Giant Cannibal Squid: The Invasion Has Begun!

Well not really. But according to this some species of squid engage in cannibalism:

Now Bruce Deagle of the University of Tasmania, Australia, and his team have analysed the gut contents of a male giant squid caught by fishermen off the west coast of Tasmania in 1999. Among the slurry of macerated prey, they found three tentacle fragments and 12 squid beaks. The beaks could not be unequivocally identified, but all of the squid DNA in the slurry, and the tentacle fragments, was found to be that of A. dux (Journal of Heredity, vol 96, p 417). "This strongly suggests cannibalism," says team member Simon Jarman of the Australian Antarctic Division in Kingston, Tasmania. The only other prey species identified was a fish, the blue grenadier.

And at the mosy inopportune times:

"The male giant squid has to use a puny 15-gram brain to coordinate 150 kilograms of weight, 10 metres of length and a 1.5-metre-long penis," he says"He physically plunges this penis into the female's arms, which are rather unfortunately right next to her beak. Because he is coordinating so much with so little, I think occasionally bits get chewed off when they inadvertently get too close to the beak."

I was looking forward to our squid overlords but if they are going to be biting penises, er, phalluses off I'm going to have to rethink that!

Mainstream Media Sucks Used Kitty Litter: Part Two

Here we go again. According to Eschaton The New Media Rules:

It looks like Republicans have learned a new trick in the media. If you give exclusive stories to journalists with the condition that no Democrats are to be allowed to comment on the story, journalists think that's a perfectly acceptable thing to do. Not only that, but they won't even bother to do any additional research for the story.

Go here and here for more.

From Media Matters:

Under a purported embargo, which the Post said prevented reporters from revealing the administration's decision until midnight -- "too late" to contact Democrats for a response -- staff writers Peter Baker and Charles Babington quoted anonymous White House officials spinning the decision regarding the documents(emphasis mine - afarensis). But while other contemporaneous print media reports noted Democrats' previously stated arguments for full disclosure of the documents, the Post omitted them for the second day in a row.

Form Kos:

Turns out Roll Call writer Lauren Whittington got the story from the GOP with the ground rule that she not call anyone else for the story.

After reading this article I couldn't help but ask myself which media outlets in West Virginia were going to be running these advertisements. I called up Lauren W. Whittington (columnist for the Roll Call) to ask her if Brian Nick went into any specifics pertaining to his comment that stated: "The initial buy, which will be concentrated in the large media markets in the state." I was interested in finding out, in specific, which television stations or "large media markets" Brian Nick was referring too. Whittington told me that Nick did not go into any specifics other than what she had presented in the article for "security reasons," security as in they do not want Democratic operatives finding out this type of information.

Security reasons? WTF?

It would be nice if these were isolated incidents - but they are not:

Days after financial services giant Morgan Stanley informed print publications that its ads must be automatically pulled from any edition containing "objectionable editorial coverage," global energy giant BP has adopted a similar press strategy.

According to a copy of a memo on the letterhead of BP's media-buying agency, WPP Group's MindShare, the global marketer has adopted a zero-tolerance policy toward negative editorial coverage.

Another magazine executive who had not heard about BP’s policy or of Morgan Stanley’s said his company has unwritten guidelines with advertisers from several industries, including auto, airlines and tobacco, to pull their ads if related negative stories are in the issue. These cases, the executive said, occur more with news magazines than lifestyle ones.

Go here and here for more info.

Comforting the afflicted and afflicting the comfortable indeed!

Humor

the Cutting Edge (52% dark, 43% spontaneous, 33% vulgar)

your humor style: CLEAN | SPONTANEOUS | DARK Your humor's mostly innocent and off-the-cuff, but somehow there's something slightly menacing about you. Part of your humor is making people a little uncomfortable, even if the things you say aren't in and of themselves confrontational. You probably have a very dry delivery, or are seriously over-the-top. Your type is the most likely to appreciate a good insult and/or broken bone and/or very very fat person dancing. PEOPLE LIKE YOU: David Letterman - John Belushi

My test tracked 3 variables How you compared to other people your age and gender: You scored higher than 99% on dark You scored higher than 99% on spontaneous You scored higher than 99% on vulgar

Link: The 3 Variable Funny Test written by jason_bateman on Ok Cupid

Dinosaur Embryos

Dinosaur Embryos 


The above is a dinosaur embryo belonging to a species called Massospondylus carinatus which is believed to be an ancestor of the giant sauropods. It (the embryo) was discovered in 1978 and just recently exposed by scientists. Apparently, according to this article enough were discovered that they could work out growth rates and changes in bodily proportions, surprisingly:

That growth pattern turned out to be highly unusual. The hatchling had a huge head and forelimbs as long as its hind legs. As the animal grew, its neck stretched dramatically, while its head got increasingly smaller relative to its body. Its hind legs grew more than twice as long as its forelimbs.

An adult Massospondylus had a head that was only 8 inches (20 centimeters) long. Its upper limbs were only half the size of its thighbones. It grew to be about 16 feet (5 meters) long, with a beanstalk-like neck and an 8-foot (2.4-meter) tail.

The earliest sauropods may have also developed with quadrupedal proportions, like their Massospondylus cousins. But these early sauropods retained their four-footed stance into adulthood.

The growth pattern of the Massospondylus could therefore provide clues about how the giant sauropods evolved.

"These animals are essentially predecessors to those large sauropods," Reisz said.

Forgive Me for I Have Sinned...

No, I have not gone and got myself all religified. I'm still the same cynical smartass who thinks we are descended from monkeys!

You see, I have realized I have done wrong - that is I have spelled a bloggers name wrong. I am refering, of course, to evolgen. I had been spelling it Evolgen, but apparently this is incorrect, so I have corrected it in my blogroll.

I am particularly apalled since a lot of people mispell my name (it's "afarensis" not Afarensis - let's be taxonomically correct) and here I go and do the same darn thing to another blogger.

Sigh

Wells and Cancer: More Evidence He's Wrong

I have written several posts on this before. They can be found here and here.
From Well's paper on TOPS:

TOPS then explicitly rejects several implications of Darwinian evolution.
These include: (1a) The implication that living things are best understood from
the bottom up, in terms of their molecular constituents. (1b) The implications
that DNA mutations are the raw materials of macroevolution, that embryo
development is controlled by a genetic program, that cancer is a genetic disease,
etc. (1c) The implication that many features of living things are useless vestiges
of random processes, so it is a waste of time to inquire into their functions.

On Science Daily I stumbled across this paper on Multi-Species Genome Comparison Sheds New Light On Evolutionary Processes, Cancer Mutations

A team of researchers from the United States, France and Singapore studied the chromosomes of eight mammals. The mammals are humans, mice, rats, cows, pigs, dogs, cats and horses. Some interesting results emerged:

Using sophisticated computer software to align and compare the mammals' genetic material, or genomes, the team determined that chromosomes tend to break in the same places as species evolve, resulting in rearrangements of their DNA. Prior to the discovery of these breakage hotspots, the prevailing view among scientists was that such rearrangements occurred at random locations.

and:

In their paper, researchers report that the chromosomal abnormalities most frequently associated with human cancer are far more likely to occur in or near the evolutionary breakage hotspots than were less common types of cancer-associated abnormalities. Researchers theorize that the rearrangements seen near breakage hotspots may activate genes that trigger cancer and/or inactivate genes that normally suppress cancer. However, they emphasize that far more work remains to be done to clarify the relationship between cancer and the breakage hotspots. One thing researchers have determined is that the regions immediately flanking the breakage hotspots contain more genes, on average, than the rest of the genome.

Note the cause of chromosome instability has nothing to do with:

Centrosomes that are too numerous or too large would produce too strong a polar ejection force, damaging chromosomes and leading to chromosomal instability.

As Wells tried to argue.

It is interesting to note that the cancer aspects of this research was done within an evolutionary paradigm:

"Science tells us that the most effective tool we currently have to understand our own genome is to compare it with the genomes of other organisms. With each new genome that we sequence, we move closer to filling the gaps in our knowledge," said Dr. Ostrander, who is chief of the Cancer Genetics Branch in NHGRI's Division of Intramural Research.

The multi-species comparison published in Science also yielded surprising results about the rate at which chromosomal evolution occurs. Based on an analysis that included a computer-generated reconstruction of the genomes of long-extinct mammals, researchers found the rate of chromosomal evolution among mammals dramatically accelerated following the extinction of the dinosaurs about 65 million years ago.

Before the sudden demise of dinosaurs and many other types of animals, which is thought to have resulted from a massive comet or asteroid striking Earth, mammals shared fairly similar body plans and also fairly similar genomes. Researchers speculate that the mass extinction opened new ecological niches for mammals, spurring their diversification and the emergence of new mammalian orders. This situation would have facilitated opportunities for the isolation of mammals into more distinct breeding groups, speeding the development of species-specific chromosomes.

"This study has revealed many hidden secrets on the nature and timing of genome evolution in mammals, and it demonstrates how the study of basic evolutionary processes can lead to new insights into the origin of human diseases," said Dr. Lewin, who is director of the Institute of Genomic Biology at the University of Illinois.

Once again proving that nothing in biology makes sense without evolution and incidentally proving wrong, yet agian, those who say evolution has nothing to offer the field of medicine.

To learn more you can go to:

National Human Genome Research Institute

Mainstream Media Sucks Used Kitty Litter

This is absolutely despicable. Yet, the mainstream media keeps wondering why people are abandoning them in droves. It concerns a missing pregnant woman from Philadelphia.

From MSNBC

CRAMER: I think we got to focus on this ratings issue for a second, because I don’t think people—we all—we all understand this because we’re in the business. I didn’t get.

If you can get a huge number of people watching a particular story, it gives you the license to do a lot of other stories. Now, some people abuse the license by going to Aruba every single night, as far as I’m concerned. But I have to—I—I—I love programing that gets watched.

CARLSON: Yes. I do, too.

CRAMER: So, I’m not going to damn this kind of story.

CARLSON: I’m not either.

MADDOW: No. And the media makes decisions based on what is going to sell advertising. And so, what is going to...

(CROSSTALK)

CRAMER: It’s commercialism.

And a little later:

MADDOW: But it’s the per—again, it’s the perception. We’ve got a woman who has been missing for nine days. She’s pregnant. She’s a young mother. It has all the components of the other stories that get covered. But because of the race, because she’s from West Philly, it’s not getting covered.

CARLSON: But...

MADDOW: So, people are trying to drive...

CARLSON: But...

MADDOW: ... the media...

(CROSSTALK)

CARLSON: But the truth is, we are covering it. It was on our air today. And it’s on our air...

MADDOW: Because of an enterprising blogger.

CARLSON: It’s...

CRAWFORD: Where would you rather vacation, Aruba or West Philly?

MADDOW: West Philly has...

(CROSSTALK)

CRAMER: Forty-second and Baltimore is nothing like Aruba.

(LAUGHTER)

(CROSSTALK)

CRAMER: I know that area.

(LAUGHTER)

So a white woman disappears in Aruba and the Mainstream Media loves it cause it brings great ratings and black woman (forgot to mention that) disappears and it is cause for laughter.

Pitiful, just pitiful.

New Species of Fly

Hybrid Fly 


According to National Geographic News the above is a relatively new species of fly that formed as a hybrid of two existing species:

The Lonicera fly evolved as a hybrid of two existing U.S. species, the blueberry maggot and the snowberry maggot, according to the study. The newfound species is named after the honeysuckle plant (scientific name: Lonicera), which the insect's life cycle revolves around.

Apparently, speciation by hybridization takes place in fish too:

German researchers have studied cichlids (a type of tropical freshwater fish) living in tiny volcano-crater lakes in Cameroon, West Africa. Their studies have shown that at least one cichlid species started off as a hybrid.

Among cichlids this process likely takes thousands of years. The Lonicera fly's evolution, however, has occurred only in the 250 years since its honeysuckle host plant arrived in North America.

You can also go here for more info.

What Democrats Need to Do

Athenae at First Draft has a perceptive post about Democrats and the need to not allow others to define us:

But what we have do, Will my love, is not "come to terms" with what our opposition says we are and promise, really promise, the American people we'll change. What we need, Will, is not some national apology session in which we say we regret opposing a war that was in fact wrong and that we did in fact lose. What we need is not some sort of press conference to announce that we're sorry we hurt all those segregationists' feelings all those years ago by opining timidly that perhaps police should not turn hoses on peaceful protestors and that we should all just drink out of the same fountain. Because when you talk about protest culture, Will, that's what you're talking about. That's what they're really mad about.

Go read it, it's great!

Tuesday Monster Movie Blogging

Although it sounds pretty cheesy (the science aspects suck), this is actually a first rate movie. Seems to be a low budget film and I don't recognize any of the stars. It was released in 1953 during the era of the "invaders from outerspace" but veers off in a different direction from most (another exception being "I Married a Creature From Outer Space").
The movie starts with some communications engineers trying to track down the source of a mysterious disturbance in their radio frequencies. They meet a lady who, along with her husband and a friend, has just been attacked by a strange person wearing what appears to be a deep sea divers outfit. Several other deaths occur and an oil refinery is blown up before it is realized the stranger is, in fact a visitor from outerspace who crashed on earth. From here the movie turns into a sensitive portrait of the alien's attempt to survive a hostile atmosphere and evade capture. Unfortunately, the protagonists realize too late what is going on and the alien dies (he is unable to survive in earths atmosphere for very long without his breathing apparatus).
Most of the films from this era dealt with horrible alien invaders hellbent on kidnapping earth women for deviant alien sex (one wonders if this would be the alien equivalent of bestiality?) and this film is a notable exception. Anyone with an hour to spare should check it out!

Bacterial Adaptations to Cold Environments

This article from Science Daily is pretty interesting. A team of researchers from The Institute for Genomic Research have sequenced the genome of Colwellia psychrerythraea - a species of cold adapted bacteria that lives in temperatures below 5 degrees celcius (brrr).

"...these analyses offer a picture of evolution in action, as C. psychrerythraea uses subtle tweaks in common bacterial biology to adapt to its chilly environs. For instance, the bacterium taps a group of four to five genes to generate polyunsaturated fatty acids and pack those acids into cell membranes, resulting in membranes that are fluid and functional--rather than a frozen chunk of biomass--below the freezing point. The genome also possesses a number of duplicated genes important to cell membrane biosynthesis. What's more, C. psychrerythraea dresses in layers, generating plenty of extracellular polysaccharides (sugars) that coat cell membranes.

Aside from its cellular outerwear, C. psychrerythraea generates a range of potential cold-protective compounds. One example is a family of polyesters, known as polyhydroxyalkanoate (PHA) compounds, that may also boost reserves of nitrogen and carbon, which could be in short supply in the extreme cold. The organism also engineers cold-hardy versions of ordinary enzymes found in free-living bacteria, such as enzymes that break down organic matter. C. psychrerythraea possesses genes that may break down complex compounds, including pollutants, as well."

Lest you think this is just pure science, the analysis does have applications:

More than just marvels of nature, cold-adapted enzymes hold industrial promise, as active ingredients in coldwater detergents, clean-up for industrial contaminants, and food treatments. Psychrophiles could hold clues to microbial life on other planets, as well, such as the frozen surface of Mars or one of Jupiter's moons, Europa.

So evolutionary theory could lead to a better way of cleaning up industrial contamination...

My Birthday

"It's my birthday and I'll blog if I want to..."
I took the day off because it's my birthday today. I plan on blogging a little , maybe watching a couple of monster movies and of course, my mom made me a german sweet chocolate cake (from scratch - not a mix) so I plan on eating some of that.

Added later: It is also, I just discovered, Josh Rosenau's birthday as well. Happy Birthday Josh! You can wish Josh a happy birthday (and see the great birthday candle) at Thoughts From Kansas

Ediacara Fauna

The above is a picture of a type of ediacaran fossil called a vendobiont.
From Geotimes:

Radiometrically dated between 551 and 538 million years old, the newly discovered vendobionts, preserved in a limestone matrix, have internal structures replaced by calcite spars, says Bing Shen, a graduate student at Virginia Tech and co-author of the paper, published in the July 11 Online Early Edition of the Proceedings of the National Academy of Sciences. The creatures have a unique body plan never before seen in living or extinct creatures, Shen says.

Shen and his colleagues plan to perform other analyses of the specimens, including some geochemical work. They will also return to the field in search of more Ediacara fossils in the previously overlooked carbonate rocks. "It is important to search more limestone for different fossil anatomies [and] ecologies," Shen says. What exactly the vendobionts were and how they lived is still a point of speculation.

Indeed, the team has several ideas about why the organisms went extinct during the Cambrian, including a change in the environment. Another possibility, they say, is that because the vendobionts were sedentary creatures — lying about on the seafloor — organisms that could burrow into and crawl across the ocean bottom may have disrupted the lifestyle of the vendobionts.

The Environmental Impact of Consumption

The Yale Journal of Industrial Ecology has an entire issue devoted to the impact of consumption on the environment. All the articles are free and dowloadable in pdf format. Check them out.

400 Million Year Old Microfossils

Although I don't know much about botany, I find this fascinating.



The above is a picture of (as near as I can tell) the fruit or seed of a type of green algae called charophytes. They are 400 million year old microfossils that scientists have recently found a new and important way to study.

Researchers at the ESRF have presented the possibilities that microtomography offers by showing the steps of a 3D non-destructive investigation by X-ray synchrotron microtomography on a gyrogonite from Late Cretaceous (Mesozoic) period, originating from the South of France. This charophyte doesn’t belong to the Sycidiales, but shows the possibilities of X-ray synchrotron microtomography on small fossils. The first step is a high resolution microradiograph (pixel size of 1.4 microns) showing the spirals twisted from base to apex. From a complete set of microradiographs taken during a half rotation, virtual slices are reconstructed (step 2). From all the slices, we obtain a 3D representation of the sample (step 3) showing its external morphology. Step 4 presents the internal cavity after the “virtual” removal of a part of the gyrogonite wall. Using these 3D data, the team reconstructed a virtual mould inside the gyrogonite (step 5). On this virtual oospore (step 6), numerous details are visible, such as the sutures, the apex, or the basal plate. Image number 7 is an observation with a polarizing microscope of a slide in an equivalent sample.

The applications of this new technique are, to say the least, extremely wide and varied:

The use of X-ray synchrotron microtomography for this pioneering study on fossil algae opens new doors to paleontology. Indeed, charophytes represent only one group among numerous others of very small fossils. This kind of investigation should hence become a reference for non-destructive three-dimensional approach of small fossils.

Incidentally, researchers found two types of structures in their study. The first, which you can see above, were a series of ridges in a spiral pattern. The second was a vertical pattern of ridges. An additional surprising find was of a uticule:

An utricule is a supplementary protective layer believed to protect the zygote (reproductive cell) against desiccation. The fact that such a structure was acquired during the evolution of these very old algae means that they probably lived in a harsh environment. This structure could be interpreted as an adaptation to strong seasonality with dry summers leading to ephemeral aquatic environments.

Amazing, the things science can do these days!

Religion in Public Life

Via Abnormal Interests comes this interesting commentary on religion in public life.

A snippet to tide you over:

All the state can do is hold on to secular values. It can encourage the moderate but it must not appease religion. The constitutional absurdity of an established church once seemed an irrelevance, but now it obliges similar privileges to all other faiths. There is still time - it may take a nonreligious leader - to stop this madness and separate the state and its schools from all religion. It won't stop the bombing now but at least it would not encourage continued school segregation for generations to come. And it might clear the air of the clouds of hypocrisy, twisted thinking and circumlocution whenever a politician mentions religion.

Abnormal Interests had some interesting things to say about this article (stop by his site and read them) and I would like to put my two cents in. Here in the US a non-christian could not get elected dog catcher much less to the Senate or House (and forget about the presidency). If you are a atheist or agnostic forget about politics. Even local races require a refelxive profession of faith in Jesus. You see it all the time. I was watching a follow up story on the local news about an ovarian transplant (which was kind of a first) guess who got credit for the success of the surgery (the recipient was able to conceive and gave birth). It wasn't the surgeons and nurses who spent years of their lives studying medicine and perfecting their craft. Worse yet, the reporter and local anchors weighed in with their own religious spin.

Reading the above paragraph a couple of things stand out.
"...encourage the moderate but it must not appease religion..." yet here in america the religious leaders that get encouraged are a bunch of lunatics like Falwell and Dobbs. Unfortunately, reliance on christian extremists has created a huge amount of political success for the Republican party and has created a runaway reaction that is pushing christianity further and further into extremism.

"And it might clear the air of the clouds of hypocrisy, twisted thinking and circumlocution whenever a politician mentions religion." Unfortunately, most folks have become adapted to the hypocrisy and twisted thinking that characterizes current politics and couldn't survive without it. Without these kind of props to their self esteem they would be left with nothing. Mosts athiests and agnostics are capable of creating their own meaning and value in their life and the lives of others. I guess another way to phrase it would be that non-believers can face the "existential question" without despair. For some people, however, the "existential question" is literally Hell and religion provides a means of escaping from it. You hear it all the time in criticisms of evolution. You know the litany: "evolution is amoral and teaches that peolple are animals so nothing is stopping us from behaving like animals, etc." For some the thought that Jesus didn't, in fact, die for their sins is a condemnation of their worth. "For God so loved the world that he sent his only begotten Son..." take God's love away and there is nothing to inform and give meaning to their lives. Which is kind of sad.

Is There Life on Titan

Titan, one of Saturn's moons, is the only satellite with a major atmosphere. It is composed largely of nitrogen, argon and methane with traces of hydrogen. Additionally, traces of hydrocarbons (ethane, propane, ethlene, etc) nitrogen compounds (hydrogen cyanide, cyanogen, etc) and carbon monoxide and dioxide have been found.

One of the things Huygens will be doing is testing for signs of life on Titan:

They think the microbes would breathe hydrogen rather than oxygen, and eat organic molecules drifting down from the upper atmosphere. They considered three available substances: acetylene, ethane and more complex organic gunk known as tholins. Ethane and tholins turn out to provide little more than the minimum energy requirements of methanogenic bacteria on Earth. The more tempting high-calorie option is acetylene, yielding six times as much energy per mole as either ethane or tholins.
“The microbes might breathe hydrogen rather than oxygen, and eat molecules drifting down from the upper atmosphere”

McKay and Smith calculate that if methanogens are thriving on Titan, their breathing would deplete hydrogen levels near the surface to one-thousandth that of the rest of the atmosphere. Detecting this difference would be striking evidence for life, because no known non-biological process on Titan could affect hydrogen concentrations as much.

What I'm Up Too

Some of the blogs I read regularly seem to be on hiatus for greater or lesser amounts of time. Others seem to be in a self reflective mood. Consequently, I've had a little time on my hands to try to catch up on my reading (I have a mound of books). So here is what I have been reading lately:

Frogs, Flies and Dandelions: The Making of Species by Menno Schilthuizen (recommended by John Wilkins on a recent post of his) with a very interesting discussion of Archirrhinos haecklii (very remarkable creatures).

Natural Selection in the Wild by John Endler - everything you ever wanted to know about natural selection - what it is, how it's studied, what's been studied.

The Neanderthals: Of Skeltons, Scientists and Scandal By Eric Trinkaus and Pat Shipman - fascinating account of the history of Neanderthal studies by one of the experts on Neanderthals.

The Wisdom of the Bones: In Search of Human Origins by Alan Walker and Pat Shipman - I wasn't sure about this one at first. Started kind of slow. Turned out to be a good book on Homo erectus (incidentally, I once met Alan Walker - UT has a Visiting Lecturer series where the bring in all types of anthropologists to talk about current research and he was one of the people they brought in - real nice guy).

The Triple Helix: Gene Organism and Environment by Richard Lewontin - (PZ Myers is always talking about this one over at Pharyngula so I thought I'd read it)interesting examination of the philosophical underpinnings of biology.

I'm currently reading:

The Nature of Selection by Eliot Sober

Up Next:

Embryos and Ancestors by Gavin de Beer
Reconstructing Human Origins by Glen Conroy
Bioarchaeology: Interpreting Behavior from the Human Skeleton
Finding Darwin's God by Kenneth Miller
The Structure of Evolutionary Theory by Stephen Jay Gould (I've had this one for about a month, keep putting off reading it because of it's length).

Bipedal Locomotion in Australopithecus afarensis

Although I can walk bipedally, there has always been some debate about whether Lucy could. John Hawkes provides us with a link to an interesting paper on that issue. The full paper is available Journal of the Royal Society Interface. The authors of the paper applied concepts from evolutionary robotics to an analysis of bipedalism in humans, great apes and Lucy. There is also a quicktime movie - below is a picture from the movie.

Results indicate that A. afarensis was a "fully competent biped." As Hawkes points out, there are several unknowns with the study that need to be addressed, but it was still interesting. Perhaps the most interesting aspect was the application of robotics and genetic algorithms (something I don't know that much about)to the study of human evolution.

When I took Paleoanthropology, my term paper was on bipedality in A. afarensis - I took the position that they were fully competent bipeds - so I was really interested in this article.

On an unrelated note, while checking out the Royal Society website I came across this article on circadian clocks. I mention in case anyone out there, who knows a lot about such things, would be interested in explaining it to us.

I've Been Sorted!

?

I'm
a Ravenclaw!



Not sure if I agree with the results. What do you think?

Is Russ Carnahan a Closet Republican?

How else can you explain his vote, in the House, for the Patriot Act.
Russ, Please read my July 4 post on Patrick Henry and in the future vote accordingly!

Friday Skunk Story Blogging

The above is a spotted skunk. Years ago when I was in junior high I was incredibly truant and got thrown into a minimum security juvenile institution. In the meantime, my oldest sister had started hanging around with a lady who taught a continuing ed course on animals and animal behavior. Because of that we had amassed quite a collection of animals - most of which are now ileagal (something I agree with). They all came from other people who had gone out and bought the cute furry animal - then when it became mature and started acting like a wild animal they started looking for ways to get rid of them. WHich is how we ended up with them.
I was woken up around 3:30 by the night attendent. He just kept babeling aboput how he had opened the door to get some fresh air and "IT" had walked in and climbed into a trash can. He knew I had some experience with wild animals so he needed me to get "IT" out of the "cottage". So I got up and went to take a look. Turns out "IT" was a spotted skunk. After finding a lid and putting it on the trash can I carried the trashcan outside about 100 feet from the cottage. Then I slowly tipped the trash can over and took off the lid. After retiring to a "safe" distance I turned to look and see what would happen. After about a minute the skunk slowly walked out of the trash can and walked into the surrounding woods.


The above is a striped skunk. Several years latter I was working for the Humane Society (a big mistake as I refused to euthanise the dogs and cats). One of the guys I worked with had a pet skunk he was trying to get rid of, so I aggreed to take. It had been descented. It was a female striped skunk the guy had named Tinkerbell. First thing I did was change her name to Raison (because she looked like a giant raison). The second thing I did was put her on a diet because she was extremely overweight. She was quite tame and we used to let her out of her cage to run around (as a matter of fact she spent considerably more time out of her cage than in). Occasionally we would "forget" to warn visitors that we had a skunk and on several occasions we had people run from the house when they saw Raison. Years later I moved into an apartment that wouldn't let me keep the skunk so I gave her to my brother-in=law. She lived for quite a while after that. I think she was about 12 or 13 years old when she passed away. Normally, wild animals do not make good pets and I, personally, am against having wild animals as pets but his is one animal I was glad to share my house with.

Friday Carnivorous Catapiller Blogging

The above is a picture of a newly discovered species of Hawaian catapiller - known as Hyposmocoma molluscivora. Hyosmocoma has a unique food and a unique method of catching that food:

In rapt fascination, they watched a caterpillar, less than 1 centimetre long, creep up to an equally tiny snail resting on the surface of a leaf, before gently lashing it to the leaf with silk threads.

Once the snail is unable to escape - by dropping to the forest floor - the caterpillar forces its way into the mouth of its shell and devours it, head first...

Such oddities are probably a result of the islands' great isolation, which means many ecological niches normally exploited by other animals remain vacant, says Rosemary Gillespie, an evolutionary biologist at the University of California at Berkeley, US. Even by these standards, though, the snail-eating caterpillars are extreme, since they involve both a novel food choice and a method of prey capture previously unknown in caterpillars.

Added Later: I have just discovered that Milk River also has a post about this, check it out. (been trying to add this for a while but blogger seems to be acting up)

Added Even Later: PZ Myers also has a post on them. I am compelled to point PZ to the comments in this post.

Added Even Later than the previous note: Those of you looking for more pictures of the carnivorous catapiller can go here

What the Blogs I Read Are Talking About

Ed Brayton over at Dispatches From The Cultures Wars has an iuntersting post on Bork and the nomination of Supreme Court Judges.

Chris Clark at Creek Running North has an interesting post called "Eft"

Michelle at The Culture of Chemistry has an interesting and skeptical look at the use of titanium in sports.

The Dharma Bums have some amazing pictures of a kingfisher.

Evolgen, who has caught a bad case of John Davisonitis, has an interesting post on genotype and phenotype.

John Wilkins at Evolving Thoughts has a post on his trip to Toronto.

Immunoblogging has a post (and videos) of predatory mice attacking albatross chicks - learned behavior apparently.

Keats' Telescope has an interesting post comparing non-coding DNA in mice and humans.

Niches has an interesting post about aphids and ants.

Pat Hayes at Red State Rabble points us to some photos of Scopes, Darrow and Bryan taken during the infamous trial. (How does he find this stuff?)

Aydin Orstan at Snail's Tales wraps up his series on Say's Snails.

Oldwhitelady at It's Morning Somewhere has an interesting take on the death of James Doohan...

My Mistake

I goofed. The article I linked to in the last post was from 1997 -silly me I thought it was new. Of course, now I have some research to do to find out what has happened to the idea since and hopefully I'll get a post out of it - maybe even for Transitions.

Incidentally, I'm always on the look out for good material for Transitions. If you know of anything or wish to contribute email me at: transistions@sbcglobal.net

Also, I'm always on the lookout for evolution related journals for the Darwinian Orthodoxy. If you know of any not already listed please let me know.

Of Embryos and Dinosaurs

This is quite interesting and unexpected. Apparently researchers in North Carolina have determined that dinosaur fingers correspond to digits 1,2 and 3 in humans whereas birds' fingers correspond to digits 2,3, and 4. Which casts some doubt on whether birds evolved from dinosaurs.

"We know that dinosaurs developed "hands" with digits one, two and three -- which are the same as the thumb, index and middle fingers of humans -- because digits four and five remain as tiny bumps or vestiges on early dinosaur skeletons," Feduccia said. "Apparently dinosaurs developed a very specialized, almost unique "hand" for grasping and raking.

"Our studies of bird embryos, however, show that only digits two, three and four develop, and this creates a new problem," he said. "How do you derive a bird "hand," for example, with digits two, three and four from a dinosaur hand that has only digits one, two and three" The answer is that you can't."

Additionaly reserchers point to some other differences:

Third, he said, if one views a chicken skeleton and a dinosaur skeleton through binoculars they appear similar, but close and detailed examination reveals many differences. Theropod dinosaurs, for example, had curved, serrated teeth, but the earliest birds had straight, unserrated peg-like teeth.

All dinosaurs had a major joint in the lower jaw that early birds did not. Birds have a reversed rear toe that opposes the front three toes and allows birds to perch. Dinosaurs had no reversed toe. Birds grow a girdle of bone in their chests quite different from dinosaur chests.

The new work involved microscopic examination of early limb development in ostriches, chickens, cormorants, alligators and turtles and comparison of chick fore- and hindlimbs.

"We know that dinosaurs developed "hands" with digits one, two and three -- which are the same as the thumb, index and middle fingers of humans -- because digits four and five remain as tiny bumps or vestiges on early dinosaur skeletons," Feduccia said. "Apparently dinosaurs developed a very specialized, almost unique "hand" for grasping and raking.

They explain dinosaur/bird similarities by proposing that dinsaurs and birds shared a common ancestor and both were adapting to upright posture.

If other researchers confirm the results this could be big.

Kennewick: A Dissenting View

John Hawks has posted some interesting thoughts on Kennewick. Pharyngula, Keat's Telescope and Savage Minds have all linked to it. Much as I like, and have learned from, Hawks' blog I have to disagree with his view on the subject. The gist of Hawks' post is that the new studies are essentially the same as the studies done prior to the court battle. In other words the new studies are essentially fact checking. He also doesn't like the way the new studies are being portrayed. The press is portraying the new studies as if these were the first on Kennewick (I agree with Hawks' on this point). Regular readers of this blog already know that there have been some studies of the Kennewick material. I have discussed some of those studies - and some of the problems with them here. Let me say at this point that previous investigations were hampered by restrictions placed on them by the conservators of the skeletal material. So let's start by comparing what has already been done with what the plaintiff's in the lawsuit are proposing to do. The plan of study can be found here.

As is standard procedure, they start with an inventory of the skeletal material. This may sound like simple fact checking but in this instance it is needed. As the proposal points out:

Among other things, there are unresolved differences between the records compiled by Dr. Owsley in October 1998 and the records compiled during the studies conducted by the National Park Service (“NPS”) in 1999. In addition, identifications of bone fragments have not been finalized. For example, the number and specific identification of all ribs (or rib fragments) recovered at the discovery site have not been determined. The inventory to be conducted during plaintiffs’ study session will attempt to resolve these and other bone identification and assignment questions.

The next step will be assembly and reconstruction of the skeletal material:

The cranium, mandible and selected postcranial bones will be reconstructed using Acryloid B-72. Some of the postcranial bones to be reconstructed are: both humeri, both femora, both tibiae and the right fibula. In addition, the right innominate and those ribs displaying pathological conditions will be reconstructed if doing so will aid in other investigations of the skeleton.

As I mentioned in my previous post, this type of reconstruction was not allowed:

Given the conservators' concerns regarding the use of permanent adhesives and consolidants, we elected to refit postcranial elements and maintain the stability of fragments by hand.

Which led to:

Prior to reconstruction of the cranium, all individual pieces of maxilla, mandible, zygomatics, and the neurocranium were measured by Powell (see Methods below). Facial bone fragments were refit by Powell and Odegaard, with input and assessment by Rose throughout the day-long process. Several times during the reconstruction process, pieces were removed, refit, and reattached to provide the best possible alignment of fragments.

Clearly a difficult situation.

Once the basics are out of the way there are 14 different analysis planned. Ranging from some of the more basic stuff (taphonomic and pathological assessment of the skeleton, age, gender, stature) to some more esoteric stuff:

Three dimensional coordinate data of the cranium will be collected using an electronic digitizer to record the x, y and z coordinates of each point touched. These data will be supplemented with measurements taken by hand instruments for those areas of the cranium (such as the mandible) not adequately measured by the digitizer.

Why is this important?

Coordinate data provide much finer characterization of morphology and allow explicit comparisons of shape. It is also possible to increase visual appreciation of variation by using wire frame models of skulls obtained by connecting landmarks. Coordinate data also allow computation of non-standard measurements, which may provide greater insights into variation among early American crania and between early and later American crania.

It goes without saying that this has not yet been done on the Kennewick cranium.

Another interesting study proposed is the laser scanning of the skull and other elements:

The purpose of the laser scan is to obtain and record accurate 3D models of the shapes of the skull and other scanned bones. Such models can be used in a variety of ways including the following: (a) to verify measurements and other data obtained by other investigators; (b) to provide data for adjusting measurements of the skull or other bones to compensate for any postmortem deformation or damage; (c) to visually compare the skull with skulls of other prehistoric (and modern) individuals; (d) to produce casts of the skull and other scanned bones. The data obtained will be recorded in a coordinate based STL file that can be archived in industry-standard formats for access by future investigators.

Also not done by NPS scientists.

They are also considering stable isotope analysis which can give information on whether they were eating terrestrial vs marine animals and what types of plants were being consumed. This analysis is contigent on finding sufficient collagen in the bones.

Another interesting study not performed by NPS scientists is the cross-sectional analysis of the femora, humeri and tibiae. Which can be used to understand activity levels (See Ruff's article in Skeletal Biology of Past Peoples: Research Methods).

NPS researchers utilized databases developed by Howells and Hanihara. The new study will uses databases developed by Jantz, Brace, Owsley and Turner to name a few.

To sum up, the original researchers were hampered by a lot more restrictions than the group that won the law suit. Consequently, although some of the analysis will be the same (gender, etc) some will be performed in more detail. For example the NPS scientists had to rely on fragmentary bones and used the humerus because they didn't have a complete femora in the interval the missing pieces to the femora have been found so a more accurate estimate can be formed. Take the age of the skeleton as another example. The age was determined based on palantine suture closure (there is some doubt about the accuracy of this method (see the Journal of Forensic Sciences 36(2):512-519)and ectocranial suture closure. Given the differences in ectocranial suture closure between, say, the Todd collection and modern forensic samples I take a second look as well. Some analysis (such as those mentioned above) will be completely new. Some of this will be mere "fact checking" in the sense used by Hawks. This is, partially, however, a fuction of proper methodology. Determining things like gender, ethnicity, stature etc, are usually done by the examiner regardless of whether this has been done before.

Having said all that, I totally agree with Hawks' assessment of the way the new studies have been portrayed. I, for one, hadn't really thought much in the way a research had been done on Kennewick till a commenter on a post concerning the peopling of the America's (back in May) caused me to do some checking (results of which are posted here). After reading a few newspaper articles concerning Kennewick I realized journalist do not know anything about anthropology and were more concerned with sensationalizing Kennewick than they were about getting the facts straight. It was at that point that I decided to do my recent four part series on the subject.

afarensis Needs a Rest

We do apologize for the previous post put up by afarensis. We think he has been working to hard, and based on that Mozart joke we think he has lost his mind (We think it is because he has been spending too much time thinking about old bones and dirt). We have taken appropriate steps to sequester him until such time as his sanity returns - if it ever does.

Until then, you can look at more pictures of us! Which I am sure you would all rather see anyway!

Pounce


Little Foot


Pounce


Little Foot

Mozart's Skull

While doing research on Kennewick I was reminded of an article published in the 1989 Journal of Forensic Sciences. The article concerned attempts to identify Mozart's skull based on pictures of Mozart. Said pictures indicated Mozart had an abnormally shaped skull. Researchers hypothesized that this was caused by the premature uniting of the metopic suture:

which can cause a deformed skull. The article itself was interesting. Even more interesting was how Mozart's skull came to be lost in the first place.

Mozart's death was somewhat unexpected and he was buried in a hurry. Several years later it was realized that they had done the great composer an injustice. His body was exhumed and the casket was put on a wagon for transport to Salzburg where a proper funeral would be held. As the wagon was rounding a corner the carriage driver was shocked to see a goat in the middle of the road. Unfortunately, they were going to fast to stop and ran the poor thing over -sending it to an unearned final resting place in a goatherd's cooking pot. The carriage carrying Mozart's mortal remains flipped over and the casket went tumbling. When it came to a stop the lid flipped open to reveal Mozart furiously erasing the scores to all his great symphonies. "Mozart!" the stunned members of the funeral procession cried "Whatever are you doing?"
To which Mozart replied "Why, I'm decomposing!"

And you thought you were going to get a serious story! Bwahahaha!

Sunday Godzilla Blogging

Usually when I go to rent movies I always check out the used videos for sale bin. Occassionally I find some good stuff for cheap prices.
Recently, I bought Godzilla vs Gigan


This is one of the cheesier movies in the series. Godzilla actually talks (although I've seen worse). Basically, giant cockroaches are trying to take over the earth because their planet is too polluted. Their plan involves a monster related theme park (with a near life size statue of Godzilla), Gigan and Ghidra. They are opposed by an artist (created the homework monster for the theme park), a girl who's brother worked for the theme park (as a scientist) and is now missing, her hippy friend (yeah, I know, but I actually liked this character) and of course Godzilla and Angilas (who was, to say the least, quite useless).

It's actually quite watchable! Of course, I've never met a Godzilla movie I didn't like.

New Post at Transitions

bootstrap analysis has allowed me to crosspost her excellent discussion of "The Poetry of Leaves" at Transitions. Check it out!

Endangered Missouri Hellbenders

The above is an Ozark Hellbender below is a picture of an Eastern Hellbender.



Both species are native to Missouri and in the past 10-15 years have suffered serious population declines - estimates range from a 60-80 percent drop in numbers.

Yue-wern Huang, an assistant professor of biological sciences at the University of Missouri at Rolla, says there seems to be a reproductive disruption among the salamanders. However, Huang says he's unsure what is causing a disruption in the hellbender's endocrine system, which regulates the secretion of hormones - although his theories include pollution, pesticides and people as possible causes.

Huang hopes water samples from the North Fork will give him insight into what pollutants might be harming hellbenders.

At Southwest Missouri State University, associate behavioral ecology professor Alicia Mathis is also trying to help keep the salamanders from extinction. Mathis and graduate student Shem Unger are raising both Ozark hellbenders and eastern hellbenders, which live between southern New York and eastern Missouri.

Tests suggest that Missouri hellbenders have lower sperm counts than their counterparts in North Carolina and Georgia, Mathis said. A similar study on humans from Columbia, Mo., Minneapolis, Los Angeles and New York City showed the Missouri men tested had the lowest sperm count.


It get's worse:

Stanley Trauth, a zoology professor at Arkansas State University in Jonesboro, showed pictures of hellbenders with open sores, tumors and missing limbs and eyes. He said that nine out of 10 animals found in the Spring River — mainly in northern Arkansas — this year had serious abnormalities.

"I'm at a loss, folks," Trauth said. "We just don't have a good explanation for what's causing this."

Max Nickerson of the University of Florida, who has worked with hellbenders for three decades, said his early research did not find nearly as many abnormalities. He called the new results baffling.

Other possible causes of the decline include introduced species of trout which juvenile Ozark Hellbenders do not seem to recognize as predators.

Additional information:
News@UMR
Northern Prairie Wildlife Research Center
St. Louis Zoo

An Open Letter to Kit Bond

Dear Kit,
I recently had the misfortune of hearing you speak about the Karl Rove outing of a CIA agent. To no one's intense surprise, your speech consisted of indiscriminent spewing of RNC talking points. Strangly enough, there was no mention of the fact that Karl Rove did indeed "out" a CIA agent. Nor was their any outrage about the damage done to our National Security by Karl Rove outing a CIA agent. Instead we were the unfortunate listeners to a smear campaign - most of which had nothing whatever to do with the fact that Karl Rove outed a CIA agent during a time when the nation is at war(in case I haven't mentioned that). I guess September 11th changed concepts of right and wrong, in addition to everything else (thus making it okay to out a CIA agent and harm national security).
Son, let me be blunt (and I don't mean our unesteemed governor either - cause he ain't that damn popular either): Karl Rove outed a CIA agent, which the last time I checked was illeagal - even for republicans hellbent on doing in their enemies (which, as I understand it consists of everyone who doesn't vote for them). See, the law applies to everybody equally or it means nothing. Just to refresh your memmory, we Missourians are proud to have voted for a dead guy and we expect at least the same level of performance and competence, displayed by the dead guy, from you. Although I don't like repeats on tv, the vote can be repeated - we can vote for dead guys instead of you! Straighten up and act like you have some morals.
Sincerely,
afarensis
Proud Voter for Carnahan

Lessons From Kennewick: Fitting it all Together

In the first post in this series I mentioned that the Kennewick skeleton had become available for scientific study. In the second post I discussed different techniques anthropologists use to study skeletal material. In the third I showed how these techniques are used in practice and tried to show how one skeleton can improve our understanding of history and of our scientific techniques. In this post I will discuss what is currently known about Kennewick and show how it impacts some of the issues discussed previously. Before continuing I would like to point you to this post for some of the archaeological background. In that post I point out some of the antecedents of North American archaeological assemblages and discuss some of the theories about how the Americas came to be populated. The one thing I left out of that post was a discussion of the people themselves.
It had long been thought that Native Americans were related to peoples somewhere in Asia (defined broadly). For example, one of the goals of the Jesup North Pacific Expedition, led by Franz Boas, in the 1890's was to trace the cultural, linguistic, archaeological and biological relationships between Asian cultures and Native Americans. Based on both skeletal and soft tissue traits it was assumed that Native Americans were related to mongoloid peoples in the old world. More specifically, it was felt that Native Americans, especially Eskimos, were related to peoples inhabiting Siberia. As anthropological methods became more sophisticated ideas changed somewhat - but not much.
E.A. Hooten, one of the more important figures in American physical anthropology, noted that the most mongoloid Native Americans were the Eskimos (coincidentally the most recent to arrive in the Americas) and the as one moved throught North America into South America populations became less mongoloid. This lead Hooten to propose that there were 2-3 separate migration events with the earliest being from non-mongoloid peoples related to populations in India, Australia and the Ainu.
J. B. Birdsell (writer of the popular - for it's time - Human Evolution: An Introduction to the New Physical Anthropology) felt that there may have been some non-mongoloid peoples (mainly the ancestors of the Ainu)involved in the peopling of the America's but felt that the America's were largely settled by mongoloid peoples.
W. Howells (author of the popular Mankind in the Making)felt that Native Americans were descended from a generalized mongoloid stock from which later, more specialized mongoloids (such as the Chinese) developed. Howells felt that populations bearing the closest resemblance to Native Americans could be found in Indonesia, Central Asian and Tibet. Unlike Hooten and Birdsell, Howells felt that mongoloids only were responsible for the peopling of the Americas. This is pretty much where things stand today. The point to take away from this is that there are two competing ideas. One allows for caucasoids in the ancestry of Native Americans. The other doesn't
The Kennewick skeletal material was found in July of 1996 Lake Wallula. It had been in a terrace, part of which claved off taking part of the skeleton with it. The remaining part of the skeleton was bleached by the sun for 1-2 months befor it to eroded out of the terrace. Elements of the skeleton were scattered, by water action, over 300 sqaure feet.


Here you can see what appears to be a tibia in situ.

Here is a view of a large part of the skeleton,



and here is a good view of the skull.

.

At first there was some uncertainty over whether the find represented, say, a homicide or was prehistoric. Preliminary analysis indicated the find was, indeed, an archaeological dicovery, which brought it under the purview of the Native American Graves Protection and Repatriation Act (NAGPRA) and under the Archaeological Resources Protection Act (ARPA). Of the two NAGPRA is the more onerus. Under NAGPRA a two step process is followed. First, One has to determine whether the remains should be considered "Native American" under NAGPRA's definition. If they are Native American the second step is to determine whether or not the remains are culturally affiliated with any modern day tribe or tribes (if so they are repatriated). Analysis of remains can be a little difficult because in most cases permanent alteration of the remains (by, say, reconstructing the skull) are not allowed. Be that as it may, in order to be in compliance with NAGPRA a number of analysis were performed upon the skeleton. First, an inventory was made of all the skeltal material. Having done that, the skelton was examined using some of the criteria mentioned in the second post. Using these methods it was determined that the skeleton was of a male between 45-50 years of age. The femurs and tibia were broken so the humerus was used to determine stature. It is estimated that the stature of the individual was between 5'8" and 5'10". The skeleton was also examined for pathology and post mortem damage. The skeleton showed some signs of osteoarthritis. There was localized trauma on the radius, and scapula. The right ilium had what has tentitively been identified as a cascade style projectile point embedded in the right ilium.


A Cascade point (only about three inches long).

Interestingly enough, this injury did not kill the individual, quite a bit of healing took place after the injury. As a matter of fact only the base and tip of the point could be clearly seen. Several of the ribs were broke, although there is some evidence that this represents post depositional damage. There were also some rodent tooth marks on the skeleton. In addition to the bleaching of some of the bones, mentioned above, the skeleton was covered with calcite deposits. Some of the bones also had alghae adhering to them. Some of the bones also had a reddish stain which may have been red ochre - but further analysis indicated the stains were caused by decaying organic matter (roots mainly).

To answer the question of biological affiliation (i.e. was Kennewick related to modern tribes) non-metric and metric techniques were used.

In terms of non-metric traits the Kennewick material contained a variety of features found in Caucasoids and Mongoloids. Caucasoid traits found in Kennewick include a large nasal spine, undulating horizontal ramus (part of the jaw) border, slanting ascending ramus profile, no wormian bones, no os japonicum (this is where a second suture divides the zygomatic bone into two pieces) and cranial sutures of medium complexity. Mongoloid traits include a large malar tubercle (a raised area on the zygomatics) blurred nasal sill, zygomatic posterior tubercle, slight nasal depression, moderate prognathism, elliptical dental arcade, straight palantine suture (the palantines are two bones that articulate with the palate in the top rear of the mouth)and possibly an angled zygomaticomaxillary suture (in caucasoids this suture is "s" shaped) and a forward facing frontal process of the maxilla (this is the area where the maxilla articulates with the frontal and nasal bones - in caucasoids the frontal process slopes steeply away from the nasals). This is where it gets interesting. Some additional traits include an nasal form intermediate between towered and tented , a medium nasal opening, vertical zygomatic bones, and a slightly rhomboidal orbital shape. These traits occur in Polynesian populations (I will get back to this later).

In terms of metric traits an extensive series of statistical analyses were carried out. In order to do this the skull had to be reconstructed, which led to several problems. Since the conservators of the skeleton would not allow permanent alterations the normal glues and what not used in restoring skulls could not be used. In order to take some of the measurements the bones literally had to be held in place by one person while the other measured them. This involved a lot of fitting and refitting of the bones (both cranial and post cranial). A CT scan was also made of the skull, which allowed a polymer cast to be made. Unfortunately, a comparison of the measuremnts of the cast with the skull revealed statistically significant differences in the measurements. Fifty two measurements of the skull were then taken and the measurments were compared to a wide variety of populations around the world. The results were interesting. In most of the tests ran Kennewick was most closely related to populations in southern Japan (i.e. the Ainu) and Polynesia (the Moriori and Easter Islanders) followed by archaic Native American populations such as Indian Knoll and, in some analysis, the Chukchi of Siberia.
The Kennewick skeleton has gotten a lot of press becuase of it's caucasoid affinities and we are now in the position to see how this came about. It should be pointed out that in this context "caucasoid" does not mean European. Rather caucasoids refers to a large highly variable population that includes Polynesians, Australians and the Ainu as well as Europeans. The way I would explain it is that Kennewick arose from the same general population that gave rise to Polynesians, Australians and the Ainu. If you refer back to my discussion of "race" in part three of this series you can see how some of those ideas play out here. In particular, the Brace et al article seems relevant. Some of the traits cluster Kennewick with, say Polynesia (this would be the common descent aspect of the Brace et al article) others are referable to the effects of different selection regimes as each population went their separate ways (my own opinion - for what it's worth - is that Kennewick seems to lend some confirmation to Hooten's theory mentioned above).
Samples were taken from the 3rd left metacarpal for DNA analysis using PCR amplification. Midway through the study analysis was terminated under orders from the Army Corps of Engineers (the skeleton was found on COE property). In the spring of 2000 permission was granted by the Department of the Interior to proceed with the analysis. Unfortunately, investigators were unable to extract DNA suitable for PCR amplification. A sample of the 3rd left metacarpal was also submitted for radiocarbon dating. The results indicvated an age range 5750 - 9510 BP. Investigators felt that there was some intrusive young carbon in the sample yielding the younger dates. But things are a little more complicated than that. Apparently, there is a discrepancy in carbon content between bone samples taken in 1996 and 1999 - which investigators found surprising.
It could be argued that the proper thing to do with Kennewick would be to make some casts (which is not without difficulty given some of the conditions posed on previous investigators) and repatriate the remains. As pointed out in this post there are several outstanding issues that need to be resolved (A better DNA analysis being one). Certainly, research on casts has some legitimacy within anthropology. However, there are precious few skeletons dating to the time of Kennewick and before we turn it over, for what amounts to it's destruction, we had better make sure we get the science right. But then, what of other skeletal material that is just as important. The Over Collection (mentioned in the previous post) has, largely been repatriated. It would not have been possible to make casts of each and every skeleton in the collection. It is, therefore, crucial that scientists be allowed to study this material in a manner consistant with the best scientific practices - which has not been done with Kennewick (which is not to say the previous investigators were less than professional - rather some very severe restrictions had been placed on their ability to perform the necessary studies).

Here are some interesting links to Kennewick:

NPS AEP: Kennewick Man Contains many of the studies used in this post.

Tri-City Herald's Kennewick Man Virtual Interpretive Center

Kennewick Man Home Page From the Burke Museum - where the Kennewick skeletal material is located.

Kennewick Update

My fourth post on Kennewick is about 1/3 finished. I'm hoping to have it completely finished tomorrow (sorry for the delay, I've been fighting off a cold for the last couple of days and it's making writing - and thinking - difficult).

Some more this and that

I'm still working on the last post in my series on Kennewick Man (okay I admit it, I didn't work on it today - I was just feeling a little lazy and needed a break). Should be up tomorrow.

Pirate Blogging

according to National Geographic News Blackbeard's flagship may have been found off the coast of North Carolina :

The wreckage includes a dozen cannon and large anchors rated for a 350-ton (355-metric-ton) ship, found amid a mound of debris where records indicate Blackbeard's flagship ran aground in 1718.

"We have extensive historical records, and there is no evidence of any [other] vessel of this kind of armament sinking anywhere during the 18th century on this coast," said Mark Wilde-Ramsing, director of the Queen Anne's Revenge Shipwreck Project, a consortium of researchers investigating the wreck.

Shipwreck records in the region are surprisingly complete. They include accounts of ships lost decades before the QAR and in more remote areas.

"There were people living in the area, and a [different] wreck of this size should not have gone unrecorded," Wilde-Ramsing said. "Beaufort was a little fishing village, and really less than a handful of ships that size were ever reported in the area."

Blackbeard captured a French slaver known as La Concorde in 1717 and renamed it Queen Anne's Revenge. He captained the ship until it ran aground, perhaps intentionally, at Beaufort Inlet in June 1718. (For more on Blackbeard, see sidebar.)

Some accounts at the time suggested that Blackbeard wanted to break up his crew of some 300 to 400 men—and keep the choicest booty for himself.

The ship is still officially classified as "believed to be" the QAR. But mounting evidence suggests to many that the wreck is that of Blackbeard's ship.

Since afarensis has a sailboat and knows how to fence he is interested in all things pirate and hopes this is indeed Blackbeard's Ship!

Unfortunately there is a fly in the ointment:

Some researchers harbor doubts that the wreck is that of the QAR. Most of their reservations center on a cannon that bears the number 1730 scratched into its surface.

"If this is a date, it definitely eliminates the identification of the site as Blackbeard's 1718 shipwreck," states a paper co-written by former QAR project conservator Wayne Lusardi and East Carolina University archaeologists Bradley Rodgers and Nathan Richards. They expressed their doubts in The International Journal of Nautical Archaeology this spring.

Still, several researchers dispute that the number is a date, suggesting that it refers instead to the weapon's price or its weight.

You can go to the Queen Anne's Revenge Website for more details.

Green Knight and Judicial Activism Or Why Does the Culture of Life Hate Congress?

This post by The Green Knight on judicial activism is brilliant! Who'd have thunk the most conservative members of the Supreme Court are the ones who vote to overturn congressional laws the most!

Lessons from Kennewick: The Value of One Skeleton

Before going any further I would recommend that you read the first and second posts in this series.

So, having learned some basic things like how to determine gender, ethnicity, age and stature you might think that nothing more can be learned. You might also think that nothing could be learned from a single skeleton. You would be wrong.

The Swan Creek site is located in South Dakota (this example comes from Skeletal Biology in the Great Plains: Migration, Warfare, Health and Subsistence edited by Douglas Owsley and Richard Jantz). It was excavated, mainly, by W. H. Over. The site dates to 1675-1725 and is Coalescent tradition village site (the Coalescent tradition has been attributed to the Arikara and Pawnee). One of the skeletons was somewhat different from the rest. It was found jumbled together with four other skeletons. The skull is labeled 2198 and that is how I will refer to it.
Skull 2198 was judged, using some of the criteria in the last post, to be a male (size, brow ridge, mastoid size, blunt eye orbits, etc) between the 40-50 years old (based on the obliteration of cranial and palatal sutures). Pathology included three healed depression fractures. To determine biological affiliation researchers first used the technique pioneered by Giles and Elliot (mentioned in the second post of this series). This is where the first problem comes in. Giles' and Elliot's method classifies white and black females and white males reasonably accurately. It missclasifies black males and native americans. Giles and Elliot used a sample of native americans from Indian Knoll (in Kentucky) which dated to around 1000 BC. Ever since Franz Boas' classic study on the changes in cranial form between immigrants and their children it has been know that a wide variety of factors effect the shape of the human skull - including environment. So the difference in environment plays a role. It is also known that the accuracy of such techniques drops off when you move outside the population the technique was developed on. Different populations have differing patterns of variability. In this case, Giles and Elliot frequently classifies northern plains indian populations incorrectly. So researchers turned to the method developed by Gill. But, you guessed it, Gill's method gives variable results for northern plains populations also - especially Arikara males. I should mention at this point that both methods classified skull 2198 as a white male. As another means of testing this researchers compared Larson (another collection of Arikara skeletal material to 300 crania from France (dating to 1500-1900 AD) and 100 Austrian crania (1700-1900 AD). They developed their own discriminant fuctions to classify the Swan Creek crania. Thsi new function classifed all Swan Creek correctly as indian - except for two. One of which was 2198 which was classified as European. You might be tempted to say "so what, you found a caucasian skull in an indian village. Big deal!" Well it is a big deal. The earliest documented evidence of European contact with the Arikara wasn't until the 1740's. There is some evidence of French trader activity prior to that time but this is the first tangible evidence. There is also some evidence that the Swan Creek village experienced a reduction in population which is part of an overall disease induced reduction of population that occured in the middle Missouri area. One explanation was that disease was passed along trade routes in advance of the arrival of Europeans. This find suggests disease pathogens were carried in directly by Europeans. This alone makes skull 2198 important. But there is more. If skull 2198 was European this raises the possibility of gene flow. Did he take a native american wife and have children? How can we tell? Presumably, they would be morphometrically intermediate but because of a shared environment would still classify as Arikara. Several of the crania from Swan Creek fell close to being classified as European (technically they were close to the sectioning point - the line that divides European from Arikara). Suggestive evidence that there may have been gene flow - but not conclusive. It would be nice if we could do more research on the issue, unfortunately the W.H. Over Collection (of which Swan Creek was a part) has been repatriated.

This brings us to Brace et al's 1993 article "Clines and Clusters Versus 'Race:' A Test in Ancient Egypt and the Case of a Death on the Nile" published in the AJPA. Ostensibly, this is a study of the biological affinities of ancient Egyptians with other populations around the world. The specific point of the article was to address the notion that Egyptians were "black". Along the way another mystery skull is found.
Let's step back a minute. When discussing ethnicity in my previous post I pointed out that I had been taught to distinguish three basic catagories - Caucasoid, Negroid and Mongoloid. As we saw with the Arikara this is very simplistic. Arikara skeletons vary from other northern plains skeletons which in turn vary with skeletal samples from other geographic areas (not to mention the issue of temporal variation). As I have mentioned a wide variety of things can affect the skeleton. Thigns like healthcare, nutrition, lifestyle (that's an interesting story and the subject of some future post) and evironment. There is one thing that can affect the skeleton that I haven't mentioned yet.
There have been a wide variety of traits used to divide people up into races. Four in particular will be discussed. The four traits in question are usually used to define Negroid or blacks. The first is the amount of melanin in the skin. There are numerous populations around the world with heavy concentrations of melanin in their skin. Such populations can be found in Africa, India, Australia and South America. Given the geographic separation of some of these groups one can say they are not all related (which you would expect if skin color was a diagnostic criteria of biological affinity). Basically the amount of melanin in skin is a response to solar radiation. As such, it is under control of selection and forms a cline or gradient that follows the amount of solar radiation. Another trait used to define the Negroid "race" is the elongation of dital limb segments (those parts of the limb furthest from the body). In point of fact the elongation of distal limbs is related to the dissapation of heat (think Allen's Rule) and is also clinally distributed. Since solar radiation and heat stress are related there is also a correlation between skin color and distal limb elongation. Nasal bridge elevation and elongation is another trait used to define race. Unlike skin pigmentation and limb elongation, nasal bridge elevation is not related to heat, rather it is related to the amount of moisture in the air. Consequently, nasal bridge elevation and elongation is also under selective control and occurs in arid environments (for example in humid areas of west Africa and the Congo nasal bridge elevation is absent. It is present in areas such as the arctic were the air is cold and dry). Jaw and tooth size are also used to define "races". Jaw size is, obviously related to tooth size - hence large teeth tend to create a certain amount of alveolar prognathism (see the previous post). Tooth size, it has been argued, is under selective control related to food processing technology. Consequently, it has a different distribution than traits related to solar radiation, heat or humidity.
So let's see how these four traits play out in Egypt. There is a cline of skin color and distal limb elongation running from the Nile Valley south to the equator. Once we reach the East Horn of Africa (Somalia and the Arabian Peninsula) we face a different situation. Since there is a large amount of solar radiation we see the dark pigmentation and distal limb elongation. It is also very dry so, unlike in other parts of Africa, we also see nasal bridge elongation and elevation. We also see a reduction in tooth size (Brace et al argue that this is because this area was one of the centers for the domestication of plants). Brace et al found that when these traits (i.e. the ones under selective control) were left out Somalis showed a definite relationship with European populations. All this, really, proves Darwin correct when he said traits under selective control can't be used to determine population relationships. Brace et al then examined traits that were not under any kind of selective control. They assumed that:

Traits that show associations with each other only within the context of a given region, then, inevitably have no adaptive significance. When a large number of features occur together in a given geographic area, the principle agent controlling their occurence is the sharing of genes between neighboring groups that are by definition relatives.

They then analyze skelatal samples from all over the world and construct a tree (for the statistically inclined the tree was based on Euclidian distance) of such clusters of populations. Since the traits underlying these clusters are, they argue, nonadaptive they do not easily yield labels such as "black", "white" or "mongoloid". I will get back to this in a bit. One of the skulls included in the analysis was skull E 597 from the 26th-30th Dynasty (dating to 664-341 BC). This skull was utterly unlike anything else in the collection - so much so that Brace almost felt that it had been included by mistake. Except for the fact that there was clear evidence that the brain had been extracted through the nasal aperture. The individual had also been embalmed with the mortuary treatment reserved for wealthy Egyptians. Discrimant function analysis of skull E 597 was more closely related to a sample of skulls from the neolithic in Germany! Leaving aside the question of how this individual came to be in Egypt, skull E 597 indicates some interesting things about Egypt. Brace et al's analysis indicated that Egyptians in Late Dynastic times shared more traits in common with Europeans than with the inhabitants of Upper Egypt 3,000 years earlier. Which indicates the extent of contact Egypt had with populations to the north and west in particular and the rest of their known world in general. In a sense, the significance of skull E597 is that simple labels such as "Caucasoid" or "Negroid" are misleading and inaccurate.
As Brace et al point out:

Where human traits have adaptive significance, their distributions are determined by the distribution of the controlling selective forces and 'their are no races, their are only clines." Where traits have no adaptivie significance, neighbors will share traits with neighbors and analysis of adjacent samples will show that they cluster together. Both these situations occur in the Nile Valley....
The old-fashioned chimerical concept of "race" is hopelessly inadequate to deal with the human biological reality of Egypt...

So there we have it. New methods for learning about history were tested. Questions that we had never tried to ask before (anthropologically speaking)were raised. One skull taught us something new about American history. One skull taught us something new about Egyptian history. Both taught us something about ourselves by leading us to questions certain notions about race - which means we might be able to have a more meaningful conversation. The value of one skelton in each case made a difference in the advancement of human knowledge.

I hope to have the next (and final post) in this series up by Tuesday.

This and That

Finally! I got the second post on Kennewick up! Took forever to write and I kind of slighted Paleopathology and it seems to have messed up the left side of my blog (I'll just have to live with that).

In the meantime Old White Lady has posted the most hysterical joke! Check it out!

Lessons from Kennewick

As I mentioned several days ago, the Kennewick skeletal material as become available for research purposes. During the course of the last 10-15 years physical anthropology has developed some powerful research methodologies to learn about how people lived in the past. In that I studied under (for a few years) one of the protangonists to the lawsuit I thought I might be able to provide some small insight into how anthropologists will proceed with the research and what they hope to lean. I will warn the reader in advance that this is going to be an extremely long post, but if you stick with it you will be rewarded in two following posts.

When examing new skeletal material the first thing to be done is to lay all the material out in correct anatomical position. This involves identifying the bones as to type (e.g. femur, mandible, vertebrate,etc.) and side (if applicable). As this is being done each bone is recorded on an inventory sheet. Once this is done a set of standard measurments (more about this below) is taken on whatever bones are in good enough conditon to measure. This is where the fun begins. There are certain other types of information that one wishes to obtain from the skeleton. In the early days of anthropology and archaeology the ethnicity, gender and stature (if possible)of the material was determined and not much else (and here I am being a little simplistic). Recent technological advances and the rise of forensic anthropology have changed things almost completely. Ethnicity, gender and stature are still recorded but there is more that we can learn (and some interesting wrinkles).
Before I go any further I need to talk about non-metric and metric methods of analysis. Non-metric traits are those that are, basically, either present ot absent. Below is a picture of a human pelvis. A probe is pointing to the greater sciatic notch.
Picture 1
In females the notch is large in males it is somewhat smaller. The size of the sciatic notch has lead to "The Rule of Thumb". If you stick your thumb into the sciatic notch and have some room to wiggle it, it is female. If you have little to know room. it is male. This is another type of non-metric trait. In this case the non-metric trait is based on variable expression of the trait.
Metric traits are those that can, obviously be measured and there are quite a few of them in anthropology. Once upon a time they were used, and abused, with abandon. The cranial index (a measure of the length vs breadth of the cranium) is a good example. The cranial index was used widely during the early days of physical anthropology. Then it was realized that a wide variety of factors (including the environment) affect the shape of the human skull and these kinds of simplistic uses of metric traits were abandoned. These days anthropologists are much more sophisticated (more of that later). A good example of a metric trait is the size of the head of the femur.

Picture 2


The diameter of the head of the femur is used to identify the gender of the skleton - diameters greater than 45mm indicate male, diameters smaller than 45mm indicate female (this method assigns gender accurately 93% of the time).

Whether one uses metric or non-metric traits in the analysis of skeletal material one should always take natural variation in populations into account. Most of the criteria for determing gender, ethnicity and stature were developed from two skletal populations (the Todd collection and the Terry collection). These collections were amassed during the 20's and 30's which means that that people makeing up the collections were born in 1800's - in some cases in the 1850's. Over time it was realized that the criteria were becoming less accurate. It turns out that things like better nutrition and healthcare were the cause. A second issue comes from applying these techniques to a different geaograhphic population than the one they were developed in. FOr example, criteria developed to identify ethnicity in the American Southwest are not as accurate when applied to populations in the great plains. With this in mind let us proceed to our analysis of the skeleton.

Gender

The following discussion concerning the determination of gender from the skeleton applies only to adult material. Determination of gender in subadult material is practically impossible. The criteria used to determine gender are reflections of secondary sexual characteristics that do not develop until puberty.
The best place to determine gender in the human skeleton is in the pelvis. In humans the pelvis been shaped by a compromise between bipedal locomotion and childbirth. Looking down on the pelvis in males the pelvic basin is narrower or heartshaped, whereas in females it is rounder.

Picture 3

This is due to modification of the the three bones that compose the pelvis. In females the pubic bone is longer than in males, the sciatic notch is wider and sacroiliac articulation (the area where the sacrum joins with the ilium)
is raised.

Picture 4

These three features increase the size of the pelvic basin and because of them there are certain other criteria diagnostic of gender. In the bottom row of picture three we see a ventral view of the male and female pelvis. Note the area labeled ventral arc. In females, due to the longer pubic bone, it is wider. On the other, dorsal, side the the pubic bone is a feature called the ventral arc - which occurs only in females.

Picture 5


Returning to picture four you will notice a area labeled "pre-auricular sulcus" this feature occurs only in females (but not in all females). Another feature that aids in the assignment of gender are dorsal pits. These occur on the dorsal surface of pubic bone and are associated, along with scarring of the preauricular groove and scarring of the groove for the interosseous ligament, childbirth. However, there is no simple correlation betwenn the number of dorsal pits and the number of offspring born. There are few metric methods for determing gender from the pelvis and they are not used that frequently.
Turning to the skull there are a number of traits the, when viewed collectively, indicate gender. Starting with the shape of the mandible. In males the chin is squarish, in females more rounded and comes to something of a point. The skull proper, in males is more rugose with muscle markings being larger and rougher. The supraorbital ridges are larger in males - as are the mastoids. The upper edges of the eye orbits are sharp in females and blunt in males.



The posterior end of the zygomatic process (in the picture above the probe is touching the zygomatic process superior to the articular eminence) extends further back in males than females. Often, it extends past the external auditory meatus (the large whole for the ear).
Gender can also be determined metrically, although this requires the use of advanced statistics. Discriminant functions are the most frequently used method. Fortunately, for the mathmatically impaired quite a few discriminant fuctions have been compiled for this purpose so that all one has to do is plug the measurements into a formula. Several computer programs, such as Fordisc, have also been developed.

Ethnicity

This is one of the most controversial areas in physical anthropology. Back in the bad old days "race" was a rigid, typological catagory. These days the anthropological approach is much more sophisticated, based in a large part on the acceptance of populational thinking (imported mainly from biology). The impact of the concept of the cline can not be underestimated as well (for example skin color follows a cline, as do several other human traits). Be that as it may, how do we identify ethnic groups when all we have is a skeleton?
When I was in school discussions of ethnic affiliation revolved around three main groupings: Caucasoids, Negroids and Mongoloids. Towards the end of my time in school the focus became wider and more populations were included (mainly due to the efforts of Forensic Anthropologists who had to deal with a wider variety of populations in widely different regions). I will start with above three and then move outwards (in the next post of this series).

Caucasoid skulls are characterised by the following: nasal sill (running along the nasal aperture, retreating zygomatics (see picture) narrow nasal opening depressed nasal root (hard to explain and I couldn't find a picture), braincase with length and width nearly equal and minimal alveolar prognathism (if you were to lay a pencil lengthwise from the nasal opening to the jaw the pencil would touch the chin).



If you were to lay a pencil where the black line is in picture "c" you would be able to insert your finger in between the zygomatic bone and the pencil in caucasoid skulls. The zygomatic bones are angled slightly back towards the rear of the skull.
Negroid skulls are characterized by the following: high, straight forhead with bregmatic depression (bregma is the point where the coronal and sagittal sutures meet), long, relatively narrow braincase, wide interorbital breadth, poorly defined nasal margin (as opposed to having a sill) and alveolar prognathism (a pencil placed with one end on the nasal spin would not touch the chin. Note: the pencil tests and the "rule of thumb" come from Bass's influential Human Osteology: a Laboratory and Field Manual).
Mongoloid skulls are characterized by the following: projecting zygomatics (see above), edge to edge bite (unlike causasoid and negroid skulls which frequently have an overbite), shoval shaped incisors, nasal overgrowth, face realtively broad compared to height and less prognathism than caucasoid or negroid skulls. Mongoloid skulls can be difficult to distingish from negroid or caucasoid skulls.
The above lists of traits are subject to a certain amount of subjectivity. What one sees in a skull can be influenced by one's views on ethnicity. This is where metric analysis really earns it's keep. The most common techniques where pioneered by Giles and Elliot in their paper "Race Identification from Cranial Measurements" and Gill in his "A Forensic Test Case for a New Method of Geographical Race Determination". Giles' and Elliot's method is basically a three step process. First gender is determined. Then eight measurements are plugged into either of two formulas. The first formula distinguishes between American white and American black skulls (there are separate formulas for male and female skulls). The second formula distinguishes between American white and American indian skulls. If the skull could be any of the three then both formulas are used and the results are plugged into a plot. The x axis of the plot reflects the American white-indian scale. The y axis reflects the American white-black scale. The scores for the skull yielded by each formula are then used to plot where the skull is on the graph and the location yields the biological affinity. The result is accurate about 82% of the time in males and 88% of the time in females.
The main problem with the above method is that it tends to misclassify native americans. Gill's paper tries to address this. Gill focused on the midfacial region, that is, the region around the nose and eye orbits. He took six measurements and combined them into three indices. The score then yielded the biological affinity. This method can distinguish American whites from American indian skulls 80% of the time. The problem with the method is that it doesn't do a good job of distinguising between Eskimos, American blacks and American indians. It also doesn't do a good job of, say, distinguishing between plains populations of American indians and southwestern populations of American indians (I will take this up in more detail in the next post in this series).

Age

There are several different methods to determine age in a skeleton. If the skeleton belongs to a subadult one could use erruption patterns of the deciduous teeth or the examine the rate of epiphyseal closure.



The above photo shows the epiphysis of the femur before and after it unites with the femur. Different epiphysis unite with their bones at different times and the number of number of united epiphysis combined with the stage of the other epiphysis can yield and estimate of age.
There are also several different methods to determine age in adult skeletons. The most frequently used involves cranial suture closure. Generally, the coronal, sagittal and lambdoidal sutures are used. The picture below shows the location of the coronal and lambdoidal sutures (the sagittal suture runs along the top middle of the skull).



Each suture is examined on a 5 point scale running from completely open (0) to completely closed (4) a composite score of all the sutures is created which indicates age. Several variants of this method exist (some use different sutures of the skull and one uses suture closure of the palate).
One can also use the pelvic bones to determine age. For example, the surface of the pubic bone can be used to determine age.



An examination is made of the different aspects of the pubic bone. Each aspect is scored and the composite (as above) yields an age estimate. Above is a picture of some of the different stages. Note there are separate criteria for males and females. A similar technique can be used on the auricular surface of the ilium (mentioned above under gender).



The surface of the bone in this area undergoes some textural changes which are associated with the aging process. The criteria, such as granularity, striations and billowing are scored (as in the above techniques) and the composite score yields an age. Speaking from experience, this technique can be difficult to use.

Stature

Most techniques of stature determination are based on regression formulae. Basically, one measures the femur or tibia and plugs that measurement into the correct formula ( depending on ethnicity and gender) and you get the stature. To date no method has been developed to accurately predict weight based on the skeleton

The one area I haven't touched on is pathology. Which will be dicussed in the next post.