a source for a nearly complete
set of skeletal characters for the actual species that REALLY belong at the nodes.
I think a good set of disparity numbers can be worked out,
given enough time and brainstorming. It could be far advanced
by now, had the victory of the cladists in "the cladist wars" not
been a complete rout of those disagreeing with them,
and had the victors not been so intolerant of the Linnean system.
> I don't see
> patristic distance as much better for this purpose than simple pairwise distance.
> Further, I think it would lead to overlapping groups if used
> in classification.
By the time I returned to s.b.p. in late 2010, I had come to realize that
the Linnean system was like an endangered species [though not as critically
endangered as s.b.p. itself was at the time], and I put all my efforts into
promoting a dual system of classification.
I made the analogy of the Dewey Decimal and Library of Congress systems
of classifying books, each promoted by its own libraries. But such
peaceful coexistence is not good enough for the victors: it's their way or the highway.
And you've made yourself a propagandist for them in s.b.p. and t.o.
> Velociraptor closer to Archaeopteryx than
> Archaeopteryx to Confuciusornis. Archaeopteryx closer to Confuciusornis
> than Confusiusornis to Icthyornis.
distance between them.
> Icthyornis closer to Passer than
> Ichthyornis to Confuciusornis.
> But where do we put the line here? And
> what's closer to Hesperornis? It would seem to be out on its own.
is that each pair is separated by a given distance, and there is no conflict between
pairwise distances. Want to know who is closest to Hesperornis? the one who
ends up with the smallest distance to it. Duh.
John Harshman
Sep 7, 2022, 8:52:06 PM9/7/22
to
regardless of where the tree is rooted or whether it's rooted at all.
patristic distance, i.e. a count of branch lengths between A and B along
the tree.
> >But these distances would depend on what
>> characters you used to make the measured tree, and there is no real
>> objective way to choose these measures of disparity.
>
> That is an extraordinarily difficult problem, but I think interested
researchers [and they still exist]
> can make a start with the tree of Equioidea in Kathleen Hunt's
excellent FAQ:
>
> http://www.talkorigins.org/faqs/horses/horse_evol.html
>
> You can see a lineage in the tree going directly from Hyracotherium
all the way to Equus,
> with a genus at each node in an old-fashioned evolutionary tree.
> The whole tree has a good number of side branches, and each node is a
great source of characters.
include, make that consistent across all taxa, decide how to score the
amount of difference among states within a character, consider how to
handle missing data (consider: how would you score, for example, the
shape of the 4th toe in Equus?). There are more problems, but that's
enough for now.
> Even if you believe that there isn't a single ancestor-descendant
relationship
> depicted there, the fossils in most cases are so nearly complete
> that the named genera can be a source for a nearly complete
> set of skeletal characters for the actual species that REALLY belong
at the nodes.
already biased the measure.
> I think a good set of disparity numbers can be worked out,
> given enough time and brainstorming. It could be far advanced
> by now, had the victory of the cladists in "the cladist wars" not
> been a complete rout of those disagreeing with them,
> and had the victors not been so intolerant of the Linnean system.
shouted down. Systematists just became convinced of proper methodology.
And the Linnean system, ranked groups within ranked groups, was not
harmed. The decline of ranked groups was a separate matter entirely.
Now, disparity numbers can in fact be useful for many purposes. But all
they are would be distances measured over trees, and they would vary
depennding on the data. They could as well be used (and are used) with
molecular data as with morphological data. They can tell us mamy things.
But using them to define closeness of relationship is not one of those
things.
>> I don't see
>> patristic distance as much better for this purpose than simple
pairwise distance.
>
> That's because of your dislike of paraphyletic taxa, in solidarity
with the victors.
paraphyletic taxa are not useful.
>> Further, I think it would lead to overlapping groups if used
>> in classification.
>
> Are you stuck in the 1990's, when I tried to interest people in such
a system?
> By the time I returned to s.b.p. in late 2010, I had come to realize that
> the Linnean system was like an endangered species [though not as
critically
> endangered as s.b.p. itself was at the time], and I put all my
efforts into
> promoting a dual system of classification.
meaning of the term that it allows, requires, or forbids paraphyly. It's
silent on the question.
> I made the analogy of the Dewey Decimal and Library of Congress systems
> of classifying books, each promoted by its own libraries. But such
> peaceful coexistence is not good enough for the victors: it's their
way or the highway.
> And you've made yourself a propagandist for them in s.b.p. and t.o.
>> Velociraptor closer to Archaeopteryx than
>> Archaeopteryx to Confuciusornis. Archaeopteryx closer to Confuciusornis
>> than Confusiusornis to Icthyornis.
>
> Where do you get these comparisons? You sure haven't worked out a
disparity-based
> distance between them.
hypothetical example if you like.
> > Icthyornis closer to Passer than
>> Ichthyornis to Confuciusornis.
>
> Really? Aren't you using the cladistic "closer to" here?
on no better basis than mine, I expect), but that's not important to the
example.
> > But where do we put the line here? And
>> what's closer to Hesperornis? It would seem to be out on its own.
>
> Wrong. The beauty of the "straight down to the LCA and straight up to
the other genus"
> is that each pair is separated by a given distance, and there is no
conflict between
> pairwise distances. Want to know who is closest to Hesperornis? the
one who
> ends up with the smallest distance to it. Duh.
would presumably be, one supposes, Ichthyornis of those listed. But
though Hesperornis would be closer to Ichthyornis than to Passer, would
Ichthyornis be closer to Passer than to Hesperornis? Relationships,
based on disparity, would appear not to be transitive. It's certainly
unclear how, if you used this measure of disparity to determine
classification, you would divide up the tree in any non-arbitrary
fashion. Simply, how would you decide where, for example, dinosaurs end
and birds begin?
Peter Nyikos
Sep 8, 2022, 1:11:29 PM9/8/22
to
On Wednesday, September 7, 2022 at 8:52:06 PM UTC-4, John Harshman wrote:
> On 9/7/22 2:08 PM, Peter Nyikos wrote:
> > On Wednesday, September 7, 2022 at 12:18:55 AM UTC-4, John Harshman
> wrote:
> >> On 9/6/22 6:53 PM, Peter Nyikos wrote:
I've snipped the text that appears above, where you added nothing new.
> On 9/7/22 2:08 PM, Peter Nyikos wrote:
> > On Wednesday, September 7, 2022 at 12:18:55 AM UTC-4, John Harshman
> wrote:
> >> On 9/6/22 6:53 PM, Peter Nyikos wrote:
Below, I'm making marked snips to get to what looks like some fundamental
miscommunications. We can talk about what I've snipped another day.
> >>> The line segment joining successive elements is given a number
> estimating degree of disparity,
> >>> and the numbers are added together to compute the length of the
> path between them.
> >
> > I should have ended that sentence with "the path between any two taxa
> on the tree,
> > assuming it is rooted."
> I don't see the need for a rooted tree here. The path is the same length
> regardless of where the tree is rooted or whether it's rooted at all.
whereby a tree lacking a root (i.e. a unique minimum element)
consists of two or more components which look like trees in the usual sense.
I take it that you mean that the tree was determined by selecting a
specimen well outside the clade to "root" the tree, as a means of
locating a unique minimum element. Correct?
> >>> The concept of "more closely related" then could be given a whole
> new meaning --
> >>> or, rather, an old meaning but now quantified. We would be able to
> say that vertebrate A
> >>> in the following example is MUCH more closely related to B than it
> is to C even though
> >>> the LCA of A and B is strictly ancestral to the LCA of B and C.
> >>>
> >>> This is the example we had earlier: A = Tiktaalik, B= Ichthyostega,
> C = Bos.
> >>> A cladist would say B and C are equally distant from A because they
> are in a clade that excludes A.
> >>>
> >>> A pheneticist would agree with the disparity measurer in this example,
> >>> but I think it is not hard to cook up an example where evolutionary
> convergence
> >>> could make the pheneticist disagree with the disparity measurer,
> >>> because the latter takes a plunge down the tree and back up to do
> the measuring,
> >>> but the pheneticist hops across the tree in a beeline from one
> species to another.
> >> If I understand your point, you are using
> >> patristic distance as a measure of relatedness, smaller distances being
> >> more close relationships.
> >
> > I am unfamiliar with the concept of patristic distance. Are there any
> > published articles about it?
> No entire articles that I'm aware of. But what you describe is a
> patristic distance, i.e. a count of branch lengths between A and B along
> the tree.
makes me suspect that patristic distance means the number of nodes,
which completely misses the role of disparity in what I wrote.
> > >But these distances would depend on what
> >> characters you used to make the measured tree, and there is no real
> >> objective way to choose these measures of disparity.
> >
> > That is an extraordinarily difficult problem, but I think interested
> researchers [and they still exist]
> > can make a start with the tree of Equioidea in Kathleen Hunt's
> excellent FAQ:
> >
> > http://www.talkorigins.org/faqs/horses/horse_evol.html
> >
> > You can see a lineage in the tree going directly from Hyracotherium
> all the way to Equus,
> > with a genus at each node in an old-fashioned evolutionary tree.
> > The whole tree has a good number of side branches, and each node is a
> great source of characters.
> Good luck with that. You would have to decide which characters to
> include,
most with nearly complete skeletons. [Of course, many would come from
distinct specimens from the same genus.]
[...]
> > Even if you believe that there isn't a single ancestor-descendant relationship
> > depicted there, the fossils in most cases are so nearly complete
> > that the named genera can be a source for a nearly complete
> > set of skeletal characters for the actual species that REALLY belong
> at the nodes.
> But are skeletal characters the only measure of disparity? You have
> already biased the measure.
Try to get your mind off extant species. Skeletons are all we have of horse fossils,
> > depicted there, the fossils in most cases are so nearly complete
> > that the named genera can be a source for a nearly complete
> > set of skeletal characters for the actual species that REALLY belong
> at the nodes.
> But are skeletal characters the only measure of disparity? You have
> already biased the measure.
and the disparity between Equus and Dinohippus is so small that we might
as well exclude Equus to level the playing field.
[...]
> [disparity distances] can tell us mamy things.
> But using to define closeness of relationship is not one of those
> things.
Three posts up to now have featured a radically different meaning
of "closeness of relationship" than the one that is second nature to you.
Please try to stick to that one when discussing disparity distances,
if only to facilitate communication between us.
[...]
> >> Further, I think it would lead to overlapping groups if used
> >> in classification.
> >
> > Are you stuck in the 1990's, when I tried to interest people in such
> a system?
> No, I am not. But that's the implication of defining relationships that way.
I completely disagree. Please try to reveal your line of reasoning.
> >> in classification.
> >
> > Are you stuck in the 1990's, when I tried to interest people in such
> a system?
> No, I am not. But that's the implication of defining relationships that way.
> > By the time I returned to s.b.p. in late 2010, I had come to realize that
> > the Linnean system was like an endangered species [though not as critically
> > endangered as s.b.p. itself was at the time], and I put all my efforts into
> > promoting a dual system of classification.
> You are misusing the term "Linnean system". It is not part of the
> meaning of the term that it allows, requires, or forbids paraphyly. It's
> silent on the question.
just to name the classes involved. And then there are what are
derisively termed "garbage taxa": Cotylosauria, Thecodonta, Insectivora, and Condylartha.
If Linnaeus had been into subclasses and infraclasses,
he might have defined Theria as a subclass of Mammalia,
split into the following infraclasses: Marsupilia, Cetacea, Chiroptera
and Terraplacentalia. After all, he was only using extant animals,
and the last named would have been a paraphyletic group.
[...]
> >> Velociraptor closer to Archaeopteryx than
> >> Archaeopteryx to Confuciusornis. Archaeopteryx closer to Confuciusornis
> >> than Confusiusornis to Icthyornis.
> >
> > Where do you get these comparisons? You sure haven't worked out a
> disparity-based
> > distance between them.
> Nope, just made them up based on a general impression. Consider it a
> hypothetical example if you like.
> > > Icthyornis closer to Passer than
> >> Ichthyornis to Confuciusornis.
> >
> > Really? Aren't you using the cladistic "closer to" here?
> No. Again, a general impression of morphology.
had a "birdlike" beak, and the rest of the skull [1] looks
more like that of a pigeon than that of Ichthyornis.
What features are you looking at to compensate for this?
[1] I'm looking at the skull in the 3rd edition of Benton's _Vertebrate_Paleontology_
[...]
> >> what's closer to Hesperornis? It would seem to be out on its own.
> >
> > Wrong. The beauty of the "straight down to the LCA and straight up to the other genus"
> > is that each pair is separated by a given distance, and there is no conflict between
> > pairwise distances. Want to know who is closest to Hesperornis? the one who
> > ends up with the smallest distance to it. Duh.
> The smallest patristic (along the tree) distance, one supposes. That
> would presumably be, one supposes, Ichthyornis of those listed. But
> though Hesperornis would be closer to Ichthyornis than to Passer, would
> Ichthyornis be closer to Passer than to Hesperornis?
California, you are closer to Hawaii than you are to Newfoundland.
But Newfoundland is closer to you than it is to Hawaii.
> Relationships, based on disparity, would appear not to be transitive.
of disparity distance is symmetry: taxon A is exactly as close to
taxon B as taxon B is to taxon A.
[...]
Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
http://people.math.sc.edu/nyikos
John Harshman
Sep 8, 2022, 3:05:01 PM9/8/22
to
your usage, the existence of a (conventially shown) "lowermost" point
dividing the tree into two subtrees. Sometimes this is done by declaring
an outgroup, but there are other ways, and it doesn't matter to the
present question how rooting is done. What matters is that the position
of the root or its absence has no effect on the lengths of paths through
the tree. Would you not agree?
magnitude of inferred change between nodes, same as what you seem to be
saying. Adding up the total length of branches between taxa gives you a
patristic distance. The number of nodes traversed is irrelevant.
>>>> But these distances would depend on what
>>>> characters you used to make the measured tree, and there is no real
>>>> objective way to choose these measures of disparity.
>>>
>>> That is an extraordinarily difficult problem, but I think interested
>> researchers [and they still exist]
>>> can make a start with the tree of Equioidea in Kathleen Hunt's
>> excellent FAQ:
>>>
>>> http://www.talkorigins.org/faqs/horses/horse_evol.html
>>>
>>> You can see a lineage in the tree going directly from Hyracotherium
>> all the way to Equus,
>>> with a genus at each node in an old-fashioned evolutionary tree.
>>> The whole tree has a good number of side branches, and each node is a
>> great source of characters.
>
>> Good luck with that. You would have to decide which characters to
>> include,
>
> All known ones for each skeleton. We are talking about extinct
species here,
> most with nearly complete skeletons. [Of course, many would come from
> distinct specimens from the same genus.]
paleontological data set? They're full of missing data. And as for
"distinct specimens from the same genus", you should know that, for
example, around half of all non-avian dinosaur genera are known from
single specimens only.
> [...]
>>> Even if you believe that there isn't a single ancestor-descendant
relationship
>>> depicted there, the fossils in most cases are so nearly complete
>>> that the named genera can be a source for a nearly complete
>>> set of skeletal characters for the actual species that REALLY belong
>> at the nodes.
>
>
>> But are skeletal characters the only measure of disparity? You have
>> already biased the measure.
>
> Try to get your mind off extant species. Skeletons are all we have of
horse fossils,
> and the disparity between Equus and Dinohippus is so small that we might
> as well exclude Equus to level the playing field.
measures dependent on that data less than ideal.
>> [disparity distances] can tell us mamy things.
>> But using to define closeness of relationship is not one of those
>> things.
>
> Three posts up to now have featured a radically different meaning
> of "closeness of relationship" than the one that is second nature to you.
> Please try to stick to that one when discussing disparity distances,
> if only to facilitate communication between us.
fact that's what I was thinking of here, but it does contribute another
reason why your definition isn't useful.
>>>> Further, I think it would lead to overlapping groups if used
>>>> in classification.
>>>
>>> Are you stuck in the 1990's, when I tried to interest people in such
>> a system?
>> No, I am not. But that's the implication of defining relationships
that way.
>
> I completely disagree. Please try to reveal your line of reasoning.
to define uniquely supported, paraphyletic groups will necessarily fail
and will imply overlapping groups.
>>> By the time I returned to s.b.p. in late 2010, I had come to
realize that
>>> the Linnean system was like an endangered species [though not as
critically
>>> endangered as s.b.p. itself was at the time], and I put all my
efforts into
>>> promoting a dual system of classification.
>
>> You are misusing the term "Linnean system". It is not part of the
>> meaning of the term that it allows, requires, or forbids paraphyly. It's
>> silent on the question.
>
> It's rife with paraphyletic taxa. Reptilia, Amphibia, Osteichthyes,
Agnatha,
> just to name the classes involved. And then there are what are
> derisively termed "garbage taxa": Cotylosauria, Thecodonta,
Insectivora, and Condylartha.
particular classification, not the one you remember from your youth, not
any other. It's about a style of classification, of ranked groups within
ranked groups.
> If Linnaeus had been into subclasses and infraclasses,
> he might have defined Theria as a subclass of Mammalia,
> split into the following infraclasses: Marsupilia, Cetacea, Chiroptera
> and Terraplacentalia. After all, he was only using extant animals,
> and the last named would have been a paraphyletic group.
ranks we use today. And claiming what Linnaeus might have done in some
alternate world doesn't seem useful. Why should we even care what groups
Linnaeus preferred, much less which ones you speculate he would have
preferred? We have advanced far beyond anything he did.
>>>> Velociraptor closer to Archaeopteryx than
>>>> Archaeopteryx to Confuciusornis. Archaeopteryx closer to
Confuciusornis
>>>> than Confusiusornis to Icthyornis.
>>>
>>> Where do you get these comparisons? You sure haven't worked out a
>> disparity-based
>>> distance between them.
>
>> Nope, just made them up based on a general impression. Consider it a
>> hypothetical example if you like.
>
> So far, so good. But the following is debatable:
>>>> Icthyornis closer to Passer than
>>>> Ichthyornis to Confuciusornis.
>>>
>>> Really? Aren't you using the cladistic "closer to" here?
>> No. Again, a general impression of morphology.
>
> Ichthyornis had long jaws with teeth, Confuciusornis
> had a "birdlike" beak, and the rest of the skull [1] looks
> more like that of a pigeon than that of Ichthyornis.
> What features are you looking at to compensate for this?
Neornithes. Of course Ichthyornis did have a birdlike beak in addition
to its teeth.
> [1] I'm looking at the skull in the 3rd edition of Benton's
_Vertebrate_Paleontology_
>
> [...]
>
>>>> what's closer to Hesperornis? It would seem to be out on its own.
>>>
>>> Wrong. The beauty of the "straight down to the LCA and straight up
to the other genus"
>>> is that each pair is separated by a given distance, and there is no
conflict between
>>> pairwise distances. Want to know who is closest to Hesperornis? the
one who
>>> ends up with the smallest distance to it. Duh.
>
>> The smallest patristic (along the tree) distance, one supposes. That
>> would presumably be, one supposes, Ichthyornis of those listed. But
>> though Hesperornis would be closer to Ichthyornis than to Passer, would
>> Ichthyornis be closer to Passer than to Hesperornis?
>
> You are talking about an everyday property of distance. If you live in
> California, you are closer to Hawaii than you are to Newfoundland.
> But Newfoundland is closer to you than it is to Hawaii.
>> Relationships, based on disparity, would appear not to be transitive.
>
> What would transitivity mean in this context? The salient property
> of disparity distance is symmetry: taxon A is exactly as close to
> taxon B as taxon B is to taxon A.
pairwise comparisons. The "closest relation", taking multiple taxa into
account, would not be a reciprocal relationship, which perhaps is a
better description than “transitive”. How would you delimit taxa on such
a basis?
Peter Nyikos
Sep 9, 2022, 7:40:34 PM9/9/22
to
This is a change of pace: A lighthearted (for me, anyway) treatment of John's reaction to a PS
of mine at the end of a reply he did to me here:
On Wednesday, September 7, 2022 at 12:18:55 AM UTC-4, John Harshman wrote:
The first time, I would try to establish rapport with them by talking about
some neat things that occurred on a pair of fossil hunts in Wyoming on which
I participated a little over a year ago.
The second time, I would get around to asking them if any of them
had one or more great-grandparents still alive, after matching any
candy bribe of yours. If it's a class of ten or more, there is an excellent chance
that at least one hand would go up, because nowadays a goodly
fraction of people live to that age.
With twenty, there might arise a longish bidding as to how many were still alive.
Once that had settled down, I would ask them whether any of those great-grandparents
had any brothers or sisters. And if any hands are raised [some might not know the answers]
I would ask the raisers whether they had any brothers or sisters.
If yes, I would turn to one of them and say,
Did you know that Dr. John's [or whatever they call you] way saying how different kinds of
animals are related is like him saying, "Your great-grandmother is more closely related
to your brother than she is to her own brother."
Once this has sunk in and the expressions of astonishment subsided,
I will say, "Now Dr. John will explain to you why this is the best way
to talk about how different kinds of animals are related."
My suggestion for you to save face is to begin by saying that we use the
same words for very different things. The one that comes to mind
is "pipe". You could make a little joke about the absent-minded
professor who tried to smoke a pipe that gas runs through,
and to run water through the pipe that he smokes. But you could
probably do better than that, given all this lead time.
And then, you could explain that the expression "more closely related"
works the same way.
But you'd still have a big problem explaining why it is the RIGHT
meaning for dealing with animal species.
TGIF.
Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of So. Carolina in Columbia
http://people.math.sc.edu/nyikos
of mine at the end of a reply he did to me here:
On Wednesday, September 7, 2022 at 12:18:55 AM UTC-4, John Harshman wrote:
> On 9/6/22 6:53 PM, Peter Nyikos wrote:
> > PS Remember those little children who thought it was "way cool"
> > that birds are dinosaurs? Do you think you [can] get them to believe
> > PS Remember those little children who thought it was "way cool"
> > that your concept is better than the one with which they
> > are familiar (aunts, uncles, cousins, etc.) and which the disparity-measurer's
> > concept so faithfully mirrors?
> I doubt children of that age would have a clue about this controversy.
> But they would probably believe my concept was better if they liked me
> or if I gave them candy.
That depends on whether you invite me twice to talk to them.
> > are familiar (aunts, uncles, cousins, etc.) and which the disparity-measurer's
> > concept so faithfully mirrors?
> I doubt children of that age would have a clue about this controversy.
> But they would probably believe my concept was better if they liked me
> or if I gave them candy.
The first time, I would try to establish rapport with them by talking about
some neat things that occurred on a pair of fossil hunts in Wyoming on which
I participated a little over a year ago.
The second time, I would get around to asking them if any of them
had one or more great-grandparents still alive, after matching any
candy bribe of yours. If it's a class of ten or more, there is an excellent chance
that at least one hand would go up, because nowadays a goodly
fraction of people live to that age.
With twenty, there might arise a longish bidding as to how many were still alive.
Once that had settled down, I would ask them whether any of those great-grandparents
had any brothers or sisters. And if any hands are raised [some might not know the answers]
I would ask the raisers whether they had any brothers or sisters.
If yes, I would turn to one of them and say,
Did you know that Dr. John's [or whatever they call you] way saying how different kinds of
animals are related is like him saying, "Your great-grandmother is more closely related
to your brother than she is to her own brother."
Once this has sunk in and the expressions of astonishment subsided,
I will say, "Now Dr. John will explain to you why this is the best way
to talk about how different kinds of animals are related."
My suggestion for you to save face is to begin by saying that we use the
same words for very different things. The one that comes to mind
is "pipe". You could make a little joke about the absent-minded
professor who tried to smoke a pipe that gas runs through,
and to run water through the pipe that he smokes. But you could
probably do better than that, given all this lead time.
And then, you could explain that the expression "more closely related"
works the same way.
But you'd still have a big problem explaining why it is the RIGHT
meaning for dealing with animal species.
TGIF.
Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
http://people.math.sc.edu/nyikos
John Harshman
Sep 9, 2022, 8:56:05 PM9/9/22
to
Popping Mad
Sep 10, 2022, 5:29:09 PM9/10/22
to
On 9/5/22 14:42, Peter Nyikos wrote:
> The heart of cladistics is found in the phylogenetic trees, which put all
> organisms at the branch tips.
nodes not tips
> The heart of cladistics is found in the phylogenetic trees, which put all
> organisms at the branch tips.
John Harshman
Sep 10, 2022, 5:49:50 PM9/10/22
to
that organisms are placed at terminal nodes, not internal nodes. In case
you are still unclear on meanings, a terminal node connects to a single
branch, while an internal node connects to three or more branches,
exactly three on a fully resolved tree.
So the claim is true.
Glenn
Sep 10, 2022, 6:25:28 PM9/10/22
to
Popping Mad
Sep 10, 2022, 8:19:44 PM9/10/22
to
On 9/6/22 21:53, Peter Nyikos wrote:
> The line segment joining successive elements is given a number estimating degree of disparity,
> and the numbers are added together to compute the length of the path between them.
>
This was correct because I was trying to write a computer program or
> The line segment joining successive elements is given a number estimating degree of disparity,
> and the numbers are added together to compute the length of the path between them.
>
algorithm that would take a CT scan of a fossil while still in the rock,
and attempt to find the placement of that fossil within the evolutionary
tree based on common attributes. In this case, the age of the fossil
would either be ignored or considered one attribute among many.
So the fundamental question is can two species, a billion years
separated, be closely related, or how closely related and how do we
define relatedness. Ideally, we know two individuals are closely
related because they share genetic material. But I don't even know what
that means and admittedly, I know less now than I did 20 years ago as an
undergrad. The older I get, the stupider I become.
Two siblings, in theory, share about 33%-50% +- random variation, of
their genetic material, since they have the same parents. It is
possible, although HIGHLY unlikely, that they share zero DNA. Or they
are some form of a twin and share 100% of their DNA.
Fine. Now Random Chimps and Humans seem to have a closer relationship
than siblings. They share 98.6% of their DNA, or so I see reported? So
in the context of siblings, I am not at all sure what that means.
Aside from that, we don't have genetic material for most species. All
we have is a fraction of skeletal material or a soft tissue imprint.
So for evidence we have
A) incomplete phenotyped characteristics
B) an imperfect time line or age of a fossil
And that is it.
The tools we have to analyze this include a few algorithms and to attach
your ego to any of them, given the limits of the data, is a colossal
error, IMO. Every way we analyze something gives us a different window
to view our specimens and their relationships to each other. These
algorithms themselves are grounded into a few evolving sciences and
mathematics which includes the study of Genetics, Geography, Cosmetology
and Astronomy, Biological computational statistics, and more to name a few.
And then we have the problem with definitions and the understanding of
concepts. Sometimes one has to step back and ask, what exactly am I
trying to learn here?
Are two species closely related despite 300 million years of evolution
if they genetics have been largely conserved other that time? There is
a molecular clock but the functional expression of genes might well be
well preserved in two species separated by by a long period of time.
Hydrothermal vent microbial organism might be more closely related to
their ancient ancestors from a billion years ago than a Moerithriun to
an African Elephant, let alone an Asian Elephant to most species in
Paenungulata. It is suggested that a Hyrax is more basal and an African
elephant, and I would ask, "how so since they are both existing species
and Elephants didn't spring from a modern Hyrax".
So the language itself, here, gets very ambiguous which fuels
disagreements and trolls alike.
And added to this amphibological language a new problem seems to have
emerged recently with core elements of evolutionary theory. It has been
a conceit that a species evolves traits to conform with its environment
through natural selection. Therefor, in theory at least, any individual
could prove to be a node to a new species if they have a mutation that
gives its linage an advantage. There has been shown to be a HUGE
conceit as we have learned from the study of the evolution of Homo and
other species. It has come to be understood that mutations that give
advantages can and do spring up multiple times, even among closely
related species... the same mutation. And then we share DNA material
outside of reproduction. And then mutation will fade if unneeded and
spring up again. Instead of a nice tree, evolution might well look more
like a river delta. Or a suppressed shared gene might become active in
two different lineages, or two species might interbreed?
Everything wants to become a crab...
None of the above is my own original ideas. They all come from reading
scientific literature both in the popular press and in peer reviewed
journals.
So are all Ceratopsidae from the same common ancestor? Maybe, likely,
not definitely.
The last common ancestor of Pachyrhinosaurus... that might be true. But
as we get more evidence of this transition, we might find that more than
once species of closely related dinosaurs evolved similarly, utilizing
similar mutations. Finding a Least common ancestor might be unknowable.
But that might not make this method of defining families and orders and
genus, any less useful. We need to use some definition.
No maybe all these ambiguities have been solved in Paleontology, I
don't know. But I do know that over my lifetime many streams of thought
within the science has come and gone and evolved. I wouldn't take a
theological attachment to any system for the analysis of the
evolutionary procession of species. Nature tends to surprise us and
these are all just tools of logic to help us understand the ancient past
and the nature of biological systems.
> The concept of "more closely related" then could be given a whole new meaning --
> or, rather, an old meaning but now quantified. We would be able to say that vertebrate A
> in the following example is MUCH more closely related to B than it is to C even though
> the LCA of A and B is strictly ancestral to the LCA of B and C.
Popping Mad
Sep 10, 2022, 8:29:24 PM9/10/22
to
On 9/7/22 00:18, John Harshman wrote:
> I don't see patristic distance as much better for this purpose than
> simple pairwise distance.
FWIW - I have no idea how Christian fathers relate to distances in a
> I don't see patristic distance as much better for this purpose than
> simple pairwise distance.
graph but....
ignoring the cost values between nodes, ie treating them all equal,will
get a wrong result every time.
Distant is a measured of a cost and that has to be defined using the
same group of attributes between two nodes to be of any use at all.
This is a mathematical fact and I am not really up to debate it. To
remove cost from the measurement of the distance between nodes gives a
senseless answer.
Popping Mad
Sep 10, 2022, 8:34:09 PM9/10/22
to
On 9/7/22 00:18, John Harshman wrote:
> But these distances would depend on what characters you used to make the
> measured tree, and there is no real objective way to choose these
> measures of disparity.
Yes and no. There is real objectivity. It is just not perfect.
> measured tree, and there is no real objective way to choose these
> measures of disparity.
Attacking those attributes is where the science is. The most attributes
you measure, FWIW, the more likely it is to reach a strong conclusion.
If you think that the ambuitiy involved in this is too difficult to
produce good science, then try your hand at quantum physics where
ambibuity is baked into the theory :)
Popping Mad
Sep 10, 2022, 8:40:13 PM9/10/22
to
On 9/7/22 00:18, John Harshman wrote:
> I think it would lead to overlapping groups if used in classification.
> Velociraptor closer to Archaeopteryx than Archaeopteryx to
> Confuciusornis. Archaeopteryx closer to Confuciusornis than
> Confusiusornis to Icthyornis.
It might. And that might be an indication that we are not choosing our
> Velociraptor closer to Archaeopteryx than Archaeopteryx to
> Confuciusornis. Archaeopteryx closer to Confuciusornis than
> Confusiusornis to Icthyornis.
attributes to the cost between nodes well. Or it can mean that we have
evidence of inter-species breeding, or something else is going on?
All we have is the observable facts, and that might not be enough to
give us a discernible outcome that we are satisfied with. It is better
than guessing and ignoring evidence.
Popping Mad
Sep 10, 2022, 8:51:03 PM9/10/22
to
On 9/7/22 20:52, John Harshman wrote:
> Now, disparity numbers can in fact be useful for many purposes. ...They can tell us mamy things. But using them to define closeness of
number of similar morphological attributes and are not closely related,
you would need a lot to explain this large coincidence. And when
talking about dozens or hundreds or thousands of attributes,
co-evolution is not going to cut it.
> Now, disparity numbers can in fact be useful for many purposes. ...They can tell us mamy things. But using them to define closeness of
> relationship is not one of those things.
Sure it does. That is its core value. It tow species have a large
number of similar morphological attributes and are not closely related,
you would need a lot to explain this large coincidence. And when
talking about dozens or hundreds or thousands of attributes,
co-evolution is not going to cut it.
Popping Mad
Sep 10, 2022, 8:54:00 PM9/10/22
to
On 9/8/22 13:11, Peter Nyikos wrote:
> All known ones for each skeleton. We are talking about extinct species here,
that is another abiguity. When a species evolves into another species,
> All known ones for each skeleton. We are talking about extinct species here,
it didn't go extinct. It evolved. Most species go extinct, but some
don't I am happy to report, as I belong to one such lineage.
John Harshman
Sep 10, 2022, 9:03:33 PM9/10/22
to
species, and this argument is about extinct ones. Is Archaeopteryx more
closely related to Deinonychus or Larus?
John Harshman
Sep 10, 2022, 9:04:33 PM9/10/22
to
On 9/10/22 5:28 PM, Popping Mad wrote:
> On 9/7/22 00:18, John Harshman wrote:
>> I don't see patristic distance as much better for this purpose than
>> simple pairwise distance.
>
> FWIW - I have no idea how Christian fathers relate to distances in a
> graph but....
>
> ignoring the cost values between nodes, ie treating them all equal,will
> get a wrong result every time.
Nobody is proposing such a thing.
> On 9/7/22 00:18, John Harshman wrote:
>> I don't see patristic distance as much better for this purpose than
>> simple pairwise distance.
>
> FWIW - I have no idea how Christian fathers relate to distances in a
> graph but....
>
> ignoring the cost values between nodes, ie treating them all equal,will
> get a wrong result every time.
> Distant is a measured of a cost and that has to be defined using the
> same group of attributes between two nodes to be of any use at all.
> This is a mathematical fact and I am not really up to debate it. To
> remove cost from the measurement of the distance between nodes gives a
> senseless answer.
Popping Mad
Sep 10, 2022, 9:40:06 PM9/10/22
to
On 9/8/22 15:04, John Harshman wrote:
>
> But that all becomes useless once you try to use it for anything except
> pairwise comparisons.
There are hundreds of algorithms that prove this to be untrue.
>
> But that all becomes useless once you try to use it for anything except
> pairwise comparisons.
Sankoff's algorthim on genetic mutation is an example.
And, BTW, much of the disagreement you are having is a matter of vector
distance versus non-vector distance.... that is if you even get an
agreement on the definition of "related"...which you do not have.
https://pubmed.ncbi.nlm.nih.gov/24639164/
https://evolution.gs.washington.edu/gs541/2010/lecture1.pdf
https://fliphtml5.com/aavh/qawv
Popping Mad
Sep 10, 2022, 9:41:16 PM9/10/22
to
On 9/10/22 21:03, John Harshman wrote:
> You're thinking about extant species,
I am talking about all species, but especially fossils.
> You're thinking about extant species,
Popping Mad
Sep 10, 2022, 9:42:42 PM9/10/22
to
On 9/10/22 21:03, John Harshman wrote:
> Is Archaeopteryx more closely related to Deinonychus or Larus?
FWIW - I don't know and I am not the person to ask.
Popping Mad
Sep 10, 2022, 9:45:26 PM9/10/22
to
On 9/10/22 21:04, John Harshman wrote:
> Nobody is proposing such a thing.
Then I am at a loss at what you are saying.
> Nobody is proposing such a thing.
I read where you said the distance between species is only relavant for
wo species but not to set up an evolutionary tree for them.
Popping Mad
Sep 10, 2022, 9:52:40 PM9/10/22
to
On 9/10/22 17:49, John Harshman wrote:
> The intended meaning is that organisms are placed at terminal nodes, not
> internal nodes. In case you are still unclear on meanings, a terminal
> node connects to a single branch, while an internal node connects to
> three or more branches, exactly three on a fully resolved tree.
Sure terminal nodes like in the RB-Tree used in the Linux scheduler.
> The intended meaning is that organisms are placed at terminal nodes, not
> internal nodes. In case you are still unclear on meanings, a terminal
> node connects to a single branch, while an internal node connects to
> three or more branches, exactly three on a fully resolved tree.
Popping Mad
Sep 10, 2022, 9:57:45 PM9/10/22
to
On 9/10/22 17:49, John Harshman wrote:
>>> he heart of cladistics is found in the phylogenetic trees, which put all
>>> organisms at the branch tips.
>>
>> nodes not tips
>
> "Branch tips" here refers to terminal nodes.
>>> organisms at the branch tips.
>>
>> nodes not tips
>
> "Branch tips" here refers to terminal nodes.
> So the claim is true.
No - it is not. Species are not branch tips but nodes. Tips are a
sub-set of nodes, as they are terminal nodes.
Are we failing basic set theory now?
In theory at lest...
All Species are NODES
Some Species are Terminal Nodes
All Species are NOT terminal Nodes, as most are just nodes.
Popping Mad
Sep 10, 2022, 10:01:08 PM9/10/22
to
On 9/10/22 21:03, John Harshman wrote:
Maybe I am not following. This group tends to take deep detours in
discussion and in fact I can often not follow the point being made.
John Harshman
Sep 10, 2022, 11:59:36 PM9/10/22
to
On 9/10/22 5:18 PM, Popping Mad wrote:
> On 9/6/22 21:53, Peter Nyikos wrote:
>> The line segment joining successive elements is given a number
estimating degree of disparity,
>> and the numbers are added together to compute the length of the path
between them.
>>
>
> This was correct because I was trying to write a computer program or
> algorithm that would take a CT scan of a fossil while still in the rock,
> and attempt to find the placement of that fossil within the evolutionary
> tree based on common attributes. In this case, the age of the fossil
> would either be ignored or considered one attribute among many.
I don't think you could write such a program. But if you could have a
> On 9/6/22 21:53, Peter Nyikos wrote:
>> The line segment joining successive elements is given a number
estimating degree of disparity,
>> and the numbers are added together to compute the length of the path
between them.
>>
>
> This was correct because I was trying to write a computer program or
> algorithm that would take a CT scan of a fossil while still in the rock,
> and attempt to find the placement of that fossil within the evolutionary
> tree based on common attributes. In this case, the age of the fossil
> would either be ignored or considered one attribute among many.
human being look at the scan and derive character descriptions from it,
then you could use an existing phylogenetic algorithm to find the placement.
> So the fundamental question is can two species, a billion years
> separated, be closely related, or how closely related and how do we
> define relatedness.
are any vertebrates. But I don't think that's a real question anyway.
> Ideally, we know two individuals are closely
> related because they share genetic material. But I don't even know what
> that means and admittedly, I know less now than I did 20 years ago as an
> undergrad. The older I get, the stupider I become.
>
> Two siblings, in theory, share about 33%-50% +- random variation, of
> their genetic material, since they have the same parents. It is
> possible, although HIGHLY unlikely, that they share zero DNA. Or they
> are some form of a twin and share 100% of their DNA.
peaked. Identical twins share 100%, but fraternal twins are like any
other siblings.
> Fine. Now Random Chimps and Humans seem to have a closer relationship
> than siblings. They share 98.6% of their DNA, or so I see reported? So
> in the context of siblings, I am not at all sure what that means.
human and any chimp share 0% of their DNA. Using the second, siblings
share around 99.95% of their DNA.
> Aside from that, we don't have genetic material for most species. All
> we have is a fraction of skeletal material or a soft tissue imprint.
>
> So for evidence we have
> A) incomplete phenotyped characteristics
> B) an imperfect time line or age of a fossil
>
> And that is it.
>
> The tools we have to analyze this include a few algorithms and to attach
> your ego to any of them, given the limits of the data, is a colossal
> error, IMO. Every way we analyze something gives us a different window
> to view our specimens and their relationships to each other. These
> algorithms themselves are grounded into a few evolving sciences and
> mathematics which includes the study of Genetics, Geography, Cosmetology
> and Astronomy, Biological computational statistics, and more to name
a few.
> And then we have the problem with definitions and the understanding of
> concepts. Sometimes one has to step back and ask, what exactly am I
> trying to learn here?
>
> Are two species closely related despite 300 million years of evolution
> if they genetics have been largely conserved other that time? There is
> a molecular clock but the functional expression of genes might well be
> well preserved in two species separated by by a long period of time.
> Hydrothermal vent microbial organism might be more closely related to
> their ancient ancestors from a billion years ago than a Moerithriun to
> an African Elephant, let alone an Asian Elephant to most species in
> Paenungulata. It is suggested that a Hyrax is more basal and an African
> elephant, and I would ask, "how so since they are both existing species
> and Elephants didn't spring from a modern Hyrax".
without having a false idea. I try to avoid it myself.
> So the language itself, here, gets very ambiguous which fuels
> disagreements and trolls alike.
>
> And added to this amphibological language a new problem seems to have
> emerged recently with core elements of evolutionary theory. It has been
> a conceit that a species evolves traits to conform with its environment
> through natural selection. Therefor, in theory at least, any individual
> could prove to be a node to a new species if they have a mutation that
> gives its linage an advantage.
(except for the rare case of polyploid speciation).
> There has been shown to be a HUGE
> conceit as we have learned from the study of the evolution of Homo and
> other species. It has come to be understood that mutations that give
> advantages can and do spring up multiple times, even among closely
> related species... the same mutation. And then we share DNA material
> outside of reproduction.
> And then mutation will fade if unneeded and
> spring up again. Instead of a nice tree, evolution might well look more
> like a river delta. Or a suppressed shared gene might become active in
> two different lineages, or two species might interbreed?
>
> Everything wants to become a crab...
>
>
> None of the above is my own original ideas. They all come from reading
> scientific literature both in the popular press and in peer reviewed
> journals.
> So are all Ceratopsidae from the same common ancestor? Maybe, likely,
> not definitely.
an individual.
> The last common ancestor of Pachyrhinosaurus... that might be true. But
> as we get more evidence of this transition, we might find that more than
> once species of closely related dinosaurs evolved similarly, utilizing
> similar mutations. Finding a Least common ancestor might be unknowable.
> But that might not make this method of defining families and orders and
> genus, any less useful. We need to use some definition.
>
>
> No maybe all these ambiguities have been solved in Paleontology, I
> don't know. But I do know that over my lifetime many streams of thought
> within the science has come and gone and evolved. I wouldn't take a
> theological attachment to any system for the analysis of the
> evolutionary procession of species. Nature tends to surprise us and
> these are all just tools of logic to help us understand the ancient past
> and the nature of biological systems.
>
>> The concept of "more closely related" then could be given a whole
new meaning --
>> or, rather, an old meaning but now quantified. We would be able to
say that vertebrate A
>> in the following example is MUCH more closely related to B than it
is to C even though
>> the LCA of A and B is strictly ancestral to the LCA of B and C.
>
> I have no idea what this means, FWIW.
here. But he's just saying that two species are more closely related if
the total branch length separating them is shorter than the total branch
length separating either of them from a third. It's a definition of
"more closely related", and it's opposed to the cladistic definition:
more recent common ancestor.
John Harshman
Sep 11, 2022, 12:00:44 AM9/11/22
to
On 9/10/22 6:39 PM, Popping Mad wrote:
> On 9/8/22 15:04, John Harshman wrote:
>>
>> But that all becomes useless once you try to use it for anything except
>> pairwise comparisons.
>
> There are hundreds of algorithms that prove this to be untrue.
> Sankoff's algorthim on genetic mutation is an example.
Explain.
> On 9/8/22 15:04, John Harshman wrote:
>>
>> But that all becomes useless once you try to use it for anything except
>> pairwise comparisons.
>
> There are hundreds of algorithms that prove this to be untrue.
> Sankoff's algorthim on genetic mutation is an example.
> And, BTW, much of the disagreement you are having is a matter of vector
> distance versus non-vector distance.... that is if you even get an
> agreement on the definition of "related"...which you do not have.
John Harshman
Sep 11, 2022, 12:02:16 AM9/11/22
to
John Harshman
Sep 11, 2022, 12:02:44 AM9/11/22
to
John Harshman
Sep 11, 2022, 12:05:01 AM9/11/22
to
On 9/10/22 6:57 PM, Popping Mad wrote:
> On 9/10/22 17:49, John Harshman wrote:
>>>> he heart of cladistics is found in the phylogenetic trees, which put all
>>>> organisms at the branch tips.
>>>
>>> nodes not tips
>>
>> "Branch tips" here refers to terminal nodes.
>> So the claim is true.
>
>
> No - it is not. Species are not branch tips but nodes. Tips are a
> sub-set of nodes, as they are terminal nodes.
Species, known species, are all terminal nodes. You can't identify
> On 9/10/22 17:49, John Harshman wrote:
>>>> he heart of cladistics is found in the phylogenetic trees, which put all
>>>> organisms at the branch tips.
>>>
>>> nodes not tips
>>
>> "Branch tips" here refers to terminal nodes.
>> So the claim is true.
>
>
> No - it is not. Species are not branch tips but nodes. Tips are a
> sub-set of nodes, as they are terminal nodes.
fossils with internal nodes; there's just no way to do that.
> Are we failing basic set theory now?
>
> In theory at lest...
>
> All Species are NODES
> Some Species are Terminal Nodes
> All Species are NOT terminal Nodes, as most are just nodes.
not the way phylogenetic trees work, because we have no way of
identifying species as ancestral.
John Harshman
Sep 11, 2022, 12:07:10 AM9/11/22
to
On 9/10/22 5:18 PM, Popping Mad wrote:
> On 9/6/22 21:53, Peter Nyikos wrote:
>> The line segment joining successive elements is given a number
estimating degree of disparity,
>> and the numbers are added together to compute the length of the path
between them.
>>
>
> This was correct because I was trying to write a computer program or
> algorithm that would take a CT scan of a fossil while still in the rock,
> and attempt to find the placement of that fossil within the evolutionary
> tree based on common attributes. In this case, the age of the fossil
> would either be ignored or considered one attribute among many.
>> The line segment joining successive elements is given a number
estimating degree of disparity,
>> and the numbers are added together to compute the length of the path
between them.
>>
>
> This was correct because I was trying to write a computer program or
> algorithm that would take a CT scan of a fossil while still in the rock,
> and attempt to find the placement of that fossil within the evolutionary
> tree based on common attributes. In this case, the age of the fossil
> would either be ignored or considered one attribute among many.
I don't think you could write such a program. But if you could have a
human being look at the scan and derive character descriptions from it,
then you could use an existing phylogenetic algorithm to find the placement.
human being look at the scan and derive character descriptions from it,
then you could use an existing phylogenetic algorithm to find the placement.
> So the fundamental question is can two species, a billion years
> separated, be closely related, or how closely related and how do we
> define relatedness.
> separated, be closely related, or how closely related and how do we
> define relatedness.
Let's just say 250 million years; a billion years puts us before there
are any vertebrates. But I don't think that's a real question anyway.
are any vertebrates. But I don't think that's a real question anyway.
> Ideally, we know two individuals are closely
> related because they share genetic material. But I don't even know what
> that means and admittedly, I know less now than I did 20 years ago as an
> undergrad. The older I get, the stupider I become.
>
> Two siblings, in theory, share about 33%-50% +- random variation, of
> their genetic material, since they have the same parents. It is
> possible, although HIGHLY unlikely, that they share zero DNA. Or they
> are some form of a twin and share 100% of their DNA.
> related because they share genetic material. But I don't even know what
> that means and admittedly, I know less now than I did 20 years ago as an
> undergrad. The older I get, the stupider I become.
>
> Two siblings, in theory, share about 33%-50% +- random variation, of
> their genetic material, since they have the same parents. It is
> possible, although HIGHLY unlikely, that they share zero DNA. Or they
> are some form of a twin and share 100% of their DNA.
No, siblings share almost exactly 50%. The distribution is very sharply
peaked. Identical twins share 100%, but fraternal twins are like any
other siblings.
peaked. Identical twins share 100%, but fraternal twins are like any
other siblings.
> Fine. Now Random Chimps and Humans seem to have a closer relationship
> than siblings. They share 98.6% of their DNA, or so I see reported? So
> in the context of siblings, I am not at all sure what that means.
> than siblings. They share 98.6% of their DNA, or so I see reported? So
> in the context of siblings, I am not at all sure what that means.
Those are two incommensurable measures. Using your first measure, any
human and any chimp share 0% of their DNA. Using the second, siblings
share around 99.95% of their DNA.
human and any chimp share 0% of their DNA. Using the second, siblings
share around 99.95% of their DNA.
> Aside from that, we don't have genetic material for most species. All
> we have is a fraction of skeletal material or a soft tissue imprint.
>
> So for evidence we have
> A) incomplete phenotyped characteristics
> B) an imperfect time line or age of a fossil
>
> And that is it.
>
> The tools we have to analyze this include a few algorithms and to attach
> your ego to any of them, given the limits of the data, is a colossal
> error, IMO. Every way we analyze something gives us a different window
> to view our specimens and their relationships to each other. These
> algorithms themselves are grounded into a few evolving sciences and
> mathematics which includes the study of Genetics, Geography, Cosmetology
> and Astronomy, Biological computational statistics, and more to name
a few.
> we have is a fraction of skeletal material or a soft tissue imprint.
>
> So for evidence we have
> A) incomplete phenotyped characteristics
> B) an imperfect time line or age of a fossil
>
> And that is it.
>
> The tools we have to analyze this include a few algorithms and to attach
> your ego to any of them, given the limits of the data, is a colossal
> error, IMO. Every way we analyze something gives us a different window
> to view our specimens and their relationships to each other. These
> algorithms themselves are grounded into a few evolving sciences and
> mathematics which includes the study of Genetics, Geography, Cosmetology
> and Astronomy, Biological computational statistics, and more to name
a few.
I'm going to assume you didn't mean Cosmetology. Autocorrect?
> And then we have the problem with definitions and the understanding of
> concepts. Sometimes one has to step back and ask, what exactly am I
> trying to learn here?
>
> Are two species closely related despite 300 million years of evolution
> if they genetics have been largely conserved other that time? There is
> a molecular clock but the functional expression of genes might well be
> well preserved in two species separated by by a long period of time.
> Hydrothermal vent microbial organism might be more closely related to
> their ancient ancestors from a billion years ago than a Moerithriun to
> an African Elephant, let alone an Asian Elephant to most species in
> Paenungulata. It is suggested that a Hyrax is more basal and an African
> elephant, and I would ask, "how so since they are both existing species
> and Elephants didn't spring from a modern Hyrax".
> concepts. Sometimes one has to step back and ask, what exactly am I
> trying to learn here?
>
> Are two species closely related despite 300 million years of evolution
> if they genetics have been largely conserved other that time? There is
> a molecular clock but the functional expression of genes might well be
> well preserved in two species separated by by a long period of time.
> Hydrothermal vent microbial organism might be more closely related to
> their ancient ancestors from a billion years ago than a Moerithriun to
> an African Elephant, let alone an Asian Elephant to most species in
> Paenungulata. It is suggested that a Hyrax is more basal and an African
> elephant, and I would ask, "how so since they are both existing species
> and Elephants didn't spring from a modern Hyrax".
The problem there lies with the use of "basal". It's hard to use it
without having a false idea. I try to avoid it myself.
without having a false idea. I try to avoid it myself.
> So the language itself, here, gets very ambiguous which fuels
> disagreements and trolls alike.
>
> And added to this amphibological language a new problem seems to have
> emerged recently with core elements of evolutionary theory. It has been
> a conceit that a species evolves traits to conform with its environment
> through natural selection. Therefor, in theory at least, any individual
> could prove to be a node to a new species if they have a mutation that
> gives its linage an advantage.
> disagreements and trolls alike.
>
> And added to this amphibological language a new problem seems to have
> emerged recently with core elements of evolutionary theory. It has been
> a conceit that a species evolves traits to conform with its environment
> through natural selection. Therefor, in theory at least, any individual
> could prove to be a node to a new species if they have a mutation that
> gives its linage an advantage.
This is nobody's theory. Individuals do not give rise to new species
(except for the rare case of polyploid speciation).
(except for the rare case of polyploid speciation).
> There has been shown to be a HUGE
> conceit as we have learned from the study of the evolution of Homo and
> other species. It has come to be understood that mutations that give
> advantages can and do spring up multiple times, even among closely
> related species... the same mutation. And then we share DNA material
> outside of reproduction.
Beg pardon?
> conceit as we have learned from the study of the evolution of Homo and
> other species. It has come to be understood that mutations that give
> advantages can and do spring up multiple times, even among closely
> related species... the same mutation. And then we share DNA material
> outside of reproduction.
> And then mutation will fade if unneeded and
> spring up again. Instead of a nice tree, evolution might well look more
> like a river delta. Or a suppressed shared gene might become active in
> two different lineages, or two species might interbreed?
>
> Everything wants to become a crab...
>
>
> None of the above is my own original ideas. They all come from reading
> scientific literature both in the popular press and in peer reviewed
> journals.
I think you may be reading the wrong scientific literature here.
> So are all Ceratopsidae from the same common ancestor? Maybe, likely,
> not definitely.
> not definitely.
Pretty sure they are, though the common ancestor would be a species, not
an individual.
an individual.
> The last common ancestor of Pachyrhinosaurus... that might be true. But
> as we get more evidence of this transition, we might find that more than
> once species of closely related dinosaurs evolved similarly, utilizing
> similar mutations. Finding a Least common ancestor might be unknowable.
> But that might not make this method of defining families and orders and
> genus, any less useful. We need to use some definition.
>
>
> No maybe all these ambiguities have been solved in Paleontology, I
> don't know. But I do know that over my lifetime many streams of thought
> within the science has come and gone and evolved. I wouldn't take a
> theological attachment to any system for the analysis of the
> evolutionary procession of species. Nature tends to surprise us and
> these are all just tools of logic to help us understand the ancient past
> and the nature of biological systems.
>
>> The concept of "more closely related" then could be given a whole
new meaning --
>> or, rather, an old meaning but now quantified. We would be able to
say that vertebrate A
>> in the following example is MUCH more closely related to B than it
is to C even though
>> the LCA of A and B is strictly ancestral to the LCA of B and C.
>
> I have no idea what this means, FWIW.
> as we get more evidence of this transition, we might find that more than
> once species of closely related dinosaurs evolved similarly, utilizing
> similar mutations. Finding a Least common ancestor might be unknowable.
> But that might not make this method of defining families and orders and
> genus, any less useful. We need to use some definition.
>
>
> No maybe all these ambiguities have been solved in Paleontology, I
> don't know. But I do know that over my lifetime many streams of thought
> within the science has come and gone and evolved. I wouldn't take a
> theological attachment to any system for the analysis of the
> evolutionary procession of species. Nature tends to surprise us and
> these are all just tools of logic to help us understand the ancient past
> and the nature of biological systems.
>
>> The concept of "more closely related" then could be given a whole
new meaning --
>> or, rather, an old meaning but now quantified. We would be able to
say that vertebrate A
>> in the following example is MUCH more closely related to B than it
is to C even though
>> the LCA of A and B is strictly ancestral to the LCA of B and C.
>
> I have no idea what this means, FWIW.
Glenn
Sep 11, 2022, 1:11:03 AM9/11/22
to
But what about asexual species?
> > There has been shown to be a HUGE
> > conceit as we have learned from the study of the evolution of Homo and
> > other species. It has come to be understood that mutations that give
> > advantages can and do spring up multiple times, even among closely
> > related species... the same mutation. And then we share DNA material
> > outside of reproduction.
> Beg pardon?
> > And then mutation will fade if unneeded and
> > spring up again. Instead of a nice tree, evolution might well look more
> > like a river delta. Or a suppressed shared gene might become active in
> > two different lineages, or two species might interbreed?
> >
> > Everything wants to become a crab...
> >
> >
> > None of the above is my own original ideas. They all come from reading
> > scientific literature both in the popular press and in peer reviewed
> > journals.
> I think you may be reading the wrong scientific literature here.
> > So are all Ceratopsidae from the same common ancestor? Maybe, likely,
> > not definitely.
> Pretty sure they are, though the common ancestor would be a species, not
> an individual.
It always takes two to tango, sexually speaking. So clearly an individual that sexually reproduces could not create a new species. But hypothetically, you could have a mutation that would only allow you to have a child with another that had the same mutation.
> > conceit as we have learned from the study of the evolution of Homo and
> > other species. It has come to be understood that mutations that give
> > advantages can and do spring up multiple times, even among closely
> > related species... the same mutation. And then we share DNA material
> > outside of reproduction.
> Beg pardon?
> > And then mutation will fade if unneeded and
> > spring up again. Instead of a nice tree, evolution might well look more
> > like a river delta. Or a suppressed shared gene might become active in
> > two different lineages, or two species might interbreed?
> >
> > Everything wants to become a crab...
> >
> >
> > None of the above is my own original ideas. They all come from reading
> > scientific literature both in the popular press and in peer reviewed
> > journals.
> I think you may be reading the wrong scientific literature here.
> > So are all Ceratopsidae from the same common ancestor? Maybe, likely,
> > not definitely.
> Pretty sure they are, though the common ancestor would be a species, not
> an individual.
Get together and walla, a barrier is born. In that sense, individuals can create new species.
jillery
Sep 11, 2022, 2:48:13 AM9/11/22
to
On Fri, 9 Sep 2022 17:55:58 -0700, John Harshman
<john.h...@gmail.com> wrote:
>On 9/9/22 4:40 PM, Peter Nyikos wrote:
>> This is a change of pace: A lighthearted (for me, anyway) treatment of John's reaction to a PS
>> of mine at the end of a reply he did to me here:
>>
>> On Wednesday, September 7, 2022 at 12:18:55 AM UTC-4, John Harshman wrote:
>>
>>> On 9/6/22 6:53 PM, Peter Nyikos wrote:
>>
>>>> PS Remember those little children who thought it was "way cool"
>>>> that birds are dinosaurs? Do you think you [can] get them to believe
>>>> that your concept is better than the one with which they
>>>> are familiar (aunts, uncles, cousins, etc.) and which the disparity-measurer's
>>>> concept so faithfully mirrors?
>>
>>> I doubt children of that age would have a clue about this controversy.
>>> But they would probably believe my concept was better if they liked me
>>> or if I gave them candy.
>>
>> That depends on whether you invite me twice to talk to them.
>> The first time, I would try to establish rapport with them by talking about
>> some neat things that occurred on a pair of fossil hunts in Wyoming on which
>> I participated a little over a year ago.
>>
>> The second time, I would get around to asking them if any of them
>> had one or more great-grandparents still alive, after matching any
>> candy bribe of yours. If it's a class of ten or more, there is an excellent chance
>> that at least one hand would go up, because nowadays a goodly
>> fraction of people live to that age.
>>
>> With twenty, there might arise a longish bidding as to how many were still alive.
>> Once that had settled down, I would ask them whether any of those great-grandparents
>> had any brothers or sisters. And if any hands are raised [some might not know the answers]
>> I would ask the raisers whether they had any brothers or sisters.
>>
>> If yes, I would turn to one of them and say,
>>
>> Did you know that Dr. John's [or whatever they call you] way saying how different kinds of
>> animals are related is like him saying, "Your great-grandmother is more closely related
>> to your brother than she is to her own brother."
>>
>> Once this has sunk in and the expressions of astonishment subsided,
>> I will say, "Now Dr. John will explain to you why this is the best way
>> to talk about how different kinds of animals are related."
>>
>> My suggestion for you to save face is to begin by saying that we use the
>> same words for very different things. The one that comes to mind
>> is "pipe". You could make a little joke about the absent-minded
>> professor who tried to smoke a pipe that gas runs through,
>> and to run water through the pipe that he smokes. But you could
>> probably do better than that, given all this lead time.
>>
>>
>> And then, you could explain that the expression "more closely related"
>> works the same way.
>>
>> But you'd still have a big problem explaining why it is the RIGHT
>> meaning for dealing with animal species.
>
>All I can say is that you would be ill-advised to quite your day job.
Perhaps PeeWee Peter could use this on his night job:
Two men are walking along, when a very noisy car goes by.
Man A says, "That's so loud, I can't hear myself think."
Man B says, "That's my sister's car. She blew the exhaust pipe."
Man A says, "I'm surprised she didn't burn her lips."
<john.h...@gmail.com> wrote:
>On 9/9/22 4:40 PM, Peter Nyikos wrote:
>> This is a change of pace: A lighthearted (for me, anyway) treatment of John's reaction to a PS
>> of mine at the end of a reply he did to me here:
>>
>> On Wednesday, September 7, 2022 at 12:18:55 AM UTC-4, John Harshman wrote:
>>
>>> On 9/6/22 6:53 PM, Peter Nyikos wrote:
>>
>>>> PS Remember those little children who thought it was "way cool"
>>>> that birds are dinosaurs? Do you think you [can] get them to believe
>>>> that your concept is better than the one with which they
>>>> are familiar (aunts, uncles, cousins, etc.) and which the disparity-measurer's
>>>> concept so faithfully mirrors?
>>
>>> I doubt children of that age would have a clue about this controversy.
>>> But they would probably believe my concept was better if they liked me
>>> or if I gave them candy.
>>
>> That depends on whether you invite me twice to talk to them.
>> The first time, I would try to establish rapport with them by talking about
>> some neat things that occurred on a pair of fossil hunts in Wyoming on which
>> I participated a little over a year ago.
>>
>> The second time, I would get around to asking them if any of them
>> had one or more great-grandparents still alive, after matching any
>> candy bribe of yours. If it's a class of ten or more, there is an excellent chance
>> that at least one hand would go up, because nowadays a goodly
>> fraction of people live to that age.
>>
>> With twenty, there might arise a longish bidding as to how many were still alive.
>> Once that had settled down, I would ask them whether any of those great-grandparents
>> had any brothers or sisters. And if any hands are raised [some might not know the answers]
>> I would ask the raisers whether they had any brothers or sisters.
>>
>> If yes, I would turn to one of them and say,
>>
>> Did you know that Dr. John's [or whatever they call you] way saying how different kinds of
>> animals are related is like him saying, "Your great-grandmother is more closely related
>> to your brother than she is to her own brother."
>>
>> Once this has sunk in and the expressions of astonishment subsided,
>> I will say, "Now Dr. John will explain to you why this is the best way
>> to talk about how different kinds of animals are related."
>>
>> My suggestion for you to save face is to begin by saying that we use the
>> same words for very different things. The one that comes to mind
>> is "pipe". You could make a little joke about the absent-minded
>> professor who tried to smoke a pipe that gas runs through,
>> and to run water through the pipe that he smokes. But you could
>> probably do better than that, given all this lead time.
>>
>>
>> And then, you could explain that the expression "more closely related"
>> works the same way.
>>
>> But you'd still have a big problem explaining why it is the RIGHT
>> meaning for dealing with animal species.
>
>All I can say is that you would be ill-advised to quite your day job.
Perhaps PeeWee Peter could use this on his night job:
Two men are walking along, when a very noisy car goes by.
Man A says, "That's so loud, I can't hear myself think."
Man B says, "That's my sister's car. She blew the exhaust pipe."
Man A says, "I'm surprised she didn't burn her lips."
Popping Mad
Sep 11, 2022, 6:56:34 PM9/11/22
to
On 9/11/22 00:07, John Harshman wrote:
> I don't think you could write such a program. But if you could have a
> human being look at the scan and derive character descriptions from it,
> then you could use an existing phylogenetic algorithm to find the
> placement.
Sure you can. It can write the enitire graph independently. Code
> I don't think you could write such a program. But if you could have a
> human being look at the scan and derive character descriptions from it,
> then you could use an existing phylogenetic algorithm to find the
> placement.
already does much of this and is commonly quoted in paleontology.
Reading the CTSCAN is the hardest part.
Writing these trees can be done without human biases and it is done so
in other areas of biological calculations in virus identification,
ecocological and epidemlogical studies etc. It is all the same
mathmatics involving distance graphing alorithms and
Markovian statistics, Baysian Statistics and
Gaussian Distribution Functions and statsitics.
Popping Mad
Sep 11, 2022, 6:59:27 PM9/11/22
to
On 9/11/22 01:11, Glenn wrote:
> So clearly an individual that sexually reproduces could not create a new species.
sure it can and it does.
> So clearly an individual that sexually reproduces could not create a new species.
Glenn
Sep 11, 2022, 7:18:19 PM9/11/22
to
Glenn
Sep 11, 2022, 7:23:48 PM9/11/22
to
John Harshman
Sep 11, 2022, 10:07:08 PM9/11/22
to
scenario is so unlikely that is probably has never happened, not even
once. So it seems useless to include it in any requirement for speciation.
John Harshman
Sep 11, 2022, 10:09:07 PM9/11/22
to
On 9/11/22 3:55 PM, Popping Mad wrote:
> On 9/11/22 00:07, John Harshman wrote:
>> I don't think you could write such a program. But if you could have a
>> human being look at the scan and derive character descriptions from it,
>> then you could use an existing phylogenetic algorithm to find the
>> placement.
>
>
> Sure you can. It can write the enitire graph independently. Code
> already does much of this and is commonly quoted in paleontology.
> Reading the CTSCAN is the hardest part.
That's the part I was talking about.
> On 9/11/22 00:07, John Harshman wrote:
>> I don't think you could write such a program. But if you could have a
>> human being look at the scan and derive character descriptions from it,
>> then you could use an existing phylogenetic algorithm to find the
>> placement.
>
>
> Sure you can. It can write the enitire graph independently. Code
> already does much of this and is commonly quoted in paleontology.
> Reading the CTSCAN is the hardest part.
> Writing these trees can be done without human biases and it is done so
> in other areas of biological calculations in virus identification,
> ecocological and epidemlogical studies etc. It is all the same
> mathmatics involving distance graphing alorithms and
> Markovian statistics, Baysian Statistics and
> Gaussian Distribution Functions and statsitics.
>
why do you need to reinvent what already exists? Only the CT scan
interpretation is new, and that's the part I don't think can be done.
Glenn
Sep 11, 2022, 11:53:03 PM9/11/22
to
I'm reminded of punctuated equilibrium. Speciation in a blink of the eye. Why do you insist that such a thing is unlikely?
But no, two individuals do not make a population, and I bet you are aware of that, as you are likely aware of your own claim, "Individuals do not give rise to new species
(except for the rare case of polyploid speciation)."
Will you now argue that an individual can be a population?
Seems it is useless as you do to claim that evolution does not require mutation.
Have you considered that your claims are useless?
Popping Mad
Sep 12, 2022, 12:05:14 AM9/12/22
to
On 9/11/22 23:53, Glenn wrote:
> However unlikely is irrelevant, nor do you provide any evidence to support your "probably".
You really need to get a basic educaiton on Biology before slashing at
> However unlikely is irrelevant, nor do you provide any evidence to support your "probably".
people.
John Harshman
Sep 12, 2022, 12:05:57 AM9/12/22
to
Eldredge N., Gould S.J. Punctuated equilibria: an alternative to
phyletic gradualism. In: Schopf T.J.M. editor. Models of Paleobiology,
1972. p. 82-115.
> But no, two individuals do not make a population, and I bet you are aware of that, as you are likely aware of your own claim, "Individuals do not give rise to new species
> (except for the rare case of polyploid speciation)."
> Will you now argue that an individual can be a population?
> Seems it is useless as you do to claim that evolution does not require mutation.
> Have you considered that your claims are useless?
you strongly desire not to?
Popping Mad
Sep 12, 2022, 12:14:11 AM9/12/22
to
On 9/11/22 22:09, John Harshman wrote:
>
> That's the part I was talking about.
>
>> Writing these trees can be done without human biases and it is done so
>> in other areas of biological calculations in virus identification,
>> ecocological and epidemlogical studies etc. It is all the same
>> mathmatics involving distance graphing alorithms and
>> Markovian statistics, Baysian Statistics and
>> Gaussian Distribution Functions and statsitics.
>>
> You understand that existing phylogeny programs work just that way. So
> why do you need to reinvent what already exists? Only the CT scan
> interpretation is new, and that's the part I don't think can be done.
There are a number of reasons. I think that more computer scientists
>
> That's the part I was talking about.
>
>> Writing these trees can be done without human biases and it is done so
>> in other areas of biological calculations in virus identification,
>> ecocological and epidemlogical studies etc. It is all the same
>> mathmatics involving distance graphing alorithms and
>> Markovian statistics, Baysian Statistics and
>> Gaussian Distribution Functions and statsitics.
>>
> You understand that existing phylogeny programs work just that way. So
> why do you need to reinvent what already exists? Only the CT scan
> interpretation is new, and that's the part I don't think can be done.
need to work on these problems directly because current theories and
procedures, I believe, lack the rigor that is applied in Medicine, for
example. And they haven't yet gone the full mile, from rocks to
analysis, which I think is technologically possible today, if not yesterday.
Aside from the raw size of these specimens, I see no reason why a fozzil
can't be scaned and identified with a report of findings and speculation
of species or where a specimen is cladistically based on phenology and
geological facts.
Popping Mad
Sep 12, 2022, 12:18:28 AM9/12/22
to
On 9/11/22 00:02, John Harshman wrote:
>>
>> Sure terminal nodes like in the RB-Tree used in the Linux scheduler.
>
> Wouldn't know, since I don't know what that is.
and that is, boardly speaking, is the problem. Folks make graphs and
>>
>> Sure terminal nodes like in the RB-Tree used in the Linux scheduler.
>
> Wouldn't know, since I don't know what that is.
trees to make mathmatical models that they don't even understand, and
then argue endlessly about how many angles live on the tip of a needle.
It is rare, in such model building, that a single method is the only
useful one and understanding how modles work is essential to gaging
usefullness of their information.
Glenn
Sep 12, 2022, 12:23:01 AM9/12/22
to
Popping Mad
Sep 12, 2022, 12:27:08 AM9/12/22
to
On 9/11/22 00:04, John Harshman wrote:
> Species, known species, are all terminal nodes.
No they are not. They are definetely NOT. That would be a broken model
> Species, known species, are all terminal nodes.
and defies linear decent.
Only species that are living today or gone exinct without ancentors are
terminal nodes.
In theory, your ancecentors form an unbroken chain of life forms,
chaining from species to species, backwards through evolution, each one
being a non-terminal node, back to the LCA of all life, if such a thing
exists. If you have been under the assuption that each species is a
terminal node, you have been working under a huge misunderstanding of
the model, and what branched trees represent.
Popping Mad
Sep 12, 2022, 12:30:52 AM9/12/22
to
On 9/11/22 00:04, John Harshman wrote:
>> All Species are NODES
>> Some Species are Terminal Nodes
>
> That isn't the theory.
yeah - that is wrong, flatly. This is exactly why more computer
>> Some Species are Terminal Nodes
>
> That isn't the theory.
scientists and mathamticians need to get involved.
Glenn
Sep 12, 2022, 12:35:25 AM9/12/22
to
> > But no, two individuals do not make a population, and I bet you are aware of that, as you are likely aware of your own claim, "Individuals do not give rise to new species
> > (except for the rare case of polyploid speciation)."
> Yep.
Yep what? You just supported the claim that speciation does not require populations, and can occur with an individual, which is contrary to your previous claim.
> > (except for the rare case of polyploid speciation)."
> Yep.
> > Will you now argue that an individual can be a population?
> > Seems it is useless as you do to claim that evolution does not require mutation.
> > Have you considered that your claims are useless?
> Have you considered the possibility that you don't understand because
> you strongly desire not to?
Popping Mad
Sep 12, 2022, 12:41:15 AM9/12/22
to
On 9/11/22 00:04, John Harshman wrote:
> But that's not the way phylogenetic trees work,
that is how ALL trees work and phylogenics is not an exception.
If you can't identify which species are ancestrial, then there is no
real point to this. Every node in the tree identifies a species, wether
you can't identify that species or not that species existed in the real
world a some such time. Eventually you can, with enough specimens and
data, identify all the nodes. And then you can point to it, this is the
ancestors of all chickens, and it is a non-terminal node. You can then
say, this species lived 30 million years ago with the presumption that
it went excint. ***But that would be scienficially WRONG***. That
species did not go excinct. It evoloved into one or more other species.
John Harshman
Sep 12, 2022, 9:06:48 AM9/12/22
to
On 9/11/22 9:17 PM, Popping Mad wrote:
> On 9/11/22 00:02, John Harshman wrote:
>>>
>>> Sure terminal nodes like in the RB-Tree used in the Linux scheduler.
>>
>> Wouldn't know, since I don't know what that is.
>
>
> and that is, boardly speaking, is the problem. Folks make graphs and
> trees to make mathmatical models that they don't even understand, and
> then argue endlessly about how many angles live on the tip of a needle.
What makes you think I don't understand the models I use? I just don't
> On 9/11/22 00:02, John Harshman wrote:
>>>
>>> Sure terminal nodes like in the RB-Tree used in the Linux scheduler.
>>
>> Wouldn't know, since I don't know what that is.
>
>
> and that is, boardly speaking, is the problem. Folks make graphs and
> trees to make mathmatical models that they don't even understand, and
> then argue endlessly about how many angles live on the tip of a needle.
have any idea what "the RB-Tree used in the Linux scheduler" is. Why
should I?
> It is rare, in such model building, that a single method is the only
> useful one and understanding how modles work is essential to gaging
> usefullness of their information.
agree with your assessment. Your method, as vaguely described, does not
seem useful. What's useful about it?
John Harshman
Sep 12, 2022, 11:23:58 AM9/12/22
to
On 9/11/22 9:40 PM, Popping Mad wrote:
> On 9/11/22 00:04, John Harshman wrote:
>> But that's not the way phylogenetic trees work,
>
>
> that is how ALL trees work and phylogenics is not an exception.
This is why computer scientists and mathematicians should learn more
> On 9/11/22 00:04, John Harshman wrote:
>> But that's not the way phylogenetic trees work,
>
>
> that is how ALL trees work and phylogenics is not an exception.
biology before presuming to revolutionize the field.
> If you can't identify which species are ancestrial, then there is no
> real point to this.
resulting trees can be used for all manner of other things, which you
could easily find in the literature if you looked.
> Every node in the tree identifies a species, wether
> you can't identify that species or not that species existed in the real
> world a some such time.
with known species.
> Eventually you can, with enough specimens and
> data, identify all the nodes.
nodes with actual specimens.
> And then you can point to it, this is the
> ancestors of all chickens, and it is a non-terminal node. You can then
> say, this species lived 30 million years ago with the presumption that
> it went excint. ***But that would be scienficially WRONG***. That
> species did not go excinct. It evoloved into one or more other species.
pseudoextinction from actual extinction using the fossil record. Also,
it's possible, even likely, for a single species to continue for some
time after giving rise to a new species, and then go extinct without
further issue.
Popping Mad
Sep 12, 2022, 9:01:44 PM9/12/22
to
On 9/12/22 09:06, John Harshman wrote:
> What makes you think I don't understand the models I use? I just don't
> have any idea what "the RB-Tree used in the Linux scheduler" is. Why
> should I?
because trees are an area of mathamatics that needs to be studied if you
> What makes you think I don't understand the models I use? I just don't
> have any idea what "the RB-Tree used in the Linux scheduler" is. Why
> should I?
are going to use them. And they have the same properties regardless
what abstraction they are modeling.
Popping Mad
Sep 12, 2022, 9:02:28 PM9/12/22
to
On 9/12/22 11:23, John Harshman wrote:
>
> This is why computer scientists and mathematicians should learn more
> biology before presuming to revolutionize the field.
No - it is the other way and the Mathamatic is now revolutionizing
>
> This is why computer scientists and mathematicians should learn more
> biology before presuming to revolutionize the field.
biology.
Popping Mad
Sep 12, 2022, 9:04:51 PM9/12/22
to
On 9/12/22 11:23, John Harshman wrote:
> Presumably. But my point is that you can't identify the internal nodes
> with known species.
and you can't assume they are edge nodes either. I am trying not to be a
> with known species.
smart alleck or snooty here, but honestly, you really are failing to
understand how silly this sounds.
If all your known species are tips, your model is broken fundementally.
Popping Mad
Sep 12, 2022, 9:05:32 PM9/12/22
to
On 9/12/22 11:23, John Harshman wrote:
> But there's no way to distinguish pseudoextinction from actual
> extinction using the fossil record.
You can if you use the data correctly.
> extinction using the fossil record.
Popping Mad
Sep 12, 2022, 9:12:33 PM9/12/22
to
On 9/12/22 11:23, John Harshman wrote:
> Also, it's possible, even likely, for a single species to continue for
> some time after giving rise to a new species, and then go extinct
> without further issue.
that is very likely a case for many species, but it still remains a
> some time after giving rise to a new species, and then go extinct
> without further issue.
node. A species can have two or three or more branches coming from it.
It is still not an edge node.
John Harshman
Sep 12, 2022, 9:29:22 PM9/12/22
to
Linux scheduler" is. I know how trees work without having any clue about
Linux.
John Harshman
Sep 12, 2022, 9:32:05 PM9/12/22
to
you need to know. And you won't listen to a biologist. Why are you even
here?
Glenn
Sep 12, 2022, 10:09:18 PM9/12/22
to
And it is no wonder why. Perhaps you should learn more about math and computer science before presuming to criticize computer scientists and mathematicians.
Biology isn't necessarily mysterious nor especially complicated to understand, and not much more than "shit happens" with respect to evolutionary theory and it's related subjects.
Why won't I "listen to" a (cough) biologist? Because you and other evolutionists say really stupid things and make really stupid claims, many of which are not anywhere near scientific.
John Harshman
Sep 13, 2022, 6:42:12 PM9/13/22
to
On 9/5/22 12:35 PM, Peter Nyikos wrote:
> On Monday, September 5, 2022 at 2:57:07 PM UTC-4, John Harshman wrote:
>
>> Wait, are you going to introduce Mayr's "evolutionary systematics",
>> which tries to combine cladistic and phenetic approaches? If so, you are
>> being oddly coy in not starting out that way.
>
> From what I've read about it, it didn't use disparity sufficiently well
> to make much of a difference. A number of researchers in various
> fields are trying to work out a measure for disparity now, but
> it is very slow going, because disparity is extraordinarily difficult
> to quantify even under the best of conditions.
>
> That's for my next post.
Your enthusiasm for posting on this subject seems to have, you should
pardon the expression, petered out.
> Here I go with the exposition on the cladist wars.
>
> The only specific event of those wars that I have ever read about (from two different sources,
> one of which I own: Kenneth S. Thompson's LIVING FOSSIL: The Story of the Coelacanth)
> is the 1978 event "the lungfish, the salmon, and the cow". It had to do with the radical
> definition by cladists of the word "related". The phenetic side claimed that it was absurd
> to regard a lungfish to be more closely related to a cow than to a salmon, but that was
> a naive choice of taxa, and the outcome was an undeserved victory for the cladist side.
>
> Had a Romer-savvy vertebrate paleontologist been involved, the choice of taxa could have been very different.
> One choice readily available at that time was "Bos, Ichthyostega, Elpistostege."
> [Nowadays, the third is better replaced by the more familiar Tiktaalik.]
> It does violence to our ordinary idea of human relationships to claim that Ichthyostega
> is more closely related to us human beings than it is to Elpistostege.
> It's almost as bad as saying that Mitochondrial Eve is more closely related to
> everyone alive today than she was to anyone in her family at the time she was born.
>
> Had the victory gone the other way, we might be far advanced in a definition of "more related"
> that combines phylogeny with measures of disparity. As it is, the theory of macroevolution,
> to which disparity is an indispensable tool, has made comparatively little progress to date.
> On Monday, September 5, 2022 at 2:57:07 PM UTC-4, John Harshman wrote:
>
>> Wait, are you going to introduce Mayr's "evolutionary systematics",
>> which tries to combine cladistic and phenetic approaches? If so, you are
>> being oddly coy in not starting out that way.
>
> From what I've read about it, it didn't use disparity sufficiently well
> to make much of a difference. A number of researchers in various
> fields are trying to work out a measure for disparity now, but
> it is very slow going, because disparity is extraordinarily difficult
> to quantify even under the best of conditions.
>
> That's for my next post.
Your enthusiasm for posting on this subject seems to have, you should
pardon the expression, petered out.
> Here I go with the exposition on the cladist wars.
>
> The only specific event of those wars that I have ever read about (from two different sources,
> one of which I own: Kenneth S. Thompson's LIVING FOSSIL: The Story of the Coelacanth)
> is the 1978 event "the lungfish, the salmon, and the cow". It had to do with the radical
> definition by cladists of the word "related". The phenetic side claimed that it was absurd
> to regard a lungfish to be more closely related to a cow than to a salmon, but that was
> a naive choice of taxa, and the outcome was an undeserved victory for the cladist side.
>
> Had a Romer-savvy vertebrate paleontologist been involved, the choice of taxa could have been very different.
> One choice readily available at that time was "Bos, Ichthyostega, Elpistostege."
> [Nowadays, the third is better replaced by the more familiar Tiktaalik.]
> It does violence to our ordinary idea of human relationships to claim that Ichthyostega
> is more closely related to us human beings than it is to Elpistostege.
> It's almost as bad as saying that Mitochondrial Eve is more closely related to
> everyone alive today than she was to anyone in her family at the time she was born.
>
> Had the victory gone the other way, we might be far advanced in a definition of "more related"
> that combines phylogeny with measures of disparity. As it is, the theory of macroevolution,
> to which disparity is an indispensable tool, has made comparatively little progress to date.
Popping Mad
Sep 14, 2022, 9:51:05 AM9/14/22
to
On 9/12/22 21:29, John Harshman wrote:
>
> Studying trees doesn't require me to know what "the RB-Tree used in the
> Linux scheduler"
an RB tree is a specific kind of common tree which just happens to be
>
> Studying trees doesn't require me to know what "the RB-Tree used in the
> Linux scheduler"
used in the scheduler.
https://en.wikipedia.org/wiki/Red%E2%80%93black_tree
Popping Mad
Sep 14, 2022, 9:54:06 AM9/14/22
to
> Your ignorance of biology convinces you
the Pharmacy Degree and I am constantly up to date on the latest in
Biological research
John Harshman
Sep 14, 2022, 11:21:54 AM9/14/22
to
have you been reading?
Peter Nyikos
Sep 22, 2022, 7:02:56 AM9/22/22
to
Sorry to be so late with this, Ruben. I have been on a posting break which was originally slated
to end on Monday. By and large that is still the case, but I've found myself with a bit of
unexpected free time due to a previously scheduled activity being canceled.
I hope you are still reading this thread, because there are some very basic things
you need to know about the phylogeneitic trees by which John Harshman swears.
On Monday, September 12, 2022 at 9:04:51 PM UTC-4, Popping Mad wrote:
> On 9/12/22 11:23, John Harshman wrote:
> > Presumably. But my point is that you can't identify the internal nodes
> > with known species.
> and you can't assume they are edge nodes either. I am trying not to be a
> smart alleck or snooty here, but honestly, you really are failing to
> understand how silly this sounds.
Harshman is thoroughly committed to the reigning orthodoxy in systematics,
which dictates that ALL species be put at branch tips = end nodes.
[It also happens to use "nodes" exclusively for "internal nodes" -- hence your use
of "node" for what he calls "branch tips" is unintelligible to Harshman.]
The traditional evolutionary tree for Equioidea which Kathleen Hunt puts in her excellent
horse FAQ is anathema to Harshman:
http://www.talkorigins.org/faqs/horses/horse_evol.html
In fact, I'm surprised that Harshman hasn't tried to have that FAQ removed and
replaced by one of his liking. As far as he is concerned, the FAQ and especially
the tree is riddled with "lies" by his standards.
Harshman is so adamant about this that he even refuses to agree to the concept of
"prime ancestor candidate" as a designator of species/genera at internal nodes.
By this I mean a species/genus with an essentially complete known skeleton
(albeit distributed among several fossils in most cases) with NO characters
that would bar it from direct ancestry to the next taxon to which it is connected upwards.
> If all your known species are tips, your model is broken fundementally.
I don't know whether Harshman would agree to a compromise such as the following:
modify Hunt's nicely branching tree to a "thorn tree" where all prime ancestor candidates
are connected to the tree by as small a thorn as feasible, with a label of 0 (zero) to indicate
the complete lack of disqualifying characters.
His usual comeback to such proposals is, "I don't see any use for such a thing."
Peter Nyikos
Professor, Dept. of Mathematics
University of So. Carolina -- standard disclaimer--
http://people.math.sc.edu/nyikos
to end on Monday. By and large that is still the case, but I've found myself with a bit of
unexpected free time due to a previously scheduled activity being canceled.
I hope you are still reading this thread, because there are some very basic things
you need to know about the phylogeneitic trees by which John Harshman swears.
On Monday, September 12, 2022 at 9:04:51 PM UTC-4, Popping Mad wrote:
> On 9/12/22 11:23, John Harshman wrote:
> > Presumably. But my point is that you can't identify the internal nodes
> > with known species.
> and you can't assume they are edge nodes either. I am trying not to be a
> smart alleck or snooty here, but honestly, you really are failing to
> understand how silly this sounds.
which dictates that ALL species be put at branch tips = end nodes.
[It also happens to use "nodes" exclusively for "internal nodes" -- hence your use
of "node" for what he calls "branch tips" is unintelligible to Harshman.]
The traditional evolutionary tree for Equioidea which Kathleen Hunt puts in her excellent
horse FAQ is anathema to Harshman:
http://www.talkorigins.org/faqs/horses/horse_evol.html
In fact, I'm surprised that Harshman hasn't tried to have that FAQ removed and
replaced by one of his liking. As far as he is concerned, the FAQ and especially
the tree is riddled with "lies" by his standards.
Harshman is so adamant about this that he even refuses to agree to the concept of
"prime ancestor candidate" as a designator of species/genera at internal nodes.
By this I mean a species/genus with an essentially complete known skeleton
(albeit distributed among several fossils in most cases) with NO characters
that would bar it from direct ancestry to the next taxon to which it is connected upwards.
> If all your known species are tips, your model is broken fundementally.
modify Hunt's nicely branching tree to a "thorn tree" where all prime ancestor candidates
are connected to the tree by as small a thorn as feasible, with a label of 0 (zero) to indicate
the complete lack of disqualifying characters.
His usual comeback to such proposals is, "I don't see any use for such a thing."
Peter Nyikos
Professor, Dept. of Mathematics
University of So. Carolina -- standard disclaimer--
http://people.math.sc.edu/nyikos
Peter Nyikos
Sep 22, 2022, 7:34:06 AM9/22/22
to
On Wednesday, September 14, 2022 at 11:21:54 AM UTC-4, John Harshman wrote:
> On 9/14/22 6:53 AM, Popping Mad wrote:
> >
> >
> >> Your ignorance of biology convinces you
Ruben was merciful to you, John, by deleting your continuation:
> On 9/14/22 6:53 AM, Popping Mad wrote:
> >
> >
> >> Your ignorance of biology convinces you
"... that you know all the biology you need to know.
And you won't listen to a biologist. Why are you even here?"
This reminds me of a statement made by perhaps the greatest amateur
ichthyologist of all time, J. L. B. Smith, who made the living coelacanth
know to the scientific world with a superbly written article in a leading journal:
"Another type of intellectual snobbery is the dictum that science has now passed beyond the understanding of the ordinary man. That, however, is very largely a matter of presentation. With the possible exception of higher mathematics, there is not a single branch of science whose broad outlines the ordinary man cannot appreciate if it is properly explained to him.
--J.L.B. Smith, _The Search Beneath the Sea_, Henry Holt and Company, 1956, p. 44
> > Your talking to the wrong guy. I studied biology for 4 years as part of
> > the Pharmacy Degree and I am constantly up to date on the latest in
> > Biological research
> Perhaps, but you don't see up to date on phylogenetics. What journals
> have you been reading?
is concerned, I told Ruben all he needs to know about phylogenetic trees a few minutes ago.
If you want to tell him how all the software used by you cladists puts every species
that is fed into it at the branch tips, you should be able to tell him yourself; he seems
to know enough about computer programming to understand if you can "properly explain"
how it goes to him.
Finally, if you want him to see the "reasoning" that puts all species at branch tips, you
should either give him a precise reference or try to explain it yourself. But I doubt that
he will impressed by your favorite terms, "objective" and "imaginary taxa" without
you justifying the ameliorative term and the pejorative term in ways to which you are unaccustomed.
Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
Univ. of So. Carolina at Columbia
http://people.math.sc.edu/nyikos
John Harshman
Sep 22, 2022, 9:27:42 AM9/22/22
to
On 9/22/22 4:02 AM, Peter Nyikos wrote:
> Sorry to be so late with this, Ruben. I have been on a posting break which was originally slated
> to end on Monday. By and large that is still the case, but I've found myself with a bit of
> unexpected free time due to a previously scheduled activity being canceled.
>
> I hope you are still reading this thread, because there are some very basic things
> you need to know about the phylogeneitic trees by which John Harshman swears.
>
>
> On Monday, September 12, 2022 at 9:04:51 PM UTC-4, Popping Mad wrote:
>> On 9/12/22 11:23, John Harshman wrote:
>>> Presumably. But my point is that you can't identify the internal nodes
>>> with known species.
>> and you can't assume they are edge nodes either. I am trying not to be a
>> smart alleck or snooty here, but honestly, you really are failing to
>> understand how silly this sounds.
>
> Harshman is thoroughly committed to the reigning orthodoxy in systematics,
> which dictates that ALL species be put at branch tips = end nodes.
>
> [It also happens to use "nodes" exclusively for "internal nodes" -- hence your use
> of "node" for what he calls "branch tips" is unintelligible to Harshman.]
You aren't reading. The term is "terminal node", as opposed to "internal
> Sorry to be so late with this, Ruben. I have been on a posting break which was originally slated
> to end on Monday. By and large that is still the case, but I've found myself with a bit of
> unexpected free time due to a previously scheduled activity being canceled.
>
> I hope you are still reading this thread, because there are some very basic things
> you need to know about the phylogeneitic trees by which John Harshman swears.
>
>
> On Monday, September 12, 2022 at 9:04:51 PM UTC-4, Popping Mad wrote:
>> On 9/12/22 11:23, John Harshman wrote:
>>> Presumably. But my point is that you can't identify the internal nodes
>>> with known species.
>> and you can't assume they are edge nodes either. I am trying not to be a
>> smart alleck or snooty here, but honestly, you really are failing to
>> understand how silly this sounds.
>
> Harshman is thoroughly committed to the reigning orthodoxy in systematics,
> which dictates that ALL species be put at branch tips = end nodes.
>
> [It also happens to use "nodes" exclusively for "internal nodes" -- hence your use
> of "node" for what he calls "branch tips" is unintelligible to Harshman.]
node".
> The traditional evolutionary tree for Equioidea which Kathleen Hunt puts in her excellent
> horse FAQ is anathema to Harshman:
>
> http://www.talkorigins.org/faqs/horses/horse_evol.html
>
> In fact, I'm surprised that Harshman hasn't tried to have that FAQ removed and
> replaced by one of his liking. As far as he is concerned, the FAQ and especially
> the tree is riddled with "lies" by his standards.
>
> Harshman is so adamant about this that he even refuses to agree to the concept of
> "prime ancestor candidate" as a designator of species/genera at internal nodes.
> By this I mean a species/genus with an essentially complete known skeleton
> (albeit distributed among several fossils in most cases) with NO characters
> that would bar it from direct ancestry to the next taxon to which it is connected upwards.
>
>
>> If all your known species are tips, your model is broken fundementally.
>
> I don't know whether Harshman would agree to a compromise such as the following:
> modify Hunt's nicely branching tree to a "thorn tree" where all prime ancestor candidates
> are connected to the tree by as small a thorn as feasible, with a label of 0 (zero) to indicate
> the complete lack of disqualifying characters.
such taxa. No special procedure necessary, as long as a taxon had zero
autapomorphies.
> His usual comeback to such proposals is, "I don't see any use for such a thing."
Peter Nyikos
Sep 22, 2022, 12:36:27 PM9/22/22
to
On Thursday, September 22, 2022 at 9:27:42 AM UTC-4, John Harshman wrote:
> On 9/22/22 4:02 AM, Peter Nyikos wrote:
> > Sorry to be so late with this, Ruben. I have been on a posting break which was originally slated
> > to end on Monday. By and large that is still the case, but I've found myself with a bit of
> > unexpected free time due to a previously scheduled activity being canceled.
Now a tiny window has opened between successive activities, just long enough
> On 9/22/22 4:02 AM, Peter Nyikos wrote:
> > Sorry to be so late with this, Ruben. I have been on a posting break which was originally slated
> > to end on Monday. By and large that is still the case, but I've found myself with a bit of
> > unexpected free time due to a previously scheduled activity being canceled.
to post this and maybe another short post.
> >
> > I hope you are still reading this thread, because there are some very basic things
> > you need to know about the phylogeneitic trees by which John Harshman swears.
> >
> > On Monday, September 12, 2022 at 9:04:51 PM UTC-4, Popping Mad wrote:
> >> On 9/12/22 11:23, John Harshman wrote:
> >>> Presumably. But my point is that you can't identify the internal nodes
> >>> with known species.
> >> and you can't assume they are edge nodes either. I am trying not to be a
> >> smart alleck or snooty here, but honestly, you really are failing to
> >> understand how silly this sounds.
> >
> > Harshman is thoroughly committed to the reigning orthodoxy in systematics,
> > which dictates that ALL species be put at branch tips = end nodes.
> >
> > [It also happens to use "nodes" exclusively for "internal nodes" -- hence your use
> > of "node" for what he calls "branch tips" is unintelligible to Harshman.]
> You aren't reading. The term is "terminal node", as opposed to "internal
> node".
"The extreme rarity of transitional forms in the fossil record persist as the trade secret of paleontology. The evolutionary trees that adorn our textbooks have data only at the tips and nodes of their branches; the rest is inference, however reasonable, not the evidence of fossils."
--Stephen J. Gould - "Evolution's Erratic Pace," _Natural History_,vol. 86(5) (May 1987): pp. 12-16, at p. 14 Reprinted in _The Panda's Thumb_, pp. 181-182.
Note, tips AND nodes. Granted, this was before the orthodoxy started to reign
in earnest on the following year, with the final victory in the cladist wars.
But make no mistake: when Gould wrote the above,
he was writing about "evolutionary trees" and NOT "phylogenetic trees".
IOW, he was writing about trees like that of Kathleen Hunt:
> > The traditional evolutionary tree for Equioidea which Kathleen Hunt puts in her excellent
> > horse FAQ is anathema to Harshman:
> >
> > http://www.talkorigins.org/faqs/horses/horse_evol.html
> >
> > In fact, I'm surprised that Harshman hasn't tried to have that FAQ removed and
> > replaced by one of his liking. As far as he is concerned, the FAQ and especially
> > the tree is riddled with "lies" by his standards.
numerous times in the FAQ and at all but the branch tips in her *evolutionary* tree?
> > Harshman is so adamant about this that he even refuses to agree to the concept of
> > "prime ancestor candidate" as a designator of species/genera at internal nodes.
> > By this I mean a species/genus with an essentially complete known skeleton
> > (albeit distributed among several fossils in most cases) with NO characters
> > that would bar it from direct ancestry to the next taxon to which it is connected upwards.
> >
> >
> >> If all your known species are tips, your model is broken fundementally.
> >
> > I don't know whether Harshman would agree to a compromise such as the following:
> > modify Hunt's nicely branching tree to a "thorn tree" where all prime ancestor candidates
> > are connected to the tree by as small a thorn as feasible, with a label of 0 (zero) to indicate
> > the complete lack of disqualifying characters.
> This would be the natural result of any usual phylogenetic analysis of
> such taxa.
Or were you referring to trees at all? or only to the character analysis which
almost never specifies the number of apomorphies?
>No special procedure necessary, as long as a taxon had zero
> autapomorphies.
every internal node has at least two branches emanating from it; so it would
be labeling the results of a fictitious cladogenesis.
> > His usual comeback to such proposals is, "I don't see any use for such a thing."
> And you have never been able to explain a use.
paraphrases of the broken record routine that I've quoted just now.
But I will be glad to repeat them if I know that an interested, knowledgeable
party is paying attention, like Ruben.
Btw I never made the "thorn tree" proposal before, so this last retort of yours is misleading.
Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
Univ. of So. Carolina in Columbia
http://people.math.sc.edu/nyikos
Glenn
Sep 22, 2022, 12:53:19 PM9/22/22
to
John Harshman
Sep 22, 2022, 3:27:02 PM9/22/22
to
case. He probably wasn't up on the language used in phylogenetics. On
the other hand, I am.
> But make no mistake: when Gould wrote the above,
> he was writing about "evolutionary trees" and NOT "phylogenetic trees".
> IOW, he was writing about trees like that of Kathleen Hunt:
mean "internal node". What is the relevance?
>>> The traditional evolutionary tree for Equioidea which Kathleen Hunt puts in her excellent
>>> horse FAQ is anathema to Harshman:
>>>
>>> http://www.talkorigins.org/faqs/horses/horse_evol.html
>>>
>>> In fact, I'm surprised that Harshman hasn't tried to have that FAQ removed and
>>> replaced by one of his liking. As far as he is concerned, the FAQ and especially
>>> the tree is riddled with "lies" by his standards.
>
> Do you deny that you have used "lies" and "lying" for exactly what Kathleen Hunt is doing
> numerous times in the FAQ and at all but the branch tips in her *evolutionary* tree?
>>> Harshman is so adamant about this that he even refuses to agree to the concept of
>>> "prime ancestor candidate" as a designator of species/genera at internal nodes.
>>> By this I mean a species/genus with an essentially complete known skeleton
>>> (albeit distributed among several fossils in most cases) with NO characters
>>> that would bar it from direct ancestry to the next taxon to which it is connected upwards.
>>>
>>>
>>>> If all your known species are tips, your model is broken fundementally.
>>>
>>> I don't know whether Harshman would agree to a compromise such as the following:
>>> modify Hunt's nicely branching tree to a "thorn tree" where all prime ancestor candidates
>>> are connected to the tree by as small a thorn as feasible, with a label of 0 (zero) to indicate
>>> the complete lack of disqualifying characters.
>
>> This would be the natural result of any usual phylogenetic analysis of
>> such taxa.
>
> Oh, really? including the part about "thorns" as opposed to longish branches?
> Or were you referring to trees at all? or only to the character analysis which
> almost never specifies the number of apomorphies?
> >No special procedure necessary, as long as a taxon had zero
>> autapomorphies.
>
> Why "autapomorphies"? phylogenetic trees use the legal fiction ("lie"?) that
> every internal node has at least two branches emanating from it; so it would
> be labeling the results of a fictitious cladogenesis.
branch is quite possible. If not that, what are you referring to?
>>> His usual comeback to such proposals is, "I don't see any use for such a thing."
>
>> And you have never been able to explain a use.
>
> There were plenty of careful explanations, and you never had a good comeback besides
> paraphrases of the broken record routine that I've quoted just now.
> But I will be glad to repeat them if I know that an interested, knowledgeable
> party is paying attention, like Ruben.
>
> Btw I never made the "thorn tree" proposal before, so this last retort of yours is misleading.
Peter Nyikos
Sep 27, 2022, 8:25:16 PM9/27/22
to
>He probably wasn't up on the language used in phylogenetics. On
> the other hand, I am.
<snip for focus>
> >>> I don't know whether Harshman would agree to a compromise such as the following:
> >>> modify Hunt's nicely branching tree to a "thorn tree" where all prime ancestor candidates
> >>> are connected to the tree by as small a thorn as feasible, with a label of 0 (zero) to indicate
> >>> the complete lack of disqualifying characters.
> >
> >> This would be the natural result of any usual phylogenetic analysis of
> >> such taxa.
> >
> > Oh, really? including the part about "thorns" as opposed to longish branches?
> Yes, really. Do you understand what branch lengths represent?
trees that we've talked about this year, branch lengths in the LITERAL
sense have to do with time elapsed. NONE of the numbers labeling
segments of those branches has anything to do with numbers
of apomorphies. Most numerical labels have to do with bootstrap values, and in
the last case below they give mya to the nearest 100,000 years.
Here they are:
fig. 5 in:
https://www.nature.com/articles/s41598-022-15535-6
branch lengths are governed by time-calibration based on stratigraphic record
[in epochs, not mya]
fig. 18 in paper coauthored by Mickey Mortimer:
https://peerj.com/articles/7247/?td=bl&fbclid=IwAR09VFddJNY8v0rvmEh9HmtINsJLScQj0B98UsoKEbTjMMNZLTdxZyA4h4w#systematic
Fig. 1 in https://academic.oup.com/gbe/article/9/9/2308/4095375
works as described, except that there is no explicit scale at top or bottom
With calibration explicitly at the top, in epochs AND mya:
Fig 1 in: https://www.researchgate.net/publication/235423191_The_Placental_Mammal_Ancestor_and_the_Post-K-Pg_Radiation_of_Placentals Fig. 1
Finally, the following was calibrated by mya at bottom and also division of periods into 2-3 sub-periods. But it also labeled every node by mya to the nearest tenth:
https://www.science.org/doi/10.1126/sciadv.abq1898
This last example was criticized by me for the way the authors didn't
expand the scale in the "G" part of the Permian. You ignored the author-elephants
in the room while exonerating the editors and reviewers:
https://groups.google.com/g/sci.bio.paleontology/c/26BZZ4NIrHw/m/LFjneBO9EgAJ
> > Or were you referring to trees at all? or only to the character analysis which
> > almost never specifies the number of apomorphies?
> No idea what you mean by that.
you as to what I was talking about. Perhaps my response
to a mostly useless question by you below could also serve this purpose.
> > >No special procedure necessary, as long as a taxon had zero
> >> autapomorphies.
> >
> > Why "autapomorphies"? phylogenetic trees use the legal fiction ("lie"?) that
> > every internal node has at least two branches emanating from it; so it would
> > be labeling the results of a fictitious cladogenesis.
> What you're trying to say there is also far from clear.
You completely ignore the "fictitious cladogenesis" issue, and the
resulting problematic use of "autapomorphies" instead of the simple "apomorphies."
> A zero-length
> branch is quite possible. If not that, what are you referring to?
to be referring to labeling, but there was no labeling of apomorphy numbers
in any of the five trees. [This is why I asked, "were you referring to trees at all?"]
[1] given that you are adamantly opposed to internal nodes being assigned
to known genera or species.
Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
http://people.math.sc.edu/nyikos
PS I will respond to the text I snipped for focus later,
and to the part I snipped at the end without marking the snip.
John Harshman
Sep 27, 2022, 9:16:05 PM9/27/22
to
>> He probably wasn't up on the language used in phylogenetics. On
>> the other hand, I am.
>
> Your use of "branch lengths" below suggests otherwise.
length" isn't a term used in phylogenetics?
>>>>> I don't know whether Harshman would agree to a compromise such as the following:
>>>>> modify Hunt's nicely branching tree to a "thorn tree" where all prime ancestor candidates
>>>>> are connected to the tree by as small a thorn as feasible, with a label of 0 (zero) to indicate
>>>>> the complete lack of disqualifying characters.
>>>
>>>> This would be the natural result of any usual phylogenetic analysis of
>>>> such taxa.
>>>
>>> Oh, really? including the part about "thorns" as opposed to longish branches?
>
>> Yes, really. Do you understand what branch lengths represent?
>
> Are you sure you know what you are talking about? In ALL the detailed
> trees that we've talked about this year, branch lengths in the LITERAL
> sense have to do with time elapsed. NONE of the numbers labeling
> segments of those branches has anything to do with numbers
> of apomorphies. Most numerical labels have to do with bootstrap values, and in
> the last case below they give mya to the nearest 100,000 years.
changes, to time, or to nothing at all. But in the case we were talking
about, it's the former. Would you like to see examples of such trees?
They're pretty common. Further, even when branch lengths aren't
displayed in a figure, the analysis used to construct the figure does
come up with branch lengths that represent the number of changes.
> Here they are:
>
> fig. 5 in:
> https://www.nature.com/articles/s41598-022-15535-6
> branch lengths are governed by time-calibration based on stratigraphic record
> [in epochs, not mya]
> fig. 18 in paper coauthored by Mickey Mortimer:
> https://peerj.com/articles/7247/?td=bl&fbclid=IwAR09VFddJNY8v0rvmEh9HmtINsJLScQj0B98UsoKEbTjMMNZLTdxZyA4h4w#systematic
> Fig. 1 in https://academic.oup.com/gbe/article/9/9/2308/4095375
> works as described, except that there is no explicit scale at top or bottom
scaled by number of changes, if that's what you mean. (Incidentally,
that's sometimes called a phylogram to distinguish from an unscaled
cladogram.)
> With calibration explicitly at the top, in epochs AND mya:
> Fig 1 in: https://www.researchgate.net/publication/235423191_The_Placental_Mammal_Ancestor_and_the_Post-K-Pg_Radiation_of_Placentals Fig. 1
don't know.
> Finally, the following was calibrated by mya at bottom and also division of periods into 2-3 sub-periods. But it also labeled every node by mya to the nearest tenth:
> https://www.science.org/doi/10.1126/sciadv.abq1898
> This last example was criticized by me for the way the authors didn't
> expand the scale in the "G" part of the Permian. You ignored the author-elephants
> in the room while exonerating the editors and reviewers:
> https://groups.google.com/g/sci.bio.paleontology/c/26BZZ4NIrHw/m/LFjneBO9EgAJ
>>> Or were you referring to trees at all? or only to the character analysis which
>>> almost never specifies the number of apomorphies?
>> No idea what you mean by that.
>
> Perhaps the five examples will serve as a wake-up call to reorient
> you as to what I was talking about. Perhaps my response
> to a mostly useless question by you below could also serve this purpose.
very commonly show branch lengths scaled to time, and many trees show
branch length scaled to nothing. But molecular trees commonly show
branch lengths scaled to number of changes, as in the one molecular
study you mention above. More importantly, such a tree is what I was
talking about, and it would show your "thorns" automatically.
>>>> No special procedure necessary, as long as a taxon had zero
>>>> autapomorphies.
>>>
>>> Why "autapomorphies"? phylogenetic trees use the legal fiction ("lie"?) that
>>> every internal node has at least two branches emanating from it; so it would
>>> be labeling the results of a fictitious cladogenesis.
>
>> What you're trying to say there is also far from clear.
>
> As usual, your question in response, below, is not designed to produce clarity.
> You completely ignore the "fictitious cladogenesis" issue, and the
> resulting problematic use of "autapomorphies" instead of the simple "apomorphies."
understand why autapomorphies would be the wrong word. Do you see, by
the way, how you constantly accuse me of dishonesty? That's not a good
way to have a discussion.
>> A zero-length
>> branch is quite possible. If not that, what are you referring to?
>
> Zero-length branches are literally impossible [1] so you would have
> to be referring to labeling, but there was no labeling of apomorphy numbers
> in any of the five trees. [This is why I asked, "were you referring to trees at all?"]
any tree scaled to number of changes. A branch with a length of zero
would not stick out from the ancestral node. I could point you to a few
real examples if you liked; they can occur on trees built from small
data sets.
> [1] given that you are adamantly opposed to internal nodes being assigned
> to known genera or species.
multiple terminal taxa per species. If all the descendant taxa belong to
that genus or species, so does the internal node. No, what I object to
is to particular fossils being placed at internal nodes, i.e. as
ancestral to particular other samples.
Peter Nyikos
Sep 30, 2022, 10:58:00 AM9/30/22
to
On Tuesday, September 27, 2022 at 9:16:05 PM UTC-4, John Harshman wrote:
> On 9/27/22 5:25 PM, Peter Nyikos wrote:
> > On Thursday, September 22, 2022 at 3:27:02 PM UTC-4, John Harshman wrote:
> >> On 9/22/22 9:36 AM, Peter Nyikos wrote:
> >>> On Thursday, September 22, 2022 at 9:27:42 AM UTC-4, John Harshman wrote:
> >>>> On 9/22/22 4:02 AM, Peter Nyikos wrote:
[to Ruben, aka Popping mad:]
> On 9/27/22 5:25 PM, Peter Nyikos wrote:
> > On Thursday, September 22, 2022 at 3:27:02 PM UTC-4, John Harshman wrote:
> >> On 9/22/22 9:36 AM, Peter Nyikos wrote:
> >>> On Thursday, September 22, 2022 at 9:27:42 AM UTC-4, John Harshman wrote:
> >>>> On 9/22/22 4:02 AM, Peter Nyikos wrote:
> >>>>> I hope you are still reading this thread, because there are some very basic things
> >>>>> you need to know about the phylogeneitic trees by which John Harshman swears.
> >>>
> >>>>>
> >>>>> On Monday, September 12, 2022 at 9:04:51 PM UTC-4, Popping Mad wrote:
> >>>>>> On 9/12/22 11:23, John Harshman wrote:
> >>>>>>> Presumably. But my point is that you can't identify the internal nodes
> >>>>>>> with known species.
> >>>>>> and you can't assume they are edge nodes either. I am trying not to be a
> >>>>>> smart alleck or snooty here, but honestly, you really are failing to
> >>>>>> understand how silly this sounds.
Unfortunately, Ruben seems to have gone incommunicado for an indefinite
> >>>>> you need to know about the phylogeneitic trees by which John Harshman swears.
> >>>
> >>>>>
> >>>>> On Monday, September 12, 2022 at 9:04:51 PM UTC-4, Popping Mad wrote:
> >>>>>> On 9/12/22 11:23, John Harshman wrote:
> >>>>>>> Presumably. But my point is that you can't identify the internal nodes
> >>>>>>> with known species.
> >>>>>> and you can't assume they are edge nodes either. I am trying not to be a
> >>>>>> smart alleck or snooty here, but honestly, you really are failing to
> >>>>>> understand how silly this sounds.
period of time, and he may never see the following explanation:
> >>>>> Harshman is thoroughly committed to the reigning orthodoxy in systematics,
> >>>>> which dictates that ALL species be put at branch tips = end nodes.
> >>>>>
> >>>>> [It also happens to use "nodes" exclusively for "internal nodes" -- hence your use
> >>>>> of "node" for what he calls "branch tips" is unintelligible to Harshman.]
> >>>
> >>>> You aren't reading. The term is "terminal node", as opposed to "internal
> >>>> node".
> >>>
> >>> I have been reading Gould, inter alia:
> >>>
> >>> "The extreme rarity of transitional forms in the fossil record persist as the trade secret of paleontology. The evolutionary trees that adorn our textbooks have data only at the tips and nodes of their branches; the rest is inference, however reasonable, not the evidence of fossils."
> >>> --Stephen J. Gould - "Evolution's Erratic Pace," _Natural History_,vol. 86(5) (May 1987): pp. 12-16, at p. 14 Reprinted in _The Panda's Thumb_, pp. 181-182.
> >>>
> >>> Note, tips AND nodes. Granted, this was before the orthodoxy started to reign
> >>> in earnest on the following year, with the final victory in the cladist wars.
> >
> >> Gould was writing for a lay audience and wasn't a systematist in any
> >> case.
> >
> > However, he was a biological polymath with a keen mind.
> True, but he wasn't that up on phylogenetic methods.
to the issue at hand, which is that these trees are designed to implicitly
deny direct ancestry to every single pair of taxa since the beginning of life on earth.
> >> He probably wasn't up on the language used in phylogenetics. On
> >> the other hand, I am.
> >
> > Your use of "branch lengths" below suggests otherwise.
> Not understanding what you mean by that. Are you saying that "branch
> length" isn't a term used in phylogenetics?
from the hip, you wouldn't have asked this asinine question.
> >>>>> I don't know whether Harshman would agree to a compromise such as the following:
> >>>>> modify Hunt's nicely branching tree to a "thorn tree" where all prime ancestor candidates
> >>>>> are connected to the tree by as small a thorn as feasible, with a label of 0 (zero) to indicate
> >>>>> the complete lack of disqualifying characters.
> >>>
> >>>> This would be the natural result of any usual phylogenetic analysis of
> >>>> such taxa.
> >>>
> >>> Oh, really? including the part about "thorns" as opposed to longish branches?
the kind of project I envision above.
> >> Yes, really. Do you understand what branch lengths represent?
> > Are you sure you know what you are talking about? In ALL the detailed
> > trees that we've talked about this year, branch lengths in the LITERAL
> > sense have to do with time elapsed. NONE of the numbers labeling
> > segments of those branches has anything to do with numbers
> > of apomorphies. Most numerical labels have to do with bootstrap values, and in
> > the last case below they give mya to the nearest 100,000 years.
> This is sometimes the case.
> Branch lengths can be scaled to number of
> changes, to time, or to nothing at all. But in the case we were talking
> about, it's the former. Would you like to see examples of such trees?
You gave one below [keyword: phylogram]. Unfortunately,
none of the branch lengths is anywhere near 0, so it doesn't
really answer my question.
Besides, what kept you from producing SEVERAL one reply earlier?
Why do you want to drag the discussion out, unlike me, who provided FIVE
examples *immediately*?
> They're pretty common. Further, even when branch lengths aren't
> displayed in a figure, the analysis used to construct the figure does
> come up with branch lengths that represent the number of changes.
(as opposed to being told by you that it has been done)
how they manage a branch length that represents 0 apomorphies.
> > Here they are:
> >
> > fig. 5 in:
> > https://www.nature.com/articles/s41598-022-15535-6
> > branch lengths are governed by time-calibration based on stratigraphic record
> > [in epochs, not mya]
> Correct.
> > fig. 18 in paper coauthored by Mickey Mortimer:
> > https://peerj.com/articles/7247/?td=bl&fbclid=IwAR09VFddJNY8v0rvmEh9HmtINsJLScQj0B98UsoKEbTjMMNZLTdxZyA4h4w#systematic
> Note that in Fig. 17 the branch lengths mean nothing.
> > Fig. 1 in https://academic.oup.com/gbe/article/9/9/2308/4095375
> > works as described, except that there is no explicit scale at top or bottom
> Not sure what "as described" means, but the branches in that tree are
> scaled by number of changes, if that's what you mean. (Incidentally,
> that's sometimes called a phylogram to distinguish from an unscaled
> cladogram.)
go to Homo sapiens vis a vis Pan paniscus, and to the walrus vis a vis sea lions.
So we are very far from a "thorn tree".
> > With calibration explicitly at the top, in epochs AND mya:
> > Fig 1 in: https://www.researchgate.net/publication/235423191_The_Placental_Mammal_Ancestor_and_the_Post-K-Pg_Radiation_of_Placentals Fig. 1
> That link goes only to the abstract and, for some reason, Fig. 3. So I
> don't know.
> > Finally, the following was calibrated by mya at bottom and also division of periods into 2-3 sub-periods. But it also labeled every node by mya to the nearest tenth:
> > https://www.science.org/doi/10.1126/sciadv.abq1898
> Correct.
> > This last example was criticized by me for the way the authors didn't
> > expand the scale in the "G" part of the Permian. You ignored the author-elephants
> > in the room while exonerating the editors and reviewers:
> > https://groups.google.com/g/sci.bio.paleontology/c/26BZZ4NIrHw/m/LFjneBO9EgAJ
> You never forget a grudge.
You keep coming across as someone with a childish belief in the magic of words
(grudge, traitor, megalomania, paranoid, etc.) whose usage you stretch well past the breaking point.
> >>> Or were you referring to trees at all? or only to the character analysis which
> >>> almost never specifies the number of apomorphies?
> >> No idea what you mean by that.
> >
> > Perhaps the five examples will serve as a wake-up call to reorient
> > you as to what I was talking about. Perhaps my response
> > to a mostly useless question by you below could also serve this purpose.
> Your sample of trees is highly biased.
lengths represent *something*.
> It's true that fossil-based trees
> very commonly show branch lengths scaled to time, and many trees show
> branch length scaled to nothing. But molecular trees commonly show
> branch lengths scaled to number of changes, as in the one molecular
> study you mention above.
And that's exactly the point of my talk about "thorn trees."
> More importantly, such a tree is what I was
> talking about, and it would show your "thorns" automatically.
to trees using only extant species. [Scroll up to where I first talk
about "thorn trees" if the preceding sentence mystifies you.]
Unfortunately, distinct extant species
don't have 0 apomorphies in molecular trees, do they?
Remainder deleted, to be replied to later (possibly today, if our
internet or electricity doesn't go down due to Tropical Storm Ian.)
John Harshman
Sep 30, 2022, 5:24:30 PM9/30/22
to
means only "internal node" in systematics, then he's wrong, and so are
you. Now how would you create a method of constructing trees that
implicitly allows direct ancestry?
(I do know of one such method, continuous track analysis, but nobody to
my knowledge has ever used it. Perhaps you might like it:
https://academic.oup.com/sysbio/article-abstract/44/2/152/1678263.)
>>>> He probably wasn't up on the language used in phylogenetics. On
>>>> the other hand, I am.
>>>
>>> Your use of "branch lengths" below suggests otherwise.
>
>> Not understanding what you mean by that. Are you saying that "branch
>> length" isn't a term used in phylogenetics?
>
> If you had understood what I wrote directly above, and below, instead of shooting
> from the hip, you wouldn't have asked this asinine question.
answered the asinine question. But here it is again: What did you mean
by that?
>>>>>>> I don't know whether Harshman would agree to a compromise such as the following:
>>>>>>> modify Hunt's nicely branching tree to a "thorn tree" where all prime ancestor candidates
>>>>>>> are connected to the tree by as small a thorn as feasible, with a label of 0 (zero) to indicate
>>>>>>> the complete lack of disqualifying characters.
>>>>>
>>>>>> This would be the natural result of any usual phylogenetic analysis of
>>>>>> such taxa.
>>>>>
>>>>> Oh, really? including the part about "thorns" as opposed to longish branches?
>
> It turns out, far below, that "usual" means "molecular" and is useless for
> the kind of project I envision above.
fossil analyses.
>>>> Yes, really. Do you understand what branch lengths represent?
>
>>> Are you sure you know what you are talking about? In ALL the detailed
>>> trees that we've talked about this year, branch lengths in the LITERAL
>>> sense have to do with time elapsed. NONE of the numbers labeling
>>> segments of those branches has anything to do with numbers
>>> of apomorphies. Most numerical labels have to do with bootstrap values, and in
>>> the last case below they give mya to the nearest 100,000 years.
>
>> This is sometimes the case.
>
> "sometimes" seems to be a huge understatement.
>> Branch lengths can be scaled to number of
>> changes, to time, or to nothing at all. But in the case we were talking
>> about, it's the former. Would you like to see examples of such trees?
>
> You are shooting from the hip again without reading further.
> You gave one below [keyword: phylogram]. Unfortunately,
> none of the branch lengths is anywhere near 0, so it doesn't
> really answer my question.
zero-length branch and you printed out the results of an analysis that
found that, you would get a tree that showed a zero-length branch. No
need for any compromise. But of course Hunt's tree was not based on an
explicit data set.
> Besides, what kept you from producing SEVERAL one reply earlier?
> Why do you want to drag the discussion out, unlike me, who provided FIVE
> examples *immediately*?
since it seems obvious what it would look like.
>> They're pretty common. Further, even when branch lengths aren't
>> displayed in a figure, the analysis used to construct the figure does
>> come up with branch lengths that represent the number of changes.
>
> Finally, you are using "branch lengths" literally. But I'd still love to SEE
> (as opposed to being told by you that it has been done)
> how they manage a branch length that represents 0 apomorphies.
J., Huddleston C.J., Bollback J., Parsons T.M., Braun M.J. True and
false gharials: A nuclear gene phylogeny of Crocodylia. Systematic
Biology 2003; 52:386-402.
In Fig. 2, the branch separating Crocodylus cataphractus from its common
ancestor with Osteolaemus tetraspis has a length of zero.
>>> Here they are:
>>>
>>> fig. 5 in:
>>> https://www.nature.com/articles/s41598-022-15535-6
>>> branch lengths are governed by time-calibration based on stratigraphic record
>>> [in epochs, not mya]
>
>> Correct.
>
>>> fig. 18 in paper coauthored by Mickey Mortimer:
>>> https://peerj.com/articles/7247/?td=bl&fbclid=IwAR09VFddJNY8v0rvmEh9HmtINsJLScQj0B98UsoKEbTjMMNZLTdxZyA4h4w#systematic
>> Note that in Fig. 17 the branch lengths mean nothing.
>
> That's why I didn't talk about Fig. 17. Duh.
>
>>> Fig. 1 in https://academic.oup.com/gbe/article/9/9/2308/4095375
>>> works as described, except that there is no explicit scale at top or bottom
>> Not sure what "as described" means, but the branches in that tree are
>> scaled by number of changes, if that's what you mean. (Incidentally,
>> that's sometimes called a phylogram to distinguish from an unscaled
>> cladogram.)
>
> Correct, now that I am looking more closely. But the shortest branch lengths
> go to Homo sapiens vis a vis Pan paniscus, and to the walrus vis a vis sea lions.
> So we are very far from a "thorn tree".
>>> With calibration explicitly at the top, in epochs AND mya:
>>> Fig 1 in: https://www.researchgate.net/publication/235423191_The_Placental_Mammal_Ancestor_and_the_Post-K-Pg_Radiation_of_Placentals Fig. 1
>> That link goes only to the abstract and, for some reason, Fig. 3. So I
>> don't know.
>
> Didn't you get two icons labeled "Download full-length PDF" and "Read full-text" in the upper right corner?
another time-calibrated tree.
>>> Finally, the following was calibrated by mya at bottom and also division of periods into 2-3 sub-periods. But it also labeled every node by mya to the nearest tenth:
>>> https://www.science.org/doi/10.1126/sciadv.abq1898
>> Correct.
>>> This last example was criticized by me for the way the authors didn't
>>> expand the scale in the "G" part of the Permian. You ignored the author-elephants
>>> in the room while exonerating the editors and reviewers:
>>> https://groups.google.com/g/sci.bio.paleontology/c/26BZZ4NIrHw/m/LFjneBO9EgAJ
>
>> You never forget a grudge.
>
> Here grudge = first time mention of something that happened less than a week ago.
>
> You keep coming across as someone with a childish belief in the magic of words
> (grudge, traitor, megalomania, paranoid, etc.) whose usage you stretch well past the breaking point.
before, but because it's a complaint gratuitously introduced into
another topic in which it's not relevant.
>>>>> Or were you referring to trees at all? or only to the character analysis which
>>>>> almost never specifies the number of apomorphies?
>>>> No idea what you mean by that.
>>>
>>> Perhaps the five examples will serve as a wake-up call to reorient
>>> you as to what I was talking about. Perhaps my response
>>> to a mostly useless question by you below could also serve this purpose.
>
>> Your sample of trees is highly biased.
>
> They are ALL THE TREES we've seen this year in s.b.p. whose branch
> lengths represent *something*.
>> It's true that fossil-based trees
>> very commonly show branch lengths scaled to time, and many trees show
>> branch length scaled to nothing. But molecular trees commonly show
>> branch lengths scaled to number of changes, as in the one molecular
>> study you mention above.
>
> Ah. There's the bias: all the others are morphological, as befits a forum on paleontology.
and fossils. It's easy enough to show morphological trees, even fossil
trees, with branch lengths scaled to character change. Presumably that's
what you want.
> And that's exactly the point of my talk about "thorn trees."
> > More importantly, such a tree is what I was
>> talking about, and it would show your "thorns" automatically.
>
> IOW, you changed the subject from trees which "correct" Kathleen Hunt's tree
> to trees using only extant species. [Scroll up to where I first talk
> about "thorn trees" if the preceding sentence mystifies you.]
> Unfortunately, distinct extant species
> don't have 0 apomorphies in molecular trees, do they?
check out Crocodylus cataphractus in the publication I cite above.
Peter Nyikos
Sep 30, 2022, 7:20:18 PM9/30/22
to
I've held off replying to this post of yours all this time, John, in
the hopes of keeping things reasonably civil. But it is kid stuff
compared to some of your behavior on the thread, "Where's Erik,"
these last three days, so there is no point in letting it go unremarked on any longer.
On Monday, September 5, 2022 at 8:07:12 PM UTC-4, John Harshman wrote:
> On 9/5/22 3:51 PM, Peter Nyikos wrote:
> > On Monday, September 5, 2022 at 2:50:32 PM UTC-4, John Harshman wrote:
> >> On 9/5/22 11:42 AM, Peter Nyikos wrote:
> >
> >>> As I looked back yesterday on some 2016 threads in s.b.p. when it was at the height of what I call
> >>> "an oasis of civilization," I came across a long exchange between Ruben Safir
> >>> [who often went under the byline Popping mad, as he does now]
> >>> and John Harshman, which I joined near the end. John and Ruben
> >>> were unable to communicate fruitfully, because John was stuck
> >>> in a dichotomy between two ways of classifying organisms:
> >>> the cladistic and the phenetic.
> >
> >> Needless to say, I reject your characterization of that argument.
> >
> > Automatic reflex reaction noted.
> Try to engage with my argument rather than just characterizing it.
You call what you wrote up there an argument??
> > You obviously haven't looked at the thread in over six years,
> > not with Giganews archives only going back a month.
> Of course I haven't. But I know my own opinions.
About yourself, based on all of the above. And they seem -- to put it mildly -- rather egotistic.
> > But I'll help you. Here is the url for the entire thread.
> > https://groups.google.com/g/sci.bio.paleontology/c/sFY6QxipSb4/m/T0QLNBF0AQAJ
> >
> > Happy surfing up and down the 148 posts. Here is a note I made on one of them:
> >
> > "Harshman is stuck in a false dichotomy between cladistics and phenetics"
> > Apr 14, 2016, 5:03:15 PM
> >
> > You may want to start there.
> >
> >
> > See you tomorrow with the post that addresses this false dichotomy of yours.
> Why begin with a personal attack? What's the point?
I only began a personal attack this time around.
If you think saying that you had been stuck in a false dichotomy is an attack,
you are taking things way too personally. The cladistic wars were
stuck in the same dichotomy. Were you too wrapped up in looking for
personal affronts to notice that herd of elephants in the room?
Sheesh.
But now, contrast your "emotional hemophiliac" behavior with
your full-bore gaslighting allegation of "megalomania" with which
I dealt two days after you wrote the above:
https://groups.google.com/g/talk.origins/c/exNELbZoE1k/m/bHyj_wb3CQAJ
Re: Hole In One
Sep 7, 2022, 10:10:05 AM
Needless to say, you haven't thought of a good comeback in
all this time. Did you think jillery let you off the hook with
the following direct reply to my linked post?
https://groups.google.com/g/talk.origins/c/exNELbZoE1k/m/TidKscYmCgAJ
Do you really want to associate yourself with the staggeringly
dishonest way jillery did it?
Peter Nyikos
PS One thing is for sure: jillery made it clear that she will
back you to the hilt no matter how despicably you behave towards me.
the hopes of keeping things reasonably civil. But it is kid stuff
compared to some of your behavior on the thread, "Where's Erik,"
these last three days, so there is no point in letting it go unremarked on any longer.
On Monday, September 5, 2022 at 8:07:12 PM UTC-4, John Harshman wrote:
> On 9/5/22 3:51 PM, Peter Nyikos wrote:
> > On Monday, September 5, 2022 at 2:50:32 PM UTC-4, John Harshman wrote:
> >> On 9/5/22 11:42 AM, Peter Nyikos wrote:
> >
> >>> As I looked back yesterday on some 2016 threads in s.b.p. when it was at the height of what I call
> >>> "an oasis of civilization," I came across a long exchange between Ruben Safir
> >>> [who often went under the byline Popping mad, as he does now]
> >>> and John Harshman, which I joined near the end. John and Ruben
> >>> were unable to communicate fruitfully, because John was stuck
> >>> in a dichotomy between two ways of classifying organisms:
> >>> the cladistic and the phenetic.
> >
> >> Needless to say, I reject your characterization of that argument.
> >
> > Automatic reflex reaction noted.
> Try to engage with my argument rather than just characterizing it.
You call what you wrote up there an argument??
> > You obviously haven't looked at the thread in over six years,
> > not with Giganews archives only going back a month.
> Of course I haven't. But I know my own opinions.
About yourself, based on all of the above. And they seem -- to put it mildly -- rather egotistic.
> > But I'll help you. Here is the url for the entire thread.
> > https://groups.google.com/g/sci.bio.paleontology/c/sFY6QxipSb4/m/T0QLNBF0AQAJ
> >
> > Happy surfing up and down the 148 posts. Here is a note I made on one of them:
> >
> > "Harshman is stuck in a false dichotomy between cladistics and phenetics"
> > Apr 14, 2016, 5:03:15 PM
> >
> > You may want to start there.
> >
> >
> > See you tomorrow with the post that addresses this false dichotomy of yours.
> Why begin with a personal attack? What's the point?
I only began a personal attack this time around.
If you think saying that you had been stuck in a false dichotomy is an attack,
you are taking things way too personally. The cladistic wars were
stuck in the same dichotomy. Were you too wrapped up in looking for
personal affronts to notice that herd of elephants in the room?
Sheesh.
But now, contrast your "emotional hemophiliac" behavior with
your full-bore gaslighting allegation of "megalomania" with which
I dealt two days after you wrote the above:
https://groups.google.com/g/talk.origins/c/exNELbZoE1k/m/bHyj_wb3CQAJ
Re: Hole In One
Sep 7, 2022, 10:10:05 AM
Needless to say, you haven't thought of a good comeback in
all this time. Did you think jillery let you off the hook with
the following direct reply to my linked post?
https://groups.google.com/g/talk.origins/c/exNELbZoE1k/m/TidKscYmCgAJ
Do you really want to associate yourself with the staggeringly
dishonest way jillery did it?
Peter Nyikos
PS One thing is for sure: jillery made it clear that she will
back you to the hilt no matter how despicably you behave towards me.
John Harshman
Sep 30, 2022, 7:39:47 PM9/30/22
to
On 9/30/22 4:20 PM, Peter Nyikos wrote:
> I've held off replying to this post of yours all this time, John, in
> the hopes of keeping things reasonably civil. But it is kid stuff
> compared to some of your behavior on the thread, "Where's Erik,"
> these last three days, so there is no point in letting it go unremarked on any longer.
>
> On Monday, September 5, 2022 at 8:07:12 PM UTC-4, John Harshman wrote:
>> On 9/5/22 3:51 PM, Peter Nyikos wrote:
>>> On Monday, September 5, 2022 at 2:50:32 PM UTC-4, John Harshman wrote:
>>>> On 9/5/22 11:42 AM, Peter Nyikos wrote:
>>>
>>>>> As I looked back yesterday on some 2016 threads in s.b.p. when it was at the height of what I call
>>>>> "an oasis of civilization," I came across a long exchange between Ruben Safir
>>>>> [who often went under the byline Popping mad, as he does now]
>>>>> and John Harshman, which I joined near the end. John and Ruben
>>>>> were unable to communicate fruitfully, because John was stuck
>>>>> in a dichotomy between two ways of classifying organisms:
>>>>> the cladistic and the phenetic.
>>>
>>>> Needless to say, I reject your characterization of that argument.
>>>
>>> Automatic reflex reaction noted.
>
>> Try to engage with my argument rather than just characterizing it.
>
> You call what you wrote up there an argument??
No, I call the argument I had with Ruben an argument. The one you just
> I've held off replying to this post of yours all this time, John, in
> the hopes of keeping things reasonably civil. But it is kid stuff
> compared to some of your behavior on the thread, "Where's Erik,"
> these last three days, so there is no point in letting it go unremarked on any longer.
>
> On Monday, September 5, 2022 at 8:07:12 PM UTC-4, John Harshman wrote:
>> On 9/5/22 3:51 PM, Peter Nyikos wrote:
>>> On Monday, September 5, 2022 at 2:50:32 PM UTC-4, John Harshman wrote:
>>>> On 9/5/22 11:42 AM, Peter Nyikos wrote:
>>>
>>>>> As I looked back yesterday on some 2016 threads in s.b.p. when it was at the height of what I call
>>>>> "an oasis of civilization," I came across a long exchange between Ruben Safir
>>>>> [who often went under the byline Popping mad, as he does now]
>>>>> and John Harshman, which I joined near the end. John and Ruben
>>>>> were unable to communicate fruitfully, because John was stuck
>>>>> in a dichotomy between two ways of classifying organisms:
>>>>> the cladistic and the phenetic.
>>>
>>>> Needless to say, I reject your characterization of that argument.
>>>
>>> Automatic reflex reaction noted.
>
>> Try to engage with my argument rather than just characterizing it.
>
> You call what you wrote up there an argument??
characterized without engaging with.
>>> You obviously haven't looked at the thread in over six years,
>>> not with Giganews archives only going back a month.
>
>> Of course I haven't. But I know my own opinions.
>
> About yourself, based on all of the above. And they seem -- to put it mildly -- rather egotistic.
>>> But I'll help you. Here is the url for the entire thread.
>>> https://groups.google.com/g/sci.bio.paleontology/c/sFY6QxipSb4/m/T0QLNBF0AQAJ
>>>
>>> Happy surfing up and down the 148 posts. Here is a note I made on one of them:
>>>
>>> "Harshman is stuck in a false dichotomy between cladistics and phenetics"
>>> Apr 14, 2016, 5:03:15 PM
>>>
>>> You may want to start there.
>>>
>>>
>>> See you tomorrow with the post that addresses this false dichotomy of yours.
>
>> Why begin with a personal attack? What's the point?
>
> I only began a personal attack this time around.
>
> If you think saying that you had been stuck in a false dichotomy is an attack,
> you are taking things way too personally. The cladistic wars were
> stuck in the same dichotomy. Were you too wrapped up in looking for
> personal affronts to notice that herd of elephants in the room?
Does any of the off-topic whatever-it-is that follows below?
Peter Nyikos
Oct 4, 2022, 7:24:12 PM10/4/22
to
On Friday, September 30, 2022 at 7:39:47 PM UTC-4, John Harshman wrote:
> On 9/30/22 4:20 PM, Peter Nyikos wrote:
> > I've held off replying to this post of yours all this time, John, in
> > the hopes of keeping things reasonably civil. But it is kid stuff
> > compared to some of your behavior on the thread, "Where's Erik,"
> > these last three days, so there is no point in letting it go unremarked on any longer.
> >
> > On Monday, September 5, 2022 at 8:07:12 PM UTC-4, John Harshman wrote:
> >> On 9/5/22 3:51 PM, Peter Nyikos wrote:
> >>> On Monday, September 5, 2022 at 2:50:32 PM UTC-4, John Harshman wrote:
> >>>> On 9/5/22 11:42 AM, Peter Nyikos wrote:
> >>>
> >>>>> As I looked back yesterday on some 2016 threads in s.b.p. when it was at the height of what I call
> >>>>> "an oasis of civilization," I came across a long exchange between Ruben Safir
> >>>>> [who often went under the byline Popping mad, as he does now]
> >>>>> and John Harshman, which I joined near the end. John and Ruben
> >>>>> were unable to communicate fruitfully, because John was stuck
> >>>>> in a dichotomy between two ways of classifying organisms:
> >>>>> the cladistic and the phenetic.
> >>>
> >>>> Needless to say, I reject your characterization of that argument.
> >>>
> >>> Automatic reflex reaction noted.
> >
> >> Try to engage with my argument rather than just characterizing it.
> >
> > You call what you wrote up there an argument??
> No, I call the argument I had with Ruben an argument.
I think I've made my point further down in the post
> On 9/30/22 4:20 PM, Peter Nyikos wrote:
> > I've held off replying to this post of yours all this time, John, in
> > the hopes of keeping things reasonably civil. But it is kid stuff
> > compared to some of your behavior on the thread, "Where's Erik,"
> > these last three days, so there is no point in letting it go unremarked on any longer.
> >
> > On Monday, September 5, 2022 at 8:07:12 PM UTC-4, John Harshman wrote:
> >> On 9/5/22 3:51 PM, Peter Nyikos wrote:
> >>> On Monday, September 5, 2022 at 2:50:32 PM UTC-4, John Harshman wrote:
> >>>> On 9/5/22 11:42 AM, Peter Nyikos wrote:
> >>>
> >>>>> As I looked back yesterday on some 2016 threads in s.b.p. when it was at the height of what I call
> >>>>> "an oasis of civilization," I came across a long exchange between Ruben Safir
> >>>>> [who often went under the byline Popping mad, as he does now]
> >>>>> and John Harshman, which I joined near the end. John and Ruben
> >>>>> were unable to communicate fruitfully, because John was stuck
> >>>>> in a dichotomy between two ways of classifying organisms:
> >>>>> the cladistic and the phenetic.
> >>>
> >>>> Needless to say, I reject your characterization of that argument.
> >>>
> >>> Automatic reflex reaction noted.
> >
> >> Try to engage with my argument rather than just characterizing it.
> >
> > You call what you wrote up there an argument??
> No, I call the argument I had with Ruben an argument.
to which you were replying on September 5. Keep reading.
> The one you just characterized without engaging with.
and identifying a specific post on it.
> >>> You obviously haven't looked at the thread in over six years,
> >>> not with Giganews archives only going back a month.
> >
> >> Of course I haven't. But I know my own opinions.
> >
> > About yourself, based on all of the above. And they seem -- to put it mildly -- rather egotistic.
> ??
results of "the cladist wars" even though they were all about cladistics vs. phenetics.
But what I documented below is even more symptomatic of egotism.
> >>> But I'll help you. Here is the url for the entire thread.
> >>> https://groups.google.com/g/sci.bio.paleontology/c/sFY6QxipSb4/m/T0QLNBF0AQAJ
> >>>
> >>> Happy surfing up and down the 148 posts. Here is a note I made on one of them:
> >>>
> >>> "Harshman is stuck in a false dichotomy between cladistics and phenetics"
> >>> Apr 14, 2016, 5:03:15 PM
> >>>
> >>> You may want to start there.
> >>>
> >>>
> >>> See you tomorrow with the post that addresses this false dichotomy of yours.
cladistics vs. phenetics was embedded in it. But I think I made you see that.
But you couldn't wait for it on the 5th:
> >> Why begin with a personal attack? What's the point?
> >
> > I only began a personal attack this time around.
> >
> > If you think saying that you had been stuck in a false dichotomy is an attack,
> > you are taking things way too personally. The cladistic wars were
> > stuck in the same dichotomy. Were you too wrapped up in looking for
> > personal affronts to notice that herd of elephants in the room?
> Does any of this trash talk serve a legitimate purpose?
"You keep coming across as someone with a childish belief in the magic of words
(grudge, traitor, megalomania, paranoid, etc.) whose usage you stretch well past the breaking point."
> Does any of the off-topic whatever-it-is that follows below?
how flagrantly you adhere to double standards.
Are you man enough to admit that what I described and documented below
was you indulging in trash talk? and that it was wrong for you to do it?
> > But now, contrast your "emotional hemophiliac" behavior with
> > your full-bore gaslighting allegation of "megalomania" with which
> > I dealt two days after you wrote the above:
> >
> > https://groups.google.com/g/talk.origins/c/exNELbZoE1k/m/bHyj_wb3CQAJ
> > Re: Hole In One
> > Sep 7, 2022, 10:10:05 AM
John Harshman
Oct 4, 2022, 8:55:16 PM10/4/22
to
On 10/4/22 4:24 PM, Peter Nyikos wrote:
I'm only responding to this because you will complain if I don't. I have
snipped all the off-topic parts and find there's nothing left. If you
would like to compose a post that is both a) on-topic and b) doesn't
reply to multiple levels of nesting, I will be glad to respond similarly.
I'm only responding to this because you will complain if I don't. I have
snipped all the off-topic parts and find there's nothing left. If you
would like to compose a post that is both a) on-topic and b) doesn't
reply to multiple levels of nesting, I will be glad to respond similarly.
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