Monday, August 29, 2005

This Has Got To Be The Stupidist Thing I have Ever Read!

Via Eschaton comes this incredibly lame column in WAPO.
It concerns, of all things, Intelligent Design.

Athletes do things that seem transcendental -- and they can also do things that are transcendentally stupid. They choke, trip and dope. Nevertheless, they possess a deep physical knowledge the rest of us can learn from, bound as we are by our ordinary, trudging, cumbersome selves. Ever get the feeling that they are in touch with something that we aren't? What is that thing? Could it be their random, mutant talent, or could it be evidence of, gulp, intelligent design?

That is how it starts. Then it goes rapidly downhill from there.

First, let's get rid of the idea that ID (intelligent design) is a form of sly creationism. It isn't. ID is unfairly confused with the movement to teach creationism in public schools.

Umm, wrong, as the wedge document clearly shows Intelligent Design is most definately a sly form of creationism.

The most serious ID proponents are complexity theorists, legitimate scientists among them, who believe that strict Darwinism and especially neo-Darwinism (the notion that all of our qualities are the product of random mutation) is inadequate to explain the high level of organization at work in the world.

And yet, all these "complexity theorists" and "legitimate scientists" have had something like fifteen years to produce some actual science and failed miserably. By the way, what the heck is a "complexity theorist" anyway? At any rate, the last I heard evolution wasn't due to random mutation. Rather it was due to a complex interplay of selection, drift and migration (to name a few) acting on genetic variabilty and mutation. I guess I should also mention historical contigency as well.

The idea, so contentious in other contexts, actually rings a loud bell in sports. Athletes often talk of feeling an absolute fulfillment of purpose, of something powerful moving through them or in them that is not just the result of training. Jeffrey M. Schwartz, a neuroscientist and research professor of psychiatry at the UCLA School of Medicine, is a believer in ID, or as he prefers to call it, "intrinsic intelligence." Schwartz wants to launch a study of NASCAR drivers, to better understand their extraordinary focus. He finds Darwinism, as it applies to a high-performance athlete such as Tony Stewart, to be problematic. To claim that Stewart's mental state as he handles a high-speed car "is a result of nothing more than random processes coming together in a machine-like way is not a coherent explanation," Schwartz said.

Darwin, it should be pointed out, wrote a whole book (called Expression of the Emotions in Man and Animals) where he did just that. But let it pass. Might not this "extraordinary focus" have something to do with the evolution of the brain? Might it not have something to do with adapting to various environments that hominids found themselves in over the course of the last 5 million years? Might come in handy if you are hunting - or being hunted.

Instead, Schwartz theorizes that when a great athlete focuses, he or she may be "making a connection with something deep within nature itself, which lends itself to deepening our intelligence." It's fascinating thought.

Umm, yes, it's called concentrating perhaps a psychology book would help with the concept. Certainly any competent neuroanatomist can explain it.

Steve Stenstrom, who played quarterback for the Bears and 49ers, works as a religious-life adviser to athletes at Stanford, where he organized a controversial forum on intelligent design last May. "I don't think it's a reach at all," he said. "Talk to any athlete, and if they really are honest, they realize that while they have worked and trained, and put a lot of effort into being great, they started with some raw material that was advantageous to them, and that it was meant to work a certain way. We all recognize that we have a certain design element."

Great, now we are getting science from football players. I think the raw material would be the genetic makeup they inherited from their parents.

A strict Darwinist would suggest this is an illusion and point out that there are obvious flaws in the body. Peter Weyand, a researcher in kinesiology and biomechanics at Rice University, observes, "Humans in the realm of the animal kingdom aren't terribly athletic."

Okay, what's the deal with Darwinism? The study of evolution has progressed quite a bit since Darwins day. Perhaps a little reading on the subject you are writing about might help.

Then we get a lot of dreck like this:

Our bodies break down a lot. If we were designed more intelligently, presumably we wouldn't have osteoporosis or broken hips when we get old. Some evolutionists suppose that the process through which people evolved from four-legged creatures to two, has had negative orthopedic consequences.

I would suggest that you consult Wilton M. Krogman's "Scars of Human Evolution" Published in Scientific American back in 1951 (VOl. 185 No. 6, pp 54-57). The fact of the matter is anyone who studies the human skeleton comes to the conclusion that the shift from quadrupedalism to bipedalism has left telltale traces. This is why Mark Prior and Kerry Woods spend so much time on the DL, this is why football players can barely walk a few years sfter retiring (ever heard of Conrad Dobler - great offensive lineman - can barely walk now).

Then we get a bunch of unitelligible stuff like this:

Schwarz finds little or nothing in natural selection to explain the ability of athletes to reinterpret physical events from moment to moment, the super-awareness that they seem to possess. He has a term for it, the ability to be an "impartial spectator" to your own actions. "The capacity to stand outside yourself and be aware of where you are," he said. "Deep within the complexities of molecular organization lies an intrinsic intelligence that accounts for that deep organization, and is something that we can connect with through the willful focus of our minds," he theorizes.

I'm not sure what any of this has to do with athletic ability?? Truth be told I'm not really sure what it has to do with, well, anything.

Crackpot speculation?

That would be my guess.

Maybe -- maybe not. ID certainly lacks a body of scientific data, and opponents are right to argue that the idea isn't developed enough to be taught as equivalent to evolution.

Ummm, actually it lacks data period. It's been something like 15 years since Intelligent Design was first proposed, so the question naturally arises. If the theory isn't developed enough now, when will it be? Surely if it's that self eveident developing Intelligent Design theory ought to be easy as crap going through a goose. Right?
But Darwin himself admitted he didn't know everything about everything. "When I see a tail feather on a peacock, it makes me sick," he once said, before he understood it was for mating.

Speaking of Darwin... in the 15 years after he published The Origin of Species he published four (I think) more works and conducted hundreds of experiments. Made it a pretty well developed theory. Why couldn't Intelligent Design do the same?

And try telling a baseball fan that pure Darwinism explains Joe DiMaggio. As Tommy Lasorda once said, "If you said to God, 'Create someone who was what a baseball player should be,' God would have created Joe DiMaggio -- and he did."

Gee, let's see... those who can hit the ball better, run faster, throw harder, catch a ball better survive and make it to the major league. Those who can't fall by the wayside. Sounds like natural selection in action to me.

None of this is to say that we shouldn't be wary of the uses for which ID might be hijacked.

One can only chuckle
In the last year, numerous states have experienced some sort of anti-evolution movement. That makes it all the more important for the layman to distinguish the various gradations between evolutionists, serious scientists who are interested in ID, "neo-Creos," and Biblical literalists.

As the Kansas school board hearing showed the difference between serious scientists who are interested in ID and "neo-Creos," and Biblical literalists is miniscule at best.
One of the things we learn in a grade school science class is a concrete way of thinking, a sound, systematic way of exploring the natural world.

Yup, that is why serious scientist don't waste their time with Intelligent Design.

Historically, scientific theorists are sandlot athletes, drawing up plays in the dirt.

I'm speechless...

Pharyngula has an excellent, and much less snarkier, take down as well.

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Word Verification

Hi All,
I just got hit with about 11 pieces of spam in my comments, so I have turned on word verification. I do apologize for any inconvenience this causes.

Now back to our regularly scheduled blogging.

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Parkway, Gays and Jesus

Parkway is a school district in St. Louis County. Recently, they ammended their disciplinary policy to include language prohibiting harrassment based on personal appearance, socio-economic status and sexual orientation. This language was included based on a survey of students:

"We have the data to support that's been a concern in our school district," said board member Karen O'Brien, who voted in favor of the changes. "We want children to feel safe and secure in our buildings, and that doesn't mean just earthquakes; it means safe from fellow human beings. (With this change) we have broadened the coverage to protect all children."

O'Brien said student surveys showed students reported being harassed or bullied primarily because of personal appearance, socioeconomic status and perceived or actual sexual orientation.

There has, of course, been protest:

Audience members said "Amen" in unison, agreeing with speakers as the discussion shifted to the use of the term "sexual orientation" in the policy. Some residents said that having special provisions protecting the sexual orientation of a person teaches children that it is acceptable to publicize sexuality.

Cunningham cited a page in a Parkway yearbook that displayed a gay and lesbian club asking students to participate in "National Come Out Day."

"They were encouraging kids to make it public about their sexual orientation, their homosexuality, their lesbian lifestyle. That's in your yearbook," she said. Cunningham said that a person's sexual orientation should be kept out of the schools.

State Rep. Allen Icet, R-Wildwood, said the policy could punish students who participate in after-school clubs, such as the Good News Group, a Christian-based group, for talking about certain kinds of sexual orientation that they feel to be morally wrong, a violation of free speech.

In other words, the fundies are pissed because they think this will prevent them from using the language of religion to express their bigotry and are pretending to be victemized. "...Let he who is without sin cast the first stone...." So, of course the fundies are casting that mutha bigtime.

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Friday, August 26, 2005

When Did Humans Start Wearing Shoes: Part Two

Abnormal Interests has linked (Thanks!)to my post on when humans started wearing shoes. He also links to a BBC News story that provides more info than the Science Daily article. As I suggested in the comments to my original article two things needed to be done to make a convincing case. First, a comparison needed to be made between shoe wearing and non-shoe wearing modern humans. From the BBC article:

To test the theory that the more delicate toes resulted from shoe use, the Washington University researcher compared the foot bones of early Native Americans, who regularly went barefoot, and contemporary Alaskan Inuits, who sported heavy sealskin boots.

Again, he identified chunkier toes in the population that routinely went without shoes. The research suggests shoe-wearers developed weaker toes simply because of the reduced stresses on them during their lifetime; it was not an evolutionary change.

Second, I was concerned about how this could be passed on to future populations. As the above quote also shows, Trinkaus is not advocating this as an evolutionary change. Adaptation can occur in many different ways. The more permanent types represent changes in the genetics of the population. Another type (from Stini in his book "Ecology and Human Adaptation") occurs in response to stress and may persist for a long period of time and occur in individuals rather than populations. Examples would be moving to a higher altitude or muscular hypertrophy (as a response to high activity levels). It is this second sense that Trinkaus is talking about. Bone has two responses to stress. More bone can be laid down or bone can be absorbed. In the case of muscular hypertrophy, mentioned above, the muscle origins and insertions would become larger in order to accomodate the increased muscle size. Another effect would be that increased muscle size means that increased force can be exerted and bone will be laid down to handle that increased force. In the case of human feet, since humans started wearing shoes, according to Trinkaus, there was a decreased stress on the toes so bone was absorbed leading to more gracile toes. As I mentioned in my first post, there was a trend towards more gracile skeletons from Neanderthals to archaic humans to anatomically modern humans (irregardless of whether you go for Out-of-Africa or Multiregional Continuity - or for that matter one's views of the taxonomy of the above species) so untangling the two is difficult. Having said that, this study certainly turned out to be more interesting than I originally thought.

Added later: Corrected a few typos and changed one sentence for clarity.

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Friday Sea Anemone Blogging

The above is a picture of a Sea Anemone. Sea Anemone are found all over the world - mainly in warm coastal waters. They range in size from five inches to six feet in diameter. They have a crown of tentacles arranged around their mouth - which are poisonous:

On the tentacles are stinging cells or nematocysts. A nematocyst is a small capsule with a thread-like tube coiled inside. When a trigger bristle is disturbed, the coiled tube shoots out and imbeds in whatever triggered it. There is a minute amount of poison injected. The nematocysts are used both for defense and capturing food.

The sexes are separate. The eggs or sperm are ejected through the mouth. The fertilized egg develops into a planula, which finally settles down somewhere and grows into a single anemone. Asexually they reproduce by pulling apart into 2 halves, or, in some species, small pieces of the pedal disc break off and regenerate into a small anemone.

Which brings us to one of the more interesting things about sea anemones. Researchers at UC Davis have studied a species of sea anemonee known as Anthopleura elegantissima. Anthopleura elegantissima are organized into large colonies of genetically identical clones. Social structure is similar to insects in that their are scouts, warriors and reproductive individuals. Differentiation depends on a combination of enemy stings and the genetics of the colony. You may have noted I said "enemy stings". From the press release:

Where two colonies meet they form a distinct boundary zone. Anemones that contact an animal from another colony will fight, hitting each other with special tentacles that leave patches of stinging cells stuck to their opponent.

This is how it works:

When the tide is out, the polyps are contracted and quiet. As the tide covers the colonies, "scouts" move out into the border to look for empty space to occupy. Larger, well-armed "warriors" inflate their stinging arms and swing them around. Towards the center of the colony, poorly armed "reproductive" anemones stay out of the fray and conduct the clone's business of breeding.

When anemones from opposing colonies come in contact, they usually fight. But after about 20 or 30 minutes of battle the clones settle down to a truce until the next high tide.

It's not just polyps along the border between two clones that clash. Polyps three or four rows away from the front will reach over their comrades to engage in fights...

The lesson to take away from the study, according to the researchers, is that:

"...very complex, sophisticated, and coordinated behaviors can emerge at the level of the group, even when the group members are very simple organisms with nothing resembling a brain..."

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Thursday, August 25, 2005

Must Read Digby

Via Eschaton comes a profound, must read Digby piece.

Go check it out! You will be glad you did.

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Wednesday, August 24, 2005

Primate Communication

An interesting study on Science News indicates a correlation between number (which I interpret to mean types) of calls, group size and length of time spent grooming. The researchers analyzed 42 different types of primates. They also used phylogenetic analysis to take evolutionary relationships between species into account - necessary to rule out spurious correlations - in the study.

The data analysis showed strong relationships between vocal repertoire size and group size, as well as between repertoire size and the amount of time spent grooming...

What the study did not indicate was causality, in other words they could not say whether one of the three variables caused the other two to develop. Look at it this way. Larger group sizes need more mechanisms to maintain social solidarity (such as grooming or increased vocal repertoire - which could serve to increase group identification). On the other hand, increased vocal repertoire could allow larger groups to exist. Chicken or egg?

One note of caution though:

It is also important to remember that there are radical differences between non-human primate vocal repertoires and human languages, says McComb (one of the researchers - afarensis). So it does not follow that languages as complex as ours will necessarily follow from increases in group sizes and social interactions. “There are other big hurdles that have to be overcome to get to human language,” she says.

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Cool Science: Part Two

Research Identifies 'Hot Spots' Of Ocean Productivity which is really interesting. Apparently, barnacles off the coast of Cape Perpetua -off the coast of Oregon - produce five times as offspring as barnacles off the coast of Cape Foulweather:

The study highlights the importance of including information on ecological processes when designing reserves and other types of marine protected areas, the scientists said. It is one of the first studies to link reproductive variation with key ecological processes on a scale that's relevant to management and conservation. The findings were published today in a professional journal, Proceedings of the National Academy of Sciences.

"This study demonstrates that not all ocean places are equivalent, and that some populations are more likely than others to contribute to future generations," said Heather Leslie, a marine ecologist at OSU. "This could serve as a model for how to link information on biodiversity patterns with underlying ecological processes."

One wonders about the efects these kinds of hotspots could have on speciation and evolution - the study was more about the implications for conservation:

Variability in ocean currents and bottom topography, as well as biological interactions, all can contribute to differences in the productivity of marine ecosystems. Biodiversity protection and enhancement of nearby fisheries are among the goals of marine reserves, the researchers said, and an important aspect of siting effective reserves would be understanding how the productivity of key populations vary.

"Not all ocean areas are the same, and the likelihood of fulfilling the objectives of reserves and other area-based management efforts would increase if we understand the ecological processes responsible for biodiversity patterns," Leslie said.

Integrating this information is particularly important, Leslie said, given the forecasts of changes in ocean currents and other biological and physical processes due to climate change.

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Cool Science: Part One

Saturn's Rings Have Own Atmosphere which came as a surprise to me - but I'm not an astronomer or astrophysicist or anything. Apparently, due to some interesting properties concerning the way water (i.e. H20) behaves in the region of Saturn an atmosphere is generated:

Water molecules are first driven off the ring particles by solar ultraviolet light. They are then split into hydrogen and atomic oxygen, by photodissocation. The hydrogen gas is lost to space, the atomic oxygen and any remaining water are frozen back into the ring material due to the low temperatures, and this leaves behind a concentration of oxygen molecules on the ring surfaces and, maybe through ion-neutral chemistry, molecular oxygen is formed, but this is not yet well understood.


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Tuesday, August 23, 2005

I Read it in the New York Times

A lot of folks have commented on the recent series of articles on Intelligent Design in the New York Times. A wrap up can be found at Pharyngula. The articles can be found here, here and here.

The author of the second paper showed up and replied here.

Pharyngula has linked to a much better article than the three New York Times articles. It can be found here. It also discusss Intelligent Design. To me this:

But legislation to require that creationism be taught as a counterpoint to evolution is being discussed in Colorado and across the country. And if history is any guide, we all should be very afraid of politicians legislating science education.

Mitton recalled an Indiana legislator's attempt in 1897 to require that schools simplify pi (the ratio of the circumference of a circle to its diameter) from the clumsy but accurate 3.141592... to 3.2.

If this had been enforced and the products of Indiana schools tried to apply it, he said, "bridges would fall down, structures couldn't be built," engineering would be impossible.

It's simple: Without pi, there is no mathematics.

And without the teaching of evolution, biology doesn't have a prayer.

Was the best quote in the article. The best thing about it was that there is none of the he said/she said style of journalism. The article educated and informed people about an important issue making news - and did not pull any punches.

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When Did Humans Start Wearing Shoes?

According to Eric Trinkaus we started wearing shoes approximately 30,000 years BP.

A 26,000 year-old early modern human, Dolni Vestonice 16 from the Czech Republic, showing the reduced strength of the bones of the lesser toes. It is one of three partial foot skeletons from Dolni Vestonice that shows the reduced lesser toe strength, all dating to about 26,000 years ago. (Photo Credit: Erik Trinkaus / Czech Academy of Sciences)

He analyzed the the feet of middle and upper Paleolithic humans and compared the strength of the toes (based on robusticity, size of muscle markings, etc.) with leg strength (I'm assuming this means the tibia and fibula - again based on robusticity, size of muscle markings, etc.). Trinkaus notes that around 30,000 years ago toe strength underwent a reduction while calf strength remained the same. He chalks up this decrease in toe strength to the full time use of supportive footwear:

During barefoot walking, the smaller toes flex for traction, keeping the toe bones strong. Supportive footwear lessens the roll of the little toes, thus weakening them.

Trinkaus is certainly one of the more original thinkers in Paleoanthropology, but I am a little bit skeptical. Granted, I haven't read the article in the October Journal of Archaeological Science (abstract available here - so if someone out there with access wants to send me a copy of the article...?). My first thought on reading the Science Daily article was what about allometry and/or sexual dimorphism?

Added Later: Go here for more.

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Monday, August 22, 2005

Culture and Chimpanzees

Culture is one of the seminal concepts in anthropology. A lot of people have tried to define it. Starting with E. B. Tyler (one of the founding fathers of anthropology) who defined culture thusly:

"culture or civilization, taken in its wide ethnographic sense, is that complex whole which includes knowledge, belief, art, morals, law, custom, and any other capabilities and habits acquired by man as a member of society"

Others, such as Linton defined culture this way:

"...the sum total of ideas, conditioned emotional responses, and patterns of habitual behavior which the members of that society have acquired through instruction or imitation and which they share to a greater or lesser degree..."

Perhaps one of the best definitions of culture - well more a list of the characteristics that define a culture - was given by Murdock in his 1940 paper for the American Sociological Review entitled "The Cross Cultural Survey". Murdock found that culture could be characterised by the following traits:

1) Culture is learned - that is it is not instinctive or biologically transmitted but is acquired by each individual through their life experiences.
2) Culture is inculcated - The above are transmitted from parent to child over successive generations. This means that not only are techniques and knowledge imparted but mistakes are corrected as well. Consequently, there is a certain amount of indepoedence between the traits being passed and the individual bearers of culture.
3) Culture is social - in other words it is shared between individuals living in groups and is kept uniform via social pressure.
4) Culture is ideational - that is certain kinds of behavior should conform to established precedent. Put another way, there are certain ideal norms or patterns of behavior (think mental template)that the bearers can use to guide their behavior.
5) Culture is gratifying - that is it satisfies - or provides a means for satisfying - biological and psychological neads
6) Culture is adaptive - to both the geographic and social environment
7) Culture is integrative - In other words, the elements of a given culture tend to form an integrated whole - although historical events - such as improved technology - exert a disturbing influence.

One could, and many people have, argue with most of these definitions. There are, however, certain commonalities in most definitions of culture. Especially, the parts about culture being shared and learned. For the longest time, cultural behavior was restricted to humans (implicit in E. B. Tylor's definiton above). For example, it used to be thought that tool use (ala Oakley's "Man the Tool-maker)was a cultural trait restricted to humans. Then tool use among chimps was discovered. Language was another cultural characteristic that - it was thought- resided only in humans. Indeed, most definitions of culture (See Kroeber and Kluckhohn's 1952 book "Culture: A Critical Review of Concepts and Definitions" for over 200 definitions collected from the literature) state overtly or imply that language, and it's ability to transmit acquired knowledge, is necessary for culture to exist. Then it was discovered that chimps, gorillas and orangs could use sign language.

A recent study at the Yerkes National Primate Research Center has cast an interesting light on culture. Researchers devised an ingenious experiment to study cultural transmission in chimps. Rather than trying to create an artificial situation like you see in some of the language experiments (usually with one chimp in isolation), researchers decided to test chimps in a group situation:

In the study, researchers introduced a naturalistic foraging task into three groups (two experimental and one control) to see if chimpanzees can learn by observation. While unseen by other chimpanzees, researchers taught a high-ranking female from each of the two experimental groups a different way, either Lift or Poke, to retrieve food from a system of tubes called Pan-pipes. Once the two females mastered the task, other chimpanzees within their groups were allowed to watch them perform the new skill over a seven-day period before all group members were allowed to use the tool. According to the researchers, group members gathered around the local expert, watched attentively and proved successful when allowed to try the task on their own. The third group, which did not have the benefit of a local expert and was left to decipher the task on its own, was unsuccessful in retrieving food from the Pan-pipes.

The upshot is that:

"This study demonstrates apes do copy members of their own species and they develop different traditions by doing so," said Dr. Horner. "It makes it likely differences in tool use between wild chimpanzee communities in Africa indeed reflect a form of culture and establishes another link between human and chimpanzee societies."

Occassionally, chimps that learned Poke would discover Lift, try it a few times, then revert to Poke. Ditto for chimps that learned lift. This has been taken to indicate a conformity bias among chimps every bit as strong as that among humans:

The conformity bias finding was an unexpected, but equally important, result of this culture study, according to Dr. Horner. A few members of each group independently discovered the alternative method for freeing food from the Pan-pipes, but this knowledge did not endanger the groups' traditions because most of these chimpanzees reverted back to the norm set by their local expert. "Choosing the group norm over the alternative method shows a level of conformity we usually associate only with our own species," said Dr. Horner. "By using the group's technique rather than the alternative method, we see the conformity is based more on a social bond with other group members than the simple reward of freeing the food."

But think about it in terms Murdock's definition of culture given above. The different methods of getting the food were learned, certainly social in that the techniques were shared among members of the group, ideational in that each group had a mental template or norm to guide their behavior, gratifying in that biological needs were satisfied, and adaptive. Whether, the behavior was inculcated, in the sense mentioned above, and integrative remains to be seen because the experiments were short term and you would need a long term study to decide those two questions. What about conformity - something getting this study a lot of attention? According to the study:

A characteristic traditionally thought to be solely human, the propensity to conform, may be part of an evolutionary progression. "These results suggest an ancient origin for the cultural conformism that is so evident in humans," said de Waal. "Further research may reveal these findings to be more widespread throughout the animal kingdom."

One thinks that here people are confusing the modern, stereotypical definition, of conformism ("Like, gaw'd Levi's are soo 15 minutes ago...") with the ideational aspects of culture. Although, in most cultures social pressure can be exerted to insure uniformity, there is room for ideosyncratic behavior. Incidentally, the studies doesn't mention whether or not social means were used to induce conformity. It just says that the chimps that discovered alternate means reverted back to the norm of their group, i. e. the mental template for getting food that they already had.

Interestingly enough, the New Scientist article mentions that the poke method was more efficient at getting food than the Lift method. Chimps that learned Lift but discovered, independently, Poke reverted to Lift. I would like to see more on this before I chalk it up to "conformity", especially because of the way the study is portrayed. "Copycat chimps are cultural conformists" is the title of the New Scientist article. The Science Daily title is better but in reading both pieces I don't get the feeling that the authors really understood the concepts they were discussing.

Leaving the conformity issue aside, what this study does indicate is that we have to look far back in human history to discover the origins of culture - and this study certainly prooves that chimps are culture bearing organisms. It goes without saying that the implications of this study for our understanding the behavior of Australopiths and early Homo will probably need to be revised somewhat.

Cool stuff!

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Sunday, August 21, 2005

Einstien Manuscript Discovered

A student working on a master's thesis has discovered the original manuscript of one of Albert Einstein's papers. According to the news report:

The paper predicted that at temperatures near absolute zero — around 460 degrees below zero — particles in a gas can reach a state of such low energy that they clump together in one larger "mono-atom."

The idea was developed in collaboration with Indian physicist Satyendra Nath Bose and the then-theoretical state of matter was dubbed a Bose-Einstein condensation.

In 1995, University of Colorado at Boulder scientists Eric Cornell and Carl Wiemann created such a condensation using a gas of the element rubidium and were awarded the Nobel prize for physics in 2001, together with Wolfgang Ketterle of the Massachusetts Institute of Technology.


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Friday, August 19, 2005

Friday Chimpanzee Blogging: The Origins of Brain Lateralization

One of the more interesting subjects paleoanthropologists are interested in is the evolution of the brain. More particulary, they are interested in the origins brain lateralization. A researcher associated with Yerkes National Primate Research Center thinks she has found the beginnings of an answer.

Elizabeth Lonsdorf studied 17 chimps at Gombe National Park in Tanzania:

She and colleague William Hopkins noted which hand mothers and offspring used and found most of the chimpanzees showed a clear preference for one hand or the other, with the majority being left-handed.

Furthermore, they determined the handedness trait runs in families, with females tending to produce offspring with the same hand preference.

They also note that:

"...wild chimpanzees are usually left-handed and pass that preference to their offspring, while chimps in captivity are usually right-handed."

The above is a picture of a chimp in a zoo - note it is holding a tube in it's left hand and using a tool to fish out treats in it's right hand.

The above picture is of a chimp in the wild, unfortunately, it is using a tool in it's right hand as well. One picture, I hasten to add, does not invalidate the theory. At any rate, this suggests that the beginnings of brain lateralization was present before the split between humans and chimpanzees and occured at least five million years ago. One of the interesting aspects to come from the Study is that:

Another interesting aspect of the new research is that it demonstrates chimpanzees learning by imitation. The adult females studied each had quite distinct patterns of using short, medium and long fishing tools to varying degrees. The lengths of tool used by daughters greatly resembled their mothers’ choices, whereas the sons’ did not. “Obviously they are paying attention to their mother’s technique, while the sons are not,”

Here is a link to some interesting, short, movies of chimps:

Images of Life on Earth

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Wednesday, August 17, 2005

Baby Octopi Blogging: An Aurora Update

Regular readers of my blog may remember this post on Aurora the octopus. To refresh your memory:

A month later, Aurora laid tens of thousands of eggs. Her sense of mothering was strong, despite the fact that her eggs didn't appear to develop and aquarists eventually believed they were sterile.

Day in and day out, she sucked in water through her mantle and sent waves of cleansing water over the eggs. She defended them against hungry sea cucumbers and starfish.

I have checking from time to time to see if I can find more information on Aurora and I finally have some, slightly old (it's dated 7/3/05) news concerning Aurora and her offspring:

Aurora's eggs appear to have mostly hatched out with a few clusters still containing embryos still to emerge. Aurora has become more active again, often seen stretching out across the tank window. The numbers of emergent paralarvae vary daily but the end of the hatch appears in sight.

Paralarva count on May 30 – 178 babies swimming and feeding in their rearing tank and they appear to have hearty appetites.

Most of these little swimmers were transferred from a separate group of Aurora’s eggs housed in a holding tank. However, Aurora’s own egg brood also continues to emerge in view of SeaLife Center visitors. This photo shows her Monday afternoon after a short bit of activity twirling her arms and casting off old sucker disk skin. She momentarily opened up her arms widely enough to allow a better examination of a few of her many remaining unhatched eggs.

Currently, the paralarvae are eating suspended daphnia and live brine shrimp nauplii larvae periodically pulsed into the rearing tank. In addition, many of the baby octopuses are now also able to rip pieces off of small shrimp suspended in the rearing tank for a few hours. This latter food item is easy to add and remove before it becomes a mess to clean up. We are still testing and evaluating various food types recognizing that probably no single food item may be a universal diet. The oncoming challenge will be anticipating and matching different foods to the growing animals’ changing food preferences.

As for the developing paralarvae held elsewhere in the SeaLife Center, we are working with a group that now contains 90+ individuals in a rearing system designed for feeding and long-term rearing. Our aquarists report there are some that have grown larger noticeably feeding on a diet of mashed krill, Mysis shrimp and clam.
Additionally many more of Aurora's brood have been added to an outdoor tank with natural plankton production during the long Alaska summer days to more or less fend for themselves. This group is less accessible for frequent evaluation until later in the year but may surprise us with survivors that grow and settle out of the water column to live on the tank bottom.

So apparently, as of July third Aurora was still alive! Which is good as in my last post I mentioned there was some indication that she might die. That's one tough, determined octopus!

According to MSNBC this is an actual picture of Aurora.

And here is a series of pictures showing the development of the baby octopi.

Are they not the cutest things you have ever seen? Well, okay Aye-Ayes are cuter but these run a close second!

Read more!

Tuesday, August 16, 2005

Why is the DNA Code Based on Codons

As everybody knows the genetic code is based on deoxyribonucleic acid (DNA). The DNA is composed of four different molecules arranged in codons with three per codon. Consequently, there are 64 possible arrangements of three molecules each. Each codon codes for one of 20 different amino acids, which in turn can make an almost infinite number of proteins. Since there are 64 arrangments but only 20 amino acids are used there is a certain amount of redundancy in the genetic code. One of the more interesting questions in genetics is how such a system developed. Recent research is beginning to answer that question.

One of quirks of the genetic code is that there are groups of codons which all translate to the same amino acid. For example, the amino acid leucine can be translated from six different codons whilst some amino acids, which have equally important functions and are translated in the same amount, have just one.

The new theory builds on an original idea suggested by Francis Crick - one of the discoverers of the structure of DNA - that the three-letter code evolved from a simpler two-letter code, although Crick thought the difference in number was simply an accident “frozen in time”.

The University of Bath researchers suggest that the primordial ‘doublet’ code was read in threes - but with only either the first two ‘prefix’ or last two ‘suffix’ pairs of bases being actively read.
By combining arrangements of these doublet codes together, the scientists can replicate the table of amino acids - explaining why some amino acids can be translated from groups of 2, 4 or 6 codons. They can also show how the groups of water loving (hydrophilic) and water-hating (hydrophobic) amino acids emerge naturally in the table, evolving from overlapping ‘prefix’ and ‘suffix’ codons.

“When you evolve our theory for a doublet system into a triplet system, you get an exact match up with the number and range of amino acids we see today,” said Dr van den Elsen, who has worked with Dr Stefan Babgy and Huan-Lin Wu on the theory.

One of the more interesting aspects of this is that it explains how the genetic code can maintain it's integrity. Because, for example, translation errors can result in another amino acid with the same charactersitics. Even more interesting is it's prediction about two amino acids (glutamine and asparagine). Both denature (or melt) at lower melting points than the other amino acids and researchers suggest that both were added somewhat later in evolution:

One possible reason for this is that the Last Universal Common Ancestor (LUCA), which evolved into all life on earth, lived in a hot sulphurous pool or thermal vent. As it moved into cooler conditions, it was able to take up these two additional amino acids and evolve into more complex organisms. This provides further evidence for the debate on whether life emerged from a hot or cold primordial soup.

Support for the theory comes from the fact that several aminoacyl-tRNA synthetases link with pairs - rather than triplettes - of bases during translation:

“There are still relics of a very old simple code hidden away in our DNA and in the structures of our cells,” said Dr van den Elsen

Which, of course, provides an avenue for future research.

I wonder what Intelligent Design advocates will make of this since it is a good example of how information content can be increased via natural selection. Something that Intelligent Design advocates say is impossible.

Read more!

Monday, August 15, 2005

Is It Worth It?

It seems the goals the administration has for Iraq keep changing. It started with WMD, then changed to Sadam was an evil that had to be destroyed, went to making Iraq a shining beacon of democracy -via draining the swamp- that will change the face of the mideast. Over the last couple of weeks it has changed again, schizophrenically divided between two competing visions.

From WAPO (via Eschaton):

The United States no longer expects to see a model new democracy, a self-supporting oil industry or a society in which the majority of people are free from serious security or economic challenges, U.S. officials say.

"What we expected to achieve was never realistic given the timetable or what unfolded on the ground," said a senior official involved in policy since the 2003 invasion. "We are in a process of absorbing the factors of the situation we're in and shedding the unreality that dominated at the beginning."

Administration officials still emphasize how much they have achieved despite the chaos that followed the invasion and the escalating insurgency. "Iraqis are taking control of their country, building a free nation that can govern itself, sustain itself and defend itself. And we're helping Iraqis succeed," President Bush said yesterday in his radio address.

Iraqi officials yesterday struggled to agree on a draft constitution by a deadline of tomorrow so the document can be submitted to a vote in October. The political transition would be completed in December by elections for a permanent government.

But the realities of daily life are a constant reminder of how the initial U.S. ambitions have not been fulfilled in ways that Americans and Iraqis once anticipated. Many of Baghdad's 6 million people go without electricity for days in 120-degree heat. Parents fearful of kidnapping are keeping children indoors.

Barbers post signs saying they do not shave men, after months of barbers being killed by religious extremists. Ethnic or religious-based militias police the northern and southern portions of Iraq. Analysts estimate that in the whole of Iraq, unemployment is 50 percent to 65 percent.

U.S. officials say no turning point forced a reassessment. "It happened rather gradually," said the senior official, triggered by everything from the insurgency to shifting budgets to U.S. personnel changes in Baghdad.

The ferocious debate over a new constitution has particularly driven home the gap between the original U.S. goals and the realities after almost 28 months. The U.S. decision to invade Iraq was justified in part by the goal of establishing a secular and modern Iraq that honors human rights and unites disparate ethnic and religious communities.

But whatever the outcome on specific disputes, the document on which Iraq's future is to be built will require laws to be compliant with Islam. Kurds and Shiites are expecting de facto long-term political privileges. And women's rights will not be as firmly entrenched as Washington has tried to insist, U.S. officials and Iraq analysts say.

"We set out to establish a democracy, but we're slowly realizing we will have some form of Islamic republic," said another U.S. official familiar with policymaking from the beginning, who like some others interviewed would speak candidly only on the condition of anonymity. "That process is being repeated all over."
(emphasis mine). Apparently, Cindy Sheehan's son died so an Islamic Republic could be built in Iraq. Or maybe he died because of "...the unreality that dominated at the beginning...". If this is too gloomy an assesment for you take comfort. There is another reason for the invasion. Also from WAPO:

Pessimists increasingly argue that Iraq may be going the way of Lebanon in the 1970s. I hope that isn't so, and that Iraq avoids civil war. But people should realize that even Lebanonization wouldn't be the end of the story. The Lebanese turned to sectarian militias when their army and police couldn't provide security. But through more than 15 years of civil war, Lebanon continued to have a president, a prime minister, a parliament and an army. The country was on ice, in effect, while the sectarian battles raged. The national identity survived, and it came roaring back this spring in the Cedar Revolution that drove out Syrian troops.

One has to ask, though, if that is enough to justify this from the New York Times:

When you talk to close relatives of men and women who have been wounded in the war, it's impossible not to notice the strain that is always evident in their faces. Their immediate concern is with the wounded soldier or marine. But just behind that immediate concern, in most cases, is the frightening awareness that they have to try and rebuild a way of life that was also blown apart when their loved one was wounded.

Ms. Olson, who is 45 and divorced, gave up everything - her work, her rented townhouse, her car - and moved from Tacoma to a hotel on the grounds of Walter Reed to be with her son and assist in his recovery.

"He was still in a coma when I got here," she said. "He didn't have his eyes open, and he was hooked up to all the machines. When he did open his eyes a couple of days later, he didn't respond. His eyes didn't follow me. That was a scary moment. But the following day his eyes started following me."

Corporal Rosendahl has improved a great deal since those days and recently has been allowed to go with his mother on brief excursions away from the hospital. "It's difficult for him," Ms. Olson said. "But in those first weeks here he couldn't move a finger. So this gives me so much hope."

Ms. Olson is a paralegal who did work for several lawyers in Tacoma. She also worked as a claims analyst for the city's transit system. With that work gone, she is now living on the $48 per diem she receives from the Army for food and lodging, along with money that she has reluctantly been drawing from her son's Army pay, and assistance she is receiving from another son, Keith, who is 27.

She has also received help from charitable organizations that assist military families.

"My son is the most important thing," she said, "and I knew that if I was going to be with him, I wouldn't be able to meet my financial obligations."

So she gave up the townhouse and "turned in" a Honda Accord that she had purchased just a year earlier. "Voluntary repossession," she said.

Voluntary that your son is of no further use you can have him back...voluntary repossession...but not before you give up your livelihood, not before you give up your house and your car...voluntary repossession...oh and here's 48 bucks - hope it helps.
It isn't right that so many have paid so much for so little.

Read more!

The Simpsons and Religion

Last nights episode had Homer and Bart converting to Catholicism. Marge, at one point, kidnaps Bart to try and show him that Protestants can have fun too. Says Homer "why does she always interfere with my occassional interest in my children" and wants to know why he can choose his own faith. Lisa chimes in with something to the effect that everybody has the right to choose their own religion "...that's why I choose Buddhism..." she says. A nearby catholic priest says "Yes, every child has an imaginary friend" I almost fell out of my chair I was laughing so hard at the irony.

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Sunday, August 14, 2005

Earth's Early Atmosphere and the Search for Life on other Planets

Model Gives Clearer Idea Of How Oxygen Came To Dominate Earth's Atmosphere

Researchers interested in how earth's atmosphere came to be dominated by oxygen have come up with an interesting model to explain why there was a lag between the origin of photosynthesis and the domination of earth's atmosphere by oxygen.

There were several processes at work. First, gasses emitted from volcanoes combined with the oxygen and acted as an oxygen sink. Second, oxidation of iron from space bombardment acted as a second sink. Researcers found that varying the estimates of iron content in the earth's crust could change the time frame by up to a billion years in one direction or the other.

Here is how it works:

Earth's oxygen supply originated with cyanobacteria, tiny water-dwelling organisms that survive by photosynthesis. In that process, the bacteria convert carbon dioxide and water into organic carbon and free oxygen. But Claire noted that on the early Earth, free oxygen would quickly combine with an abundant element, hydrogen or carbon for instance, to form other compounds, and so free oxygen did not build up in the atmosphere very readily. Methane, a combination of carbon and hydrogen, became a dominant atmospheric gas.

With a sun much fainter and cooler than today, methane buildup warmed the planet to the point that life could survive. But methane was so abundant that it filled the upper reaches of the atmosphere, where such compounds are very rare today. There, ultraviolet exposure caused the methane to decompose and its freed hydrogen escaped into space, Claire said.

The loss of hydrogen atoms to space allowed increasingly greater amounts of free oxygen to oxidize the crust. Over time, that slowly diminished the amount of hydrogen released from the crust by the combination of pressure and temperature that formed the rocks in the crust.

"About 2.4 billion years ago, the long-term geologic sources of oxygen outweighed the sinks in a somewhat permanent fashion," Claire said. "Escaping to space is the only permanent escape that we envision for the hydrogen, and that drove the planet to a higher oxygen level."

The most intersting part of the article is the last sentence:

"There is interest in this work not just to know how an oxygen atmosphere came about on Earth but to look for oxygen signatures for other Earth-like planets," Claire said.

Note that the one thing missing in this search for life on other planets is Intelligent Design

Read more!

Saturday, August 13, 2005

I'm All Alone...

I'm all alone, there's no one here beside me,
My troubles are all gone, there's no one here to deride me..."

I've been getting over 200 hits a day lately, but few comments outside of a small group of great people. So I just thought I would mention that I do like comments and try to respond to each and every one of them. Really, it's okay, I don't bite!

I also just noticed that I have received over 20,000 visitors since I started this site (which is a heck of a lot more than what I thought I'd have so (imagine this next bit in your best Eyore voice):

Thanks for noticing, I'm just grateful for the attention, don't leave any comments if you don't feel like it, I'm just happy to have you visit. I don't really need comments...

Have I whined enough yet?

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Life is Sooo Unfair

Do to some recent feedback on my Naked Mole Rat posts I thought there might be a way of making some money off of it - maybe millions - so I could retire in style. My first thought was I could create a Naked Mole Rat stuffed animal or maybe a beanie baby (could you imagine the reaction of some kid pulling one of these ugly spuds out of a toy meal?). But then I found this:

from here

Oh well, back to the drawing board.

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Ancient Ozone Holes and Mass Extinctions

This blog is, primarily, about evolution. Whenever possible I like to publish stories about some of the interesting techniques scientists use to learn things about the past. This is another along those lines.

Lycopodium magellanicum is a species of clubmoss native to South America, and islands in the southern Atlantic and Indian oceans.

The leaves are arranged in cones which bear sporangia containing spores of one type only.

Reserchers examined the spores of Lycopodium magellanicum for UV-B screening pigments. The idea being that as the ozone layer thins an increase in UV-B screening pigments should be observed. This is exactly what they found. Basically this first step was a test to see if the methodology (examining spores for UV-B screening pigments) would yeild results relevant to the question of whether or not we can detect ozone depletion in the past. Having answered the question in the affirmative, the researchers are turning their attention to the Permian-Triassic boundry some 250 million years ago (I should mention that the chemical traces of UV-B screening pigments can be detected in the geological record).
One of the important events, geologically speaking, to occur around the end of the Permian was the volcanic eruption of the Siberian traps, a byproduct of which is the destruction of the ozone layer. Hypothetically, this would mean we should detect an increase in UV-B screening pigments in spores from that time period.

For more info:


New Window Into Ancient Ozone Holes

Permian Extinction

Rocks Reveal Details of Mass Extinction

Read more!

Friday, August 12, 2005

Naked Mole Rat Porn: or This Means War

One of the blogs I visit on a regular basis is Dharma Bums There, the stories are always interesting, the writing is always great and the pictures would make Ansel Adams weep in jealousy. Today, I visit their site and what do I discover but Squirrel Porn! I was very shocked...that I didn't think of it first. So without further ado I am proud to present: NAKED MOLE RAT PORN!

I'd really like to see someone top that!

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Friday Naked Mole Rat Blogging

Naked mole rats have a pretty distinctive social structure - which in some ways is similar to that found in social insects.

From Science Daily:

They live in Somalia, Ethiopia and Kenya. They are 3-6 inches long, have pink furless skin, tiny eyes which never see the light of day, and long front teeth for digging. Despite their tiny size, the naked mole-rat family den may stretch for 2 miles entirely underground, with various rooms. In one room, a plant root protrudes to provide a meal; in another is the "potty." When a new hallway is needed, usually for new food supplies, the naked mole-rat siblings form an earth moving chain to pass dirt out a hole which later is covered to block out intruders.

The most unusual room is the largest. It's where Momma naked mole-rat produces more babies – as many as 12 at a time every couple of months. Here she is stoked by her numerous mates and tended to by any number of offspring whose lot in life - if not to dig tunnels - is to keep Momma happy.

Apparently, this is a really good case of altuistic social behavior in mammals, where some mole rats give up reproduction and help related mole rats care for the young. Researchers are currently investigating the relationship between DNA and social structure:

Ingram looked at regions of DNA - specifically the microsatellites, which represent distinct DNA bands, much like a satellite, which separate from the main DNA band. These rapidly changing regions of DNA don't code for any particular trait, as far as scientists can tell. Ingram thought these regions shouldn't be overlooked.

"If there is a random-mating population, there are a lot of sizes of those DNA bands, but a child only gets one set from the mother and one from the father," Ingram noted. These markers are used in paternity cases for humans, she said.

She looked for changes in the processes and patterns of this strand in mole-rats, she said.

"The current methods of analyses of microsatellite markers are oversimplified and may lead to incorrect conclusions when looking at natural populations and their social structures," Ingram said. "The relationship among members of the mole-rat family are well-accepted. Some species (of mole-rat) are strictly solitary while others, such as the naked mole-rat, are highly social."

DNA markers, like the satellites, are important because they can reveal how traits pass from one mother to her multitude of babies conceived by various interrelated fathers. That may help understand why scores of offspring in the family are willing to support the mother naked mole-rat.

Read more!

Thursday, August 11, 2005

4,000 Year Old Archaeological Site In Danger

The above is a picture of a squirrel pipe found at the Davis site in Eureka, MO (a town not all that far from St. Louis). The site dates to the Archaic and also has Woodland and Mississippian occupations as well.

The above is a picture of a cookpot of the Mississippi Plain variety.

The problem is threefold. First, the site has not been carefully explored - only a preliminary survey was carried out. Second, developers want the land to build a subdivision:

Owned now by Buccaneer Properties, the knoll was included in a recent development proposal before the St. Louis County Council for a zoning change to build 80 homes on 55 acres on Eureka Road, just east of Eureka.

That proposal got bad reviews from the county planning and zoning commission. But the fate of the knoll, where two civilizations appear to be on a collision course, still is in limbo.

Third, Missouri law regardin archaeological sites:

"Missouri has no laws requiring investigation of important artifact sites before they are built over, and only the flimsiest requirements for notification to authorities if a developer uncovers bodies..."

A complete excavation of the Davis site could add critical missing pieces to the puzzle. Harl said that would cost between $50,000 and $100,000.

Illinois law requires the developers of such a site to bear this cost, but Missouri has no such obligation, although a seller of the property could make the sale contingent upon the developer paying for the dig.

A preliminary study was done of the site several years back:

Jack Davis took his squirrel pipe and other pieces to be examined by archaeologists from the Missouri Archaeological Society in 1987. Two society members, professors Michael and Neathery Fuller of St. Louis Community College, returned to the Davis home, documented the collection and later set up a Web site to display the squirrel pipe, at Davis Site.

That site exploration was a preliminary survey, not a major field effort.

Read more!

Tuesday, August 09, 2005

Cindy Sheehan

A lot of bloggers have written about this sory so it should be pretty familiar to everyone. A woman loses her son in Iraq and wishes to question the president - her president - about it. The President hides at his ranch and threatens to have her arrested in the name of national security.

So, a greiving mother stands on the side of the road waiting for an answer that will never come while the President - her President - sits in his ranch surrounded by all the panoply of power and avoids a question - and really it's such a simple question - that every mother has the right to ask and every mother should demand the answer. Yet the President - her President avoids the question. Perhaps the question strips all the false pretenses and vanities that our President has built up about himself. Perhaps the answer would reveal something in the soul of our President that he dare not face. Perhaps answering the question would be like looking in the mirror and seeing Richard the Third staring back at him.
Perhaps his reflection would say:
"Perjury, perjury, in the high'st degree,
Murder,stern murder, in the dir'st degree -
all several sins, all used in each degress,
Throng to the bar, crying all 'Guilty, guilty!'
I shall despair. There is no creature loves me,
And if I die, no soul shall pity me."

It seems strange to see a woman standing in the road asking for so little while the leader of the most powerful nation on earth sits behind fences, sits behind the Secret Service, sits behind the pretense of national security. Some moral clarity is lacking here that perhaps an answer might reveal. I think it is shame that prevents the President from going out in the street and answering this woman, I think if he were to come face to face with her the facade would crumble - being stripped of all the illusions you hold about yourself can be painful.
So, I say Mr. President you are no gentleman, you are no christian, you are no leader until you can face the grief of a mother crying - and perhaps dying a little - for her son.

Read more!

New Species of Lemur Discovered

Ain't it cute? It's called Microcebus lehilahytsara and was discovered in Madagascar (where else).

You can find more info here

Added Later: Thoughts from Kansas has a more indepth post on the lemur - as well as pictures of the second new lemur. Check it out.

Added Even Later: One of the more interesting things about Josh's post is the few tidbits of info we learn about Steve Goodman. We need more of this kind of thing. Not because we should all be name droppers but because it puts a human face on science and makes it harder for those who oppose science. If one knows about someone like Steve Goodman who "...basically lives in the field, coming back to the Field Museum now and then to drop off specimens..." it becomes harder to believe scientists are engaged in some shadowy conspiracy to silence critics and enforce ideological conformity, etc.

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Forensic Science

This is interesting - and scary! Apparently, Forensic science isn't quite as scientific as we all thought:

"The underlying principles of the identification forensic sciences have never been rigorously scientifically proven," said Jay Siegel, director of the undergraduate forensic science program at Indiana-Purdue University in Indianapolis.

"This includes handwriting, fingerprints, and firearms, and tool marks," he said.

According to a new study, traditional forensic analysis often relies on untested assumptions and semi-informed guesswork. It can also sometimes produce the wrong results.

Drawing on data from 86 DNA exoneration cases, the researchers found that forensic science testing errors and false or misleading testimony by forensic scientists had been leading causes in the false convictions.

In other words, folks are being convicted based on the prestige value of having "scientific" evidence?

One of the researchers, Jonathan Koehler, says it's time for forensic sciences to adopt the culture of other sciences.
"This includes being more conservative, requiring empirical support for claims, adopting higher professional standards, and generally conceding the important role that the possibility of error plays in interpreting results," said Koehler, a professor of behavioral decision-making at the University of Texas in Austin.

Wonder what the intelligent design community will make of that since ID frequently claims Forensic Science as an ally?

Error rates range from 20% (fingerprint analysis) to above 60% (bite marks, voice identification):

During the past decade, scores of people who were convicted of serious crimes have been exonerated by DNA analyses of crime-scene evidence that had not been tested at the time of their trials.

Drawing on data from 86 such cases, Koehler and his colleague, Michael Saks, a law professor at Arizona State University in Tempe, found that forensic science testing errors played a part in 63 percent of the wrongful convictions. Only eyewitness error was a more common factor.

The study also found that forensic scientists are the witnesses most likely to present misleading or fraudulent testimony. In 27 percent of the cases reviewed, expert witnesses were found to have given false testimony.

Part of the problem concerns a concept called discernable uniqueness which states that if two marks appear indistinguishable, they must have been produced by the same object:

"Forensic scientists will likely say that they know it, because they've never found different objects that have identical markings across many years of forensic science. At first blush, this might seem like an impressive boast. But consider this: Suppose that exactly a hundred pairs of firearms out of the estimated 100,000 guns in a Texas town do, in fact, share indistinguishable rifling markings."

"If each of a hundred firearms experts examined ten pairs of guns from the town's gun population every day for ten years, there is about a 93 percent chance that none of the indistinguishable pairs will have come under examination. That is, despite a thousand 'collective years' of forensic science experience—and more than three million gun-pair examinations—the failure to find even a single pair of guns with indistinguishable markings would offer little basis for drawing conclusions about whether bullet markings on guns in this town are indeed unique."

So, if I understand this correctly you would get a lot of false positives - which have to due with sampling procedure.

It goes without saying that this has profound implications for how expert testimony is used by the criminal justice system (and I may do a post on how this impacts fornesic anthropology) - but that is not the point of this post. The point is that those aspects of forensic science which ID proponents argue give the most support to ID are being abandoned by forensic science. They are being replaced by a more rigorous scientific procedure that gives no support to ID.

Read more!

Monday, August 08, 2005

Bilateral Symmetry and the Cambrian Explosion

This is cool.

Bilateral symmetry is a character of most organisms (except sponges, jellyfish, ctenophores and echinoderms). According to my book on vertebrate structure (An Analysis of Vertebrate Structure, 2nd ed, by Milton Hildebrand) this is a fundamental characteristic of vertebrates. A 2004 discovery has pushed the origins of bilateral symmetry back to approximately 600 million years ago - to the Precambrian.

From the article:

The discovery is crucial. It suggests that the earliest ancestors to modern-day animals developed before the Cambrian explosion. That so-called explosion period, 488 to 542 million years ago, envelops the time on Earth when most animal groups first appeared.

In his article, Bottjer suggests that the famous Cambrian explosion was more accurately "the exploitation of newly present conditions by animals that had already evolved the genetic tools to take advantage of these novel habitats."

Rather than solely genetics, it may have been the critters' ability to grow large that led to the explosion. The growth spurt, Bottjer said, may have been caused by a drastic rise in dissolved oxygen in seawater. More oxygen for breathing reduces size constraints.
(emphasis mine - afarensis)

Even more interesting is the process underlying the discovery:

But it took incredible patience and work to uncover the fossils, which measure about 200 micrometers across. The team sliced the samples into thousands of see-through-thin layers and examined them under a microscope. Finally, among the 10,000 slides, the collaborators discovered 10 examples of the fossil type they had been seeking. After more months of painstaking analysis, the group confirmed the examples were fossils of miniscule bilaterian animals.

So after plenty of hard work a phenomenal new discovery was made - one that throws some light on Precambrian life and the Cambrian explosion. Another talking point knocked out from beneath ID proponnents.

Teach the Controversy says I.

Note: those of you with a digital subscription to Sciantific American can go here for more info

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More This and That: Dembski and Human Evolution

Why is it when you do a Google search on Ape Human DNA you get a bunch of creationist sites?

While searching for the above I stumbled across Reflections on Human Origins by Dembski. Haven't had time to read it yet but apparently we get Dembski's notions on human evolution - should be hysterical. Soon as I print and read it I'll do a post on it.

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Globalization and Diet

Malnutrition And Obesity Increasingly Co-exist In Global Community

The part of the impact of globalization is an increase in diabetes and hypertension:

"A global nutrition transition has and is occurring on a continuum. While problems of under-consumption and poor nutritional status continue to exist, increasingly problems of diet/chronic diseases are emerging as significant public health issues globally," says Kennedy. A demographic shift has resulted in increased life expectancy in many countries, and in some countries, this means an older population. Closely tied with this change in age structure is an epidemiological shift which has decreased communicable diseases and increased chronic diseases, such as diabetes and hypertension, she reports.

"An increase in availability of more high-fat and sugar-laden foods has led to a surge of nutrition-related chronic diseases around the world. At the same time that diets have changed, physical activity has decreased. The highest rates of overweight and obesity are now often found in low-income groups. Many populations have been left in the midst of an obesity crisis that exists with food insecurity and under-nutrition," Kennedy summarizes. "Chronic diseases can no longer be labeled as 'diseases of affluence.' Unfortunately, the message that the global nutrition profile is changing hasn't reached policy makers, and they need to be aware that it is occurring."

This happens whenever people change to a western style diet (the New World Syndrome is a good example).

In a separate article published in the May 2005 American Journal of Clinical Nutrition, Kennedy and co-author Linda Meyers, PhD, Director of the Food and Nutrition Board, Institute of Medicine, note that large parts of the developing world are plagued with micronutrient deficiencies. "Deficiencies of micronutrients, such as iron, iodine, zinc and vitamin A, contribute to 'hidden hunger' and while the statistics on micronutrient status for women in developing countries are scarce," she says, "it is clear that a large percentage of women from developing countries suffer negative health and nutrition consequences."

Read more!

Sunday, August 07, 2005

WHich Harry Potter Character Are You?

Pirate Monkey's Harry Potter Personality Quiz
Harry Potter Personality Quiz
by Pirate Monkeys Inc.

Explanation of the Results:
This type of personality test uses four indexes of personality and the combination of the four is your personality type. The first index relates to how you interact with other people and can be Extroverted (E), meaning you're more outgoing or Introverted (I), meaning you keep more to yourself. The second relates to how you make decisions; whether you're Intuitive (N), getting answers from within, or you rely on Sensing (S) information from your surroundings, using your five senses. The third relates to whether you're more emotional and Feeling (F) or rational and Thinking (T). The fourth relates to whether you prefer things to be organized, meaning you're Judging (J), or you prefer things to be more unbound, meaning you're Perceiving (P).

I can live that!

Note: This is actually your standard Myers-Briggs personality test with a Harry Potter theme added. I've taken these before and the results (for me) are pretty consistent (They are always INTJ).

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Bipedal Locomotion and Semicircular Canals

I am currently working on a post for Transitions involving the molecular evidence for the common ancestry of apes and humans (Note: this is slow going because I am having trouble finding websites with age appropriate discussions of this material - if you know of any let me know as I hate doing posts without giving links for people to get further information). While searching the internet I kept stumbling across a lot of creationists sites disputing this relationship. An incidental finding was an argument concerning bipedality in Australopithicines based on CAT scans of the inner ear morphology. Which is what this post is about.

An example of the creationist argument:

High-resolution computed tomography, known as CT or Cat Scan, was used to scan the inner ear labyrinth of 53 humans, a few dozen apes consisting of pygmy chimps, chimps, gorillas, orangutans, and other species. They also scanned fossil humans (early Homo and H. erectus), Australopithecus and Paranthropus. Reporting in Nature, Wood and his coworkers made height and width measurements of the arc of each semicircular canal from the CT scans. From these measurements, they calculated the radius of the arc's curvature. Among the living specimens, they correlated the arc size of the three semicircular canals with the body mass. Taking body mass into account, modern humans have larger anterior and posterior canals and a smaller lateral canal than the great apes. According to Wood, Homo erectus is the earliest fossil hominid to demonstrate the modern human morphology of the inner ear. The dimensions of Australopithecus and Paranthropus inner ears resemble those of living great apes. Wood says,

"Modern human locomotor behaviour [walking] makes particular demands on the vestibular apparatus for it involves the maintenance of an upright body posture by balancing on very small areas of support."

In other words, humans have the correct inner ear configuration for obligatory upright walking, while apes, australopithecines, and Paranthropus do not.

Finally, Wood concludes his report by saying,

"This study demonstrates that the morphology of the bony labyrinth has the potential to provide information about both the locomotor behaviour and the phylogenetic relationships of early hominids." [Wood, 1994]

Another example:

Some interesting new work has also helped to demolish the idea that the australopithecines habitually walked upright. Computerized X-ray scans are able to reveal the bony structure of the inner ear. The shape of this has been shown to directly reflect patterns of movement. Understandably, humans (the only creatures alive that walk habitually upright) have an inner ear structure which stands out from the rest. When this analysis is carried out on fossil skulls, the results are completely in line with modern creationist expectations. So-called Homo erectus (which even some evolutionists are saying should be reclassified as Homo sapiens) has an inner ear structure just like ours; whereas that of all australopithecines (and habilines) studied are 'decidedly ape-like'.

There is also this Intelligent Design version:

Other recent studies have found that the handbones of Lucy are similar to those of a knucklewalking ape, and that their inner ear canals, responsible for balance and related to locomotion, resemble small inner-ear canals of the great apes rather than larger canals found in humans and other members of the genus Homo.
(Note: I may do something on this article as it purports to lay out an ID theory of human evolution.)

So what does it all mean? Let's start with some basic anatomy. The picture below is a cross section of the inner ear.

The anterior and posterior semicircular canals are labeled "B" (the horizontal canal is not labeled). Note that both of these travel through the bone. Below is a picture showing the semicircular canals in relation to blood vessals and nerves, note also the two organs called utricle and saccule.

The function of this complex is to help maintain balance. The Utricle and saccule respond to linear acceleration (turning your head left or right, for example)and the orientation of the head relative to gravity (tilting your head left or right for example). The horizontal semicircular canal also has a role in the vstibulo-ocular reflex - which allows you to keep you gaze fixed on an object while your head is moving (trying to read a sign in a moving car for example). The semicircular canals respond to angular accelerations.

In humans the horizontal semicircular canal and utricle are at an angle to the naso-occipital plane.

When a person walks or runs they tilt their head forward causing the plane of the horizontal semicircular canal and utricle to be parallel to the earth horizontal and perpendicular to gravity. The anterior and posterior semicircular canals are positioned verticall in the skull and at angles to each other.

Note that the anterior on one side is oriented in the same fashion as the posterior on the other side.

Back to the creationists. Two studies are usually cited by creationists in order to claim that Australopithecines were apes. The first is by Spoor. The second is by Spoor et al and is available here. Spoor et al used CT scans to examine the morphology of the inner ear of 31 extent primates and 12 fossil hominids. They used height and width measurements to compute the radius of curvature of the arc. One of the findings of the study was that arc size of each of the three semicircular canals scaled with body mass. When body size is taken into consideration, humans have larger anterior and posterior and smaller horizontal semicircular canals than apes. They also discovered that the naso-occipital and sagittal orientation of the semi circular canals was the same in apes, humans and fossil hominids (this is not surprising since inner vestibular anatomy is a highly conservative trait in evolution). Spoor et al state that this implies that the ape condition was the likely ancestral condition and that the functional consequences of the elarging semicircular canal arc are not fully understood. They also point out that:

"...if the enlargment of the anterior and posterior canals is functionally related to modern human-like obligatory bipedalis, then at least in this respect the vestibular apparatus of the australopithicines was not adapted to this type of locomotor behavior(Spoor et al 1994, Nature 369:645-648)"

Basically then, what Spoor et al concludes is that australopithicine semicircular canals were somewhat different (in size but not orientation) from humans but they aren't sure what the functional meaning of the differences are. Which isn't quite what the creationists were arguing. One other note, Australopithecus afarensis was not included in the study.

For more on semicircular canals go here

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Organic Molecules in the Early Universe

Nasa's infrared telescope (the Spitzer Telescope) has found traces of organic molocules that are believed to be about 10 billion years old:

Using Spitzer, scientists have detected organic molecules in galaxies when our universe was one-fourth of its current age of about 14 billion years. These large molecules, known as polycyclic aromatic hydrocarbons, are comprised of carbon and hydrogen. The molecules are considered to be among the building blocks of life.

These complex molecules are very common on Earth. They form any time carbon-based materials are not burned completely. They can be found in sooty exhaust from cars and airplanes, and in charcoal broiled hamburgers and burnt toast.

The molecules, pervasive in galaxies like our own Milky Way, play a significant role in star and planet formation. Spitzer is the first telescope to see these molecules so far back in time.

The interesting part about this, to me, is that these molecules play a role in star and planet formation. Not being an astronomer I can only wonder at how many other organic molecules play a role in these processes.

You can also go here for more info.

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Saturday, August 06, 2005

Teaching the Controversy? (ID Blogwhoring)

The ID movement is placing a premium on teaching the controversy. On the other hand they have been roundly criticized for not allowing comments on their blogs. What just dawned on me (I'm a bit slow on the uptake, being a hominid of very little brain - 380 to 450 glorious centimeters), however, is that they don't link to science websites or blogs. Which is odd. I have several links to ID or creationist websites and blogs - granted, they are under a snarky header, but a link is a link. So how 'bout it all you ID and creationist believers? Link to me and truely "teach the controversy"! Be as snarky as you wish about it - just like I am - come on put your money where your mouth is!

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Friday, August 05, 2005

This and That

Philosophy of Biology has two interesting posts on evolutionary biology and ID.

I'll be working on a post for Transitions so posting wil be light.

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Big Game Hunting may have caused giant ground sloths to go extinct

To the right is a picture of two skulls from different types of sloth. The bigger skull belongs to a species that weighed up to three tons and lived 15,000 years ago. The smaller skull belongs to a species that lives 6,000 years ago and weighed about 10 pounds.
Recent research on giant ground sloths provide support for the hypothesis that big game hunting was responsible for the extinction of megafauna:

Determining whether the first arrival of humans or the warm-up of the American continent at the end of the last Ice Age was responsible for the demise of prehistoric sloths has puzzled scientists because both events occurred at the same time, about 11,000 years ago. But by using radiocarbon to date fossils from Cuba and Hispaniola, where humans appeared later than on the North American continent, long after the last Ice Age occurred, UF ornithologist David Steadman was able to separate the two events.

He and his colleagues found the last record of West Indian ground sloths coincided with the arrival of humans 4,400 years ago. The results are published in a Proceedings of the National Academy of Sciences paper this week.
"If climate were the major factor driving the extinction of ground sloths, you would expect the extinctions to occur at about the same time on both the islands and the continent since climate change is a global event," Steadman said.

Steadman said he was not surprised to find that humans were more significant than changes in climate because most species of plants and animals can adjust to changes in temperature. However, the transition between the glacial and inter-glacial period, which resulted in shifts in habitat and the ranges of plants, may have made animal species more vulnerable than they otherwise would have been, he said.

"This is the first time it's been demonstrated for West Indian ground sloths, and West Indian ground sloths are sort of the poster child of big extinct West Indian mammals," he said. "I think this will go a long way to finally put to rest this whole idea that large extinct animals from the West Indies died out in the Ice Age during the Pleistocene Epoch."

You can go here, here, and here for an overview on what the debate is about.

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Thursday, August 04, 2005

Culture of Life Hates Rape Victems

From here (follow the links) the culture of life in Wisconsin has introduced a bill to ban contraceptives and counselling for rape victems because it leads to promiscuity. This has got to be the most idiotic idea to come from the culture of life yet.

With this bill, rape victims will no longer be able to turn to campus health services to obtain emergency contraceptives to prevent an unwanted pregnancy, or receive postrape counseling and education — adding even more stress to a traumatic event.

I've said it before and I will say it again "I will die before I vote republican" and this kind of nonsense is a perfect example of why.

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Dental Microwear Analysis and Australopithecines

This is pretty cool.
Researchers examined several species of monkey teeth in order to determine the microwear patterns produced by a variety of different diets. They then turned their attention to the teeth of Australopithecus africanus and A. robustus:

The new study by Ungar, Brown, and colleagues suggests that, on average, A. africanus probably ate a greater share of soft and tough foods than P. robustus, which probably ate more hard and brittle foods.

The researchers found, however, that there was substantial overlap between the two species in their dental microwear, and presumably, in their diets.

Both species would probably have preferred to eat easy-to-consume, energy-rich foods, such as fruits, when they were available.

A similar phenomenon can be seen in modern chimpanzees and gorillas that live in the same geographical area. These so-called sympatric animals share food resources much of the year, but differ mostly during times of food scarcity.

At these times, gorillas fall back on tougher foods, such as leaves and stems, because their teeth and guts allow them to do so.

This study tends to confirm the idea that A. africanus and A. robustus were specializing in different diets - although not to the extent one would have thought. Seems like a good example of the competitive exclusion principle.

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