20 January 2008

Third Meeting of the International Society for Phylogenetic Nomenclature

The ISPN's third biennial meeting has just been officially announced.



Third Meeting of the International Society for Phylogenetic Nomenclature
Halifax, Nova Scotia, July 21 – July 23, 2008

We are pleased to announce that the 3rd Meeting of the International Society for Phylogenetic Nomenclature (ISPN) will be held in conjunction with a joint meeting of the International Society of Protistologists and the International Society for Evolutionary Protistology (https://protist2008.dal.ca/). In addition to featuring communications on the theory and practice of phylogenetic nomenclature, this meeting will be an opportunity to discuss the forthcoming release of the PhyloCode and publication of the Companion Volume, as well as development of the on-line registration database (RegNum). All systematists interested in the development of phylogenetic nomenclature are welcome. Discussions and presentations at this meeting may influence the future development of the PhyloCode.

Venue:
The meeting and associated social gatherings will be held on the campus of Dalhousie University, in the centre of Halifax. In order to make the meeting accessible to all scientists, on-campus dormitory-style accommodation will be available, in addition to nearby hotels. Note that U.S. Citizens traveling to Canada will be required to carry passports.

Conference Language:
English

ISPN Organizing Committee:
Harold Bryant, Chair, Royal Saskatchewan Museum, Canada
Nico Cellinese, University of Florida, U.S.A.
Walter Joyce, Yale University, U.S.A.
Michel Laurin, CNRS, Paris, France

Registration and Abstract Submission:
Instructions on how to register and submit abstracts will be provided in the second circular, which will be distributed in the very near future.

For More Information:
Download the First Circular (PDF)



I'd better brush up on my protistology. Oh, and hurry up with Names on NEXUS....

16 January 2008

Vermin the Size of Cars

I have to say, I've never understood why certain animals are kept as pets. Dogs and cats I like. You can play with them. They're your buddies. But my girlfriend has four chinchillas (Andean rodents that look like grey Pikachus), and, while I suppose they're kind of cute, sometimes I fail to see the point. Sometimes I feel like we're intentionally harboring vermin.

Anyway, Bernard, Lily, Hyzenthlay, and Half-Pint might be interested (if they had larger intellects) to know that an extinct cousin of theirs was recently discovered which outweighed some of the dinkier automobiles on the road. To be more precise, Josephoartigasia monesi weighed about a metric tonne. (Well, based on allometric inferences, anyway -- only the skull is known.)

Wonderfully, the paper is freely available.

How close was it to my messy housemates? Reasonably close -- since they're both caviomorphs (a group named after the guinea pig genus), their shared ancestry goes back at furthest to the middle Oligocene, roughly 28 million years ago. (J. monesi itself is from the Pleistocene, roughly a million years ago.) But J. monesi is much closer another living South American rodent called the pacarana, Dinomys branickii. Basically, it's a stem-pacarana.

Illustrations of a) Josephoartigasia monesi and b) its close living relative, the pacarana (Dinomys branickii), to scale, by G. Lecuona. A larger version is available in the paper, linked above.

And it's not the only giant South American rodent. The type species of Josephoartigasia, J. magna, was a smaller giant, as were some other stem-pacaranas less close to pacaranas, like Phoberomys pattersoni (about 700kg) and Phoberomys insolita (even bigger, but poorly known). Even today, the largest rodent in the world is the South American capybara*, Hydrochoerus hydrochaeris, weighing up to 65 kg. And the pacarana itself is no slouch, at 15 kg.

South America was until recently host to a number of large-to-gigantic animals we'd find strange today. There were ground sloths; tank-like stem-armadillos called glyptodonts; ground-dwelling killer birds called phorusrhacids; the aforementioned huge caviomorphs; and two groups of hoofed mammals unrelated to any of the modern groups: notoungulates, including the hippo-like Toxodon, and litopterns, including the bizarre Macrauchenia, which looked something like a llama with the head of a tapir.

On the subject of tapirs, clearly not all of the weird South American fauna has died out. While much of it seems to have been done in by invaders from North America, some of it has continued to flourish. A couple of groups, including the opossums, Didelphis, and certain armadillos, Dasypus, have even "swum against the tide" and colonized North America from South America.

And, of course, there are the four little furballs sitting in my downstairs. Oh, maybe I'll go give them some raisins -- they are kind of cute when they hold them.

Susan's cat, Caspian, at left, with one of her chinchillas, Bernard, at right. Photo by Susan Havens. (Not one of her best, but....)

* Apparently also known as the carpincho, according to the paper. Sounds kind of rude, somehow.

14 January 2008

March of Man: Information Upgrade

The information in the "Field Guide" at March of Man is fairly vague, unsubstantiated, and really just a first pass. I started to collect more complete, referenced entries in a Google Docs document:

March of Man Taxa

This is publicly viewable. If anyone wishes to help out with this (and receive credit on the March of Man website, of course), leave a comment and I'll share the document with you.

Here's a sample of one of the more complete entries so far:

Orrorin tugenensis

Time Range: 6.1 to 5.8 Mya

Author: Senut et al. 2001

Definition: The species typified by BAR 1000'00.

Synonyms: Praeanthropus tugenensis Cela-Conde and Ayala 2003

Hypodigm: at least 5 individuals -- BAR 1000a'00 (fragment of left mandible with molars 2 and 3; holotype); BAR 1000b'00 (fragment of right mandible with molar 3; holotype); BAR 349'00 (manual phalanx; paratype);
BAR 1001'00 (upper central incisor; paratype); BAR 1002'00 (left femur; paratype); BAR 1003'00 (proximal left femur; paratype); BAR 1004'00 (right humeral shaft; paratype); BAR 1215'00 (proximal right femur; paratype); BAR 1390'00 (lower 4th premolar; paratype); BAR 1425'00 (upper right canine; paratype); BAR 1426'00 (upper left 3rd molar; paratype); BAR 1900'00 (upper right 3rd molar; paratype); KNM LU 335 (lower molar; paratype)

Systematics: Originally proposed as the earliest species closer to Homo than to Australopithecus (Senut et al. 2001). However, this poses temporal difficulties, since it dates from a time when, according to genetic evidence, the human and chimpanzee lineages had only just begun to diverge, or perhaps had not diverged at all (Patterson et al. 2006). Instead it may be a very early species in the human lineage (Cela-Conde et al. 2003) or, given the timing, something close to the human-chimpanzee concestor. See: Hominini (concestor), stem-Hominini

Cranial Capacity: unknown, but probably about 350 cc

Description: Probably somewhat chimp- or bonobo-like, but with a more habitually upright posture.

Adult Female Height: 0.7 to 1m

Adult Male Height: 0.9 to 1.2m

References:
  • Cela-Conde, C. J. and F. J. Ayala (2003). Genera of the human lineage. Proceedings of the National Academy of Sciences 100(13):7684-7689. doi:10.1073/pnas.0832372100
  • Patterson, N., D. J. Richter, S. Gnerre, E. S. Lander and D. Reich (2006 June 29). Genetic evidence for complex speciation of humans and chimpanzees. Nature 441:1103-1108. doi:10.1038/nature04789
  • Senut, B., M. Pickford, D. Gommery, P. Mein, K. Cheboi and Y. Coppens (2001). First hominid from the Miocene (Lukeino Formation, Kenya). Comptes Rendus de l'Académie de Sciences 332:137-144.

06 January 2008

My Reading List: Or, Why I Should Not Buy Any Books for the Next Two Years At Least

Yuletide has ended, and now I have even more books that I'm "currently reading" (translation: currently keeping bookmarks in). I compiled a list of the the books I've started but have not yet finished. I left out reference books, as well as my best Christmas present: Susan got me a freakishly gigantic compilation of Little Nemo in Slumberland comic strips (by Winsor McKay). The book is so large that you don't read the strips so much as enter into them, in all their meticulous detail.

I also omitted any books that are best browsed rather than read cover-to-cover, for example, The Onion's new atlas, Our Dumb World (which is pretty hilarious).

Anyway, here's the list:
  • The Amber Spyglass by Philip Pullman. I read though the first two His Dark Materials books pretty quickly last month, but I seem stuck halfway through this one. One of the key things these books have going for them is a great main character, Lyra, and she hasn't been present much in this volume so far.
  • Cocktail Time by P. G. Wodehouse. I barely started it when Susan absconded with it.
  • Collapse: How Societies Choose to Fail or Succeed by Jared Diamond. I keep reading this in spurts and am currently a little over halfway through. Very interesting, although I prefer the author's Guns, Germs, and Steel so far.
  • The Complete Gospels ed. by Robert J. Miller. I'm not sure if I should include this or not. I did read The Gospel According to Mark in its entirety (and it turns out to be written in a much more colloquial style than more "orthodox" translations indicate) and skimmed the rest, but it seems better as a reference than something to read cover-to-cover. (And for that reason I should probably return it to the friend who loaned it and buy my own durn copy.)
  • Darwin's Dangerous Idea: Evolution and the Meanings of Life by Daniel C. Dennett. Almost done with chapter two — excellent read so far.
  • Did God Have a Wife? by William G. Dever. I started reading this while visiting Scott in Wyoming. Now I have my own copy so I can finish it.
  • The Elegant Universe: Superstrings, Hidden Dimensions, and the Quest for the Ultimate Theory by Brian Greene. Got two-thirds through and then forgot about it.
  • From Lucy to Language by Donald Johanson and Blake Edgar, principal photography by David Brill. Haven't really started reading this cover-to-cover yet, but I should.
  • The Great Human Diasporas by Luigi Luca Cavalli-Sforza and Francesco Cavalli-Sforza. I've read a bit, but it seems so far to be stuff covered by other Cavalli-Sforza books I've read (although going into more detail on African pygmies).
  • How We Believe: Science, Skepticism, and the Search for God by Michael Shermer. I seem to have gotten halfway through this one and then forgot about it. I really enjoyed the author's Why People Believe Weird Things.
  • The Impact of Science on Society by Bertrand Russell. Really excellent stuff so far — has aged surprisingly well.
  • The Inflationary Universe: The Quest for a New Theory of Cosmic Origins by Alan H. Guth. Stalled two-fifths of the way through.
  • The Life and Adventures of Tristram Shandy, Gentleman by Laurence Sterne. Let's face it, I'm never going to finish this one.
  • Lucy's Child: The Discovery of a Human Ancestor by Donald Johanson and James Shreeve. Haven't gotten too far, but so far it's pretty interesting. More about how discoveries have been made than about what discoveries have been made.
  • The Orthodox Corruption of Scripture by Bart D. Ehrman. I'm about a quarter through. Very interesting stuff.
  • Sociobiology: The New Synthesis by Edward O. Wilson. I've been "reading" this classic tome for years. (To be fair, it's pretty large.)
  • Species: New Interdisciplinary Essays ed. by Robert A. Wilson. I've read a few of the essays and wonder if I'll ever read them all. I probably should.
  • The Stuff of Thought: Language as a Window into Human Nature by Steven Pinker. This book caps off not one but two trilogies by the author, one on language and the other on mind. Having read and throughly enjoyed the four preceding books (The Language Instinct, Words and Rules; How the Mind Works, The Blank Slate), I figured I owed it to myself to check this one out. So far pretty good.
  • The Text of the New Testament: Its Transmission, Corruption, and Restoration by Bruce M. Metzger and Bart D. Ehrman. Very detailed, somewhat laborious but fascinating, account of what, exactly, our sources for the New Testament are.
  • Under the Banner of Heaven: A Story of Violent Faith by Jon Krakauer. I finished the first two chapters, which are so distressing that it's taken me a while to work up to reading the rest.
  • Using Language by Herbert Clark. Not far.
  • Voyage of the Beagle by Charles Darwin. I sort of inherited this one and will make it through some day....


I'm sure I left some stuff off, and I'm really sure I left some stuff off the next list: a list of the the books I haven't even started yet!

  • Annals of the Former World by John McPhee
  • The Autobiography of Charles Darwin by (duh) Charles Darwin
  • The Chicken Qabbalah of Rabbi Lamed ben Clifford by Lon Milo Duquette.
  • The Coming Global Superstorm by Art Bell and Whitley Strieber
  • The Evolution of Living Things by H. Graham Cannon
  • The Lucifer Principle by Howard Bloom
  • Sanksrit Grammar by Willian Dwight Whitney. This one'll probably end up more of a reference book, but I should read the first few chapters at least.
  • Scenes From Deep Time: Early Pictorial Representations of the Prehistoric World by Martin J. S. Rudwick.
  • Speeches That Changed the World by various authors.
  • Spook: Science Tackles the Afterlife by Mary Roach. The author's Stiff, about various topics to do with corpses, was quite good.
  • The Structure of Scientific Revolutions by Thomas S. Kuhn
  • The Rough Guide to Climate Change: The Symptoms, the Science, the Solutions by Robert Henson
  • Write It in Arabic by Naglaa Ghali. It's a workbook, actually, and I should start it sometime.


I really need to take a month or two off and just read, read, read. (Or get caught in a bank vault while an atomic bomb destroys Los Angeles ... time enough at last!)

04 January 2008

Resolutions for 2008

I'm not going to bother you with personal resolutions (lose weight, save money, blah blah blah), but rather creative resolutions.

2007 was kind of a watershed year for me in many ways.
My girlfriend, Susan, also had a very productive year, since she started USC film school a year ago.

Of course, it wasn't entirely positive. I dropped the ball on Parry & Carney, and the Dinosauricon continues to languish. (Some day I plan to re-use code from March of Man and Names on NEXUS for a new version, but that day is still far off.)

Well, with 2007 in mind, here's what I'd like to get done in 2008:
  • Launch Names on NEXUS and give a talk on it at this year's ISPN meeting in Halifax, Nova Scotia (and also try for an SVP talk or poster). Perhaps start working on a related paper, if applicable.
  • Continue developing March of Man and add several dozen images to it. Continue promoting it and get at least another dozen artists to contribute. Perhaps do a poster or something at SVP.
  • Fix a few remaining issues with the PhyloCode website.
  • Help Susan on her filmic endeavors, and continue to develop a sci-fi concept we started.
  • Continue translating Genesis.
  • Release some ActionScript 3.0 source code into the public domain.

03 January 2008

Ape Taxonomy Is Confusing

Homininans, including us humans, are a type of hominin. Hominins are part of Homininae. Hominidae includes hominines. These are all subsets of Hominoidea.

Confused yet? You should be. Welcome to the not-so-wonderful world of typological, ranked taxonomy.

Traditionally, taxonomy had little to do with how organisms were actually related (Linnaeus having preceded Darwin by a good century). Taxonomy was just a way of sorting specimens: these ones go in this box (a species), and the little box goes in this bigger box (a genus), and the bigger box goes in this even bigger box (a family), and so on.

Eventually a typological system arose from this: one specimen (ideally) would be the standard, the archetype, the name-bearer for a given little box. One little box would be the "type" for a larger box, and so on. The box sizes were also strictly regulated: species, genus, family, order, class, phylum/division, kingdom. Eventually, new intermediate sizes, or ranks, were also added: subgenus, subfamily, superfamily, infraorder, suborder, etc.

Several taxonomic codes arose to govern this style of taxonomy, primarily the ICZN for fauna and the ICBN for flora. To simplify matters, they mandated that the name of a type genus should be used with the appropriate suffix for some of the taxa that include that genus. The codes don't agree on which suffixes to use for ranks (for example, the ICZN uses -idae for families while the ICBN uses it for subclasses), but they are standardized within each code.

Under the ICZN, our own taxonomy below the ordinal level looks like this:
RankTaxonEnglish vernacular form
SuperfamilyHominoideahominoid
FamilyHominidaehominid
SubfamilyHomininaehominine
TribeHomininihominin
SubtribeHomininahomininan
GenusHomo
SubgenusHomo (Homo)
SpeciesHomo sapiens
SubspeciesHomo sapiens sapiens


Anyone whose skin isn't crawling by now isn't paying attention.

Not only are these names comically and confusingly similar, but they're ambiguous. "Hominidae" means "the family that includes Homo", but what constitutes a "family" is entirely up to the whims of the taxonomist. As I've discussed on this blog earlier, some researchers restrict to to Homo and a few close, extinct relatives, while others have included all great apes as well, or even all apes.

Recently there has been a movement to coöpt these names into a phylogenetic framework. Something like this is emerging as a consensus (extinct taxa omitted):

Hominoidea
|--Hylobatidae (gibbons)
`--Hominidae
|--Ponginae
| `--Pongo (orangutans)
`--Homininae
|--Gorillini
| `--Gorilla (gorillas)
`--Hominini
|--Panina
| `--Pan (chimpanzees, including bonobos)
`--Hominina
`--Homo
`--Homo sapiens (humans)


In some ways this is a good scheme, but it has two big problems: 1) the Homo-typified names are still all horribly similar, and 2) many people still use those names in the more traditional way, where, for example, Gorilla, Pan, and Pongo are not in Hominidae.

So here's a brainwave: why not just think of new names for these clades? Seriously!

We already have some good vernacular names as a basis: "apes" for Hominoidea, "great apes" for Hominidae, and "African apes" for Homininae. Admittedly there's not a convenient term for the chimp-human crown group (besides "the chimp-human crown group", of course). Maybe something like "hunting apes" (humans and common chimps are the only apes to go on hunts, I think) or "sexy apes" (humans and bonobos are the only apes to engage in certain sexual positions and activities). Translate these into Latinized Greek and we get:

Pithecoi
|--Hylobatidae (gibbons)
`--Megapithecoi
|--Pongo (orangutans)
`--Afropithecoi
|--Gorilla (gorillas)
`--[insert clever name here]
|--Homo (humans)
`--Pan (chimpanzees, including bonobos)


Isn't that much nicer? All of these could be defined as crown groups (except for Homo).

Well, just a little dream of mine, anyway....

01 January 2008

March of Man: Collage Backgrounds

Merry 2008, everyone!

In an attempt to beautify the collages on March of Man, I've added a more naturalistic background than the old grey tiles. Check it out.

I also added a few more figures. I sketched a bunch over my vacation, inspired by the chimpanzees at the Chicago Zoo (who, incidentally, love snow—or love eating it, anyway). Despite this, though, over half of the taxa are still not illustrated. Now would be a great time for other people to start making contributions. (Thanks again to Stephen O'Connor for his Homo erectus!)

Here are some sample collages—as always, figures are in chronological order from left to right:


Vertical distribution of figures based on phylogeny.


Vertical distribution of figures based on geography (Cape of Good Hope at top, Tierra del Fuego at bottom).


Vertical distribution of figures based on a combination of phylogeny and geography.


This won't be the final word on the background, but I think it's a bit of a step up (even if it does look a bit like barf). Unfortunately, it also drastically increases the size of the application. I need to do some file restructuring at some point. I've been neglecting my other projects, though, so I may have to push this off for a bit.





Update: Here is a much larger version (with phylogeny-based vertical arrangement).