Species and systematics

Comparative limb growth of a bat (top) and a mouse, in utero development. From the paper below. One of my favourite statistics is this: one in every four mammal species you meet is a rat or rodent, and one in every five is a bat. That's right, nine in every 20 mammal species is covered by one of these taxa: we may as well treat rodents and bats as the standard mammalian species type. So a paper that combines them has to be good. Quintessence of Dust (what a title!) gives an excellent summary and discussion of a paper that tested evolutionary hypotheses of the evolution of bat wings by…
I have been called, for my denial of outright atheism, a Chamberlainist. Well I never felt so much like Neville Chamberlain today as I walked through the corridors of the Seat of Learning* with a contract from the publishers for my book Species: A history of an Idea. I felt like shouting as I waved it, "Peace in our time!" except that the corridors are empty and I'd have felt like a right loon doing that. As has been noted recently, by the way, Neville Chamberlain noticed that his rapprochement with Hitler had failed and rearmed Britain for the coming war, and responded to Hitler's…
No, not the use of Java to archive his music. This presence: A trapdoor spider named after him. This cute fellow: Hat tip: David Williams
So much has been happening in the world while I was giving a talk on the adaptiveness of religion in Sydney. The Platypus thing was one item I'd have blogged on if the rest of the blogosphere hadn't beaten me to it. All I can say is that no matter how many bloggers write on the mosaic nature of the platypus genome, at least I got to hold one. And I would never have used the meaningless term "reptile". And although I have only been to NYC twice, I can say I have a favourite store there, and I saw it on CSI: NY recently (although they obviously tidied up the counter for the shoot). And…
Duck and cover, folks. I'm about to upset somebody. I have previously been fairly critical of DNA barcoding, the proposal to use a small fragment of the COI gene - a mitochondrial gene cytochrome c oxidase, subunit I - as a surrogate marker for species. That is, in simple terms, the use of COI sequences to "barcode" species so that straightforward molecular gene sequencing will tell you if you have a species or not, and how many there are in a given area. Now I'm going to defend a new paper that proposes a barcoding method, for philosophical reasons. Here's the paper: Inferring Species…
John Hawks has a very nice post for people with basic math, explaining why a recent press release announced that 70,000 years ago the human species encountered a population bottleneck of 2000 individuals, and why it's most likely wrong. In the process he explains effective population size. It's a tad too complex even for an Intermediate Concepts post, but still worth the effort. Larry Moran at his blog has opened a comments thread, as the Hawks blog is comment free (I am unsure if I should be censorial or jealous), and John promises to come back and answer them.
One of the enduring patterns of the history of the history of evolution is for historians to claim that their favourite individual, or their country's best and brightest, invented evolution. The most recent appears to be this guy from New Zealand, claiming that evolution was actually invented by an artist, Augustus Earle, who visited Australia and New Zealand, and spent some time on board the Beagle with Darwin. Earle wrote a book entitled A narrative of a nine months' residence in New Zealand in 1827: together with a journal of a residence in Tristan D'Acunha, an island situated between…
I just wanted to give you all a heads up to a couple of wonderful blogs: Tetrapod Zoology's post on the lost lynxes and wildcats of Britain, and Catalogue of Organism's post on spiders that lose their lungs. It's things like these posts that make me wish I had been a proper biologist,
First, the good news. The inestimable John van Whye has added, with the help of his team of course, 90,000 scanned images of Darwin's journals, manuscripts and letters. Now the bad news. The Utrecht Herbarium is closing, and no plans have been made to store and make available its collection of type specimens. Why this matters is that the very name of species depend on there being type specimens. Go read Catalogue of Organisms, an amazing blog in any case, on the matter.
Watch the video under the fold, from Chang Mai in Thailand. There's a moment where you realise what the elephant is representing, and a shock that comes when you see that it is representing something. I don't know if it's been trained to do this but it looks real to me.
Ernst Rutherford, the "father" of nuclear physics, once airily declared "In science there is only physics. All the rest is stamp collecting". By this he meant that the theory of physics is the only significant thing in science. Such mundane activities as taxonomy in biology were just sampling contingent examples of physics. So it is with some amusement that I note that in order to make sense of string theory, a group of physicists have been trying to do taxonomy over string theories. Why this is more than a "gotcha!" is that since the late nineteenth century, philosophers of science have…
So here's a neo-Thomist talking about species, and not getting it due to (i) prior metaphysical commitments, and (ii) not understanding Aristotle - dude, he never called anything a species, not in the biological sense. Eidos and genos were just ordinary words he coopted for the Metaphysics and Posterior Analytics. He used them interchangeably in the Liber Animalia, and sometimes didn't use either words for living kinds. Rule Number One: You can't do science by definitions. Here's a furore (is that pronounced "few-roar" or "few-ror-ay"?) about whether to respond to the Expelled gaff. Nisbet…
The ever-interesting blog of Moselio Schachter, Small Things Considered has another post of thought-provoking microbes: hyperthermophiles. These wee beasties live at 90°;C in anoxic conditions. I particularly liked the passing comment: Growth and division of these organisms was observed at 90°;C under anoxic conditions using a dark-field light microscope (which takes quite a set-up). Um yes. I'm betting that was a Herculean effort! In particular this is interesting because there is a bias in identifying microbes that do not culture in ordinary lab conditions. These researchers are to be…
So, here I am in Phoenix airport, waiting to go back home, and I read T Ryan Gregory's snark about me and barcoding. Apparently I am to learn only from his blog posts and not from (perish the thought) critics. One should never attend to critics. My crime was, of course, to say that I thought Brent Mishler of UC Berkeley and others (including mein host in Phoenix, Quentin Wheeler, and Kip Will) were correct in their concerns that barcoding was being touted as a replacement for proper taxonomy and that it will draw resources from it. What are the issues? There are three, as I see it. One…
Ever since Gould's Wonderful Life: The Burgess Shale and the Nature of History, the popular view has been that the Cambrian was an "explosion" of living forms, and for some, usually but not always creationists, this has been touted as contrary to "Darwinism" (whateverthehell that is) or even evolutionary theory. PvM at Panda's Thumb has a nice post about this and recent work. And I'm not just saying that because he links to one of my articles on the web. One point I would make, that he doesn't mention, is that figures derived from "genera" or "classes" in the fossil record are weak signals…
Roberta is a great philosopher from UC Davis and she's talking about the notion of populations. Known she needed a definition of population for a long time - this is a first stab. "Population" has many definitions by biologists. Most try to limit it by space or time or interbreeding. But very little analysis. We invoke it often - it needs a proper definition. Uses include conspecificity, arbitrary delimitation, geography, area and time, interbreeding, etc. Second motivation based on selection and drift, which are processes that occur in populations. These processes become arbitrary if…
Jon is a Utah biologist. His talk is on population genetics. He is talking about an unusually clean evolutionary experiment that leaves natural populations just as messy as they were before. Real populations are so complicated they frustrate basic models and general principles of population genetics. The whale lice of right whales are the case study used. The speciated about 5 million years ago and have distinct habitats.[Coalescent theory has completely changed how we do this work.] Okay: species are communities of genes, he says. Various problems - ring species, clines, yadda yadda. […
This is a session on paleontology that I missed the start of because I had to go get my power supply. Julia, a paleontologist, is discussing the evolution of birds, and how paleontology was misled by hypotheses that used the wrong taxa and characters. I'd love to blog it more extensively, but I missed the start. She is noting the telic nature of some hypotheses, and how she and her colleagues worked in a different way, phylogenetically. Adopting a method used in molecular phylogeny, they supposed that character states might be decomposeable into smaller subregions, anatomically. They…
Jay is an ecological philosopher. He wants to sketch how ecologists have used boundaries, and outline both a skepticism and an interactive approach. He's not talking about types of ecosystems but tokens; not biomes, for example. Second, some ecosystems are sociopolitical objects (Greater Yellowstone). In 1935, A. G. Tansley distinguished ecosystems - the abiotic and biotic resources - and rejected communities - set of interacting species. Ecosystem ecology focused on the flow of nutrients and energy through organisms and their environments. Organisms are transducers of energy and…
Lunch being had we crowd into a new room to hear Stephen Peck, a biologist from Brigham Young University down the road a ways in Provo. Stephen is talking about ecological boundaries. A group of ecologists set up seven different ecosystem groups for agroecosystem studies. They debated how to define an ecosystem, and it simply got harder. They needed a biological indicator to determine the state of the ecosystem and couldn't even get to defining the latter. Over fifteen years, he hasn't been able to figure it out. Properties of ecosystem boundaries: Fuzzy Non-regulated -> Highly…