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

Mon Dec 28 09:12:04 EST 2020

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 <marcus at snoutfarm.com> 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 <friam-bounces at redfish.com> *On Behalf Of *David Eric Smith
> *Sent:* Sunday, December 27, 2020 12:15 PM
> *To:* The Friday Morning Applied Complexity Coffee Group <
> friam at redfish.com>
> *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, <thompnickson2 at gmail.com> <
> thompnickson2 at gmail.com> 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
>
> ThompNickSon2 at gmail.com
>
> https://wordpress.clarku.edu/nthompson/
> <https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fwordpress.clarku.edu%2fnthompson%2f&c=E,1,UnB7k63SKcvaBW394o4XX8Kr918viefJc1jU_wc73MRPbogV-4MFPjtAV2C4BKWHTH_3Esdm4WZ0egV3stJQ4BQ7hDY1jALoe1ZElHwDVPvEvSE,&typo=1>
>
>
>
>
>
> *From:* Friam <friam-bounces at redfish.com> *On Behalf Of *David Eric Smith
> *Sent:* Sunday, December 27, 2020 11:53 AM
> *To:* The Friday Morning Applied Complexity Coffee Group <
> friam at redfish.com>
> *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 <gary at naturesvisualarts.com>
> 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 <thompnickson2 at gmail.com> wrote:
>
>
> https://www.theguardian.com/environment/2020/dec/25/discovery-of-cryptic-species-shows-earth-is-even-more-biologically-diverse-aoe
> <https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fwww.theguardian.com%2fenvironment%2f2020%2fdec%2f25%2fdiscovery-of-cryptic-species-shows-earth-is-even-more-biologically-diverse-aoe&c=E,1,d8ssUiHUP3tLETjJmf50cEcV2upLKBND2qQAnwF__EwkcPtRZ4gDe8VeZoMCaUPYDxPsgQn0SuGFhkQvCAdrBxfgzxgbKmjGgeVhwULSGv75Zs7h4RD5BgK8B7U,&typo=1>
>
> 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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