The Dover Lawyers

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

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

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

“It’s not the last you’ve heard from me and Steve on this,” Rothschild said.

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

New Species of Mammal Discovered in Australia

From National Geographic News:

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

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

Why cadburyi?

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

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

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

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

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

Back to the fossil:

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

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

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

I’ve not been able to find any pictures of the fossil…

Evolution in Action

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

http://www.msnbc.msn.com/id/10644538/from/RS.5/

The virus, Clostridium difficile, is particularly nasty:

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

There are two possible causes. First:

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

*snip*

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

*snip*

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

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

Second:

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

One of the reasons the virus is “meaner and nastier”:

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

Finally, an interesting epidemiological tidbit:

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

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

Abstracts can be found by following the links below:

http://content.nejm.org/cgi/content/abstract/353/23/2433

http://content.nejm.org/cgi/content/abstract/353/23/2442

http://content.nejm.org/cgi/content/extract/353/23/2491

http://content.nejm.org/cgi/content/extract/353/23/2503

Zooarchaeology, Pokemon Archaeology and Climate Change

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

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

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

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

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

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

*snip*

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

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

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

Back to the Grayson article for the final word:

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

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

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

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

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

For additional info on zooarchaeology the following books are recommended:

Vertebrate Taphonomy by R. Lee Lyman
Bison Kills and Bone Counts by John D. Speth
Fossils in the Making: Vertebrate Taphonomy and Paleoecology by Behrensmeyer and Hill
Environment and Archaeology by Karl Butzer
Quantitative Zooarchaeology: Topics in the Analysis of Archaeological Faunas by D.K. Grayson.

Update 03/31/2013: Edited to fix pictures and correct typos.

New Post at Transitions

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

Late Archaic Projectile Points

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

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

*snip*

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

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

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

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

Sevens Meme

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

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

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

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

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

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

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

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

Open Access Journals and the Evil Darwinian Orthodoxy

Geotimes has an interesting discussion of open access journals:

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

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

Does anybody know the URL of this Online Database?

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

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

Transitions News

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

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

Tangled Bank Reminder

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