On 9/7/22 00:18, John Harshman wrote:
> But these distances would depend on what characters you used to make the
> measured tree, and there is no real objective way to choose these
> measures of disparity.

Yes and no. There is real objectivity. It is just not perfect.
Attacking those attributes is where the science is. The most attributes
you measure, FWIW, the more likely it is to reach a strong conclusion.

If you think that the ambuitiy involved in this is too difficult to
produce good science, then try your hand at quantum physics where
ambibuity is baked into the theory :)

On 9/7/22 00:18, John Harshman wrote:
> I think it would lead to overlapping groups if used in classification.
> Velociraptor closer to Archaeopteryx than Archaeopteryx to
> Confuciusornis. Archaeopteryx closer to Confuciusornis than
> Confusiusornis to Icthyornis.

It might. And that might be an indication that we are not choosing our
attributes to the cost between nodes well. Or it can mean that we have
evidence of inter-species breeding, or something else is going on?

All we have is the observable facts, and that might not be enough to
give us a discernible outcome that we are satisfied with. It is better
than guessing and ignoring evidence.

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 9/8/22 13:11, Peter Nyikos wrote:
> All known ones for each skeleton. We are talking about extinct species here,

that is another abiguity. When a species evolves into another species,
it didn't go extinct. It evolved. Most species go extinct, but some
don't I am happy to report, as I belong to one such lineage.

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?

On 9/10/22 5:28 PM, Popping Mad wrote:
> On 9/7/22 00:18, John Harshman wrote:
>> I don't see patristic distance as much better for this purpose than
>> simple pairwise distance.
>
> FWIW - I have no idea how Christian fathers relate to distances in a
> graph but....
>
> ignoring the cost values between nodes, ie treating them all equal,will
> get a wrong result every time.

Nobody is proposing such a thing.

> 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.

Again, nobody is proposing such a thing.

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.

https://pubmed.ncbi.nlm.nih.gov/24639164/
https://evolution.gs.washington.edu/gs541/2010/lecture1.pdf
https://fliphtml5.com/aavh/qawv

On 9/10/22 21:03, John Harshman wrote:
> You're thinking about extant species,

I am talking about all species, but especially fossils.

On 9/10/22 21:03, John Harshman wrote:
> Is Archaeopteryx more closely related to Deinonychus or Larus?

FWIW - I don't know and I am not the person to ask.

On 9/10/22 21:04, John Harshman wrote:
> Nobody is proposing such a thing.

Then I am at a loss at what you are saying.

I read where you said the distance between species is only relavant for
wo species but not to set up an evolutionary tree for them.

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 9/10/22 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 9/10/22 21:03, John Harshman wrote:
> 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?
>

<<They can tell us mamy things. But using them to define closeness of
relationship is not one of those things.>>

YOu wrote that - Not I :)

Maybe I am not following. This group tends to take deep detours in
discussion and in fact I can often not follow the point being made.

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 name
a few.
I'm going to assume you didn't mean Cosmetology. Autocorrect?

> And then we have the problem with definitions and the understanding of
> concepts. Sometimes one has to step back and ask, what exactly am I
> trying to learn here?
>
> Are two species closely related despite 300 million years of evolution
> if they genetics have been largely conserved other that time? There is
> a molecular clock but the functional expression of genes might well be
> well preserved in two species separated by by a long period of time.
> Hydrothermal vent microbial organism might be more closely related to
> their ancient ancestors from a billion years ago than a Moerithriun to
> an African Elephant, let alone an Asian Elephant to most species in
> Paenungulata. It is suggested that a Hyrax is more basal and an African
> elephant, and I would ask, "how so since they are both existing species
> and Elephants didn't spring from a modern Hyrax".
The problem there lies with the use of "basal". It's hard to use it
without having a false idea. I try to avoid it myself.

> So the language itself, here, gets very ambiguous which fuels
> disagreements and trolls alike.
>
> And added to this amphibological language a new problem seems to have
> emerged recently with core elements of evolutionary theory. It has been
> a conceit that a species evolves traits to conform with its environment
> through natural selection. Therefor, in theory at least, any individual
> could prove to be a node to a new species if they have a mutation that
> gives its linage an advantage.
This is nobody's theory. Individuals do not give rise to new species
(except for the rare case of polyploid speciation).

> There has been shown to be a HUGE
> conceit as we have learned from the study of the evolution of Homo and
> other species. It has come to be understood that mutations that give
> advantages can and do spring up multiple times, even among closely
> related species... the same mutation. And then we share DNA material
> outside of reproduction.
Beg pardon?

> And then mutation will fade if unneeded and
> spring up again. Instead of a nice tree, evolution might well look more
> like a river delta. Or a suppressed shared gene might become active in
> two different lineages, or two species might interbreed?
>
> Everything wants to become a crab...
>
>
> None of the above is my own original ideas. They all come from reading
> scientific literature both in the popular press and in peer reviewed
> journals.
I think you may be reading the wrong scientific literature here.

> So are all Ceratopsidae from the same common ancestor? Maybe, likely,
> not definitely.
Pretty sure they are, though the common ancestor would be a species, not
an individual.

> The last common ancestor of Pachyrhinosaurus... that might be true. But
> as we get more evidence of this transition, we might find that more than
> once species of closely related dinosaurs evolved similarly, utilizing
> similar mutations. Finding a Least common ancestor might be unknowable.
> But that might not make this method of defining families and orders and
> genus, any less useful. We need to use some definition.
>
>
> No maybe all these ambiguities have been solved in Paleontology, I
> don't know. But I do know that over my lifetime many streams of thought
> within the science has come and gone and evolved. I wouldn't take a
> theological attachment to any system for the analysis of the
> evolutionary procession of species. Nature tends to surprise us and
> these are all just tools of logic to help us understand the ancient past
> and the nature of biological systems.
>
>> The concept of "more closely related" then could be given a whole
new meaning --
>> or, rather, an old meaning but now quantified. We would be able to
say that vertebrate A
>> in the following example is MUCH more closely related to B than it
is to C even though
>> the LCA of A and B is strictly ancestral to the LCA of B and C.
>
> I have no idea what this means, FWIW.
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 9/10/22 6:39 PM, Popping Mad wrote:
> On 9/8/22 15:04, John Harshman wrote:
>>
>> But that all becomes useless once you try to use it for anything except
>> pairwise comparisons.
>
> There are hundreds of algorithms that prove this to be untrue.
> Sankoff's algorthim on genetic mutation is an example.

Explain.

> 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.

No, that has nothing to do with our disagreement.

On 9/10/22 6:44 PM, Popping Mad wrote:
> On 9/10/22 21:04, John Harshman wrote:
>> Nobody is proposing such a thing.
>
>
> Then I am at a loss at what you are saying.
>
> I read where you said the distance between species is only relavant for
> wo species but not to set up an evolutionary tree for them.

Not quite what I said.

On 9/10/22 6:51 PM, Popping Mad wrote:
> 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.

Wouldn't know, since I don't know what that is.

On 9/10/22 6:57 PM, Popping Mad wrote:
> On 9/10/22 17:49, John Harshman wrote:
>>>> he heart of cladistics is found in the phylogenetic trees, which put all
>>>> organisms at the branch tips.
>>>
>>> nodes not tips
>>
>> "Branch tips" here refers to terminal nodes.
>> So the claim is true.
>
>
> No - it is not. Species are not branch tips but nodes. Tips are a
> sub-set of nodes, as they are terminal nodes.

Species, known species, are all terminal nodes. You can't identify
fossils with internal nodes; there's just no way to do that.

> Are we failing basic set theory now?
>
> In theory at lest...
>
> All Species are NODES
> Some Species are Terminal Nodes

That isn't the theory.

> All Species are NOT terminal Nodes, as most are just nodes.

Well, it's true that some species are ancestral to others. But that's
not the way phylogenetic trees work, because we have no way of
identifying species as ancestral.

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 name
a few.
I'm going to assume you didn't mean Cosmetology. Autocorrect?

> And then we have the problem with definitions and the understanding of
> concepts. Sometimes one has to step back and ask, what exactly am I
> trying to learn here?
>
> Are two species closely related despite 300 million years of evolution
> if they genetics have been largely conserved other that time? There is
> a molecular clock but the functional expression of genes might well be
> well preserved in two species separated by by a long period of time.
> Hydrothermal vent microbial organism might be more closely related to
> their ancient ancestors from a billion years ago than a Moerithriun to
> an African Elephant, let alone an Asian Elephant to most species in
> Paenungulata. It is suggested that a Hyrax is more basal and an African
> elephant, and I would ask, "how so since they are both existing species
> and Elephants didn't spring from a modern Hyrax".
The problem there lies with the use of "basal". It's hard to use it
without having a false idea. I try to avoid it myself.

> So the language itself, here, gets very ambiguous which fuels
> disagreements and trolls alike.
>
> And added to this amphibological language a new problem seems to have
> emerged recently with core elements of evolutionary theory. It has been
> a conceit that a species evolves traits to conform with its environment
> through natural selection. Therefor, in theory at least, any individual
> could prove to be a node to a new species if they have a mutation that
> gives its linage an advantage.
This is nobody's theory. Individuals do not give rise to new species
(except for the rare case of polyploid speciation).

> There has been shown to be a HUGE
> conceit as we have learned from the study of the evolution of Homo and
> other species. It has come to be understood that mutations that give
> advantages can and do spring up multiple times, even among closely
> related species... the same mutation. And then we share DNA material
> outside of reproduction.
Beg pardon?

> And then mutation will fade if unneeded and
> spring up again. Instead of a nice tree, evolution might well look more
> like a river delta. Or a suppressed shared gene might become active in
> two different lineages, or two species might interbreed?
>
> Everything wants to become a crab...
>
>
> None of the above is my own original ideas. They all come from reading
> scientific literature both in the popular press and in peer reviewed
> journals.
I think you may be reading the wrong scientific literature here.

> So are all Ceratopsidae from the same common ancestor? Maybe, likely,
> not definitely.
Pretty sure they are, though the common ancestor would be a species, not
an individual.

> The last common ancestor of Pachyrhinosaurus... that might be true. But
> as we get more evidence of this transition, we might find that more than
> once species of closely related dinosaurs evolved similarly, utilizing
> similar mutations. Finding a Least common ancestor might be unknowable.
> But that might not make this method of defining families and orders and
> genus, any less useful. We need to use some definition.
>
>
> No maybe all these ambiguities have been solved in Paleontology, I
> don't know. But I do know that over my lifetime many streams of thought
> within the science has come and gone and evolved. I wouldn't take a
> theological attachment to any system for the analysis of the
> evolutionary procession of species. Nature tends to surprise us and
> these are all just tools of logic to help us understand the ancient past
> and the nature of biological systems.
>
>> The concept of "more closely related" then could be given a whole
new meaning --
>> or, rather, an old meaning but now quantified. We would be able to
say that vertebrate A
>> in the following example is MUCH more closely related to B than it
is to C even though
>> the LCA of A and B is strictly ancestral to the LCA of B and C.
>
> I have no idea what this means, FWIW.
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 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 name
> a few.
> I'm going to assume you didn't mean Cosmetology. Autocorrect?
> > And then we have the problem with definitions and the understanding of
> > concepts. Sometimes one has to step back and ask, what exactly am I
> > trying to learn here?
> >
> > Are two species closely related despite 300 million years of evolution
> > if they genetics have been largely conserved other that time? There is
> > a molecular clock but the functional expression of genes might well be
> > well preserved in two species separated by by a long period of time.
> > Hydrothermal vent microbial organism might be more closely related to
> > their ancient ancestors from a billion years ago than a Moerithriun to
> > an African Elephant, let alone an Asian Elephant to most species in
> > Paenungulata. It is suggested that a Hyrax is more basal and an African
> > elephant, and I would ask, "how so since they are both existing species
> > and Elephants didn't spring from a modern Hyrax".
> The problem there lies with the use of "basal". It's hard to use it
> without having a false idea. I try to avoid it myself.
> > So the language itself, here, gets very ambiguous which fuels
> > disagreements and trolls alike.
> >
> > And added to this amphibological language a new problem seems to have
> > emerged recently with core elements of evolutionary theory. It has been
> > a conceit that a species evolves traits to conform with its environment
> > through natural selection. Therefor, in theory at least, any individual
> > could prove to be a node to a new species if they have a mutation that
> > gives its linage an advantage.
> This is nobody's theory. Individuals do not give rise to new species
> (except for the rare case of polyploid speciation).

Well then individuals can give rise to new species.
But what about asexual species?
> > There has been shown to be a HUGE
> > conceit as we have learned from the study of the evolution of Homo and
> > other species. It has come to be understood that mutations that give
> > advantages can and do spring up multiple times, even among closely
> > related species... the same mutation. And then we share DNA material
> > outside of reproduction.
> Beg pardon?
> > And then mutation will fade if unneeded and
> > spring up again. Instead of a nice tree, evolution might well look more
> > like a river delta. Or a suppressed shared gene might become active in
> > two different lineages, or two species might interbreed?
> >
> > Everything wants to become a crab...
> >
> >
> > None of the above is my own original ideas. They all come from reading
> > scientific literature both in the popular press and in peer reviewed
> > journals.
> I think you may be reading the wrong scientific literature here.
> > So are all Ceratopsidae from the same common ancestor? Maybe, likely,
> > not definitely.
> Pretty sure they are, though the common ancestor would be a species, not
> an individual.

It always takes two to tango, sexually speaking. So clearly an individual that sexually reproduces could not create a new species. But hypothetically, you could have a mutation that would only allow you to have a child with another that had the same mutation.
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.
> >
> >> The concept of "more closely related" then could be given a whole
> new meaning --
> >> or, rather, an old meaning but now quantified. We would be able to
> say that vertebrate A
> >> in the following example is MUCH more closely related to B than it
> is to C even though
> >> the LCA of A and B is strictly ancestral to the LCA of B and C.
> >
> > I have no idea what this means, FWIW.
> 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 Fri, 9 Sep 2022 17:55:58 -0700, John Harshman
<john.harshman@gmail.com> wrote:

>On 9/9/22 4:40 PM, Peter Nyikos wrote:
>> This is a change of pace: A lighthearted (for me, anyway) treatment of John's reaction to a PS
>> of mine at the end of a reply he did to me here:
>>
>> On Wednesday, September 7, 2022 at 12:18:55 AM UTC-4, John Harshman wrote:
>>
>>> On 9/6/22 6:53 PM, Peter Nyikos wrote:
>>
>>>> PS Remember those little children who thought it was "way cool"
>>>> that birds are dinosaurs? Do you think you [can] get them to believe
>>>> that your concept is better than the one with which they
>>>> are familiar (aunts, uncles, cousins, etc.) and which the disparity-measurer's
>>>> concept so faithfully mirrors?
>>
>>> I doubt children of that age would have a clue about this controversy.
>>> But they would probably believe my concept was better if they liked me
>>> or if I gave them candy.
>>
>> That depends on whether you invite me twice to talk to them.
>> The first time, I would try to establish rapport with them by talking about
>> some neat things that occurred on a pair of fossil hunts in Wyoming on which
>> I participated a little over a year ago.
>>
>> The second time, I would get around to asking them if any of them
>> had one or more great-grandparents still alive, after matching any
>> candy bribe of yours. If it's a class of ten or more, there is an excellent chance
>> that at least one hand would go up, because nowadays a goodly
>> fraction of people live to that age.
>>
>> With twenty, there might arise a longish bidding as to how many were still alive.
>> Once that had settled down, I would ask them whether any of those great-grandparents
>> had any brothers or sisters. And if any hands are raised [some might not know the answers]
>> I would ask the raisers whether they had any brothers or sisters.
>>
>> If yes, I would turn to one of them and say,
>>
>> Did you know that Dr. John's [or whatever they call you] way saying how different kinds of
>> animals are related is like him saying, "Your great-grandmother is more closely related
>> to your brother than she is to her own brother."
>>
>> Once this has sunk in and the expressions of astonishment subsided,
>> I will say, "Now Dr. John will explain to you why this is the best way
>> to talk about how different kinds of animals are related."
>>
>> My suggestion for you to save face is to begin by saying that we use the
>> same words for very different things. The one that comes to mind
>> is "pipe". You could make a little joke about the absent-minded
>> professor who tried to smoke a pipe that gas runs through,
>> and to run water through the pipe that he smokes. But you could
>> probably do better than that, given all this lead time.
>>
>>
>> And then, you could explain that the expression "more closely related"
>> works the same way.
>>
>> But you'd still have a big problem explaining why it is the RIGHT
>> meaning for dealing with animal species.
>
>All I can say is that you would be ill-advised to quite your day job.

Perhaps PeeWee Peter could use this on his night job:

Two men are walking along, when a very noisy car goes by.
Man A says, "That's so loud, I can't hear myself think."
Man B says, "That's my sister's car. She blew the exhaust pipe."
Man A says, "I'm surprised she didn't burn her lips."

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 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 Sunday, September 11, 2022 at 3:59:27 PM UTC-7, Popping Mad wrote:
> 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.

Perhaps you don't realize that it takes two to tango.

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:
> > > 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 name
> > a few.
> > I'm going to assume you didn't mean Cosmetology. Autocorrect?
> > > And then we have the problem with definitions and the understanding of
> > > concepts. Sometimes one has to step back and ask, what exactly am I
> > > trying to learn here?
> > >
> > > Are two species closely related despite 300 million years of evolution
> > > if they genetics have been largely conserved other that time? There is
> > > a molecular clock but the functional expression of genes might well be
> > > well preserved in two species separated by by a long period of time.
> > > Hydrothermal vent microbial organism might be more closely related to
> > > their ancient ancestors from a billion years ago than a Moerithriun to
> > > an African Elephant, let alone an Asian Elephant to most species in
> > > Paenungulata. It is suggested that a Hyrax is more basal and an African
> > > elephant, and I would ask, "how so since they are both existing species
> > > and Elephants didn't spring from a modern Hyrax".
> > The problem there lies with the use of "basal". It's hard to use it
> > without having a false idea. I try to avoid it myself.
> > > So the language itself, here, gets very ambiguous which fuels
> > > disagreements and trolls alike.
> > >
> > > And added to this amphibological language a new problem seems to have
> > > emerged recently with core elements of evolutionary theory. It has been
> > > a conceit that a species evolves traits to conform with its environment
> > > through natural selection. Therefor, in theory at least, any individual
> > > could prove to be a node to a new species if they have a mutation that
> > > gives its linage an advantage.
> > This is nobody's theory. Individuals do not give rise to new species
> > (except for the rare case of polyploid speciation).
> Well then individuals can give rise to new species.
> But what about asexual species?
> > > There has been shown to be a HUGE
> > > conceit as we have learned from the study of the evolution of Homo and
> > > other species. It has come to be understood that mutations that give
> > > advantages can and do spring up multiple times, even among closely
> > > related species... the same mutation. And then we share DNA material
> > > outside of reproduction.
> > Beg pardon?
> > > And then mutation will fade if unneeded and
> > > spring up again. Instead of a nice tree, evolution might well look more
> > > like a river delta. Or a suppressed shared gene might become active in
> > > two different lineages, or two species might interbreed?
> > >
> > > Everything wants to become a crab...
> > >
> > >
> > > None of the above is my own original ideas. They all come from reading
> > > scientific literature both in the popular press and in peer reviewed
> > > journals.
> > I think you may be reading the wrong scientific literature here.
> > > So are all Ceratopsidae from the same common ancestor? Maybe, likely,
> > > not definitely.
> > Pretty sure they are, though the common ancestor would be a species, not
> > an individual.
> It always takes two to tango, sexually speaking. So clearly an individual that sexually reproduces could not create a new species. But hypothetically, you could have a mutation that would only allow you to have a child with another that had the same mutation.
> 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.
> > >
> > >
> > > No maybe all these ambiguities have been solved in Paleontology, I
> > > don't know. But I do know that over my lifetime many streams of thought
> > > within the science has come and gone and evolved. I wouldn't take a
> > > theological attachment to any system for the analysis of the
> > > evolutionary procession of species. Nature tends to surprise us and
> > > these are all just tools of logic to help us understand the ancient past
> > > and the nature of biological systems.
> > >
> > >> The concept of "more closely related" then could be given a whole
> > new meaning --
> > >> or, rather, an old meaning but now quantified. We would be able to
> > say that vertebrate A
> > >> in the following example is MUCH more closely related to B than it
> > is to C even though
> > >> the LCA of A and B is strictly ancestral to the LCA of B and C.
> > >
> > > I have no idea what this means, FWIW.
> > 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.