Exoskeletons!

That would be the Raytheon version (snagged from the Danger Room).



This latter one is from the guys that did the BLEEX work at UC Berkeley but now as a spin off company (Berkeley Bionics). The stuff they show for the latter as far as mobility goes is pretty darned impressive. They just don't have the upper body segment at this point unlike the Raytheon guys.

Now we just need to armor these things and...

ahem. No personal hobby horses involved here. Move along, move along.

Research on the Dessication of the Sahara

(Lake Yoa via NatGeo)

The grassy prehistoric Sahara turned into Earth's largest hot desert more slowly than previously thought, a new report says—and some say global warming may turn the desert green once again.

The new research is based on deposits from a unique desert lake in remote northern Chad.

Lake Yoa, sustained by prehistoric groundwater, has survived for millennia despite constant drought and searing heat.

The body of water contains an unbroken climate record going back at least 6,000 years, said study lead author Stefan Kröpelin of the Institute of Prehistoric Archaeology at the University of Cologne in Germany.

Ancient pollen, insects, algae, and other fossil clues preserved in the lake's sediments point to a gradual transformation to a desert environment.

The study contradicts past research that suggested the region dried up within a few hundred years. That research was based on windblown Saharan dust found in Atlantic Ocean sediments.

"This was a hypothesis used by most of the modelers and many of the scientific community who were not working themselves in the Sahara," Kröpelin said.

"To a large degree we can now show that such an abrupt drying out of the Sahara was a myth," he said.

The new study, which appears tomorrow in the journal Science, instead found evidence for a slow decline in tropical plants, followed by the gradual loss of savanna-type grasslands, and then the eventual spread of desert species.

Pollen samples revealed, for example, that the decrease in tropical trees accelerated after 4,800 years ago, while desert plants took root between 3,900 and 3,100 years ago.

A related, ealier paper's abstract is here.

Koehle suggests at the end of the NatGeo article that with global warming happening and absed on some data from the eastern Sahara that it will end up greening again due to increased rain fall from increased evaporation. It would be interesting if that happened since most of the climate sims I have seen have indicated that Africa as a whole is going to get drier. Then again, the tropical cells are on the move north and we may see the tropics move up and decrease the desert latitudes nontrivially.

That's thinking out loud, btw.

Platypus Genome Published...and Analyzed

Animal's reptilian-mammalian mix reflected in its DNA

The first analysis of the genome sequence of the duck-billed platypus was published today by an international team of scientists, revealing clues about how genomes were organized during the early evolution of mammals. The research was supported in part by the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health (NIH).

[...]

n a paper published in today’s issue of the journal Nature, researchers analyzed a high-quality draft genome sequence of Glennie, a female platypus from Australia. The consortium included scientists from the United States, Australia, England, Germany, Israel, Japan, New Zealand and Spain. Sequencing of the platypus genome was led by the Genome Sequencing Center at Washington University School of Medicine in St. Louis, a part of NHGRI’s Large-Scale Sequencing Research Network.

Once the sequence was produced, researchers began comparing the genome of the platypus, whose ancestors split from the rest of mammalian lineage some 166 million years ago, with the well-characterized genomes of the human, mouse, dog, opossum and chicken, as well as the draft genome sequence of the green anole lizard. The chicken genome was chosen because it is descended from the ancestral group of egg-laying animals, including extinct reptiles, which passed on much of their DNA to animals like the platypus. Scientists were particularly interested in finding features within the platypus genome that could explain the odd mix of characteristics seen in the platypus, those that were more like reptile and birds and which were like mammals.

The team found that the platypus genome contains about the same number of protein-coding genes as other mammals -- approximately 18,500. The platypus also shares more than 80 percent of its genes with other mammals whose genomes have been sequenced. Next, researchers combed the platypus genome looking for genetic evidence of sequences unique to platypuses, which have been lost from mammalian genomes. Scientists were also eager to find out what characteristics of the platypus were linked at the DNA level to reptiles or mammals.

“The mix of reptilian, mammalian and unique characteristics of the platypus genome provides many clues to the function and evolution of all mammalian genomes,” said Richard K. Wilson, Ph.D., director of Washington University School of Medicine’s Genome Sequencing Center and the paper’s senior author. “Now, we’ll be able to pinpoint genes that have been conserved throughout evolution, as well as those that have been lost or gained.”

Alright, first argh: mix of reptilian, mammalian and unique...that hurt to read. As we all now know, mammals did not evolve from reptiles. They both came from basal amniotes. That said there are some interesting bits of information that have come out.

First, platypus venom is genetically encoded in the same way as in diapsids: through gene duplication of the same genes. This seems to be a case of parallel evolution - so say the paper authors - rather than conserved basal genes.

Second, its RNA evolution is...interesting. There seems to be I am wholly unqualified to comment though.

Third, the sex detemination genes for the platypi have de nada to do with XY chromosomes. That's a therian...thing. Instead, their sex chromosomes share extensive homology to those of birds.” Waters notes that this finding suggests our ancient mammal-like reptile ancestor may have had bird-like sex chromosomes and sex determination system.

Then...well...nuts. Go read it yourself.

Here's a link with all of the above.

This has a lot of exciting potential for uncovering some of the basal traits for the therapsids and, indeed, the ancestral amniotes. Based on this and previous studies it seems highly likely that the therapsids were egg layers and had a sex determination system that was inherited from the amniote ancestors. I am stoked that they have looked at least a bit at the echidna genome and I hope that the same sort of analysis will be conducted there too relatively soon.

wow

Couldn't Resist

Uber Climate HPC Platform

Abstract:

Towards Ultra-High Resolution Models of Climate and Weather

Michael Wehner

CRD/NERSC, Lawrence Berkeley National Laboratory, Berkeley, CA 94720

Leonid Oliker

CRD/NERSC, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, loliker@lbl.gov

John Shalf

CRD/NERSC, Lawrence Berkeley National Laboratory, Berkeley, CA 94720

We present a speculative extrapolation of the performance aspects of an atmospheric general circulation model to ultra-high resolution and describe alternative technological paths to realize integration of such a model in the relatively near future. Due to a superlinear scaling of the computational burden dictated by stability criterion, the solution of the equations of motion dominate the calculation at ultra-high resolutions. From this extrapolation, it is estimated that a credible kilometer scale atmospheric model would require at least a sustained ten petaflop computer to provide scientifically useful climate simulations. Our design study portends an alternate strategy for practical power-efficient implementations of petaflop scale systems. Embedded processor technology could be exploited to tailor a custom machine designed to ultra-high climate model specifications at relatively affordable cost and power considerations. The major conceptual changes required by a kilometer scale climate model are certain to be difficult to implement. Although the hardware, software, and algorithms are all equally critical in conducting ultra-high climate resolution studies, it is likely that the necessary petaflop computing technology will be available in advance of a credible kilometer scale climate model.

The full paper is here. The Pop sci version is here. The Press release version is here.

That's Mike whom I have collaborated with for the SC05 Tri Challenge where we ran a copy of CAM on bassi, reduced the data on PDSF, and visualized it on a system that was based in Seattle that is very similar to davinci while using a wide area instance of GPFS as the only method of communication. It worked okay, but that was because we hit a bug. Alas. That same bug would come out and nail us a few weeks later at work. We did win a prize and some very nice recognition for the effort though.

That said, because of my mischief I have been attending conferences for embedded and real-time coding that have de nada to do with work. Or so it was planned. After all, I work in HPC with an emphasis on file systems. My research interests there are wide area file systems, on demand system aggregation, and the odd bit of paleoclimate work (emphasis Permian). The Mischief has de nada to do with that, as I said. Well, it turns out that NERSC & LBNL in general is making a push to make a raid on the next set of commodity computing parts and I had walked into the middle of it all. Yep, you guessed it, the embedded chip guys: those chips that run in your cell phones or printer or even in your car.

You see, what's killing PCs and everything higher is the economics of it all: single CPUs are pretty flat for processor speed. They're not getting faster. There are a few single core CPUs left that are making any progress doing faster computation: the power and heat requirements are killing them. Ever notice that the CPU of the 386 didn't require that monster fan you have on your current x86? Ever think about that power supply? Now we have hit the point where power consumption (and the heat dissipation associated with it) are now growing faster than the computational speed. The answer was to start adding cores onto the chip.

Starting a few years back, the chip companies started putting more and more cores on a single "CPU." Really these were more like multiple CPUs on the same silicon real estate than anything else. However, they were tied together more closely than the older SMPs. However, the cores tend to be 'simpler' than the one CPUs before. One reason being to save power. In some ways this strikes me as very amusing. It's like revenge of the RISC. Even so, the costs of developing those chips for the CPU monsters is still obscene.

Think rocket cost and then some. I can't share a lot of what I know, but I will just blurb that its shocking. I'll also say I have to tread carefully here due to NDAisms. (oy)

So why is the HPC world - or at least LBL - interested in the embedded products? One: cost. The cost of developing an embedded chip is cheaper. By a lot. Second is power consumption. Now, your desktop might consume a good 500 watts. In an oversimplification, Franklin has 9k sockets with 2 cores per socket. If you were to merely scale up the power requirements: you're talking 4.5 megawatts there for a 100 teraflop system. Not Good. Then for a petaflop system do at least a 10x. Now consider the next 'frontier:' the exaflop system. Yes, 1000x the speed of the systems not yet built (but coming in the next year or two). Yep. That power requirement kills the exaflop system based on current or extrapolated PC/server processor tech.

The embedded guys are very concerned if the processors start using more than single digit watts. Our guys were intrigued by that and started plying with the concept. I wasn't involved at all until quite recently. Even now I am only involved to a degree: I happen to have contacts that the Lab would like to use. They already have when we pulled an Intel embedded chip architect I connected to at a conference I was invited to by one of my mischief sponsors. What I have learned about their plans for the nextgen supercomputer is rather interesting.

John, Mike, and Lenny's design for the above is to develop a HPC platform that is cheaper, tailored to a specific application but able to run others, and fast. Really fast. The goal for the above was an exaflop according to the presentations I was at for this. The whole idea was to be able to simulate a 1 km grid for the CCSM climate simulations. It would allow for accurate cloud simulations which is something they can only approximate now. The power consumption and the cost of the machine would be far, far lower than now. The design they talked about was...interesting.

One of the key ideas though is the transition from single core to multicore and then the projected, in the center's opinion, to manycore. They are expecting around 1024 cores per chip, but much, much smaller and simpler cores. Consider that you put together 64 of those chips and you have a machine witha s many cores as the old CM2-64k that I used back in the early 90s. 256 of these chips and you would have more cores than in the Blue Gene at LLNL. (note: it wouldn't be as fast, but far cheaper and less power consumptive). The proposal though is that John, Mike, and Lenny have proposed that the machine they want would have 170,000 sockets and each with a chip not too dissimilar to what I outlined above living in that socket. o.O

That is not to say I don't have my worries. I am not working largely as the application guy. I do dabble in it. I do have interest there. Programming models that scale past 1k cores are not very common now. What would need 170k sockets? let alone the cores therein. In fact, there are a nontrivial number of 'supercomputer users' that really don't belong on our machines anymore. They just need a cluster of medium to small size in their department rather than the big iron we have. Now try to imagine those few that are actually able to use our monster here. Not very many. In this case, the machine was designed with the use of one code only and the others can run on it as they can.

However, I have to think about the times I spend on rotation too here. If we were to acquire one of those ubersocketed monsters, then there would be a constant rain of dead or dying processors even in the lightest weight of nodes. Even with a 99.999% reliability you are still going to have nearly two nodes down at a time. That's not so good to have to deal with. Now, about all that memory too...

There's much more to go on, but I don't have time at the moment. I have yet another dreaded meeting. bah. Just ponder what they are talking about when they talk supercomputers of the future and that infernal Singularity nonsense.

Now About that 65 Million Year Old Carbon Layer!

he asteroid presumed to have wiped out the dinosaurs struck the Earth with such force that carbon deep in the Earth's crust liquefied, rocketed skyward, and formed tiny airborne beads that blanketed the planet, say scientists from the U.S., U.K., Italy, and New Zealand in this month's Geology.

The beads, known to geologists as carbon cenospheres, cannot be formed through the combustion of plant matter, contradicting a hypothesis that the cenospheres are the charred remains of an Earth on fire. If confirmed, the discovery suggests environmental circumstances accompanying the 65-million-year-old extinction event were slightly less dramatic than previously thought.

"Carbon embedded in the rocks was vaporized by the impact, eventually forming new carbon structures in the atmosphere," said Indiana University Bloomington geologist Simon Brassell, study coauthor and former adviser to the paper's lead author, Mark Harvey.

The carbon cenospheres were deposited 65 million years ago next to a thin layer of the element iridium -- an element more likely to be found in Solar System asteroids than in the Earth's crust. The iridium-laden dust is believed to be the shattered remains of the 200-km-wide asteroid's impact. Like the iridium layer, the carbon cenospheres are apparently common. They've been found in Canada, Spain, Denmark and New Zealand.

But the cenospheres' origin presented a double mystery. The cenospheres had been known to geologists only as a sign of modern times -- they form during the intense combustion of coal and crude oil. Equally baffling, there were no power plants burning coal or crude oil 65 million years ago, and natural burial processes affecting organic matter from even older ages -- such as coals from the 300-million-year-old Carboniferous Period -- had simply not been cooked long or hot enough.

"Carbon cenospheres are a classic indicator of industrial activity," Harvey said. "The first appearance of the carbon cenospheres defines the onset of the industrial revolution."

The scientists concluded the cenospheres could have been created by a new process, the violent pulverization of the Earth's carbon-rich crust.

For a time it was thought this carbon layer was a sign of a global conflagration: the asteroid impact incinerated the world, essentially. However, they ought to be more large chunks of charcoal scattered about the KT Boundary. AFAIK, this hasn't been found, except in a few places, yet there was this fine layer of carbon made of cenospheres more globally. That was odd because as far as we knew, these could only be made through industrial processes. What the researchers are proposing here is that Chicxulub Impact event vaporized a lot of carbon rich content (oil, iirc) and that was spread across the world. The suggestion is that the impact would be able to generate the cenospheres. Interestingly, the cenosphere mass distribution centered their origin on the Chicxulub Crater: the closer the researchers sampled to the crater, the heavier the cenospheres became.

It makes for an interesting - and difficult - item for the vulcanists to explain unless there were tons of exposed coal fields in the path of the lava flows...they'd have to be exposed only at the time of the KT boundary being laid down - not before! not after! - since the Deccan Traps erupted for a long time (over 2 million years). Furthermore, why it'd be centered on Chicxulub is even more difficult to explain.

Now seriousness aside, if the only way we have seen is to produce the cenospheres by industrial methods...sounds like an sf book plot not yet written! Y'know, if you ignore some important science bits. Unless, of course, the lone sapient dinosaurian city was centered on Chicxulub and the impact was an alien race's way of wiping out a future problem. hmmmm...

Small Delay

Sorry to play the tease. We're getting there. I've handed off the website to someone else to tinker with the code for the next few days. When he's done, the website will go up. Sorry for the delay.

Diapsid MOLESTED by Vicious Synapsid

An Antarctic fur seal has been observed trying to have sex with a king penguin.

The South African-based scientists who witnessed the incident say it is the most unusual case of mammal mating behaviour yet known.

The incident, which lasted for 45 minutes and was caught on camera, is reported in the Journal of Ethology.

The bizarre event took place on a beach on Marion Island, a sub-Antarctic island that is home to both fur seals and king penguins.

Why the seal attempted to have sex with the penguin is unclear. But the scientists who photographed the event speculate that it was the behaviour of a frustrated, sexually inexperienced young male seal.

Equally, it might be been an aggressive, predatory act; or even a playful one that turned sexual.

"At first glimpse, we thought the seal was killing the penguin," says Nico de Bruyn, of the Mammal Research Institute at the University of Pretoria, South Africa.

The brazenness of the seal's behaviour left those who saw it in no doubt as to what was happening.

De Bruyn and a colleague were on Trypot beach at Marion Island to study elephant seals when they noticed a young, adult male Antarctic fur seal, in good condition, attempting to copulate with an adult king penguin of unknown sex.

whoa.

Antarifornication doesn't roll that well off the tongue.

(o.O)

A Thought

Disasters are opportunities with fangs.

Fox News Frak Up: Lincoln-Douglass Debate Pic

oh. ouch. It was impossible for a Black Man in 1860 to be running for President. Really. Fox didn't catch this?! N/m the very famous Lincoln-Douglass debates were with a different Douglass too.

*stunned bunny look*

New Tower Development in San Francisco

Manhattanization is a foregone conclusion at this point.

Small Update Teaser

The website will go live (as in having real info) either on Sunday or Monday.