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 <[email protected]> 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 <[email protected]> *On Behalf Of *David Eric Smith > *Sent:* Sunday, December 27, 2020 12:15 PM > *To:* The Friday Morning Applied Complexity Coffee Group < > [email protected]> > *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, <[email protected]> < > [email protected]> 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 > > [email protected] > > 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 <[email protected]> *On Behalf Of *David Eric Smith > *Sent:* Sunday, December 27, 2020 11:53 AM > *To:* The Friday Morning Applied Complexity Coffee Group < > [email protected]> > *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 <[email protected]> > 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 <[email protected]> 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 > > - .... . -..-. . -. -.. -..-. .. ... -..-. .... . .-. . > FRIAM Applied Complexity Group listserv > Zoom Fridays 9:30a-12p Mtn GMT-6 bit.ly/virtualfriam > <https://linkprotect.cudasvc.com/url?a=http%3a%2f%2fbit.ly%2fvirtualfriam&c=E,1,foGr69X29NwVBuhs5_OYQsbJMROEpdBEUDaYJD1iY8L2FLC2CV4ss33T0HL7EUm_QBBNKm3Lx2dp7GjtkILLrvvsBdt7_3M3zwUnWvS4_jC-Ll6X-uo,&typo=1> > un/subscribe http://redfish.com/mailman/listinfo/friam_redfish.com > <https://linkprotect.cudasvc.com/url?a=http%3a%2f%2fredfish.com%2fmailman%2flistinfo%2ffriam_redfish.com&c=E,1,fIgA-f_L-FPHCVSbwL_DIGYAiH3XWc41guN_B0ayBDafV2MTyIO_tWpra4FLXDFX4xAqAyUcyc7pYm6Hw6vK0x_JkrIA7CgSiLRu2qWznPU,&typo=1> > archives: http://friam.471366.n2.nabble.com/ > FRIAM-COMIC http://friam-comic.blogspot.com/ > <https://linkprotect.cudasvc.com/url?a=http%3a%2f%2ffriam-comic.blogspot.com%2f&c=E,1,Dqlg85Dlbuh8fbdXUEq7uvapBNdOg8XOpZzaapnWLbLn2rRUWnzaTwvIkcLtX3s3LKD4I_M1k4B6yN24IPubDI5mFl6poR6n1wpp0m1O&typo=1> > > - .... . -..-. . -. -.. -..-. .. ... -..-. .... . .-. . > FRIAM Applied Complexity Group listserv > Zoom Fridays 9:30a-12p Mtn GMT-6 bit.ly/virtualfriam > <https://linkprotect.cudasvc.com/url?a=http%3a%2f%2fbit.ly%2fvirtualfriam&c=E,1,jmctWcs0EWdvH9drKBvUOSNsbVH5V2YIJQRTuJIS0_9JKfi6CClx-Rzm9Aq-HeBCrRwHKzqz-xX4Si_c29h5pNwYBZy56JG3w3SYKxOtrzk,&typo=1> > un/subscribe > https://linkprotect.cudasvc.com/url?a=http%3a%2f%2fredfish.com%2fmailman%2flistinfo%2ffriam_redfish.com&c=E,1,y_Hvb_aasSNzzcMDqntU2KFzJv3N3lbHwjuRS0OptrCSlKUFotBrXNXU20_UjsE7JPfODuGECNKv3NgxJJQOY6mDsU4y_X02_PEO9Lrvg-vgqmOqtrc,&typo=1 > archives: http://friam.471366.n2.nabble.com/ > FRIAM-COMIC > https://linkprotect.cudasvc.com/url?a=http%3a%2f%2ffriam-comic.blogspot.com%2f&c=E,1,rt2S6zpgWOLuXwtQXbSXIEwoHSy-RBi8nR31x0zs29bhQROtIQJsvnX2OCxdVDn5UDf6w52Z_vc3Cg5iKj0RZAzSDNKtmMrXM0u8WW-3yfCMcN_rLnU,&typo=1 > > > > - .... . -..-. . -. -.. -..-. .. ... -..-. .... . .-. . > FRIAM Applied Complexity Group listserv > Zoom Fridays 9:30a-12p Mtn GMT-6 bit.ly/virtualfriam > un/subscribe > https://linkprotect.cudasvc.com/url?a=http%3a%2f%2fredfish.com%2fmailman%2flistinfo%2ffriam_redfish.com&c=E,1,4nVhTUnZALCzJi85X8z6-y6ZMiHncl4TSFvt3UovfSxZo-bDvdyHKwv8sJIpzHq3lHU1qjzxOMCqghiGiIyymQntWgNL_tYMM-_BpPz80QbOHPRmLQut3uNxlA,,&typo=1 > archives: http://friam.471366.n2.nabble.com/ > FRIAM-COMIC > https://linkprotect.cudasvc.com/url?a=http%3a%2f%2ffriam-comic.blogspot.com%2f&c=E,1,M4vbTmxEUeW3Fd5W6gvUI2oxFeGi5KiT_tiSA2TQFNlbmVlEx_7sIzvFjjAT0QtvnWCI7enE7AwTSNQapRT_ssmGJ-A1pDQYKGEKCCJixcULq44wofaMmDxLOdVB&typo=1 > > > - .... . -..-. . -. -.. -..-. .. ... -..-. .... . .-. . > FRIAM Applied Complexity Group listserv > Zoom Fridays 9:30a-12p Mtn GMT-6 bit.ly/virtualfriam > un/subscribe http://redfish.com/mailman/listinfo/friam_redfish.com > archives: http://friam.471366.n2.nabble.com/ > FRIAM-COMIC http://friam-comic.blogspot.com/ >
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