Saturday, December 31, 2005

Papers I Have Read This Week

One of the things Santa brought me for Christmas was a subscription to Current Anthropology. So I have read a bunch of articles from that:

Sealy and Pfeieffer, 2000. Diet, Body Size and Lanscape Use among Holocene People in the Southern Cape, South Africa. CA 41(4):642-654. Stable isotope (nitrogen) analysis of a series of Kalahari San skeletons spanning the last 10,000 years

Dobson and Geelhoed, 2001. On the Chatelperronian/Aurignacian Conundrum: One Culture, Multiple Human Morphologies. CA 42(1):139-140. Totally unconvincing paper that tries to relate Neandertal morphology to thyroid problems and/or iodine deficiency.

Karavanic and Smith, 2000. More on the Neanderthal Problem: The Vindija Case. CA 41(5):838-839. Short article discusses a issue conected with interpreting lithics discovered at Vindija.

Russell, Martin and Buitebhuis, 2005. Cattle Domestication at Catalhoyuk Revisted. CA 46 (Supplement):S101-S108. This was an interesting article. The Anatolian city of Catalhoyuk was primarily excavated by Mellaart during the 1960's. Excavations started again in 1995 (under the direction of Ian Hodder)and have continued to the present. Catelhoyuk has always been considered a "center" of animal domestication. However, this paper indicates this picture is erroneus. The authors conclude that domestication occured first in the northern Levant and spread west through Anatolia reachin Hoyucek and Asikli Hoyuk by the end of the occupation at Catalhoyuk (Yes,I know they all have accent marks but I don't have the fonts to do them). Below is a map of the Region. South of Ankara is a city called Konya. Catalhoyuk is south and a little east of Konya.

James and Petraglia, 2005. Modern Human Origins and the Evolution of Behavior in Later Pleistocene Record of South Asia. CA 46 (Supplement):S3-S26. Discusses the archaeological and fossil records of South Asia - mainly from an Out-Of-Africa perspective.

Bonneuil, Noel, 2005. Fitting to a Distribution of Deaths by Age with Application to Paleodemography: The Route Closest to a Stable Population. CA 46 (Supplement): S29-S45. Esoteric issues in paleodemography.

Cyphers, Zuniga and Castro, 2005. Another Look at Bufo marinus and the San Lorenzo Olmec. CA 46 (Supplement):S129-S133. Current ideas have Bufo toxins being used among the early Preclassic Olmecs in shamanistic rites. The authors examine the archaeological context of toad remains in San Lorenzo and conclude that, in the early Preclassic, the Olmec were not exploiting marine toads. Rather most of the toad remains represent modern toads " and dying in their preferred habitat." Consequently, they are secondary intrusions in the early Preclassic strata.

Dennell and Roebroeks, 2005. An Asian persperctive on early human dispersal from Africa. Nature 438:1099-1104. Fascinating discussion of early hominin presence in Asia. I will be doing a post on this when time permits. Definately a must read for anyone interested in Paleoanthropology.

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The Dover Lawyers

Others have already mentioned this article on Eric Rothschild and Stephen G. Harvey - the lawyers who were instrumental in the Dover Trial. There are two sentences in the article that I find fascinating:

The next scheduled talk, and by no accident, will be in Kansas, where an intelligent design battle is brewing.

Rothschild and Harvey said they feel connected to this controversy and will not stop their involvement with it now that the case is over.

"It's not the last you've heard from me and Steve on this," Rothschild said.

I don't know what their future plans are in this regard, but I am happy to see them say that. I've read all the testimony and cross exams, some of the amicus briefs and the entire decision. I am not a lawyer, or legal expert, but all I can say is that the trial was a work of art.

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Friday, December 30, 2005

New Species of Mammal Discovered in Australia

From National Geographic News:

Dubbed Kryoryctes cadburyi—as in Cadbury chocolate—the dinosaur-era mammal was roughly the size of a large cat, covered with quills, and toothless.

A distant relative of today's spiny anteater, the species lived about 106 million years ago alongside dinosaurs in what is now Australia.

Why cadburyi?

Helen Wilson, then a student at Australia's Monash University, was one of the bone diggers in the summer of 1987.

"The food at the dig was terrible, and all of us students lived on chocolate," Wilson said. "I asked Tom what we'd get if we found a dinosaur jaw, and he said he'd give me a kilo [2.2 pounds] of chocolate"—which she went on to win and consume almost single-handedly.

If a dinosaur jaw was worth two pounds of chocolate, what would a mammal specimen merit?

"For Tom, a mammal bone was the holy grail," Wilson said.

Quite certain that a mammal bone wouldn't be found, Rich promised a cubic meter [35 cubic feet, or about a ton] of chocolate to anyone who came up with a specimen.

Back to the fossil:

The specialists determined that the fossil was in fact a mammal bone, from an early echidna, to be exact.

Echidnas are insect-eating burrow dwellers that, unlike other mammals, lay eggs. The two living species of echidnas, also known as spiny anteaters, occur only in Australia and New Guinea.

The mammal experts wrote up the scientific description for publication, and the newfound mammal was announced this week in the December issue of the Journal of Mammalian Evolution.

I've not been able to find any pictures of the fossil...

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Evolution in Action

Wow, according to the CDC a new mutated virus (actually a bacterium - afarensis) is going around.

The virus, Clostridium difficile, is particularly nasty:

“…a growing number of young, otherwise healthy Americans who are being stricken by the bacterial infection known as Clostridium difficile -- or C. diff -- which appears to be spreading rapidly around the country and causing unusually severe, sometimes fatal illness.”

There are two possible causes. First:

"This may well be another consequence of our use of antibiotics," said John G. Bartlett, an infectious-disease expert at Johns Hopkins University in Baltimore. "It's another example of an organism that all of a sudden has gotten a lot meaner and nastier."


The antibiotics Flagyl (metronidazole) and vancomycin still cure many patients, but others develop stubborn infections like Shultz's that take over their lives. Some resort to having their colon removed to end the debilitating diarrhea. A small but disturbingly high number have died, including an otherwise healthy pregnant woman who succumbed earlier this year in Pennsylvania after miscarrying twins.


The infection usually hits people who are taking antibiotics for other reasons, but a handful of cases have been reported among people who were taking nothing, another unexpected and troubling turn in the germ's behavior.

The infection has long been common in hospital patients taking antibiotics. As the drugs kill off other bacteria in the digestive system, the C. diff microbe can proliferate. It spreads easily through contact with contaminated people, clothing or surfaces.


Canadian researchers, however, have found one possible culprit: popular new heartburn drugs. Patients taking proton pump inhibitors, such as Prilosec and Prevacid, are almost three times as likely to be diagnosed with C-diff , the McGill University researchers reported in the Dec. 21 issue of the Journal of the American Medical Association. And those taking another type called H2-receptor antagonists, such as Pepcid and Zantac, are twice as likely. By suppressing stomach acid, the drugs may inadvertently help the bug, the researchers said.

One of the reasons the virus is meaner and nastier:

In addition to being resistant, the dangerous C. diff strain also produces far higher levels of two toxins than do other strains, as well as a third, previously unknown toxin. That would explain why it makes people so much sicker and is more likely to kill.

Finally, an interesting epidemiological tidbit:

In the Dec. 8 issue of the New England Journal of Medicine, the CDC reported that an analysis of 187 C. diff samples found that the unusually dangerous strain that caused the Quebec cases was also involved in outbreaks at eight health care facilities in Georgia, Illinois, Maine, New Jersey, Oregon and Pennsylvania.

"This strain has somehow been able to get into hospitals widely distributed across the United States," said Dale N. Gerding of Loyola University in Chicago, who helped conduct the analysis. "We're not sure how."

Abstracts can be found by following the links below:

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Thursday, December 29, 2005

Zooarchaeology, Pokemon Archaeology and Climate Change

The above are pictures of pika's, small north american species related to rabbits and hares:

Pikas breed in March or April and have a litter of three or four young after a gestation period of about 30 days. Some females have a second litter. Like many mammals, pikas shed in late spring from their long winter coats to a shorter summer coat, then shed again in the fall. Because of the short warm season, the end of spring shedding can actually overlap the beginning of the fall shed so the animals look scruffy most of the summer.

Maximum life span is four to seven years. Predators of pikas include long-tailed weasels, ermines and martens. Coyotes and hawks probably take their toll as well, but pikas are fairly well protected from larger predators by their rocky habitat.

Additionally, Pikas are the inspiration for one of the characters in the popular children's show, Pokemon.

Zooarchaeology, on the other hand, is a subset of archaeology. Zooarchaeologists are a diverse lot who study the patterened distribution of animal remains in order to learn something about subsistence patterns of humans and their ancestors. Consequently, zooarchaeology covers a wide amount of territory. One aspect falls under the rubric of taphonomy - where zooarchaeologist study how critters become fossils. In particular, how fossils can be used to study and reconstruct past environments. Another example would be studying wild sheep and goats in order to make predictions about how these animals were first domesticated. A better example would be John Speth's Bison Kills and Bone Counts. The book is, primarily, an examination of a bison kill site. Along the way we learn about portability of bison parts based on nutrional value (and examine predictions this makes about the archaeological record - calculate sex ratios based on a variety of body elements, for example)and seasonal variation in nutrional value. He then examines various groups such as northern Native Americans and European fur trappers in light of the above (if your diet is primarily meat, make sure you have some fat in it).
One of the leading zooarchaeologists is D. K. Grayson - who's "Quantitative Zooarchaeology: Topics in the Analysis of Archaeological Faunas" is a classic. Grayson has recently been studying Pikas and the results are interesting:

New research indicates the small mammals, which are very sensitive to high temperatures, are being pushed upward in their mountain habitat and are running out of places to live. Climate change and human activities appear to be primary factors imperiling the pika, reports University of Washington archaeologist Donald Grayson in the current issue of the Journal of Biogeography.

Grayson's research which looks at a 40,000-year record of archaeological and paleontological sites, combined with yet unpublished work by several other researchers, paints a bleak future for the American pika (Ochotona princeps) in the Great Basin.


Grayson's analysis of 57 well-dated archaeological sites, dating as far back as 40,000 years, shows that pikas have been pushed to higher and higher elevations. During the late Pleistocene and early Holocene epochs, 40,000 to about 7,500 years ago, now-extinct populations of Great Basin pikas were found at an average elevation of l,750 meters (5741 feet). The average minimum elevation of 18 surviving Great Basin populations surveyed in 2003 by Erik Beever, now with the National Park Service, was 2,533 meters (8,310 feet). These populations are scattered across Nevada, eastern California and southern Oregon.

Nine populations of Pikas have become extinct, while the remaining populations have been pushed to higher elevations. Beever's recent (2004 - afarensis) research indicates:

...American pika (Ochotona princeps) populations were detected at only five out of seven re-surveyed sites that possessed pikas in Beever's research in the mid- to late-1990s. The original research documented local extinctions at seven of twenty-five sites in the Great Basin – the area between the Sierra Nevada and Rocky Mountains. The recent re-sampling brings the total number of sites at which American pika populations have suffered local extinction to nine out of twenty-five or 36 percent. Continued loss of populations raises concern, as does the fact that these results and other lines of evidence suggest that many of the losses have occurred towards the more recent end of the 14 to 91-year period since their scientific discovery.

Back to the Grayson article for the final word:

Beever recently discovered two more pika population extinctions in the Great Basin and another increase of 132 meters (433 feet) in the lower elevation range of the animals at the locations where populations still remain. Patton, who has been studying wildlife in Yosemite National Park, which is in the Sierra Nevada Mountains adjacent to the Great Basin, has reported a 1,700-foot upward increase in the range of pikas there over the past 90 years. Found as low as 7,800 feet in the first decade of the 20th century, the animals now can't be found below 9,500 feet in Yosemite.

"We might be staring pika extinction in the Great Basin, maybe in Yosemite, too, right in the face. Today, the Great Basin pika is totally isolated on separated mountain ranges and there is no way one of these populations can get to another," said Grayson. "They don't have much up-slope habitat left."

"Pikas are an iconic animal to people who like high elevations. They are part of the experience. What's happening to them is telling us something about the dramatic changes in climate happening in the Great Basin. Climate change will have a dramatic effect including important economic impacts, such as diminished water resources, on people.

So, studying the effects of climate change is another intersting facet of zooarchaeology...

The abstract to Grayson's article can be found here.
The absract to Beever et al's 2003 paper can be found here.

For additional info on zooarchaeology the following books are recommended:

Vertebrate Taphonomy by R. Lee Lyman
Bison Kills and Bone Counts by John D. Speth
Fossils in the Making: Vertebrate Taphonomy and Paleoecology by Behrensmeyer and Hill
Environment and Archaeology by Karl Butzer
The Grayson book mentioned above.

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New Post at Transitions

Aydin Orstan has a new post up over at Transitions. It is about Baracles:Darwin's Old Buddies. The title is a reference to the fact that Darwin spent eight years classifying baracles and made several interesting discoveries concerning them. Check it out!

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Late Archaic Projectile Points

This is cool...
Michael J. Rogers, associate professor of anthropology at Southern Connecticut State University and his student, Nancy Parsons, have found almost 5,000 stone artifacts at the site, including several unfinished points and at least one unbroken dart point.

The discovery reveals the importance of stone ridges to the hunter-gatherers of 3,000 to 4,000 years ago and adds details to the sparse knowledge of the Late Archaic period of North America.”


"Quartz was probably not their first choice" for making stone points, he said. Although very hard, quartz cracks unpredictably and is difficult to work. The hunter-gathers probably selected fist-sized lumps of quartz and broke them into two parts. The ancient craftspeople then used rocks to shape the quartz, Rogers says.

Once the quartz gained a sufficiently triangular shape, pieces of wood or antler were then pressed against the edges to flake off small pieces to shape the final product.

Parsons says she wondered why the site contained so many imperfect points. The answer is probably that the "good" points were used for hunting, while less-than-perfect pieces were discarded, she says.

In case you are wondering the projectile points are of a type known as Squibnocket Triangles which date to the Late Archaic (6,000-3,700 BP)
New England Projectile Point Typology contains an interesting overview of projectile points found in the New England Region as well as pictures illustrating each type.

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Tuesday, December 27, 2005

Sevens Meme

Oldwhitelady has tagged me with the "Sevens" meme so here goes:

Seven Things To Do Before I Die
1)Get a Ph.d
2)Finish The Structure of Evolutionary Theory
3)When 2 is done read everything in the Library of Congress
4)Visit Greece
5)Visit the Smithsonian
6)Sail around the world
7)After 1 is complete publish a paper in a professional peer-reviewed science journal so I can legitimately claim that I have outproduced the intelligent design advocates (currently we are tied)

Seven Things I Cannot Do
1)Anything that involves artistic talent (drawing, painting, coloring inside the lines)
2)Stop smoking (but if at first you don't succeed...)
3)Get the words to "I'll be Home for Christmas" out of my head (been looping through for about three days now - driving me crazy)
4)Join the Republican party
5)Stop being cynical
6)Think of something for number seven (or is that cheating...)

Seven Things That Attract Me to...Blogging (this is a tough one)
1)It allows me to put my education to use
2)Forces me to try and stay current about what's happening in the world
3)Allows for me to be creative
4)Makes me write everyday
5)The interchange of ideas can be fun
6)Outlet for my sense of humor (see my mistletoe post)although other's might characterize it differently
7)Gives me an excuse to avoid chores "...but Honey, I'm writing a post...", "...but Sweetie, I have to respond to these comments..." etc. (I hope Mrs. afarensis doesn't read this post).

Seven Things I Say Most Often
1)good luck with that
2)How does it feel to want (usually when my teenage offspring produce a long, long list of things they want me to buy them)
3)All righty roo usually in response to a bad idea
4) I'll put it on my to do list (usually after number 7 above)
5)Oh, for the love of Pete (usually after the excuses in number seven above don't work)
6)Fine! also used when excuses in number seven don't work
7)Oh noooo, a shark winked at me! (it's a phobia, I can't explain it so don't ask - and yes some sharks, lemon sharks spring to mind, have eyelids and can wink)

Seven Books That I Love
1)The Origin of Species
2)Lucy: The Beginnings of Humankind
3)The Anubis Gates (Tim Powers)
4)Lord Foul's Bane (Stephen Donaldson)
5)The Best of Corwainer Smith
6)Complete Works of William Shakespear
7)A Tale of Two Cities

Seven Movies That I Watch Over and Over Again
1)Underworld (Sequel is coming out soon)
3)Anything with Godzilla
4)The Mummy and The Mummy Returns (Brendan Fraser)
5)Tremors (and it's three sequels)
6)My Cousin Vinny
7)Oh, Brother, Where Art Thou?

Seven + People I Want To Join In Too
I'll leave this open for whoever wants to do it...

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Saturday, December 24, 2005

Open Access Journals and the Evil Darwinian Orthodoxy

Geotimes has an interesting discussion of open access journals:

Open-access publishing has been heralded both as the savior of scientific literature and the death of publishing, but after less than a decade of the practice, its impact remains uncertain. A new review indicates that the success of these free and open journals also remains to be seen.
The movement to make scientific journals freely available has been growing worldwide in recent years.

About 1,600 journals have followed the open-access model, whereas more than 20,000 non-open-access journals are regularly published around the world. The movement to make scientific journals freely available has been growing worldwide in recent years, with added attention in the United States due partly to a policy introduced last year by the National Institutes of Health. The federal agency encourages its researchers to enter their papers in an online database open to the public, within six months of publication.

Does anybody know the URL of this Online Database?

The entire article is worth reading in it's own right, but I have different motives for mentioning it. You may notice a section on my sidebar, named "The Evil Darwinian Orthodoxy". It contain's link to a number of scientific journals dealing with evolution. I am alway's on the lookout for more and since the above quote mentions 1,600 open access journals and 20,000 non-open access journals I figure I've barely scratched the surface here. In a word, even though I beg and plead some of my readers are holding out on me! So I'm going to beg and plead some more! Please, pretty please with sugar on top, leave some journal titles in the comments (links would be nice but are not required). Don't make me show up at your site and whine pathetically! You won't (to paraphrase Bruce Banner) like me when I get whiney!

I was inspired to create the list based on an idea of Josh Rosenau at Thoughts From Kansas. You see Josh created The Evolution Prject and the Non-Evolution Project wherein he documents the relative contibutions of evolutionists and Intelligent Design proponents to the advancement of science (we are still waiting for a contribution from ID ...). So I thought wouldn't it be a grand idea if we had a list of all the science journals dealing with evolution. So that we could refer people to them. Refering people to say, Talk Origins or the NCSE, is great but I think it would be helpful if we could also send to to some journals where they could see how science actually works. Doesn't that sound worthwhile? How can you still hold out? You will be amply rewarded with the warm fuzzies that come from knowing you helped halt the spread of stupidity in America, so come on pony up with the Journals!

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Transitions News

The next post in Evolgen's series on Detecting Natural Selection has been crossposted on Transitions: The Genetics Page. The series gets more fascinating with each post, and would dare I say, make a great book (just a hint)! Check it out!

In the meantime, I am in the process of selecting a new site of the week but the competition is tough!

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Friday, December 23, 2005

Tangled Bank Reminder

Just a reminder, I'll be hosting Tangled Bank 44 on January 4th. You all know what to do...

The Tangled Bank

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Footprints are Springing Up All Over the Place

From Yahoo News:

Hundreds of human footprints dating back to the last Ice Age have been found in the remote Australian Outback, an official and media reported Thursday.

The 457 footprints found in Mungo National Park in western New South Wales state is the largest collection of its kind in the world and the oldest in Australia, The Sydney Morning Herald newspaper reported.

The prints were made in moist clay near the Willandra Lakes 19,000 to 23,000 years ago, the newspaper reported ahead of archeologists' report on the find to be published in the Journal of Human Evolution.


"We see children running between the tracks of their parents; the children running in meandering circles as their parents travel in direct lines," Debus told Australian Broadcasting Corp. radio.

"It's a most extraordinary snapshot of a moment or several moments in the life of Aboriginal people living on the edge of the lake in western New South Wales 20,000 years ago," he added.

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Interesting Website

I'll probably do a post later, but in the meantime I thought I would bring this website to your attention Paleobiology Website.

It's pretty cool to play around with.

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Thursday, December 22, 2005

Fish with Two Mouths


"It's probably a genetic deformity," he said. "I don't think there's anything wrong with it."

Ummm, I don't really have anything to add (other than to recommend that somebody should check pollution levels in the lake it came from - Montgomery Burns would be so proud).

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Mammoth Nuclear DNA says African Elephant, Mitochondrial DNA Says Asian

Okay, now I'm confused! I have posted on the Mammoth DNA study several times. One The articles I read stated that one of the conclusions was that Mammoths are more closely related to Asian elephants than African. Yet the story linked to above claims the exact opposite:

A mammoth was chosen for the study, in part, because of its close evolutionary relationship to the African elephant, whose nuclear DNA sequence has been made publicly available by the Broad Institute in Cambridge, Massachusetts (USA). Using comparisons with elephant DNA, the researchers identified 13-million base pairs as being nuclear DNA from the mammoth, which they showed to be 98.5 percent identical to nuclear DNA from an African elephant.

This, I hasten to point out, is a completely different study than the one I posted about previously. One obvious difference is that the first article used mitochondrial DNA while this one used nuclear DNA. I don't see how this would make a difference in basic results though. One of these studies has to be flawed...

At any rate here is what the Penn State (the mitochondrial DNA study was done by the Max Planck Institute)team did:

The project became possible through the discovery of exceptionally well preserved remains of a mammoth skeleton in the permafrost soil of northern Siberia, in combination with a novel high-throughput sequencing technique that could cope with the heavily fragmented DNA retrieved from the organism's mandible, its jaw bone. "The bone material used in this study is approximately 28,000 years old, as was shown by beta carbon dating analysis," said Hendrik N. Poinar, associate professor of anthropology at McMaster University. "This was a surprising finding, as it demonstrated that the analyzed material was frozen for more than 10,000 years before the maximum of the last ice age." The research team used a comparative computational approach to demonstrate that an unprecedented large percentage of the bone DNA was indeed mammoth DNA, while the remaining genetic material was shown to belong to microorganisms and plants living the tundra soil.
"Analyzing DNA from the organelles of mitochondria has been the only method of studying ancient DNA in the past, as it is more tractable due to its 1000-fold higher copy number per cell," Schuster explains. However, the mitochondrial genome codes for only a tiny fraction of an organism's genetic information -- 0.0006 percent in the case of a mammal. "We focused on sequencing nuclear DNA in this study because most hereditary information is organized on chromosomes located in the cell's nucleus," Schuster says.

The mitochondrial research appears in Nature and the Penn State research will appear in Science...

Added Later: Ahh, here is the explanation:

Poinar sent the DNA-rich sample to genomicist Stephan C. Schuster at Pennsylvania State University, University Park, who is working with a new genome sequencer developed by a team at Stanford University and 454 Life Sciences Corp. of Branford, Connecticut (Nature, 15 September, p. 376). This rapid, large-scale sequencing technology sidesteps the need to insert DNA into bacteria before amplifying and sequencing it. Instead, scientists break DNA into small fragments, each attached to a tiny bead and encapsulated by a lipid bubble where the DNA is multiplied into many copies for sequencing. Because each fragment is isolated before copying, the method avoids bias from copying large amounts of contaminant DNA from bacteria or humans.

The researchers were stunned by how well the method worked on ancient DNA, which is notoriously difficult to extract and sequence: "I would have been happy if we got 10,000 bases of mammoth DNA," said Poinar. Instead, they got 28 million basepairs, 13 million from the mammoth itself. Their preliminary analysis shows that the mammoth was a female who shared 98.55% of her DNA with modern African elephants. But mammoths were apparently closest kin to Asian elephants, as shown by Pääbo's mitochondrial study, which retrieved about 17,000 basepairs.

Apparently, both groups helped each other...

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Wednesday, December 21, 2005

More on Mammoth DNA

Added Later: Sorry for the weird formatting. I have been experimenting with posting via email.

National Geographic News has a story on mammoth DNA:
"The DNA revealed that woolly mammoths had more genetic similarities to modern Asian elephants than to the African species, though not by much, Hofreiter's team reports.

The DNA also showed that elephant species split from each other more quickly than had been thought.

Modern elephants and woolly mammoths share a common ancestor that split into separate species about 6 million years ago, the study reports.

At that time African elephants branched off first. Then just 440,000 years later, a blink of an eye in evolutionary time, Asian elephants and mammoths diverged into their own separate species."

One of the implications of the study:

Geneticists may now be able to put those samples to better use.

"Using the knowledge we've gained, this technology can be used quite widely on ancient DNA to resolve the [evolutionary histories] of both extinct and extant species," Hofreiter said.

"We may even be able to conduct population studies using ancient mitochondrial DNA. There will be some things to resolve and maybe some interesting surprises as well."

I'm looking forward to this later, sounds intriguing!

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Is MSNBC Spending to Much Time on Discovery Institute Propaganda

<a href="">You be the judge</a>

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Tuesday, December 20, 2005

More on Dover


In addition, Professor Behe
agreed that for the design of human artifacts, we know the designer and its
attributes and we have a baseline for human design that does not exist for design of
biological systems. Professor Behe’s only response to these
seemingly insurmountable points of disanalogy was that the inference still works in
science fiction movies.


In the midst of this panoply, there arose the astonishing story of an evolution mural that was taken from a classroom and destroyed in 2002 by Larry Reeser, the head of buildings and grounds for the DASD. At the June 2004 meeting, Spahr asked Buckingham where he had received a picture of the evolution mural that had been torn down and incinerated. Jen Miller testified that Buckingham responded:
“I gleefully watched it burn.” Buckingham disliked the mural because he thought it advocated the theory of evolution, particularly common

Given, say Dembskis obsession with putting Darwin's head in a vise and pile driving him one has to wonder about this violent streak among creationists and ID proponents.
Better yet, should the guy have been allowed with miles of a child?


Remarkably, the 6-3 vote at the October 18, 2004 meeting to approve the
curriculum change occurred with absolutely no discussion of the concept of ID, no
discussion of how presenting it to students would improve science education, and
no justification was offered by any Board member for the curriculum change.
Furthermore, Board members somewhat candidly conceded that they lacked sufficient
background in science to evaluate ID, and several of them testified with equal
frankness that they failed to understand the substance of the curriculum change
adopted on October 18, 2004.
In fact, one unfortunate theme in this case is the striking ignorance concerning the concept of ID amongst Board members. Conspicuously, Board members who voted for the curriculum change testified at trial that they had utterly no grasp of ID.

Actually, now I'm starting to wonder why they were put in charge of determining educational curriculum:

Despite this collective failure to understand the concept of ID, which six Board members nonetheless felt was appropriate to add to ninth grade biology
class to improve science education, the Board never heard from any person or
organization with scientific expertise about the curriculum change, save for
consistent but unwelcome advices from the District’s science teachers who
uniformly opposed the change.


While there is no requirement that a school board contact any of
the afore-referenced organizations prior to enacting a curriculum change, in this
case a simple glance at any one of their websites for additional information about
ID and any potential it may have to improve science education would have
provided helpful information to Board members who admittedly had no
comprehension whatsoever of ID.

Although the case was largely about ID the underlying story is about a board of education that failed in its duty to promote education. They displayed a total lack of concern about what would be the best way to educate the children of Dover. Even more appalling, their behavior was the exact opposite of the open minded critical examination of facts they were trying to foster.

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Some Snark about Dover

Redesign the strategy Bill:

The first mention of the Vise Strategy appeared on this blog here. I devised the Vise Strategy to aid the Thomas More Law Center in interrogating the ACLU’s expert witnesses in the Dover Trial. Since all witnesses in that trial have now been called (all that remains is for Judge Jones to render his verdict), I am making available the full-blown Vise Strategy here.

Worked like a charm didn't it? So what will the next incarnation od creationism be? I favor "Random Design" myself. How about you?

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Sour Grapes from the Discovery Institute

I am laughing too hard at this to say morehehehehe!

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The Decision

The decision can be found and it's big!

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Wohooo, We WON!

Added later: I posted this via email and the formatting wasn't good, so I have tidied it up.

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Monday, December 19, 2005

Mammoth Mitochondrial DNA Partially Decoded

According to BBC News the mitochondrial genome of the mammoth has been partially decoded:

It shows that the mammoth was most closely related to the Asian rather than the African elephant.

The three groups split from a common ancestor about six million years ago, with Asian elephants and mammoths diverging about half a million years later.

"We have finally resolved the phylogeny of the mammoth which has been controversial for the last 10 years," lead author Michael Hofreiter of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, told the BBC News website.


The DNA of several extinct ice age mammals, preserved in permafrost, has been analysed before, but not in such detail.

"It is the longest stretch of DNA [decoded to date] from any Pleistocene species," said Professor Hofreiter.


The team of researchers - from Germany, the UK, and the US - extracted and analysed mammoth DNA using a new technique that works on even the tiny quantities of fossilised bone - in this case 200 milligrams.

Some 46 chunks of DNA sequence were matched up and arranged in order, giving a complete record of the mammoth's mitochondrial DNA - the circular scrap of genetic material found outside the cell's nucleus.

A write up of the research will appear in Nature Online...

Read more!

Sunday, December 18, 2005

Luzia, Kennewick and the Peopling of the Americas

National Geographic News has an interesting story on some research on a large collection of skeletons found in Brazil. The skulls themselves date to about 10,000 years ago. The story is incredibly interesting, since it impacts theories about the peopling of the americas.

The skeletal material comes from the Lagoa Santa region of Brazil. Caves containing skeleatal material were first discovered in 1842/1843. The first prefessional archaeological excavations were conducted in 1956 and further excavations were made in the 1970's (the skull above came from the 1970's excavations). During that time at least 250 skeletons were discovered:

The scientists examined 81 skulls unearthed over many decades in Brazil's Lagoa Santa region. They represent the largest collection of early American remains, many of which had to be tracked down in European museums.

The results of the study, which is actually one paper in an ongoing program, were recently published in the Proceedings of the National Academy of Science(Thanks for sending me the article Aydin!). I also managed to track down an earlier paper published in Genetics and Molecular Biology. I'll get to some of the results below, but would like to describe some of the things that are a part of the research program of Neves and Hubbe. At this point they are trying to date as many skeletons as possible via accelerator mass spectrometry, trying to get minimum dates for some of the skeletons by dating cristaline calcite layers sealing the deposits, excavating new sites to increase the number of skeletal material and to better understand the stratigraphy of the area and rexamining some of the original sites.

Absolute dates have been obtained on 22 of the skeletons and range from 7500 - 8500 years ago. An interesting aside, most of the sample was buried in a hypeflexed position in shallow graves covered with blocks of limestone or quartz. A small hearth was usually adjacent to the pit and burning coals werethrown into the pit before sealing.

A series of measurements (61 according to the data set - although not all of them were used de to missing value, etc.) was taken on the skulls and the measurments were compared to those Howells datbase (which can be found here). To assess morphological affinities three different principal components analysis (an explanation of principal component analysis can be found here, here and here) were conducted. The first, of a type I'm not terribly familiar with (and will research and post on later), compared principal coordinates on heritability corrected data (as I understand it this technique tries to get at how much of the variation in skull morphology is due to genetic contributions). The second principal component analysis compared individual measurments within the Lagoa Santo and Howells samples. The third compared group centroids.

The resilts of all three analysis indicated that the Lagoa Santo sample has a distinctly different cranial morphology compared to late and modern Northeastern Asians and Amerindians. The Lagoa Santo sample was more similar to present Australian/Melanesian and African samples than any other group. At this point you should be asking yourselves "Where have I heard afarensis talk about old bones being related to Melanesians and Australians before?"
The picture below is another hint.

I'll get back to that in a minute. First we have to talk about the National Geographic article:

Recent genetic studies of modern human populations have also suggested multiple early migrations across the Bering land bridge.

Neves and colleagues have not been able yet to extract ancient DNA from the Lagoa Santa remains—but excavations are yielding additional ancient remains.

"We have already found at least 20 new skeletons older than 8,000 years that are not part of our paper," he said.

Still, not all scientists are convinced that the variations found in the skulls are proof of multiple migrations to the Americas.

"There is a huge amount of variation among the first Americans, more than you see among any other population outside of the Pacific," said Joseph Powell, an anthropologist at the University of New Mexico in Albuquerque.

"Much of that is genetic, and it comes from the fact, I think, that these first Americans had very small colonizing populations, and they have a great degree of genetic variation due to genetic drift."

There two questions here. First, how many populations settled the America? We know of at least two, possibly three: those populations ancestral to modern day Native Americans and those ancestral to Athabascans and the Eskimoos. All of whom originated in Northeast Asia. Neves and Hubbe, and Neves et al, put a slightly different on this question. They argue that the Americca's were first populated by "...a generalized population of Homo sapiens very similar to the one that departed from East Asia to Australia around 50,000 BP..."(from Neves et al). Later in the paper, Neves et al go into a little more detail:
In the beginning of this paper we stated that the settlement of the Australian continent is currently seen as a direct expansion of early modern people from Africa...while the settlement of the America's is viewed as a much later colonization event, namely the expansion of the specialized Mongoloids from North Asia in relatively recent times...
If this view is accepted, it becomes clear that Native Americans had an ancestral population in mainland Asia which was not shared with Native Australians."

In essence, Neves et al, is saying that Paleoindians were part of the expansion of H. sapiens out of Africa, whereas Native Americans represent a later expansion of specialized populations. I find this suggestion intriguing. There are skeptics, as you can see from the above quote from The National Geographic article. Powell is arguing that because America was populated by small populations, genetic drift would kick in and you would see a lot of variation between populations and that the Lagoa Santo populations fit within the pattern af variation seen in Native American populations. If that is the case, I would expect one or two populations to display morphology similar to Australians and Melanesians. Instead, what we have is a series running from southern Chile to Florida - and now Kennewick in Washington (which was not included in either study)- all of which display morphology similar to Australians, Melanesians and Polynesians. As Neves and Hubbe put it:

One is a local microevolutionary process that transformed, in situ, the Paleoamerican morphology into that prevailing today among Native Americans. The other is that the Americas were successively occupied by two morphologically differentiated human stocks, with the Paleoamerican morphology entering first.

We believe the second hypothesis is more plausible for three reasons: first, it would be very unlikely that the same evolutionary event (directional morphological change) happened in the Americas and in East Asia in parallel at approximately the same time (the parsimony principle)...; second, because in South America, at least, the transition between the two morphological patterns was, as far as we know, abrupt...; and third, cranial morphology has recently been shown to respond adaptatively only to extreme environmental conditions, being therefore much less plastic than originally thought...

It would have been interesting to have included Kennewick in this study since it is withing the date range of some of the other skulls studied, not to mention some of the similar morphology...but considering the legal difficulties involved in previous attempts...

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Whats Your Elf Name?

PZ is cranky cause his elf name is Ditzy Slave O' Santa. All I have to say is it could be worse. Check out my elfname!

Your Elf Name Is...

Candy Fluffernutter

Which would you rather be?

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Saturday, December 17, 2005

The War on Christmas: Santa Launches a Counterattack

Santa's pissed according to this article on MSNBC:

A group of 40 people dressed in Santa Claus costumes, many of them drunk, rampaged through New Zealand’s largest city, robbing stores and assaulting security guards, police said Sunday.

The rampage, dubbed “Santarchy” by local newspapers, began early Saturday afternoon when the men, wearing ill-fitting Santa costumes, threw beer bottles and urinated on cars from an Auckland overpass, said Auckland Central Police spokeswoman Noreen Hegarty.

afarensis expected a Clause counterattack on mistletoe not on New Zealand so he was somewhat surprised at the news. However, Santa is doing what is necessary to keep Christmas safe, so it is not our place to question his strategy...remind afarensis to be good next year (see the bolded sentence)

The remaining Santas entered a downtown convenience store and carried off beer and soft drinks.

“They came in, said ’Merry Christmas’ and then helped themselves,” store owner Changa Manakynda said.

Dang strait, Santa knows how to celebrate Christmas.

Alex Dyer, a spokesman for the group, said Santarchy was a worldwide movement designed to protest the commercialization of Christmas.

Sure, of course they are going to Swift-Sleigh Santa Clause by trying to say he's against what makes Christmas great...
On the other hand, afarensis could just be drinking too much caffiene?

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Bush Admits Spying on Americans

Added Even Later: Dear Kitty has more. I think is important to stress that this is not just one agency that has been given permission to spy on american citizens. The Pentagon has as well. My guess is that all intelligence agencies are doing so - but I can't prove it.

In the meantime, if you have done a post on the subject I would be happy to link to it...

Added Later: A good sign is that according to this survey 70% of the approximately 95000 people surveyed said Bus authorizing the NSA to spy on Americans is unconstitutional.

I Say Impeach Him:

President Bush said Saturday he personally has authorized a secret eavesdropping program in the U.S. more than 30 times since the Sept. 11 attacks and he lashed out at those involved in publicly revealing the program.

Totally disgusting. We are a nation based on the Rule of Law, not the whims oof any one person. Either it applies to everybody or it means nothing.

Really, why did you people vote for him. Was it because you enjoy the government invading your pprivacy in a massive abuse of power (beacuse don't forget, it's not just the NSA the Pentagon is doing it too)? One wonders how many other groups are spying on american citizens? One also wonders whether those resource couldn't actually be put to better use?

Eschaton has a several posts on it.
Daily Kos
Political Animal
Talking Points Memo
Thoughts From Kansas
It's Morning Somewhere on the Pentagon spying on American citizens.
First Draft
Rude Pundit
TPM Cafe
Shakespeare's Sister
Badtux the Snarky Penguin
Abnormal Interests
Think Progress
Stranger Fruit

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This is Brilliant!

From BBC News and Science:

A road ramp that uses passing cars to generate power has been developed.


Plates in the ramp move up and down as vehicles pass over them, driving a generator.

"The ramp is silent, comfortable and safe for vehicles," Mr Hughes said. (the inventor of the ramp - afarensis)

Depending on the weight of the vehicle passing overhead, between five and 50kW can be generated.

One wonders how much energy the US could save by installing these ramps?

Read more!

Genome Complexity and Population Size

Added Later: I think one of these is the original 2003 paper (scroll down to the technical comments papers - those by Daubin and Moran and Lynch and Conery are both accessible without a subscription).

This is interesting:

Biologists at Georgia Tech have provided scientific support for a controversial hypothesis that has divided the fields of evolutionary genomics and evolutionary developmental biology, popularly known as evo devo, for two years. Appearing in the December 2005 issue of Trends in Genetics, researchers find that the size and complexity of a species’ genome is not an evolutionary adaptation per se, but can result as simply a consequence of a reduction in a species’ effective population size.


Their test consisted of analyzing data from 1,043 species of fresh and saltwater ray-finned fish. Previous data on genetic variability had established that freshwater species have a smaller effective population size than their marine counterparts. If the hypothesis was correct, the genome size of these freshwater fish would be larger than that of the saltwater dwellers. It was.

Then they matched the data with estimates of heterozygosity, a measure of the genetic variation of a population. Again they found that species with a smaller effective population had larger genomes.

“We see a very strong negative linear relationship between genome size and the effective population size,” said Soojin Yi, assistant professor in the School of Biology and lead author of the study. “This observation tells us that the mutations that increase the genome tend to be slightly deleterious, because population genetic theories predict such a relationship.”

The interesting thing here is that biological complexity may passively evolve,” said Yi. “We show that at the origins, it’s not adaptive mutations, but slightly bad ones that make the genome larger. But if you have a large genome, there is more genetic material to play with to make something useful. At first, maybe these mutations aren’t so good for your genome, but as they accumulate and conditions change through evolution, they could become more complex and more beneficial.”

Interesting, I may do a more detailed post on this in the future, but in the meantime, I just thought I would point this out for (Evolgen seems to be really busy otherwise I wuld pester him about it) others to consider or maybe do a post on...

Incidently, here is a link to the recent paper. I'm still trying to track down the 2003 paper mentioned in the press release.

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Dwarf Mistletoe Joins War on Christmas, Attacks Christmas Trees

“It’s ironic that the plant associated with love and well-being at Christmas can be the kiss of death for the trees we’ve come to associate with the same holiday,” said one individual at hearing the news.
It was recently revealed that dwarf mistletoe has been routinely attacking christmas trees for years. A picture of the christmas hating plants in action is below.

Even more disturbing:

Dwarf mistletoe (dmt), an evergreen parasitic plant found on conifers in Canada, can significantly reduce a tree’s life expectancy. Even more important in beetle-infested British Columbia, the almost-invisible dwarf mistletoe species that prefers pines can weaken a tree and make it more susceptible to attack by micro-organisms and insects.

In other words, they are in Canada, heading towards the North Pole and Santa Clause. One source indicates the christmas hating mistletoe has opened a fifth column here in the United States. A map of known mistletoe terrorist cells is below.

Terrorist christmas hating misletoe in the US are particularly virulent (goes without saying since we are the greatist nation on earth our terrorist christmas hating misletoe has to be of the worst sort):

Because of its widespread occurrence on limber and whitebark pines, and the high level of mortality it causes, limber pine dwarf mistletoe is considered to be one of the most important diseases of high-elevation 5-needle pines in the West. Only white pine blister rust (Cronartium ribicola Fisch.) is considered more damaging.

From another source:

“Dwarf mistletoe is a serious forest pest,” says Ross. “Its effects can change habitat, compromise timber quality, create a fire hazard due to dead trees, and weaken a tree to the extent that it dies from other factors.”

afarensis was so alarmed at the thought that he might be harboring christmas hating terrorist mistletoe that he took his christmas tree outside and burned it. He was much embaressed, however, when Mrs. afarensis pointed out that we had a fake tree...dwelling on the failures in the war on Christmas only aides and abets the enemy so let's move on...

Apparently, these evil christmas hating mistletoe have come up with a clever and heinous method of attack:

While they may have different appetites, all of the dmt species spread their seeds through explosion, an unusual method of propagation unrivalled by any other member of the plant kingdom.


Essentially, the process works like this: water initially accumulates in the viscin mucilage, creating a steady rise in pressure, then changes in cell chemistry instigate a major influx of water into the mucilage, triggering a rapid increase in pressure. A resistant cell layer makes sure the fruit doesn’t expand in all directions, but rather accumulates pressure in the viscin, so when the cell layer where the fruit joins the stalk dies, pressure is suddenly released, bursting the fruit and dispersing the seed.

“The outer fruit shell is elastic but resistant to pressure build-up, like the skin of a balloon, and the dying cell layer that forms at the fruit stalk mimics the result of putting a pin in the balloon,” says Ross.

It’s a deadly discharge that plays a mean prank on neighbouring trees, and it’s particularly threatening in single-species stands like lodgepole pine plantations.

Shocking! I can fondly remember, from years past, kissing Mrs. afarensis under the mistletoe. Little did I know the evil nature of the christmas hating terrorist mistletoe that was hanging above our heads. So the next time someone stands under mistletoe and wants a smooch politly explain how mistletoe is a heinous member of war on Christmas then take the mistleoe outside and burn it (children should ask their parents to do this or at least be supervised by a responsible adult). They will thank you for it, our country will thank you and I will thank you.

Read more!

Friday, December 16, 2005


Within the past 24 hours I have had an unusually large number of hits on some of my posts on ID (including some of my older ones). Curious. I wonder why?

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Thursday, December 15, 2005

Napoleon, Body Lice and the Russian Retreat

Added Later: Tara over at Aetiology has also posted on this. Check it out.

Added Even Later: Honesty compells me to point out that Tara catches afarensis having a "Homer Simpson" moment. DOH!

Everyone is familiar, or should be, with the story of Napoleon's unfortunate invasion of Russia. Long story short, Napoleon marched into Russia with an army of approximately 500,000 soldiers. Winter came, Napoleon crawled out of Russia with a few thousand soldiers.

An interesting study in the Journal of Infectious Diseases sets out to examine the story from a novel perspective. In 2001 construction workers unearthed a mass grave containing 2,000-3,000 corpses:

Construction work in 2001 unearthed one such grave, containing between 2,000 and 3,000 corpses. Didier Raoult, MD, PhD, from the Université de la Méditerranée in Marseille, France, and colleagues identified body segments of five lice in a forensic excavation of two kilograms of earth containing fragments of bone and remnants of clothing. Three of the lice carried DNA from Bartonella quintana, which causes the disease commonly known as trench fever, which afflicted many soldiers in World War I.
Not content with stopping there, the researchers examined the pulp in the teeth cavity (from 72 teeth representing 35 soldiers) and were able to extract DNA from the pulp. Turns out some of the DNA belonged to B. quintana:

In all, 29 percent of the soldiers tested had evidence of either R. prowazkii or B. quintana infection...

It should be stressed that this represents what happened to those fleeing Russia, not what caused Napoleon's defeat.

One of the interesting sidenotes is that the authors of the study indicate that searching for DNA of infectious agents in the dental pulp of teeth will become an importatn tool in investigating the history of infectious diseases. I will also be the first to admit that I have no idea how the DNA got into the pulp cavity in the first place...I guess I have some research to do.

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Wednesday, December 14, 2005

afarensis is Going to Seed!

Since the cat has poked his nose out of the bag I'll help it out a little further. I have been asked to join to Seed Magazine's new blog consortium as well. It looks like a fascinating opportunity. As Ed Brayton says, arrangements will be made so you won't even have to change your bookmarks.
Unlike Ed, however, I do plan on using this opportunity to make a few - minor - changes that I have been considering for awhile. For example, I have found it a little difficult to blog about anthropological subjects since at this point I am not a practicing anthropologist. The problem is that I haven't, until now, had much access to the anthropological literature, but Santa has promised to bring afarensis some journals for Christmas. The main exception being I am still looking for two people to sponsor me so I can get the AJPA. With that in mind, you may notice a little more focus on anthropology. Instead of quoting chunks of articles as background I am going to do a lot more of the background myself. As I said, minor changes.
Unlike Ed, I have no idea who else is going to Seed - part of the fun at this point is trying to figure that out!

Added Later: Stranger Fruit as well

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Stuff I Probably Won't Have Time to Blog About , But Find Incredibly Cool!

From the BBC Humans may have moved into England 200,000 years earlier than previously thought. The tools above were found at a sight dating to approximately 700,000 years ago:

A team of researchers from the UK, Italy and Canada found a total of 32 flint tools in a fossil-rich seam at Pakefield. They say it represents the earliest unequivocal evidence of human activity in northern Europe.

New Scientist has a good article on the subject as well. Some perspective:

"We don't know for sure what species it was," says team member Chris Stringer of the Natural History Museum in London, "but my bet is it's an early form of Homo heidelbergensis or Homo antecessor."

H. heidelbergensis is known to have been present in central Europe about 500,000 years ago. Bones were first discovered in 1907 near Heidelberg, Germany, and have since been found in France and Greece. Hominin remains about 800,000 years old have been found in Spain and Italy, indicating that early humans had colonised southern Europe by this time. These early humans have been classed as another species, H. antecessor, though arguments remain over whether it is a really separate species to H. heidelbergensis.

Ancient Humans Brought Bottle Gourds To The Americas From Asia:

Thick-skinned bottle gourds widely used as containers by prehistoric peoples were likely brought to the Americas some 10,000 years ago by individuals who arrived from Asia, according to a new genetic comparison of modern bottle gourds with gourds found at archaeological sites in the Western Hemisphere. The finding solves a longstanding archaeological enigma by explaining how a domesticated variant of a species native to Africa ended up millennia ago in places as far removed as modern-day Florida, Kentucky, Mexico and Peru.
This was an open access article in PNAS and I will probably be doing a post on it.

This is probably going to blow my reputation at the Hairy Museum of Natural History since it took me a day to post about it.
The above is Hongshanornis longicresta a 125 million year old fossil bird found in China:

Primitive land birds, or enantiornithines, were among the earliest known birds. Mainly tree dwellers that were poor fliers, these birds warmed their bodies by basking in the sun, like lizards and other reptiles.

The newly found bird, meanwhile, belonged to ornithurines, a group that maintained body temperature internally by dilating or contracting blood vessels, sweating, or shivering.

This trait, known as endothermy, is associated with a more active lifestyle. The prehistoric wading bird may have developed the trait as a result of shoreline living, says Zhonghe Zhou, a palaeontologist at the Chinese Academy of Sciences in Beijing.

Finally, enjoy the squid:

here and

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Torture - Pentagon Re-writes the Rules

Via Eschaton
This is just sick...

Added Later:Apparently, the defense department is also spying on americans:

A year ago, at a Quaker Meeting House in Lake Worth, Fla., a small group of activists met to plan a protest of military recruiting at local high schools. What they didn't know was that their meeting had come to the attention of the U.S. military.

A secret 400-page Defense Department document obtained by NBC News lists the Lake Worth meeting as a “threat” and one of more than 1,500 “suspicious incidents” across the country over a recent 10-month period.

“This peaceful, educationally oriented group being a threat is incredible,” says Evy Grachow, a member of the Florida group called The Truth Project.

Read more!

Tuesday, December 13, 2005

Mayan Mural Discovered Dating to 100 B.C.

The above is one panel the oldest known Mayan Mural. It was discovered in 2001 and tells the Mayan story of creation:

The first part of the mural shows the establishment of order to the world.

The world is propped up by trees with roots leading to the underworld and branches holding up the sky, Saturno said.

Four deities, who are representations of the maize god's son, provide a blood sacrifice and a unique offering before each tree.

"The story starts with this deity, who is patron of kings, standing in water. He's running a large spear through his own penis, letting blood. Blood is squirting all over the place," Saturno said.

The sacrificial bloodletting is accompanied by the offering of a fish to represent the watery underworld.

The second offering is a deer to represent the land, the third a turkey representing the sky, and the fourth is the scent of fragrant blossoms wafting from the flowery east.

The east is the direction of paradise and where the sun is reborn every day, Saturno explained.

Next the mural shows the maize god setting up the tree at the center of the world and crowning himself king.

This section of the story traces the maize god's birth, death, and resurrection, which brings sustenance to the world.

The final scene shows a historic coronation of an actual Maya king.

His name and title are written in hieroglyphics. Taube said the writing style is different than that known from later periods, but is nevertheless sophisticated.

By receiving the crown in the company of the gods, the king in the mural likely claimed the right to rule from the gods themselves—not from parents, as did later kings, Saturno said.

As mentioned, the mural dates to 100 B.C., previously archaeologists believed this type of art did not become established prior to 700 A.D.

Another find at the same site:

In addition to the mural, the researchers found the oldest known Maya royal burial, dating to 150 B.C. It serves as further proof for the existence of early Maya kings.

Finally, the site has promise for the future:

"This is a tip of iceberg," he said. "The site is one square kilometer [0.4 square mile] in area. This room we've spent so much time in … it's a four-meter-by-nine-meter [13-by-30-foot] space."

Read more!

Science Comes to Daily Kos

Fellow science blogger (and one of the first contributors to Transitions) Darksyde has been asked to be one of the guest bloggers at Daily Kos. Congratulations DarkSyde!

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Monday, December 12, 2005

More on PNAS

The Abstract:

Comparative morphological studies of the earliest human skeletons of the New World have shown that, whereas late prehistoric, recent, and present Native Americans tend to exhibit a cranial morphology similar to late and modern Northern Asians (short and wide neurocrania; high, orthognatic and broad faces; and relatively high and narrow orbits and noses), the earliest South Americans tend to be more similar to present Australians, Melanesians, and Sub-Saharan Africans (narrow and long neurocrania; prognatic, low faces; and relatively low and broad orbits and noses). However, most of the previous studies of early American human remains were based on small cranial samples. Herein we compare the largest sample of early American skulls ever studied (81 skulls of the Lagoa Santa region) with worldwide data sets representing global morphological variation in humans, through three different multivariate analyses. The results obtained from all multivariate analyses confirm a close morphological affinity between South-American Paleoindians and extant Australo-Melanesians groups, supporting the hypothesis that two distinct biological populations could have colonized the New World in the Pleistocene/Holocene transition.

Sigh, I guess this will have to do...
Sigh, I really need to get a job in academia...anybody out there need someone with a B.A. in anthropology (plus 2 years of grad school)... have knowledge of old bones and dirt, won't travel... sigh!

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AAARGH! PNAS is Driving Me Crazy!

No Really, it's a plot! You see MSNBC has an article on some 7,500-11,000 year old Brazillian skulls. That's one below:

It's of a female the discoverers have nicknamed Luzia:

However, a new study examining the largest collection of South American skulls ever assembled suggests that a different population may have crossed the bridge to the New World 3,000 years before those Siberians.

Scientists occasionally discover skulls in South America that look more like those belonging to indigenous Australians and Melanesians than Northern Asians, but researchers tend to regard these skulls as anomalies due to natural variation rather than a norm, mainly because there were too few to study.


Now scientists have compared 81 skulls from the Lagoa Santa region of Brazil to worldwide data on human variation.

While the skulls of Native Americans and Northern Asians — the descendents of the early Siberian settlers — generally feature short, wide craniums, a broader face and high, narrow eye sockets and noses, this collection was remarkably different.

You get the picture, it's totally my cup of tea. Unfortunately, it's published in PNAS Early Online See! just scroll down a little and you'll find it - right above the OPEN ACCESS ARTICLE on "Introduction of an additional pathway for lactate oxidation in the treatment of lactic acidosis and mitochondrial dysfunction in Caenorhabditis elegans" like anyone would choose to read an article on lactic acidosis in nematodes when they could be reading about old bones and dirt! AAARGH! Come on PNAS make "Cranial morphology of early Americans from Lagoa Santa, Brazil: Implications for the settlement of the New World" Open access too...

Added a few minutes later: I apologize for to any Caenorhabditis elegans that I may have offended by implying they were less than interesting...

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Sunday, December 11, 2005

Skhul CT Scans

Incidently, CT scans and animations(such as the one below)

Can be found atThe Peabody Museum of Archaeology and Ethnology. Though, special software is required to saee it, which is available here

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Papers I have Read This Week

Adami, C, Ofria, C, and Collier, T. C., (2000) Evolution of Biological Complexity. PNAS 97(9):4463-4468

Cameron, C. B., Garey, J. R., and Swalla, B. J. (2000) Evolution of the Chordate Body Plan: New Insights from Phylogenetic Analysis of Deutersome Phyla. PNAS 97(9): 4469-4474. Still reading this one actually.

A new hominid from the Upper Miocene of Chad, Central Africa
Nature 418, 145–151 (2002). On the Toumai fossils. Note: This paper, along with some of the other important papers in Paleoanthropology (published in Nature) can be found at Focus on Human Origins

Palaeoanthropology: Hominid revelations from Chad
The story of human origins in Africa takes a twist with the description of a 6–7-million-year-old cranium from Chad. The discovery hints at the likely diversity of early hominids.
Nature 418, 133–135 (2002). See above.

Backwell, L. R. and d'Errico, F. (2001) Evidence of Termite Foraging by Swartkrans Early Hominids. PNAS 98(4):1358-1363. Macroscopic and microscopic analysis of bones at Swartkrans and Sterkfontein reveal they were used for termite fishing.

Niewoehner, W. A. (2001) Behavioral inference from the Skhul/Qafzeh Early Modern Human Hand Remains. PNAS 98(6):2979-2984. I'm still reading this one (well, actually rereading it - I'm still trying to figure out if I'm convinced or not). Compares the Skhul/Qafzeh hand remains with Neanderthals, early and late Paleolithic humans and holocene humans and finds: 1)Skhul/Qafzeh hand remains are similar to the upper Paleolithic humans and are significantly different from Neanderthals.

Roseman, Charles (2004) Detecting Interregionally Diversifying Natural Selection on Modern Human Cranial Form by Using Matched Molecular and Morphometric Data. PNAS 101(35):12824-12829. Still reading.

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One Reason Why I Don't Fly

Passengers: Shot suspect mentioned no ‘bomb’:

The airline passenger shot to death by federal marshals who said he made a bomb threat was agitated even before boarding and later appeared to be desperate to get off the plane, some fellow travelers said.

One passenger said he “absolutely never heard the word ’bomb’ at all” during the uproar as the Orlando-bound flight prepared to leave Miami on Wednesday.


“I can’t conceive that the marshals wouldn’t be able to overpower an unarmed, single man, especially knowing he had already cleared every security check,” Carlos Alpizar told The Orlando Sentinel.

Some passengers said they noticed Alpizar while waiting to get on the plane. They said he was singing “Go Down Moses” as his wife tried to calm him. Others said they saw him having lunch and described him as restless and anxious, but not dangerous.

“The wife was telling him, ’Calm down. Let other people get on the plane. It will be all right,”’ said Alan Tirpak, a passenger.


“The first time I heard the word ’bomb’ was when I was interviewed by the FBI,” McAlhany said. “They kept asking if I heard him say the B-word. And I said, ’What is the B-word?’ And they were like, ’Bomb.’ I said no. They said, ’Are you sure?’ And I am.”


Armed police boarded the aircraft after the shooting, with some passengers in hysterics. McAlhany said he remembers having a shotgun pressed into his head by one officer, and hearing cries and screams from many passengers aboard the aircraft after the shooting in the jetway.

But here is the kicker:

David Stempler, president of the Air Travelers Association, said he thinks the shooting may prove more “reassuring than disturbing” to the traveling public his organization represents. “This is a reminder they are there and are protecting the passengers and that it is a seriously deadly business,” he said.

Now I, personally, have never felt comfortable flying (think William Shatner in Twilight Zone) so contrary to David Stempler, the fact that I might get my ass shot off or have a shotgun presed up against my head while someone else gets shot is not at all comforting. Nor does it particularly make me want to fly. What it does, in point of fact, is makes me want to stay as far away from airplanes and airports as possible. But tha's just me.

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Saturday, December 10, 2005

Mirecki Threatens to Sue KU

More atEvolving Thoughts

Added Later: Thoughts From Kansas also has info on the story.

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Friday, December 09, 2005

Major Triumph for Bush!

In a major triumph for Bush polls indicate he has succeded in raising his poll numbers to...42%! Oh, never mind. The way the media was portraying it I thought he was back in the 60's:

Shifting into campaign mode to reverse his slide in public opinion polls, Bush has boosted his support among key constituency groups — particularly in the Northeast and West — on his handling of Iraq and the economy, an AP-Ipsos poll found.

Really, the headline said "Ratings Boost" and "Bush's Job Approval Rebounding" Sorry. Go back to whatever you were doing...

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More on Dawgs, Gigantopithecus and Mayan Women

Evolgen has solved the mystery of the shared 5% between mice, dogs and humans...

National Geographic News has a story about the gigantopithecus find I blogged about here. You may remember I complained about the fact that gigantopithecus is frequently drawn as some kind of giant gorilla looking thing, even though it is believed that they are more closely related to Orangs... Well:

Much Better! The National Geographic article mentioned Russell Ciochon has something to do with this, so I did a little searching and found a sight detailing the process of creating the reconstruction. It can be found here. For a quick overview of gigantopithecus you can go here. You can also see some of the fossil specimens here - they are the last three.

Finally, Alun has a post about the Mayan stela picturing a Mayan woman - one of the earliest representations in Mayan art. I have found pictures (rather than drawings) of the stela.

The above is a picture to tide you over till you get there. The rest of the pictures can be found here. There are also two quicktime movies, one shows the raising of the stela and the other shows some preliminary cleaning of it.

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Wednesday, December 07, 2005

"...But They are Still Dogs..."

Added Later: Here is a link to the NIH press release and, for those with Real Player, here is a link to a webcast about it. Concerning the 5% issue this is the only further info I have - in case it gives a clue to those who know a lot more about genetics than I do:

While dogs occupy a special place in human hearts, they also sit at a key branch point, relative to humans, in the evolutionary tree. It was already known that humans share more of their ancestral DNA with dogs than with mice; the availability of the dog genome sequence has allowed researchers to describe a common set of genetic elements - representing about 5 percent of the human genome - that are preferentially preserved among human, dog and mouse. Rather than being evenly distributed, some of these elements are crowded around just a small fraction of the genes in the genome. Future studies of these clusters may give scientists the critical insight needed to unravel how genomes work.

Those so inclined can also go to NCBI Dog Genome Resources.

National Geographic News and New Scientist have both done stories on the sequencing of the dog genome.

Meet Tasha. Tasha is the boxer who supplied the DNA for the study. Researchers used the shotgun sequencing technique to map her genome. This is how it works:

With this technique the genome is first broken into fragments and the DNA sequence of each determined. Then a computer stitches the fragments back together.

The process must be repeated several times to ensure accuracy, and the new draft is the product of 7.5 repetitions. The genome of Shadow, the poodle owned by gene-entrepreneur Craig Venter, had only 1.5 times coverage. The boxer was chosen as it is highly inbred. That means the difference between its paired chromosomes are smaller, making sequencing easier.

Researchers examined the sequences of 2.4 billion bases - equivalent to 39 pairs of chromosomes. Several interesting findings stand out. First, domestic dogs genomes are 99.85% similar:

The boxer and the poodle, for example, differ by about a single nucleotide change in every 900 bases. “A dog is a dog in a genomic sense,” says Lindblad-Toh.

Researchers also sequenced smaller parts from 10 other breeds of dog (such as german shephards, beagles and italian greyhounds) as well as coyotes and grey wolves:

The greater than 99% coverage of the 2.4 billion letters of Tasha’s genome has also revealed an important twist in our understanding of how natural selection works on DNA. Much of the non-coding DNA in dogs is the same as that in humans, indicating that it is under strong natural selection.

“Hence, non-coding DNA is not just ‘junk’,” says Hans Ellegren, of the department of evolutionary biology at Uppsala University, Sweden. Instead, he says that such sequences may constitute non-coding RNA or may have a regulatory function.

Even more interesting:

Scientists had previously found that about 5 percent of the human genome sequence appears in the mouse genome. The new study shows that 5 percent of the human genome is also shared with dogs.

This is interesting because dogs split off from the common ancestor before mice did, but the shared sequences are virtually the same:

"For genes this is not unexpected, since most mammals share a rather similar set of genes," said Hans Ellegren, an evolutionary biologist at Uppsala University in Sweden.

"However … this indicates that there is a core set of noncoding sequences needed to make a mammal."

The researchers have also found that many of the conserved sequences are clustered around developmental genes.

The most interesting aspect, to me was the genetic history. The research indicated a genetic bottleneck sometime around 10,000-15,000 years ago - roughly the time when dogs were first domesticated. Withing some of the breeds there are genetic bottlenecks ranging from 50-200 years ago which suggests that some breeds have a recent origin.

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Big Brains Means Small Testes

According to a new study reported by New Scientist there is a correlation between brain size ans testes size in...bats. Researchers examined 334 species of bats for the studies. They found an inverse correlation between brain size and testes size. They relate the results to breeding systems. In bat species with highly promiscuous females, male bats had smaller brains but larger testes - related to sperm competition (something also seen in chimps). They attribute the effect to:

Both brain tissue and sperm cells require a lot of metabolic energy to produce and maintain. The different species appear to have evolved a preference for developing one organ more than the other, presumably determined by which will help them produce more offspring.


“An extraordinary range of testes mass was documented across bat species - from 0.12% to 8.4% of body mass. That exceeds the range of any other mammalian order,” says Scott Pitnick, from Syracuse University in New York, US, one of the research team. Primate testes vary between species from 0.02% and 0.75% of body mass.

Apparently, then, you can have a large brain (such as in humans) or large testes (such as in some bats and chimps) but not both.

If I remember corectly, one of the areas where researchers recently found differences between chimps and humans was in the genes for sperm production. So a change in mating patterns and social structure between chimps and humans may be one, of several, forces driving the evolution of large brains in humans.

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