Evolution of Complex Protein Machines

This has been a controversial idea in the past year or so. An article in Science Daily gives us some more info on the subject that clears up some of the controversy:

It all begins with the way that the cell repairs breaks in the double strands of DNA that are its genetic blue print. Usually, when this happens, special protein machinery in the cell copies the missing DNA from another chromosome and rejoins the broken ends around the newly synthesized genetic material.

"It fixes the hole in the DNA by copying similar information," said Rosenberg. However, when the process goes wrong, the repair process introduces errors into the DNA.

Researcher Rebecca Ponder set up experiments to control where the break occurred and examined where the increased mutations were located:

"...she found that errors occurred right next to the break in the stressed cells, and that the rate of errors was 6,000 fold higher than in cells whose DNA was not broken. "It's really about local repair," said Rosenberg. Not only that, but subsequent experiments proved that this mechanism of increased mutation at sites of DNA repair occurs only in the cells under stress. "Even if you get a break in a cell, it won't process it in a mutagenic way," said Rosenberg. "The cell repairs it, but does not make mutations unless the cell is stressed."

Not all cells increase their mutation rates in this fashion when stressed. Not being a geneticist my guess would be that somehow stress interferes with repair mechanisms in some cells - which might be the next step in investigating the issue.

Among the small percentage that do increase mutations, most of the errors are neutral, not affecting cells at all. Many are deleterious, resulting in cell death. But a small percentage is advantageous, allowing the cells to survive in an adverse environment.

The fact that the changes in the rate of mutation occur only in a certain physical space at a certain time gives the cells advantage because it reduces the risk to the whole colony. DNA breaks occur only rarely in each individual cell. If the mutations are restricted in time and space, it reduces the risk that the mistakes in repair will affect some other gene. It can also enhance the likelihood of two mutations occurring in the same gene or neighboring genes.

Normally, in discussions of natural selection an entire organism is being talked about. I think the idea of selection between cell lines or even individual cells is fascinating - though I don't know much about it.

At any rate, the article ends with two statements that give no comfort to intelligent design advocates:

"This can speed evolution of complex protein machines."

The implications of this statement for intelligent design are obvious.

There is a second statement that affects the argument some are making for intelligent design. Namely the argument that evolutionary theory contibutes nothing to modern medicine. Well:

"...which was supported by grants from the U.S. Department of Defense Breast Cancer Research Program and the National Institutes of Health."

Now why would the U.S. Department of Defense Breast Cancer Research Program and the National Institutes of Health support research into evolutionary theory when it contributes nothing to modern medicine??

I'll eagerly await the response from the intelligent design community...

*sound of cicadas chirping*

In Memorium: Hermann Bondi

BBC Science News is reporting that astrophysicist Sir Hermann Bondi has passed away due to Parkinon's. Apparently, he died on 9/10/05 and was 85.

From the BBC article:

Sir Hermann Bondi was an astrophysicist who helped formulate the steady-state theory of the universe - which said it has always existed.

When this theory was supplanted by the Big Bang in the 1950s, Sir Hermann did pioneering work on black holes.

Hermann Bondi graduated from Cambridge University in 1940 but as an Austrian was immediately interned as an "enemy alien" first in Britain then in Canada.

He met Thomas Gold in one of these prison camps and the pair struck up a working relationship.

Once the value of the two scientists was recognised they were set a task of developing radar systems for the British Admiralty and they met Fred Hoyle.

In 1948, the three presented their theory that the universe has always existed in a steady state.

His view that the gravitational pull of a black hole builds up gas in its vicinity led to a mathematical exercise by scientist Stephen Hawking who suggested that radiation can emerge from these mysterious objects.

In the 1960s, Sir Hermann promoted space exploration and was director-general of the European Space Research Organization between 1967 and 1971.

Me as a Superhero

Your Superhero Profile

Your Superhero Name is The Suicide Gorilla Your Superpower is Piracy Your Weakness is Atomic Explosions Your Weapon is Your Fungal Bludgeon Your Mode of Transportation is Sleigh

What's your Superhero Name?

oldwhitelady has a link to the worlds shortest personality test. I took it several times but didn't agree with any of the results. The site did have other tests including the one above. Which, in a strange way is accurate... I have an anthropology background so the gorilla part is accurate. I have a sailboat and know how to fence so I'm almost a pirate and have been tepmted in the past to obtain a new sailboat through looting, pillaging and plundering (Commodore Mrs. afarensis keeps overuling me on this method of getting a new boat). (Theological note: since pirates have a place in the theology of the Flying Spaghetti Monster I'm wondering if this isn't a sign? Am I being spoken to by "His Noodly Appendage"?)Like everybody, my weakness is an atomic explosion... Not sure what a "Fungal Bludgeon" is, but it sounds groovy! I'm not thrilled about the sleigh though (unless it's pulled by skeletal reindeer like in "A Nightmare Before Christmas")

A New Method of Determining Age From Teeth

This is way cool!

The new technique, developed by researchers at Lawrence Livermore National Laboratory (LLNL) and the Karolinska Institute in Sweden, determines the amount of carbon-14 in tooth enamel. Scientists can relate the extensive atmospheric record for carbon-14 to when the tooth was formed and calculate the age of the tooth, and its owner, to an accuracy of within about 1.6 years.

“Unlike most other tissue, dental enamel doesn’t turn over,” said Bruce Buchholz of LLNL’s Center for Accelerator Mass Spectrometry, where the enamel samples were analyzed. “Whatever carbon gets laid down in enamel during tooth formation stays there, so tooth enamel is a very good chronometer of the time of formation.

“We were surprised at how well it worked,” he said. “And if you look at multiple teeth formed at different times, you can get (the age range) even tighter.” Previous techniques, such as evaluating skeletal remains and tooth wear, are accurate only to within five to 10 years in adults, Buchholz said.

Here is how it works:

Carbon-14, or radiocarbon, is naturally produced by cosmic ray interactions with air and is present at low levels in the atmosphere and food. Atmospheric testing of nuclear weapons from 1955 to1963 produced a dramatic surge in the amount of radiocarbon in the atmosphere, Buchholz said.

“Even though the detonations were conducted at only a few locations, the elevated carbon-14 levels in the atmosphere rapidly equalized around the globe,” he said. Since atmospheric testing was banned in 1963, the levels have dropped substantially as the carbon-14 reacted with oxygen to form carbon dioxide, which was taken up by plants during photosynthesis and mixed with the oceans.

“Because we eat plants and animals that live off plants, the carbon-14 concentration in our bodies closely parallels that in the atmosphere at any one time,” he said.

Buchholz and his colleagues analyzed 33 teeth from 22 different people whose ages were known. The enamel separations were done at the Karolinska Institute, and sample preparation and accelerator mass spectrometry analysis was done at Lawrence Livermore.

The enamel dating technique doesn’t work for people born before 1943, because all of their teeth would have been formed before testing began in 1955.

New Reconstruction of A Titanosaur Skull

This is a rather interesting story from Science Daily.
The skull of a titanosaur



has been reconstructed.

The largest animals known to have walked the earth, sauropods were common in North America during the middle of the dinosaur era but were thought to have been pushed to extinction by more specialized plant-eaters at the end of that era. New discoveries, however, are showing that one lineage of sauropods diversified at the end of the dinosaur era, University of Michigan paleontologist Jeffrey Wilson says.
Wilson's recent restudy and reconstruction of the skull of a Mongolian sauropod adds to a growing body of evidence for sauropod diversity at the end of the dinosaur era. Wilson described the reconstruction and the conclusions he drew from it in a paper published Aug. 24 in the Journal of Systematic Palaeontology.

The reconstruction is important for several reasons:

"Most animals walk with a narrow gauge, with their feet close to the midline, because it's energetically more efficient to walk that way. But some sauropod trackways tell us that a group of sauropods were walking with a new wide-gauge stance. We can identify characteristics of titanosaurs that would have allowed that stance, and we can tie the appearance of those features with the proliferation of wide gauge tracks everywhere in the fossil record at the end of the dinosaur era." Wilson wonders if the change in locomotion—from typical sauropod narrow-gauge walking to titanosaur wide-gauge walking—corresponded to lifestyle changes, such as different feeding habits. But without skulls to study, it has been hard to draw conclusions about how and what titanosaurs ate.

One feature of the skulls is particularly intriguing. "They have elongate, sort of horse-like skulls with many openings and grooves on the outer surface of their snouts," said Wilson, who worked closely with U-M Museum of Paleontology artist Bonnie Miljour over the course of a year preparing the paper's many illustrations of the skull reconstruction. "Blood vessels and nerves passed through these holes and may suggest an especially sensitive snout. This probably had some role in feeding, but we haven't investigated it at all."

Oddly, a group of distantly related sauropods evolved a similarly grooved snout. "Apparently, these two different branches of sauropods gravitated toward similar anatomical structures, perhaps because they were specialized for eating certain types of vegetation."

Titanosaurs are found in widely scattered locations from Patagonia to Madagascar to Mongolia and have yeilded some interesting insight into dinosaur evolution. For example this find (first picture above) in Madagascar allowed the resolution of an interesting issue:

The discovery of the skull of Rapetosaurus showed Curry Rogers and Forster that two enigmatic sauropods from Mongolia (Nemegtosaurus and Quaesitosaurus) are actually titanosaurs, and not, as theorized, more closely related to other sauropod families. Rapetosaurus was key in this resolution, since it provides both a skull and skeleton for comparing titanosaurs (previously only known from skeletons) to these two Mongolian dinosaurs (known only from skulls).

Are Tanukis Pastafarians?

But there is more to the tanuki story! For you see, in Japan they have become legendary creatures and cultural icons. From Wikipedia:

Tanuki have been part of Japanese myth since ancient times. The mythical tanuki is reputed to be mischievous and jolly, a master of disguise and shapeshifting, but somewhat gullible and absent-minded.

WARNING: TANUKI PORN BELOW(Don't say I didn't warn you)

The current humorous image of tanuki is thought to have been developed during the Kamakura era. The wild tanuki has unusually large testicles, a feature often comically exaggerated in artistic depictions of tanuki. Tanuki may be shown with their testicles flung over their backs like a traveller's pack, or using them as drums. Tanuki are also typically depicted as having large bellies. They may be shown drumming on their bellies instead of their testicles, especially in children's art.

Here are several portrayals...





Kind of makes sense. Chimps - a highly promiscuous species - have large testicles due to among other things sperm competion between males. Since tanukis live in groups, one wonders if the same competition between male sperm might happen...?

This does not exhaust the list of remarkable things about the tanuke though. For you see the tanuki have theological implications as well. From Wikipedia:

Statues of tanuki can be found outside many Japanese temples and restaurants, especially noodle shops. These statues often wear a big, cone-shaped hat and carry a bottle of sake. Tanuki statues always have a large belly, although contemporary sculptures may or may not show the traditional large testicles. These exaggerated features represent fertility and plenty.

Note the bolded words "...especially noodle shops." Which, of course, implies some kind of relationship between the Flying Spaghetti Monster and tanuki. If you think about it the relationship becomes really clear. Pastafarians belive there is a beer volcanoe in heaven. What happens when you drink lot's of beer for long periods of time? You get a beer belly just like the tanuki. Pastafarians also belive there is a stripper factory in heaven, which leads us to the other prominent characteristic of tanukis...

Friday Tanuki Blogging

The animals to the left are tanuki, or more scientifically, Nyctereutes procyonoides. Prosaically they are raccoon dogs. They come in six subspecies.



* N. p. procyonoides -- Asia
* N. p. koreensis -- Korea
* N. p. orestes -- Yunnan
* N. p. ussuriensis -- Russia
* N. p. viverrinus -- Japan (Honshu,Shikoku and Kyushu)
* N. p. albus -- Japan (Hokkaido)

They are also quite remarkable creatures. Let's start with one of the Japanese forms. N. p. viverrinus entered Japan some 18,000 years BP. By approximately 12,000 BP the Sea of Japan had cut Japan off from the rest of asia and N. p. viverrinus went on it's merry way. Incidently, in Japan the raccoon dog is called a Tanuki - but more on that later. On the mainland, raccoon dogs have 54 chromosomes, in Japan 38 - mainly due to Robertsonian translocations. Interestingly enough there is some evidence that the raccoon dog karyotype is the most primitive of the canine species. There is also some evidence indicating homologies between some raaccoon dog chromosome fragments and cat chromosomes. The Japanese species are smaller than mainland species and may live in groups. The mainland species are larger, able to accumulate more fat reserves, have thicker fur and are dormant during the winter. They are also monogamous and hence very little sexual dimorphism exists in mainland species. In Japanese raccoon dogs (or tanuki) the molars are especially large compared to mainland populations. This is largely attributed to differences in diet. Japanese tanuki tend to eat insects, other invertebrates and course plant material. Mainland raccoon dogs are more omnivorous.

This is where the story starts to get interesting. Between 1929 and 1955 about 9,100 raccoon dogs were imported into the former Soviet Union - mainly the European part. From there they spread far and wide reaching places such as Belarus and Finland. As a matter of fact they pose an invasive species problem for much of eastern Europe. This is largely because the raccoon has one of the highest litter sizes in the canine family (I forgot to mention they were canines didn't I?). Mean litter size in some areas is 9 cubs but can reach a maximum of 16. Their omnivorous diet and the fact that they sleep through the winter also aides in their spread. The one place they have not been able to spread to is Lapland. This is because Lapland summers are too short for raccoon dog cubs to accumulate enough fat to survive the long Lapland winter.

More info:

here,
here,
here,
here and
here

Pharyngula Has Cursed St. Louis

Not in the sense of calling it a bunch of bad names. Allow me to explain. PZ did a post on a creationist ninny who happened to be from my own home city of St. Louis. Being properly apalled and not wanting people to mistake St. Louis for Kansas I left a comment apologizing for the creationist ninny on the cities behalf (no need to thank me Mayor Slay - just doing my bit to help make the world a better place). What was the response?

Afarensis, we won't hold your city accountable unless by some godawful freakish curse of contrariness, you elect Birdnow to the school board.

He actually said that on his blog, just flung it out there for the wingnuts to read and act on. It's like saying "What could possibly go wrong" as soon as you say it something goes wrong. St. Louis is doomed. My one consolation is that I actually live in St. Louis County and my school district wouldn't be affected. None the less, we do need to be careful about what we say out loud.

Right Whales, Cyamids and Evolution

The above is a southern right whale. Below is a picture of a cyamid. The genetics of both tell a common story.



Recent genetic studies indicate that there are three species of right whale (North Atlantic, North Pacific and Southern Ocean) which diverged from a single ancestral species some 5-6 million years ago. Scientists studying cyamids (a crustacean parasite on whales)have confirmed the gentic results:

Cyamids were nicknamed "whale lice" by early whalers, who often were infested with real head and body lice. Whale lice are related to crabs and shrimp, and cling to the whales' raised, callus-like patches of skin -- named callosities -- the grooves and pits between callosities, and also to skin in slits that cover mammary glands and genitals. The white whale lice covering the callosities create distinct markings that stand out against the whales' dark skin, making it possible for scientists to distinguish individual whales.

*snip*

Whale lice infest only whales, just as bird lice infest only birds and human lice infest only people. Recent genetic studies of head and body lice have revealed details of human evolution. Whale lice hang onto the whales throughout their lives, so they share a common ecological and evolutionary history with the whales. Genes from whale lice actually may reveal more about the whales than the whales' own genes do, because the parasites are much more abundant and reproduce more often than whales. As a result, the parasites have much greater genetic diversity and scientists have more mutations to track.

The results mirror the results obtained by studying whale genetics - with one surprising wrinkle:

The same three whale louse species -- Cyamus ovalis, Cyamus gracilis and Cyamus erraticus -- were thought to infest each of the three different species of right whale. But the new study revealed that like the whales, each whale louse species also split into three species, so North Pacific, North Atlantic and southern ocean species of right whales each are infested by three distinct species of cyamid. That tripled -- from three to nine -- the number of cyamid species infesting right whales.

*snip*

Some 20 million years ago, North and South America were separated by deep seas, but 18 million years ago, undersea volcanism slowly began forming a volcanic island chain. By 3 million years ago, the chain formed solid land, the Isthmus of Panama, linking the two continents. By 5 million or 6 million years ago, the sea between the two continents was so shallow that whales could not swim between the North Pacific and North Atlantic, Rowntree says. Changing circulation patterns established warm currents that discouraged right whales from moving between southern and northern oceans.

"Right whales have such thick blubber they can't cross the equator," Rowntree says. "The waters are too warm. They can't shed heat."

Seger says: "The genetics of whale lice show conclusively that the three species of right whales have been isolated in the North Pacific, North Atlantic and Southern Hemisphere for about 5 million to 6 million years," with a possible range of error from 3.6 million to 9.9 million years.

One other interesting result. Gentic studies of right whales indicated that north Atlantic right whales have lower genetic diversity than southern ocean right whales. The Cyamid study, however, indicates that north Atlantic cyamids have just as much genetic diversity as cyamids on whales in the north Pacific and southern oceans. This indicates that north Atlantic right whale populations were just as large as those in the north Pacific and southern ocean - but suffered recent declines:

North Atlantic right whales have lower genetic diversity than southern ocean right whales. But the new study showed "the genetic diversity of whale lice is virtually as great for the North Atlantic right whale as for the southern right whale, suggesting that historically (but before whaling) the North Atlantic right whale population was comparable in size to that in the Southern Hemisphere," Seger says. "This suggests that the reduced genetic diversity of North Atlantic right whales happened recently, possibly due to whaling, not because the whale population was small even before whaling."

Whale louse populations correlate with population sizes of right whales, so if North Atlantic right whales had small populations before whaling, the diversity of their whale lice would not be as great as those on the southern right whales.

Limited data from North Pacific whale lice suggest right whales also were abundant there before whaling began, in line with early whaling records, Rowntree says.

Small population size can be harmful because it is impossible to avoid inbreeding and an increased risk of genetic disease. The study raises hope for endangered Northern Hemisphere right whales by suggesting that their reduced genetic diversity is a relatively recent phenomenon and perhaps not as severe overall as it appears to be in the particular genes that were studied, Seger says.

Okay, Bats are Weirder than I Thought

Okay,
Bats are weirder than I thought. Specifically, Greater Horseshoe bats.


According to National Geographic News several generations of female greater horseshoe bats mate with the same male:

During their life span, most female greater horseshoe bats (Rhinolophus ferrumequinum) revisit and breed with a specific male, according to a new study.
That means offspring born in different breeding seasons are full siblings. In addition, the researchers believe that daughters follow their mothers to mating sites to breed with the same male.
" … sharing sexual partners strengthens social ties and promotes greater levels of cooperation within the [bat] colony," said Stephen Rossiter, a zoologist at the School of Biological Sciences, Queen Mary, University of London.
"The females are choosing their mates. We still don't know how they do it, how they pass along the information to their daughters, or how they mostly avoid inbreeding," added Rossiter. The zoologist is the lead author of the new study, which is described in tomorrow's issue of the science journal Nature.
Mate sharing among bats can make for some confusing relationships. In several cases genetic tests showed that a female bat and her maternal half-aunt also were half sisters on their father's side.

Between 1991 and 2002, Rossiter and his colleagues caught bats in nets and collected samples of skin from their wings. The scientists were able to analyze 19 different genes in a group of 452 bats, which included mothers, offspring, and potential fathers.
The researchers positively identified the mothers of 371 individual bats and the fathers of 232. The researchers also determined breeding pairs.
Further study showed that specific males and females paired together on multiple occasions more times than would have occurred at random. This finding suggests that mothers and their female offspring are selecting one male and returning to him for subsequent mating.

An Interesting Inovation On DNA Extraction from Fossil Bones

According to New Scientist an new technique has been developed to extract DNA from bones. Before going further a little background information is in order.



Above is a picture of the structure of bone. Bones are made up of two components. One component is the cellular component - which are called osteocytes. The other component is the matrix component. The matrix component is composed of collagen fibers with hydoxyapatite crystals, which form in the holes between fibers. The fibers are lined in arrays



and the orientation of the array determines the type of bone (more or less).

The bone matrix is formed by cells called osteoblasts which lie on the surface of the bone and secrete a substance - mainly collagen - that is then mineralized. Occasionally the osteoblast becomes embedded in the matrix (as hydroxyapatite crystals stick to the collagen fibers) and is then referred to as an osteocyte. With this, somewhat simplistic, overview of bone microstructure in mind we can now look at the new DNA extraction technique.

Most attempts to extract DNA from bone involve:

"...grinding up bone, decalcifying it, and converting the collagen matrix to gelatin. "

The DNA is then subjected to the PCR technique (a subject for another post) which multipies the amount of DNA present. Their are two problems however. First, DNA degrades quickly and burial in soil leads to contamination with foriegn DNA. Second, fossil bones can contain substences that inhibit the PCR reation.

The new technique seems to provide a way around this. This is the way New Scientist describes the new technique:

Bones form as cells mineralise, depositing tiny crystals of hydroxyapatite in a matrix of collagen fibres. Some DNA remains in the structure, and earlier studies extracted it by grinding up bone, decalcifying it, and converting the collagen matrix to gelatin. However, much of the DNA had been damaged, and samples were vulnerable to contamination.

Looking for alternatives, the team turned to crystal aggregates inside bone. They extracted the clumps by soaking bone powder in a solution containing sodium hypochlorite, the active agent in chlorine bleaches and disinfectants. Further processing showed the clumps contained strings of DNA.

More of the DNA sequences from the clumped crystals can be reproduced than DNA sequences taken from ground-up whole-bone samples, team member Noreen Tuross of Harvard University in Cambridge, Massachusetts, US, told New Scientist. The crystals also contain longer strings of better-preserved DNA, with fewer contaminants than DNA from whole bone.

Essentially, then, they are looking at extracting material trapped between clumps of the hydroxyapatite crystals that mineralize the collagen fibers, rather than trying to grind up a slice of the bone.

Added 9/20/05: The BBC has a story on this here a fact I learned from Abnormal Interests. The BBC also mentions the impact this will have on the neanderthal/homo issue quoting Stringer:

"The mitochondrial DNA on its own can't tell us if we're a distinct species," he explains.

"It depends what mammal you take. There are some species where the difference in mitochondrial DNA between us and Neanderthals would say they were a different species.

"Whereas in chimpanzees, our closest relative, you could contain the variation between us and Neanderthals in a single species alive today in Africa."

Scientists need to recover better DNA from our fossils, especially the nuclear DNA.

"Each gene has a separate evolution so to understand Neanderthals properly we will need different bits of their DNA to see if they're all telling us the same story," he adds.

Blackwater Mercenaries in New Orleans

Overkill: Feared Blackwater Mercenaries Deploy in New Orleans

Scary Stuff!

In Memorium: Gatemouth Brown

Blues legend Gatemouth Brown passed away Saturday due to cancer, he was 81.
From the Houston Chronicle
Although his career first took off in the 1940s with Okie Dokie Stomp and Ain't That Dandy , Brown bristled when he was labeled a bluesman.

In the second half of his career, he became known as a musical jack-of-all-trades who played a half-dozen instruments and culled from jazz, country, Texas blues, and the zydeco and Cajun music of his native Louisiana.

By the end of his career, Brown had more than 30 recordings and won a Grammy award in 1982.

"I'm so unorthodox, a lot of people can't handle it," Brown said in a 2001 interview.

Clarence Gatemouth Brown

SARS Linked to Bats

To the left are Horseshoe bats. They come from China, Australia, Wales and Wales respectively. In a paper to be published in PNAS, researchers have discovered a genetic relative of the SARS virus in Horeshoe bats.

From The Globe and Mail:

Scientists from State Key Laboratory of Emerging Infectious Diseases and the University of Hong Kong found a new coronavirus that was 40 per cent similar to the human SARS coronavirus in cave-dwelling Chinese horseshoe bats in Hong Kong. They proposed that the newly identified virus be known as the bat SARS coronavirus.
Their findings were published online Friday by the journal the Proceedings of the National Academy of Sciences.

Bats have previously been identified as important reservoirs for a number of zoonotic viruses — viruses that can jump from animals to humans — including rabies, the Hendra and Nipah virus and St. Louis encephalitis.

The scientists ran tests on anal swabs taken from 59 bats; 39 per cent of them carried the virus. Blood drawn from the bats suggested between 67 and 84 per cent (the differences related to the test used) had previously been infected with the virus.

The team has yet to test the bat virus to see how pathogenic it is, or whether it can infect other species.

Molecular analysis of the virus showed it is the closest known virus to the human SARS virus, with the exception of a SARS virus isolated from palm civets and raccoon dogs.

The story is a little more complicated, however. The research indicates that the bat and human coranaviruses are serparated by about 100 years of evolution. Which implies some other species are carrying the virus that jumped into humans. Previously, it had been thought that the disease jumped into humans from civets...



or tanuki...



However, recent tests on wild civets found no trace of the coronavirus:

But evidence later emerged that threw that theory into question. For instance, the virus was found only in civet cats in the crowded markets, not in wild or farmed civet cats. That suggests the market cats were infected by another as-yet unidentified animal.

Dr. Brown (an expert in viral evolution at the University of Ontario - afarensis)said the finding underscores the importance of learning more about the range of viruses lurking in nature.

“Historically we worry about viruses that infect ourselves or our pets or the things we eat. And otherwise we just don't care,” he noted.

“I think probably in the long run we have to care a bit more about the whole biosphere to try to link things up. We do have to know a bit of what's out there and moves into people and that sort of thing.”

To learn more about bats go here.

Sounds of Freetailed Bats

Why I Loved Living in Knoxville!

From 1990 to 1996 I was a resident of Tennessee - I was attending UT. I formed quite an attachment to Knoxville (has one of the best used book stores) and only moved back to St. Louis out of economic necessity. Here is an example of why.


More on this story can be found here. I'll quote some of the interesting bits picking up the story were snags start appearing:

We were now desperate to find a contact on the ground at the New Orleans airport to help triage ambulatory medical patients into these planes. FEMA in Washington was non responsive. We spoke to the aide to one of the deputies at FEMA and was told they did not need or want our help since the hospital evacuation was going fine. We looked at the reports from CNN about the conditions at the field hospital at the airport and discounted that opinion immediately.

*snip*

Around 8 pm this was the situation: We had planes for two flights at least. We had hospitals in Tennessee and Chicago for 290 and 200 patients respectively. We had two doctors for the plane. We needed landing slots at the airport and patients for the planes. We needed a contact on the ground.

Gore called Secretary of Transportation Norm Mineta and obtained two landing slots for Saturday. All we needed now was a medical contact at the airport. I contacted Casey Decker at the HHS Command Center, a highly advanced, high tech center for tracking and dealing with public health crises of all kinds. I asked Decker for help contacting TRANSCOM, which was running operations at the airport, as well as a medical coordinator on the ground. Decker explained they had not been able to maintain communications with TRANSCOM on the ground or the medical staff. That was troubling.

*snip*

Starting right after midnight I began receiving calls from FEMA, HHS, TRANSCOM and other groups whose acronyms I still cannot explain. LCDR Kennedy from FEMA called to understand what I was trying to do. I told him. Fifteen minutes later Mimi Riley, Deputy Director from NDMS called to beg me in a plaintive and exhausted voice not to carry out this mission. She had many reasons – you need doctors on the plane, Chicago is too far from their home, how will we track the patients, this is a military operation and we were not military.

I explained to her that we had two doctors on the plane one of whom was a retired Air Force Doctor who had run the military hospital in Baghdad after the invasion. I thought we could trust him to run an airplane of people from New Orleans to Knoxville. We were working with NDMS hospitals in Tennessee and Chicago so they would have a good tracking system. (I guess Mimi never heard of the Great Migration of African Americans from New Orleans and the south to Chicago after the flood of 1927 and during the Depression. Many people from New Orleans are more at home in Chicago than Houston. )

Mimi was unmovable. We were not military and that was that. She tried to sound grateful for our intentions but she was not going to have outsiders help. I even offered to GIVE her the planes and the crews and the hospitals and let her run it through her NDMS system but she would have none of it. She asked me at least to delay until noon the next day and I said I would try.

*snip*

Over the next three hours (from 2a.m. to 5 a.m.) I was called by an array of Majors and Lieutenant Commanders telling me to stop. (“I don’t mean to be rude, sir, but you must not do this. You must stop this now.”) Major Webb from GPMRC (don’t ask), Grant Meade from ESF. Major Lindquist from TRANSCOM (at last!) all telling me they would not cooperate and they did not know how we had gotten permission to land. I never mentioned Gore’s name because no one ever asked me who was paying for the flights or how we had come so far.

Finally at 5 a.m. Major Lindquist said if we landed he would not put any patients on the plane and we should expect no cooperation and there was no place to store the plane so we would have to leave.

Success:

At 7 a.m. on Saturday September 3^rd, the American Airlines plane with Gore and the doctors and Gore’s son Albert left Dallas for New Orleans. They landed at 8:30, got off the plane and Col LaFon immediately established contact with the Colonels running the operation on the ground, most of whom he had served with. He had trained many of the doctors on the scene. He explained why they were there and the doctors began a triage process to fill the plane. Two hours later the plane was loaded and headed to Knoxville.

*snip*

By now, it was too late to return to New Orleans, load up and leave before dark and American Airlines refused to have its personnel stay in New Orleans after dark. Gore and the team headed to Dallas for the night. Around midnight Saturday night, the FAA called American airlines and pulled their landing slots for Sunday saying only FEMA planes could fly in. Gore called Mineta again who promised to honor our initial agreement for two landing slots.

On Sunday morning Gore and the team landed in New Orleans to a much improved scene. Many more patients had been airlifted out after our flight and there were only ten ambulatory patients for our plane so we took 120 evacuees with us to Chattanooga. The welcoming reception in Chattanooga was so large that Gore said it looked like there was an ambulance for everybody on the plane.

We decided not to return to New Orleans because the medical patients we could take had been helped. (We could not take bedridden patients on stretchers on this plane.) Gore said that on the second trip to New Orleans, the doctors at the airport told him that the evacuation of the first 90 ambulatory patients had been the tipping point in their ability to adequately care for the other bedridden patients. They also noted that the military evacuations did not really pick up steam until after we “motivated” them with our private effort.

Of note:
Throughout the entire operation in Tennessee, EMS operations in Chicago had stayed prepared to handle patients or evacuees. None ever arrived because the military did not want us to use Chicago. The volunteers in Chicago were amazing in their desire to help. Mayor Daly had been rebuffed earlier when he offered a complete mobile hospital unit for the airport and a tent city as well. Sen. Barack Obama called Gore and asked how had Gore managed to land in New Orleans when the Senator had been refused landing rights to help.

Several things stand out that reinforce the pattern we have seen in the response to hurrican Katrina. First, the complete disconnect between what was happening in the devastated areas and what FEMA knew (The hospital evac for example). I have to wonder... Chertoff denies people are in the convention center, the FEMA officials mentioned above say the Charity Hospital evacuation was going fine. The question is, was there really a disconnect or were they simply covering for lack of response? Second the complete refusal of help. Here we have Daley offering a complete mobile hospital and being refused? Third, it took a private effort - by a Democrat - before the military evacuation picked up steam?



Added later: I added the pictures of Al Gore a few days later - should have done it when I first posted this.
P.S. I liked the beard - made him look like Will Ryker.

Oh, and one other thing

I heard on NPR that a Federal Appeals court has given Bush to detain American citizens on American soil as enemy combatants...
Nothing about it elsewhere though. Strike that:

"The exceedingly important question before us is whether the president of the United States possesses the authority to detain militarily a citizen of this country who is closely associated with al Qaeda," wrote Judge J. Michael Luttig in the opinion for the three-judge panel.

"We conclude that the president does possess such authority," wrote Luttig, a conservative whom the Bush administration has been considering for a possible Supreme Court nomination.

The ruling by the court based in Richmond, Virginia, was a major victory for the Bush administration. Andrew Patel, an attorney for Padilla, said he thought it would be appealed to the
U.S. Supreme Court.
"It is very troubling that a court would be willing to uphold executive detentions in a democracy. Terrorism does not change over 200 years of legal tradition," he said in New York.

He acknowledged in a footnote that Padilla cannot be held indefinitely. But he can continue to be detained for the duration of hostilities and Luttig said the United States remained engaged in the conflict with al Qaeda in Afghanistan.

Fortunately, there is one voice of sanity:

U.S. Rep. Adam Schiff said the ruling required congressional action to set out standards on what constituted an enemy combatant and what review should be mandated.

"The executive cannot have the unilateral authority to designate an American citizen as an enemy combatant and lock them up for life without meaningful standards and judicial review," the California Democrat said.

All I can say is be afraid, be very afraid.

A Followup to Comments

Comments on my previous post call for a more indepth folloup - because they are on target. So let's develop it a bit more.

From Eschaton:

THERESA ROY, RESIDENT OF ST. GABRIEL: I'd rather have them here dead than alive. And at least they're not robbing you and you have to worry about feeding them.

From St. Louisans survive lawlessness in French Quarter:

A St. Louis lawyer and his wife spent most all of four days in a French Quarter hotel while the streets outside were filled with looters. Finally, they escaped New Orleans in the back of a pickup.

"There was mass looting going on, the Walgreens next to us was wiped out clean," said Scheer, 36, a self-employed lawyer. "We never once saw a National Guard presence anywhere in the Quarter. We had to walk by gangs of thugs on the sidewalks with lead pipes, golf clubs, pistols under their shirts. We tried to maintain tunnel vision."

From Workbench:

As we approached the bridge, armed Gretna sheriffs formed a line across the foot of the bridge. Before we were close enough to speak, they began firing their weapons over our heads. This sent the crowd fleeing in various directions. As the crowd scattered and dissipated, a few of us inched forward and managed to engage some of the sheriffs in conversation. We told them of our conversation with the police commander and of the commander's assurances. The sheriffs informed us there were no buses waiting. The commander had lied to us to get us to move.

A little background on this second quote:

Around 500 people stuck in downtown New Orleans after the storm banded together for self-preservation, making sure the oldest and youngest among them were taken care of before looking after their own needs.

When buses charted by the group to escape New Orleans never showed up, they camped out beside a police command center on Canal Street, believing it was the best place to get aid, protection, and information. They were told they could not stay there and should leave the city on foot over Highway 90, which crosses the Mississippi River from New Orleans to the suburb of Gretna, a city of 17,500 people.

As pointed out at Pandagon there are two competing naratives at work here. One posits anarchy and violence in the wake of the complete collapse of government in New Orleans - and note only in New Orleans (at least I haven't heard of looting elswhere). The shows people trying to save themselves in the wake of govenmental collapse:

Well, yesterday we talked about how the media exaggerated and spread unsubstantiated rumors that made it sound like a riot in New Orleans. And now that survivors are getting out and getting comfortable and telling their stories, it's looking like what could be predicted by the theory that good crowds produce good thinking is shaping up to be true. I point everyone to this Kos diary by two survivors that Steve Gilliard has highlighted. The people who wrote it tell a compelling story of good crowd rule--people leaning on each other, bouncing ideas off each other, protecting each other. But there's another side of it, which is that the predominant, negative view of crowds--that they are automatically prone to violence--caused the police and military routinely to overreact and disperse crowds, which was counterproductive.

You can see both themes competing with each other in the St. Louis Post-Dispatch article (linked to above):

A group of about 200 Monteleone guests decided to try to walk out of the city to the east, and got to the on-ramp at the Crescent Connection bridge, where they were met by Gretna, La., police with shotguns. "They told us the bridge was closed to foot traffic," Scheer said. "Some locals had joined us and became extremely unruly, threatening to rush the officers. They fired their shotguns into the air."

In one paragraph you have both. A group joins together for mutual aide, the police overreact and of course there are unruly locals. Here's another paragraph - one that really makes you think:

In an interview with UPI, Gretna Police Chief Arthur Lawson confirmed that his department shut down the bridge to pedestrians: "If we had opened the bridge, our city would have looked like New Orleans does now: looted, burned and pillaged."

The increasingly desperate group set up camp on the New Orleans side of the bridge, where they were seen by several media outlets, until they were chased off at gunpoint by Gretna police:

Reduced to a small group of 8 people, in the dark, we sought refuge in an abandoned school bus, under the freeway on Cilo Street. We were hiding from possible criminal elements but equally and definitely, we were hiding from the police and sheriffs with their martial law, curfew and shoot-to-kill policies.

Criminals or the Police... who do you think they felt they were more in danger from?

The point here is that is still time to counteract the perception of lawless anarchy. Most of the stories I am hearing follow a similar pattern. People in an extremely desperate situation band together to try and survive in the face of a neglectful government are treated as roving bands of criminals by the people who are supposed to help them. Reversion to anarchy and criminal thuggary in the face of disaster is a common theme in fiction and being in that situation, I suppose it's inevitable that this assumption rears it's ugly head. "We were hiding from possible criminal elements..." one thinks it would be hard to tell, in that situation, whether the group you see is just a collection of people trying to survive or something worse. Such is the power of the mob rule mythology.
I use the word mythology deliberately because a lot of these news reports and stories have a certain "just so" quality that serve no purpose other than to confirm preexisting stereotypes and seem to be nothing but boundry maintenence mechanisms (simplistically, boundry maintenece mechanisms create sharp ideological boundries between two groups - reinforcing a positive image of one group and a negative image of the other).

What Gives Me Hope

Coturnix at Science and Politics has an incredibly interesting post about "mob rule", "crowd rule" and heroism. I strongly recommend it to everyone.

Why I'm Starting to Get Really Pissed Off

Let's start with Nixon sues to shut some relief Web sites. Apparently the web sites were run by someone with ties to racist groups:

Missouri's attorney general filed suit Wednesday seeking to shut down at least 10 hurricane relief Web sites that he said are quietly run by a man with ties to a racist group - and that may not benefit storm victims at all.

"This is a horrendous use of the victims of Hurricane Katrina to the benefit of a hate group," Attorney General Jay Nixon said at a news conference. He said Weltner is associated with the National Alliance, which Nixon's office described as "listed by the Southern Poverty Law Center as one of the nation's most active neo-Nazi hate groups."

So if you are looking for a place to donate stay away from these sites:

donate-katrina.com,
katrina-donations.com,
katrinafamilies.com,
katrinafund.name
neworleanscharities.com
katrinafund.ws,
christiandonations.org,
parishdonations.com,
clergydonations.com
internetdonations.us.

One of the sites, katrinafamilies.com, featured pictures of people in the flooded streets of New Orleans and the appeal, "We Need Your Help Now!" When a visitor to the site clicked on "Make a Donation," he was transferred to another site, internetdonations.org.

From there we move via Eschaton to The Raw Story where we learn of plans for rebuilding New Orleans:

"The power elite of New Orleans -- whether they are still in the city or have moved temporarily to enclaves such as Destin, Fla., and Vail, Colo. -- insist the remade city won't simply restore the old order. New Orleans before the flood was burdened by a teeming underclass, substandard schools and a high crime rate. The city has few corporate headquarters.

"The new city must be something very different, Mr. Reiss says, with better services and fewer poor people. "Those who want to see this city rebuilt want to see it done in a completely different way: demographically, geographically and politically," he says. "I'm not just speaking for myself here. The way we've been living is not going to happen again, or we're out."

From there we move to War and Piece:

The guy who callled me back yesterday who was supposedly a spokesman for FEMA? It turns out the WaPo reported as recently as March 2005 that he had been hired as one of three staffers to run a Bush administration Social Security "war room", modeled on the "Coalition Information Centers that promoted the administration message around the world during the war in Afghanistan"

Read the rest to understand what this means.

Onwards to The TPMCafe for an excellant analysis on the Bush Personality Cult. Pay attention to the comments.

Then to here where we learn 11 Republican congressman have voted NO on the bill to provide aid to the victems of Katrina.

Then of course there is the farcial "Bi-partisian" investigation concocted by the Republicans ans announced at a news conference with no bipartisianship in evidence.

Yup, I'm pissed.

Bush and Katrina

From the Preamble:

We the People of the United States, in Order to form a more perfect Union,
establish Justice, insure domestic Tranquility, provide for the common
defence, promote the general Welfare, and secure the Blessings of Liberty to
ourselves and our Posterity, do ordain and establish this Constitution for the
United States of America.

Well, they failed to insure domestic tranquility, they failed to promote the general welfare, and the verdict is not in on providing for the common defense. As for securing Blessings of Liberty....

Amendment I
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.

Let's see...

At first the evidence was scattered and anecdotal. But now it's pretty clear that a key aim of the Bush administration's takeover of the NOLA situation is to cut off press access to report the story.

First, there were the FEMA orders barring members of the press from photographing anything to do with the recovery of the bodies of the dead.

Perhaps there could be guidelines about photographs which in any way clearly identified the deceased. No one wants to get first confirmation of the death of a loved one by seeing their body on the nightly news. But a blanket ban serves only to prevent the public from knowing what really happened last week. And the right of FEMA or any branch of the federal government for that matter to issue such a ban on American soil seems highly dubious to me. It's one thing with military casualties: the military operates under its own legal code and not under normal civilian rules. But this is happening on American soil. This isn't a war zone. Nor is it any longer a situation where police or National Guard troops are in the midst of retaking control from mobs or looters. This is a recovery from a natural disaster.

Now comes this post from Brian Williams, which suggests a general effort to bar reporters from access to many of the key points in the city.

Take a moment to note what's happening here: these are the marks of repressive government, which mixes inefficiency with authoritarianism. The crew that couldn't get key aid on the scene in time last week is coming in in force now. And one of the key missions appears to be cutting off public information about what's happening in the city.

This is a domestic, natural disaster. Absent specific cases where members of the press would interfere or get in the way of some particular clean up operation, or perhaps demolition work, there is simply no reason why credentialed members of the press should not be able to cover everything that is happening in that city.

Think about it.

From Brian Williams:

At one fire scene, I counted law enforcement personnel (who I presume were on hand to guarantee the safety of the firefighters) from four separate jurisdictions, as far away as Connecticut and Illinois. And tempers are getting hot. While we were attempting to take pictures of the National Guard (a unit from Oklahoma) taking up positions outside a Brooks Brothers on the edge of the Quarter, the sergeant ordered us to the other side of the boulevard. The short version is: there won't be any pictures of this particular group of guard soldiers on our newscast tonight. Rules (or I suspect in this case an order on a whim) like those do not HELP the palpable feeling that this area is somehow separate from the United States.

At that same fire scene, a police officer from out of town raised the muzzle of her weapon and aimed it at members of the media... obvious members of the media... armed only with notepads. Her actions (apparently because she thought reporters were encroaching on the scene) were over the top and she was told. There are automatic weapons and shotguns everywhere you look. It's a stance that perhaps would have been appropriate during the open lawlessness that has long since ended on most of these streets. Someone else points out on television as I post this: the fact that the National Guard now bars entry (by journalists) to the very places where people last week were barred from LEAVING (The Convention Center and Superdome) is a kind of perverse and perfectly backward postscript to this awful chapter in American history.

So the first ammendment has gone by the wayside as well. Granted, no laws have been created to bar the press from New Orleans but freedom of the press is being abridged none the less. The question is, what is going to be done about it?

Katrina Death Toll

From ABC News Reporter's Blog:

Death Toll Mounts

Dennis Powell
Rich Esposito Sept. 5, 2005

Two senior-level state and federal sources say that the death toll could top 6,000. Both believe that the majority of deaths — 80 to 90 percent — were caused by a slow response from FEMA and Department of Homeland Security.

In the meantime, several blogs are reporting that the press is being banned from New Orleans. I have been searching for more since it first hit Eschaton. So far, there is nothing in the MSM...
I would take it with a large amount of caution until further proof shows up...

Americablog has more... more proof would be nice. Anybody out there have anything more solid?

Irish Elk and Fallow Deer

The above is a picture of the skull of an Irish Elk.

According to National Geographic News a study in Nature has linked Irish Elk to Fallow Deer:

Scientists at University College London studied DNA and skeletal remains of the extinct giant deer, or Irish elk, to construct its family tree. This is the first time this method has been used to reveal an extinct animal's living descendants, according to the study team.

The researchers found that the giant deer, which stood seven feet (two meters) tall at the shoulder, is closely related to the modern fallow deer, a much smaller species that still inhabits the former haunts of its Ice Age relative throughout Europe.

The giant deer (Megaloceros giganteus) roamed Europe and Central Asia alongside humans until its extinction some 8,000 years ago. The animal was just one of a number of colossal deer species that no longer exist today.

The team identified skeletal features that are unique to both fallow and giant deer. They also found that the vertebrae of the fallow deer were once adapted to support very large antlers.

Further evidence of a close ancestral link came from mitochondrial DNA taken from both animals' bones. Mitochondrial DNA is passed down through generations from mothers to their offspring.

The NGN article also contains an interesting discussion on using a similar techniques with Homo floresiensis:

Recent technological advances have raised hopes that scientists may be able to pinpoint our own closest relatives in the human family tree.

Researchers are currently trying to extract the DNA of Homo floresiensis, whose remains were found last year on the island of Flores in Indonesia.

Nicknamed "the Hobbit" because of its tiny stature, H. floresiensis is believed to have diverged from modern humans some two million years ago.

However researchers are skeptical about whether techniques that worked for extinct Ice Age animals like the giant deer will work on this diminutive species of human, which lived only some 18,000 years ago.

The problem, says Ian Barnes, is that the remains come not from Ireland or Siberia, as in the case of the giant deer, but from a tropical island.

"DNA degrades over time, and like any chemical reaction, it will degrade faster if the temperature's higher," he said. "The problem with a lot of the remains that we are asked to look at is that they've been at too high a temperature for too long a period of time.

"Our best estimate is that there won't be any DNA surviving in that [H. floresiensis] material."

Comets and Organic Molecules

Deep Impact collision ejected the stuff of life


Millions of kilograms of fine dust particles and water and a "surprisingly high" amount of organic molecules sprayed into space when NASA crashed its Deep Impact spacecraft into Comet 9P/Tempel 1 on 4 July 2005, reveal a trio of new studies.

The observations bolster theories that comets may have seeded Earth with the raw materials for life and suggest they may be sponge-like – rather than hardened – at their cores.

Observers estimate the impact released about 5 million kilograms of water from beneath the comet's surface and between two and five times as much dust. There was so much dust, in fact, that mission members have not been able to see the impact crater with the high-resolution camera on the mission's flyby spacecraft, about 500 km away.

But here is the interesting part:

The team estimates the impact blasted away a crater about 100 metres wide and up to 30 m deep. Crucially, organic molecules were among the material ejected. Neither the full range of molecules nor their abundances have been determined yet, but researchers say they have found a surprisingly high amount of methyl cyanide, a molecule seen in large quantities in another comet.

This supports theories that comets may have brought water and the building blocks of life to Earth, and the team hopes to eventually "identify all the species comets brought in abundance to early Earth", says A'Hearn.

Interesting!

Vikings!

King loses mother but gains a daughter

Mitochondrial DNA and forensic anthropology has been used to identify the remains long thought to be the mother of Sven Estridsen,apparently the last viking king.

Jorgen Dissing, at the Institute of Forensic Medicine in Copenhagen, Denmark, extracted mitochondrial DNA from the pulp of molars from the skeletons. Mitochondrial DNA is useful for analysing ancient remains because there are many copies per cell so DNA breakdown causes fewer problems during analysis than it can in nuclear DNA samples.

If Estrid is Sven's mother the DNA should be identical because mitochondria are passed exclusively from a mother to her offspring. But they weren't. Moreover, the condition of the teeth and bones suggest that the woman was around 35 when she died, Dissing told the International Association of Forensic Science meeting in Hong Kong last week. Historical records tell us Sven's mother died aged around 75.

For more about how anthropologists determine age, gender, stature and ethnicity from a skeleton you can go here

Just for kicks, here is an interesting article on viking hoards.


A replica of a viking ship...

And finally a link to where you can get your own viking helmet

Now if we could only get the church of the FSM to incorporate vikings into it's services...

Here's the Question

Josh Marshall has a slightly different take The real story about the Brown memo below is, How did it get public? The knives, or rather, not the knives, but the long knife seems to be out for Michael Brown now. Now I for one have never seen Bush fire anyone, but assuming Bush and company decide to scape goat Brown (who deserves to be fired) does Bush come out of this unscathed?

Also from Josh Marshall:

But according to this August 30th article in the St. Petersburg Times, on Sunday the 28th, Mayfield arranged a video conference call with President Bush himself at the Crawford Ranch during which he explained the hurricane's force and destructive potential.

So the question is, if Bush makes a sacrificial lamb out of Brown does it end there?

From Daily Kos:

As specific orders began arriving to the firefighters in Atlanta, a team of 50 Monday morning quickly was ushered onto a flight headed for Louisiana. The crew's first assignment: to stand beside President Bush as he tours devastated areas.

A link is provided to Frustrated: Fire crews to hand out fliers for FEMA:

The firefighters, several of whom are from Utah, were told to bring backpacks, sleeping bags, first-aid kits and Meals Ready to Eat. They were told to prepare for "austere conditions." Many of them came with awkward fire gear and expected to wade in floodwaters, sift through rubble and save lives.
"They've got people here who are search-and-rescue certified, paramedics, haz-mat certified," said a Texas firefighter. "We're sitting in here having a sexual-harassment class while there are still [victims] in Louisiana who haven't been contacted yet."
The firefighter, who has encouraged his superiors back home not to send any more volunteers for now, declined to give his name because FEMA has warned them not to talk to reporters.

From later in the same article:

But as specific orders began arriving to the firefighters in Atlanta, a team of 50 Monday morning quickly was ushered onto a flight headed for Louisiana. The crew's first assignment: to stand beside President Bush as he tours devastated areas.

So who do we focus on and hold accountable?

This Could Be Big

Yahoo News is reporting that:

The government's disaster chief waited until hours after Hurricane Katrina had already struck the Gulf Coast before asking his boss to dispatch 1,000
Homeland Security employees to the region — and gave them two days to arrive, according to internal documents.
Michael Brown, director of the
Federal Emergency Management Agency, sought the approval from Homeland Security Secretary Mike Chertoff roughly five hours after Katrina made landfall on Aug. 29. Brown said that among duties of these employees was to "convey a positive image" about the government's response for victims.
Before then, FEMA had positioned smaller rescue and communications teams across the Gulf Coast. But officials acknowledged Tuesday the first department-wide appeal for help came only as the storm raged.

Brown's memo to Chertoff described Katrina as "this near catastrophic event" but otherwise lacked any urgent language. The memo politely ended, "Thank you for your consideration in helping us to meet our responsibilities."

Homeland Security spokesman Russ Knocke said Brown had positioned front-line rescue teams and Coast Guard helicopters before the storm. Brown's memo on Aug. 29 aimed to assemble the necessary federal work force to support the rescues, establish communications and coordinate with victims and community groups, Knocke said.

Instead of rescuing people or recovering bodies, these employees would focus on helping victims find the help they needed, he said.

"There will be plenty of time to assess what worked and what didn't work," Knocke said. "Clearly there will be time for blame to be assigned and to learn from some of the successful efforts."

Brown's memo told employees that among their duties, they would be expected to "convey a positive image of disaster operations to government officials, community organizations and the general public."

"FEMA response and recovery operations are a top priority of the department and as we know, one of yours," Brown wrote Chertoff. He proposed sending 1,000 Homeland Security Department employees within 48 hours and 2,000 within seven days.

Knocke said the 48-hour period suggested for the Homeland employees was to ensure they had adequate training. "They were training to help the life-savers," Knocke said.

Question: Why wern't they already properly trained?
Second Question: Doesn't saying "They were training to help the life-savers," contradict "...Instead of rescuing people or recovering bodies, these employees would focus on helping victims find the help they needed..." or am I missing something?

The same day Brown wrote Chertoff, Brown also urged local fire and rescue departments outside Louisiana, Alabama and Mississippi not to send trucks or emergency workers into disaster areas without an explicit request for help from state or local governments. Brown said it was vital to coordinate fire and rescue efforts.

Meanwhile, the airline industry said the government's request for help evacuating storm victims didn't come until late Thursday afternoon...

Republicans are, however impressed with Brown:

Sen. Ted Stevens, R-Alaska, said the administration is "getting a bad rap" for the emergency response.

WTF?? You have the head of FEMA telling local first responders not to save lifes until they get an explicit request from local and state governments, and the federal government doesn't ask the airline industry for help evacuating storm victems till 3 days later - but they are getting a bad rap?

Let's look at this again, maybe I'm missing something:

The same day Brown wrote Chertoff, Brown also urged local fire and rescue departments outside Louisiana, Alabama and Mississippi not to send trucks or emergency workers into disaster areas without an explicit request for help from state or local governments. Brown said it was vital to coordinate fire and rescue efforts.

State authorities suspected a political motive behind the request. "Quite frankly, if they'd been able to pull off taking it away from the locals, they then could have blamed everything on the locals,

From the New York Times:

Under the command of President Bush's two senior political advisers, the White House rolled out a plan this weekend to contain the political damage from the administration's response to Hurricane Katrina.

It orchestrated visits by cabinet members to the region, leading up to an extraordinary return visit by Mr. Bush planned for Monday, directed administration officials not to respond to attacks from Democrats on the relief efforts, and sought to move the blame for the slow response to Louisiana state officials, according to Republicans familiar with the White House plan.

The effort is being directed by Mr. Bush's chief political adviser, Karl Rove, and his communications director, Dan Bartlett.

Okay, that makes more sense.

Chimpanzee Fossils

As recently reported in Nature, fossil teeth of chimpanzees have been found. They date to about 545,000 years ago. Besides being some of the few chimp fossils found, they also demonstrate that chimps - in the past - were not confined to the same dense forest environments they are found in today. Who knows, maybe competitive exclusion is the reason why chimps and humans separated.

In Memorium

Bob Denver passed away today due to complications from cancer treatments. He was 70 years old.

"I certainly didn't set out to have a series rerun forever, but it's not a bad experience at all,"

How Cool Is That!

In my recent post on Ichthyostega I mentioned I didn't have access to Nature. Low and behold when I checked my email On Friday I had all the articles on Ichthyostega - sent by none other than Per Ahlberg the lead author of the paper! Thanks again!

The article is even more interesting than than descriptions of it in the press. Before I go into it a little background information is necessary (Run away! afarensis is going to talk about bones again!).
Below is a picture of human vertebrae. There are three different types pictures: (7)cervical, (12)thoracic and (5)lumbar. Additionally, humans have sacral and caudal (or coccygeal - the remnants of the tail) vertebrae. This differentiation - based on form and function - is called regionalization



Human vertebrae share several common features. First, a round heavy body. Second, a round opening (the vertebral foramen). Third, several processes (two - usually - transverse and one spinous). The tranverse processes and spinous processes (along with the pedicle) form the vertebral arch. Additionally, the thoracic vertebrae contain facets for articulation with the ribs. The human vertebral column forms an S-shaped curve.



If you look closely at the middle picture above you will note that the spinous processes change orientation based on where they are on the vertebral column (I will get back to this later). So what does this have to do with a Devonian fossil?

In order to reconstruct Ichthyostega Ahlberg et al used 9 different fossils to create a composite vertebral column (necessary because none of the fossils had a complete vertebral column). This was possible because the fossils contained overlapping segments. It should be pointed out here that the osteology of these early vertebrates is somewhat different from that of humans. The Ichthyostega vertebrae has several pieces as you can see in the drawing below.



Several interesting features of the new reconstruction stand out. First, was the identification of regionalization in Ichthyostega vertebrae. As I understand it (having a background in anthropology rather than say comparitive anatomy or paleontology) this is not seen in fish and can be construed as an adaptation to life on land. This is where things get interesting. Ichthyostega vertebral arches change in orientation based on where they are in the vertebral column and in the lumbar area there is some overlap. Additional changes in the reconstruction involve the ribs. Previous reconstructions showe Ichthyostega with no neck. Which is not the case in the new reconstruction. Another change involves the ribs - which overlap. Taken all together the osteology of Ichthyostega indicates some interesting things about locomotion. The zygapophysis, pictured above, stiffen the spine and are adaptations to life on land. The morphology of the ribs and vertebrate restricts lateral flexion - but the lumbar vertebrate allow for some vertical flexion. I should also point out that Ichthyostega has ears specialized for underwater hearing. Taken all together the morphology shows one, ultimately unsuccesful, attempt to solve the problems of life on land.

Speaking of the Devil

As I am blogging this morning I'm watching the news (first time in a while) and low and behold Fox news is following the Republican "shift the blame" policy in their interview with Chertoff. I don't have transcripts but there were several leading questions during the interview. So Chertoff got to talk about how local officials were telling him a different story than what the press was and about how much easier it is to work with republican governors like Haley Barbour than it is to work with democrats like Kathleen Blanco...

And now Britt Hume is whining about how people are blaming the White House but not local officials - didn't mention all the budgett cuts that affected the situation. Wankers!

WOW! and now Kristol is bowing to political winds and criticizing the head of FEMA - wonders why he's in charge...

Political fallout...
Kristol... folks are proud of what Bush achieved and think Bush is a good leader...fallout won't matter to Bush

Wallace and Kristol... should proceed with plans to repel estate tax, social security, etc.

Wankers!

You Heard it Here First

Deep Scope is starting to get a lot of attention here and here for example. But you heard it here and here first!

Our Government at Work

From MSNBC:

Behind the scenes, a power struggle emerged, as federal officials tried to wrest authority from Louisiana Gov. Kathleen Babineaux Blanco (D). Shortly before midnight Friday, the Bush administration sent her a proposed legal memorandum asking her to request a federal takeover of the evacuation of New Orleans, a source within the state's emergency operations center said Saturday.

The administration had sought control over National Guard units, normally under control of the governor. Louisiana officials rejected the request, noting that such a move would be comparable to a federal declaration of martial law. State authorities suspected a political motive behind the request. "Quite frankly, if they'd been able to pull off taking it away from the locals, they then could have blamed everything on the locals," said the source, who is an adviser and does not have the authority to speak publicly.

Blanco made two moves Saturday that protected her independence from the federal government: She created a philanthropic fund for the state's victims and hired James Lee Witt, Federal Emergency Management Agency director in the Clinton administration, to advise her on the relief effort.

Bush, who has been criticized, even by supporters, for the delayed response to the disaster, used his weekly radio address to put responsibility for the failure on lower levels of government. The magnitude of the crisis "has created tremendous problems that have strained state and local capabilities," he said. "The result is that many of our citizens simply are not getting the help they need, especially in New Orleans. And that is unacceptable."

In a Washington briefing, Homeland Security Secretary Michael Chertoff said one reason federal assets were not used more quickly was "because our constitutional system really places the primary authority in each state with the governor."

Then, of course, there is this and this

Up till now I have refrained from posting about Hurricane Katrina, but the tactics we are seeing from the government has repulsed me beyond measure. As Aaron Broussard, President of Jefferson Parish, said to Tim Russert "Shut up and send help"

Of Crabs and Hagfish

There are a number of videos available from the Deep Scope missions mentioned in a previous post.
One of the more interesting is a confrontation between some crabs and a hagfish

here
Other videos are available atNOAA Ocean Explorer

New Species of Squid Discovered

After dodging Hurricane Katrina, researchers in the Deep Scope exepediton reports the discovery of a new species of squid pictured above.

From Science Daily:

The ship's crew took special precautions as they cruised from Texas back to the Viosca Knoll to avoid hurricane debris. They encountered extensive garbage, but nothing that threatened the ship. They also saw signs of damage on oil rigs and heard reports from other ships that all rigs within a 50-mile-wide swath beneath the hurricane's path appeared to be thrashed beyond operable condition.

Last year, the system captured footage of a six-foot squid believed to be a new species. This year, at a site hundreds of miles away, the camera caught footage of what appears to be the same species, which would suggest that the squid is not rare, and would also illustrate how poorly explored the deep sea remains if such a large animal could have gone undiscovered. The squid appears to have been attracted by a flashing light lure designed to mimic a deep-sea jellyfish's bioluminescent display. Much remains unknown about how animals use bioluminescence, and one of the key goals for Eye-in-the-Sea beyond basic observation is to use the bioluminescence lure and other techniques to learn how animals use the light they produce.

Even more interesting is news about a new species of crab:

Frank has been conducting detailed studies of how the eyes of animals on the deep seafloor work, in collaboration with others aboard. Working with animals collected in special light-tight devices that avoid damage to delicate deep-sea eyes, Frank has discovered a species of deep-sea crab that can detect ultra-violet light, despite there being no known ultraviolet light in deep water. UV sensitivity is common in animals that live closer to the surface, but has never been discovered in a deep species. The reasons for this seemingly bizarre ability are not clear, but the sensitivity could point to a deep-sea light source about which researchers are not aware, or to some unknown characteristic of known light sources such as bioluminescence--the light chemically produced by countless open ocean organisms.

More info on Deep Scope - includes more pictures and periodic dipatches.

Grasshoppers Being Murdered By Hairworms

The above is a picture of a parasitic hairworm - a species of Nematamorph. They have a unique pattern of reproduction:

Gordian worms or hair worms are nematamorphs, a phylum of freshwater invertebrates. Gordian worms live most of their lives as foot long, ribbon thin animals, in the rivers, where they mate and produce eggs. Once eggs develop into larvae, larval gordian worms must infect an aquatic insect larvae, which metamorphosizes and carries the gordiid onto shore. Once onshore, the gordiid encysted inside the aquatic insect must be eaten by a cricket or grasshopper, in which the gordian worm feeds and matures. Gordian worms only feed while inside their cricket or grasshopper host. For the gordian to complete its lifecycle, the infected cricket must then die and fall into water.

A mystery has always been how they get their hosts to fall into the water. Recent research has taken a step towards solving this mystery

Now Biron and his colleagues have shown that the worm brainwashes the grasshopper by producing proteins which directly and indirectly affect the grasshopper’s central nervous system.

Two different proteins seem to be involved. One mimics the hosts protiens and affects the central nervous system. The second is:

"...linked to geotactic behaviour – the orientated movement of an organism in response to gravity."

You can watch a video of a grasshoper plunging to it's death here

Added About an Hour Later: National Geographic News also has a story on this:

"It's one of the most horrific things I've ever seen," Loxdale said. "It makes the science fiction film Alien look pretty tame in comparison."

For example, a type of parasitic flatworm targets cockles in New Zealand, driving the marine mollusks to the surfaces of muddy bottoms in shallow waters. There, oystercatcher birds snap the cockles up and eat them, flatworms and all. The shorebirds serve as the final hosts in the flatworms' complex life cycle.

"Parasitic wasps can also make the host weave a special cocoon-like structure to protect the wasp pupae [offspring] against heavy rain," Thomas added.

While revelations about the hairworm's antics may inspire a new generation of sci-fi aliens, the study team says their findings may also help the development of new medical treatments.

Biron says mind-altering human pathogens—such as those that cause rabies, sleeping sickness, and toxoplasmosis—may manipulate their victim in similar ways.

So apparently, this is not unprecedented. Given the rampant amount of chemical warfare going on in the insect world I can't say I surprised to find out that some parasites use chemical means to control their hosts behavior.

Opus and Intelligent Design

Via Stranger Fruit comes OPUS on Intelligent Design



I'm not surprised considering the strips he did on creationism back around the time of the Arkansas trial (see "Loose Tails" - here's a memorable quote "Did penguins evolve through the ages or were they created in Newark, New Jersey in 1912, as according to Scientific Penguinism?").

Ichthyostega and the Origins of Land Vertebrates

One of the problems with being a science blogger but not a scientist is that stories come along that you can't really cover in the detail you would like. The Chimp genome is a good example. I don't have access to Nature (other than the free stuff they have put up)short of wandering into the library of one of the local colleges here in St. Louis - something I don't always have time to do. Decoding the chimpanzee genome is an incredibly important piece of science that we will all be hearing more about (I may do something on it later).

In the meantime, several interesting pieces of science news are just crying out to be covered.


Ichthyostega Hindlimb


Ichthyostega Skull



The above are fossils of Ichthyostga - one of the first land dwelling vertebrates. They evolved in the Devonian (some 410-360 mya)and are found in Greenland. A recent study - published in the most recent issue of Nature - indicates some interesting facts about Ichthyostega (from National Geographic News):

The team's reconstruction differs from all previously published reconstructions of the animal.

Unlike in other reconstructions, the vertebrae that make up the backbone in Ahlberg's rendering are regionalized: They have different shapes in different parts of the column. Therefore, different parts of the backbone flexed in different ways, Ahlberg speculates.

The shapes of the vertebrae would have prevented Ichthyostega from sideways movement. The vertebrae generally resemble those of mammals, suggesting that this part of the backbone could flex vertically to some extent, Ahlberg said.

While regionalization of the backbone is fairly common in living land vertebrates, it's not seen in the lobe-finned fishes from which Ichthyostega is thought to have evolved. Lobe-finned fishes have thick, fleshy fins, as opposed to the delicate fins of most fish. Only two types of lobe-finned fishes survive today, coelacanths and lungfishes.

This has interesting implications for how Ichthyostega moved:

As such, the researchers hypothesize that Ichthyostega probably used two different gaits on land, depending on how fast it needed to move.

"On the one hand it could have 'walked' with the body held rigid and the limbs moving in [an] alternating diagonal sequence," Ahlberg wrote in an e-mail to National Geographic News.

In this gait the strong front limbs likely allowed the creature to hold its body off the ground, while the flipperlike hind limbs and rear end dragged behind, Ahlberg noted.

In the other, inchworm-like gait Ichthyostega likely used the limited up-and-down movement of the backbone in combination with symmetrical limb movement "to achieve a weird gait approximating to a slow and extremely stumpy-legged gallop," Ahlberg said.

Since most paleontologists assume that land vertebrates evolved from an organism that could flex their vertebral column from side to side, this means Ichthyostega probably wasn't a direct ancestor of later vertebrates:

In other words, Ichthyostega's body design was a failure. Few, if any, fossils representing descendants of this lineage are known after about 360 million years ago, Carroll noted in a commentary on this research in Nature. The creatures, it seemed, simply died out.

"Remember, the origin of land vertebrates from fish took 15 million years," Carroll said in a telephone interview. That's a long time, he added, for lobe-finned fish to have evolved various designs—with varying degrees of success.

Ahlberg said that another Devonian tetrapod from Greenland, Acanthostega, which is more primitive and less terrestrial looking than Ichthyostega, appears closer to the "main line" of tetrapod evolution. Below is a fossil Acanthostega.


For more info you can go to:

Palaeos

Tree of Life

Also, I am cross-posting this at Transitions

ADDED LATER: Welcome Pharyngulans! After checking out my site I recommend following the Palaeos link for some interesting additional info - and controversy - surrounding Ichthyosyega.