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Discovery of 'cryptic species' shows Earth is even more biologically diverse | Wildlife | The Guardian

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thompnickson2

Discovery of 'cryptic species' shows Earth is even more biologically diverse | Wildlife | The Guardian

https://www.theguardian.com/environment/2020/dec/25/discovery-of-cryptic-species-shows-earth-is-even-more-biologically-diverse-aoe

So what IS a species? A level of distinctness of design, a degree of genetic differentiation, or an interbreeding population? And what happens to Darwinism when these things turn out to be not particularly well correlated, in the way that the signs and symptoms of hunger turned out to be not so well correlated as the Cartesian model would require? Steve Guerin: if you want to demolish Darwinism, here is where you start.

Nick

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Gary Schiltz-4

Re: Discovery of 'cryptic species' shows Earth is even more biologically diverse | Wildlife | The Guardian

When I studied biology at university back in the 1970s, my recollection is that most biologists in those days thought of species as an interbreeding population of individuals. Over the years, I've seen this definition give way more and more to defining species by genetic differences alone. Though I haven't been professionally a biologist for over 40 years (if ever), my life as a birdwatcher (and occasional keeper of coveted lists of species seen) has been affected by this shift. Based on genetic analysis (possibly tempered by studies of behavior, range, morphology), bird species are frequently "split" into two or more separate groups, either "subspecies", "races", or even full blown "species" (yay!! I've seen both those, add another species to my life list). Or the converse is also true - based on genetic analysis (tempered as above), ornithological consensus will deem two or more species to be merely different races or subspecies of one species, which we refer to as "lumping" (boo!!! lost some bragging rights about my life list).

I asked an ornithologist friend about this a couple of years ago. I've always been a "lumper" at heart, even if it does result in my life list being shorter. To me, if two individuals decide to mate, and produce offspring, they ought to be considered the same species. Maybe adding the requirement that the offspring are themselves fertile and able to produce fertile offspring. My ornithologist friend seems pretty firmly in the camp that defines species by their genetics. I asked him if this wasn't rather arbitrary, and the only thing I remember him mentioning (which I never followed up on studying) was the notion of a "clade". I won't comment further on that, since I know absolutely nothing about clades.

As a side note, we certainly don't classify currently living Homo sapiens individuals into different species, but then I don't know if the genetic differences among different races of people are more, or less, significant than that of some other animal species. This would, of course, be hugely (and justifiably, I believe) unpopular among us humans. I asked my parrots what they think, and they just chewed on the furniture more. I don't know if that signifies agreement or disagreement with my ornithologist friend.

On Sun, Dec 27, 2020 at 11:54 AM <[hidden email]> wrote:

https://www.theguardian.com/environment/2020/dec/25/discovery-of-cryptic-species-shows-earth-is-even-more-biologically-diverse-aoe
So what IS a species? A level of distinctness of design, a degree of genetic differentiation, or an interbreeding population? And what happens to Darwinism when these things turn out to be not particularly well correlated, in the way that the signs and symptoms of hunger turned out to be not so well correlated as the Cartesian model would require? Steve Guerin: if you want to demolish Darwinism, here is where you start.
Nick
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David Eric Smith

Re: Discovery of 'cryptic species' shows Earth is even more biologically diverse | Wildlife | The Guardian

My late colleague Harold Morowitz once made a comment in an afternoon working conversation, which I found funny and fun. He said something like “I remember only 45 years ago when the lagomorphs split off from the rodents”.

Kind of like Paul Erdos, the 4 billion year old man.

Eric

On Dec 27, 2020, at 12:44 PM, Gary Schiltz <[hidden email]> wrote:

When I studied biology at university back in the 1970s, my recollection is that most biologists in those days thought of species as an interbreeding population of individuals. Over the years, I've seen this definition give way more and more to defining species by genetic differences alone. Though I haven't been professionally a biologist for over 40 years (if ever), my life as a birdwatcher (and occasional keeper of coveted lists of species seen) has been affected by this shift. Based on genetic analysis (possibly tempered by studies of behavior, range, morphology), bird species are frequently "split" into two or more separate groups, either "subspecies", "races", or even full blown "species" (yay!! I've seen both those, add another species to my life list). Or the converse is also true - based on genetic analysis (tempered as above), ornithological consensus will deem two or more species to be merely different races or subspecies of one species, which we refer to as "lumping" (boo!!! lost some bragging rights about my life list).

I asked an ornithologist friend about this a couple of years ago. I've always been a "lumper" at heart, even if it does result in my life list being shorter. To me, if two individuals decide to mate, and produce offspring, they ought to be considered the same species. Maybe adding the requirement that the offspring are themselves fertile and able to produce fertile offspring. My ornithologist friend seems pretty firmly in the camp that defines species by their genetics. I asked him if this wasn't rather arbitrary, and the only thing I remember him mentioning (which I never followed up on studying) was the notion of a "clade". I won't comment further on that, since I know absolutely nothing about clades.

As a side note, we certainly don't classify currently living Homo sapiens individuals into different species, but then I don't know if the genetic differences among different races of people are more, or less, significant than that of some other animal species. This would, of course, be hugely (and justifiably, I believe) unpopular among us humans. I asked my parrots what they think, and they just chewed on the furniture more. I don't know if that signifies agreement or disagreement with my ornithologist friend.

On Sun, Dec 27, 2020 at 11:54 AM <[hidden email]> wrote:
https://www.theguardian.com/environment/2020/dec/25/discovery-of-cryptic-species-shows-earth-is-even-more-biologically-diverse-aoe
So what IS a species? A level of distinctness of design, a degree of genetic differentiation, or an interbreeding population? And what happens to Darwinism when these things turn out to be not particularly well correlated, in the way that the signs and symptoms of hunger turned out to be not so well correlated as the Cartesian model would require? Steve Guerin: if you want to demolish Darwinism, here is where you start.
Nick
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jon zingale

Re: Discovery of 'cryptic species' shows Earth is even more biologically diverse | Wildlife | The Guardian

*Kind of like Paul Erdos, the 4 billion year old man.* Paul Erdos C.D.

Sent from the Friam mailing list archive at Nabble.com.

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jon zingale

Re: Discovery of 'cryptic species' shows Earth is even more biologically diverse | Wildlife | The Guardian

In reply to this post by David Eric Smith

*Kind of like Paul Erdos, the 4 billion year old man.*

Paul Erdos C.D.

thompnickson2

Re: Discovery of 'cryptic species' shows Earth is even more biologically diverse | Wildlife | The Guardian

In reply to this post by David Eric Smith

Gary, and EricS,

Well my vote is for Species, genus, etc., to be descriptive categories, levels of difference in the possession of traits. As soon as we put our foot down, there, we discover that species differences are NOT as well correlated with levels of genetic differentiation or with gene flow as our theories would require. “WHY are species?” then becomes a real and difficult question. Which, I think, relates to the question of why the genome is as modular as it is. I whose interest is THAT?

I agree that cladistics, with its weird terminology that only a ideologue could love, is impenetrable. But I think we have to penetrate it. It is, after all, a descriptive method of arraying organisms on the basis of their manifest traits. It does allow us, for instance, to make a distinction between convergent evolution (where creatures that are fundamentally different look superficially similar) and divergent evolution (where creatures that are fundamentally similar look superficially different) because it can breath life into the notions of fundamentally and superficially.

Nick

Nicholas Thompson

Emeritus Professor of Ethology and Psychology

Clark University

[hidden email]

https://wordpress.clarku.edu/nthompson/

From: Friam <[hidden email]> On Behalf Of David Eric Smith
Sent: Sunday, December 27, 2020 11:53 AM
To: The Friday Morning Applied Complexity Coffee Group <[hidden email]>
Subject: Re: [FRIAM] Discovery of 'cryptic species' shows Earth is even more biologically diverse | Wildlife | The Guardian

Kind of like Paul Erdos, the 4 billion year old man.

Eric

On Dec 27, 2020, at 12:44 PM, Gary Schiltz <[hidden email]> wrote:

When I studied biology at university back in the 1970s, my recollection is that most biologists in those days thought of species as an interbreeding population of individuals. Over the years, I've seen this definition give way more and more to defining species by genetic differences alone. Though I haven't been professionally a biologist for over 40 years (if ever), my life as a birdwatcher (and occasional keeper of coveted lists of species seen) has been affected by this shift. Based on genetic analysis (possibly tempered by studies of behavior, range, morphology), bird species are frequently "split" into two or more separate groups, either "subspecies", "races", or even full blown "species" (yay!! I've seen both those, add another species to my life list). Or the converse is also true - based on genetic analysis (tempered as above), ornithological consensus will deem two or more species to be merely different races or subspecies of one species, which we refer to as "lumping" (boo!!! lost some bragging rights about my life list).

I asked an ornithologist friend about this a couple of years ago. I've always been a "lumper" at heart, even if it does result in my life list being shorter. To me, if two individuals decide to mate, and produce offspring, they ought to be considered the same species. Maybe adding the requirement that the offspring are themselves fertile and able to produce fertile offspring. My ornithologist friend seems pretty firmly in the camp that defines species by their genetics. I asked him if this wasn't rather arbitrary, and the only thing I remember him mentioning (which I never followed up on studying) was the notion of a "clade". I won't comment further on that, since I know absolutely nothing about clades.

As a side note, we certainly don't classify currently living Homo sapiens individuals into different species, but then I don't know if the genetic differences among different races of people are more, or less, significant than that of some other animal species. This would, of course, be hugely (and justifiably, I believe) unpopular among us humans. I asked my parrots what they think, and they just chewed on the furniture more. I don't know if that signifies agreement or disagreement with my ornithologist friend.

On Sun, Dec 27, 2020 at 11:54 AM <[hidden email]> wrote:
https://www.theguardian.com/environment/2020/dec/25/discovery-of-cryptic-species-shows-earth-is-even-more-biologically-diverse-aoe
So what IS a species? A level of distinctness of design, a degree of genetic differentiation, or an interbreeding population? And what happens to Darwinism when these things turn out to be not particularly well correlated, in the way that the signs and symptoms of hunger turned out to be not so well correlated as the Cartesian model would require? Steve Guerin: if you want to demolish Darwinism, here is where you start.
Nick
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thompnickson2

Re: Discovery of 'cryptic species' shows Earth is even more biologically diverse | Wildlife | The Guardian

In reply to this post by Gary Schiltz-4

I think according to cladistics humans are a pretty primitive species.

Nicholas Thompson

Emeritus Professor of Ethology and Psychology

Clark University

[hidden email]

https://wordpress.clarku.edu/nthompson/

From: Friam <[hidden email]> On Behalf Of Gary Schiltz
Sent: Sunday, December 27, 2020 11:45 AM
To: The Friday Morning Applied Complexity Coffee Group <[hidden email]>
Subject: Re: [FRIAM] Discovery of 'cryptic species' shows Earth is even more biologically diverse | Wildlife | The Guardian

On Sun, Dec 27, 2020 at 11:54 AM <[hidden email]> wrote:

https://www.theguardian.com/environment/2020/dec/25/discovery-of-cryptic-species-shows-earth-is-even-more-biologically-diverse-aoe
So what IS a species? A level of distinctness of design, a degree of genetic differentiation, or an interbreeding population? And what happens to Darwinism when these things turn out to be not particularly well correlated, in the way that the signs and symptoms of hunger turned out to be not so well correlated as the Cartesian model would require? Steve Guerin: if you want to demolish Darwinism, here is where you start.
Nick
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David Eric Smith

Re: Discovery of 'cryptic species' shows Earth is even more biologically diverse | Wildlife | The Guardian

In reply to this post by thompnickson2

Yes, Nick, I think you already are where the discussion should have gone.

Questions posed, like “what _IS_ a species” are just trolling to rile up people like me, since it is clear I will respond in the same way I do to questions like “what _is_ emergence”, or “what _is_ a gene”.

The amazing thing about the levels K, P, C, O, F, G, S, from Linnaeus, are that the animals (+ fungi) and plants he needed to handle with them were so similar despite their superficial diversity, that the categories held up so well for so long. Presumably this is a reflection of underlying nestedness in developmental regulatory systems, which then get reflected in affordances for diversification that can at least be shoehorned into roughly-corresponding levels by people committed to doing so because they want an invariant classification system.

Then we get Ernst Mayr, who will declare that they are breeding-able groupings, a criterion that of course is largely useless for asexuals (the nearest parallels one can find to it, for restriction/modification controls on gene transfer, are vastly more ad hoc and idiosyncratic). But then this is the same Mayr who insisted that Woese would not bring any new thoughts into _his_ biology, where men were men and prokaryotes were prokaryotes, (and the prokaryotes knew their place) and so on.

On the “why do certain kinds of classes seem to show up, and how are they driven?” question, I have heard some fun things whose status today I don’t know. I think one of them was that in many folk classifications worldwide, there tend to be category names corresponding much better-than-randomly to genus-level Linnaean categories. (I’m almost sure I got this from Murray, and it is the kind of little factoid that he loved knowing and relating; as for some others of that kind, caveat lector.) I may once have heard something about genera and the idea of “phylotypic” stages of development, but in saying that here I am incoherent, since the phylotypic stage, to the extent that there is one, tends to span much larger clades than genera. There might yet be something to see here, though, to the extent that development has natural “kernels”, as Doug Erwin and Eric Davidson called them, and to the extent that diversification follows outlines written into the modularization of development.

Wish I knew more about this problem at a professional level, because I agree the causation versions of the question are interesting.

Eric

On Dec 27, 2020, at 2:22 PM, <[hidden email]> <[hidden email]> wrote:

Gary, and EricS,

Well my vote is for Species, genus, etc., to be descriptive categories, levels of difference in the possession of traits. As soon as we put our foot down, there, we discover that species differences are NOT as well correlated with levels of genetic differentiation or with gene flow as our theories would require. “WHY are species?” then becomes a real and difficult question. Which, I think, relates to the question of why the genome is as modular as it is. I whose interest is THAT?

I agree that cladistics, with its weird terminology that only a ideologue could love, is impenetrable. But I think we have to penetrate it. It is, after all, a descriptive method of arraying organisms on the basis of their manifest traits. It does allow us, for instance, to make a distinction between convergent evolution (where creatures that are fundamentally different look superficially similar) and divergent evolution (where creatures that are fundamentally similar look superficially different) because it can breath life into the notions of fundamentally and superficially.

Nick

Nicholas Thompson
Emeritus Professor of Ethology and Psychology
Clark University
[hidden email]
https://wordpress.clarku.edu/nthompson/

From: Friam <[hidden email]> On Behalf Of David Eric Smith
Sent: Sunday, December 27, 2020 11:53 AM
To: The Friday Morning Applied Complexity Coffee Group <[hidden email]>
Subject: Re: [FRIAM] Discovery of 'cryptic species' shows Earth is even more biologically diverse | Wildlife | The Guardian

My late colleague Harold Morowitz once made a comment in an afternoon working conversation, which I found funny and fun. He said something like “I remember only 45 years ago when the lagomorphs split off from the rodents”.

Kind of like Paul Erdos, the 4 billion year old man.

Eric

On Dec 27, 2020, at 12:44 PM, Gary Schiltz <[hidden email]> wrote:

When I studied biology at university back in the 1970s, my recollection is that most biologists in those days thought of species as an interbreeding population of individuals. Over the years, I've seen this definition give way more and more to defining species by genetic differences alone. Though I haven't been professionally a biologist for over 40 years (if ever), my life as a birdwatcher (and occasional keeper of coveted lists of species seen) has been affected by this shift. Based on genetic analysis (possibly tempered by studies of behavior, range, morphology), bird species are frequently "split" into two or more separate groups, either "subspecies", "races", or even full blown "species" (yay!! I've seen both those, add another species to my life list). Or the converse is also true - based on genetic analysis (tempered as above), ornithological consensus will deem two or more species to be merely different races or subspecies of one species, which we refer to as "lumping" (boo!!! lost some bragging rights about my life list).

I asked an ornithologist friend about this a couple of years ago. I've always been a "lumper" at heart, even if it does result in my life list being shorter. To me, if two individuals decide to mate, and produce offspring, they ought to be considered the same species. Maybe adding the requirement that the offspring are themselves fertile and able to produce fertile offspring. My ornithologist friend seems pretty firmly in the camp that defines species by their genetics. I asked him if this wasn't rather arbitrary, and the only thing I remember him mentioning (which I never followed up on studying) was the notion of a "clade". I won't comment further on that, since I know absolutely nothing about clades.

As a side note, we certainly don't classify currently living Homo sapiens individuals into different species, but then I don't know if the genetic differences among different races of people are more, or less, significant than that of some other animal species. This would, of course, be hugely (and justifiably, I believe) unpopular among us humans. I asked my parrots what they think, and they just chewed on the furniture more. I don't know if that signifies agreement or disagreement with my ornithologist friend.

On Sun, Dec 27, 2020 at 11:54 AM <[hidden email]> wrote:
https://www.theguardian.com/environment/2020/dec/25/discovery-of-cryptic-species-shows-earth-is-even-more-biologically-diverse-aoe
So what IS a species? A level of distinctness of design, a degree of genetic differentiation, or an interbreeding population? And what happens to Darwinism when these things turn out to be not particularly well correlated, in the way that the signs and symptoms of hunger turned out to be not so well correlated as the Cartesian model would require? Steve Guerin: if you want to demolish Darwinism, here is where you start.
Nick
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Eric Charles-2

Re: Discovery of 'cryptic species' shows Earth is even more biologically diverse | Wildlife | The Guardian

And, of course, this conversation conflates two (or more) very different questions.

One question is: How should we distinguish animals of the same type vs. a different type? That corresponds, roughly, to the "What is a species?" question that seemed to start us off.

A different question is: Once we have those basic groups, how do we expect the groups to relate to each other? This is the issue Eric S pointed to previously. Once we start to great the King Philip Came Over For Great Sex system to both animals, plants, and fungi, we find that the system seems to be working very differently in the different kingdoms... which is unsatisfying.

[hidden email]

Eric C

On Sun, Dec 27, 2020 at 3:15 PM David Eric Smith <[hidden email]> wrote:

Yes, Nick, I think you already are where the discussion should have gone.

Questions posed, like “what _IS_ a species” are just trolling to rile up people like me, since it is clear I will respond in the same way I do to questions like “what _is_ emergence”, or “what _is_ a gene”.

The amazing thing about the levels K, P, C, O, F, G, S, from Linnaeus, are that the animals (+ fungi) and plants he needed to handle with them were so similar despite their superficial diversity, that the categories held up so well for so long. Presumably this is a reflection of underlying nestedness in developmental regulatory systems, which then get reflected in affordances for diversification that can at least be shoehorned into roughly-corresponding levels by people committed to doing so because they want an invariant classification system.

Then we get Ernst Mayr, who will declare that they are breeding-able groupings, a criterion that of course is largely useless for asexuals (the nearest parallels one can find to it, for restriction/modification controls on gene transfer, are vastly more ad hoc and idiosyncratic). But then this is the same Mayr who insisted that Woese would not bring any new thoughts into _his_ biology, where men were men and prokaryotes were prokaryotes, (and the prokaryotes knew their place) and so on.

On the “why do certain kinds of classes seem to show up, and how are they driven?” question, I have heard some fun things whose status today I don’t know. I think one of them was that in many folk classifications worldwide, there tend to be category names corresponding much better-than-randomly to genus-level Linnaean categories. (I’m almost sure I got this from Murray, and it is the kind of little factoid that he loved knowing and relating; as for some others of that kind, caveat lector.) I may once have heard something about genera and the idea of “phylotypic” stages of development, but in saying that here I am incoherent, since the phylotypic stage, to the extent that there is one, tends to span much larger clades than genera. There might yet be something to see here, though, to the extent that development has natural “kernels”, as Doug Erwin and Eric Davidson called them, and to the extent that diversification follows outlines written into the modularization of development.

Wish I knew more about this problem at a professional level, because I agree the causation versions of the question are interesting.

Eric

On Dec 27, 2020, at 2:22 PM, <[hidden email]> <[hidden email]> wrote:

Gary, and EricS,

Well my vote is for Species, genus, etc., to be descriptive categories, levels of difference in the possession of traits. As soon as we put our foot down, there, we discover that species differences are NOT as well correlated with levels of genetic differentiation or with gene flow as our theories would require. “WHY are species?” then becomes a real and difficult question. Which, I think, relates to the question of why the genome is as modular as it is. I whose interest is THAT?

I agree that cladistics, with its weird terminology that only a ideologue could love, is impenetrable. But I think we have to penetrate it. It is, after all, a descriptive method of arraying organisms on the basis of their manifest traits. It does allow us, for instance, to make a distinction between convergent evolution (where creatures that are fundamentally different look superficially similar) and divergent evolution (where creatures that are fundamentally similar look superficially different) because it can breath life into the notions of fundamentally and superficially.

Nick

Nicholas Thompson
Emeritus Professor of Ethology and Psychology
Clark University
[hidden email]
https://wordpress.clarku.edu/nthompson/

From: Friam <[hidden email]> On Behalf Of David Eric Smith
Sent: Sunday, December 27, 2020 11:53 AM
To: The Friday Morning Applied Complexity Coffee Group <[hidden email]>
Subject: Re: [FRIAM] Discovery of 'cryptic species' shows Earth is even more biologically diverse | Wildlife | The Guardian

My late colleague Harold Morowitz once made a comment in an afternoon working conversation, which I found funny and fun. He said something like “I remember only 45 years ago when the lagomorphs split off from the rodents”.

Kind of like Paul Erdos, the 4 billion year old man.

Eric

On Dec 27, 2020, at 12:44 PM, Gary Schiltz <[hidden email]> wrote:

When I studied biology at university back in the 1970s, my recollection is that most biologists in those days thought of species as an interbreeding population of individuals. Over the years, I've seen this definition give way more and more to defining species by genetic differences alone. Though I haven't been professionally a biologist for over 40 years (if ever), my life as a birdwatcher (and occasional keeper of coveted lists of species seen) has been affected by this shift. Based on genetic analysis (possibly tempered by studies of behavior, range, morphology), bird species are frequently "split" into two or more separate groups, either "subspecies", "races", or even full blown "species" (yay!! I've seen both those, add another species to my life list). Or the converse is also true - based on genetic analysis (tempered as above), ornithological consensus will deem two or more species to be merely different races or subspecies of one species, which we refer to as "lumping" (boo!!! lost some bragging rights about my life list).

I asked an ornithologist friend about this a couple of years ago. I've always been a "lumper" at heart, even if it does result in my life list being shorter. To me, if two individuals decide to mate, and produce offspring, they ought to be considered the same species. Maybe adding the requirement that the offspring are themselves fertile and able to produce fertile offspring. My ornithologist friend seems pretty firmly in the camp that defines species by their genetics. I asked him if this wasn't rather arbitrary, and the only thing I remember him mentioning (which I never followed up on studying) was the notion of a "clade". I won't comment further on that, since I know absolutely nothing about clades.

As a side note, we certainly don't classify currently living Homo sapiens individuals into different species, but then I don't know if the genetic differences among different races of people are more, or less, significant than that of some other animal species. This would, of course, be hugely (and justifiably, I believe) unpopular among us humans. I asked my parrots what they think, and they just chewed on the furniture more. I don't know if that signifies agreement or disagreement with my ornithologist friend.

On Sun, Dec 27, 2020 at 11:54 AM <[hidden email]> wrote:
https://www.theguardian.com/environment/2020/dec/25/discovery-of-cryptic-species-shows-earth-is-even-more-biologically-diverse-aoe
So what IS a species? A level of distinctness of design, a degree of genetic differentiation, or an interbreeding population? And what happens to Darwinism when these things turn out to be not particularly well correlated, in the way that the signs and symptoms of hunger turned out to be not so well correlated as the Cartesian model would require? Steve Guerin: if you want to demolish Darwinism, here is where you start.
Nick
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Marcus G. Daniels

Re: Discovery of 'cryptic species' shows Earth is even more biologically diverse | Wildlife | The Guardian

In reply to this post by David Eric Smith

Incompatible nested developmental regulatory systems as a definition for species doesn’t seem to jibe with companies like eGenesis who are adapting pigs to grow organs for human use. The latter says to me a relatively small genomic patch and not a rewrite. When are species differences and exon edit distance contrary? In other words, could one have a small exon edit distance and a difference in species, or a large edit distance and no difference in species? I guess I am assuming some reasonably intelligent generative function that would create the a minimum length patch even if the raw DNA differences were quite large.

From: Friam <[hidden email]> On Behalf Of David Eric Smith
Sent: Sunday, December 27, 2020 12:15 PM
To: The Friday Morning Applied Complexity Coffee Group <[hidden email]>
Subject: Re: [FRIAM] Discovery of 'cryptic species' shows Earth is even more biologically diverse | Wildlife | The Guardian

Yes, Nick, I think you already are where the discussion should have gone.

Wish I knew more about this problem at a professional level, because I agree the causation versions of the question are interesting.

Eric

On Dec 27, 2020, at 2:22 PM, <[hidden email]> <[hidden email]> wrote:

Gary, and EricS,

Well my vote is for Species, genus, etc., to be descriptive categories, levels of difference in the possession of traits. As soon as we put our foot down, there, we discover that species differences are NOT as well correlated with levels of genetic differentiation or with gene flow as our theories would require. “WHY are species?” then becomes a real and difficult question. Which, I think, relates to the question of why the genome is as modular as it is. I whose interest is THAT?

I agree that cladistics, with its weird terminology that only a ideologue could love, is impenetrable. But I think we have to penetrate it. It is, after all, a descriptive method of arraying organisms on the basis of their manifest traits. It does allow us, for instance, to make a distinction between convergent evolution (where creatures that are fundamentally different look superficially similar) and divergent evolution (where creatures that are fundamentally similar look superficially different) because it can breath life into the notions of fundamentally and superficially.

Nick

Nicholas Thompson

Emeritus Professor of Ethology and Psychology

Clark University

[hidden email]

https://wordpress.clarku.edu/nthompson/

From: Friam <[hidden email]> On Behalf Of David Eric Smith
Sent: Sunday, December 27, 2020 11:53 AM
To: The Friday Morning Applied Complexity Coffee Group <[hidden email]>
Subject: Re: [FRIAM] Discovery of 'cryptic species' shows Earth is even more biologically diverse | Wildlife | The Guardian

My late colleague Harold Morowitz once made a comment in an afternoon working conversation, which I found funny and fun. He said something like “I remember only 45 years ago when the lagomorphs split off from the rodents”.

Kind of like Paul Erdos, the 4 billion year old man.

Eric

On Dec 27, 2020, at 12:44 PM, Gary Schiltz <[hidden email]> wrote:

When I studied biology at university back in the 1970s, my recollection is that most biologists in those days thought of species as an interbreeding population of individuals. Over the years, I've seen this definition give way more and more to defining species by genetic differences alone. Though I haven't been professionally a biologist for over 40 years (if ever), my life as a birdwatcher (and occasional keeper of coveted lists of species seen) has been affected by this shift. Based on genetic analysis (possibly tempered by studies of behavior, range, morphology), bird species are frequently "split" into two or more separate groups, either "subspecies", "races", or even full blown "species" (yay!! I've seen both those, add another species to my life list). Or the converse is also true - based on genetic analysis (tempered as above), ornithological consensus will deem two or more species to be merely different races or subspecies of one species, which we refer to as "lumping" (boo!!! lost some bragging rights about my life list).

I asked an ornithologist friend about this a couple of years ago. I've always been a "lumper" at heart, even if it does result in my life list being shorter. To me, if two individuals decide to mate, and produce offspring, they ought to be considered the same species. Maybe adding the requirement that the offspring are themselves fertile and able to produce fertile offspring. My ornithologist friend seems pretty firmly in the camp that defines species by their genetics. I asked him if this wasn't rather arbitrary, and the only thing I remember him mentioning (which I never followed up on studying) was the notion of a "clade". I won't comment further on that, since I know absolutely nothing about clades.

As a side note, we certainly don't classify currently living Homo sapiens individuals into different species, but then I don't know if the genetic differences among different races of people are more, or less, significant than that of some other animal species. This would, of course, be hugely (and justifiably, I believe) unpopular among us humans. I asked my parrots what they think, and they just chewed on the furniture more. I don't know if that signifies agreement or disagreement with my ornithologist friend.

On Sun, Dec 27, 2020 at 11:54 AM <[hidden email]> wrote:

https://www.theguardian.com/environment/2020/dec/25/discovery-of-cryptic-species-shows-earth-is-even-more-biologically-diverse-aoe

So what IS a species? A level of distinctness of design, a degree of genetic differentiation, or an interbreeding population? And what happens to Darwinism when these things turn out to be not particularly well correlated, in the way that the signs and symptoms of hunger turned out to be not so well correlated as the Cartesian model would require? Steve Guerin: if you want to demolish Darwinism, here is where you start.

Nick

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Frank Wimberly-2

Re: Discovery of 'cryptic species' shows Earth is even more biologically diverse | Wildlife | The Guardian

All this reminds me of when my now middle-aged daughter said to me scornfully, "What do you know about speciation, Dad?" I have no memory of what the issue was. She was in highschool.

---
Frank C. Wimberly
140 Calle Ojo Feliz,
Santa Fe, NM 87505

505 670-9918
Santa Fe, NM

On Sun, Dec 27, 2020, 11:06 PM Marcus Daniels <[hidden email]> wrote:

Incompatible nested developmental regulatory systems as a definition for species doesn’t seem to jibe with companies like eGenesis who are adapting pigs to grow organs for human use. The latter says to me a relatively small genomic patch and not a rewrite.   When are species differences and exon edit distance contrary? In other words, could one have a small exon edit distance and a difference in species, or a large edit distance and no difference in species? I guess I am assuming some reasonably intelligent generative function that would create the a minimum length patch even if the raw DNA differences were quite large.



From: Friam <[hidden email]> On Behalf Of David Eric Smith
Sent: Sunday, December 27, 2020 12:15 PM
To: The Friday Morning Applied Complexity Coffee Group <[hidden email]>
Subject: Re: [FRIAM] Discovery of 'cryptic species' shows Earth is even more biologically diverse | Wildlife | The Guardian

Yes, Nick, I think you already are where the discussion should have gone.

Questions posed, like “what _IS_ a species” are just trolling to rile up people like me, since it is clear I will respond in the same way I do to questions like “what _is_ emergence”, or “what _is_ a gene”.

The amazing thing about the levels K, P, C, O, F, G, S, from Linnaeus, are that the animals (+ fungi) and plants he needed to handle with them were so similar despite their superficial diversity, that the categories held up so well for so long. Presumably this is a reflection of underlying nestedness in developmental regulatory systems, which then get reflected in affordances for diversification that can at least be shoehorned into roughly-corresponding levels by people committed to doing so because they want an invariant classification system.

Then we get Ernst Mayr, who will declare that they are breeding-able groupings, a criterion that of course is largely useless for asexuals (the nearest parallels one can find to it, for restriction/modification controls on gene transfer, are vastly more ad hoc and idiosyncratic). But then this is the same Mayr who insisted that Woese would not bring any new thoughts into _his_ biology, where men were men and prokaryotes were prokaryotes, (and the prokaryotes knew their place) and so on.

On the “why do certain kinds of classes seem to show up, and how are they driven?” question, I have heard some fun things whose status today I don’t know. I think one of them was that in many folk classifications worldwide, there tend to be category names corresponding much better-than-randomly to genus-level Linnaean categories. (I’m almost sure I got this from Murray, and it is the kind of little factoid that he loved knowing and relating; as for some others of that kind, caveat lector.) I may once have heard something about genera and the idea of “phylotypic” stages of development, but in saying that here I am incoherent, since the phylotypic stage, to the extent that there is one, tends to span much larger clades than genera. There might yet be something to see here, though, to the extent that development has natural “kernels”, as Doug Erwin and Eric Davidson called them, and to the extent that diversification follows outlines written into the modularization of development.

Wish I knew more about this problem at a professional level, because I agree the causation versions of the question are interesting.

Eric

On Dec 27, 2020, at 2:22 PM, <[hidden email]> <[hidden email]> wrote:

Gary, and EricS,

Well my vote is for Species, genus, etc., to be descriptive categories, levels of difference in the possession of traits. As soon as we put our foot down, there, we discover that species differences are NOT as well correlated with levels of genetic differentiation or with gene flow as our theories would require.   “WHY are species?” then becomes a real and difficult question. Which, I think, relates to the question of why the genome is as modular as it is. I whose interest is THAT?

I agree that cladistics, with its weird terminology that only a ideologue could love, is impenetrable. But I think we have to penetrate it. It is, after all, a descriptive method of arraying organisms on the basis of their manifest traits. It does allow us, for instance, to make a distinction between convergent evolution (where creatures that are fundamentally different look superficially similar) and divergent evolution (where creatures that are fundamentally similar look superficially different) because it can breath life into the notions of fundamentally and superficially.

Nick

Nicholas Thompson

Emeritus Professor of Ethology and Psychology

Clark University

[hidden email]

https://wordpress.clarku.edu/nthompson/

From: Friam <[hidden email]> On Behalf Of David Eric Smith
Sent: Sunday, December 27, 2020 11:53 AM
To: The Friday Morning Applied Complexity Coffee Group <[hidden email]>
Subject: Re: [FRIAM] Discovery of 'cryptic species' shows Earth is even more biologically diverse | Wildlife | The Guardian

My late colleague Harold Morowitz once made a comment in an afternoon working conversation, which I found funny and fun. He said something like “I remember only 45 years ago when the lagomorphs split off from the rodents”.

Kind of like Paul Erdos, the 4 billion year old man.

Eric

On Dec 27, 2020, at 12:44 PM, Gary Schiltz <[hidden email]> wrote:

When I studied biology at university back in the 1970s, my recollection is that most biologists in those days thought of species as an interbreeding population of individuals. Over the years, I've seen this definition give way more and more to defining species by genetic differences alone. Though I haven't been professionally a biologist for over 40 years (if ever), my life as a birdwatcher (and occasional keeper of coveted lists of species seen) has been affected by this shift. Based on genetic analysis (possibly tempered by studies of behavior, range, morphology), bird species are frequently "split" into two or more separate groups, either "subspecies", "races", or even full blown "species" (yay!! I've seen both those, add another species to my life list). Or the converse is also true - based on genetic analysis (tempered as above), ornithological consensus will deem two or more species to be merely different races or subspecies of one species, which we refer to as "lumping" (boo!!! lost some bragging rights about my life list).

I asked an ornithologist friend about this a couple of years ago. I've always been a "lumper" at heart, even if it does result in my life list being shorter. To me, if two individuals decide to mate, and produce offspring, they ought to be considered the same species. Maybe adding the requirement that the offspring are themselves fertile and able to produce fertile offspring. My ornithologist friend seems pretty firmly in the camp that defines species by their genetics. I asked him if this wasn't rather arbitrary, and the only thing I remember him mentioning (which I never followed up on studying) was the notion of a "clade". I won't comment further on that, since I know absolutely nothing about clades.

As a side note, we certainly don't classify currently living Homo sapiens individuals into different species, but then I don't know if the genetic differences among different races of people are more, or less, significant than that of some other animal species. This would, of course, be hugely (and justifiably, I believe) unpopular among us humans. I asked my parrots what they think, and they just chewed on the furniture more. I don't know if that signifies agreement or disagreement with my ornithologist friend.

On Sun, Dec 27, 2020 at 11:54 AM <[hidden email]> wrote:

https://www.theguardian.com/environment/2020/dec/25/discovery-of-cryptic-species-shows-earth-is-even-more-biologically-diverse-aoe

So what IS a species? A level of distinctness of design, a degree of genetic differentiation, or an interbreeding population? And what happens to Darwinism when these things turn out to be not particularly well correlated, in the way that the signs and symptoms of hunger turned out to be not so well correlated as the Cartesian model would require? Steve Guerin: if you want to demolish Darwinism, here is where you start.

Nick

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