Tuesday, May 31, 2005

Yet More on New World Origins

According to this article in Science Daily. Humans arrived in america 12,000-14,000 years ago. The interesting part is how the estimate was determined.

"The estimated effective size of the founding population for the New World is about 70 individuals," Hey said. "Calculations also showed that this represents approximately 1 percent of the effective size of the estimated ancestral Asian population."

"Effective size" in population genetics is often thought of as the number of adults of reproductive age. One rule of thumb is the effective size might be about one third of the 'census population size' which, in this case, comes out to about 200 people.

In addition to population size, Hey's rigorous and complex methodology also generated historical estimates of when the divergence occurred. His dates are consistent with much of the archaeological record -- in the range of 12,000-14,000 years ago.

The full article will be published in the June edition of PLoS Biology. I can hardly wait!

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Monday, May 30, 2005

Biology and Machines: Part II

Intelligent Design advocates like to make an analogy between cellular processes and machines. For example Behe says:
And in the past 50 years, science has discovered that at the very foundation of life there are sophisticated molecular machines, which do the work in the cell. I mean, literally, there are real machines inside everybody’s cells and this is what they are called by all biologists who work in the field, molecular machines. They’re little trucks and busses that run around the cell that takes supplies from one end of the cell to the other. They’re little traffic signals to regulate the flow. They’re sign posts to tell them when they get to the right destination. They’re little outboard motors that allow some cells to swim. If you look at the parts of these, they’re remarkably like the machineries that we use in our everyday world.
The argument is that we know from experience that machinery in our everyday world that we use in our everyday world required design, required an intelligent agent that put it together, who understood how it was going to be used and who assembled the parts. By an inductive argument, when we find such sophisticated machinery in other places too, we can conclude that it also requires design. So now that we found it in life and in the very foundation of life, I and other ID advocates argue that there is no reason to not reach the same conclusion and that in fact, these things were indeed designed.

Actually the correct conclusion would be that since all the machines we are familiar with were designed by humans, cellular machines were designed by humans as well - but note the shifting language of the premise.

Also here Behe says:

In many biological structures proteins are simply components of larger molecular machines. Like the picture tube, wires, metal bolts and screws that comprise a television set, many proteins are part of structures that only function when virtually all of the components have been assembled.

And here is Calvert:
We intuitively infer design when we observe the awesome complexity of the living information processing systems that comprise life. When we look into the black box of the cell we see a biological language, input devices, application programs, information processors, output devices, and systems designed to collect and process energy, make decisions and direct the construction, maintenance and operation of cellular machines and systems. DNA is a blue print that has a semantic or meaningful characteristic found in any writing produced by a mind. That semantic characteristic has not been explained by natural law and chance. Non-natural machines and information processing systems are the kinds of effects that are produced only by human minds. Hence, analogy leads to a reasonable inference that intelligence may also be the cause of similar biological machines and information processing systems.

So, how acurate is the analogy? Let's look at protein synthesis. Before proceeding, however, let me mention that the following synopsis is drawn from Genes VI by Benjamin Lewin and Molecular Biology of the Cell by Alberts et al. Any mistakes (and I hope there are few) are mine.

Ribosomes Posted by Hello

Anyone who has had biology knows the process (the picture above is a graphic overview of the process). The DNA helix unwinds, the mRNA makes a complementary template, ribosomes bind to the mRNA strand and tRNA brings the amino acids that will form the protein. This is the way it is usually presented (with a little more detail) and it all sounds very straight forward and machine like. In reality, there is a lot more to the process than that. In bacteria free RNA polymerase collide randomly with DNA , with most sticking very weakly to the DNA. When the RNA polymerase hits the promotor region, however, it binds tightly and transcription begins (which in and of itself is a good argument against the whole notion of irreducible complexity - which is related to the machine analogy).
In eucaryotic cells (cells with a nucleus) the transcription part of the process occurs in the nucleus. The DNA strands are opened by an RNA polymerase which exposes a short section of nucleotides (I'm still simplifying greatly) . The RNA polymerase then binds incoming ribonucleoside triphosphate monomers to form a chain. Once a RNA chain is completed it moves out in the cytoplasm for the translation process. It is here where I really want to pick up the story in more detail.
In order for the translation process to occur the mRNA molecule has to be unwound and there are several factors ( called, in eucaryotic cells, eIF-4, eIF-4A and eIF-4B) that actually start unwinding the mRNA molecule at the 5' end.

mRNA Posted by Hello

Ribosomes then attach to the 5' end and migrate towards the initiator codon - a sequence of the three bases AUG. The distance between the 5' end and the initiator codon varies between 50 and 1000 bases (imagine if the timing chain on your car displayed similar variation in where it was set - while the car was running, would it still run?). As it moves down the mRNA the ribosome occasionally encounters obstacles - called secondary structure hairpins - that prevent it from moving further. At that point the ribosome disassociates into it's two smaller subunits and the process starts over again (imagine if you car had a blocked gas line - could it over come that and continue running?). The optimum start sequence is GCCA/GCAUGG. The A or G three sequences before the start codon and the G immediately after are particularly important, they increase the efficiency of translation by a factor of 10 (which would be like having a car that got 10 mpg when you put regular in it but 100 mpg when you put unleaded).

tRNA Cloverleaf Posted by Hello

Okay, we have the ribosome at the initiator sequence. What happens next? Well, the initiator sequence (AUG) actually codes for methionine and two different types of tRNA can carry it. One type of tRNA is used in initiation and one type is used in elongation. If you look at the picture above at the top of the picture (labeled acceptor region) the initiator would read ACCA-met-formyl. The anti-codon arm would have 3 G-C pairs in the stem. This is where things really get interesting. Although I mentioned above that the initiator site is AUG, the initiator tRNA can also recognize GUG and UUG. The kicker is that when GUG is used elongation efficiency is reduced by half and when UUG is used elongation is reduced by half again (it would be like if your car ran okay when gas was used as fuel, half as well if beer was used and a quarter as well if water was used - but your car don't work like that does it?). The process is even more variable (that's an important word I will get back to later). I mentioned above that the initiator tRNA has a formyl group on it, but this is actually not necessary, but it does increase the efficiency with which tRNA is bound by a factor (IF-2 for those that know a lot about this) that aids the process. One final wrinkle before I proceed to a description of the process itself. The last two bases in the acceptor stem of the initiator tRNA are unpaired. This prevents the initiator tRNA from being used in elongation. Mutations, however, frequently occur which create a base pair in this position and allow it to function in elongation (in my opinion this undermines everthing Dembski is arguing for and the whole notion of irreducible complexity - but I'm not a biologist so I could be wrong).

Translation Posted by Hello

So, shall we build a protein? The top portion of the above picture shows a mRNA strand with an intact ribosome. This is about half a step ahead of where we need to be. Ribosomes are composed of two units - a small and a large which exist in a pool of free ribosomes. Initiation of synthesis is undertaken by the separate subunits. The small subunit binds to the the mRNA and travels to the initiator region. At this point the P-site (see picture above) on the ribosome lies over the initiator region on the mRNA strand forming an initiation complex. The only tRNA that can join the complex, at this point, is the initiator tRNA. The larger subunit joins the complex and makes the A-site available for a tRNA complementary to the second codon on the mRNA. This also is quite variable. Sometimes the process stalls and the the subunits and tRNA are released and the process starts over. Assuming it continues, the tRNA in the P-site transfers it's product to the tRNA in the A-site and the ribosome moves forward one codon. This moves the tRNA in the A-site to the P-site making room for another tRNA in the A-site. The previous occupant of the P-site is released via a third site on the ribosome called the e-site. Here again, there is some variability. Sometimes the wrong tRNA enters the A-site, binds temporarily and is released. Ocassionally, a tRNA enters the A-site with four codons instead of the normal three. Most of the time it is released but occasionally, it's product is incorporated into the protein. At any rate, the ribosome travels down the mRNA strand until it reaches the termination codon, at which point the finished protein is released and the ribosome is released back into the pool. The mRNA usually has more than one ribosome traveling down it and after a while degrades.
The picute below is the real thing. In the bottom portion you can see ribosomes (the round things) traveling down a mRNA strand. Sticking out of the ribosomes are long strings - which are actually proteins in the making ( I don't see any machines, do you?)

Elongation Posted by Hello

Summing things up, protein synthesis is a variable process. There are approximately 20,000 ribosomes in cell (and they compose 1/4th of the cell mass). There are approximately 3000 copies of each tRNA as well as 1500 mRNA's in various states of synthesis and decomposition. They all exist in a dynamic equilibrium. To quote Tom Misteli:

"No longer can we think of cellular machines as stable, static, and precisely-assembled complexes, akin to man-made machines."

Instead, researchers found that polymerase subunits came together and formed a complex each time a gene was read, on average every 1.4 seconds. Computer simulations suggest that each formation resulted from random, chaotic interactions between protein subunits that eventually came together in the proper configuration. (emphasis mine) Once a complete polymerase finished reading a gene, the subunits quickly disassembled and scattered throughout the cell. Researchers speculate that the dynamic nature of cellular machines allows components to assemble as needed in response to changing environmental conditions.

All through this post I frequently made comparisons to cars. The point was that designed objects are characterized by their lack of tolerance for variability. I recently put together a book shelf. Problem was, apparently, the manufacturers drill press was out of alignment so the bolt holes didn't match. Which meant I couldn't put the shelf together and so it was completely useless as a book shelf. Cars, motors, planes - anything made by human hands show the same characteristics. Change the operating environment they were designed for (the chronic problems of military hardware in Iraq is a good example) and they rapidly break down. We do not see these qualities in nature though. During protein synthesis any number of things can and do go wrong yet the process continues (it goes without saying that the ability to overcome variability. Phrased another way, biological processes adapt to variability in their environment, designed things don't.

Coming Soon: Part III Semantics and Logic

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Biology and Machines: Part I

Regular readers of this blog are no doubt aware that ocassionally have a few things to say about intelligent design/creationism. Particularly in regards to the analogy intelligent design advocates make between cells and machines. Here for example. I have been doing research on this with an eye to writing a post examining how well the analogy holds up in protein synthesis (which I mentioned earlier in the week. In the blogosphere, if you procrastinate you get pre-empted. In this case Pharyngula has written an excellent post on the analogy between genes and machines. Normally, when I come across a post similar to one I am thinking about I usually scrap the idea (seems too me too-ish to continue). Especially if the writer says pretty much everything I was planning on saying. After reading PZ Myers post I decided to proceed with mine since I am approaching the issue from a somewhat different angle.

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Sunday, May 29, 2005

A Change of Pace

You may have noticed a section in my links called "Here There be Monsters..." I am actually quite addicted to Monster Movies. I prefer the older ones especially anything staring Boris Karloff, Lon Chaney Jr or Bela Lugosi. I also like anything with Chris Lee (last seen as Saruman)or Peter Cushing (last seen as Darth Vader's right hand man Grand Moff Tarkin) - anything with Godzilla in it is also good.
I bring this up because yesterday I watched all three Jurassic Park movies and had a couple of thoughts on them - the fact that I just did a longish post on Stegosaurs also factored into it.
There is a tradition in horror movies dating back to 1925's The Lost World to portray dinosaurs as nothing but killing machines wandering from one killed beast to the next with nary a pause for dinner.
Lost World 1925 Posted by Hello

King Kong continued the tradition. While they are still on Skull Island Kong has to fight off any number of dinosaurs. There is also the scene with the Stegosaurus and the scene with the bronto - umm - apatosaurus (where a large majority of the crew are killed).

King Kong 1933 Posted by Hello

Valley of the Gwanji , made in 1969, continued the trend. Gwanji (I have never quite made up my mind whether it was supposed to be a T-rex or an allosaurus) roamed the valley indiscriminately killing anything that moved.

Valley of the Gwanji 1969 Posted by Hello

In some ways the Jurassic Park movies are a continuation of this trend. Granted the herbivorous dinosaurs are portrayed somewhat realistically, but the carnivores still kill anything that moves - even if it just ate.

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Intelligent Design and the Evolution of the Eye

As part of their response to Dawkins, ID the Future has the following post Dawkin's Eye-con of Evolution Unravels. It's pretty pathetic really.

Dawkin's says:

"The eye is today a showpiece of the gradual, cumulative evolution of an almost perfect illusion of design. The relevant chapter of my Climbing Mount Improbable is called 'The fortyfold Path to Enlightenment' in honour of the fact that, far from being difficult to evolve, the eye has evolved at least 40 times independently around the animal kingdom."

The Response:

Only someone who does not know, or does not care to know, the myriad problems with eye evolution could make such a claim with a straight face.

Then they provide a link to Belinski totally distorting and misunderstanding research published in the Proceedings of the Royal Society of London. This whole issue has been addressed elswhere.

I would just like to recommend that the folks over at ID the Future read the following three books:

Evolution above the Species Level, B. Rensch
Vertbrate Eye and It's Adaptive Radiation, G. Walls
Visual System in Vertebrates, Crescikilli

They will straighten you out on all those areas on the evolution of the eye that are confusing you. You might also want to reread the first paragraph of Dawkin's article.

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Is afarensis Going Senile?

Really, totally forgot to supply some interesting Dinosaur links I found while working on the previous post. Been doing that a lot lately. Forgot about the Friday Ark again (two weeks in a row, no less)! So here they are:


Some Interesting Lecture Notes

Dinosauria Online

DinoData Home Page

(I'll be adding this one to my blog roll - along with a few others when I get time)

Added a few minutes later: I will definately be adding Palaeoblog to my blog roll - dudes got some excellent journal links, wonder if he will let me steal them for the Evil Darwinian Orthodoxy? Which, let me say, I am always on the look out for more journals (hint, hint).

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Stegosaur Plates and Intelligent Design

Stegosaur Skeleton Posted by Hello

This and this is really interesting.
Stegosaurs roamed the earth from the Middle Jurassic to the Late Cretaceous. They are related to ankylosaurs and form a larger grouping (the Thyreophora) with them in the order Ornithischia (named after the shape of the ischium). Stegosaurs are one of the more popular dinosaurs and have been used in movied such as "Fantasia" and "Jurassic Park II:The Lost World" One of the reasons, perhaps the only reason, for their popularity is the series of plates running down their back and ending in four massive spikes on thier tail (used to incredibly dramatic effect in Fantasia). Paleontologists have always been somewhat puzzled as to what these plates were for. There are four theories to explain these plates.

2)Heat Regulation
3)Sexual Selection
4)Species Identification

A study to be published in the upcoming issue of the journal Paleobiology examines these exlanations and concludes that number four is probably correct. The study is authored by Paidan, Main, Horner and de Ricqles.
They examined the histology of the plates and scutes of stegosaurs and their relatives (the Ankylosaurs and Scutellosaurus among others).
They ruled out the use of the plates as a defense mechanism because they are very thin and only lie along two rows on the back - which doesn't provide that much protection (especially when the amount of energy required to grow them). They also ruled out the role of sexual selection because female stegosaurs had the plates too - so they couldn't be the result of male-male competition or female choice.

Stegosaurus Plate Posted by Hello

This leaves thermoregulation and species identification as possible explanations. Stegosaur plates have large blood vessals leading into them, and, as mentioned above, are extremely thin. This has lead to the idea that they are involved with heat exchange with the environment (as are, for example, the ears of elephants and the flippers and tails of seals). From the press release:

As for heat exchange, one major reason earlier scientists proposed such a function for stegosaur plates is that these plates have large blood vessels piercing their interior, perhaps channels to carry blood to be cooled or heated. But it turns out that these "pipes" lead to dead ends, so their roles as major blood vessels are difficult to establish.

To probe the possibility that the plates and spikes were heat exchangers, the paleontologists looked at the evolution of these skin growths in the thyreophoran family, which included the stegosaurs. The team obtained fossils from a half-dozen different species of thyreophorans, ranging from the stegosaurs' earliest ancestors - "armored" dinosaurs that lived 200 million years ago - to the first stegosaurs and related ankylosaurs - which had bony plates or scutes all over their bodies - to the last stegosaurs, which died out in the Early Cretaceous period more than 120 million years ago. All were plant eaters with formidable flat or erect plates on the neck, back and tail. The team sliced through about 10 fossil scutes to study their internal structure.
Added a few days later: Here is an example of one of the thin sections.

Stegosaurus Plate Posted by Hello

The earliest thyreophorans, such as the North American dinosaur Scutellosaurus, which measured about four feet from nose to tail, had small bony plates lying flat over their backs and tails, each with a slightly raised keel. These scutes, about a half-inch across, had an internal structure similar in some aspects to the much larger plates of the stegosaurs, yet were obviously useless in regulating the internal temperature of the animal, Main said. The same is true of the later Scelidosaurus, a 13-footer covered with larger scutes with bigger keels; the scutes had the same type of blood vasculature as stegosaur plates and spikes. Ankylosaurs, a sister group to the stegosaurs that survived into the late Cretaceous and went extinct with the rest of the dinosaurs 65 million years ago, had more diverse scutes and ossicles that nevertheless were plumbed in the same way as those on stegosaurs.

Based on this analysis, the team argued that it was unlikely that the larger plates that evolved in the stegosaur ancestors of Scutellosaurus and Scelidosaurus were used for heat exchange.

Below is a picture of the skeleton of a species related to stegosaurus - called Huayangosaurus. It was found in China and is from the Middle Jurassic. Note that it has small plates intermixed with spines. Paidan et al are argueing that becuase Huayangosaurus and Stegosaurus were related their plates and spikes would have come from a common ancestor and would serve roughly the same purpose. If that purpose was thermoregulation they would be a lot similar than what they are.

Padian and Main point out, too, that the horns or antlers of many living animals contain large vessels to supply blood needed for fast growth. None of these horns or antlers function as heat exchangers. A possible role of the large "pipes" in the scutes of stegosaurs and their ancestors was to carry the large blood supply needed for the fast growth that was thought to be typical of dinosaurs.

In addition, not all stegosaurs living at the end of the Jurassic had the big, flat plates of Stegosaurus stenops that most people associate with stegosaurs. Kentrosaurus of Africa and the Asian Huayangosaurus, which were about the same size as Stegosaurus, had mostly spikes with a few "dinky" plates, Main said. These spikes and small plates would have been useless for heat exchange.

"You get quite a large variety in the types of osteoderm arrangements in these animals, but they are not specialized in the way that one would expect if they were built specifically for a thermoregulatory function," he said. "What it looks like is the scutes simply show hypertrophic growth of the keel region, it's simply a modification of an already existing growth pattern."

Huayangosaurus Posted by Hello

This leaves us with species identification as the explanation:

"There is a natural tendency that leads to elaborate displays for social group recognition, like the calls of birds," Padian said. "This underscores the importance of behavior to evolution."

And from National Geographic News:

"The skeletons of these dinosaurs [stegosaurs] below the neck are identical," Horner said. He points to deer as a modern-day analog: While the skeletons of mule deer and white-tailed deer look very similar, the animals themselves have different colors, and their ears and tails are also different.

Horner says these deer attributes serve a similar function to that of the elaborate frills, crests, and back spikes found in dinosaurs. They allow mule and white-tailed deer to identify members of their own species.

Referring to the dinosaurs, Horner noted that "all of these big features on dinosaurs are very expensive" in terms of the energy required to grow them. He added that such features must therefore be extremely important.

At this point, three out of four hypothesis' concerning the function of stegosaur plates have been eliminated. Some of the evidence suggests that the fourth (species recognition) may be correct. A note of caution, however:

De Ricqlès cautioned, however, that "an accessory role in thermoregulation cannot be ruled out for the Stegosaurus plates. Being so large, well vascularized (and available) they may have been inevitably exapted for such a function. This is so even if the primary explanation of their occurrence in an evolutionary context may be elsewhere: namely in some sort of 'display' (mate or species recognition), as suggested by the comparative, phylogenetic, context of plates development among Stegosauria."

So how do we proceed? Let's ask for a few outside opinions. What's your advice William Dembski?:

But is the problem ignorance of the material causes needed to bring about biological complexity or an inherent inability of such causes to do so?

So, we should just infer intelligent design and call it a day.
Richard Dawkins what is your advice?

Science mines ignorance.
Mystery – that which we don’t yet know; that
which we don’t yet understand – is the mother lode
that scientists seek out. Mystics exult in mystery
and want it to stay mysterious. Scientists exult in
mystery for a very different reason: it gives them
something to do. Maybe we don’t understand yet,
but we’re working on it! Each mystery solved
opens up vistas of unsolved problems, and the scientist
eagerly moves in.

So we have two different opinions. One says stop, enjoy blissful ignorance and say God did it. The other says don't despair, accept the unknown as a challenge and go forth to meet it.

To investigate further whether the elaborate horny displays of stegosaurs and other dinosaurs are involved in sexual displays, Padian is going to South Africa in May and June to measure skulls and bodies of African antelopes to look at the range of sexual dimorphism. Such studies have never been done on a full range of African bovids, he noted. Meanwhile, Main at Harvard is studying bone growth and skeletal mechanics in animals such as goats and emus to see how they change with age.

"We know more about growth in some dinosaurs than we do about growth in large living mammals," Padian said.

Looks like Dawkins wins! A wonderful example of how science operates!

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Friday, May 27, 2005

Dawkins and Dembski

Richard Dwakins has a new article here.
The Interesting bit:

Science feeds on mystery. As my colleague Matt
Ridley has put it, “Most scientists are bored by
what they have already discovered. It is ignorance
that drives them on.” Science mines ignorance.
Mystery – that which we don’t yet know; that
which we don’t yet understand – is the mother lode
that scientists seek out. Mystics exult in mystery
and want it to stay mysterious. Scientists exult in
mystery for a very different reason: it gives them
something to do. Maybe we don’t understand yet,
but we’re working on it! Each mystery solved
opens up vistas of unsolved problems, and the scientist
eagerly moves in.
Admissions of ignorance and mystification are vital
to good science. It is therefore galling, to say the
least, when enemies of science turn those constructive
admissions around and abuse them for political
advantage. It is worse than galling. It threatens the
enterprise of science itself. This is exactly the effect
creationism or ‘intelligent design theory’ (ID) is
having, especially because its propagandists are
slick, superficially plausible and, above all, wellfinanced.
ID, by the way, is not a new form of creationism.
It simply is creationism disguised, for political
reasons, under a new name.

IDthe Future has a response. The Interesting bit:

And William Dembski takes on Dawkins' argument-from-ignorance objection here.
So I followed the link and this is what we get: "He claims that ID is an argument from ignorance. But is the problem ignorance of the material causes needed to bring about biological complexity or an inherent inability of such causes to do so? Dawkins can’t seem to get his mind around this latter possibility."

At first I thought Dembski had just missed the point Dawkins was making. That it is the desire to demystify the mysterious and explore the unknown that drives the scientific enterprise. I especially thought this because Witt, the author of the ID the Future post, mischaracterises Dawkins argument as "an argument from ignorance" - birds of a feather and all. Then I realized that Dembski was just being perverse and really believes ignorance is proof of Intelligent Design. Biblical literalism has a way of doing that to people!

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Thursday, May 26, 2005

Interesting Stuff on the Maya

This is fascinating!

The Maya lived in what is now Mexico, Guatemala, Honduras, and Belize since at least 2600 BC. Their hieroglyphic texts were inscribed mostly from AD 250 to 900. This is called the "Classic Period" of the Maya. After that, the Maya mysteriously abandoned many of their major cities, and their civilization collapsed.

Thanks to the work of many other epigraphers (eh-PIG-ruh-fers, people who decipher and classify ancient inscriptions), we now know that Maya writing has two kinds of symbols. Some represent whole words. For example, a picture of a spotted animal with long teeth means "jaguar." Other symbols represent sounds, such as "la," "ka," or "ma." When put together — la-ka-ma — they form "lakam," which means "banner." We know that from a 16th-century Spanish/Maya dictionary. The Maya used around 500 glyphs. They are inscribed in columns that are read in pairs from left to right, top to bottom.

Another breakthrough happened in 1960. Russian-American architect Tatiana Proskouriakoff noticed that when the ancient Maya drew a picture of a man being dragged by his hair, they often drew similar glyphs nearby, like a caption for the picture. She identified the symbols for "was captured" — chu-ka-ja, or "chukaj." Ms. Proskouriakoff was eventually able to prove that glyph texts told stories of real events in Maya history.

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Wednesday, May 25, 2005

More on New World Origins

In comments to the previous post Dior had asked for some links to sources. As I was working on a response I realized I had more to say on the subject.
First some terminological issues. The words Pre-Projectile Point Horizon actually have some meaning in archaeological jargon. The term horizon is defined, in Willey and Phillips "Method and Theory in American Archaeology" as "...a primarily spatial continuity represented by cultural traits and assemblages whose nature and mode of occurence permit the assumption of a broad and rapid spread. As applied to Clovis, then, you have a simple technology (the Southeast Asian Chopper-Chopping Tool Traditon mentioned above) which somewhere evolves a new trait (Clovis) which spreads like wildfire (in some respects it is like punctuated equilibria with it's emphasis on peripatric speciation followed by a rapid spread). Other examples of a horizon would include the spread of shell tempered pottery in the southeast and the spread of the Southern Cult, also in the Southeast.

You will also note I did not say much about skeletel remains. The reason is that with a few rare exceptions, such as the Kennewick material, skeletal material from this time range does not exist ( go here, here and here for more info on Kennewick - especially the first site). Kennewick does have an impact on the debate and I may do a post about it some time in the next couple of weeks.
Now to answer Dior.
The only magazine reference I used was from the May National Geographic. The article doesn't seem to be in the online edition. For the rest, I basically summarized part of Chapter One of Willey's Introduction to American Archaeology - a two volume classic. I would recommend it to anyone interested in archaeology. You might also check out Jennings and Norbeck's Prehistoric Man in the New World. Macgowan and Hester's Early Man in the New World is also quite good. In terms of journal articles the following are pretty interesting:

Chard 1959 New World Origins: A Reappraisal, Antiquity 33(129): 44-49
Chard 1959 Old World Sources for Early Lithic Cultures, Actas del 33ra Congresso de Americanistas pp314-320
Chard 1963 The Old World Roots: Reviews and Speculations Anthro. Papers 10(2) University of Alaska, Fairbanks
Wilmsen 1964 Flake Tools in the American Arctic: Some Speculations
Wormington 1957 Ancient Man in North America, Popular Series # 4, Denver Museum of Natural History.
Finally, for the climate stuff Butzer has a good book called "Environment and Archaeology"

The above references, you may have noticed, are from the 50's and 60's. Although old, these are the papers that set the framework for the debate over Clovis and the Pre=Projectile point horizon. As matters stand now, archaeologists are at something of an impasse older material like Lewisville, Tule Springs, Topper, Meadowcraft and Monte Verde keep cropping up, but unfortunately none of them provide definitive answers (one way or the other).

To answer Henry: My advice would be to take the point to a university anthro department. However, if you want to solve the riddle yourself I would consult Willey's book - or a similar book. Fluted points are pretty distictive - unfortunately, I couldn't find a pic where the fluting really stands out. The flutes are broad long grooves running the length of the point (Clovis and related points are spear points - you can tell by the size). I haven't read Diamond's book yet, so I can't really comment on it. There are valid arguments for the younger dates. I, personally, find the above sites (and quite a few others that are similar) to be suggestive. They are, IMHO a legitimate phenomena that needs to be explained.

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Tuesday, May 24, 2005

The Peopling of America: Clovis and The Pre-Projectile Point Horizon

One of the main goals of Americanist archaeology is to elucidate the cultural history of North America. Perhaps, the biggest problem concerns how and when North America was first settled. Recent finds at the Topper site in North Carolina may provide an answer to the when. Before I can discuss that, however, a little background is necessary. The following account is drawn from Gordon Willey's excellent "Introduction to American Archaeology Volume One: North and Middle America (1966).

The Climatic Background

The Pleistocene, in North America, is divided into four glacial and interglacial periods. The periods of glacial advance and retreat (called interstadials) are presented for the last (Wisconsin) stage below (these are for the Laurentide ice sheet, which covered eastern North American).

Glacial stages Posted by Hello

Three other periods need to be mentioned. The Anathermal climatic stage occured from 8,000 to about 5,00 BC. During the Anathermal a minor glacial advance called the Cochrane advance occured. The Anathermal was followed by a period of warmer climates called the Altithermal. This is followed by the Medithermal - or period of climatic optimum, which lasted from around 5,000 to 2,500 BC. The medithermal was characterized by a climate much like that which we experience now.
ClimatePosted by Hello

It is within this context that most of the discussion of the "how" and "when" of North American Settlement takes place. There is abundant amount of evidence to indicate that the first immigrants to America came via the Bearing Land Bridge (so I won't discuss it). The problem has always been with the timing. There are only certain periods during which routes from Siberia to North America were passable. The main timeframe was 10,000-12,000 years ago and it had always been assumed that this was the time during which North America was settled. The first inhabitants of North America participated in a cultural tradition called the Big Game Hunting Tradition. The Big Game Hunting Tradition was adapted to and developed in a grasslands environment and most of the significant sites are found on the North American Plains. The Big Game Hunting Tradition, was, largely centered around the hunting of large mammals such as mammoth and buffalo. It is characterized by bifacially flaked fluted projectile points (such as Clovis - pictured below - Fulsom, Sandia and Plano) which date to around 10,000-9,000 years BC (or during the Two Creeks Interstadial which preceeded the Valders advance). Associated with the projectile points were a series of specialized and unspecialized choppers, scrappers, knives and drills.

clovis Posted by Hello

clovis and beyond Posted by Hello

However, there are a number of sites that may, or may not be older and which may or may not have earlier, more primitive technology. Such sites are found in both North and South America. They are characterized by crude, percussion flaked tools. Mainly scrapers, flakes and pebble choppers. They are also characterized by the absence of bifacially flked projectile points (such as Clovis). They are usually found in geological associations (or with faunal associations) that imply great age - if accepted.
For example, a site was found in Lewisville, Texas which consisted of pebble-choppers, hammerstones and flakescrapers in association with what were believed to be hearths. Radiocarbon dating of the hearths yielded dates of around 38,000 years old. There are several problems with the site however. First, it is entirely possible that the hearths were in fact not hearths. Rather the blackened areas excavators identified as hearths could actually be the results of burned vegetation (through lightening strikes, etc.). Second, the site was excavated through the use of heavy earth moving equipment and suffered some post-depositional mixing. A, possibly, intrusive Clovis point was found at the site.
Another interesting site is at Tule Springs, Nevada. The site was discovered in an erosion channel, later dated to 28,000-23,500 BC. It appeared to be a camp on the edge of an ancient lake. Remains of camel, bison, horse, mammoth and groundsloth were found near what seemed to be a fire area or charcoal lense. A number of scrapes and flakes as well as two bone implemets were also found. The entire site was covered with several feet of lake deposited clay and silt interbedded with fine sand and gravel. Unfortunately, later research indicated the site dated to approximately 11,000 BC.
These two sites are typical of pre-Clovis archaeology. There are a number of sites in both North and South America that contain - in the words of Gordon Willey - "...chipped stone complexes whose typology and isolation from technologically more advanced implements suggests the possibility of great age (Willey, see above pg 33)". These complexes have been christened the Pre-Projectile Point Horizon.
There are two possibilities, then, for the development of the Big Game Hunting Tradition.
First, people arrived in America much earlier than 10,000-12,000 years ago. They carried with them a tool kit reminiscent of the Southeast Asian Chopper-Chopping Tool tradition (characteized by rough core tools, chopppers and scrappers and the lack of bifaceial blades and points). Which would explain the tantilizing sights such as Lewisville and Tule Springs. This tradition eventually evolved into the Big Game Hunting Tradition. In this view, Clovis was an in situ development and humans arrived in North America considerably earlier.
Second, Clovis and related points evolved out of Asiatic and Eurasiatic prototypes - in particular complexes in western and southwestern Siberia. Some of these prototypes were related to Mousterian, Solutrean and Magdalenian antecedents. Ust'Kanskaia in western Siberia is a good example. The site is found in a cave in the Altai Mountains. Tools found at the site (bifaces, scrappers, burins, retouched flake points) reflect the Mousterian Tradition. It is argued that assmblages such as this blended, further east, with the Southeast Asian Chopper-Chopping Tool Tradition and were then carried into the new world. Interestingly enough, sites in Alaska and the Yukon share some of the same Mousterian flaking techiques as at, say Ust'Kanskaia.
In order to resolve which of these is correct, either of two things are needed. First, indiputable associations of pre-Clovis artifacts with middle or early Pleistocen deposits and convincing radiocarbon dates. Second, a complex of materials attributable to pre-Clovis assmblages are found stratigraphically beneath artifacts of the well known clovis tradition.
Posted by Hello

In 2004 Albert Goodyear found material he claims will satisfy on or possibly both of the above conditions. The Topper site, located on the banks of the Savannah River in South Carolina, is dated to 16,000-20,000 years ago and may be as old as 50,000 years (I am skeptical of this latter date as it pushes things to close to the neanderthals and early modern humans - remember neanderthals are found as late as 35,000 years ago in Europe). The picture above is of the stratigraphy of the site. The artifacts were found in the layer labeled Pleistocene Terrace. The artifacts themselves were a mixture of primitive scappers, flakes and points and they were found below Clovis. They were also found in association with a blackened area believed to be a hearth.

From thePress Release:
“The dates could actually be older,” Goodyear says. “Fifty-thousand should be a minimum age since there may be little detectable activity left.”
The dawn of modern homo sapiens occurred in Africa between 60,000 and 80,000 years ago. Evidence of modern man’s migration out of the African continent has been documented in Australia and Central Asia at 50,000 years and in Europe at 40,000 years. The fact that humans could have been in North America at or near the same time is expected to spark debate among archaeologists worldwide, raising new questions on the origin and migration of the human species.

Which would satisfy the second condition also. There are two problems. First, are the artifacts really human made tools or are they just rocks that look like they might be something? The Jury is out. Second concerns the date and the association with the hearth.

preclovis chert tools Posted by Hello

It would be nice if we had a reliable way of determining whether any given hunk of rock is human made or not. There are several techniques such as trace wear analysis that do help. It gets difficult the closer you get to the origination of stone tools and there comes a point where the boundry is pretty muddled.

the dig Posted by Hello

At any rate, I would be skeptical of the 50,000 year old date and certainly question dates older than that. I do, however, think that the 16,000 to 20,000 date (mentioned in the May National Geographic) is probably correct. I have always been somewhat skeptical of the notion that humans have only been in America for 10,000-12,000 years. The Pre-Projectile Point Horizon is a real phenomena - there are too many sites with this type of material to dismiss. Consequently, an explantion is needed and the best, to date, is that humans did indeed arive earlier than currently believed. Of course more proof is needed and Topper, like the other sites, is a tantilizing piece of the puzzle.

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This is why I don't like the mainstream media

Via Eschaton

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.

Great, our news is being managed by advetising. Wonderful. So really, everything we read has to be friendly to whoever has paid for the advertising. So if BP has a pipeline break and kill tons of wildlife and do huge amounts of damage to the environment they can manage the news by threatening to pull their advertising and none of us will know about it.

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Happy Anniversery Mrs. Afarensis!

Lovers, Rovers and Songs of Sidhe

We roamed the world over,
She and I , we played the rovers,
I, following fortune,
She, her four leaf clover.

We searched for gold,
and secrets of olden times,
She, with beauty like cathedral chimes,
I, with the hunger to know other minds.

We lay by a stream,
we lay by a brook,
we slept in a ship,
far out on the foamy sea.

Then some siren call,
or song of Sidhe,
lured her beyond the love of me.
We parted,
Her, with sparkles of magic in her mind,
I with the sad fate of being left behind.

We roamed the world over,
She and I, we played the rovers.
I following fortune,
But she, She followed the magic of elven tunes.
We Loved. We parted. Will I follow soon?

Sixteen years and she still loves me. Amazing!

Lovers, Rovers and Songs of Sidhe, Part Two

Come softley, come swiftly, come, come away.
Leave farming, leave trading, come what may.
Sleep softly, wake swiftly, today is a new day.
Leave plowing, leave forestin, come, come away.

The waves break upon the shore,
as I morn for days that are no more.
I see the sun shine,
and far off, I hear something that hints of cathedral chimes.

leave the sea, forsake the sea,
come with us, your destiny,
leave the castle noble lord,
forsake it's treasure,
sheath it's bloody sword.

Something calls,
A siren from earlier times,
something calls,
reminding me of cathedral chimes,
Something calls,
A shadow looms,
and calls,
tinkling with elven tunes...

Soft beauty,
You and I,
together once more,
watch the sun rise.

I wrote both of the above poems a long time ago when Mrs. afarensis and I were first dating. I could probably rewrite them into much better poems, but Mrs. afarensis has a sentimental attachment to them (they are her favorites of all the poems I have written for her) so I don't mess with them.
Oddly enough, I took a creative writing class in college and showed both of them to my teacher - he liked the second one better (I've always thought the first was the best) especially the "something calls" part (he thought it was a very intense bit of writing). He didn't like the fact that the lines numbered 4, 4, 5, 8 and 4 and really strongly encouraged me to rewrite it but I didn't want to make Mrs. afarensis mad - which I explained to him. He thought I was being silly. But that's the effect love has on some people.

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Monday, May 23, 2005

Odds and Ends

I am currently working on three kind of long posts on North American Archaeology, Biology and Machines, and the skeletal anatomy of several of the Australopithecines. Hope to have them up soon.

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Sunday, May 22, 2005

Chapter 13, the Mainstream Media and the New Bankruptcy Bill

The Consumer Federation
Makes chapter 13 plans to save homes and cars far more difficult. Contrary to the supposed aim of encouraging more chapter 13 payment plans, numerous provisions in the bill will make chapter 13 much harder and less attractive. For many debtors, the bill will require five year plans (up from three years), assuring that the failure rate will be even higher than the current two-thirds who can’t complete plans because of unexpected income or job loss.


Most Chapter 13s fail before completion. The most authoritative study revealed that 18% of Chapter 13 filings are dismissed before confirmation. Of confirmed plans, 32% are successful and 49% are dismissed after confirmation, which translates to a postconfirmation failure rate of 60%, according to "Consumer Bankruptcy's New Clothes: An Empirical Study of Discharge and Debt Collection in Chapter 13."

From the The Department of Justice

Federal Judicial Center

The most recent draft of proposed bankruptcy legislation requires debtors to visit a debt counseling agency before filing a bankruptcy petition. All are watching the proposed legislation to determine if it will create more than a million new customers who will need to pay dollars to a debt counseling agency to obtain an entry pass into the bankruptcy court. This would result in a huge new revenue source for the industry.

The failure rates are excessive, particularly in the DMP program.

Now I don't know if this provision made it into the recently approved Bankruptcy law, but if it did here is what we have. Consumers would be directed into a totally unrealistic debt counseling plan with high failure rates. From there they could enter into a Chapter 13 which also has unrealistically high payment rates ( I know one person -not me- who filed a Chapter 13. That individual makes 1200 a month gross, the bankruptcy court is taking 890 a month.) Two-thirds of all Chapter 13's are dismissed before they are completed.

Yet, by and large I saw no discussion of this issue in the mainstream media nor by politicians. Why? Why is congess mandating that people participate in a Chapter 13 when for the most part this plan is an abject failure? Why was there no discussion of this issue in the mainstream media? I mean WTF? This is insane. If I only got successful results 30% of the time I'd be fired. For the most part Chapter 13's only work for peaople with a large amount of secured debt -and a large amount of assets to begin with it sounds like they were designed for people with cash flow problems not to help people got in over their heads. Yet there is no discussion in the mainstream media of the large -and negative - impact these things have on most of the people who get them.
As near as I can tell the new Bankruptcy law was desirned to help two groups. Creditors and Debt Counseling companies.

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Friday, May 20, 2005

Ohh, Crap it's Friday

Boy is my face red. I totally lost track of what day it was and did not do anything for the Friday Ark! I am sooooo glad this week is over!

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I have come across several excellant analysis of Intelligent Design.

The first, by Stan Cox (on AlterNet), entitled Monkey Trial or Kangaroo Court describes the proceeding from the viewpoint of one who was there.

A snipet:
For three long days, many in the audience had been wondering which witnesses were correct -- those who said the new standards would not inject religion into the curriculum or those who said or implied that they would.

In his testimony, Calvert cleared up that confusion. To meet the legal requirement of neutrality as he defined it, schools either must allow religious teaching in biology classes or else allow nothing at all to be taught about how biological species come to be.

The ID forces' reliance on federal law is significant. After the hearings, Irigonegaray told reporters, "What we saw in there was religious extremism, and what we are seeing in Kansas is happening all across this country."

The second, by Andrew Gumbel (in the LA City Beat), entitled Not in Kansas Anymore is an excellent analysis of what creationists are trying to accomplish.
A snipet:

Another manifestation of the misdirection of the ID movement is the ludicrous notion that high schools are the appropriate venue for intricate debate about the finer points of evolutionary science. Any public school science teacher will tell you it’s already a minor miracle if a 16-year-old can accurately summarize The Origin of Species, or pinpoint the Galapagos Islands on an atlas. Raising questions about the cellular structure of the flagellum is unlikely to exercise most students until grad school.

The only reason for raising such questions before state education authorities is not to deepen the scientific understanding of teenagers but rather to sow deliberate confusion. It is about denigrating mainstream science as biased against religion – which it is not; it merely regards questions of the supernatural to be outside the realm of scientific inquiry – and by extension bringing God and open avowals of faith into the public school system.

The hearings in Kansas made that abundantly clear. The state school board members who sat in on the witness testimony – Christian fundamentalists all – were so ignorant of the subject matter it was laughable. Board member Connie Morris talked about the Darwinian notion of a prebiotic soup like a patron in a restaurant who decides to launch an irrational boycott campaign against mulligatawny. “There was a speck that landed in the soup?” she asked one witness. “What was that? Was it a cell?” Her colleague Kathy Martin admitted on day two she hadn’t even read through the competing science standards documents before her.

His comment about the press two paragraphs earlier is definately worth reading.

Finally, Burt Humburg (at the Panda's Thumb) has a fascinating post called Creationist Fears, Creationst Behaviors. The piece is an interesting analysis of the what motivates creationists and also of the strategy used by scientists to respond to the creationist challenge.

A snipet:

One thing that was interesting about the creationist’s arguments was the certainty with which he held his YEC positions. As anyone who has read Robert Pennock’s book Tower of Babel knows, there is a great diversity of creationist thought in the US. So, I asked the obvious question:

“Sir, there are forms of creationism other than YEC, such as OEC and ID creationism. How can you be so certain about the age of the earth when it appears to be a legitimate controversy within the creationist community?”

His answer was, “All those other forms of creationism allow for the possibility of an old earth. If death entered the world before the fall, then there is no need for Christian salvation. That is why YEC is true.”

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Thursday, May 19, 2005

Post Darwinist?

From Law Evolution Science and Junk Science comes this amusing quote:

I concluded that Darwinian evolution cannot, on the evidence, be the whole explanation of the history of life on Earth. Clearly, intelligent design was also involved. But because I do not subscribe to any brand of creationism, I call myself a post-Darwinist.

Ummm, wouldn't Post Darwinist thought be considered the Modern Synthesis? The next logical question after that would be "If you don't subscibe to any brand of creationism doesn't that make you a 'Darwinist'?"

Here is a link to the site in question. The rest of it is pretty haughty.

Having been an editor for many years, I am comfortable exercising divine powers, and rarely even notice the offender’s anger. Many blogs encourage the very trends I deplore, so there is no need to remain in my universe when so many kinder ones beckon.

Post comments by all means, but I suggest this simple self-test first:

"Has it ever occurred to me that even my nearest and dearest find me a thunderous bore?"

Answer: If that thought has never occurred to you, my precious little party sox, be cautious about posting here.

She hasn't posted since 5/2/05 so apparently she took her own advice and realized she was a "thunderous boar" and by her own criteria couldn't post anymore and is now knitting precious little party soxs. (I don't know, I haven't been sailing since last year - maybe that's why I'm feeling so snarky).

On a more serious note, this just kind of shows the continued fundie embrace of post modernism. If they really knew what it was about they would avoid it like the plague becuase it totally undermines any straightforward interpretation od the bible. Although I must say, I am suprised at the path post moderism has taken. It blew through anthropology during the mid nineties. I recently spotted a commenter over at the Preposterous Universe (a physics website) offering a post modernist critique of physics (scientific knowledge is dictated by the politics of science) and of course Phillip Johnson has been playing with it (no pun intended) for years. I may have to dust off some of my cultural anthropology and archaeology articles and do a post on it.

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ID as Politics

Via Red State Rabble comes this interesting editorial.

A little to tide you over till you get there:
The battleground that I.D. supporters have chosen for their theory - their scientific theory - is political, not scientific, although they deny this. They do not seek the validation of fellow scientists. They seek validation from local and state Boards of Education in culturally conservative states such as Kansas and Ohio. This is preaching to the choir, not gaining converts...
It seems extremely important to the proponents of intelligent design that children are exposed to their theory before the scientific community has accepted even the smallest part of it. No other central scientific theory has ever sought or won approval in this manner.

Intelligent Design is a political movement not a scientific movement. It will continue to find supporters in churches and on school boards, but it will never be considered seriously by the scientific community because the movement refuses to acknowledge any need for acceptance.

This last is really important. ID proponents arn't aiming any scientific arguements at scientists - there are no experiments coming from ID. There is just enough science in ID to make them look like they know what they are talking about when they are in front of pople with little knowledge of science.

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Prehensile Tailed Porcupine: Part Two

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A few weeks back I wrote this post on the prehensile tailed porcupine. In an interesting bit of science the gender of the porcupine has been determined through the analysis of quill DNA! But I'm not going to tell you. You will just have to go read for yourself!

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Wednesday, May 18, 2005

Megalodon and the Great White Sharks: Conclusion

I had originally planned the first post in this series as a companion piece to the Cheetah post for the Friday Ark. One of the points I wanted to address was the issue of great whites preying on juvenile Megalodon. Since cheetahs have extremely high infant mortality I thought the two would complement each other nicely. Unfortunately, I got extraordinarily busy and didn't have time to do it then.
At any rate, I ended up somewhere else from where I intended. Originally, I was going to recount the evidence favoring the relationship with mako sharks, mention the predation on juvenile Megalodon and pretty much end it there. However this raised the broader question of what caused the extinction of Megalodon and I ended up talking about reproductive isolation between two populations of killer whales. Although I didn't perform any experiments or do any paleontological fieldwork, this is a good example of how science works. Start with a simple observation or question (Megalodon looks like a Great White - are they related?) find evidence (the characteristics of all those teeth as well as their position in the fossil record)then take stock of the implications of that evidence for your hypothesis (nope - not related). The evidence raised new questions (well then, if Megalodon didn't evolve into Great White sharks, then what happened to them (my answer: they were outcompeted by killer whales). At this point we could frame a new hypothesis and ask ourselves what kind of evidence would confirm or deny the theory (noticible absence of megalodon in areas with a lot of killer whale fossils or maybe a statistical analysis of the incidence of Megalodon in areas with great whites, bite marks on what few parts of Megalodon would fossilize, demonstration that the territories and niches of either great whites or killer whales overlapped with that of Megalodon - there are other, better types of evidence that would support or refute the idea, but you get the picture). then the process would start over, but at a higher, more general level. Whatever questions we asked of the data and whatever answers we received would apply at a wider, more generalized level till we ended up with...? (Hint: Something of great explanatory power that unites a wide variety of phenomena.) Note, though, that in this example, we did not work in a lab -we worked out in the field. Nor were we trying to explan something we personally witnessed (kind of like the resurection - no one saw that either - just saw an empty tomb and made assumptions - yes I'm feeling snarky) yet we are still able to make predictions and test our hypothesis.

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Just When I Thought the Pandering Couldn't Get Any Worse!

20/20 is devoting a full hour to the resurection of Jesus Christ!

From the webpage:

Sometime between the year 30 and 33 of the first century, a young Jewish preacher named Jesus of Nazareth was crucified in Jerusalem. It was a brutal and humiliating death that should have ended his tiny movement right there. And yet his followers carried on, planting the seeds of a religion that would eventually rule the Western world. What convinced them to continue? The Bible says that after Jesus died, his mother and other women who had followed him actually took his body down off the cross and that he was laid to rest in a tomb owned by Joseph of Arimathea. What happened next is a mystery.

Vargas also interviews Jewish scholars in Jerusalem who are experts in the history of the early Christian movement there. Professor Daniel Schwartz of Hebrew University and professor Albert Baumgarten of Bar Ilan University help shed light on the mindset of the first followers of Jesus. While neither obviously believes a physical resurrection occurred, both concur that something extraordinary took place shortly after Jesus' death. "I think definitely something happened," said Schwartz of Hebrew University in Jerusalem, "I don't know how they convinced themselves. But the historical fact is, you've got people who are convinced he was resurrected."

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What to do with the Press

Couldn't have said it better myself!

Even better!

To tide you over till you get there:

Some of these efforts at balance can involve some even more volatile issues than abortion, particularly when they fall outside allowable circles of discourse in the U.S. Former CIA Middle East analyst Kathleen Christison recently wrote that state violence against the Palestinians by Israel has become so widespread and brutal that it is no longer possible to ethically treat the subject with balance.

To do so, she says, would be morally akin to providing balance on slavery, giving the pro and con of slave owning:

"Neutrality in any conflict in which there is a gross imbalance of power is probably impossible and certainly immoral. It effectively removes all restraints on behavior by the powerful party...Thinking back to some of the colonial conflicts of the twentieth century, is it possible to imagine a scenario in which peacemakers or public commentators and opinion molders ever believed these conflicts could be resolved by simply splitting the difference? ... The notion of being 'neutral' is soothing to most people because it is ostensibly fair, it is optimistic, it is positive, obviating the need for negativity and unpleasantness.

"But a balanced position in an unbalanced situation inevitably is a miscarriage of justice. Neutrality in Palestine-Israel is no different from refusing to take a stand between slaves and slave owners, or between children and abusive priests."

But that is exactly what is done in U.S. journalism. One can argue about whether Christison is correct about the level of savagery against Palestinians, but it's important to ask why U.S. journalism has created a reality in its news coverage of the Palestinians that exists in the journalism of only one other nation.

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Megalodon and Great White Sharks: Part Two

So the question becomes, if Megalodon did not evolve into great whites ( i.e., if they were not a chronospecies) then what happened to cause them to go extinct? One site argues that it was competition with great whites. Specifically, early great whites were outcompeting/preying on juvenile Megalodon which caused Megalodon to go extinct. As the cheetah post, of a few days ago, shows high infant mortality came be overcome. It is adult survivorship that is important. Another theory has it that oceanic temperature cooled off around the end of the Pliocene. My own hypothesis on the subject is that they were outcompeted by early killer whales (which go back at least 5 million years). Killer whales are warm blooded and travel in packs - which makes them efficient predators. They frequently team up to kill larger whales (such as blue whales)and occasionally eat great white sized sharks. They are, approximately, the same size as Megalodon and would have been trying to fill the same niche. What would it take to confirm my hypothesis and how can I broaden it into a theory? That is a subject for another post.

In the meantime, awhile back I had written a post on killer whales. Killer whales (in the Pacific Northwest, that is) are divided into three different forms: residents, transients and offshores. These three forms differ in morphology, ecology, behavior, and genetic composition and,it should be added, cultural behavior. The resident population is divided into northern and southern residents and thes two populations are reproductively isolated from each other even though there is a partial overlap in territory. I am wondering if this is the beginnings of a sympatric speciation event?

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Tuesday, May 17, 2005

Megalodon and Great White Sharks

Regular readers of this blog may recall that I have a certain quirky prediliction for shark movies) I say quirky because they a) give me the heebe jeebies and b) have given me nightmares about sharks winking at me - but let's not discuss that). Awhile back I had the misfortune to watch the movie "Megalodon". I say misfortune because quite frankly it sucked! It did, however, get me thinking about shark evolution. In the movie Megalodon is portrayed as a giant great white shark, so I was curious about what the evolutionary relationship between the two.
Megalodon was a giant shark (believed to be 40-50 feet long) that lived from 25 to 1.6 mya. It is believed that megalodon evolved in conjuction with whales. The evolutionary lineage leading to megalodon can be traced fairly well (see chart below). Below is a megalodon tooth.

Posted by Hello

Great white sharks, on the other hand, can be traced back 5 million years to the pliocene. This is where the controversy begins. Until recently, Megalodon was placed in the sam genus (Carcharodon) as the great white and reconstructions of megalodon portrayed it as looking almost exactly like a great white. In recent years this view has been challanged. Scientists and amateurs alike have challenged the view.

Posted by Hello

Above is a comparison of the teeth of Megalodon (right) and a great white (left). On the surface they both look pretty similar. It should be pointed out at this point that the Megalodon tooth is from a small juvenile and the great white tooth is from an adult. Look a little closr and you will start to notice differences. One of the more pronounced differences is in the area of the collum - the transitional are between crown and root. In megalodon this area is large and broad. In the great whites it almost doesn't exist. Another difference is in the shape of the roots. The roots in Megalodon form a "V" shape, whereas in the great white the roots are horizontal. What can't be seen in the picture is that Megalodons teeth are almost 3 times as broad as great white teeth. About the only thing the teeth share in common is the serration.

Posted by Hello

Above is a comparison of a great white tooth with Isurus hastalis (an ancestor of the makos). Note that, like the great white, Isurus hastalis does not have much of a collum and has flat roots. About the only difference is the lack of serration in Isurus hastalis. This has lead to the theory (see links above) that makos and great whites are related and that great whites evolved from mako ancestor. Interestingly enough, a series of finds in Peru, in layers ranging from the late Miocene to early Pliocene, has buttressed this argument. In the late Miocene layers one finds Isurus hastalis in the early Pliocene layers one finds Carcharodon carcharias (the great white). In between one finds several transitional species and in point of fact identifying how many is difficult. Finally, studies in molecular biology indicate great whites and makos are related. Below is a phylogeny based on the great white/mako relationship.

Posted by Hello

See here and here for additional info.

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Monday, May 16, 2005

Another Reason Not To Fly

This is another reason why I will never fly! A few quotes to tide you over till you get there:
Security workers using the machines can see through clothes and peer at whatever may be hidden in undergarments, shirts or pants. The images also paint a revealing picture of a person's nude body.

But Homeland Security Secretary Michael Chertoff told a Senate subcommittee last month that he wants to employ the technology and doesn't want an "endless debate" over privacy issues.(empasis mine)
Perverts! What else would you expect from the Republican party?

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Bill Moyers

Bill Moyers was in town on Sunday and had a few things to say about the media . Unfortunately, I wasn't there - would have loved to have seen it.
A quote to tide you over till you get there:
Bill Moyers denounced on Sunday the right wing and top officials at the White House, saying they are trying to silence their critics by controlling the news media.
He also took aim at reporters who become little more than willing government "stenographers." And he said the public increasingly is content with just enough news to confirm its own biases.

You can also listen to the entire speech here - on second thought, ignore the Post-Dispatch link and go here and listen to the whole thing. I'm kind of mad at the Post-Dispatch because they have not published my response to the creationist letter.

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Friday, May 13, 2005

Culture of Life Just Keeps Getting Weirder

Blame oldwhitelady for this "Culture of Life" rant! Seems some folks think it's perfectly okay to "do" anything that is warm, damp and vibrates according to Lab Kat! The story is about Neal Horsley the Republican candidate for governor in Georgia. Apparently, he thinks it is okay to engage in bestiality and post the name of abortion doctors on websites (one doctor has been killed because of it) but gay rights is out? The Southern Poverty Law Center has a good profile on him. You can also go here and here for more info. Sad thing is, this guy will probably get elected! I worry about our country, I really do!

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Homo erctus Doing What??

I am sure I do not want to know the answer to this...probably, but would the person, from New York, New York, who did the following search to end up at my blog:

www.google.com/search?hl=en&ie=ISO-8859-1&q=homo erctus sucking dick

Please tell me what you were looking for? Did you find it? Perhaps if you substituted "erectus" (if you are looking for fossil hominids to date - you arn't a flaming bible thumping hetero by any chance are you?) for erctus you might find what you were looking for. Although, I must say my sight is pretty much G-rated. You might try Pharyngula he's always writing posts about spider porn and nematode vulva's and such.

Yup, I'm feeling mean, time for another patch.

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Creationist Letter In the St. Louis Post-Dispatch and Flaming Bible Thumping Heteros

I was reading the letters to the editor in today's St. Louis Post Dispatch when I discovered this letter bashing evolution.

Both evolution and creationism (or "Intelligent Design") are worthy of discussion. Both are reasonable, both have their ardent believers, and both are theories. Neither is provable through scientific testing. It may be an error to introduce the term "science" in reviewing evolution or creationism, since neither theory can be tested in any laboratory environment.

So, of course I had to respond to it:

Dear Editors,
I am writing to correct some misconceptions about science and evolution expressed in a previous letter (Prove It, by Karl Zickler). He writes that neither science nor creationism "...can be tested in any laboratory environment". This is incorrect and is a misunderstanding about the nature of science. For example, scientists at the Howard Hughes Medical Center were doing research - in a lab - on the evolution of spines in stickleback fishes. One of the byproducts of this research was that they managed to link the gene responsible for forming stickleback spines to a gene in humans that plays a role in the disease ectodermal dysplasia. In reality though, science doesn't occur in just a lab. Ask any field biologist, ecologist, anthropologist, geologist or paleontologist. Contrary to Mr. Zickler, evolution is capable of being proven through scientific testing and many scientist have devoted their lives to the experimental testing of evolution. This process requires rigorous standards of evidence and proof. We have heard a lot about the supposed scientific nature of creationism (and it's offshoot Intelligent Design) so I would ask Mr. Zickler to provide just one experiment -it doesn't have to be in the lab, it can be fieldwork - that would give evidential support to the any of the creationist (or ID) "theories". I, personally, have been following the evolution/creation debate since I was in college and have yet to find any experimental evidence that would support creationism (or Intelligent Design).

As a follow up, I should point out that the pseudo attempt at fairness "Both are reasonable, both have their ardent believers, and both are theories. Neither is provable through scientific testing." Is a favorite creationist tactic. They try to appear reasonable and fair - but you know they really think "God did it"

There was also a second letter that I wanted to respond to, but I felt that I would have a better chance of getting published if I only wrote one letter. It reads:

It's not the person

I don't think you understand the reason why the "conservative element that is pushing hardest against gay rights" (Leonard Pitts, May 8) is pushing so hard. Our opposition is not against the homosexual as a person but the homosexual activity in which the person chooses to participate. We accept the person but decry the abnormal behavior.

For the past 5,000 years, societies have recognized homosexuality as an abnormal behavior.

Where to start? "We accept the person" this is pure nonsense. Most of the people against gay rights are total bigots - they take all their hatred for the "abnormal behavior" (note the perjorative way it's phrased) and hurl it at living, breathing people (I feel a rant about the Culture of Life coming on - don't get me started). People who have just as much right to love and be loved, to be happy, as bible thumping heteros.

"For the past 5,000 years, societies have recognized homosexuality as an abnormal behavior." Oh, learn some anthropology will you. Human societies have been around a lot longer than 5,000 years. Among the many societies that have come and gone, there were quite a few that accepted homosexuality. Ancient greece comes to mind, as does the Etoro of Papua New Guinea.

If anybody wants to write the St. Louis Post Dispatch on either of these letters (especially the second)the addresses are:

Letters to the Editor
St. Louis Post Dispatch
900 N. Tucker Blvd
St. Louis, MO 63101

Fax: (314)340-3139
E-Mail: letters@post-dispatch.com

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Friday Baby Cheetah Blogging

Following up on a post from a few days ago, here are some picturtes of baby cheetahs.

Cheetah Posted by Hello

Cheetah 2 Posted by Hello
Be afraid, we are wild, ferocious, jungle kitties

Here is a link to an interesting discussion concerning predation on cubs (from lions and hyenas) vs. habitat destruction and genetic issues.

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