The renaissance of technicolour dinosaurs continues (and the gloves come off…) [Not Exactly Rocket Science]
National Geographic should have a 3-D animation up soon
The pursuit of accurate dinosaur colours just turned into a race, and a heated one at that. Just last week, I wrote about a group of scientists who claimed to have accurately identified the colours of some feathered dinosaurs by microscopically analysing three fossils. According to that study, Sinosauropteryx had a tail covered in ginger stripes. Now, another group have revealed the palette of an entire dinosaur, Anchiornis. This tiny predator had a dark grey body and the limbs bore long, white feathers tipped with black spangles. Its head was mostly grey with reddish-orange and black specks, and an extravagant reddish-orange crown.
Both reconstructions are based on microscopic structures called melanosomes. They're partly responsible for the brilliant colours of modern bird feathers, they're packed with pigments, and they happen to fossilise well. There are two major types. Spherical 'phaemelanosomes' contain a reddish-brown or yellow pigment while the rod-like 'eumelanosomes' have black-grey tints.
The technique of inferring colours from fossil melanosomes was pioneered by Jakob Vinther at Yale University. He used it to show that a Cretaceous bird feather probably had black and white stripes and, later, that another fossil feather had an iridescent starling-like sheen. But these were analyses of single papers and even last week's paper coloured Sinosauropteryx by looking at just one part of a single individual.
Vinther isn't impressed with his rivals. "They are in the Stone Age when it comes to understanding melanosome fossilization and interpretation of original colors," he says. To him, it's simply not enough predict colours based on the presence of one type of melanosome. Even the hues of single feathers can depend on a mix of the two melanosome types with different concentrations of pigments. So you need to know the distribution of melanosomes across an animal and even then, you still need to work out how that translates to different colours.
And that's exactly what he's done. When I spoke to Vinther last week, he said, "We are still far from putting colours on dinosaurs [but] the future is promising. Eventually we will have dinosaurs in technicolour. We are working seriously on that currently." He wasn't kidding!
He had been working on a new specimen of Anchiornis with the catchy name of BMNHC PH828. The tail is missing but the rest of the skeleton is beautifully preserved, including the skull and both sets of limbs with their elegant plumes. Rather than looking at individual body parts, Vinther took 29 samples from the specimen, representing every type of feather types across different body parts. In each one, he thoroughly analysed the size, shape, density and distribution of melanosomes.
To interpret this goldmine of data, he worked with his colleague Matt Shawkey to catalogue the melanosomes from a wide variety of living birds, from ravens to finches to mallards. This modern data set was a cross between a paint catalogue and a Rosetta stone. It told Vinther how different combinations of melanosomes led to different colours and allowed him to correctly paint his Anchiornis.
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Things I Have Learned From Blogging at Science Blogs, Part I [Casaubon's Book]
I've now been at scienceblogs for a couple of months, and it is fascinating to me - I went from a stand-alone blog to one with a whole lot of other people, and getting to know the local culture is a really interesting exercise. Overwhelmingly, it has been really wonderful and fascinating. Still, I have learned some new-to-me things about this culture. I thought I would do a series, seeing if I could sum up the lessons learned here as I adapt to this strange new world. So here is the first one.
#1 - The phrase "American Conservative Evangelical Protestantism" is spelled "R-E-L-I-G-I-O-N. In some cases, admittedly, the category of "religion" is diversified to include the Inquisition and Moslem suicide bombers.
In response to what is clearly a custom of the country, I feel obligated to try and conform. I will thus resist the attempt to observe that there are difference on a whole host of subjects between the perspective of say, a leftist Jew, a neo-pagan, a zen Buddhist or even an American Liberal Evangelical Protestant vs. an American Conservative Evangelical Protestant, much less a Grand Inquisitor.
In conformation with this custom of priveleging the general over the inconvenient specificity that details and distinctions bring, I am also going to start referring always to "scientists" rather than specifying what scientific discipline they specifically belong to, what their training is and what their goals are. I think this will enhance clarity, or at least bring me more traffic. I will also refrain from distinguishing between whether this is something that scientists actually know what they are talking about or not - after all, it is said by a scientist, and therefor goes into the catetgory of things about scientists.
So here goes - all observations gleaned form my months of reading scientists on sciencblogs:
Scientists are definitely trying to contain global warming. Scientists are also trying to cause global warming by developing new ways to consume fossil energies. Scientists believe that global warming is anthropogenic and accellerating. Scientists believe that global warming is not anthropogenic (well, 2 or 3 of them, anyway, but let's not muddy the water with specificities). Scientists are trying to reduce chemical contamination of the waterways. Scientists are also trying to increase chemical contamination of the waterways by developing new pesticides. Scientists believe women should count equally with men. Scientists believe that women just make the problems of inequality up. Scientists believe in cutting the vocal cords of barking dogs. Scientists believe this is inhumane. Scientists don't have a problem with eating meat. Scientists are vegetarians. Scientists live in Sweden. Scientists have no fashion sense. Scientists really like highly fashionable shoes and have a great deal of fashion sense. Scientists believe that duck sex can unite duck sex fetishists and scientists. Scientists can teach high level physics to dogs. Scientists can comment on blogs in entire sentences using only the word "fuck." Scientists are getting laid. Scientists are lonely. Scientists are good at creating ways to destroy the whole world. Scientists are good at fixing the world, but not quite as good as they are at destroying it. Scientists have breasts. Scientists are sadly without breasts. Scientists are concerned that there aren't enough scientists with breasts. Scientists believe that the Yellowstone mega-caldera is not likely to explode. Scientists believe NASA has conducted secret tests on the best sexual positions for space nookie. Scientists have determined that marshmallow peeps are better than twinkies. Scientists consume marshmallow peeps. Scientists think stuff is cool. Scientists think we should have sex like the Swedes. Scientists think having sex like the Swedes might be depressing. Scientists think that population will be best controlled by instituting communism and then collapsing it. Scientists believe blogs should be civil. Scientists are not always civil. Scientists are religious. Scientists are athiests. Scientists really like more blog traffic.
See, now I know about scientists!
Sharon
Even Dogs Can Go Local [Casaubon's Book]
We spent about 8 months looking for a suitable dog before we acquired Mac the Marshmallow last month. Until a little over a year ago, we had two American Working Farmcollies, half siblings. Rufus, our senior dog was an unusually large dog for his breed - half again the size of either parent or his sister, Mistress Quickly, and he died suddenly at 7 of a hidden heart condition that our vet says sometimes affects unusually large dogs.
We knew that we did not want another farmcollie - or rather we did, we had loved Rufus, but that what we needed in working dog for our family was slightly different than what we'd had. In both the case of Rufus and Mistress Quickly, their strong herding instincts had reduced their utility has guardian dogs - both were wonderful at driving off strange predators, but had difficulty letting the livestock be in normal circumstances. They both had a tendency to respond excessively to normal situations, and to try and herd the animals back to the barn if they ranged too far or even minor abnormalities occurred. Despite a lot of work, we were never able to fully curb these practices, so the dogs couldn't be out entirely unattended with the livestock.
We decided we needed a dog that would be primarily a guardian, whose instincts would be protective, but more mellow. Because our barnyard is within a few meters of the house, however, we wanted the dog to be both protective of our livestock and also part of our family. We were given a mix of information about whether this was possible - if we selected a guarding breed, we were told, they might or might not be able to bond to both humans and animals, but enough people reported success this way that we decided we'd attempt it. We were looking for a dog of mixed or single ancestry that would have the livestock guarding instincts that we wanted.
No dog is perfect, and the expression of what they have been bred for is only part of knowing what they will do. We ruled out adult dogs for two reasons. The first is that we have younger children, and many adult dogs have endured some kind of trauma that could have made them unsafe around kids. The second is that it is impossible to know whether an older dog will have the instinct to chase and kill small livestock - we could do the best guessing we could, picking dogs who genetic heritage inclined them to be protective, but a dog who has had experience killing poultry or rabbits was not an acceptable option for us, and there's simply no way to know. Many shelters cat and other dog test their dogs, but "chicken testing" is less common 
.
We looked at rescue dogs for months, and found that we really couldn't meet our needs there, which was disappointing. Several of the breed rescues we contacted required us to sign papers permitting them to come at any time to our property to inspect the dogs - that just wasn't going to happen - this is a working farm, and giving up legal right to our privacy wasn't something we would do. A number of the shelters we contacted didn't want to place LGD breeds on working farms - their policy was that they only wanted the animals to be household pets. Others would have required we sign a contract keeping the animals in a fenced yard all the time - which sort of defeats the purpose of a working animal. The cost of adopting a rescue puppy was as high as purchasing an animal bred for working (I don't blame the rescue organizations who use the more desirable puppies to fund the care of older dogs for this at all), without the assurances that a breeder would be able to offer us that the animal wouldn't be disabled by hip displasia.
One of the things our search taught us was this - that the culture of animal rights and love of animals (some of which has been a very good thing) has become profoundly suspicious of the idea of using animals to work - even when they have been bred to work. For example, we inquired about a litter of Great Pyrenees/Old English Sheepdog cross puppies that were available at a shelter in an affluent suburb of Boston. I wrote that we were looking for a dog with the characteristics that these were likely to have, and described our farm, room to roam on a quiet street and the fact that the dogs would be doing what they had been bred for. The respondent told me that they thought that the puppies should be placed locally, in community where they could be pets. I actually know this suburb fairly well - I didn't grow up very far from it, and what fascinated me was the idea that dogs who genetic history is pushing them to master a fairly large territory and work with other animals will mostly be put in small suburban backyards by people who will not give them any work to do. This was deemed to be preferrable. I admit, I find this hard to understand.
I love dogs, and I find it equally hard to understand why people so often choose dogs inappropriate to the environment they live in. I do grasp that many inappropriate dogs are beautiful and wonderful, but I also think that dogs, like everything else biological, have appropriate and inappropriate placements in sustainable systems. I've seen Newfies and Komondors in South Florida in agony from the heat, and keep high energy dog breeds alone for 10 hours a day in an apartment. I've seen families with young children and no experience with dogs choose dogs that are difficult to control and require strong alpha behavior, with the inevitable results. In today's New York Times, there's an article about the practice of cutting the vocal cords of dogs, making them unable to bark. I tend to agree with the article that the practice is probably more humane than euthanizing a dog because of its barking, but I also tend to think that in many cases, the problem arises because we are trying to make dogs live in ways deeply unsuitable to them - that the people with the barking problems may have chosen their dogs without regard to their environment.
I think dogs have an important role in the future - yes, they are another creature to feed, but they also provide a measure of security for many people. Even a smaller dog with a decent bark can be the difference between getting a good night's sleep and being terrified for many people. A dog as companion for a walk for an older person in neighborhood with rising crime dramatically increases their safety. As we use less energy, dogs often detect fire quickly - an important supplement to (not replacement for) smoke detectors in tightly built neighborhoods where more people are using space heaters or other risky techniques to keep warm and cook. For the elderly, disabled and alone, dogs and cats provide comfort, companionship, warmth and a reason to get up in the morning.
And for those of us on farms, for hunters, for those in icy climates who can travel by dogsled at least part of the year, for the disabled with assistance dogs, dogs are a major part of sustainable systems - they allow us to live better. Coyotes den across the road from us - if we didn't have dogs, the choice would be a major economic loss of livestock, giving up livestock keeping, or killing the coyotes. I don't want to see harm come to the coyotes - we have an insufficiency of larger predators in my region, and coyotes have in some respects moved into the ecological niche that was once occupied by wolves. My dogs mean that we can listen to the coyotes sing and also keep them away from our animals - achieve a kind of detente.
Our working dogs are beloved by us - they get attention and brushing and good food. They also have jobs to do, and my observation is that the signs of dog happiness are never more in evidence than when the dogs are doing their job and doing it well - Mistress Quickly's tail is flying with joy when she rounds up the goats, and when Mac and MQ drove off a fox, they were manifestly pleased with themselves. They did good - and of course, we let them know that too. Dogs are not humans, but the signs of pride are unmistakable.
There are a lot of issues around pets - the biggest one may be the meat that they eat and the way that the pet food market subsidizes and supports the industrial food system - but I don't think pets are going away anytime soon. But what we do need to do is to think hard about the animals we raise and care for - just as we need to live lives appropriate to our place and climate, so should our pets. That is, they need to be well adapted to the lives. Picking a dog should take some thought and serious consideration. Ideally, one will be able to adopt a rescue - we weren't able to do that, but that doesn't mean we won't ever go that route - we made a serious attempt at it, and when the kids are older will have more options.
In the end, we found a wonderful couple who breed Great Pyrenees dogs. Mac was a 7 month old puppy who had been raised with goats and horses, had the mellow temprament we were looking for, and also strong abilities to bond with the family. We were impressed immediately by him - he was nervous taken out of his familiar environment to meet us, but he expressed his nervousness gently, and gravitated towards the children, who he treated with consummate gentleness. We saw him around the animals, and he was calm, and the goats came right up to him. We watched a 6lb pomeranian take food out of his brother's mouth.
So Mac came home with us, and after a few days, settled in comfortably. He's a warm, affectionate sweet dog, and while there have been some adjustments (having a dog on eye-level with the kitchen counters was a new thing!), he's been wonderful. So we're currently working on teaching him his new role. This is a slow process - the goats are still afraid of him, although he's in no way aggressive to them, and because he'd never seen poultry before, he's not really clear on what these things are yet. He's not aggressive at all with them, just puzzled. Our job is to show him what we expect from him, to praise him lavishly when he does well, and to show alternatives when he makes a mistake. He's a good student, and we're working on good teaching.
For us, a gentle, mellow but serious guardian dog the size of a small pony (he weighs 84lbs now, but will probably top out near 150) is a good thing - but he'd be out of place in a lot of places. It has been a long process for us, figuring out what kind of dog suited our place, and I hope that most people, when choosing their dog, will also be thinking about their local conditions and how their dog fits into their attempts to adapt in their place.
Sharon
"Eruption" in Azerbijian [Eruptions]
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A 2010 mud flow from Lok-Batan, a mud volcano in Azerbijian.
So, first there was all the Yellowstone talk. Then the unsubstantiated reports of a volcanic eruption in a decidedly unvolcanic part of Pakistan (what part isn't), then submarine volcanism off Japan. Now, we have a nrews report about an eruption in Azerbijian. Luckily, although the headline implies a magmatic event, the text of the article shows that this is, in fact, a mud volcano. The mud volcano is called Lok-batan (or Lokbata) and has erupted quite a few times over the last 150 years, as recently as 2005. Azerbijian has quite a few mud volcanoes, some of which are quite impressive. Remember, "mud" in the ground is just a viscous fluid - water and soil more or less - so it too can behave like lava if it becomes pressurized, especially thanks to heating of the mud. Earthquakes (common along the shores of the Caspian Sea in Azerbijian) could provide a route to the surface for the pressurized mud, leading to the "eruption". The most famous mud volcano in the world is like the Lusi Mud Volcano in East Java, Indonesia - a feature that was likely triggered by man-made action.
Quite the volcano week, eh?
Submarine eruption near Japan [Eruptions]
The plume from submarine volcano Fukutoku-Okanoba, erupting in February 2010.
Almost a year after the Hunga Tonga Hunga Ha'apai eruption, where an undersea volcano sprang forth from the deep - quite spectacularly, we have new footage of another undersea eruption. Fukutoku-Okanoba, off the coast of Minami Iwo, started to erupt yesterday (or, at least, erupt enough to manifest a plume out of the ocean). A Japanese coast guard vessel was able to capture the plume on video as it reached 100 m / ~300 feet. The plume appears to be dominated by white steam along with some grey ash mixed in. Additional footage shows the water stained brown/tan with ash and volcanic debris from the eruption as well.
Fukutoku-Okanoba is actually a quite active submarine volcano, last erupting in 2005. The sea is often discolored near the volcano and a number of ephemeral islands have formed due to its activity over the last 100 years - my favorite being Shin-Iwo-jima, or "New Sulfur Island" in 1904. Most of the eruptions appear to be VEI 0-2 based on what manifests at the surface, however the 1904 eruption was VEI 3, producing significant andesitic (intermediate) ash and lava. The summit of the volcano lies only 14 m / ~50 feet below the ocean surface.
The History Of Cooking in Five Courses [Greg Laden's Blog]
FROM OPEN FLAMES TO SOUS VIDE: The History Of Cooking in Five Courses
Tuesday, February 9, 2010 - 7 p.m., doors open at 6 p.m.
Cost . Reservations required. Call 612-624-9050
Join Chef Chris Olson and local experts on an exploration of the evolution of cooking in five delicious courses. With the Bell Museum's wildlife dioramas as a backdrop, Olson, cook at St. Paul-based Meritage and co-creator of Paired, will take diners on a culinary journey through the ages, from the invention of fire to the scientific approach to food through molecular gastronomy. Biological anthropologist Greg Laden, whose work focuses on diet and human evolution, will join Olson in this deliciously illustrated tale. The event is co-sponsored by the Heavy Table, a Twin Cities-based online magazine devoted to telling the stories of food and drink in the Upper Midwest.
Lawrence Lessig: How To Get Our Democracy Back [The Primate Diaries]
Harvard professor Lawrence Lessig has a new article in The Nation entitled "How to Get Our Democracy Back." In the piece he challenges both the Right and the Left on the ineffective means to create real change in this country. Attempts to shrink government by conservatives or to reform government by liberals have been useless because the underlining problem has not been addressed: the power of corporate lobbies that control policy.
In an earlier post (see: The Shadow of Scientific Opinion) I quoted the education reformer and philosopher John Dewey:
[P]olitics is the shadow cast on society by big business, the attenuation of the shadow will not change the substance.
There is a growing consensus by both sides of the political spectrum that our current governmental system is broken. By taking this dirty money out of Congress it would do far more for democracy than mere reforms or reducing the size of government could ever accomplish. For more see FixCongressFirst.org.
Top Posts in January [The Primate Diaries]
Deconstructing Social Darwinism, Part I
Deconstructing Social Darwinism, Part II
Deconstructing Social Darwinism, Part III
How Can Haiti Be Sustainable?
Uniting Primates and Cetaceans Through Personhood
Bonobos and the Emergence of Culture
Civility, Science Communication, and the White Patriarchy
Robert Sapolsky on the Uniqueness of Humans
Deconstructing Social Darwinism, Part IV
The Huffington Post Publishes the Craziest Things
Looking inside the structure of the Yellowstone Caldera [Eruptions]
With all the talk of the current Yellowstone earthquake swarm, I thought it would worth it to write a post on the the structure and caldera - and why we get earthquake swarms that are structurally rather than magmatically-related.
First off, lets think about why calderas formed. This is relatively simple - at least superficially. The land (or volcano) above a magmatic system is partially supported by that magma, especially because magma is hot and buoyant. The isostatic support by the magma holds up the land surface or volcanic edifice, so when an eruption expels a large volume of magma, this support is removed. This collapse forms the caldera - the negative topographic expression of the eruption. The collapse of the land surface plays a dual role - not is it a result of the eruption, but also helps the eruption along, like a piston pushing of hot gas out of a cylinder. After the eruption, the collapsed caldera continues to subside as the isostatic equilibrium is reached. After the caldera-forming eruption {caution, large PDF}, the system may have eruptions that produce resurgent domes in the middle of the caldera as the last dregs of the caldera-forming magmatic system leak out. This is referred to as the "caldera cycle", originally defined by Howell Williams for the collapse of Mt. Mazama ~7,700 years b.p. (see below).
Modified illustration of the caldera cycle by Howell Williams.
The collapse of the caldera produced what is called the "ring fracture," the fracture along the edge of the caldera. This fracture was formed during the collapse, but was then likely also exploited by the erupting magma during the caldera-forming eruption. These fractures then become long lived zones of weakness around the edge of the caldera (see below) - the down-dropped part of the caldera is no longer supported by either the emptied magma chamber or the crust around it.
Map of the extent of Yellowstone Caldera. The ring fractures from the caldera-forming eruptions are roughly coincident with the caldera.
We can look at the general structure of caldera systems by looking at the Long Valley Caldera (see below). The ring fracture is present on the edge of the Long Valley caldera, with the down-dropped caldera material in the middle - filled in by the tephra from the caldera-forming eruption and resurgent dome material. The caldera may continue to settle for hundreds of thousands of years after the caldera-forming eruption - all happening at depths at or above the current "top" of the magmatic system.
A schematic look at the structure of the Long Valley caldera in California.
If we take a look at historical seismicty around Yellowstone (see below), we can see that quite a bit it is near the ring fracture of the caldera. This means that thesuggested structural source of the current seismicity makes sense - as I've mentioned, the earthquakes in these locations in historic times have not lead to eruptions. In fact, we should expect to see a lot of low scale seismicity along the ring fracture that represents the many faults related to the ring fracture system.
Historic seismicity around Yellowstone Caldera.
However, as zones of weakness, you might expect that magma could exploit the ring fracture to reach the surface. Magma rising would need corroborating evidence, though. Magma doesn't do a good job of disguising its present, especially large volumes. The ground should deform from the additional volume of magma displacing the crust and this displacement with our current methods of measuring ground changes should be detected well in advance of an eruption. We should also expect changes in the hydrothermal system as the hot body of magma moves higher into the system, possibly in the form of new mud pots, geysers or hot pools. The chemistry of springs might change as well, reflecting the input of magmatic components into the water - which goes hand-in-hand with changes in gases being released by the magma. Volatiles like water vapor, CO2, SO2 and He are constantly being released by a cooling, depressuring magma, so we should see the signal of this in the gases being released at Yellowstone, especially by monitoring dissolved gases in springs. The type of earthquakes should also change - not only becoming shallower, but also taking on the classic pattern of harmonic volcanic tremor - the harbinger of moving magma.
YVO monitors many, if not all, of these factors, so we are not likely to be "surprised" by any new eruptions at Yellowstone. While the current earthquake swarm does appear to be getting shallower, you can see how it is part of life at an active caldera system. You can check the current status of the Yellowstone Caldera on the YVO website.
James Ray arrested, charged with three counts of manslaughter in Sedona sweat lodge debacle [Terra Sigillata]
A few weeks ago, we discussed (1, 2) some of the drugs confiscated by authorities who searched the Sedona resort room occupied by self-help guru, James Ray, following the October 2009 deaths of three followers who paid nearly ,000 each for his Spiritual Warrior retreat program.
Late this afternoon, Ray was arrested - the best news and supporting information continues to come from The Prescott (AZ) News, with a sidebar to the lower right of the story that links to their extensive timeline of coverage:
The Yavapai County Grand Jury returned a "true bill" on 3 counts of Manslaughter against Ray early this afternoon. The Yavapai County Superior Court issued a warrant for James Ray as a result of the indictment.
The warrant was served by YCSO detectives at Ray's attorney's office in Prescott and he was arrested around 3:30 P.M.
Sheriff Waugh would like to thank the victim's families for their patience while the Sheriff's Office completed a thorough and comprehensive investigation. The County Attorney's Office also provided assistance to YCSO detectives as they conducted hundreds of interviews and gathered evidence to support today's indictment. With the arrest of James Ray, Sheriff Waugh hopes the families of the three victims will now have some measure of closure to this tragedy.
Ray was transported to the Sheriff's Prescott Office to begin booking procedures. He will eventually be transferred to the Camp Verde Detention Center for final processing.
Ray's bond has been set at 5 million dollars.
Indeed, it is the families of the victims that deserve justice and some sense of closure.
If nothing else comes out of the tragic deaths of these three people, perhaps self-styled gurus will be on notice that their pocket-lining antics will fall under greater scrutiny and accountability.
Photo source: Prescott News