Friday, April 29, 2005

Ask and Ye Shall Receive....

Rexroth's Daughter asked me to provide a link to the Delay column, so here it is Delay Non-apologizes . On rereading the post it I also mentioned John Thune. The ggogle search that got Sargent at Arms here was "john thune remarks tom delay". Could be a coincidence but just in case:

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Is Tom Delay Spying On afarensis?

Hi ho, hi ho it's off to gitmo I go!

Yikes Posted by Hello

Apparently, my post on Tom Delay has been visited by the US Senate Sergent at Arms office! Although Delay is in the House... Hmm. Maybe I'll continue to live in St. Louis for a little while longer. Hope they found what they were looking for - wonder if they are going to go all Patriot Act on my sad, sorry, hominid behind? They wouldn't throw a 3.5-2.8 my old hominid in the slammer would they (no, but since A. afarensis comes from Ethiopia we are going to render you for -er - questioning!)

In case they come back:

The first ten amendments comprise the Bill of Rights. The first amendment protects religious freedom by prohibiting the establishment of an official or exclusive church or sect. Free speech and free press are protected, although they can be limited for reasons of defamation, obscenity, and certain forms of state censorship, especially during wartime. The freedom of assembly and petition also covers marching, picketing and pamphleteering.

Amendment I (1791)

Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof; or abridging the freedom of speech, or of the press; or the right of the people peaceably to assemble, and to petition the Government for a redress of grievances.

From The US Sergeant at Arms website.

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Friday Baby Prehensile-Tailed Porcupine Blogging

Baby Porcupine Posted by Hello

From the "Isn't it just sooo darned cute!!" catagory of blogging .

It's a … well, we don't know the sex yet. A female prehensile-tailed porcupine gave birth to this baby at the Smithsonian Institution's National Zoo in Washington, D.C., earlier this month. (The zoo released the photo Tuesday.) Staff say they wouldn't normally know if the newborn is a boy or a girl for another six months, but this time they'll use DNA tests to solve the mystery sooner.
Native to South America, prehensile-tailed porcupines (Coendou prehensilis) are mostly nocturnal. The plant-eaters use their nimble tails to climb and hang from trees and are known to stamp their hind feet when excited. As for their big noses, the rodents' keen sense of smell helps compensate for their nearsightness.

In case you're wondering, the recent birth at the zoo wasn't as painful as the animal's porcupine name might imply. C. prehensilis infants are born with fur, not quills.

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Friday Horshoe Crab Blogging

My mother is from Cape Cod, MA. Periodically (when I was younger) we would go visit her parents in Provincetown. Which, of course, also meant a swim in the ocean. One of my mother's sisters was a slightly mischievious individual who used to delight in telling us horror stories about horsehoe crabs. How they hid in the sand and stung unwary childre, how if you got stung you would bleed for months. Needless to say when we went to the ocean we tiptoed very cautiously around the beach. Everytime we saw a rock buried in the sand, evertime we saw anything slightly unusual we would start screaming for all we were worth "Horseshoe crabs! Help, they are going to get us!" We thought they were far meaner than sharks! Turns out they are related to spiders (and possibly trilobites).

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Below is some horseshoe crab porn for all the Pharyngulans!
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Rated M for mature.

Finally, there is, apparently, a museum devoted to horseshoe crabs! This is an intersting paper on horseshoe crab phlogeny. This site contains a lot of interesting info on horshoe crabs.

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Friday Seal Blogging

I am in the process of reading "New Directions in Ecological Physiology" and I came across something I had to write a post about. It falls in the catagory of "My god, that is so obvious, why didn't I think of it?"

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The northern fur seal (Callorhinus ursinus) is adapted for heat retention while in the water. However, this causes problems when the seal is on land, for example some seals have died of heat shock in 10 c temps.

Artocephalus galapagoensis (galapagoes southern fur seal) has the same problem. It is adapted to cold water - radiates heat (in the water) through highly vascular flippers.
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Zalophus californiansus (California sea lion) also faces this problem. Interestingly enough the California sea lion also occurs in the Galapagoes. So the we can compare how it solves the heat problem with A. galapagoensis. A. galapagoensis
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Both the California sea lion and the Galapagos fur seal are highly polygamous. Males compete for large territories and try to acquire large harems of female seals. So, the question is how do you compete and avoid heat stress? The Galapagos fur seal competes for territory and mates on land, however, its land habitat of choice are wave cut caves and talus slopes containg large boulders (to hide in the shade of). The California sea lion competes for territory in the ocean and comes ashore primarily at night for mating purposes.

Two points need to be made. The first is that, as the above example shows, behavior can be used to expand niches. The second is that adaptations have unintended consequences. Adaptation to cold oceans can lead to problems when it is time to come ashore. The interaction between being adapted to a cold environment and needing to inhabit a warm environment (for however short a time) has yielded a complex answer.

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Thursday, April 28, 2005

Intelligent Design and Kansas On NPR

NPR's Science Friday is doing a segment on the Kansas ID issue. Tune in it should be interesting.

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Holy Crap!!

Holy crap this may be kind of old but it is the first I've heard about it.

The US military is funding development of a weapon that delivers a bout of excruciating pain from up to 2 kilometres away. Intended for use against rioters, it is meant to leave victims unharmed. But pain researchers are furious that work aimed at controlling pain has been used to develop a weapon. And they fear that the technology will be used for torture.


New Scientist contacted two researchers working on the project. Martin Richardson, a laser expert at the University of Central Florida, US, refused to comment. Brian Cooper, an expert in dental pain at the University of Florida, distanced himself from the work, saying "I don't have anything interesting to convey. I was just providing some background for the group." His name appears on a public list of the university's research projects next to the $500,000-plus grant.

John Wood of University College London, UK, an expert in how the brain perceives pain, says the researchers involved in the project should face censure. "It could be used for torture," he says, "the [researchers] must be aware of this."

Amanda Williams, a clinical psychologist at University College London, fears that victims risk long-term harm. "Persistent pain can result from a range of supposedly non-destructive stimuli which nevertheless change the functioning of the nervous system," she says. She is concerned that studies of cultured cells will fall short of demonstrating a safe level for a plasma burst. "They cannot tell us about the pain and psychological consequences of such a painful experience."

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Well, This is Freaking Wonderful

From the New Scientist apparently the network of satellites that monitor environmental health is detiorating badly.

The US network of satellites monitoring the environmental health of the Earth is on the verge of collapse, according to a highly critical report released on Wednesday by the country’s National Research Council.

Six recent NASA Earth-observing missions have been delayed, scaled back or completely cut. Several of the cancelled missions were follow-ups to successful satellite projects.

The US is probably responsible for about half of the Earth-science satellites currently in orbit, says Richard Anthes, president of the University Corporation for Atmospheric Research and co-chair of the committee that produced the report.

Most of the document focuses on research satellites, and Anthes warns that, for example, these map bulges in the Earth that may signal impending volcanic eruptions, track the depleted ozone layer, and analyse changes in soil moisture that may precede a famine. Furthermore, if observational satellites are not replaced weather and hurricane forecasting would suffer.

When current satellites retire, scientists fear there may be a serious data gap. “The planning for new missions should probably have been started five to 10 years ago,” says Anthes. “But the community is now waking up.”

As always, our president is on top of the situation:

President George W Bush’s proposed budget for Fiscal Year 2006 lists Earth studies as one of NASA’s five national objectives. But in that budget, NASA’s Earth science programmes would get $1.37 billion, about 8% less than they received the year before.

Apparently, he's going to fix the problem by underfunding it - I guess if there is no data all those hard questions about global warming will go away. On the hand, he might be replacing the current program with faith based satellites!

I really don't get it. One of the main reasons why we enjoy the standard of living that we do is because of the strength of our science and technology and it is vital that we continue to have a strong and vibrant research base. Yet in the last few months we have seen several key areas of research go by the wayside (see here for example). Now I don't know about y'all but I really don't want to live in a third world country. Nor do I want my children to live in a third world country. So could we PLEASE go back to doing science. I should also mention Santorum's attempts to destroy the National Weather Service .

Do you want a seven-day weather forecast for your ZIP code? Or hour-by-hour predictions of the temperature, wind speed, humidity and chance of rain? Or weather data beamed to your cellphone?

That information is available for free from the National Weather Service.

But under a bill pending in the U.S. Senate, it might all disappear.

The bill, introduced last week by Sen. Rick Santorum, R-Pa., would prohibit federal meteorologists from competing with companies such as AccuWeather and The Weather Channel, which offer their own forecasts through paid services and free ad-supported Web sites.
"I believe I've paid for that data once. ... I don't want to have to pay for it again," said Scott Bradner, a technical consultant at Harvard University.

He says that as he reads the bill, a vast amount of federal weather data would be forced offline.

"The National Weather Service Web site would have to go away," Bradner said. "What would be permitted under this bill is not clear — it doesn't say. Even including hurricanes."

And in a bit of hypocrisy:

"It is not an easy prospect for a business to attract advertisers, subscribers or investors when the government is providing similar products and services for free," Santorum said.

AccuWeather has been an especially vocal critic of the weather service and its parent agency, the National Oceanic and Atmospheric Administration.

The company has accused the federal agencies of withholding data on hurricanes and other hazards, and failing to ensure that employees don't feed upcoming forecasts to favored investors in farming and energy markets.

Which is ironic considering these comapnies get the dat for their forcasts from the National Weather Service.

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Wednesday, April 27, 2005

A Challenge to ID

An intrepid archaeologist has been out exploring. He stumbles across some interesting structures/formations. The question is are they designed or caused by nature? Using the principles of intelligent design analyze the picture below and tell me what our archaeologist is standing in the middle of.
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Is this caused by intelligent or stochastic mechanisms?

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Just for Fun!

In honor of my 3,000th visitor to this site, I hereby present two fun and interesting links: go here to be insulted in shakespherean prose it's great!

Then go here to kill some Simpsonian zombies. Hint: shoot Krusty (repeatedly). Great for hours of entertainment!

Speaking of clowns - does anybody remember the name of the tv show staring Queen Latifah? The one that had the guy who was afraid of clowns, but who's girlfriend was a clown? Queen Latifah played a magazine editor? Ringing any bells?

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From New Scientist Cassini has found complex organic chemicals on Titan.

Some complex organic molecules - such as benzene and diacetylene - had already been picked up on an earlier approach to Titan, but the latest encounter has yielded an even wider range.

It includes nitriles and scores of different hydrocarbons, some with up to seven carbon atoms. And the results suggest that Titan's upper atmosphere holds even heavier and more complex organics, which are beyond the instrument's mass range.
Scientists do have some idea about how they are formed, however. Methane and molecular nitrogen are thought to be smashed apart by ultraviolet radiation from the Sun and by high energy particles trapped in Saturn's magnetic field. That creates highly reactive radicals that can combine to form more complex molecules.

Similar processes might have operated on the Earth a few hundred million years after it formed, generating the raw materials for life. On the other hand, Earth's organics may have been created in deep space and then delivered by comets.

Cool stuff!

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Tuesday, April 26, 2005

I'm Glad I'm not an Educational Psychologist

Mark Hartwig, an educational psychologist has written an op-ed on intelligent design in the York Daily Record. It's pretty bad.

“Intelligent design.” To hear some folks talk, you’d think it’s a scam to sneak Genesis into science classrooms. Yet intelligent design has nothing to do with the six days of creation and everything to do with hard evidence and logic.

For example, consider the cell. Even the simplest cells bristle with
high-tech machinery. On the outside, their surfaces are studded with sensors, gates, pumps and identification markers. Some bacteria even sport rotary outboard motors that they use to navigate their environment.

Inside, cells are jam-packed with power plants, assembly lines, recycling units and more. Miniature monorails whisk materials from one part of the cell to another.

Some people actually need to look at a cell through a microscope. Below is a diagram for a prokayotic cell. Notice their are no high tech machines, no power plants, no assembly lines or monorails. Not even an outboard motor. Granted this is a metaphor but it's a really bad one. Although I am curious, are those power plants "nucular" and are the republicans going to want to privitize our cells now?

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Below is an eucaryotic cell. Note there are still no power plants, high tech gadgets or monorails (although one is reminded of the song from the Simpsons). I think somebody needs to go here and learn a few things about the cell .

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See if you can identify the parts in the above picture. The picture below contains the answers - so don't look.
ID theorists contend that living organisms like the cell appear designed because they are designed. And they’ve developed rigorous new concepts to test their idea.
In contrast to what is called creation science, which parallels biblical theology, ID rests on two basic assumptions: namely, that intelligent agents exist and that their effects are empirically detectable.

I'm sorry but that doesn't sound rigorous to me. Compare that with this study discussed by PZ Myers. Note the rigourus research design. First the researchers experimented to determine the type of gene acting to produce spots on the wing of D. biarmipes then they experimented to determine the location of the gene. The experiments were elegant (in the scientific sense of the term) and produced interesting results. Compare with the rigor displayed by ID:

Its chief tool is specified complexity. That’s a mouthful, and the math behind it is forbidding, but the basic idea is simple: An object displays specified complexity when it has lots of parts arranged in a recognizable pattern.

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The effectiveness of such thinking is confirmed by massive experience . As William Dembski, author of “The Design Inference,” points out, “In every instance where we find specified complexity, and where (its) history is known, it turns out that design actually is present.”

Yes but in all those cases it has been because humans made the design, so the logical conclusion is that humans are the intelligent designer the ID crowd is looking for.

To see how this applies to biology, consider the little outboard motor that bacteria such as E. coli use to navigate their environment. This water-cooled contraption, called a flagellum, comes equipped with a reversible engine, drive shaft, U-joint and a long whip-like propeller. It hums along at a cool 17,000 rpm. And flagellum is integrated into a sensory/guidance system that maneuvers the bacterium toward nutrients and away from noxious chemicals — a system so complex that computer simulation is required to understand it in its entirety. That system is meshed with other systems.

Which brings us back to the flagella. I have a sailboat. I used to have an outboard motor. It looked nothing like the flagella on the organisms pictured below. I should also point out that it worked in a completely different fashion from the flagella pictured below. Anybody who has ever seen movies of flagella in operation can tell this is complete nonsense.

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In fact, if you want to run the numbers, as Dembski does in his book “No Free Lunch,” it boils down to the following: If every elementary particle in the observed universe were cranking out mutation events at the cosmic speed limit for a billion times the estimated age of the universe, they still could not produce the genes for a working flagellum.

For somebody who's specialty is statistics and research design this is just pitiful. Probability is meaningless without a model. In other words I could calculate probabilities all day long but they mean nothing unless they are based on a realistic model - in this case a model of evolution.

Of course, what’s important here is not what we conclude about the flagellum or the cell, but how we study it. Calling design theorists religious is just a cheap way to dodge the issues.

And calling them scientists is more then they deserve. All in all, if you strip the op-ed of it's overblown rhetoric ("...everything to do with hard evidence and logic...", "The effectiveness of such thinking is confirmed by massive experience...","...the math behind it is forbidding...") and what you have is a couple of bad metaphors repeated add nauseum. Rotary motors, power plants, monorails...does anybody really believe this junk? More importantly, do the ID crowd really think the rest of us are that stupid?

ADDED LATER: To follow up on a comment from an anonymous commenter go here , here , here or here - should probably go here first. Fascinating stuff. Heavy going though.

ADDED LATER: Abnormal Interests has an interesting discussion of the same op-ed.

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Monday, April 25, 2005

Frist and the Evangelical Love Fest

From Frist's Evangelical Love Fest :

Putting more evangelicals on the court will mean rulings more in tune with the
religious convictions of churchgoers, said R. Albert Mohler Jr., president of
the Southern Baptist Theological Seminary in Louisville.
"We are not asking
for persons merely to be moral," Mohler said. "We want them to be believers in
the Lord Jesus Christ."

So, there you have it. Frist is pandering to folks who want to force you to become Christian. I guess radical activist judges who ignore the constitution are okay after all!

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Sunday, April 24, 2005

New Blogs on the Blog Roll

I have added two new blogs to my Blogroll. They are Orange Quark and Henry's Webiocosm Blog. Check them out, they are both interesting.

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PZ Myers Op-Ed

PZ Myers (of Pharyngula fame) has an interesting op-ed in the Star-Tribune on teaching ID creationism in the classroom. It is well worth reading.

A few snippets to tide you over:

ID proponents have not only failed to provide any evidence for their thesis, they aren't even trying. There are no labs doing research on this subject; all the papers the Discovery Institute has tried to publish are exercises in spin, in which they try to distort biology researchers' work to fit their preconceptions.

With no established body of results, no current work and no promising prospects for future research, why should ID be supported? It's a dead end. It is absurd to propose that our kids learn about a subject that no legitimate scientists are pursuing and that has no utility.


My own discipline of developmental biology has been revolutionized in the last few decades as we've embraced evolution more fully than before; new papers in the rapidly growing field of evo-devo, or evolutionary developmental biology, pile up on my desk faster than I can read them.
This is a genuinely exciting time to be studying biology. When students ask me about the hot fields that promise great careers, I steer them toward evo-devo (and developmental biology in general), bioinformatics, proteomics and genomics, all fields in which knowledge of evolution is indispensable.

Note that I do not and cannot recommend anything to do with ID, whose proponents spend their time lobbying school boards, producing nothing new, and with no promise of new ideas for the future.
(all emphasis are mine- afarenis)

Go, read the whole thing.

While we are on the subject of ID creationism. Let me just mention this exchange between a chemistry student at the University of Minnesota-Morris and Paul Nelson of the Discovery Institute :

Here’s the question, from a bright young woman who identified herself as a chemistry major. “What you’ve said so far,” she remarked, “sounds like magic to me. I’ve tried magic chemistry, and it just doesn’t work. Aside from poking holes in evolution, what evidence can you show me for intelligent design?


Evidence is a funny thing, I said to her. There was a titter of laughter from the audience –- and now the reader must picture what follows as being spoken in sentence fragments at roughly 375 miles per hour."

What followed was the usual spiel about SETI research. Note, the chemistry student was asking for some experimental evidence from chemistry, or some current studies, basically any kind of actual scientific research. What she got instead was a hypothetical situation about the search for intelligent life. Now thought experiments have a noble and illustrious career in science. The most famous being that of Einstien in his book "Relativity". The difference between Nelson's example and Einstein's is that Einstein's yeilded predictions about what the results of certain experiments should be. Nelson's don't. Nelson draws the following moral from his thought experiment:

Note that the data themselves in my thought experiment are exactly the same for the design skeptic and the design proponent. What renders the narrow band and primes evidence of intelligence is a causal impotence claim –- no natural mechanism exists to cause x –- coupled with a causal sufficiency claim –- intelligence, uniquely in our experience, produces narrow band radio transmissions and prime numbers. Because of its logical form, however (a universal negation), the causal impotence claim cannot be proven. No failed search for a natural mechanism, a necessarily finite search in any instance, can turn back one’s prior conviction that a mechanism nevertheless exists, lying perhaps just beyond the horizon of our current investigations. Until we find that natural mechanism, say the design skeptics, “we can content ourselves with regularities, chance, and ‘don’t know’ explanations” (Wilkins & Elsberry, Biology & Philosophy 16 [2001]:721).

Impasse. As Bill Dembski puts it, “the universe of unknown material mechanisms can never be exhausted” (The Design Revolution, p. 222). To exhaust that universe would be to solve the problem of induction. It is a logical impossibility.

Thus to elevate data to the status of “evidence” requires a decision that is not, strictly speaking, supported by the data themselves. This is an instance of the classical problem of the underdetermination of theory by data, and one of the reasons that the design debate is so heated.

Yet, this isn't about what we should see in any experiment we could perform. Which is what the chemistry student asked for - one wonders how the scientist involved in SETI research would actually deal with an event like that described by Nelson. Surely, there is more involved than that. One just has to go back and reread , say Carl Sagan, to relize that this is a gross oversimplification of SETI research.

Nelson then followed up by citing an article on RNA from 1989, pretty much ignoring the intervening 16 years of research on RNA , Origins of Life, more Origins of Life and as a matter of fact there is a journal devoted to this issue .

Which brings us back to the beginning and PZ Myers op-ed. Allow me to mention again an earlier quote from the op-ed:

With no established body of results, no current work and no promising prospects for future research, why should ID be supported? It's a dead end.

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Saturday, April 23, 2005

Bible stickers

From Red State Rabble comes this interesting article concerning putting warning stickers on the bible.

Since religious conservatives in the United States have been unsuccessful in preventing evolution from being taught in public- school science classes, they have had to resort to other tactics to inject their religious ideology into secular education. One such tactic has been the attempt to place stickers, which provide a cautionary disclaimer about the theory of evolution, on biology textbooks. This practice first began in Alabama in 1996, where stickers on biology textbooks proclaimed that evolution is a "controversial theory which some scientists present as a scientific explanation for the origin of living things."

Other states have since followed suit. In Cobb County, Georgia, the site of the most recent legal dispute over the matter, the stickers reads, "This textbook contains material on evolution. Evolution is a theory, not a fact, regarding the origin of living things. This material should be approached with an open mind, studied carefully, and critically considered." Proponents of the stickers argue that science textbooks present the theory of evolution as fact and that such warnings are necessary to counterbalance the effect of such a presentation. The goal, they argue, is not to restrict the teaching of evolution but rather to foster critical thinking among students, to promote tolerance and diversity, and to ensure a posture of neutrality toward religion.

I love this part of the article:

In reality, however, we all know what reaction this compromise would prompt among religious conservatives. They would be livid, most likely claiming that the sticker violates their constitutional right to religious freedom. And therein lies the hypocrisy that ultimately bankrupts their position. In reality, religious conservatives are only interested in encouraging skepticism and critical thinking when it comes to questioning evolution. They have little real desire to encourage critical thinking generally and even less if that critical thinking is directed toward their religion.

Check it out!

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Icons of Creationism: The Bombardier Beetle

I had originally intended to do this post yesterday in time for the Friday Ark, but got sidtracked. Normally I like to research what I post about for the Friday Ark and this time is no exception. Which is part of the reason why I didn't get it written. My original intention was to post a couple of picts, find a few links to interesting info about the beetle and discuss how it could evolve. One of the great things about trying to provide interesting scientific information about whatever I post for the Friday Ark is that sometimes I stumble across some really fascinating stuff. This time I struck the mother load. I think, to be more than a little snarky, George Bush should have looked to the insect world for weapons of mass destruction! To be an insect is to be immersed into a nightmare world of chemical warfare.

Chrysomeline (Leaf) beetles, for example, have chemical defense glands. Originally, they synthesized the chemicals themselves. During the course of their evolution, however, the became dependent on plant hosts to acquire the chemicals they use for defense (in other words, they incorporate the host plants toxins into their own defense system). One group within the Chrysomelines (the interuptus group)however, has managed to adapt to a wide variety of plant hosts and uses a wide variety of chemical defenses. One of the more interesting things about this is that in order to go from self synthesized to use of host derived chemicals only requires the change of one or two enzymes. To go from the use of host derived metabolites to use of many hosts also requires the change of one or two enzymes.

Fireflies illustrate another, creepy, way insects can acquire chemical defenses. Female fireflies of the genus Photuris imitate females of the genus Photinus. Once they attract a male of the genus Photinus they eat him! Photinus species have a chemical called lucibufagin (similar to a chemical found in the chinese toad) which are extremely noxius to the insects that prey on fireflies (mainly jumping spiders). So female Photuris acquire the chemical by ingesting male Photinus. Then when attacked they engage in what is called reflexive bleeding and the chemical in their blood drives the predator away. They also incorporate the chemical into eggs when they lay them so their offspring is protected.

Peruvian fire sticks (related to the walking sticks) also use chemical defenses. They are rather unique in that a lot of species, when molting, shed their defensive glands. Fire sticks shed the cuticle lining, but do not shed the gland itself. Consequently, they do not have to wait as long after molting to use their chemical defense. The glands are located near their neck. The chenical is sometimes ejected as a spray but more often is oozed out as a froth and spreads down the thorax. The chemical is related to quinoline and other species of walking stick do not have this type of chemical. In that sense Peruvian firesticks are unique.

Opilionid beetles are similar to the Peruvian fire sticks in the way the use their chemical defenses, but not identical. A bubble of enteric fluid is dribbled out their mouth and onto a track which runs by their glands, where quinonoid paste is injected into the enteric fluid. This bubble then moves down a groove on the beetles carapace. The beetles use it back legs to scoop some of this mixture of and tries to smear it on it's attacker.

Which brings us to the Bombardier beetle. Bombardier beetles compose two branches in family Carabidae (brachinoid and paussoid). The Paussoid branch is believed to be older and more primitive (in evolutionary terms). One of these (Metrius contractus) is believed to be close to the ancestral condition for Bombardier beetles. It has two gland openings near the abdominal tip. The glands themselves are cuticle lined and have two chambers (as in all Bombardier beetles). When attacked the froth is emitted and either runs down a track (if attacked in the front)or builds up near the glands (if attacked from the rear). M. contractus is unusual in that the froth develops into a mist, whereas in brachinoid species it is sprayed in any direction. M. contractus is also unique in that the froth is only 50 degrees centigrade rather than one hundred degrees centigrade as in brachinoid species.

Which brings us to the Bombardier species proper. The species pictured below is Stenaptinus insignis.

A single bombardier beetle can discharge upward of 20 times
before depleting its glands (6). The discharges are accompa-nied
by audible detonations, and they have been shown to be
potently deterrent to a number of predators, including ants (6,
The spray of bombardier beetles is ejected at 100°C (13).
This is because the quinones are generated explosively at the
moment of ejection by the mixture of two sets of chemicals
ordinarily stored separately in the glands. Each gland consists
of two confluent compartments. The larger of these (storage
chamber or reservoir) contains hydroquinones and hydrogen
peroxide while the smaller one (reaction chamber) contains
special enzymes (catalases and peroxidases). To activate the
spray, the beetle mixes the contents of the two compartments,
causing oxygen to be liberated from hydrogen peroxide and the
hydroquinones to be oxidized by the freed oxygen. The oxygen
also acts as the propellant, causing the mixture to ‘‘pop’’ out
(16–18). The heat that accompanies the formation of the spray
is perceptible (13) and contributes to the defensive effective-ness
of the secretion (14, 15). An early explorer, reporting on
large bombardier beetles from the neotropics, commented that
when these ‘‘play off their artillery’’ they are so hot to the touch
‘‘that only few (can) be captured with the naked hand’’ (19).
Although it was known that bombardier beetles can aim their
spray by revolving the abdominal tip (6), the degree of
precision with which they target their ejections had escaped
notice. (from THOMAS EISNER AND DANIEL J. ANESHANSLEY, (1999) Spray aiming in the bombardier beetle: Photographic evidence. Proc. Natl. Acad. Sci. USA
Vol. 96, pp. 9705–9709, August 1999)

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This first picture shows a bettle directing the spray to the front. Note the glob of stuff on it's back. They attached a wire to the beetle by embedding it in wax. They then used the wire to handle the beetle.

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This second picture shows a beetle directing the spray backwards.
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The third shows the beetle directing the spray to the right rear - note the forceps, they had to pinch it's leg to set it off.

In addition to the insects mentioned above, a wide variety of other insect use some form of chemical defense including: millipedes, cockroaches, ants, termites earwigs and grasshoppers to name a few (but I'm still in shock about the male-eating fireflies. I am used to that kind of thing in, say, black widow spiders, but not in lightening bugs!).

So, we have a wide variety of different chemicals, a large number of different ways of getting the chemicals and delivering them (we could have given details on Opilionid beetles and millipedes as well). In some cases, the differences are caused by differences in a few enzymes. I have done much research into the origins and evolution of these systems, but from what I have read so far Bombardier beetles don't represent that much of a challenge to evolutionary theory. Rather, they seem to be a specialization of several traits already present in nature in one form or another - benzoquinones, for example, are used by a wide variety of insects.
I will probably write some more about this in the future. I just need to do some more research into a really fascinating area of biology (it's referred to as chemical ecology in the literature I've read).

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Friday, April 22, 2005

Friday Staphylococcus aureus Blogging

I think this is the one that put me in the hospital. Still can't figure out how I caught it though.

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Posted by Hello

Here is an interesting story on the subject though.

Staphylococcus aureus, a common germ that infects countless scrapes and scratches a year, is fast becoming an uncommon public health threat. Drug-resistant strains of staph known as MRSA, once confined to hospitals and nursing homes, have been turning up among pro football players in St. Louis, Marine recruits in North Carolina, inmates in Georgia prisons, gay men in Los Angeles, native Americans in Minnesota and pediatric wards in Atlanta.

"Close to one-fifth of what used to be a hospital-specific problem is now a community problem, and that's a large number," said Scott Fridkin of the Centers for Disease Control and Prevention. "We didn't think it would be anywhere near that high when we started the study."

Now to scare you a little:

Until a few years ago, reports of MRSA were so rare outside of hospitals that many doctors may have unwittingly aided its spread by treating it with antibiotics that didn't work.

In the last few years, outbreaks of several new staph strains have been reported in dozens of states, as well as in England, France, Switzerland, Saudi Arabia, India, Australia and New Zealand. In the United States, at least two dozen people have died of MRSA pneumonia during the last two flu seasons.

Overall, health authorities have only a piecemeal picture of MRSA's prevalence — much of it based on isolated outbreaks and limited surveillance of a few communities.

A 2002 survey by the Georgia Division of Public Health, for instance, found that nearly 600 people seeking treatment for staph infections at hospitals and clinics in the eight-county metro Atlanta area were infected by MRSA. The rate doubled in just a year, but the study was discontinued for budgetary reasons.

The Georgia survey found that 70 percent of people treated for such infections were getting antibiotics to which the microbe was already resistant — an error that gave otherwise mild infections an opportunity to fester and spread.

Fortunately, association with necrotizing faciitis is rare (only 14 cases so far -all in Los Angeles).

Part of the problem is caused by an evolutionary response to the overuse of antibiotics:

MRSA struck the St. Louis Rams in September 2003, when five linebackers who did not cover their artificial turf abrasions were infected. Investigators suspect players passed the bug to each other by sharing towels, using a whirlpool without showering, and by only sporadic hand washing. They also passed the bacteria — through contact on the field — to three San Francisco 49ers during a game in St. Louis on Sept. 14.

CDC epidemiologist Sophia Kazakova, who headed the Rams study, said the reasons for the outbreak are unclear, but the team's heavy use of antibiotics may have been a contributing factor.

"The players in our investigation were receiving 10 times the number of anti-microbial prescriptions dispensed to the public," she said.


In the 1940s, when modern medicine first used antibiotics, no one realized that was the beginning of an arms race between man and microbe that would rage across the medical landscape for the next 60 years.

Penicillin, introduced during World War II, greatly reduced staph as a threat in hospitals and operating rooms. But within two years, a strain of penicillin-resistant staphylococcus had emerged. By the 1950s, the germ was universally present in hospitals. And by the 1970s, it had spread to the community at large. Today, 95 percent of all staph strains in the world are resistant to penicillin.

Modern medicine fought back. And so did staph. A new class of antibiotics, led by methicillin, was introduced in the early 1950s. And within a few years, methicillin-resistant staph had emerged in hospitals and nursing homes, where the new antibiotics were most heavily used.

Today, staph is one of the leading causes of the estimated 2 million infections and 88,000 deaths among people who get an infection in a hospital. At least 55 percent of all hospital staph infections, 60 percent of infections in intensive care units and 71 percent in nursing homes are now caused by MRSA.

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Thursday, April 21, 2005

Baby Aye-Ayes!

What could be cooler then an Aye-Aye? Baby Aye-Ayes! (Note: Daubentonia is afarensis' favorite primate.)Posted by Hello
Cutest Thing I have Seen in Quite A Long Time

National Geographic News has the rest of the story.

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First Draft Says It All

This post by Athenae at First Draft is great!

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Wednesday, April 20, 2005

Oviraptors, Archaeopteryx and Horses Toes

The recent discovery of of dinosaur eggs still inside the mother is important for several reasons. First, it is another piece of evidence confirming the relationship between reptiles and birds. Second, and more importantly, it is a piece of evidence that demonstrates how. The oviraptor demonstrated that this particular dinosaur developed and laid eggs in a fashion intermediate between the primitive repilian form and that of birds.
Let's consider this from the perspective of avian evolution for a moment. Birds originated in the late mesozoic (245-66 mya) and differentiated in the early cenozoic (66-37 at the end of the eocene). The best example of this is archaeopteryx from the upper jurassic (208-144 mya). The most amazing thing about archaeopteryx is that it had feathers. Why is that amazing? Archaeopteryx share a large number of similarities to dinosaurs such as composgnathus. Archaeopteryx does not have a large sternum as in birds, its bones are thickwalled and lack the pneumatic ducts seen in birds. The front limbs show typically reptilian features such as three fully developed digits, flexible carpus and unaltered radius and ulna (in humans this is the forearm). Other characteristics similar to that of reptiles include the retention of teeth and limited fusion of bones in the skull. Birds have a unique pelvic morphology and also posses a furcula (wishbone). Archaeopteryx has a birdlike pelvis and has a furcula - unfortunately, these two traits have been found in several theropod dinosaurs. An Asian genera, for example, has a posteriorly rotated pubis similar to that in birds. Others have fused clavicles that form a wishbone structure. The most birdlike features of Archaeopteryx, not including the feathers, are in the rear limbs. The head of the femur is turned inwards, the knee and ankle joints form simple hinge joints and three of the toe digits face forwards while the first toe digit is turned to the rear. Some of these traits are found in theropods as well. So where does that leave us in the reptile-bird transition? We have some traits that link Archaeopteryx firmly with reptiles, others are found in both birds and reptiles, and none link Archaeopteryx to birds only. With the recent oviraptor discovery, we now have a dinosaur that lays eggs in a fashion intermediate between the primitive reptillian pattern and birds.
Which, of course, brings us to horses.
Posted by Hello

The above is a neat chart (which I swiped from Pharyngula ) that shows the broad outlines of horse evolution. Horse evolution is really fascinating because there are so many different things all going on at once. Some species were increasing in size, others were decreasing in size. Some were reducing the number of toes, others weren't. Some were increasing the thickness of the enamel on their teeth and increasing the size of the ridges on thier teeth. Some were browsers, others were grazers and still others were mixed feeders. At this point the parallels between horse evolution and the reptile-bird transition should be obvious (and to go even further the reptile-mammal transition). With horse evolution we have several genera with a mosaic of traits some of which we see in modern horses. In the reptile-bird we also have a wide variety of species with traits that link them to modern birds, although none of them had the complete set of characteristics that we use to define the class Avis.
The above discussion is a prelude to my directing you to these two articles:
Gould on Phyla (while you are at Pharyngula check out the post on hot-blooded crocodiles)
and Down With Phyla .
The point you should take with you to these other articles is that, although Archaeopteryx presents some radically new characteristics that define a new class, it is still just an animal trying to survive as best it can. It is linked to other animals by the traits it shares with them. Perhaps the biggest difference between Archaeopteryx and the other theropods is that it had more traits that it shared with birds than the other theropods did. It is very easy to forget the animal and reify the mosaic of traits that came to be called Avis. This is where, in my opinion, creationists tend to make their biggest mistake in talking about "Macroevolution".

Wicander, R and Monroe, J. (1989)Historical Geology: Evolution of the Earth and Life Through Time
Carroll, R. (1988) Vertebrate Paleontology and Evolution

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Tuesday, April 19, 2005

Creationist Classroom

This Creationist Classroom movie looks like it might be pretty cool. Unfortunately, I can't get it to play with sound. I'm downloading it to see if I can figure it out. Meantime, check it out and let me know what you think.

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Basilosaurus isis: or 'Does Phillip Johnson Know About This"

In my post on the oviraptisaurian I had mentioned that I was starting to feel sorry for the creationists. At least one of the people commenting on that post thought I was being silly. Well, it's happening again. Philip Gingerich (who has also done some good work on early primate origins, oh, and he is NOT related to Newt)and his team have uncovered a nearly complete Basilosaurus isis. Previously, remains of Basilosaurus had been found (for those of you who are unfamiliar with whales Basilosaurus is one of the first oceangoing species. It still has legs and does not have a blowhole) but none are as complete as the one recently found.

Basilosaurus isis Posted by Hello

You can go to National Geographic News or Yahoo News for more info. You can also go to Philip Gingerich's site which has a good overview of whale evolution. It also has some free .pdf's of some of his papers so I'll be checking it out more thouroughly! When I saw the above picture I had this mental image of Phillip Johnson lip sinking "Poor, Poor Pitiful Me" in my head - but that could be the medication.
So the proof just keeps piling up on the poor creationists. One step at a time, bit by small bit -which is how science works really, until the evidence becomes overwhelming.

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National Poetry Month

It is national Poetry Month so:

she walks in beauty,
and as you reach out to touch her,
you wish you could see her face.

she walks in serenity,
and as you reach out to touch her,
smoke curls and writhes winding 'round your face.

she walks in grace,
and as you reach out to touch her,
tears fall and you lick your lips for a taste.

she walks in sorrow,
and as you reach out to touch her,
sadness lingers and a heart breaks.

she walks in love,
and as you reach out to touch her,
love blossoms and pains no longer ache.

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Monday, April 18, 2005

To Qoute The Who "I am Free"

Hi everybody,
I have finally been sprung from the hospital! As Mrs. afarensis informed you on Friday, I have been held, webless, for several days. I had a lump on my forehead, later diagnosed as a keritinaceous cyst, which became infected with aome form of staph along about thursday of last week. Managed to get a doctors appointment on Friday and was promptly admitted to the hospital. It was very primitive - no internet, no cable, just network tv. Fortunately I was brought several books (Genetics and the Evolutionary Procees by Dobzhansky and New Directions in Ecological Physiology by Feder- a really interesting book, I highly recommend it) in a care package (which also contained a large supply of milk duds and tootsie rolls -along with the perpetual supply of coffee my wife brought me kept me alive and sane). The downside was that my eyes were kind of swollen so I could only read for a short time. I was almost reduced to listening to the Revelations Miniseries (hey, I was really desparete for something to do). Even worse, I had a IV unit that plugghed into to the wall so I couldn't sneak around the hospital at night. One of the big questions in Forensic Anthropology (which is what I was specializing in in college) is how soft tissue disease and what not affect the skeleton. Usually, unless the skeleton is directly involved in a disease process skeletal affects are considered incidental. I had been planning to sneek into radiology and take a cat scan of my skull to find out how all the gook from the staph infection affected my frontal bone - maybe some x-rays too - but I was foiled by an electrical cord. Dang it!
Fortunately, my hospital did not practice faith based medicine - the only laying of hands occured when the plastic surgeon lanced the cyst and squeezed all the gook out of it. Which is, of course, why I survived to blog about it! I was supposed to be set free this morning but they lost the orders saying I could go home - result is I didn't get home until about 6:00 St. Louis time. What really sucks is they didn't even give me any time off work to recuperate so it's back to the salt mines tomorrow.
Thanks to all who wrote to express concern. Those of you who had questions, I will try to get them answered in the next few days as time permits.

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Saturday, April 16, 2005

Hello from Mrs Afarensis

Hello, this is "Mrs. Afarensis." Afarensis asked me to do a short guest blog in his absence. He was admitted to the hospital yesterday for observation - nothing too serious. I think, however that 23 hours without contact from this community and being able to post to his blog and read the postings of others is really about to get to him.

Of course, I told him I would post something that would make his skin crawl - I think he believed me because he turned white as ghost and had that 'Maybe I should have thought this through more carefully' look on his face. That in itself was worth a chuckle.

He should be home tomorrow and I KNOW that the first thing he will do is check this site and make sure there is a "fresh" posting for everyone.

Thanks for stopping by this site - sorry you had to put up with me instead!


Mrs. Afarensis

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Friday, April 15, 2005

Dinosaurs Layed Eggs Like Birds Not Crocodiles

Posted by Hello

(A) The pair of eggs sit at the bottom of the fossilised pelvis (B) An egg found inside the female oviraptorosaurian. The blue color of the egg shell fragments is not the original color, though the texture of the shell pieces probably resembles the original texture of the egg.

From New Scientist .
This is incredible. Paleontologist in China have found dino eggs in the body of the mother!

The first dinosaur eggs found complete with shells in the body of the mother has solved the long-standing mystery of how dinosaurs laid their eggs. The evidence shows they laid a clutch in a series of sittings, like birds, rather than all at once like crocodiles and other living reptiles.

Oviraptors are part of the wide-ranging group called theropods, which also includes Tyrannosaurs and the ancestors of birds. Their fossilised nests are well known in China, typically including over a dozen elongated oval eggs in two rings.

Too little is preserved of the new find to identify the particular species, but the newly eggs looked ready to be laid, says Tamaki Sato of the Canadian Museum of Nature in Ottawa.

The best-preserved egg of the find is nearly 20 centimetres long and 6 to 8 cm wide, although somewhat deformed. Sato says the egg's shape and microscopic structures match those of some previously found eggs.

The pair of eggs show the oviraptor developed one egg at a time in each of its two oviducts, most probably laying one pair at a time in the nest, Sato suggests.

That puts it somewhere between the primitive reptilian form of crocodiles and the more advanced form of the birds, consistent with the theory that birds evolved from dinosaurs related to oviraptors.

Gee, sounds like a transitional fossils to me. An yet more eveidence of "macroevolution". With finds like this happening on a regular basis I'm almost starting to feel sorry for the creationists!

More Info

Added later: Pharyngula has a post as well - didn't realize he was doing a post on it but he approaches it from a slightly different angle.

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Friday Hagfish Blogging

Hagfish are eel-like critters that, at one time, were put in the same group as lampreys. Recently, however, some have suggested that they are the sister group to lampreys (and hence vertebrates. One of the interesting things about hagfish is that they can tie themselves in knots!
Hagfish knots Posted by Hello

The also look like what comes out of the Graboids mouth in Tremors (if you haven't seen the Tremors movies you should - there are four of them now)!

;Posted by Hello

Finally, they produce a lot of slime when nervous!
;Posted by Hello

The Hagfish Page
Francis Creek Shale Fossils
(video/quicktime Object)

Taxonomy of Hagfish

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