Friday, October 31, 2008

Which Hurricane Season Will It Be In the Future?

In a paper published in the journal Science today, scientists Gabriel A. Vecchi of NOAA's Geophysical Fluid Dynamics Laboratory, Kyle L. Swanson of the University of Wisconsin - Milwaukee Atmospheric Sciences Group and Brian J. Soden from the University of Miami's Rosenstiel School of Marine and Atmospheric Science teamed up to study hurricane data observed over more than 50 years. The study explores the relationship between sea surface temperature (SST) and seasonal hurricane activity, and show how differing interpretations of the observational record can imply vastly different futures for Atlantic hurricane activity due to global warming. The two interpretations arise from assumptions of whether it is the local SST in the Atlantic in isolation, or whether it is the SST in the Atlantic 'relative' to the rest of the tropics, that drives variations in Atlantic hurricane activity.

If one assumes the former (the local SST hypothesis), then by 2100, the lower bound on Atlantic hurricane activity is comparable to that of 2005, when four major hurricanes struck the continental United States, causing more than $100 billion in damage. The upper bound exceeds 2005 levels by more than a factor of two. However, if one assumes the latter (the relative SST hypothesis), then the future is similar to the recent past, with periods of higher and lower hurricane activity relative to present-day conditions due to natural climate variability, but with little long-term trend.

If the upper bound is 8 hurricanes per 'average' year for the more catastrophic model, does that cross the threshold of making building (and rebuilding) there uneconomical. 21st century population shifts are going to be interesting. Safe Bet: Alaska gets a 10x increase in people.

Smilodon: Pack Cat?

The sabertooth cat (Smilodon fatalis), one of the most iconic extinct mammal species, was likely to be a social animal, living and hunting like lions today, according to new scientific research. The species is famous for its extremely long canine teeth, which reached up to seven inches in length and extended below the lower jaw.

Instead of relying on the bones and teeth of the sabertooths to make their findings, scientists from UCLA and the Zoological Society of London concluded that the sabertooth cat was social by using a novel technique: They compared numbers of present-day carnivores competing for kills in Africa with those of mainly extinct species found in a North American fossil deposit.

The research is published in the current issue of the Royal Society's journal Biology Letters (Oct. 28). Co-authors also included scientists from South Africa's Tshwane University of Technology and University of Pretoria.

Smilodon existed in North and South America between 1.8 million and 10,000 years ago and is one of the most common species preserved at the Rancho La Brea tar pits of Los Angeles, a fossil deposit in which dying herbivores trapped in sticky asphalt attracted numerous dire wolves and sabertooth cats, some of which also died there.

Because most living cats are solitary, controversy has persisted over the social life of Smilodon.

The study reported in Biology Letters took a new approach to the question by comparing data from the La Brea fossil record and data obtained from "playbacks" used in Africa, in which the recorded calls of distressed prey and the sounds of lions and hyenas are used to attract carnivores. This technique has been used by scientists to estimate carnivore densities in eastern and southern Africa.


Glacial Advances in Antarctic Climate Change Studies

Antarctica, which seemed to have largely escaped the global warming affecting the rest of the planet, is melting too, according to a study.

The new research, published in the journal Nature Geoscience, also provides the firmest proof to date that climate change at both poles is not the result of natural fluctuations.

"Our results demonstrate that human activities have already caused significant warming in both polar regions," said Alexey Karpechko, a professor at the University of East Anglia and a co-author of the study released Thursday.

Earlier investigations left no doubt that Earth's northern extremity has warmed at nearly twice the global average over the last century, causing a dramatic shrinking of sea ice and disrupting the region's ecosystems.

"However in Antarctica, such detection was so far precluded by insufficient data," said Karpechko.

The new study goes a long way toward filling that gap, and factoring out the causes.

Another piece of the puzzle...

Thursday, October 30, 2008

Tracking Paleo Forests Through PhytoGenetics

A "living fossil" tree species is helping a University of Michigan researcher understand how tropical forests responded to past climate change and how they may react to global warming in the future.

The research appears in the November issue of the journal Evolution.

Symphonia globulifera is a widespread tropical tree with a history that goes back some 45 million years in Africa, said Christopher Dick, an assistant professor of ecology and evolutionary biology who is lead author on the paper. It is unusual among tropical trees in having a well-studied fossil record, partly because the oil industry uses its distinctive pollen fossils as a stratigraphic tool.

About 15 to 18 million years ago, deposits of fossil pollen suggest, Symphonia suddenly appeared in South America and then in Central America. Unlike kapok, a tropical tree with a similar distribution that Dick also has studied, Symphonia isn't well-suited for traveling across the ocean---its seeds dry out easily and can't tolerate saltwater. So how did Symphonia reach the neotropics? Most likely the seeds hitched rides from Africa on rafts of vegetation, as monkeys did, Dick said. Even whole trunks, which can send out shoots when they reach a suitable resting place, may have made the journey. Because Central and South American had no land connection at the time, Symphonia must have colonized each location separately.

Once Symphonia reached its new home, it spread throughout the neotropical rain forests. By measuring genetic diversity between existing populations, Dick and coworker Myriam Heuertz of the Université Libre de Bruxelles were able to reconstruct environmental histories of the areas Symphonia colonized.

"For Central America, we see a pattern in Symphonia that also has been found in a number of other species, with highly genetically differentiated populations across the landscape," Dick said. "We think the pattern is the result of the distinctive forest history of Mesoamerica, which was relatively dry during the glacial period 10,000 years ago. In many places the forests were confined to hilltops or the wettest lowland regions. What we're seeing in the patterns of genetic diversity is a signature of that forest history."

In the core Amazon Basin, which was moist throughout the glacial period, allowing for more or less continuous forest, less genetic diversity is found among populations, Dick said. "There's less differentiation across the whole Amazon Basin than there is among sites in lower Central America."

The study is the first to make such comparisons of genetic diversity patterns in Central and South America. "We think similar patterns will be found in other widespread species," Dick said.

The extent of the tropical rain forests such as the Amazon during the glacial periods is an extraordinarily contentious subject in their study. Part of the reason is that the rain forests may have been very, very small pockets and the current Amazon rain forest as we know it is a very recent phenomenon that is a run together of many, many smaller forests. That has two points that cause irritation: 1. that might mean that the modern cut back can be recovered from in a very quick manner (1000 years or less, geologically quick, btw!) and two, the celebrated diversity of the Amazon and other tropical rain forests may be only temporary as the ecosystem sorts itself out between all those former isolated faunas now competing with one another. Both of those ideas are less than popular with some.

Who's Your Phoenician Daddy?

Ancient maritime traders of the Mediterranean may have left behind a large genetic footprint in the region, where 1 in 17 men still harbors Phoenician DNA, according to a new study.

The findings could fill a gap in the history of the Phoenician civilization, which originated two to three thousand years ago in the eastern Mediterranean—in what is now Lebanon and Syria—and included prominent traders, according to Chris Tyler-Smith, lead author and associate researcher at National Geographic Society's Genographic Project. (The National Geographic Society owns National Geographic News.)

kewl. I ahve to say, though, that it would not entirely be correct to say the Phoenicians had disappeared by the time the Romans appeared. Tyre and Carthage and all those types were around. A little.

PS Mild soft spot for the Phoenicians. I know you all would have never guessed that...

Methane's Rise

New surge ends a decade of stability

The amount of methane in Earth's atmosphere shot up in 2007, bringing to an end a period of about a decade in which atmospheric levels of the potent greenhouse gas were essentially stable, according to a team led by MIT researchers.

Methane levels in the atmosphere have more than doubled since pre-industrial times, accounting for around one-fifth of the human contribution to greenhouse gas-driven global warming. Until recently, the leveling off of methane levels had suggested that the rate of its emission from the Earth's surface was approximately balanced by the rate of its destruction in the atmosphere.

However, since early 2007 the balance has been upset, according to a paper on the new findings being published this week in Geophysical Review Letters. The paper's lead authors, postdoctoral researcher Matthew Rigby and Ronald Prinn, the TEPCO Professor of Atmospheric Chemistry, in MIT's Department of Earth, Atmospheric and Planetary Science, say this imbalance has resulted in several million metric tons of additional methane in the atmosphere. Methane is produced by wetlands, rice paddies, cattle, and the gas and coal industries, and is destroyed by reaction with the hydroxyl free radical (OH), often referred to as the atmosphere's "cleanser."

One surprising feature of this recent growth is that it occurred almost simultaneously at all measurement locations across the globe. However, the majority of methane emissions are in the Northern Hemisphere, and it takes more than one year for gases to be mixed from the Northern Hemisphere to the Southern Hemisphere. Hence, theoretical analysis of the measurements shows that if an increase in emissions is solely responsible, these emissions must have risen by a similar amount in both hemispheres at the same time.

A rise in Northern Hemispheric emissions may be due to the very warm conditions that were observed over Siberia throughout 2007, potentially leading to increased bacterial emissions from wetland areas. However, a potential cause for an increase in Southern Hemispheric emissions is less clear.

First off, this is bad. Methane is one of the major contributors to the PT Extinction.

The source of the methane is really, really important. Is it the tundra? There's a lot of carbon sequestered there. Is it directly from man made pollution? Or is it the methane calthrates? Which of these is the perpetrator tells us whether this is a train we can stop...or not.

Wednesday, October 29, 2008

Russian "Relations" With Georgian Provinces Formalized

Russia's parliament on Wednesday quickly ratified treaties cementing close economic and military ties with Georgia's two breakaway provinces.

The State Duma, or lower house, voted unanimously to endorse the friendship treaties with Abkhazia and South Ossetia which were signed in the Kremlin last month. The Duma, dominated by Kremlin-controlled parties, quickly rubber stamps government proposals.

Russia recognized both provinces as independent states following its war with Georgia in August. The treaties envisage the deployment of 3,800 Russian troops in each of the two provinces.

Russia's Foreign Ministry said in a letter to lawmakers that the treaties were necessary to create the legal basis for the deployment of Russian troops to the territories. "The Russian troops presence is necessary to protect peace in the region and ensure reliable security," the ministry said, adding that the treaties envisage aid in case of aggression.

I wish I had time to comment, but...I don't. More later.

Son of a Mule

Noah talks development plan for the Mule project at DARPA. Quite interesting, especially for those of us that remember the walking robot NOVA program waaaaaaay back. Talk about Future is Now moment.

Tuesday, October 28, 2008

Whoa: Pyrite Armour Footed Snails

Hat Tip to Doug.


The Ever Thinner Arctic Sea Ice

he thickness of sea ice in large parts of the Arctic declined by as much as 19% last winter compared to the previous five winters, according to data from ESA's Envisat satellite.

Using Envisat radar altimeter data, scientists from the Centre for Polar Observation and Modelling at University College London (UCL) measured sea ice thickness over the Arctic from 2002 to 2008 and found that it had been fairly constant until the record loss of ice in the summer of 2007. Unusually warm weather conditions were present over the Arctic in 2007, which some scientists have said explain that summer ice loss. However, this summer reached the second-lowest extent ever recorded with cooler weather conditions present.

Dr Katharine Giles of UCL, who led the study, said: "This summer's low ice extent doesn't seem to have been driven by warm weather, so the question is, was last winter's thinning behind it?"

The research, reported in Geophysical Research Letters, showed that last winter the average thickness of sea ice over the whole Arctic fell by 26 cm (10%) compared with the average thickness of the previous five winters, but sea ice in the western Arctic lost around 49 cm of thickness.

Giles said the extent of sea ice in the Arctic is down to a number of factors, including warm temperatures, currents and wind, making it important to know how ice thickness is changing as well as the extent of the ice.

"As the Arctic ice pack is constantly moving, conventional methods can only provide sparse and intermittent measurements of ice thickness from which it is difficult to tell whether the changes are local or across the whole Arctic," Giles said.

"Satellites provide the only means to determine trends and a consistent and wide area basis. Envisat altimeter data have provided the critical third dimension to the satellite images which have already revealed a dramatic decrease in the area of ice covered in the Arctic."

Global Warming Makes Canada HAPPY!

okok...I had to say something rather than just link to it.

Saturday, October 25, 2008

Permian Extinction Refugium Found

During the worst apocalypse the planet has ever known, somehow, life found a way to survive. But how? Scientists now think they have an answer: a nurturing refuge in the shallow continental shelf waters of northwestern Pangea.

During the end of the Permian era 250 million years ago, global warming ran rampant on Earth, extinguishing 95 percent of life in the ocean, and 70 percent of life on land.

Through the darkest days, the planet was a barren wasteland. Ocean circulation, so vital to our modern climate, had shut off. Huge algal blooms sucked the seas dry of oxygen. Poisonous hydrogen sulfide built up to lethal concentrations in the water and may have even been belched into the atmosphere, suffocating organisms on shore.

The fossil record of the Permian-Triassic extinction is a stark one -- rocks go from teeming with life to nearly empty in the geologic blink of an eye. But searching through deposits left at the height of the extinction event, Tyler Beatty of the University of Calgary discovered something nobody ever expected to see: an almost fully-intact marine ecosystem.

This is pretty exciting! An intact refugium from that time period can tell us a lot about what and why everything died. What's interesting from the article is that the refugium only extended down to 50m depth. Everything below that was extremely anoxic. This one site just licked out in that - the investigators posit - the wave action oxygenated the waters just enough for life to pull through. I'll have more thoughts about this in the future, but my paleo article writing is a little curtailed these days. Rockets, HPC, family and more, oh my!

Gasping for Paleo Air

Musings of a Beginning

It's funny. Sometimes you find that you have an interest in something when you didn't even know it existed and only just happen to stumble across it happenstance. I always have been fascinated by the paleo world, but during the 1990s I ran off into the purely techno end of my interests and, frankly, mostly within the computer or IT world. This culminated in me returning to the supercomputing world and my job at NERSC.

What do you do once you've attained what is probably the highest point you can with respect to computing? Well, I could branch out and either go into the very smallest computing devices instead of the largest (from HPC to peewee?) or I could go into theoretical bleeding edge CS with quantum computing...which, as it turns out, I am undereducated for at present (to be fixed, math and quantum physics need a little more advancing to work there). So I was left with the situation of what to do...

I ended up participating in the Tri Challenge at SC05 as my something to do. This was a competition where I put together a team that participated in the Bandwidth Challenge, StorCloud Challenge, and Analytics Challenge. We supported science - climate sims and the frequency of hurricanes. It was a blast and we were noted for the science and the innovative set-up we'd done. I looked what to do next as a project and since my paleo interests had been rekindled and especially the start of my passion for mass extinctions and the ecology just prior to the Great Dying, I thought swapping some teraflops for participation in their project and help with mine. That didn't turn out so well, but I learned a few thing along the way.

The Atmosphere of Argument

One of the most important - and contentious! - has been that whenever someone does a simulation of the past atmosphere, they really, really need to make sure that they don't cut'n'paste the current gas mix into their simulation. That mixture ratio really messes with the results. Easy Example: a different amount of carbon dioxide would change the amount of heat retained by the atmosphere which in turn would change the speed of the winds and the speed of evaporation and those together would change the amount of precipitation that would get transported into the continental interior. The gases are equally important, but for different reasons. One of the researchers that I listened to as they presented got eviscerated as they stated they used the modern gas ratios. Since it really impacts the results, it's something that's really important.

Another reason that the gas ratios are so important is that the evolution of life absolutely must have been impacted by the level of oxygen available at different time periods. We know that this was the case in the Carboniferous: giant insects were possible through the massively higher oxygen level than now (somewhere around 30% of the atmosphere). Additionally, it has been hypothesized that the ups and downs of oxygen percentiles have triggered diversification (ups) or innovation (downs) in evolution. This was Ward's central hypothesis in Out of Thin Air.

Taste That Original Stale Paleo Air!

Since its so important, how do you figure out the atmospheric content of the past? After all, you don't have samples you can go pick up! Right? In fact, you can occasionally get samples, but that's not the only way to track the amount of oxygen, carbon dioxide and other gases in the atmosphere. Let's take a moment and explore the ways that are

The first and most obvious way is to measure the ratios directly from samples of the paleo-atmosphere. Wuh?! How do you do that, you ask? There are two ways that we have found that seem to produce repeatable, reliable results. Both are from trapped gas bubbles. The first only works for relatively recent history: say from some point in the Pleistocene to present. That would be trapped gas bubbles in glacial ice from Greenland and Antarctica. The second source of trapped paleo atmospheric samples is in volcanic glass. In both cases, it's possible to check, albeit carefully, the ratios directly. So what about the cases where there are no trapped bubbles?

The evidence for atmospheric content from the Deep Time when not actually encased in various bubbles is only found indirectly. That indirect evidence is in the form of isotope ratios in the sediments. Different isotope measurements and chemical traces have different meanings. Sometimes the ratios reflect the temperature of the region where the sediment was laid down: the ratio of O16 to O18, for example. The ratios of carbon dioxide tell us a lot about the productivity of the ecosystems at the time. The amount oxidized - or unoxidizied - materials in the sediment, especially iron, tell us about the amount of oxygen present. Other chemicals have other meanings. Sulfur compounds are another indicator, frex.

By studying the sulfur compounds, especially, groups of researchers have made claims about the percentile of oxygen in the atmosphere at any given time. Some have claimed that during the Jurassic that the oxygen fraction was as low as six percent - 6%! - and that it would explain why the dinosaurs were the dominant megafauna. The airsack system of the bird-dinosaur clade was superior to anything else out there supposedly: nothing else could scale up large enough to be that large and still not suffer from hypoxia, not even our diaphram based system that we mammals, and possibly therapsids, share. More frequently, I hear the number 11% tossed around for the Jurassic oxygen minimum.


However, one researcher and his collegues have been modeling the atmopshere extensively for the whole of the Phraenozoic at least as far as the gas fractions are concerned. Dr Berner and his crew's model is called GEOCARBSULF and has produced some interesting results. You can read the abstract here and the paper here (warning, pdf), but a much simplified explanation, perhaps overly so, is that the oxygen levels in the atmosphere traclk well with the rise and fall of the seas, plant cover of the terrestrial environment, and volcanic events such that the weathering of the rock gives a strong indicator of the oxygen level. They do some computer simulation work to try to match up the atmospheric content with their data collection points. Their most recent round of modeling puts a lower limit for the oxygen fraction taking place at the Permian Extinction at around 15% and possibly 12% during the Triassic. The upper limit was 30% during the early Permian(!), not the Carboniferous. This would imply, to me, that the fall of sea levels would expose more rock to be oxidize and, thus, regulate the O2 content of our atmosphere. Even so, there are other researchers that maintain the atmospheric oxygen fraction was far, far lower during the Mesozoic, especially the Jurassic. How do we independently check that if there are arguments using the sulfur data?

Flame Out?

One of the oft cited criticisms of the models for Carboniferous Period's oxygen fraction is that it is too high! After a certain point, even wet vegetation will burn at that oxygen concentration and that would indicate that wild fires were common in that point of the Paleozoic. So, to counter, some scientists went looking for evidence of more common wild fires during the Carboniferous oxygen maximum. Low, and behold, there was a plethora of evidence of burned carbon chunks in the sediments. The fires were very frequent at the time.

Others have then wondered if that couldn't be used as a litmus test for other time periods. Tests have been done with respect to the opposite end of the spectrum of oxygen content. How low can you go? And still have forest fires! In the past, others have tested and reported that it is possible to burn plant material at oxygen fractions as low at 11%. A recent paper attempted to repeat these experiments and found something rather different: it is only possible to get plant material to burn at fractions of 15% at the lowest and really to match the observed pattern in the fossil record that it most be closer 18%.

Why did they get such a higher percentile? It's a little odd, isn't it? The suggestion from the paper itself is that the experimental apparatus of the previous experiments was deficient: the lit materials were tossed in through an open door and allowed to burn under the imperfect oxygen environment. This time, the researchers developed a triggering mechanism that started the fires without ever contiminating the experiment with the modern atmosphere: it was a purely sealed experiment. That would be why they found rather different results.

What does that mean though? It means that so long as there is evidence of a forest fire, or fire in general, in the fossil record, it is patently impossible for there to have had the uber low oxygen level reported. 12%? Not possible if there are Triassic and Jurassic wildfires: that appears to be the case too. That's an exciting result. A very exciting result.

The reason for the excitement is that there has been the idea out there that the oxygen content levels have been one of the great driving forces in evolution. (see Ward above). Other times, it must be admitted, there was some thought that maybe the oxygen level was higher during the Mesozoic to explain the gigantism of the dinosaurs. That has been ruled out. Now its in question whether or not the O2 content was even something that impacted the evolution and dominance of the Mesozoic at all. This paper certainly adds fuel to the, erm, um fire...

A Few Thoughts

(Ward's oxygen vs paleobiotic events graph)

I have to admit that I have been skeptical of the idea that oxygen fraction has dropped that low and the consequences extrapolated there from. If you go to the altitudes where the equivalent partial pressure of oxygen is present today as was in the Mesozoic hypoxic periods, the birds - the extant dinosaurs - are hardly the dominant megafauna present. Wait, you say, where do those conditions exist? Mountains. Where are the large ground forms? Even moderate ones? Or flightless small ones?

Then there's the fact there were six to eight inch insects during the Triassic and, as the partial pressure of oxygen drops, just as inversely when you increased it during the Carboniferous, bug sizes scale down; yet, the Goliath Beetles and other large insects of the present day are hard pressed to get even close to 5 inches in length. Sooo did the isects of back then happen to be more efficient breathers? *uber skeptical look*

I also have to admit that I am unsure whether or not Ward's "retreat from the land" even took place. Yes, we have not seen much in the way of fossils of tetrapods during Romer's Gap. Yet at the same time there are, iirc, a nontrivial amount of fossil footprints from the period, just not bones. I have a feeling, but its not really backed by much, that the Gap is really just a case of a lack of sampling from the sediments where the tetrapods were. We shall see.

Thursday, October 23, 2008

Really Bummed

I'm not in Las Cruces.

I am not flying a rocket.

I am afflicted with very conflicting feelings: I would like to see the teams that are flying do well...yet I also want them to not get the prizes! argh!

Wednesday, October 22, 2008

The Not-So-Isolated Aborigines

Thousands of Aborigine rock paintings discovered in the remote ranges of northern Australia may force a rewrite of the nation's history books.

That's because the art—which ranges from 15,000 years old to 50 years old—depicts contact with other cultures possibly centuries before the arrival of the British.

The library of Aborigine history shows ships—including WWII destroyers and ocean liners—extinct animals, and modern inventions, such as bicycles, planes, and cars sketched onto the walls of rock shelters in the Aborigine territory of Arnhem Land.

"Everything that passed by or through the area is represented one way or another," said Paul Tacon, a professor of anthropology and archaeology at Griffith University in Queensland, Australia.

The main site, Djulirri, was documented by rock-art expert George Chaloupka in the 1970s, but the area hadn't been visited.

When researchers working with Aborigine elder Ronald Lamilami went to find the site again in August 2008, they were surprised to find hundreds of other well-preserved galleries nearby.

"Some of these images have unique depictions not found anywhere else," said Tacon, who is part of the research project.

"One site, previously undocumented, is the largest painting site in the whole of Australia," he said. "It is truly amazing."


Contrary to a long-held belief that Aborigines were isolated, northern communities may have interacted with visitors, such as the Makassans—indigenous people from the city of Ujungpandang (Makassar) on the Indonesian island of Sulawesi.

Drawings of Makassan-style houses and Indonesian sailing boats called praus suggests that Aborigines had extensive contact with Makassans—perhaps hundreds of years before British began to settle Australia in the late 1700s.

So much for that isolation that brought about their supposed Baxterian social implosion and near miss with evolution into nonsapients. sheesh.

oh my

I always knew Tigh looked like McCain, which I thought was intentional,

Tuesday, October 21, 2008

Polar Dinosaurs Had TO Deal With The Polar Winter

Contrary to popular belief, polar dinosaurs may not have traveled nearly as far as originally thought when making their bi-annual migration.

University of Alberta researchers Phil Bell and Eric Snively have suggested that while some dinosaurs may have migrated during the winter season, their range was significantly less than previously thought, which means their treks were shorter. Bell and Snively's findings were recently published in Alcheringa: An Australasian Journal of Paleontology.

The idea that these animals may have travelled distances nine times further than mule deer or four times those of wildebeest would have made them the greatest migrators in history. "There are strong opinions regarding dinosaur migration, but we decided to take a different approach, looking at variables such as energy requirements," said Bell. Their research led them to suggest that migrating dinosaurs could have travelled up to 3,000 kilometres in a round trip—lasting perhaps up to six months—half of the distance suggested previously.

According to Bell, the notion of migrating polar dinosaurs is not new; however, previously-held beliefs were that the animals followed the centrally shifting sunlight, or latitudinal "sun line," as part of their migration and would travel as far as 30 degrees of latitude, or 3,200 kilometres, in order to survive. Given their size and physiology, Bell and Snively have concluded that dinosaurs would have been incapable of sustaining the effort needed to make the trip. "When we looked at the energy requirements needed to support a three-tonne Edmontosaurus over this distance, we found it would have to be as energy efficient as a bird. No land animal travels that far today," said Bell.

Bell does not dispute the evidence of migration and points to discoveries of large bone beds as evidence that many dinosaurs also traveled. In order to sustain the herd, "it seemed to make sense that they would be moving to and from the poles," he said.

While this view of migration is feasible for some species of polar dinosaurs, it does not hold for all, Bell noted. "Many types of dinosaurs were surviving in polar latitudes at the time, and getting along quite fine," said Bell. "They were not physically able to remove themselves from the environment for a variety of reasons and had to adapt to the cold, dark winters just as the rest of us mammals do today."

More nontime for commentary. He, Zach...interesting, no?

Monday, October 20, 2008

Late Cretaceous Ocean Current Patterns

Even though the Cretaceous Period ended more than 65 million years ago, clues remain about how the ocean water circulated at that time. Measuring a chemical tracer in samples of ancient fish scales, bones and teeth, University of Missouri and University of Florida researchers have studied circulation in the Late Cretaceous North Atlantic Ocean. The Late Cretaceous was a time with high atmospheric levels of carbon dioxide and warm temperatures. Understanding such ancient greenhouse climates is important for predicting what may happen in the future. The new findings contradict some previous models.

Water masses are naturally imprinted with a chemical signature that reflects the geology in the land masses surrounding the area where they form. They carry this signature with them as they travel through the oceans, and the signature is recorded by fish skeletal material. If this fish debris is fossilized, so is the signature. MU and UF researchers collected 45 samples of 95- to 65- million-year-old fish debris from the Demerara Rise in the tropical western North Atlantic Ocean. They measured the chemical signature of these samples to estimate the source and circulation of intermediate waters during the Cretaceous Period.

"This technique allows us to track how water flowed in the Cretaceous oceans better than has been possible previously," said Ken MacLeod, a professor of geological sciences in the MU College of Arts and Science. "Constraining ocean circulation patterns during greenhouse times, especially across the very large changes in the global carbon cycle that occurred during the interval we studied, is giving us a better understanding of how greenhouse oceans behave."

Late Cretaceous atmospheric carbon dioxide levels were two to four times higher than today, which resulted in a greenhouse climate with tropical sea-surface temperatures rising to more than 34 degrees Celsius, 4 to 7 degrees Celsius (7 to 12 degrees Fahrenheit) warmer than today.

"The chemical signatures we measured presented two surprising findings. Values were extremely low for open-ocean sites for most of the time between 95 and 65 million years ago, but they were interrupted by a shift that was larger and more rapid than anything previously documented in marine sediments. This shift happened precisely at the time of the largest disturbance to the global carbon cycle of the past 200 million years," MacLeod said.

Based on the results, the researchers proposed the Late Cretaceous North Atlantic was characterized by sinking of warm, salty, equatorial waters, and that circulation became more vigorous or a new source of the chemical signature was introduced at the time of the disturbance to the carbon cycle. Both the persistent formation of warm, saline intermediate waters and enhanced mixing contradict leading paleoceanographic models for these times.

Interesting, interesting...some contrarian data. No time to comment today.

Friday, October 17, 2008

Hadrosaur Voices

ESA Delays Mars Rover

[ESA member governments] tentatively have agreed to delay the launch of Europe's first-ever Mars rover by a little more than two years, to 2016, as part of a broader effort to rein in project costs and seek deeper cooperation with NASA and the Russian space agency, European government officials said.

The decision, made at an Oct. 15-16 meeting of ESA member governments at the agency's headquarters here, remains fragile because some governments still are resisting the price tag of the Enhanced ExoMars mission: 1 billion euros ($1.34 billion), not including the 23 instruments to be paid for by various national laboratories.

ESA had received informal estimates from Enhanced ExoMars prime contractor Thales Alenia Space-Italy that the upgraded ExoMars project demanded by scientists would cost about 1.2 billion euros for a launch in late 2013.

Several governments, including Italy, balked at the price and said they would not participate at the expected level in the program.

That's too bad! It'd be really kewl to see more than just the USA running around on Mars. Don't get me wrong! The nationalist in me wants to see 2:1 minimum for USA:all others probes out there, but I do want to see some minimal competition.

Thursday, October 16, 2008

Russia's Agenda at the Talks over the Russo-Georgian War?

Russia seeks to use the Geneva process to cement its territorial gains, erode Georgian sovereignty further, and disseminate propaganda against the Georgian government from a Geneva tribunal. Minister of Foreign Affairs Sergei Lavrov spelled out Russia’s goals in Moscow on the eve of the Geneva conference and Karasin did so during the Geneva event (Interfax, Itar-Tass, October 13-15). The stated goals include the following:

1) Georgia should sign legally binding agreements on the non-use of force with Abkhazia and South Ossetia in the Geneva framework, as well as “develop normal relations” with the Abkhaz and South Ossetian authorities. The proposed agreements and “normalization” could, however, amount to recognition of the two territories’ secession, which is a central objective for Moscow in this Geneva process;

2) Pending such agreements, the EU should “guarantee” security in “zones adjacent to” Abkhazia and South Ossetia, on rump Georgia’s territory, working out the modalities with the secessionist authorities and Russia in the Geneva process. Such arrangements, however, would carve out special-status zones in Georgian territory and could turn the EU’s Monitoring Mission (EUMM) into de facto border guards along the new, illegitimate “borders”;

3) An international ban should be imposed on sales of “heavy” and/or “offensive” weapons to Georgia. This purely propagandistic demand seeks to stigmatize Georgia as an “aggressor” state necessitating international restraining measures. Meanwhile, Russia is continually objecting to the idea of Georgia receiving purely defensive weapons, such as anti-tank and air-defense systems, the lack of which ultimately laid Georgia wide open to the invasion in August.

It almost sounds like either A) the Russians are trying to derail the talks so they can claim the gave the jawboning a try but it was those darn Westerners that screwed everything up or B) they're trying to set up Georgia to be uberweak to either take it or, after the talks are done, just outright claim the errant territories.

So which is it, Mr Putin?

Frog Extinction Ecosystem Impact Study

Streams that once sang with the croaks, chirps and ribbits of dozens of frog species have gone silent. They're victims of a fungus that's decimating amphibian populations worldwide.

Such catastrophic declines have been documented for more than a decade, but until recently scientists knew little about how the loss of frogs alters the larger ecosystem. A University of Georgia study that is the first to comprehensively examine an ecosystem before and after an amphibian population decline has found that tadpoles play a key role keeping the algae at the base of the food chain productive.

"Many things that live in the stream depend on algae as a base food resource," said lead author Scott Connelly, a doctoral student who will graduate in December from the UGA Odum School of Ecology. "And we found that the system was more productive when the tadpoles were there."

The results, which appear in the early online edition of the journal Ecosystems, demonstrate how the grazing activities of tadpoles help keep a stream healthy. The researchers found that while the amount of algae in the stream was more than 250 percent greater after the amphibian population decline, the algae were less productive at turning sunlight and nutrients into food for other members of the ecosystem. Without tadpoles swimming along the streambed and stirring up the bottom, the amount of sediment in the stream increased by nearly 150 percent, blocking out sunlight that algae need to grow.

The study is part of a larger effort known as the Tropical Amphibian Declines in Streams (TADS) project, which also involves researchers from Southern Illinois University, Drexel University and the University of Alabama. The project is now in its third round of funding by the National Science Foundation and was initiated by Catherine Pringle (UGA Odum School of Ecology) and Karen Lips (Southern Illinois University) in 2000 through a Small Grant for Exploratory Research (SGER) from the NSF. Connelly and Pringle are monitoring in-stream effects of the population decline on algae, while other team members are studying how the loss of frogs impacts other organisms and the transfer of energy between streams and the terrestrial communities that surround them. Preliminary data show that the number of snakes that feed on frogs, for example, has plummeted after the population decline.

"We were there before, during and after the extinction event and were able to look at the ecosystem and measure how it changed," said Pringle, Distinguished Research Professor in the Odum School and study co-author. "Very rarely have scientists been able to do that with respect to any organism."

Now, this is alarming from a the POV of a normal citizen of the world. OTOH, this is something that the paleo types ought to take note. When we discuss mass extinctions there are impacts that ought to be traceable in the fossil record. The fungal/algal spike at the Permian Extinction might be a case in point: whatever kept the fungi or algae in check suddenly died off and left a mark. Do we see this in other extinction events? Like, oh, say the TJ Extinction? If there was no disruption, why? Looking for these kinds of ecological imbalance markers may well allow us to have a tool to verify that the mass extinction took place instead of us just having a bad case of sampling error.

Wednesday, October 15, 2008

Florida State University Faculty Position (Climate related)

Faculty Position in Coupled Ocean-Atmosphere Modeling at Florida State University

The Center for Ocean-Atmospheric Prediction Studies (COAPS) ( at the Florida State University (FSU) invites applications for a tenure earning Assistant Professor in Coupled Ocean-Atmosphere Modeling. The Center seeks candidates with research interests focusing on understanding either coastal/regional phenomena or large-scale climate variability and predictability. Specific research issues could include, but are not limited to, extreme events, mesoscale processes, seasonal to decadal prediction, global climate change and its feedback on regional climates, and climate scale interactions of the atmosphere with terrestrial, oceanic and/or cryospheric processes. Candidates with multidisciplinary interests (biogeochemical, fisheries ecology, hydrology) are encouraged to apply. The successful candidate will be expected to a) conduct state of the art research, b) assist in developing applications based on the above mentioned research activities, and c) interact with a team of interdisciplinary scientists. The candidate will have her/his tenure earning home in either the department of Meteorology or the department of Oceanography, depending on background, and will be expected to teach at both the graduate and undergraduate levels.

COAPS is a center of excellence which promotes interdisciplinary research in air-sea interaction, the coupled ocean-atmosphere-land-ice earth system, and climate prediction on scales of weeks to decades in order to increase our understanding of the physical, social, and economical consequences of coupled ocean-atmospheric variations. Located in the capital city of Tallahassee, Florida, the Florida State University is a comprehensive, graduate-research university with a liberal arts base. We invite you to learn more about Florida State University by visiting

Please send a comprehensive vita, a statement of research interest, and the names and addresses of at least three scientific references by email to by December 5, 2008. Salary and start-up costs are nationally competitive. A Ph.D. is required.

The Florida State University is committed to a policy of non-discrimination for the university community on the basis of race, creed, color, sex, religion, national origin, age, disability, veteran’s or marital status, or any other protected group status.

Pass this one along...

Tiktaalik: The Transitional Gift That Keeps On Giving

Tuesday, October 14, 2008

Oldest Full-Body Impression of an Insect?

Scientists have uncovered what they are calling the oldest full-body impression of a flying insect, possibly an ancient mayfly.

"[The fossil] captures a moment in time over 300 million years ago when a flying insect just happened to land on a damp, muddy surface leaving almost a perfect impression of its body behind," said researcher Jake Benner, a paleontologist at Tufts University in Massachusetts.

Benner and Tufts geologist Richard Knecht discovered the insect imprint in a shale and sandstone outcropping hidden in a wooded field behind a strip mall in North Attleboro, Mass. Knecht had learned of the site while reading a master's thesis written in 1929.

With a length of about three inches (eight centimeters), the 310 million-year-old impression did not include wings. But Knecht and Benner said the insect's body structure was similar to that of primitive flying insects. In addition, "there are no walking tracks leading up to the body impression, indicating that it came from above," Benner said.

The insect may have been a mayfly.

"We can tell from the imprint that it has a very squat position when it lands," said researcher Michael Engel, an entomologist at the University of Kansas. "Its legs are sprawled and its belly is pressed down. The only group that does that today is the mayfly."

There's a bit more about the Carboniferous ecosystem. Mayfly esque body casts. sweet.

Monoculture Extromophile Ecosystem

The first ecosystem ever found having only a single biological species has been discovered 2.8 kilometers (1.74 miles) beneath the surface of the earth in the Mponeng gold mine near Johannesburg, South Africa. There the rod-shaped bacterium Desulforudis audaxviator exists in complete isolation, total darkness, a lack of oxygen, and 60-degree-Celsius heat (140 degrees Fahrenheit).

D. audaxviator survives in a habitat where it gets its energy not from the sun but from hydrogen and sulfate produced by the radioactive decay of uranium. Living alone, D. audaxviator must build its organic molecules by itself out of water, inorganic carbon, and nitrogen from ammonia in the surrounding rocks and fluid. During its long journey to the extreme depths, evolution has equipped the versatile spelunker with genes – many of them shared with archaea, members of a separate domain of life unrelated to bacteria – that allow it to cope with a range of different conditions, including the ability to fix nitrogen directly from elemental nitrogen in the environment.

D. audaxviator was captured and its unusual genome sequenced and analyzed using the techniques of environmental genomics, also called metagenomics, by scientists from the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab), Joint Genome Institute (JGI), and Pacific Northwest National Laboratory (PNNL), working with colleagues from Princeton University, Indiana University, National Taiwan University, Massachusetts Institute of Technology (MIT), Florida State University, the Desert Research Institute, and the University of Western Ontario. The work was a project of the Virtual Institute for Microbial Stress and Survival (VIMSS), supported by DOE and directed by Berkeley Lab’s Adam Arkin and Terry Hazen, and the Indiana Princeton Tennessee Astrobiology Initiative (IPTAI) of NASA’s Astrobiology Institute, directed by Tullis Onstott of Princeton University and Lisa Pratt of Indiana University. The researchers report their results in the 10 October, 2008 issue of the journal Science.


Yes, CoLabbies are involved. sheesh.

Another Pachyrhinosaur lakustai

Now that's schnoz.

Monday, October 13, 2008

New Books

I ordered some new books. Most were used, so they were cheap. I still got a bunch of them though. I thought I'd be further along in Krauze's book though (1/2 way instead of 3/4): there's lots of good what-if's in there. One of my favourites has been that Obregón succeeds in killing himself. I can't help, but see that as throwing the Mexican train off its historical tracks.

I only picked up two paleo books this time: Dinosaurs, Spitfires, and Sea Dragons by Christopher McGowan and The Evolution of Vertebrate Design by Lewis Radinsky. I also picked up a few politics books: United States and Mexico: Between Partnership and Conflict; and in the same series Canada and the United States: Ambivalent Allies. I am not quite Mexico'ed out yet - I want to get to Noel's books soon - so I picked up Caste War of Yucatan by Nelson Reed. I also picked up the tangentially related to my Byzantine obsession: The Crusades Through Arab Eyes by Amin Maalouf. I also picked up Six Degrees by Mark Lynas (it really ought to be up to 10 C, but nevermind...)

I also got Sleeping Beauty for my daughter...y' own little princess Avrora.

Thursday, October 09, 2008

Perfect for Darren: Sauropods Grew Huge By Not Chewing!!!

Dinosaurs known as sauropods—the largest land animals that ever lived—grew huge and were an evolutionary success in part because they didn't bother to chew their food, new research suggests.

Sauropods weighed up to 88 tons (80 metric tons)—ten times more than an African elephant—and measured as high as 23 feet (7 meters).

The group of dinosaurs, which included the brachiosaurus and diplodocus, loomed over the animal kingdom for more than 140 million years until the late Cretaceous period, 65 million years ago. (See a brachiosaurus herd.)

Scientists think the animals evolved to be so large to discourage big predators, like Tyrannosaurus rex, from eating them. But how they maintained such massive body sizes has remained mysterious.

The herbivores, or plant-eaters, had hardly any teeth and are thought to have swallowed their food whole—an entire bush in one gulp, for example. They browsed large areas, barely moving and consuming vast quantities in short periods of time.

So they needed long necks to reach food high in trees and a huge gut to process and break down their unchewed meals, said Martin Sander, a palaeontologist at the University of Bonn in Germany and co-author of the study, published tomorrow in the journal Science.

"You can only have this long neck if you don't chew your food, otherwise your head would be full of teeth and too heavy to support," he said.

Paul Upchurch, an expert on sauropods from University College London, said that "most palaeontologists agree that feeding is the key to understanding sauropod gigantism."

Sooooo...what was the news in this? Help? Please?

Need a Paper Again!

Anomalously diverse Early Triassic ichnofossil assemblages in northwest Pangea: A case for a shallow-marine habitable zone

Tyler W. Beatty1, J-P Zonneveld2, and Charles M. Henderson1

1 Department of Geoscience, University of Calgary, Calgary, Alberta T2N 1N4, Canada
2 Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Alberta T6G 2E3, Canada

Early Triassic trace fossil assemblages from the northwest margin of Pangea record a diverse suite of postextinction infauna. These ichnofossil assemblages occurred within well-oxygenated, shallow-marine refuges in a Panthalassa Ocean otherwise characterized by widespread anoxia. We propose an environmentally controlled model for their distribution, in which wave aeration, enhanced by frequent storms, gave rise to an optimal zone for benthic colonization. Within this habitable zone extinction pressures were ameliorated and postextinction recovery duration was minimized.

I am sure we have a few readers that have this one! anzhalyu at gmail dot com.


Now That's What I Call Crop Diversification!

Work by researchers at North Carolina State University is leading to a new kind of crab harvest – blue crabs grown and harvested from freshwater ponds, instead of from the sea.

Crab lovers shouldn't worry, researchers say, because the pond-raised crabs look and taste just like their ocean-raised brethren.

North Carolina's native blue crab population has been at historic lows since 2000. Dr. Dave Eggleston, director of NC State's Center for Marine Sciences and Technology (CMAST) and professor of marine, earth and atmospheric sciences, looked at various methods for helping the population recover. He hit upon a solution which not only reduces pressure on existing crab populations, but also benefits farmers looking to diversify their crops: using irrigation ponds on farms to grow blue crabs.

"We started out by catching small crabs in the wild and stocking them into farm ponds loaded with bass and bluegill predators, and were still able to get 12 percent survival," Eggleston says.

"So we teamed with the University of Maryland's Center of Marine Biotechnology who had the expertise to growth hatchery-reared blue crabs, and stocked these blue crabs in freshwater experimental aquaculture ponds at NC State's Vernon James Research and Extension Center in Plymouth, N.C., where the crabs exhibited some of the highest growth rates on record."

Eggleston then noticed that a lot of farmers in Eastern N.C. were trying to diversify their crop offerings in response to the decline in tobacco demand.

Mmmm....Crabs. I have to wonder if we might see a return to a multicrop farm? Monocultures are the norm these days, right?

Wednesday, October 08, 2008

Sauron Found

New Paleozoic Sediment Curve

...A new sediment curve (which shows where sediment-on-the-move is deposited), derived from sediments of the Paleozoic Era 542 to 251 million years ago, scientists report in this week's issue of the journal Science. The sediment curve covers the entire Paleozoic Era.

"The new Paleozoic sea-level sediment curve provides a way of deriving predictive models of sediment migration on continental margins and in interior seaways," said Bilal Haq, lead author of the Science paper and a marine geologist at the National Science Foundation (NSF). The paper's co-author is geologist Stephen Schutter of Murphy Oil International in Houston, Tx.

"The sediment curve is of interest to industry, and also to scientists in academia," said Haq, "as the rise and fall of sea-level form the basis for intepretations of Earth history based on stratigraphy."

Through stratigraphy, the study of rock layering (stratification), scientists can derive a sequence of time and events in a particular region. Recent advances in the field of stratigraphy, including better time-scales for when sediments were deposited, and availability of data on a worldwide basis, are allowing scientists to reconstruct sea level during the Paleozoic.

The rises and falls of sea level during this period form the basis of stratigraphic interpretations of geology not only in the sea, but on land. These sea level increases and decreases are used extensively, Haq said, in predictive models of sediment movements.

The current Science paper is a shorter version of the results of a global synthesis of Paleozoic stratigraphy on which the authors have worked for many years.

news, news, news.

Why Didn't They Have This When *I* Was a Child?!

Introducing Kota, the walking, ridable dinosaur! Just in time for Xmas!

I was soooo born too early.

Tuesday, October 07, 2008

Boneyard XXIV is up!

Woo! I got in! The Caste Ecology rides again! (oy on some major typos) I'll go back later this week and try to fix them.

Ediacaran Arthopods?!

The fossilized trail of an aquatic creature suggests that animals walked using legs at least 30 million years earlier than had been thought.

The tracks -- two parallel rows of small dots, each about 2 millimeters in diameter -- date back some 570 million years, to the Ediacaran period.

The Ediacaran preceded the Cambrian period, the time when most major groups of animals first evolved.

Scientists once thought that it was primarily microbes and simple multicellular animals that existed prior to the Cambrian, but that notion is changing, explained Loren Babcock, professor of earth sciences at Ohio State University.

"We keep talking about the possibility of more complex animals in the Ediacaran -- soft corals, some arthropods, and flatworms -- but the evidence has not been totally convincing," he said. "But if you find evidence, like we did, of an animal with legs -- an animal walking around -- then that makes the possibility much more likely."

Soo-Yeun Ahn, a doctoral student at Ohio State, presented the discovery in a poster session at the Geological Society of America meeting Sunday in Houston. Coauthors included Margaret Rees of the University of Nevada, Las Vegas, and J. Stewart Hollingsworth of the Institute for Cambrian Studies.


If the disccovery holds up, this trace fossil has some profound implications. It'd do a mighty blow to the multiple origination hypothesis of complex life.

More Research on the TJ Mass Extinction

Bottjer and many others have published studies suggesting that the end-Permian extinction 250 million years ago happened in essence because "the earth got sick."

The latest research from Bottjer's group suggests a similar slow dying during the extinction 200 million years ago at the boundary of the Triassic and Jurassic eras.

At the 2008 Joint Annual Meeting of the Geological Society of America, USC doctoral student Sarah Greene drew similarities between ocean conditions at the Triassic-Jurassic boundary and after the end-Permian extinction.

At both those times, bouquet-like structures of aragonite crystals formed on the ocean floor. Such structures are extremely rare in Earth's history, Greene said.

"The fact that these deposits have only been found at these two specific times that are associated with mass extinction suggests at the very least that maybe there's some shared ocean geochemistry … that could be related to the cause of the extinctions," Greene said.

"The Triassic-Jurassic extinction cause is totally up for grabs at the moment," she added.

Also at the meeting, USC doctoral student Rowan Martindale presented results from her studies of coral reefs during the Triassic-Jurassic extinction.

"The coral reefs look actually very similar to modern coral reefs," she said. "At the end-Triassic mass extinction, you lose all your reef systems. And nobody's figured out why that is."

Martindale identified two distinct types of ancient reefs: one dominated by coral and another consisting mainly of mud and debris, possibly held together by bacteria.

A theory for the end-Triassic extinction needs to explain how both types of reefs could have been killed off, Martindale said.

The impression I have from reading about the TJ Extinction is not whether or not an asteroid did the deed: it appears not to have been the case whatsoever. However, it appears now that there are issues with dating and samples sizes with respect to the TJ Event. Hallam brought it up in is books. Now some of the beds there seems to be some dating issues that have been recently raised, so stay tuned. The TJ Extinction is likely to be a battleground.

Our Kid's Hummer?

The army's working on replacing the Hummer and the MRAPs. This is Textron et al's version. It looks like a Dutch vehicle that I remember...

Monday, October 06, 2008

Planet Twice the Density of Lead?

Last May, the COROT satellite discovered another exoplanet to add to the stack of 228 confirmed exoplanets. Follow-up investigations of the object, named Corot-exo-3b, have revealed it to be quite a curiosity as far as exoplanets are concerned, and some of its characteristics – such as its density of twice that of lead – may force astronomers to rethink the distinction between massive planets and low-mass brown dwarfs.


Via universe Today.

Help Needed: My Google Fu is Weak

Okay Folks.

I have Yet Another Pitch to make for backing on the Team Phoenicia.

I need an image. My google fu is failing me. I need a picture - and don't laugh - of inflated pants. Jeans, whatever. It needs to look like they were blown up like a balloon and tied off at the ends.

I need it for a presentation. Anyone able to find one?

I am sucking at my google-fu atm.

Friday, October 03, 2008

Birds, Alligators and Thumbs

Bird wings only have three fingers, having evolved from remote ancestors that, like humans and most reptiles, had five fingers. Biologists have typically used embryology to identify the evolutionary origin (homology) of structures; the three fingers of the bird wing develop from cartilage condensations that are found in the same positions in the embryo as fingers two, three and four of humans (the index, middle and ring fingers). However, the morphology of the fingers of early birds such as Archaeopteryx corresponds to that of fingers one, two and three in other reptiles (thumb, index and middle finger). The fossil record clearly shows that fingers four and five (ring and pinky finger) were lost and reduced in the dinosaur ancestors of birds.

Further, the lack of expression of the HoxD-11 gene in the first finger of the wing makes it most similar to finger one (the "thumb") of the mouse, consistent with comparative morphology. However, the mouse is only distantly related to birds; crocodilians, in turn, are bird's closest living relatives.

To see whether the evidence from mouse HoxD-11 expression held up, Vargas and colleagues, working at the lab of Gunter Wagner at Yale, have examined the expression of this gene in alligators; they found the expression to be, as in mice, absent only in finger one (the "thumb").

Developmental and evolutionary biologists are familiar with the phenomenon of homeotic transformations, in which one structure begins to develop at a different position within the body. A famous example is the case of the fruitfly mutant antennapaedia, which develops legs on its head instead of antennae. The new work by Vargas et al. rekindles the hypothesis that a "hometic frameshift" occurred in the evolution of the bird wing, such that fingers one, two and three began to develop from the embryological positions of fingers two, three and four.

MB's strike again, Zach!

Wednesday, October 01, 2008

Some "Junk" DNA Ultra Conserved!

Small stretches of seemingly useless DNA harbor a big secret, say researchers at the Stanford University School of Medicine. There's one problem: We don't know what it is. Although individual laboratory animals appear to live happily when these genetic ciphers are deleted, these snippets have been highly conserved throughout evolution.

"The true function of these regions remains a mystery, but it's clear that the genome really does need and use them," said Gill Bejerano, PhD, assistant professor of developmental biology and of computer science. In fact, these so-called "ultraconserved" regions are about 300 times less likely than other regions of the genome to be lost during mammalian evolution, according to research from Bejerano and graduate student Cory McLean to be published in the Oct. 2 issue of Genome Research.

Although some of the ultraconserved regions, which were first identified by Bejerano in 2004, are involved in the regulation of the expression of neighboring genes, previous research has shown that mice missing each of four regions seem perfectly normal.

"It's very surprising that none of the four has any observable phenotype," said Bejerano. "In some ways it just doesn't make sense."

This lack of effect is usually taken as a strong argument against an important functional role for the missing segments of DNA — either because they don't do much or because other bits of DNA serve as understudies when the primary actors are missing. But in this most recent study, evolution roars over the squeak of the seemingly contented mice.

"When we tried to determine whether similar deletions occur in the wild," said Bejerano, "we found that this is almost never seen in nature."

McLean and Bejerano compared the likelihood that ultraconserved elements of at least 100 base pairs shared by humans, macaques and dogs would have been deleted in rats and mice, with the likelihood of a similar pattern in non-conserved DNA. Less than one-tenth of 1 percent of segments completely identical among the primates and dog were missing in the rodents. In contrast, about 25 percent of non-conserved segments were absent in the mice and rats.

It's not that these regions are somehow protected against change: they are mutated in about one in 200 healthy humans. Rather, these changes seem to be swept away over time by the tides of evolution in a process called "purifying selection." Bejerano and McLean believe that something similar may be happening in the laboratory mice on a scale too subtle to be seen under carefully controlled experimental conditions.

After establishing how infrequently the ultraconserved segments are deleted, the researchers investigated whether the degree of homology (the percent of nucleotides shared between species) or the extent of conservation (the evolutionary distance between species that share a version of the sequence) correlated most closely with the likelihood that it would be lost in primates or rodents. Sequences shared among many distantly related species are likely to be older than sequences found only in closely related species. The researchers found that less-highly conserved sequences shared among several distantly related species — including opossum, platypus, chicken, frog and fish — are more likely to also occur in humans than are more-homologous sequences that occur in only a few closely related species. The likelihood that a sequence will be found in humans increases as the evolutionary age of the sequence increases.

"Interestingly," said Bejerano, "the longer the sequence has been in us, the less likely it is to be lost. It's almost like the bricks in the foundation of a building, which hold up the rest of the structure."

huh. I wonder why. IIRC, anything that's not important, not used gets mutated PDQ. That's where all those noisy pseudogenes come from and why they disappear over time. yet...this stuff is conserved for 300 million years. Why? Any guesses?

(no, they don't know either)

Russia to Ukraine: Remain Out of NATO...or Else

Most recently Vladimir Zhirinovsky, the Russian ultranationalist leader who often acts as the Kremlin’s unofficial spokesman, warned that “if someone attempts to drag Ukraine into NATO and the people start to protest against this and they are harassed…then Russia will have the right to defend its citizens in Ukraine.” He added that “it would be ideal for both Georgia and Ukraine to remain neutral.”

The Russians have expanded the passport program in Ukraine. Anyone who is "Russian" can pick up a passport and Russian citizenship. They had been doing this only in Crimea. They just expanded it to the rest of the country. They're tauting it as the way to help those poor souls that had been lost on the other side of the USSR's split to allow them to come home.

That might have been plausible a decade ago. However, the Russians did a similar stunt in Georgia's break away regions a year or so before the Russo-Georgian War. Now they're testing the waters in Ukraine? Where Ukraine lacks a military to protect herself, really? huh. Sounds like the Bear is getting set to chew on the helpless again.

If only Europe would drop its objections! A lot of resentment by Ukrainians against NATO, EU, and the West is because of the difficulty in getting visas and the perception that the West outright rejects them. *sighs*