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.
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.
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.
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.
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 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.
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.
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.
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.
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.There is no post with that time stamp. Is there perhaps a typo? Or does 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.
On Monday, September 5, 2022 at 5:14:48 PM UTC-7, 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:There is no post with that time stamp. Is there perhaps a typo? Or does
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.
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.
Note that you made two posts, one stamped 5:00 and another 5:03 in that thread on that day, according to my server.
I think you misunderstand what Peter said and meant above.
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 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.
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.
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.
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 >> 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.
Take another look at the post:
On 4/14/16 1:28 PM, ruben safir wrote:
On 04/14/2016 12:09 AM, John Harshman wrote:No it won't, unless by "closely related" you just mean "similar". But
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.
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--
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.
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:No it won't, unless by "closely related" you just mean "similar". But
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.
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.
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?
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:No it won't, unless by "closely related" you just mean "similar". But
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.
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
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."
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.
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.
On Wednesday, September 7, 2022 at 12:18:55 AM UTC-4, John Harshmanwrote:
be trueOn 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
makingNo it won't, unless by "closely related" you just mean "similar". Butif 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.
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
hasn't replied yet.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
he will explain himself.
I've told him about this new thread in direct reply to him, but he
I certainly hope he does join, because he might learn a lot about allthree methods of
defining "more closely related." Back in 2016, he wrote that he wasworking on a
Master's degree and I wish I had known then what I know now.
estimating degree of disparity,The line segment joining successive elements is given a number
path between them.and the numbers are added together to compute the length of the
I should have ended that sentence with "the path between any two taxaon 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.
new meaning --The concept of "more closely related" then could be given a whole
say that vertebrate Aor, rather, an old meaning but now quantified. We would be able to
is to C even thoughin the following example is MUCH more closely related to B than it
C = Bos.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,
are in a clade that excludes A.A cladist would say B and C are equally distant from A because they
the measuring,
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
species to another.but the pheneticist hops across the tree in a beeline from one
No entire articles that I'm aware of. But what you describe is a
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.
I am unfamiliar with the concept of patristic distance. Are there any published articles about it?
>But these distances would depend on whatresearchers [and they still exist]
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
can make a start with the tree of Equioidea in Kathleen Hunt'sexcellent FAQ:
http://www.talkorigins.org/faqs/horses/horse_evol.htmlall the way to Equus,
You can see a lineage in the tree going directly from Hyracotherium
with a genus at each node in an old-fashioned evolutionary tree.great source of characters.
The whole tree has a good number of side branches, and each node is a
Even if you believe that there isn't a single ancestor-descendantrelationship
depicted there, the fossils in most cases are so nearly completeat the nodes.
that the named genera can be a source for a nearly complete
set of skeletal characters for the actual species that REALLY belong
I think a good set of disparity numbers can be worked out,You take "wars" much too literally here. Nobody was harmed or even
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.
pairwise distance.I don't see
patristic distance as much better for this purpose than simple
That's because of your dislike of paraphyletic taxa, in solidaritywith the victors.
a system?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
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 ascritically
endangered as s.b.p. itself was at the time], and I put all myefforts into
promoting a dual system of classification.You are misusing the term "Linnean system". It is not part of the
I made the analogy of the Dewey Decimal and Library of Congress systemsway or the highway.
of classifying books, each promoted by its own libraries. But such
peaceful coexistence is not good enough for the victors: it's their
And you've made yourself a propagandist for them in s.b.p. and t.o.That's a pejorative characterization of a reasoned and reasonable position.
disparity-basedVelociraptor 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
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 thanNo. Again, a general impression of morphology. You may disagree (though
Ichthyornis to Confuciusornis.
Really? Aren't you using the cladistic "closer to" here?
> But where do we put the line here? Andthe other genus"
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
is that each pair is separated by a given distance, and there is noconflict between
pairwise distances. Want to know who is closest to Hesperornis? theone who
ends up with the smallest distance to it. Duh.The smallest patristic (along the tree) distance, one supposes. That
On 9/7/22 2:08 PM, Peter Nyikos wrote:
On Wednesday, September 7, 2022 at 12:18:55 AM UTC-4, John Harshmanwrote:
On 9/6/22 6:53 PM, Peter Nyikos wrote:
estimating degree of disparity,The line segment joining successive elements is given a number
path between them.and the numbers are added together to compute the length of the
I should have ended that sentence with "the path between any two taxaon 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.
new meaning --The concept of "more closely related" then could be given a whole
say that vertebrate Aor, rather, an old meaning but now quantified. We would be able to
is to C even thoughin the following example is MUCH more closely related to B than it
C = Bos.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,
are in a clade that excludes A.A cladist would say B and C are equally distant from A because they
the measuring,
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
species to another.but the pheneticist hops across the tree in a beeline from one
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.
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 interestedresearchers [and they still exist]
can make a start with the tree of Equioidea in Kathleen Hunt'sexcellent FAQ:
http://www.talkorigins.org/faqs/horses/horse_evol.html
You can see a lineage in the tree going directly from Hyracotheriumall the way to Equus,
with a genus at each node in an old-fashioned evolutionary tree.great source of characters.
The whole tree has a good number of side branches, and each node is a
Good luck with that. You would have to decide which characters to
include,
Even if you believe that there isn't a single ancestor-descendant relationshipat the nodes.
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
But are skeletal characters the only measure of disparity? You have
already biased the measure.
[disparity distances] can tell us mamy things.
But using to define closeness of relationship is not one of those
things.
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 sucha 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.
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 adisparity-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.
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?
Relationships, based on disparity, would appear not to be transitive.
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 Harshmanwrote:
On 9/6/22 6:53 PM, Peter Nyikos wrote:
I've snipped the text that appears above, where you added nothing new.
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.
sense.estimating degree of disparity,The line segment joining successive elements is given a number
path between them.and the numbers are added together to compute the length of the
on the tree,
I should have ended that sentence with "the path between any two taxa
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.
I was using "rooted" the way graph theorists and set theorists use it, 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
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?
example,new meaning --The concept of "more closely related" then could be given a whole
say that vertebrate Aor, rather, an old meaning but now quantified. We would be able to
is to C even thoughin the following example is MUCH more closely related to B than it
C = Bos.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,
are in a clade that excludes A.A cladist would say B and C are equally distant from A because they
A pheneticist would agree with the disparity measurer in this
beingconvergencebut I think it is not hard to cook up an example where evolutionary
the measuring,could make the pheneticist disagree with the disparity measurer,
because the latter takes a plunge down the tree and back up to do
species to another.but the pheneticist hops across the tree in a beeline from one
[...]
If I understand your point, you are using
patristic distance as a measure of relatedness, smaller distances
"addition"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.
What do you mean by branch lengths? The word "count" rather than
makes me suspect that patristic distance means the number of nodes,
which completely misses the role of disparity in what I wrote.
species here,researchers [and they still exist]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
can make a start with the tree of Equioidea in Kathleen Hunt'sexcellent FAQ:
all the way to Equus,
http://www.talkorigins.org/faqs/horses/horse_evol.html
You can see a lineage in the tree going directly from Hyracotherium
with a genus at each node in an old-fashioned evolutionary tree.great source of characters.
The whole tree has a good number of side branches, and each node is a
Good luck with that. You would have to decide which characters to
include,
All known ones for each skeleton. We are talking about extinct
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 relationshipat the nodes.
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
horse fossils,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
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.
that way.a system?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
No, I am not. But that's the implication of defining relationships
I completely disagree. Please try to reveal your line of reasoning.
realize thatBy the time I returned to s.b.p. in late 2010, I had come to
efforts intothe 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
Agnatha,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,
just to name the classes involved. And then there are what areInsectivora, and Condylartha.
derisively termed "garbage taxa": Cotylosauria, Thecodonta,
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.
ConfuciusornisVelociraptor closer to Archaeopteryx than
Archaeopteryx to Confuciusornis. Archaeopteryx closer to
disparity-basedthan Confusiusornis to Icthyornis.
Where do you get these comparisons? You sure haven't worked out a
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:
No. Again, a general impression of morphology.Icthyornis closer to Passer than
Ichthyornis to Confuciusornis.
Really? Aren't you using the cladistic "closer to" here?
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?
[1] I'm looking at the skull in the 3rd edition of Benton's_Vertebrate_Paleontology_
[...]to the other genus"
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
one whois 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
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.
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.
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.
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.
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 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.
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.
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.
All known ones for each skeleton. We are talking about extinct species here,
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.
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
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.
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.
But that all becomes useless once you try to use it for anything except pairwise comparisons.
Is Archaeopteryx more closely related to Deinonychus or Larus?
Nobody is proposing such a thing.
You're thinking about extant species,
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.
On 9/10/22 5:50 PM, Popping Mad wrote:
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
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.
I don't believe you are following this. You're thinking about extant
species, and this argument is about extinct ones. Is Archaeopteryx more closely related to Deinonychus or Larus?
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.
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.
On 9/6/22 21:53, Peter Nyikos wrote:estimating degree of disparity,
The line segment joining successive elements is given a number
I don't think you could write such a program. But if you could have aand 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.
So the fundamental question is can two species, a billion yearsLet's just say 250 million years; a billion years puts us before there
separated, be closely related, or how closely related and how do we
define relatedness.
Ideally, we know two individuals are closelyNo, siblings share almost exactly 50%. The distribution is very sharply
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 relationshipThose are two incommensurable measures. Using your first measure, any
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. Alla 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
And then we have the problem with definitions and the understanding of concepts. Sometimes one has to step back and ask, what exactly am IThe problem there lies with the use of "basal". It's hard to use it
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 fuelsThis is nobody's theory. Individuals do not give rise to new species
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 HUGEBeg 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,Pretty sure they are, though the common ancestor would be a species, not
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, Inew meaning --
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
say that vertebrate Aor, rather, an old meaning but now quantified. We would be able to
is to C even thoughin the following example is MUCH more closely related to B than it
It would work better with pictures, but those aren't easy to producethe LCA of A and B is strictly ancestral to the LCA of B and C.
I have no idea what this means, FWIW.
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.
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.
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.
On 9/6/22 21:53, Peter Nyikos wrote:estimating degree of disparity,
The line segment joining successive elements is given a number
I don't think you could write such a program. But if you could have aand 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.
So the fundamental question is can two species, a billion yearsLet's just say 250 million years; a billion years puts us before there
separated, be closely related, or how closely related and how do we
define relatedness.
Ideally, we know two individuals are closelyNo, siblings share almost exactly 50%. The distribution is very sharply
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 relationshipThose are two incommensurable measures. Using your first measure, any
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. Alla 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
And then we have the problem with definitions and the understanding of concepts. Sometimes one has to step back and ask, what exactly am IThe problem there lies with the use of "basal". It's hard to use it
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 fuelsThis is nobody's theory. Individuals do not give rise to new species
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 HUGEBeg 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,Pretty sure they are, though the common ancestor would be a species, not
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, Inew meaning --
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
say that vertebrate Aor, rather, an old meaning but now quantified. We would be able to
is to C even thoughin the following example is MUCH more closely related to B than it
It would work better with pictures, but those aren't easy to producethe LCA of A and B is strictly ancestral to the LCA of B and C.
I have no idea what this means, FWIW.
On 9/10/22 5:18 PM, Popping Mad wrote:
On 9/6/22 21:53, Peter Nyikos wrote:estimating degree of disparity,
The line segment joining successive elements is given a number
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 fossilI don't think you could write such a program. But if you could have a
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 yearsLet's just say 250 million years; a billion years puts us before there
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, ofNo, siblings share almost exactly 50%. The distribution is very sharply peaked. Identical twins share 100%, but fraternal twins are like any
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.
other siblings.
Fine. Now Random Chimps and Humans seem to have a closer relationshipThose are two incommensurable measures. Using your first measure, any
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 windowa few.
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
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 evolutionThe problem there lies with the use of "basal". It's hard to use it
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 beenThis is nobody's theory. Individuals do not give rise to new species
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 HUGEBeg 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,Pretty sure they are, though the common ancestor would be a species, not
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.
new meaning --The concept of "more closely related" then could be given a whole
say that vertebrate Aor, rather, an old meaning but now quantified. We would be able to
is to C even thoughin the following example is MUCH more closely related to B than it
the LCA of A and B is strictly ancestral to the LCA of B and C.
I have no idea what this means, FWIW.It would work better with pictures, but those aren't easy to produce
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.
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.
So clearly an individual that sexually reproduces could not create a new species.
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.
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.
On Saturday, September 10, 2022 at 9:07:10 PM UTC-7, John Harshman wrote:
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 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.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.
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.No, siblings share almost exactly 50%. The distribution is very sharply 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.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.
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 namea 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 isThe 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.
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.
Well then individuals can give rise to new species.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).
But what about asexual species?
There has been shown to be a HUGEBeg 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...
mutation.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 sameNone 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.
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.
new meaning --The concept of "more closely related" then could be given a whole
say that vertebrate Aor, rather, an old meaning but now quantified. We would be able to
is to C even thoughin the following example is MUCH more closely related to B than it
the LCA of A and B is strictly ancestral to the LCA of B and C.
I have no idea what this means, FWIW.It would work better with pictures, but those aren't easy to produce
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.
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.
On Saturday, September 10, 2022 at 10:11:03 PM UTC-7, Glenn wrote:mutation.
On Saturday, September 10, 2022 at 9:07:10 PM UTC-7, John Harshman wrote: >>> On 9/10/22 5:18 PM, Popping Mad wrote:
Well then individuals can give rise to new species.On 9/6/22 21:53, Peter Nyikos wrote:estimating degree of disparity,
The line segment joining successive elements is given a number
between them.and the numbers are added together to compute the length of the path
I don't think you could write such a program. But if you could have a
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 yearsLet's just say 250 million years; a billion years puts us before there
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 closelyNo, siblings share almost exactly 50%. The distribution is very sharply
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 relationshipThose are two incommensurable measures. Using your first measure, any
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. Alla 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
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 IThe problem there lies with the use of "basal". It's hard to use it
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 fuelsThis is nobody's theory. Individuals do not give rise to new species
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).
But what about asexual species?
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 sameThere has been shown to be a HUGEBeg 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 andI think you may be reading the wrong scientific literature here.
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,Pretty sure they are, though the common ancestor would be a species, not >>> an individual.
not definitely.
Get together and walla, a barrier is born. In that sense, individuals can create new species.
So, as you have claimed, that "evolution does not require mutation", it is not only accurate but appropriate to say that speciation does not require populations.
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.new meaning --
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
say that vertebrate Aor, rather, an old meaning but now quantified. We would be able to
is to C even thoughin the following example is MUCH more closely related to B than it
It would work better with pictures, but those aren't easy to producethe 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.
On 9/11/22 4:23 PM, Glenn wrote:mutation.
On Saturday, September 10, 2022 at 10:11:03 PM UTC-7, Glenn wrote:
On Saturday, September 10, 2022 at 9:07:10 PM UTC-7, John Harshman wrote: >>> On 9/10/22 5:18 PM, Popping Mad wrote:
Well then individuals can give rise to new species.On 9/6/22 21:53, Peter Nyikos wrote:estimating degree of disparity,
The line segment joining successive elements is given a number
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.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.
So the fundamental question is can two species, a billion yearsLet'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. >>>> Ideally, we know two individuals are closely
separated, be closely related, or how closely related and how do we >>>> define relatedness.
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 anNo, siblings share almost exactly 50%. The distribution is very sharply >>> peaked. Identical twins share 100%, but fraternal twins are like any
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.
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.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.
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. >>>>I'm going to assume you didn't mean Cosmetology. Autocorrect?
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?The problem there lies with the use of "basal". It's hard to use it
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 fuelsThis is nobody's theory. Individuals do not give rise to new species
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).
But what about asexual species?
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 sameThere has been shown to be a HUGEBeg 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 andI think you may be reading the wrong scientific literature here.
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.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.
So, as you have claimed, that "evolution does not require mutation", it is not only accurate but appropriate to say that speciation does not require populations.
Well, a population of two, in that scenario. More importantly, that
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.
The last common ancestor of Pachyrhinosaurus... that might be true. But >>>> as we get more evidence of this transition, we might find that more thannew meaning --
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
say that vertebrate Aor, rather, an old meaning but now quantified. We would be able to
is to C even thoughin the following example is MUCH more closely related to B than it
It would work better with pictures, but those aren't easy to producethe 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.
That's the part I was talking about.
Writing these trees can be done without human biases and it is done soYou understand that existing phylogeny programs work just that way. 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.
However unlikely is irrelevant, nor do you provide any evidence to support your "probably".
On Sunday, September 11, 2022 at 7:07:08 PM UTC-7, John Harshman wrote:mutation.
On 9/11/22 4:23 PM, Glenn wrote:
On Saturday, September 10, 2022 at 10:11:03 PM UTC-7, Glenn wrote:
On Saturday, September 10, 2022 at 9:07:10 PM UTC-7, John Harshman wrote: >>>>> On 9/10/22 5:18 PM, Popping Mad wrote:
Well then individuals can give rise to new species.On 9/6/22 21:53, Peter Nyikos wrote:estimating degree of disparity,
The line segment joining successive elements is given a number
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.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.
So the fundamental question is can two species, a billion yearsLet'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. >>>>>> Ideally, we know two individuals are closely
separated, be closely related, or how closely related and how do we >>>>>> define relatedness.
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.No, siblings share almost exactly 50%. The distribution is very sharply >>>>> peaked. Identical twins share 100%, but fraternal twins are like any >>>>> other siblings.
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.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.
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. >>>>>>I'm going to assume you didn't mean Cosmetology. Autocorrect?
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?The problem there lies with the use of "basal". It's hard to use it
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 fuelsThis is nobody's theory. Individuals do not give rise to new species >>>>> (except for the rare case of polyploid speciation).
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.
But what about asexual species?
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 sameThere has been shown to be a HUGEBeg 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 andI think you may be reading the wrong scientific literature here.
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.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.
So, as you have claimed, that "evolution does not require mutation", it is not only accurate but appropriate to say that speciation does not require populations.
Well, a population of two, in that scenario. More importantly, that
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.
However unlikely is irrelevant, nor do you provide any evidence to support your "probably".
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?
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.new meaning --
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
It would work better with pictures, but those aren't easy to produce >>>>> 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 ofor, 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.
"more closely related", and it's opposed to the cladistic definition: >>>>> more recent common ancestor.
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 people.
Sure terminal nodes like in the RB-Tree used in the Linux scheduler.
Wouldn't know, since I don't know what that is.
Species, known species, are all terminal nodes.
On 9/11/22 8:53 PM, Glenn wrote:same mutation.
On Sunday, September 11, 2022 at 7:07:08 PM UTC-7, John Harshman wrote:
On 9/11/22 4:23 PM, Glenn wrote:
On Saturday, September 10, 2022 at 10:11:03 PM UTC-7, Glenn wrote:
On Saturday, September 10, 2022 at 9:07:10 PM UTC-7, John Harshman wrote:
On 9/10/22 5:18 PM, Popping Mad wrote:Well then individuals can give rise to new species.
On 9/6/22 21:53, Peter Nyikos wrote:estimating degree of disparity,
The line segment joining successive elements is given a number
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,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.
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.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. >>>>>> Ideally, we know two individuals are closely
related because they share genetic material. But I don't even know whatNo, siblings share almost exactly 50%. The distribution is very sharply
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? SoI'm going to assume you didn't mean Cosmetology. Autocorrect?
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.
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 ofThe 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.
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 fuelsThis is nobody's theory. Individuals do not give rise to new species >>>>> (except for the rare case of polyploid speciation).
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.
But what about asexual species?
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 theThere has been shown to be a HUGEBeg 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 andI think you may be reading the wrong scientific literature here. >>>>>> So are all Ceratopsidae from the same common ancestor? Maybe, likely, >>>>>> not definitely.
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.
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.
So, as you have claimed, that "evolution does not require mutation", it is not only accurate but appropriate to say that speciation does not require populations.
Well, a population of two, in that scenario. More importantly, that
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.
However unlikely is irrelevant, nor do you provide any evidence to support your "probably".That's not what punctuated equilibrium is. You should probably read
I'm reminded of punctuated equilibrium. Speciation in a blink of the eye. Why do you insist that such a thing is unlikely?
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 speciesYep.
(except for the rare case of polyploid speciation)."
Will you now argue that an individual can be a population?Have you considered the possibility that you don't understand because
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?
The last common ancestor of Pachyrhinosaurus... that might be true. ButIt would work better with pictures, but those aren't easy to produce >>>>> here. But he's just saying that two species are more closely related if
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 --I have no idea what this means, FWIW.
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. >>>>>>
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.
But that's not the way phylogenetic trees work,
All Species are NODES
Some Species are Terminal Nodes
That isn't the theory.
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.
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.
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.
This is why computer scientists and mathematicians should learn more
biology before presuming to revolutionize the field.
Presumably. But my point is that you can't identify the internal nodes
with known species.
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?
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.
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
biology.
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
are going to use them. And they have the same properties regardless
what abstraction they are modeling.
On 9/12/22 6:01 PM, Popping Mad wrote:
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 revolutionizingYour ignorance of biology convinces you that you know all the biology
biology.
you need to know. And you won't listen to a biologist. Why are you even
here?
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.
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.
Studying trees doesn't require me to know what "the RB-Tree used in the
Linux scheduler"
Your ignorance of biology convinces you
Your ignorance of biology convinces you
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
On 9/12/22 11:23, John Harshman wrote:
Presumably. But my point is that you can't identify the internal nodesand 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.
with known species.
If all your known species are tips, your model is broken fundementally.
On 9/14/22 6:53 AM, Popping Mad wrote:
Your ignorance of biology convinces you
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?
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 nodesand 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.
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."
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 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.
This would be the natural result of any usual phylogenetic analysis of
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."
And you have never been able to explain a use.
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:Now a tiny window has opened between successive activities, just long enough to post this and maybe another short post.
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.
reasonable, not the evidence of fossils."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".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
--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
Do you deny that you have used "lies" and "lying" for exactly what Kathleen Hunt is doingIn 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.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 zeroWhy "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.
autapomorphies.
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
Professor, Dept. of Mathematics -- standard disclaimer--
Univ. of So. Carolina in Columbia
http://people.math.sc.edu/nyikos
On Thursday, September 22, 2022 at 9:27:42 AM UTC-4, John Harshman wrote:reasonable, not the evidence of fossils."
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 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".
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
--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.
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.
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.
On 9/22/22 9:36 AM, Peter Nyikos wrote:reasonable, not the evidence of fossils."
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
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".
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
--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.
He probably wasn't up on the language used in phylogenetics. On
the other hand, I am.
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?
Or were you referring to trees at all? or only to the character analysis whichNo idea what you mean by that.
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.
What you're trying to say there is also far from clear.
A zero-length
branch is quite possible. If not that, what are you referring to?
On Thursday, September 22, 2022 at 3:27:02 PM UTC-4, John Harshman wrote:reasonable, not the evidence of fossils."
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:
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
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.
You aren't reading. The term is "terminal node", as opposed to "internal >>>> node".
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.] >>>
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
--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.
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.
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.
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 whichNo idea what you mean by that.
almost never specifies the number of apomorphies?
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.
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."
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?"]
[1] given that you are adamantly opposed to internal nodes being assigned
to known genera or species.
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.
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 nodesand 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.
reasonable, not the evidence of fossils."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
--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.
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?
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.
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?
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]
Correct.
fig. 18 in paper coauthored by Mickey Mortimer: https://peerj.com/articles/7247/?td=bl&fbclid=IwAR09VFddJNY8v0rvmEh9HmtINsJLScQj0B98UsoKEbTjMMNZLTdxZyA4h4w#systematicNote that in Fig. 17 the branch lengths mean nothing.
Fig. 1 in https://academic.oup.com/gbe/article/9/9/2308/4095375Not sure what "as described" means, but the branches in that tree are
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:That link goes only to the abstract and, for some reason, Fig. 3. So I
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:Correct.
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
You never forget a grudge.
Or were you referring to trees at all? or only to the character analysis whichNo idea what you mean by that.
almost never specifies the number of apomorphies?
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.
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.
More importantly, such a tree is what I was
talking about, and it would show your "thorns" automatically.
On Tuesday, September 27, 2022 at 9:16:05 PM UTC-4, John Harshman wrote:reasonable, not the evidence of fossils."
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:]
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 nodesand 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.
Unfortunately, Ruben seems to have gone incommunicado for an indefinite 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
--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.
Methods of constructing phylogenetic trees are irrelevant
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?
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.
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.
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.
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.
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.
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:Note that in Fig. 17 the branch lengths mean nothing.
https://peerj.com/articles/7247/?td=bl&fbclid=IwAR09VFddJNY8v0rvmEh9HmtINsJLScQj0B98UsoKEbTjMMNZLTdxZyA4h4w#systematic
That's why I didn't talk about Fig. 17. Duh.
Fig. 1 in https://academic.oup.com/gbe/article/9/9/2308/4095375scaled by number of changes, if that's what you mean. (Incidentally,
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
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:That link goes only to the abstract and, for some reason, Fig. 3. So I
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.
Didn't you get two icons labeled "Download full-length PDF" and "Read full-text" in the upper right corner?
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:Correct.
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
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.
Or were you referring to trees at all? or only to the character analysis whichNo idea what you mean by that.
almost never specifies the number of apomorphies?
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 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?
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 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.
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'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?
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.
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 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 this trash talk serve a legitimate purpose?
Does any of the off-topic whatever-it-is that follows below?
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
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