Wednesday, November 30, 2005

Platynereis dumerlii, Acropora millepora and the Human Genome: Part Two

Let's approach this from another direction we can look at nematodes and compare their genome with flies and humans. So researchers compared more than 100 nuclear protein alignments. The original study used the 18S rRNA. In nematodes this has particularly long branches, indicating an increased rate of sequence change. What this means is that, basically, nematodes have an increased rate of nucleotide substitution which creates a longer branch phlogenetically - in essence high rates of sequence change give the appearance of greater age and are pushed further down on the phylogentic tree (called long branch attraction).

Which is where they are placed in the coelomata hypothesis. Supporters of the alternative view argues that this is because of long branch attraction. The writers of the papers linked to above reasoned that if nematodes cluster at the base of the phylogeny because of long branch attraction then the best place to find support for the alternative, Ecdysoza, hypothesis is in slowly evolving proteins. Their results actually supported the Coelomata hypothesis - that is that humans are more closely related to flies than nematodes. They suggest that the linkage of nematodes with flies is an artifact of of analysing only one gene.
But there is another wrinkle, which I will discuss tomorrow.

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My International Readers

There is a post over at Pharyngula comparing international readership on liberal vs. conservative blogs . Here are my stats. I'm happy to note that 44% of my visitors came from overseas.

56 56.57% United States United States
7 7.07% United Kingdom United Kingdom
6 6.06% Denmark Denmark
6 6.06% Canada Canada
4 4.04% Ireland Ireland
4 4.04% Australia Australia
4 4.04% Netherlands Netherlands
4 4.04% Czech Republic Czech Republic
2 2.02% Taiwan Taiwan
2 2.02% India India
1 1.01% Sweden Sweden
1 1.01% Switzerland Switzerland
1 1.01% Puerto Rico Puerto Rico
1 1.01% Germany Germany

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Tuesday, November 29, 2005

You Know You Have Been Reading Too Much Biology When...

You know you have been reading too much biology when everytime you get an idea for a post you discoverPZ Meyers has already written a post on the same topic! I started on mine yesterday, got lazy and decided to turn it into a two parter - that's what I get for procrastination! The sad thing is, I have been reading a lot of anthropology lately (I'm currently reading L.S.B. Leakey's "By the Evidence")but for some reason I keep posting on biological topics. As soon as I get over being befuddled by it, I'll finish that post becuase I'm actually going somewhere slightly different with it. In the meantime I think I'll try to forget about biology by immersing myself in Walker and Leakey's "The Nariokotome Homo Erectus Skeleton" I'd like to see a post on that over at Pharyngula!

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Prehistoric Settlements Discovered in Greece

The above is a map of the area around Ptolemaida Greece. It's about 330 miles northwest of Athens and is home to some interesting archaeological finds. According to a story on MSNBC two neolithic sites, dating to some 5,000-6,000 years ago, have been found. The two sites join approximately 25 others found in the area:

The first site, located on a plot earmarked for coal mining by Greece's Public Power Corporation, yielded five human burials, as well as artifacts including clay figurines of humans and animals, sealstones, pottery and stone tools.

The second site dates to around the same time period and seems to be a stone tool workshop.

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Intelligent Design and the Need for Jesus

Dembski says:

God, as understood by the world’s great monotheistic faiths, is an infinite personal transcendent creator. The designer responsible for biological complexity, by contrast, need only be a being capable of arranging finite material objects to display certain patterns. Accordingly, this designer need not even be infinite. Likewise, that designer need not be personal or transcendent (cf. the “designer” in Stoic philosophy).

That being the case, would that mean we are not created in gods image and that Jesus didn't die for our sins? Wouldn't that mean the bible was fallible. SHouldn't we then worship the non-infinite, non-transcendent material arranger? I'd really like to see Dembski discuss the theological implications for christianity behind that statement!

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Monday, November 28, 2005

Platynereis dumerlii, Acropora millepora and the Human Genome



It all started several years ago. Scientist were trying to decide the relationships between vertebrates, arthropods and nematodes. There were two competing theories. The first is based on the fact that the nemetodes lack a true body cavity, rather they have a false coelom sandwhiched between endoderm and mesoderm tissue layers.

In contrast true coelomates have a coelom entirely surrounded by mesoderm.

The Coelemates are divided into deuterostomes (which includes vertbrates) and protostomes (based on whether the blastophore develops into the anus or the mouth respectively).

The second, based on small subunit ribosomal RNA analysis, revamps this placing acoelemates (lacking a coelom) and pseudocoelomates (such as nematodes) in a clade with protostomes. More specifically, they placed nematodes in a clade with arthropods. This clade is defined based on the fact that they moult. Both phylogenies are pictured below.

This is where things get really interesting. There have been a number of studies designed to settle the question. During the course of the research some interesting, and unexpected phenomena came to light. In the meantime, researchers studying primates discovered theat the rate of molecular evolution in humans and apes was slower than the rate of molecular evolution in monkeys....

Look for Part Two tomorrow (hopefully).

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Sunday, November 27, 2005

Frankenstein Has Tea

I had someone land at my site by doing a Google image search on "Karloff, Tea, Cigarette". Since I had mentioned on my Halloween post that this was one of my favorite pics, here it is:

The picture was taken on the set of Frankenstein during a break in filming. Note Boris Karloff is holding a tea cup in his right hand and Colin Clive has a cigarette in his mouth and is in the process of striking a match. The juxiposition of the image of Frankenstein (brutal, mindless murderer - or at least he is often portrayed that way) with the tea cup is priceless.

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Venom, Snakes and a Slapdown

As I mentioned in a previous post. Snake taxonomy has recently been completely revamped based on research on the evolution of snake venom. Zimmer has an interesting post on the subject. The Panda's Thumb has a post as well. Note comments 60039, 60220, and 60221. Note also the very diplomatic, but total, slapdown of those comments in 60050, 60089, and 60247. Classic! The moral of the exchange is that one should do ones research before trying to criticize.
There is also a thread on the same subject here. One intersting note concerning fossil snakes. This and this provide some interesting info on snake evolution.

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Saturday, November 26, 2005

Movie Meme

Tony at Milkriverblog has a movie meme he would like everyone to participate in. Tony explains:

Now they can name as many as they would like, but i'm asking for only one. They name it in a post, and i'll check all the blogs and collect the nominees and compile a master list here. They also should challenge their readers to post one also, and then notify me so i can add them to the master list.

I have three I would like to suggest. Two are science fiction, the third may or may not be fantasy.

1)The Phantom from Space. This movie is somewhat ahead of it's time. It starts with communications engineers looking for the cause of some interference. Along the way they come to the aide of a woman, her husband, and a friend. They had been attacked by a mysterious man with no face. As the police investigate it becomes clear thatt the police and communications engineers are looking for the same thing. A man from outer space. It also becomes clear that what is motivating the aliens behavior is the need to survive. You see his space ship is wrecked at the bottom of the ocean and the only thing he has left is his space suit which is rapidily running out of power, correct atmosphere, etc. The movie was made in 1953 when all men from outer space when all aliens were out to kidnap earth women for nefarious purposes, so it's sympathetic view is years ahead of it's time (don't see it again till Starman or ET).

2)The Magnetic Monster. In the 1950's most science fiction revolved around bug eyed monsters - either made in the lab or coming from outer space. Although, the magnetic monster was made in a lab it definately did not have bug eyes. The monster of the story is a weird radioactive isotope that sucks down massive amounts of energy and actually reproduces. The heroes of the story have to figure out a way to stop it before it destroys the world. It is a low budgett film by Curt Siodmak that was actually well done - although I don't think you will find it at any of the movie stores.

3)Secrets of the Roan Innish. What does a ten year old girl and seals have in common? And what's up with the mysterious "dark" branch of the family? Absolutely phenomenal! Great acting, great cinematography, great story. When it was over I found myself saying "It can't be over, I want more!" See it if you can.

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Friday, November 25, 2005

Transitions News

RPM at Evolgen has allowed me to cross post his series on "Detecting Natural Selection". I have decided to create a new page for genetics at Transitions. The first two parts of RPM's series can be found here.

I have also selected the next Site of the Week Check both out. Be sure to visit Evolgen while you are at it.

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Papers I have Read in the Last Two Weeks

Fry, B. G. and Wuster, W, 2004, Assembling an Arsenal: Origin and Evolution of Snake Venom Proteome Inferred from Phylogentic Analysis of Toxin Sequences. Mol. Biol. Evol. 21(5):870-883. Background for a post I was thinking about doing, but Zimmer beat me to it. May still do the post anyway.

Vidal, N. and Hedges, S. B., 2005, The Phylogeny of Squamate Reptiles (Lizards, Snakes, and Amphisbaenians) inferred from Nine Nuclear Protein-Coding Genes. C. R. Biologies 328:1000-1008. See above.

Bleiweiss, Robert, 1998, Slow Rate of Molecular Evolution in High-Elevation Hummingbirds. PNAS 95:612-616 Background for a post I'm working on.

Martin, A. P., Palumbi, S. R., 1993, Body Size, Metabolic Rate, Generation Time, and the Molecular Clock. PNAS 90:4087-4091. Same as the previous article, although it may be awhile before I post it. I'm thinking of going out and buying several books on the subject as I'm really developing an interest in the effects of body size, etc, on metabolism.

Seino, S., Bell, G. I., and Li, WH, 1992, Sequences of Primate Insulin Genes Support the Hypothesis of a slower Rate of Molecular Evolution in Humans and Apes than in Monkeys. Mol. Biol. Evol. 9(2):193-203. See above.

Fielding, S, Martill, D., and Naish, D., 2005, Solnhofen-Style Soft-Tissue Preservation in a New Species of Turtle from the Crato Formation (Early Cretaceous, Aptian) of North-East Brazil. Paleontology 48(6):1301-1310. I did a post on this a few days ago.

Bell, G. L., and Polcyn, M. J., 2005, Dallasaurus turneri, A New Primitive Mosasauroid from the Middle Turonian of Texas and Comments on the Phylogeny of Mosasauridae (Squamata). Netherlands Journal of Geosciences 84(3):177-194. I did a post on this as well. Strangely enough, it is relevant to the above two articles on snakes. I'll mention how it is relevant if I actually get round to writing the post. I say strangely because a paper I mentioned here has bearing on the above articles on body size, metabolic rates and molecular evolution.

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Turkey: A Thanksgiving Myth Debunked

Most of you are familiar with Tryptophan. It's the ingredient in turkey that is widely rumoured to put folks to sleep on Thanksgiving. Pure Tryptophan is a mild sleep inducing agent and because it is found in turkey, many believe that it is responible for many of the food induced coma's commonly experienced on Thanksgiving. According to National Geographic News this is a myth!

But tryptophan can't get to the human brain in large amounts when ingested as part of a massive Thanksgiving feast—it needs an empty stomach.

"Tryptophan is taken to the brain by an active transport system shared by a number of other amino acids [the chief components of proteins], and there's competition among them—like a crowd of people trying to get through a revolving door," said Simon Young, a neurochemist at McGill University in Montreal, Canada.

Consuming tryptophan-rich foods may cause blood levels of the amino acid to rise. But not enough tryptophan will reach the brain to have a sedative affect.

"Brain levels of tryptophan could even go down after a big meal because of the [amino acid] competition," Young said.

Apparently, even the amount of Tryptophan in turkey has been overstated:

Turkey isn't even unusually high in tryptophan. Many foods, such as beef or soybeans, boast higher concentrations.

So, why the need for a nap?

The slumber may be caused by the stressful hustle and bustle of the holidays, alcohol consumption, and the massive caloric intake of the year's biggest feast.

"There have been many studies citing a post-lunch dip in performance, from factory output to single-car accidents," McGill's Young explained.

"These things tend to peak in the early afternoon. A thousand-calorie lunch causes a sedative effect that a smaller meal doesn't have."

So the next time you slip into a coma on Thanksgiving day, don't malign the Turkey. Jest fess up and say "My relatives are stressing me out and I drank to much!"

Added Later: RPM at Evolgenexplains some genetics connected with tryptophan.

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More on KU

Recently, I posted on a class at KU called “Special Topics in Religion: Intelligent Design, Creationisms and other Religious Mythologies.” The class has raised the ire of the intelligent design community and conservatives in Kansas. Which is kid of shocking. ID advocates have made a big show of talking about how not teaching ID violates academic freedom and amounts to viewpoint discrimation. They constantly talk about how purveyors of "Darwinian ideology" are censoring and intimidating ID advocates into silence. Well:

And John Altevogt, a conservative columnist and activist in Kansas City, said Tuesday that state officials should require the university to change the name of the Department of Religious Studies to the “Department of Religious Intolerance.”

“If we can’t do that,” Altevogt said, “maybe we settle for some cuts in spending.”

Sen. Roger Pine, R-Lawrence, said he doesn’t believe KU’s move to offer the course should have a negative effect in the Legislature as long as the course is handled in a serious and intellectually honest way.

“They should be commended for taking the challenge — if it’s done in that manner,” Pine said.

But O’Connor said anything was possible in the Legislature.

“If they press forward in this area and continue to kick sand, the ultimate will be a negative of some sort,” she said. “I don’t know what the negative will be ... You can’t kick sand in someone’s face and then expect a positive. And that’s what this is — a sand-kicking contest.”


“Why poke a stick in somebody’s eye if you don’t have to?” she said. “If you’re going to have an intelligent design course and call it mythology, I think in the very least it’s a slap in the face to every Judeo-Christian religion that’s out there.”

Gee, I though ID had nothing to do with any religion, much less Judeo-Christian ones.

Altevogt was still angry.

“There’s nothing intellectually honest about this at all,” he said Tuesday. “This is purely hate-mongering, just for the purpose of hate-mongering. It’s not a religion class. It’s a class of religious intolerance.”

So there ya go. Create a class to explore intelligent design in an academically meaningfull way and the prevailing religious orthodoxy circles the wagons, starts making threats and is trying to intimidate Professor Paul Mirecki into silence. It is interesting to note that ID advocates always protest when people say ID is a way of sneaking religion into science class. ID doesn't say anything about who the designer is "could be space aliens" (if space aliens are the designers does that mean folks don't have to worship God and Jesus anymore?) yet the response to Professor Mirecki's class has come primarily from the conservative christian community. Why is that?

Red State Rabble has an interesting take on the subject as well.

Added slightly later: Thoughts From Kansa also has a couple of posts on the subject.

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Too Much to Blog About, Not Enough Time

Really, there has been an explosion of interesting stories that I'm hoping to blog about. I hoping to get to all of them by the end of the weekend. I'm pessamistic though because I keep finding interesting things to blog about quicker than I can actually post on them.

By the way, have you donated to Harry McDonald yet? I have!

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Wednesday, November 23, 2005

Donating to Kansas

I almost forgot... in line with this post. I have sent my donation to the Committee to Elect Harry McDonald.

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Tuesday, November 22, 2005

Way to Go KU!

"Teach the Controversy" is the battle cry of the Discovery Institute. Kansas University has taken them up on it:

“The KU faculty has had enough,” said Paul Mirecki, chairman of KU’s religious studies department. He said he planned to teach “Special Topics in Religion: Intelligent Design, Creationism and other Religious Mythologies” next semester.


Mirecki said the course would be capped at 120 students, exploring intelligent design as a modern American mythology. Intelligent design is the idea that life is too complex to have evolved without a “designer,” presumably a god or other supernatural being.

The course also will cover the origins of creationism, why it’s an American phenomenon, and why Americans have allowed it to pervade politics and education, Mirecki said. He said several KU faculty have volunteered to be guest lecturers.

“Creationism is mythology,” Mirecki said. “Intelligent design is mythology. It’s not science. They try to make it sound like science. It clearly is not.”

You'd think the DI would be elated! But instead they throw a hissy fit!

“I would predict that (Mirecki’s) effort will go down in history as one of the laughingstocks of the century,” said John Calvert, an attorney and managing director of the Intelligent Design Network in Johnson County.


“To equate intelligent design to mythology is really an absurdity, and it’s just another example of labeling anybody who proposes (intelligent design) to be simply a religious nut,” Calvert said. “That’s the reason for this little charade.”

Calvert questioned Mirecki’s expertise, saying the teaching of intelligent design requires an extensive understanding of evolution and science. (He's telling a half truth here, it does take a lot of time, effort and knowledge to debunk ID - afarensis)

“I think the guy is going to fall all over himself,” Calvert said. “I would love to go to his class and say, ‘Explain to me how DNA arose in the primordial soup?’”

John Altevogt, a conservative columnist and activist in Kansas City, said the situation was the equivalent of David Duke teaching about race relations or Fred Phelps teaching about homosexuality.

Teach the controversy indeed!
I guess the title of the article was correct after all ("KU class angers ‘design’ advocates, Course would be taught as religion, not as science")

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Monday, November 21, 2005

Magnetic Bacteria

The above is a picture of Magnetospirillum gryphiswaldense a unique type of bacteriathat is magnetotactic. That is it uses the earth's magnetic field to find suitable environmental conditions. How does it work? Well, Magnetospirillum absorb large amounts of iron to produce an oxide called magnetite. The magnetite is formed into magnetosomes which are strung out in a chain.

This raises two interesting questions. First, what are the genetics behind it? Second, how does the bacteria accomplish this? The two questions are related. Researchers, at the Max Planck Institute, first focused on identifying the part of the DNA that carried the code for magnetosome formation. They found a fragment containing about 25-30 different magnetosome genes. One gene had a product (MamJ) that was similar to proteins that control crystallization processes in bones, teeth and mussel shells among others. Once this gene was removed they discovered something interesting.

The picture on the left shows normal bacteria, the one on the right shows mutant bacteria with the Mamj gene disabled. Notice the magnetosomes form a straight chain in the normal but are clumped in the mutant. What was going on here? Researchers then used a relatively new technique called cyroelectron tomography to examine the magnetosome chain in more detail. This is what they saw:

The blue is cell membrane, the red are the magnetosomes, the green is a previously unknown filamentous structure (resembling a cytoskeleton)and the yellow is the MamJ product. Apparently, the MamJ product develops on the magnetosome and the filament and this is what allows them to form a chain. In the mutant bacteria, which lacks the MamJ, the magnetosomes clump toghether one they reach a certain size. This is fascinating, but there is an interesting evolutionary wrinkle. Some organisms, such as salmon and homing pidgeons, also orient themselves to magnetic fields. Interestingly, they also have magnetite chains in some of their tissue and may develop through similar mechanisms. I eagerly await further developments.

For more info:

Science Daily

The Press Release (where some of the pics and info for this post came from)

Magneto-Lab: Research(where some of the pics and info for this post came from)

The Research is also being published in Nature, Advanced Online Publication, November 20, 2005

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Sunday, November 20, 2005

Kansas Needs Your Help

Added Later: I'm keeping this at the top for awhile.

I don't know how many of my readers live in Kansas, but if you do I would like to direct your attention to two posts at Red State Rabble. In the first we learn:

"In private interviews with employees," reports Rothschild, "the transition team, appointed by Corkins after he was hired last month, has asked, 'What is your general reaction to school choice, charter schools and parental empowerment?'”

"Christy Levings, president of the Kansas-National Education Assn., said the question was unfair," according to Rothschild.

“'It’s a difficult position to put state employees in,' Levings said because Corkins is a known supporter of vouchers, which allows the use of state tax dollars to send students to private schools."

As the appointment of Corkins, the hiring of David Awbrey, and the contract with Harden demonstrate, political loyalty -- not competence -- will now be the standard by which all things are judged at the department of education.

I, for one find this appalling and urge you, if you live in Kansas, to stand up and make a difference. From the second post:

The painful irony for Kansans is that opposition to public education -- once the preoccupation of a few isolated individuals on the lunatic fringe -- is now being organized out of the State Board of Education and by the top administrators in the Kansas State Department of Education.

That is why it is absolutely essential for the people of Kansas -- the overwhelming majority of whom take justifiable pride in the state's history of support for public education -- to take the state school board away from the fanatics who now control it and put it back into the hands of experienced adults.

I urge those of you who don't live in Kansas to read these to posts and take notes because if this works in Kansas in will be showing up in your state next. It is time to stand up and put a stop to this kind of nonsense - whether you live in Kansas or not. To that end let's take Pat Hayes' advice and donate to those who are striving to keep rationality in education:

To win, McDonald believes he will have to raise nearly $100,000. He needs your help. RSR strongly urges supporters of public education in Kansas to support McDonald by writing a check to the Committee to Elect Harry McDonald and sending it to 11917 W. 143rd St., Olathe, KS 66062.

If you live out of state, as many RSR readers do, you should remember that much of the funding for the far right candidates will come from wealthy out-of-state donors who give regularly to right-wing causes.

Several blog sites have made much ado about supporting bloggers but this is so much more important. Please give what you can to the address above (Pat says he will be talking about other candidates in the coming weeks and I urge you to watch for them and donate whatever you can). I, personally, live from paycheck to paycheck but am going to donate $20 to Mr. McDonald out of my next paycheck (I'll let you know when this happens) and challange my readers to donate (no set amount - whatever you can) as well.

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This and That

Pharyngula links to an intersting version of the big bang.
He also links to a warning label generator here is my attempt:

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Saturday, November 19, 2005

Transitions: Site of the Week

I have instituted a new "Site of the Week" category over at Transitions (which I hope will actually be weekly).

You can find out about the first site here. As always if you have a post that you think will fit with the mission of Transitions drop me a line. For example, if somebody had an interesting post on theEvolution of the Cichlid Mandible... or some such (you can also consult the posts already up for examples of what I am looking for).

I am also on the look out for more sites to link to, please consult the list of links at Transitions to get an idea of what I'm looking for. I'm especially interested in finding the following: interactive sites, sites with activities that teachers can bring into the classroom and sites dealing with the evolution of organisms other than hominins. This later is particularly important since at the moment there is a pronounced bias towards human evolution. So, if you know of any good sites relating to the evolution of you favorite organsism (note: I also don't have much on invertebrates, viruses, etc.)leave a link in the comments section or email me. I should also mention that I'm looking for links on the "Cambrian Explosion".

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Most People Want Evolution Taught In Schools!

A recent poll by Scripps Howard/Ohio University finds that even though 54% of the people surveyed believe that "God" created the world in six days:

"Sixty-nine percent agreed that evolution is what most scientists believe, so it should be taught in public school science classes..."

Now the bad news. 20% think scientists are wrong about evolution and about half agree with Bush that Intelligent Design should be taught alongside evolution.

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I Know What Santa afarensis is Getting Me for Christmas

Cool, ain't it!

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Thursday, November 17, 2005

Intelligent Design and Human Origins:The Final Post

I have been discussing Casey Luskin's article "Human Origins and Intelligent Design" in a series of posts. My last one covered Luskin's views on Eocene primates. I'm going to skip his, brief, discussion of the Miocene and jump strait to the hominins. The first thing that stands out is his total misunderstanding of the role of Ramapithecus in current paleoanthropological thinking. Luskin's article was written in 2004, yet we still find him talking about Ramapithecus as a human ancestor. Once upon a time, Ramapithecus used to be considered a human ancestor (for example, by Richard Leakey in his book "People of the Lake: Mankind and it's Beginings"), however, by the 1980's molecular evidence and cladistic analysis indicated this was incorrect. As a matter of fact Ramapithecus, as a taxon, was sunk into Sivapithecus (a species related to the Orangutan).

It gets better. By 2004 the following species of early hominin were known:

Ardipithecus ramidus ramidus
Ardipthecus ramidus kadabba
Australopithecus anamensis
A. afarensis
A. garhi
A. barelgazeli
A. aethiopicus
A. robustus
A. africanus
A. boisei

Kenyanthropus platyops
Orrorin tugenensis

Yet all we here about from Luskin is A. afarensis, A. africanus, A. robustus and A. boisei (he does mention Ardipithecus ramidus). In reading the article, one gets the distinct impression that Luskin really doesn't understand the material he is discussing (more on this in a bit). After giving the creationist arguement about Oxnard an australopith locomotion. After which he starts in on "Lucy" :

Other recent studies have found that the handbones of Lucy are similar to those of a knucklewalking ape. (pg. 7)

At which point he cites two articles, one a 2000 paper by Collard and Aiello and the other a 1971 paper by Richard Leakey - the citing of which is an example of really poor scholarship. However, let's address the question head on. Assume that A. afarensis was a knucklewalker, does this rule out a possible ancestor-descendent relationship with Homo? This is a good example of where Luskin really doesn't understand the material he is discussing. Among primates three species knucklewalk. Chimps, gorillas and orangs (more or less). In chimps and gorillas, when knucklewalking, the weight is born on the middle phlanges

primarily of the second and third digits. Below is a picture of knucklewalking.

Technically, orangutans, when on the ground, fist-walk. Their hand is curled into a fist and the weight is primarily born on the proximal phlanges. Because of this chimps, gorillas and orangs have certain modifications to their hand and wrists to allow for stability and weightbearing. In chimps and gorillas the radius is concave and the distal edge projects downwards to form an edge which abuts a ridge on the scaphoid (in humans this is not the case - see the picture above). Below is a picture comparing the radius of a chimp, early australopiths and humans.

Additionally, the metacarpals have transverse ridges that abut the proximal phlanges and more or less lock them in place. Orangutans hands and wrists are more adapted to suspensory activity. One side note, pygmy chimps have hand and wrist morphology intermediate between Chimps and gorillas ont the one hand and orangs on the other. A. afarensis lacks these features (except perhaps the concave radius with a distal projecting edge). Molecular and anatomical evidence indicates humans are closely related to the african apes. In particular, humans are more closely related to chimps than to gorillas and are more closely related to african apes than to the orang. The larger question, then, is one of trait polarity and it's implications for human evolution. If the common ancestor of orangs, gorillas and chimps was a knucklewalker then the condition is a shared primitive trait in the apes and humans have a derived condition. It gets trickier. For example, if the common ancestor of chimps and humans was a knucklewalker and the common ancestor of gorillas and chimps was not what does that say? Well, this would imply that knucklewalking evolved independently in chimps and gorillas but was lost in humans. Either way, it has no impact on the question of whether A. afarensis and humans are evolutionarily related.
He then mentions semicircular canals, which I have discussed here.

Luskin then jumps to Homo habilis and again displays poor scholarships and a total lack of understanding of the material he is discussing. Consider the following:

H. habilis remains were first discovered in 1960, and were named in 1964 by famous paleoanthropologist Richard Leakey and his team. (pg. 9)

Hello, excuse me? Let's explore. A new Species of Genus Homo from Olduvai Gorge, Leakey, L. S. B., Tobias, P. V. and Napier, J. R. He actually cies two papers for the claim. One being Stern and Susman's paper on The Locomotor Anatomy of Australopithecus afarensis published in vol 60 of the AJPA (he gets the page numbers wrong in his citation by the way). I have a copy of the Stern and Susman article and nowhere in it do they say that Richard Leakey discovered Homo habilis since, of course, they both know Louis Leakey discoverd H. habilis.

Even worse is his mangling of Wood and Collard's paper "The Human Genus". At this point I had encountered so many errors and spent so much time tracking down sources that I just gave it up as being a bad job. I have heard people say debunking this kind of writing takes a lot more time and energy than it took to write it, but I didn't believe it until now. One thing more, though, Luskin makes much of the sudden emergence and rapid development of various groups of primates, hominins etc, and given Dembskii's recent preoccupation with Stephen Gould one wonders if the next incarnation of creationism/ID might not be some sort cheap imitation of punctuated equilibria. Might explain ID advocates recent attempt to say Gould didn't believe in natural selection.

If you wish to torture yourself with bad scholarship and worse paleoanthropology (most first year anthro students have a better understanding of the material) you can find Luskins article here.

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Wednesday, November 16, 2005

Turtle Fossils

While I'm on the subject of fossils...
The BBC has some interesting pics of fossil turtles.

This one is a juvenile:

From the accompanying article:

Representatives of the turtle lineage are known from the fossil record as far back as 200 million years. But these examples look more like tortoises, suggesting they were still very much adapted to life on land.

The latest find has front feet shaped like paddles, much like modern turtles.

Which kind of sounds like a transitional fossil to me, but I coould be wrong.

"Tortoises have very short foot bones and not very much soft tissue," lead author Sarah Fielding, of the school of Earth and environmental sciences at Portsmouth, told the BBC News website.

"This specimen has slightly longer foot bones and quite a lot of webbing in between."

Nope, I was right...

"We're fortunate the deposit it was found in has fine mud which has preserved the webbing - which is quite rare for turtles."

But the hind feet in this specimen seem to be more tortoise-like, suggesting this creature was not fully adapted to a marine lifestyle and spent some significant amount of time on land.

Researchers determined the turtle was a new species, which they named Araripemys arturi.

Read more!

New Transitional Fossil Found: Dallasaurus turneri

Added Even Later: John Wilkins at Evolving Thoughts has some interesting thoughts on the subject as well.
Added Later: The Hairy Museum of Natural History has more. Including links to pics of the fossil, the paper it was described in and more!

The mosasaurs are species of aquatic reptiles that are related to lizards (to be more precise the varanoid lizards - of which the Komodo dragon is a good example). During the upper cretaceous they reached their peak. Almost 20 genera are recognized for this period with the largest approaching 30 feet. They were ocean going carnivores that ate almost anything that swam in the sea. Below are some representitive species.

And here are some fossils.

One with a person in it for scale.

However, we are not concerned with one of the larger species. We are interested in a little three foot long specimen discovered in Texas. Most Mosasaurs have flippers, Dallasaurus turneri has limbs similar to other land lizards. From Science Daily:

Until the discovery of Dallasaurus, however, only five primitive forms with land-capable limbs were known, all of them found in the Middle East and the eastern Adriatic.


The advanced fin-bearing mosasaurs have been grouped into three major lineages. Although a small number of primitive mosasaur have been known to retain land-capable limbs, they were thought to be an ancestral group separate from the later fin-bearing forms. Dallasaurus represents a clear link to one lineage of the later forms and the first time researchers can clearly show mosasaurs evolved fins from limbs within the different lineages of mosasaurs.

I was unable to find any pictures of the fossil, but here is a reconstruction of what it is believed to look like.

For a quick overview of Mosasaurs you can do no better than Oceans of Kansas

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Monday, November 14, 2005

“The size of these specimens – the crown of the molar, for instance, measures about an inch across – helped us understand the extraordinary size of the primate" so this tooth is about twice the actual size!

The above are pictures of Gigantopithecus fossils. Gigantopithecus is a genus composed of two species G. blacki and G. giganteus. G. giganteus lived during the Late Miocene/Early Pliocene and G. blacki is known from the Pleistocene and both are generally considered to be the largest primates ever. Incidentally, G. giganteus is considered to be directly ancestral to G. blacki (so they are really a chrono species). They are estimated to have reached 10 feet in height and about 1,200 pounds in weight. Most specimens come from the Siwalik hills in Pakistan and India. Currently it is thought that Gigantopithecus is actually related to the orangutans, via Sivapithecus (a widespread genus that contains all of the material previously reffered to as Ramapithecus - but that's a long story). At any rate, recent research has thrown an interesting wrinkle into the story:

Using a high-precision absolute-dating method (techniques involving electron spin resonance and uranium series), Jack Rink, associate professor of geography and earth sciences at McMaster, has determined that Gigantopithecus blackii, the largest primate that ever lived, roamed southeast Asia for nearly a million years before the species died out 100,000 years ago. This was known as the Pleistocene period, by which time humans had already existed for a million years.

So it's possible that anatomically modern humans would have encountered them (certainly H. erectus would have also).

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Saturday, November 12, 2005

Papers I Have Read This Week

The Position of Hippopotamidae Within Cetartiodactyla
PNAS 102:1537-1541. Fascinating discussion of the phlogeny of Hippos (apparently, they are related to whales). I'll probably do a post about it - maybe on Transitions

Coding Sequences of Functioning Human Genes Derived Entirely from Mobile Element Sequences.
PNAS 101:16825-16830. The title pretty much says it all.

The Rate of DNA Evolution: Effects of Body Size and Temperature on the Molecular Clock
PNAS (yes I've been reading a lot of PNAS lately) 102:140-145. Interesting article that ties in with this post. It explores the impact of body size, temperature and metabolic activity (the first two affect the third) on nucleotide substitution rates. Absolutely fascinating and I will be doing a post on it.

Molecular Origins of Rapid and Continuous Morphological Evolution.
ONAS 101:18058-18063. Pharyngula did a great post on this paper.

Modeling Gene and Genome Duplications in Eukaryotes
PNAS 102:5454-5459. Actually, I'm still in the process of reading this one.

A Hominid from the Lower Pleistocene of Atapuerca, Spain: Possible Ancestor to Neandertals and Modern Humans.
Science 276:1392-1395. Discussion of the Gran Dolina fossils. Places them in a new species (Home antecessor).

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Thursday, November 10, 2005

Evo-Devo and Cichlids

Added Later: Pharyngula has a fascinating post on the same subject. A must read!

The above is a picture of a cichlid. I have blogged about them before. A new studies illustrates the link between evolutionary development and embryonic development in the jaws of cichlid fishes. From Science Daily:

In a study illustrating the apparent linkages between the evolutionary development and embryonic development of species, researchers have uncovered the genetic elements that determine the structure and function of a simple biomechanical system, the lower jaw of the cichlid fish. In addition, they've shown that increasing expression of a particular gene in an embryo can lead to physical changes in the adult fish. The results appear in the November 11, 2005 issue of the Proceedings of the National Academy of Sciences.

Researchers predicted that functionally or developmentally related componets of the cichlid jaw would be controlled by the same set of genes. The researchers compared two species of cichlid from Lake Malawi:

One species had force modified jaws that are more adept at biting prey; the other had speed modified jaws, which are more accomplished at using suction to feed on plankton. Each jaw system is essentially a lever system made up of one out-lever and two in-levers.

The predator cichlid is the first picture above. Below is a picture of the plankton eating cichlid.

But when the researchers mapped the part of the genome that controlled the system they found that the levers were controlled by genes on different chromosomes (i.e. the short lever genes are on a different chromosome than the long gene). Or to phrase it another way:

“We were surprised to see that the genetic basis of components involved in opening the jaw is independent of the jaw-closing system,” said Streelman. (one of the researchers involved - afarensis)

Taking it a step further:

In another part of the study, researchers showed that the gene bmp4 is a major factor in controlling the jaw-closing system. When the team injected bmp4 protein into the developing embryos of another fish species, the zebrafish, they saw that the mechanical advantage (and thus the biting power) of the jaw increased.

The researchers sum up their work thusly:

"We've demonstrated that important functional differences operating in adult organisms are elicited by changes in early development. Our next goal is to understand the genetic bases underlying the differences between the simple biomechanical system of the lower jaw and complex systems of the anterior jaw in these fish."

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Intelligent Design Thread on the St. Louis Post-Dispatch Blog: Could it be Kent Hovind?

The St. Louis Post-Dispatch Blog has another thread on Intelligent Design The question posed to start the thread was:

Supporters of the change (introduced by the Kansas Board of Education - afarensis) say it promotes “academic freedom.” Opponents, that it unconstitutionally will introduce religion into a public school framework.

Further, the standards would rewrite the definition of science, so that it is no longer limited to the search for natural explanations of phenomena.

What is science? Do you have a clear idea of the definition of science? What makes one thing a scientific theory, but another religious dogma?

It has attracted the usual hodgepodge of people both for and against, but one comment (257) stands out. It reads, in part:

The test of any theory is whether or not it provides answers to basic questions. Some well-meaning, but misguided, people think evolution is a reasonable theory to explain man’s questions about the universe. Evolution is not a good theory—it is just a pagan religion masquerading as science. The following questions were distributed to the 750-plus people who attended my debate at Winona State University in Winona, Minnesota, on January 9, 1993. (The videotaped debate is #6, $9.95.) Questions added since the debate remarked with an asterisk (*).

1. Where did the space for the universe come from?

2. Where did matter come from?

3. Where did the laws of the universe come from (gravity, inertia, etc.)?

4. How did matter get so perfectly organized?

5. Where did the energy come from to do all the organizing?

6. When, where, why, and how did life come from non-living matter?

7. When, where, why, and how did life learn to reproduce itself?

8. With what did the first cell capable of sexual reproduction reproduce?

9. Why would any plant or animal want to reproduce more of its kind since this would only make more mouths to feed and decrease the chances of survival? (Does the individual have a drive to surviv e, or the species? How do you explain this?)

10. How can mutations (recombining of the genetic code) create any new, improved varieties? (Recombining English letters will never produce Chinese books.)

After scrolling past a bunch more of this junk you find the comment mas made by Matthew. Click on the name Matthew and you end up at I vaguely recall seeing a list of questions exactly like this and I want to say it was by Kent Hovind - does anybody out there have any info on this list of questions?

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Crocodiles and Godzilla!

The above is a picture of a new fossil crocodile discovered in South America. Christened Dakosaurus andiniensis, the crocodile lived about 135 mya.

Here's another pic.


"This species was very unusual, because other marine crocodiles that were around at the same time had very delicate features – long, skinny snouts and needle-like teeth for catching small fish and mollusks," said Ohio State University researcher Diego Pol, who determined the crocodile lineage. "But this croc was just the opposite. It had a short snout, and large teeth with serrated edges. It was definitely a predator of large sea creatures."

It has been nicknamed "Godzilla". It sheds some interesting light on crocodile evolution:

"This [animal] forms a very distinct lineage that appears early on in the evolutionary history of crocodiles—invading the sea and showing outstanding adaptation to the marine environment," Pol said.

Unlike today's crocodiles, Dakosaurus andiensis lived entirely in the water. It measured 13 feet (4 meters) from nose to tail. Instead of legs, Dakosaurus had four paddle-like limbs, used mostly for stability. A fish-like tail propelled the beast through the water.

What made it especially unusual was its snout and teeth.
The animal's unusual features suggest that it had completely different feeding habits from its relatives. While other marine crocs fed on small fish, Dakosaurus hunted for marine reptiles and other large sea creatures, using its jagged teeth to bite and cut its prey.

"The most perplexing thing about the animal is that its head shape does not appear to be well suited to a fast swimming crocodilian, because rather than being streamlined, it is somewhat high and flattened from side to side," said Clark, who was not involved with the research.

"Presumably it moved its head mainly up and down rather than sweeping it from side to side, like fish-eating crocodilians."

New Scientist also has a story on it.

Here is another pic:

Added Later: Welcome Pharyngulans! I have added some more stuff below. Also, for your viewing pleasure (and to satisfy those unhealthy cravings for squid pictures here is a link to the video).

And yet more:

A closer view of one of the pics above:

The relationship between Dakosaurus andiniensis and other crocodylians:

The original press release can be found here

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Humboldt Squid Video

National Geographic has an interesting story on filming Humboldt Squid - complete with video here

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Tuesday, November 08, 2005

Intelligent Design and Human Evolution

The Dover trial is in the hands of the judge and in Kansas the fundies have approved the destruction of their education system. Meantime, Dembski is hallucinating loudly about the stunning legal strategy he provided the Thomas More Law Center (giggle), apparently we have him to thank for the endless amusement obtained from reading the transcripts of the trial - available here.
I think the scientists came off just a little bit better the Dembski's people (giggle).

At any rate, now seems to be a good time to continue my series on Intelligent Design and Human Evolution.

The Fossil Record of Non-Hominid Primates

As I pointed out, in a very simplistic overview here, here and here the study of primate evolution is quite rich with many theories, debates and fossils. How does Luskin describe this? First, it is immediately obvious that Luskin does not really understand the material he is writing about. For example he states that the "...standard primate phylogeny, constructed by comparing DNA sequences of living primates..."(pg. 4). Well, no, actually primate phylogeny was created based on fossil evidence. When biochemical and anatomical studies of living primates started being used it led so some conflict with the paleontological evidence. Then he sites the Encyclopedia Britannica to support his contention that primates fossils from 40 mya are rare. Then he goes into a discusion of some the work by R. D. Martin. For example, he states that Martin found that "...many characteristics linking adapid fossils with simians are so common in mammals, and primates inparticular, that they cannot serve as conclusive evidence of an evolutionary link." (pg. 4) Anyone who read my post on defining primates will immediately recognize this. Luskin here completely misunderstands the discussion. After this, which completely dismisses a large amount of primate evolution, Luskin moves on to anthropoid origins. Which consists of a few remarks about Parapithecus and Aegyptopithecus. So lets talk about anthropoids. The earliest evidence of anthropoids comes from the Oligocene deposits in the Fayum, Egypt. So far seven genera and 12 species have been named as follows:

Family Parapithecidae

Family Propliopithecidae
(both of which are catarrhines - or old world monkeys)

Family Cebidae
Tremacebus (a new world platyrrhine from Patagonia)

Family incertae sedis
Branisella (found in Bolivia)
Dolichocebus (found in Patagonia)

Infraorder incertae sedis
Amphipithecus (found in Burma and considered to be a transitional fossil linking adapids and higher primates)
Pondaungia (found in Burma, also considered to be a transitional fossil linking adapids and higher primates)

Family Tarsiidae

Not to mention the the most recent find.

There are quite a few anthropoid features in the Fayum primates (metopic suture that fuses early in life, almost complete postorbital closure, fused mandibular symphysis, etc) as well as some primitive retentions (some have nontubular ectotympnics and relatively small brains). There are four competing phylogenies for the above groups, which I won't go into, suffice to say there is more to anthropoid origins than Luskin would have you believe (and I haven't even mentioned the origins of new world monkeys).

Tomorrow: Early Hominid Fossils and Taxonomy.

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Sunday, November 06, 2005

New Posts at Transitions

I have slightly updated two of my recent posts on primates and posted them at Transitions. I am hoping to have the third up tomorrow. I have also found several interesting sites and will be adding them to the links section as well. In the meantime, I'm always on the lookout for new material or links. If you have anything you think fits in feel free to contact me!

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My Take on The National Geographic Home floresienses Show

First off, enough with the cheesy CGI dramatizations! Really, they added nothing and took time away from actually imparting information. I think the producers must have spent too much time watching shows about dinosaurs.

Having said that, it was actually okay. Parts were actually filmed on Flores and in Ling Bua (which we learned how to pronounce). There were sections on the discovery, on Falk and her work (including some other neuroanatomists), on how Homo erectus might have got to Flores (which was one of the more interesting parts), island dwarfing, and the eventual fate of the "hobbits" - which included a brief discussion of the Abu Gogo.

It was obviously filmed well before the recent Nature article as in the article the discoveres moved away from the interpretation of H. floresiensis as H. erectus selected for small size.

Mrs. afarensis and my 15 year old both found it interesting.

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Saturday, November 05, 2005

Papers Read This Week

Aydin over at Snail's Tales has a post up about the papers he has read this weak and it seemed like a good idea so I'm doing the same.

Martin, R. 1986. Primates: A Definition. In Major Topics in Primate and Human Evolution, ed B. Wood, L. Martin, and P. Andrews, pp 1-31, Cambridge Univ. Press. An interesting discussion of how to define primates. Also has some interesting ideas on the primates fossil record.

Rassmusen, D. T. 1986. Anthropoid Origins: A Possible Solution to the Adapidae-Omomyidae Paradox. J. Hum. Evol. 15:1-12.

A Toxic Mutator and Selection Alternative to the Non-Mendelian RNA Cache Hypothesis for hothead Reversion by Comai and Cartwright. Discusses some interesting genetics in Arabidopsis thaliana.

EST Analysis of the Cnidarian Acropora millepora Reveals Extensive Gene Loss and Rapid Sequence Divergence in the Model Invertebrates Subject of some controversy since a post on a creationist blog was refused at 'Circus of the Spineless". So I decided to track it down to see if what it was about.

Metazoan Evolution: Some Animals Are More Equal than Others I decided to do a little more research on the subject and this paper puts it into context. Seems to me ID types should do a little bit more research rather than stopping at whater phrase reinforces their preconceived notions.

Andrew, P. 1995. Ecological Apes and Ancestors. Nature 376:555-556. Cited by Luskin, will have more to say about it in my next post - but, again, ID types really need to do a bit more research before they start citing articles.

Unknown, 'Deviant' Burials Reveal Death on the Fringe in Ancient Societies. Science 310:613. Interesting discussion of some unusual burials in England - and the light they cast on the standard practive of examining "status burials" in anthropology.

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Homo floresiensis on the National Geographic Channel

Tomorrow at 7:00 the National Geographic channel is airing a program on Homo floresiensis. Looks like it is going to be interesting.

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Thursday, November 03, 2005

Get Your Own Pirate Name, Arrrgh!

I discovered this at a blog called Pen to Paper.

My pirate name is:

Iron Tom Bonney

A pirate's life isn't easy; it takes a tough person. That's okay with you, though, since you a tough person. You can be a little bit unpredictable, but a pirate's life is far from full of certainties, so that fits in pretty well. Arr!

Get your own pirate name from

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Bush, Cronies and Intelligence

Now I'm really scared! According to Newsweek Bush has appointed nine campaign donors (who laid out hundreds of thousands of dollars on the Bush campaign) to the Foriegn Intelligence Advisory Board:

After watching the fate of Michael Brown as head of FEMA and Harriet Miers as Supreme Court nominee, you might think the president would be wary about the appearance of cronyism—especially with a critical national-security issue such as intelligence. Instead, Bush reappointed William DeWitt (afarensis - one has to wonder if this is the same Bill DeWitt who is a part owner of the St. Louis Cardinals?), an Ohio businessman who has raised more than $300,000 for the president’s campaigns, for a third two-year term on the panel. Originally appointed in 2001, just a few weeks after the 9/11 attacks, DeWitt, who was also a top fund-raiser for Bush’s 2004 Inaugural committee, was a partner with Bush in the Texas Rangers baseball team.

Other appointees included former Commerce secretary Don Evans, a longtime Bush friend; Texas oilman Ray Hunt; Netscape founder Jim Barksdale, and former congressman and 9/11 Commission vice chairman Lee Hamilton. Like DeWitt, Evans and Hunt have also been longtime Bush fund-raisers, raising more than $100,000 apiece for the president’s campaigns. Barksdale and five other appointees—incoming chairman Stephen Friedman, former Reagan adviser Arthur Culvahouse, retired admiral David Jeremiah, Martin Faga and John L. Morrison—were contributors to the president’s 2004 re-election effort.

To be fair Clinton also appointed campaign donors to the same committee - two of them! The some of Clintons other appointees are:

"...former chairman of the Joint Chiefs of Staff Adm. William Crowe, former Defense secretary Les Aspin, former House speaker Tom Foley and former GOP senator Warren Rudman."

What is the purpose of the Foriegn Intelligence Advisory Board?

According to the White House, the intelligence advisory board offers the president “objective, expert advice” on the conduct of foreign intelligence, as well as any deficiencies in its collection, analysis and reporting. Created during the Eisenhower administration, the board has played a role in determining the structure of the intelligence community. Indeed, its members have been considered important presidential advisers, receiving the highest level security clearance and issuing classified reports and advice to the president.

So one naturally has to ask "Who do you trust more on national security?"

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Adapidae, Omomyidae and Anthropoid Origins

The Eocene saw the rise of the euprimates (a term coined by Elwyn Simons). An alternative term is "primates of modern aspect". Going back to R. D. Martin's definition of fossil primates the euprimates share claws replaced by nails, opposable hallux (big toe) and postorbital closure (among other things) in common with all modern primates.The euprimates are divided into two families, the adapidae and omomyidae. The adapidae are composed of two subfamilies: nothartinae (5 genera) and adapinae (14 genera). The omomyidae are divided into three subfamilies: anaptomorphinae (15 genera), omomyinae (12 genera) and microchoerinae (4 genera) Plus two species (Arapahovius and Loveina) of uncertain affinities (for those who know something of taxonomy they are Omomyidae incerta sedis).

In general, Omomyids are tarsierlike in their morphology. For example, the dental formula (which gives the number of each type of tooth) is often similar (in particular the lower dental formula is sometimes 1 incisor, 1 canine, 3 premolars and 3 molars - as seen in tarsiers). The crania have tapered snouts and the ectotympanic bone is tubular - as in tarsiers. The nasal and olfactory regions are diminished in size and the eye orbits are expanded.

The adapids, on the other hand, are generally considered to be related to lemurs. They have a divergent hallux, flattened nails on the digits. Some (such as notharctus)have a postorbital bar and a petrosal bulla. Encephalization quotients (a ration of brain and body weight) have been calculated ad are withing the range of other Eocene mammals and are slightly lower than say, the Oligocene anthropoid Aegyptopithecus. In the middle ear region they bear some resemblance to lemurs. The ectotympanic bone (which supports the tympanic membrane) is variable in adapids ranging from a free ringlike structure (as in lemurs) to one that is expanded to form part of the lateral bull wall (as in lorises and Aegyptopithecus).

The morphology of both leads to several interesting problems. First, what are the phylogenetic relationships? There are three competing theories.

1) Omomyids share some characteristics with plesiadapiformes and at one time the plesiadapiformes were thought to have given rise to omomyids. In this theory the adapids were considered ancestral to anthropoids and the prosimians (other than tarsiers).

2) Since no shared derived characters link tarsiers and anthropoids to the other prosimians it has been suggested that plesiadapiformes gave rise to the euprimates which split into two branches. One branch was composed of adapids, lemurs and lorises, the other was composed of omomyids, tarsiers and anthropoids. In this theory, tarsiers are more closely related to omomyids than to anthropoids.

3)A variant of number 2, except tarsiers are more closely related to anthropoids than they are to omomyids.

There is a further complication. In both 2 and 3 above tarsiers are grouped with anthropoids and adapids are grouped with lemurs and lorises. The problem is adapids share quite a few traits with anthropoids, tarsiers share some traits with anthropoids but not lemurs and lorises. Paleontological data supported a linking of adapids and anthropoids. Comparitive anatomy (hemochorial placenta, presence of a retinal fovea, for example) and biochemical data supported a relationship between tarsiers (and consequently omomyids) and anthropoids. This led to something of a stalemate. If tarsiers (and hence omomyidae) were more closely related to the anthropoids (as the anatomical and biochemical data suggested) then adapids (as the paleontological data suggested) couldn't be. Which was right. A very intersting solution to this problem was presented by Gingerich and Schoeninger in 1977. The suggestion wasn't paid much attention to until 1986, when Rasmussen (in his 1986 paper "Anthropoid Origins: A Possible Solution to the Adapidae-Omomyidae Paradox") revived it. Grant the paleontological evidence that relates the omomyidae to tarsiers and adapidae to anthropoids. Lemurs and lorises would then form a sister group to both the omomyidae-tarsier group and the adapidae-anthropoid group. Consequently, tarsiers would be more closely related to anthropoids than to lemurs and lorises - which satifies the anatomical and biochemical evidence and the omomyid-tarsier and adapid-anthropoid groups could still be kept - satisfying the paleontological evidence. It's a good theory, unfortunately, one small fact stands in the way. This is the traits which seem to relate adapids to lemurs and lorises. In this theory, the traits relating adapids to lemurs and lorises are due to parallel evolution. Which has raised some objections since parsimony requires little or no parallel evolution.
It's been my experience that these kinds of situations come up a lot in primate - and human - evolution. No matter what phylogenies you create parallel evolution always comes into play. Personally, I consider a certain amount of parallel evolution to be a fact of life in primate evolution.

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Wednesday, November 02, 2005

A Slight Delay

I'm still Working on the post on Adapidae, Omomyidae and Anthropoid Origins. It should be ready tomorrow.

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NPR, Wickipedia and Luskin: A Little Snark

I know I'm getting a little ahead of myself but I couldn't resist this. I was listening to Talk of the Nation on NPR today. They were doing a section on Wickipedia. They were talking to a person who called in named Rick, who said he always writes nasty notes saying bad resources when his students used Wickipedia as a reference. Jimmy Wells - who has something to do with Wickipedia - agreed saying he frequently gets emails from college students complaining because they got F's for using Wickepedia. His response was "You are in college now, you shouldn't be citing an encylcopedia at all" (This exchange occurs from around 12:50 - 14:00 in the audio file).

I find this amusing because Casey Luskin, in his paper "Human Origins and Intelligent Design" says that some of the earliest anthropoid fossils are known only from jaw fragments. His source? Encyclopedia Brittanica - GIGGLE - 1984 edition!
BWA HAHAHAHA....afarensis breaks down in hysterical laughter...

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Tuesday, November 01, 2005


I examined several definitions of the order primates in a previous post and looked at how any definition of primates has to be constricted when applied to the fossil record. In particular, the closer one gets to the common ancestor between primates and other mammals (insectivores for example) the harder it becomes to tell what is a primate and what is not.

The earliest identifiable primates are the plesiadapiformes. The plesiadapiformes occur from the mid Paleocene to the Eocene (from about 65 mya to about 53 mya). They inhabited both North America and Europe. The plesiadapiformes are an infraorder composed of six families and almost forty genera. The families are:

1) Plesiadapidae (five genera)
2) Carpolostidae (three genera)
3) Saxonellidae (one genus)
4) Microsyopidae (24 genera)
5) Paromomyidae (three genera)
6) Picrodontidae (two genera)

The phylogeny of most of these groups has been worked out in greater or lesser detail. Consider the Plesiadapidae. The earliest genus was Pronothodectes. In North America the earliest member of this genus was Pro. matthewi. Pro. matthewi gave rise to Pro. jepi. From here it gets complicated. Pro. jepi gave rise to two different groups, Nanodectes and Plesiadapis. The Nanodectes lineage goes as follows: N. intermedius, N. gazini, N. simpsoni, and N. gidleyi. The Plesiadapid branch goes as follows: Ples. praecursor, Ples anceps. Ples anceps gave rise to two lineages. The first goes: Chiromyoides minor, C. caesor, C. potior, C. major. The second lineage of Ples. anceps goes as follows: Ples. res, Ples. churchilli. Ples. churchilli also split into two lineages. The first goes: Ples. fodinatus, Ples. dubius. The second lineage is Ples. simonsi, Ples. cookei. The phylogeny of the other families is equally complicated.

Comparitive work on modern primate dentitions has allowed us to come up with some general guidelines on determining things like diet. Based on this we say that the plesiadapiformes were primarily insectivorous with diets resembling modern prosimmians such as lemurs and galagos. However by the late Paleocene - Early Eocene some plesiadapiformes were adopting diets of fruit or leaves.

How are plesiadapifomes related to later primates? There are actually three different views on this question. One view is that plesiadapiformes are not primates because they are distinct from later primates. A second view places them in a suborder with tarsiiformes (because both groups share some traits in common - enlarged, protruding incisors, similar configurations of inner ear anatomy among others). A third view is that they are the earliest primate radiation (because they have primatelike teeth that make them important for understanding primate origins).

Tomorrow I will look at Adapids, Omomyids and anthropoid origins. On Thursday I will resume the discussion of ID and human origins.

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