Species and systematics
evolvingthoughts | August 22, 2007
The National Geographic and the news services are touting a new ape fossil found in Ethiopia as "forcing a rethink on human evolution". As usual, the headlines are hyperbolic. This ape is fragmentary, and so far only teeth and a jaw bone have been found, and the teeth are similar to gorilla teeth. Gorillas are thought on molecular grounds to have split off from the chimp-human clade about 7 million years ago, but this specimen is 10 million years old. What gives?
I can think of a couple of options. One is that, as I have reported previously, teeth are not great diagnostic material for…
evolvingthoughts | August 22, 2007
Historian Mary P. Winsor published recently (2006b, in the December 2006 edition, but it just came out) a paper discussing how the Essentialism Story was constructed by Arthur Cain, Ernst Mayr, and David Hull.
The Essentialism Story is the claim that before Darwin systematists and biologists in general treated natural kinds such as species as being defined by necessary and sufficient conditions. That is, to be a member of a species, an organism has to have all the right properties. After Darwin, goes the story, "population thinking", which denies that there are such necessary properties…
evolvingthoughts | August 14, 2007
I have a book forthcoming, Species definitions: a sourcebook from antiquity to today, which gives and commentates definitions of "species" in logic and biology for 2,500 years, from Plato to Templeton and beyond. It's designed as a reader for scholars to see how the notion[s] have evolved separately in the logical definitional sense - for Aristotle, eidos, which we translate as "form", "species", and "kind", was a logical term, not a biological one, which had to wait until the 16th century, and even then they were distinct notions.
I argue in the commentaries that there was nothing…
evolvingthoughts | August 12, 2007
I have a review of the centenary festschrift for Mayr, published by the National Academies of Science, in the latest Biology and Philosophy here. I worked pretty hard on this one, so it's more than your average dashed off review article...
Hey, Jody; Fitch, Walter M.; Ayala, Francisco J., eds. 2005. Systematics and the origin of species: On Ernst Mayr’s 100th Anniversary. Washington, DC: National Academies Press. Pages: 367 + xiii. ISBN: 0-309-09536-0
evolvingthoughts | August 11, 2007
Laelaps has a very nice essay that ranges from the number of ribs humans have, the book of Genesis, creationism, and the variety of stories told about human evolution from the nineteenth century to now. Go read it. It's one of the few blog posts in which you'll read of petrified testicles...
[HT: Afarensis]
evolvingthoughts | August 10, 2007
Rob Wilson has a new entry up at the Stanford Encyclopedia of Philosophy, entitled "The Biological notion of an individual". It discusses an interesting problem, one that goes back to discussions by Julian Huxley in 1911. What is an individual in biology?
The term "individual" means, etymologically, that which is not divisible. Of course we can divide up organisms, but if we do this physically, they immediately thereafter cease to be the organism. Except... there are colonial organisms that can be so divided - sponges, hydras, slime molds, and so on. To make matters worse (much worse, as…
evolvingthoughts | August 3, 2007
So I'm home from Ish, and the front part of my brain is giddy and tired while the rest has just shut down. I don't travel well, I'm afraid.
One thing that I came back fired up over are the unfinished projects I have running. So I intend to finish them. They are, in no particular order:
1. Denying that genes have information [heresy #1] Status: Written and needing to be submitted.
2. Denying that functions in biology exist outside models [heresy #2] Status: Written but badly in need of a rewrite.
3. Denying that essentialism ever existed in biology [#3. Four more and I get a free auto…
evolvingthoughts | July 18, 2007
In recent years it has becoming increasingly obvious that there is a considerable amount of lateral, or cross phylogenetic, transfer of genetic material. In bacteria, this happens by several mechanisms, such as uptake of gene fragments from cells that have disintegrated, or by mechanisms such as conjugation ("bacterial sex"). Sometimes genetic material has transferred this way from bacteria into mammal cells. How important this turns out to be for the novelty of evolutionary processes remains to be seen.
But until recently there has been little evidence of lateral transfer (apart from sex…
evolvingthoughts | July 7, 2007
Naturalised Brazilian, Dutch biologist Marc van Roosmalen, has been sentenced to 14 years jail in Brazil for running a monkey refuge without a permit from Ibama, the local environmental agency. Not that he didn't apply, mark you, but Ibama didn't respond, and the received local wisdom is that if they don't within 45 days, it's approved. Van Roosmalen was convicted because although this is indeed what happens, it's not in the legislation.
This is egregious sucky. Brazil ought to be ashamed of itself.
Late note: See Marc's own site for a background. This looks like, as I expected, corrupt…
evolvingthoughts | July 4, 2007
Back from the drinking sessionconference, with many good thoughts.
One in particular is due to the talk by Aiden Lyons at ANU on probability and evolution - after more than two decades trying to figure it out, I had to wait for a grad student to put it all neatly into perspective. His argument that there are at least three if not four senses or interpretations of probability and chance in evolution that - apart from anything else - prevents fitness being tautological, raises many more questions, but that is the nature of good papers.
Another, in no particular succession, is whether we…
evolvingthoughts | June 26, 2007
Run by Matt Haber at Utah, it's a forum for discussions of work in progress, student matters like employment, tech issues and biology and society topics, to mention only a few. It's in alpha form now, but expect it to grow. The sidebar blurb is this:
Thank you for visiting the Philsophy of Biology Cafe. Our forums are currently under construction and are in ALPHA testing stages.
This forum is a place to come, sit down, and have a hearty swig of the many topics concerning philosophy and biology.
We try to keep things in a coffee-house theme (in case you didn't notice) so if you have any…
evolvingthoughts | June 21, 2007
I'm putting this up because I will use it to discuss the history of species definitions in a forthcoming talk. It's very interesting for a number of reasons, one of which is the species nominalism, and another that Lewes argues from evidence for biparental inheritance some years before Mendel, and against eugenics, despite his evident racism, and well before Galton.
Footnotes follow their paragraph, and have been slightly retagged for clarity.
Published anonymously by George Henry Lewes, (1856). “Hereditary Influence, Animal and Human.” Westminster Review 66 (July): 135-162. Parts of…
evolvingthoughts | June 20, 2007
A new paper in New Mexico Geology has the following rather tendentious title:
Fassett, J.E. 2007. The documentation of in-place dinosaur fossils in the Paleocene Ojo Alamo Sandstone and Animas Formation in the San Juan Basin of New Mexico and Colorado mandates a paradigm shift: dinosaurs can no longer be thought of as absolute index fossils for end-Cretaceous strata in the Western Interior of North America. New Mexico Geology 29(2):56.
Ack! He mentioned the p-word! Now I have to find him and extract his teeth without anesthetic.
So here's the abstract:
Extensive geochronologic…
evolvingthoughts | June 19, 2007
No! Not orgasmic! [There, that should bump up the hits]
You all know, of course, the inestimable Darren Naish and his wonderful blog Tetrapod Zoology. What? You don't? Go there immediately and come back when you've read it all, and the old site too.
[Fifteen days later]
So, I wanted to mention a similar blog, by a student working on spider systematics (way cool), name of Christopher Taylor, called Catalogue of Organisms. In this 300th anniversary of the first real such catelogue by Linnaeus, that's a way cool title. And of course you have an almost endless supply of cool material, even…
evolvingthoughts | June 14, 2007
New Scientist is reporting that a case in Austria (not Australia - we share a love of beer, but that's about it) is set to decide if chimps have rights. They already do in Spain, and in New Zealand (which was, I think, the first country to enact rights for chimps).
They do not have rights in Australia, or America, or most of the world apart from these few countries that have what I consider are sensible and inescapable laws. Why do I think so?
Chimps, and indeed most of the great apes if not all of them, share an enormous genetic heritage in common with humans; they are capable of…
evolvingthoughts | June 12, 2007
Marc Ereshfsky's entry on "Species" in the Stanford Encyclopedia of Philosophy has been updated, though not to remove the classic "Essentialism Story" that has been called into question by a number of scholars lately. Under the fold, I will quote Marc's comments and critique them. [I can do this because Marc is a hell of a nice guy, and not at all precious about such stuff, at least not so far. I will test him, though. I should stress that Marc is not the originator of the Essentialist Story - it was developed between 1958 or so and 1982 largely by Mayr.]
Since Aristotle, species have been…
evolvingthoughts | June 11, 2007
So the record for the "world's largest organism" has again been claimed for a fungus, something Stephen Jay Gould wrote about in his wonderfully titled essay "A Humongous Fungus Among Us" back in 1992, and which was included in his volume A Dinosaur in a Haystack.
The previous fungus, Armillaria gallica, is now replaced by a related mushroom stand, Armillaria ostoyae, in Oregon's Blue Mountains. But I have my doubts. The term "organism" here has a meaning rather different to "relatively undifferentiated mass of related stands". In fact, I want to talk about the notion of an organism, and…
evolvingthoughts | June 10, 2007
The Flood is perhaps the most scientifically interesting story in Genesis, and it has, in fact, been discussed by scientists for over 400 years. Now we are taking the text to tell us of a world, not taking the world to tell us what to think of the text, but let's consider what the Flood story might mean for a world in which it occurred.
First the P author gives us a list of genealogy from Adam to Noah. These individuals live very long times - in Methuselah's case almost a thousand years, so obviously the harm caused by the Fall did not take effect immediately. In fact, the collapse of YHWH…
evolvingthoughts | June 4, 2007
This three-part series is a talk I gave a while back to some ecologists and molecular biologists. It is a brief overview of the aims and relationship between science and philosophy of science, with a special reference to the classification wars in systematics, and the interface of science and the broader community. I will present my own overview of the elements of science - as a dynamic evolving entity of knowledge gathering rather than as a timeless methodology or as a purely social movement.
[Part 2, Part 3]
It isn't often that an ornithologist gets to talk to birds. It's even less…
evolvingthoughts | May 31, 2007
We're in the third day, and Elohim has made dry land, but no sun or stars or moon. Still, he's keen to see something growing, so he tells the land to produce, by spontaneous generation as it was later known, "seed bearing plants and plants bearing fruit with their proper seed inside". Seed here is crucial - God creates things that reproduce themselves through some innate generative power, but at first they come out of the land. Augustine, in De Genesi ad litteram declared that God acted out of a secondary power here - he didn't create these plants directly, but indirectly, by putting a…