Wednesday, January 25, 2006


I will be picking a new Site of the Week for Transitions soon. Be sure to check out my new blog at ScienceBlogs

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Wednesday, January 11, 2006


ScienceBlogs is an effort of Seed Media, publishers of Seed Magazine. The goal is to get some of the best and brightest science bloggers to all blog in the same place. Below is a list of the people posting at ScienceBlogs:

Chris Mooney
Dispatches from the Culture Wars
Stranger Fruit
Cognitive Daily
Adventures in Ethics and Science
Gene Expressions
Living the Scientific Life
No Se Nada Commentary
Uncertain Principles

Quite a collection...what they didn't count on was a 3.5-2.8 million year old hominin would catch wind of it and use his tree climbing abilities to climb a tree and scamper in through an open window...

The past year, or so, has been interesting and I have made many friends while writing this blog. I hope you will visit me at my new blog.
Especially because I am one of the few who does not have a Ph.D in the group so venturing out into the savanah to play with the big boys is going to be quite an experience (I hope I don't meet any leopards [those of you who don't get that joke should read the works of C.K. Brain]).

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Tuesday, January 10, 2006

Afarensis Goes to Seed: Part II

As mentioned previously, I have been asked to join a new blog effort created by Seed Media. Future posts of mine can be found at: afarensis:Anthropology, Evolution and Science

My most recent post is on Redating the Vindija Fossils
I may occasionally put up a post here, but for the most part my blog home will be at the above address (and at Transitions, of course). Please look for me there and update your links and blogroll accordingly!

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People from the Bog


From BBC News comes this story about bog people:


“Archaeologists have unveiled two Iron Age "bog bodies" which were found in the Republic of Ireland.

The bodies, which are both male and have been dated to more than 2,000 years old, probably belong to the victims of a ritual sacrifice.

In common with other bog bodies, they show signs of having been tortured before their deaths. “


“Clonycavan man was a young male no more than 5ft 2in tall (1.6m). Beneath his hair, which retains its unusual "raised" style, was a massive wound caused by heavy cutting object that smashed open his skull.

Chemical analysis of the hair showed that Clonycavan man's diet was rich in vegetables in the months leading up to his death, suggesting he died in summer.

It also revealed that he had been using a type of Iron Age hair gel; a vegetable plant oil mixed with a resin that had probably come from south-western France or Spain.”


“Old Croghan man was also young - probably in his early to mid 20s - but much taller than his counterpart from 25 miles away. Scientists worked out from the length of his arms that he would have stood around 6ft 6in tall (2.0m).

He had been horrifically tortured before death. His nipples had been cut and he had been stabbed in the ribs. A cut on his arm suggested he had tried to defend himself during the attack that ended his life. “

Other Stories on the subject:




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Excavations in the Cyclades

Photo from the Museum of Cycladic Art

Archaeologists are to begin new excavations on the Greek island of Keros in April 2006. From ABC News:

British and Greek archaeologists are preparing a major excavation on a tiny Greek island to try to explain why it produced history's largest collection of Cycladic flat-faced marble figurines.


Now experts are seeking insight into the island's possible role as a major religious center of the enigmatic Cycladic civilization some 4,500 years ago.


"What is particularly impressive is not just the bulk of the finds, which is larger than the total from the rest of the Cyclades, but also that they were intentionally broken during ancient times," Sotirakopoulou said. "Therefore, this is a very important, a unique site."

The Cycladic culture a network of small, sometimes fortified farming and fishing settlements that traded with mainland Greece, Crete and Asia Minor is best known for its elegant artwork: mostly naked, elongated figures with their arms folded under their chest. The seafaring civilization was eclipsed in the second millennium B.C. by Crete and Mycenaean Greece.


"The prevailing explanation is that this was a sacred repository, a sort of pan-Cycladic sanctuary where people left objects within the framework of rituals which included their intentional smashing," said Sotirakopoulou.

From the "Dean" of Classical Studies:

"We hope the forthcoming excavations will clarify further the nature of the occupation and activities at Dhaskalio and Kavos," Renfrew (that would be Colin Renfrew - afarensis) said.

"It is clear Kavos was an important site where high prestige artifacts were deliberately broken and left. It is possible, but not yet certain, these were ritual actions relating to ceremonies in honor of the dead."

Fascinating stuff.

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Sunday, January 08, 2006

Mystery of Mozart's Skull Continues

According to a story on ABC News the question of Mozart's skull remains unresolved. Researchers were testing DNA extracted from the skull against skeletal material that came from the graves of his maternal grandmother and a niece. They assumed this would settle the question once and for all. An unexpected problem has defeated the attempt:

Experts had assumed the remains were of Mozart's maternal grandmother and a niece. But DNA analysis showed that none of the skeletons in the grave were related, making it impossible to prove that the skull was Mozart's, Parson said.

So basically, the material from the grandmother's grave is unrelated to the material from the niece's grave and neither is related to the skull (picture below).

Which means that grandma or the niece, or both, may not be members of the Mozart family (i.e. that one, or both, of the graves are not correctly identified).

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Howard Dean Rules!

Via Eschaton Howard Dean destroys Blitzer and demonstrates what's wrong with the MSM. WOW!

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How Does a Tyrannosaurus rex Sit Down?

In most movies, such as Jurassic Park (and it's sequels), Tyrannosaurs are portrayed running about eating anything that moves. Presumably, at some point they require rest. So the question naturally arises as to what is the resting posture of the T. rex.
An attempt to answer this question was presented at the June 2005 Symposium "100 Years of Tyrannosaurus rex". Rex,Sit examines the question:

The challenge was to try to understand how Tyrannosaurus rex might have transitioned between a bipedal, standing posture and a resting pose. It has long been expected that the great theropod would have settled its weight upon its pubic boot. Just how might it have sat down and gotten up again?

In order to address the question:

The appendicular skeleton and head were digitized; the remainder of the axial skeleton was represented in a more schematic form, with important parameters (e.g., centrum length, neural spine height, and intervertebral separations) accurate based on measurements taken off of the specimen.

Two Quicktime movies were created based on this. One shows T. rex going from a standing to a sitting position and the other shows it rising from a sitting position. Unfortunately, I can't provide direct links to the movies so you will have to follow the link above. The movies are at the very bottom of the page.

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Transitions Site of the Week

I have selected a new Site of the Week for Transitions. If you love fossils you will like this site, check it out! Really, you will love all the fossil pics!

In the meantime, I am working on cross posting the next two posts in Evolgen's series on detecting natural selection, but am having formatting issues with the Punnet squares. As soon as I get that fixed I'll post links.

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Saturday, January 07, 2006

Oh Hell, What Next?

Homeland Security opening private mail:

In the 50 years that Grant Goodman has known and corresponded with a colleague in the Philippines he never had any reason to suspect that their friendship was anything but spectacularly ordinary.

But now he believes that the relationship has somehow sparked the interest of the Department of Homeland Security and led the agency to place him under surveillance.

Last month Goodman, an 81-year-old retired University of Kansas history professor, received a letter from his friend in the Philippines that had been opened and resealed with a strip of dark green tape bearing the words “by Border Protection” and carrying the official Homeland Security seal.


“All mail originating outside the United States Customs territory that is to be delivered inside the U.S. Customs territory is subject to Customs examination,” says the CBP Web site. That includes personal correspondence. “All mail means ‘all mail,’” said John Mohan, a CBP spokesman, emphasizing the point.

“This process isn’t something we’re trying to hide,” Mohan said, noting the wording on the agency’s Web site. “We’ve had this authority since before the Department of Homeland Security was created,” Mohan said.

However, Mohan declined to outline what criteria are used to determine when a piece of personal correspondence should be opened, but said, “obviously it’s a security-related criteria.”

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Bush and Spying

Analysts: Bush spying rationale legally shaky: Memo questions use of presidential power in wiretapping without approval:

A report by Congress's research arm concluded yesterday that the administration's justification for the warrantless eavesdropping authorized by President Bush conflicts with existing law and hinges on weak legal arguments.


The 44-page report said that Bush probably cannot claim the broad presidential powers he has relied upon as authority to order the secret monitoring of calls made by U.S. citizens since the fall of 2001. Congress expressly intended for the government to seek warrants from a special Foreign Intelligence Surveillance Court before engaging in such surveillance when it passed legislation creating the court in 1978, the CRS report said.

The report also concluded that Bush's assertion that Congress authorized such eavesdropping to detect and fight terrorists does not appear to be supported by the special resolution that Congress approved after the Sept. 11, 2001, terrorist attacks, which focused on authorizing the president to use military force.


Bush has said that he has broad powers in times of war and must exercise them to target not only "enemies across the world" but also "terrorists here at home." The administration has argued, starting in 2002 briefs to the FISA court, that the "war on terror" is global and indefinite, effectively removing the limits of wartime authority -- traditionally the times and places of imminent or actual battle.

Some law professors have been skeptical of the president's assertions, and several said yesterday that the report's conclusions were expected. "Ultimately, the administration's position is not persuasive," said Carl W. Tobias, a University of Richmond law professor and an expert on constitutional law. "Congress has made it pretty clear it has legislated pretty comprehensively on this issue with FISA," he said, referring to the Foreign Intelligence Surveillance Act. "And there begins to be a pattern of unilateral executive decision making. Time and again, there's the executive acting alone without consulting the courts or Congress.

I think my response is the following:

For my own part, I consider it as nothing less than a question of freedom or slavery; and in proportion to the magnitude of the subject ought to be the freedom of the debate. It is only in this way that we can hope to arrive at truth, and fulfill the great responsibility which we hold to God and our country.


Is life so dear, or peace so sweet, as to be purchased at the price of chains and slavery? Forbid it, Almighty God! I know not what course others may take; but as for me, give me liberty or give me death!

Patrick Henry, March 23, 1775.

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Friday, January 06, 2006

6th Century Greek Temple Discovered in Albania

According to this press release a new greek temple dating to the 6th century BC has been found in Albania:

The temple they have discovered, located in coastal Albania, is only the fifth known stone temple in Albania. It stands out both because of its age and its size.

The site is just outside of the ancient Greek city-state of Apollonia, and dates back to the late 6th century B.C. That would put its use in the Archaic and Classical periods, a time from which little has been recovered from inside the acropolis of Apollonia.

So far, in addition to remains of sacrificial meals and broken fineware pottery, substantial numbers of Classical and Hellenistic figurines have been found, although the principal deity of the sanctuary remains undetermined at this point

The site is important because:

"It now seems likely that the life of the sanctuary began not long after the founding of the Apollonia colony," Davis says. "What we discover here will contribute much to our understanding of religious life in the 6th and 5th centuries B.C., a period that is hardly known from previous excavations inside the borders of Apollonia itself."

Science Daily also has an article on the find.

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PZ Myers on Daily Kos

In case you haven't stumbled across this elsewhere, Darksyde interviewed PZ Myers here. Fascinating stuff...

A couple of my favorites:

"...if I started babbling about tiny changes in feeding behavior in different strains of zebrafish, or error rates in cell migration in the presence of teratogens, there'd be maybe two or three people in the world who'd care, and they'd just check in once every six months to see what was new!"

The changes in feeding behavior sounds interesting.

As far as the charge of being too liberal -- no one can be too liberal. We can only be not liberal enough.

This is my favorite quote from the interview. I get really torqued when I hear some lame brain bragging about how he is getting more conservative now that he's getting older...

When religious superstition dissipates and wafts away before reason like a fog in the noonday sun, then we will have achieved an appropriate balance.

Poetically said, and all the more poetic for being true...

You will have to read the rest at Daily Kos.

(P.S. Good job Darksyde!)

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In Memorium: Lou Rawls



Lou Rawls, the velvet-voiced singer who started as a church choir boy and went on to record such classic tunes as “You’ll Never Find Another Love Like Mine,” died Friday of cancer. He was 72.

Rawls died at Cedars-Sinai Medical Center, where he was hospitalized last month for treatment of lung and brain cancer, said his publicist, Paul Shefrin. His wife, Nina, was at his bedside when he died.

You can find out more at the link below:

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Hippos and Tortoises

From National Geographic News comes this interesting story:

The strength of a unique male bond between a young hippopotamus and a 130-year-old tortoise will be tested later this spring when conservation workers introduce a female hippo to the mix.

The pending introduction serves as an intriguing plot twist to the unlikely story of a hippo and tortoise brought together at Haller Park wildlife sanctuary in Mombasa, Kenya, in the wake of the December 26, 2004, Indian Ocean tsunami.
The conservationists hope the two hippos will bond with no objection from the tortoise, named Mzee. Such an outcome will allow Mzee's return to the safety of his original enclosure.

While other tortoises, monkeys, and antelope roam in that enclosure, Mzee has shown no affection toward any of them. But he has surprisingly become attached to the young hippo, Owen.


"He will grow to anywhere between three and four tons—he's gonna be a big male hippopotamus," said Paula Kahumbu, the general manager of Lafarge Ecosystems, the Kenyan environmental restoration firm that manages the wildlife sanctuary.

"He's already quite playful, already quite strong," she said. "He could injure Mzee at any moment. He's very childlike in his behavior. As he gets older he will get rougher. Mzee is not a flexible animal—he could be injured."

But how Mzee and Owen will react to the presence of Cleo, the female hippo, and a subsequent separation is unknown, Kahumbu said. If one cannot live without the other, some sort of accommodations will be made.

The really fascniating part:

Nevertheless, Mzee follows Owen around, nudges him to go for walks, initiates play in the water, and even stretches his neck out so Owen can give him a lick.

There has been growing evidence of physical communication between the pair, with Owen nibbling Mzee's back feet to get him to walk in a desired direction. The two have even developed a sort of vocal communication of their own, Kahumbu said.

The vocalizations are not the honking of hippos or the grunts and hisses of tortoises, but rather a soft whimpering that emanates from one and is mimicked by the other.

"It's very high pitched; definitely not a stomach sound, as some had suggested," Kahumbu said. "They're vocalizing towards each other."

What the animals are trying to communicate is not yet understood, but researchers think it is a contact call made to get the other's attention.

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Thursday, January 05, 2006

Viking Teeth

According to New Scientist VIKING warriors may have filed deep grooves into their teeth to indicate class or military rank.

From the article:

Caroline Arcini of Sweden's National Heritage Board analysed 557 skeletons from four major Viking-age Swedish cemeteries and discovered that around 10 per cent of men, but none of the women, bore horizontal grooves across the upper front teeth.

The marks, which were cut deep into the enamel, are often found in pairs or triplets and appear precisely made. They might have marked certain men as members of a group of tradesmen or warriors, or signified their ability to withstand pain, says Arcini...


Most of the men bearing the grooves were young, but in the absence of any distinctive injuries or artefacts buried with the skeletons, the exact reason for the marks remains a mystery.

This is the first known case of tooth filing in Europe, but it was common practice in the Americas between AD 800 and 1050. Since the skeletons date from around the same time, this raises the possibility that the Vikings picked up the practice during their travels. Arcini hopes future finds will reveal where the practice arose and how it spread.

The research has been published in the AJPA...

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Maya Writing Found Dating to 2,300 BP

From National Geographic News:

Evidence of Maya writing that dates to 2,300 years ago has turned up in a pyramidal structure in Guatemala.

Researchers excavating the site—ruins at San Bartolo in the northeastern part of the country—say the finding could be among the earliest Maya written material ever found.

Currently the oldest known writing system in all of Central and South America dates to about 400 B.C. and is from cultures based in what is now Oaxaca, Mexico.

The researchers did radiocarbon dating on five charcoal samples from deposits found in three layers of the site. Samples from the area where the writing was found dated to approximately 400 to 200 B.C.

Taken together with other radiocarbon dates from the site, the authors have concluded that the text was written between 300 and 200 B.C.—placing writing among the Maya much closer to the earliest known writing systems from other Mesoamerican cultures.

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Wednesday, January 04, 2006

Tangled Bank #44

The Tangled Bank

Welcome to Tangled Bank # 44! When I volunteered to host this edition of the Tangled Bank I was expecting to read a lot of good science writing on a lot of interesting subjects. Even so, I fear I have underestimated how good and interesting science bloggers really are! Pat yourselfs on the back you are good!

I originally thought that I would do a clever layout involving the stratigraphy of the Hadar site (where Australopithecus afarensis was first discovered), but after reading all the posts I decided to let the science, scientists and science writers speak for themselves...

I did, however, find the perfect post (this will come as a surprise to the author - since it wasn't actually submitted) to start off. It contains all the that make The Tangled Bank what it is - science, mystery and Blue Smurf Pee, Rabbits and Buckthorn - a reason for visiting Bootstrap Analysis is that she is hosting Circus of the Spineless as well.

The always interesting Coturnix has an interesting post at Cirdiana on the effects of global warming on circadian systems. In line with that I have a discussion about how Zooarchaeology can be used to study climate change in Zooarchaeology, Pokemon Archaeology and Climate Change.

Zygote Games asks Why do Narwhals Have Horns and gives a surprising answer.

Aydin Orstan discusses Barnacles: Darwin’s old buddies in a piece he generously crossposted at Transitions as well as at Snail's Tails.

Which brings us to a section of posts on how science affects society and vice versa.

Political Calculations asks What Your Kids Know About Science... and comes up with some interesting - if scary - answers.

A Concerned Scientist wonders What Scientists Owe the Public - a fascinating piece that everyone should read!

Elia Diodati inThe Biggest Losers, South Korean Style discusses the plight of the grad students in Hwang's lab. Certainly gives a new perspective to the story (and one I had never thought of).

In a more upbeat piece, the Daily Transcript discusses The Best Things About Science.

Centrerion tells Time Magazine about the link between protion size and obesity - although afarensis thinks this is more common sense than science.

I will get back to the impact of science on society in minute. It's time for a visit to what I call Wilkinspalooza.

You see John Wilkins (also know as PZ's worst nightmare) has written a series of posts on speciation (anyone who has visited John's blog will not be surprised):

Modes of Speciation Organizing the Mess
Modes of Speciation 2 Flow verses Place
Relating Speciation
Speciation Genes
At this point Evolgen objected to the characterization of molecular biologists (to his credit Wilkin's took not of the objection)and responded with Why Study Speciation Genes (in keeping with upright decent and honest behavior among scientists and science bloggers Evolgen was the person who submitted all the posts in this section).
Wilkin's series concludes with Speciation Conclusion. Teach the Controversy says I!

Since we are on the subject of controversy.

Is the Cambrian explosion real? How can we tell one way or another?A signature of a radiation in metazoan evolution by PZ Myers gives us the latest on the subject - you should bookmark this one for future confrontations with creationists!

Chris Clarke takes on a creationist textbook in Crown clade of Creation

Tara at Aetiology has an interesting post that discusses Shelley's criticism of Paley's Natural Theology and points out thatThose who do not learn from history... also should be bookmarked!

The Daily Duck tackles ID, Sex Combs and Theodicy.

Archy debunks a creationist in Another Mammoth Story.

Darksyde follows up with a story about The One That Got Away (Note: If you have ever wondered why earth isn't ruled by lightening fast land octopi and intelligent squid you will find the answer here).

Grey Thumb submitted one post, but I found another equally worthy of inclusion. Testing Intelligent Design With Artificial Life and Incompetent Design and the No Free Lunch Theorems.

Dan Keane at Science Gate discusses why Dover Ain't Over... Very Interesting!

Adaptive Complexity talks about the difference between evolution and abiogenesis in Evolutionary Biology is not "Origins of Life" Research. Bookmark this one for furture use!

While at Science Notes there is a discussion about Flagellum Structure is Not so Irreducibly Complex.

Switching to a little anthropology...
Kambiz Kamrani at discusses The anthropology of race and the discovery of a skin color gene, SLC24A5 as does Sunil at Balancing Life in Happy hour: The color of our skin from a slightly different perspective.

Hedgwig the Owl at living the Scientific Life tells us about how tsunamis are formed in Tsunami: One Year Later, Part I,What We Know About The Event Itself.
While Hsien-Hsien Lei at Genetics and Health tells us how DNA is being used to identify tsunami victems in DNA Identification of Indian Ocean Tsunami Victims.

Mike at 10,000 Birds tells us about Another Avian Ailment but it's not what you think.

The Bad Astronomy Blog talks about being number four in We're Number Four.

Sophistpundit asks What Can We Hope To Leave Our Children? I'm not so sure I agree with his conclusion (like some of the commenters), but it is still interesting.

The Biotec Weblog dicusses Anthrax and Tobacco.

Orac at Respectful Insolence debunks some Alternative Medicine. I found this one interesting...

The Invasive Species Weblog discusses an interesting vector for invasive species in What the Hull.

Finally, science isn't just words on a page, it can also be art and music as the Hairy Museum of Natural History shows in The Devonian Blues.

Tangled Bank # 45 will be hosted at GreyThumb on Jan 18, 2006. So start getting those new ideas!

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Hysterical! If I had known about it I would have included it in the Tangled Bank. Really, check it out!

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This is good news!

From the link above:

Ted Koppel has joined the Discovery Channel to make news documentaries, bringing his former top producer and eight other ex-"Nightline" staff members, the cable channel announced Wednesday.


Koppel will host and produce long-form programming examining major global topics and events exclusively for Discovery, said network President Billy Campbell. Koppel will also conduct some of the town hall-style meetings that were a staple of "Nightline" programming, Campbell said.

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Tuesday, January 03, 2006

This is cool! From National Geographic News (link above):

"The next morning Yaowalak and her Bangkok-based team from the Thailand Department of Mineral Resources traveled to the site. The scientists soon began unearthing a treasure trove of fossils: skulls of a gavial (a crocodile-like reptile) and a spotted hyena, deer antlers, and a buffalo horn.

"I've never seen such a community of large mammals in one excavation," said Yaowalak, who has since been studying the remains. "

"The preservation [of the fossils] is exceptional," said Jean-Jacques Jaeger, a professor of paleontology at Montpellier II University in France.

Jaeger, who has announced past discoveries of primate fossils in Thailand, is working with Yaowalak on the latest excavation.

The scientists have not yet established the exact age of the fossils, but they estimate the remains are about 400,000 years old.

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Sunday, January 01, 2006

Tangled Bank Reminder

I will be hosting the next Tangled Bank on 1/4/06. Please send me links to your submissions!

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What Kind Of World Leader Are You?

Via Buridan's Ass comes the following quiz!

First I was shocked by the "emaciated do gooder" label, but then I read the description and had to agree...

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