## DNA Sequenced from the Fossilized Femur of a 400,000 Year Old Hominin

A new DNA sequencing technique allowed the sequencing of mitochondrial DNA from the remains of a 400,000 year old hominin found in Spain. From “Scientists Just Sequenced the DNA From A 400,000-Year-Old Early Human“:

Since its discovery in 1990, La Sima de los Huesos, an underground cave in Northern Spain’s Atapuerca Mountains, has yielded more than 6,000 fossils from 28 individual ancient human ancestors, making it Europe’s most significant site for the study of ancient humans. But despite years of analysis, the exact age and even the species to which these individuals belonged has been in doubt.

Now, though, an international group of scientists has extracted and sequenced DNA from the fossilized femur of one of these individuals for the first time. The resulting data—which represent the oldest genetic material ever sequenced from a hominin, or ancient human ancestor—finally give us an idea of the age and lineage of these mysterious individuals, and it’s not what many scientists expected.

The fossilized bone tested, a femur, is roughly 400,000 years old. But the big surprise is that, although scientists had previously believed the fossils belonged to Neanderthals because of their anatomical appearance, the DNA analysis actually shows they’re more closely related to Denisovans, a recently-discovered third lineage of human ancestors known only from DNA isolated from a few fossils found in Siberia in 2010. The findings, published today in Nature, will force anthropologists to further reconsider how the Denisovans, Neanderthals and the direct ancestors of modern-day humans fit together in a complicated family tree.

The analysis was enabled by recent advances in methods for recovering ancient DNA fragments developed at the Max Planck Institute for Evolutionary Anthropology in Germany, previously used to analyze the DNA of a cave bear fossil found in the same cave. “This wouldn’t have been possible just two years ago,” says Juan Luis Arsuaga, a paleontologist at the University of Madrid who led the initial excavations of the cave and collaborated on the new study. “And even given these new methods, we still didn’t expect these bones to preserve DNA, because they’re so old—ten times older than some of the oldest Neanderthals from whom we’ve taken DNA.”

H/T Geek Press

Posted in Science_Technology | | Comments Off

Parallella is a company that manufactures and sells boards that can be combined to produce a supercomputer. From Parallella’s website:

Project Goals

Making parallel computing easy to use has been described as “a problem as hard as any that computer science has faced”. With such a big challenge ahead we need to make sure as many people as possible have access to open parallel hardware and development tools.

Inspired by great hardware communities like Raspberry Pi and Arduino, we also see a critical need for a truly open, high-performance computing platform that will enable us to close the knowledge gap in parallel programming.

The goal of the Parallella project is to democratize access to parallel computing through providing an affordable open hardware platform and open source tools, and supporting learning and the development of software which is able to harness the power of parallel systems.

Hardware Platform

To make parallel computing ubiquitous, developers need to have access to a platform that is affordable, open and easy to use.

The Parallella platform will be built on the following principles:
Open Access: Absolutely no NDAs or special access needed! All architecture and SDK documents must be published on the web.
Open Source: The Parallella platform will be based on free open source software (FOSS) development tools and libraries. All board design files will be provided as open source once the Parallella boards are released.
Affordability: Hardware cost and SDK costs have always been a a huge barrier to entry for developers looking to develop high performance software. The goal is to bring the Parallella high performance computer cost below $100, making it an affordable platform for all. Software Platform Although the initial focus has been on delivering the hardware platform this is only part of the story and Parallella is also very much an open source software project. One important goal of Parallella is to teach parallel programming and the project will strive to be objective with respect to programming models. The only hard requirement is that the language/method chosen must be supported by free and open source development tools. Parallel programming projects and examples will be published based on all influential parallel programming languages and frameworks. Beyond the Parallella SDK and learning materials we will support the development of open source languages, frameworks and applications that are able to unlock the potential of massively parallel computing architectures. Working closely with other open source communities and fostering cross-project collaboration. An extensive review of Parallella’s board can found in “Supercomputing on the cheap with Parallella: Blowing open the doors to low-power, on-demand supercomputing” by Federico Lucifredi. Packing impressive supercomputing power inside a small credit card-sized board running Ubuntu, Adapteva‘s$99 ARM-based Parallella system includes the unique Ephiphany numerical accelerator that promises to unleash industrial strength parallel processing on the desktop at a rock-bottom price. The Massachusetts-based startup recently ran a successfully funded Kickstarter campaign and gained widespread attention only to run into a few roadblocks along the way. Now, with their setbacks behind them, Adapteva is slated to deliver its first units mid-December 2013, with volume shipping in the following months.

What makes the Parallella board so exciting is that it breaks new ground: imagine an Open Source Hardware board, powered by just a few Watts of juice, delivering 90 GFLOPS of number crunching. Combine this with the possibility of clustering multiple boards, and suddenly the picture of an exceedingly affordable desktop supercomputer emerges.

This review looks in-depth at a pre-release prototype board (so-called Generation Zero, a development run of 50 units), giving you a pretty complete overview of what the finished board will look like.

This is a very interesting development that immediately brings to mind a few business ideas.

First, is to build supercomputers for sale using Parallella’s boards. Of course other components must be added, namely memory and cooling, to form a complete system. This is akin to building a high end gaming pc using components from different manufacturers. Here, I note that liquid cooling may be a useful option (see “Cooling Personal Computers and Servers“).

Such supercomputers could be a series of standard units, a base standard unit that can be expanded in a modular fashion, or custom built systems. I can see a market for all of these approaches.

Second is to start a company that builds supercomputers in house and sells access to them via the cloud. This can certainly be done now with existing supercomputers (see “Supercomputer Apps“). However, Parallella offers the chance of constructing a system that is cheaper than buying one from Cray or IBM. Also, it allows a company to test the idea with relatively little capital at risk and if the business thrives, additional capacity can be constructed modularly. Additionally, Parallella wants to foster a community of developers using open source software tools. If they are able to do this, then it becomes easier to set up a company offering supercomputing access as the software tools will be readily accessible.

The third idea is a variant of the first two: construct a supercomputer optimized for machine learning. Current supercomputers are optimized for massively parallel physics-like computations (i.e. solution of coupled partial differential equations) in which the focus is on increasing the speed of pure number crunching. For machine learning, the bottleneck in speed is accessing information from memory. I do not have the expertise to even make suggestions on how to build a supercomputer for machine learning applications. However, the facts that Parallella is selling hardware components that memory and other components can be purchased separately, suggest that a clever engineering team should be able to construct a system that provides high speed at reasonable costs.

I strongly suspect that there are already groups formed to work on the ideas expressed above.

## A Weekly Dose of Hazlitt: No End to Superspending?

No End to Superspending?” is the title of Henry Hazlitt’s Newsweek column from May 18, 1953. Here, Hazlitt shows president Eisenhower backtracking on his early rhetoric about cutting spending. This is the usual game played by politicians who even deign to mention fiscal restrained. At the end of the day, spending increases.

The announcement of President Eisenhower on
April 30 that he would ask Congress “to appropriate
$8,500,000,000 less new money for fiscal year 1954 than had been asked for by the previous Administration” made a good one-day headline. But it will not bring much comfort to taxpayers who examine the situation closely. This$8,500,000,000 is not a proposed cut compared
with the previous rate of Truman spending. It is
merely a cut from President Truman’s estimate for a fiscal
year when he would not be in office and for which he
knew he could not be held responsible. And it is a cut only
in requested new appropriations, not necessarily a cut in
actual rate of spending. In last week’s issue, Newsweek
estimated that the Eisenhower spending budget for the
fiscal year 1954 would approximate $74,200,000,000. This would be about the same as is being spent in the present Truman-Eisenhower fiscal year which ends on June 30. But it would be$8,000,000,000 more than was
actually spent in the last full Truman fiscal year of 1952
and almost $30,000,000,000 more than was spent in the Truman fiscal year 1951. The Korean war was being fought during the whole of both these years. Mr. Eisenhower complains that when he took office he found “a total carry-over of$81,000,000,000
in appropriated funds, largely committed. . . . It’s just
ordered $81,000,000,000 of goods, which we’ve got to pay for as they’re delivered, in addition to paying the regular household running expenses.” But two questions must be raised about this: (1) Is the whole of this$81,000,000,000 in fact so irrevocably
committed (in the form of noncancelable contracts,
for instance) that no appreciable part of it can either
be rescinded or used for new purposes? (2) Isn’t Mr.
Eisenhower planning to continue the same sort of carryover
to make it just as difficult to balance the budget in
future years? A simple calculation leads, in fact, to the
conclusion that on his present proposed spending and
appropriation program he will end even the fiscal year
1954 with a carry-over of more than \$70,000,000,000
unspent appropriations into 1955.

Posted in Political_Economy | | Comments Off

## Syria, Sarin, and Subterfuge: They Made It All Up by Justin Raimondo

Justin Raimondo of Antiwar.com published an interesting article that details the enormity of the lies told by the Obama administration in their failed quest to invade Syria.

The real smoking gun in Hersh’s piece is the statement attributed to a former senior intelligence official that the “intelligence” cited by administration officials as justification for bombing Syria was simply made up in much the same way that the Bush administration manipulated intelligence-gathering in the run up to the Iraq war. Apparently those sensors had gone off last December, and the NSA had picked up transmissions that seemed to indicate a sarin attack was imminent – but it turned out to be a training exercise. According to Hersh, in making their case for war the administration tried to pass off the December intercepts as having occurred in the days prior to the August 21 incident:

“The former senior intelligence official explained that the hunt for relevant chatter went back to the exercise detected the previous December, in which, as Obama later said to the public, the Syrian army mobilised chemical weapons personnel and distributed gas masks to its troops. The White House’s government assessment and Obama’s speech were not descriptions of the specific events leading up to the 21 August attack, but an account of the sequence the Syrian military would have followed for any chemical attack. ‘They put together a back story,’ the former official said, ‘and there are lots of different pieces and parts. The template they used was the template that goes back to December.’”

Putting together a “back story” is spook-talk for outright lying. There are laws against government officials doing that in testimony before Congress, and it appears those laws were broken.

Let’s be clear about what administration officials yet to be identified did: they described NSA intercepts detailing preparations for a military drill that had occurred months earlier as communications sent in the days prior to August 21.

Posted in Political_Economy | | Comments Off

## Political Economy Quote of the Week for 20131209

Posted in Political_Economy | | Comments Off

Eades has thundered against the use of statins for years. In “Statin madness” he relates an incident involving his elderly father that indicates the depths of unethical medical practice that is all to common these days when statins are involved.

The statin madness infecting the greater part of the tribe of physicians has finally reached out and touched me personally.

We all hear horror stories about all kinds of occurrences, but, although we feel empathy for the victims, we don’t truly understand until it happens to us directly.

I’ve railed in numerous posts and to anyone who would stand and listen to me about the idiocy of prescribing statins to the vast majority of those they’re prescribed for. I read comments from female readers of this blog telling me how their doctors are insisting they go on statins despite there not being any evidence that statins provide any benefit to women. I hear about young men with no history of heart disease but minimally elevated cholesterol levels being put on a statin with the understanding that they need to be on this drug for life. This despite there not being any evidence that statins prolong the lives of those young men who take them.

Based on these examples and a thousand others, I’ve become convinced that prescribing statins is a reflex action for many doctors. And I have to shake my head because these are not benign drugs. In fact, they come with a contingent of fairly serious side effects, many of which can last long after the drugs have been discontinued.

But back to the statin prescription.

How could any doctor in his/her right mind write such a prescription for an 86 year old, totally paralyzed man who has normal cholesterol? Even one who has elevated cholesterol? After about age 50, the higher the cholesterol, the greater the longevity. So, again, why would anyone write a prescription for a non-benign drug to an elderly patient? Plus, the chance for rhabdomyolysis is greater in the elderly who take statins as well as those who are taking a ton of other drugs, as is my dad. It’s a set up for disaster with no potential upside to balance the risk. It is blind stupidity to prescribe a statin under these circumstances.

And not just any old statin. The script was for a large dose of Lipitor, a fat-soluble statin. Fat soluble statins are much more likely to be involved in drug interactions, and they can induce insulin resistance and possibly cause diabetes. If you’re going to give an unnecessary drug, why wouldn’t you at least give one with the fewest side effects?

Lipid (fat) soluble statins make their way into the cell membranes, which are basically fats. But fats that are highly functional in terms of their relationship to the cells they enclose. Anything absorbed into fatty tissues is more difficult to get rid of than that absorbed into a water-based part of the cell. Whenever I think of these drugs socked away in the fat cells and cell membranes of the people who take them (unnecessarily), I always remember the words of Dr. Ernest Curtis, cardiologist and author of The Cholesterol Delusion, a book I highly recommend:

As severe as some of these short-term side effects can be, they pale into relative insignificance when compared to the potential long-term problems. The chief difficulty here is that no one knows what the long-term effects may be from altering the basic biochemistry of the human body over a period of time. Because cholesterol is the key element in the formation of cell membranes, which are the protective coat for the cells, it may be that blocking cholesterol’s production will weaken the protective barrier and allow the entry of toxins or carcinogens that were previously excluded. There are disturbing reports of increased cancer in some cholesterol-lowering studies, but, in fact, this process may take many years to play out. It’s enough at this point to acknowledge that the long-term effects are completely unknown. This is a risk that should receive serious attention before half the population is placed on these drugs, that, in effect, accomplish nothing more than low-dose aspirin or an extra glass or two of water each day.

Posted in Paleolithic_Lifestyle, Science_Technology | Tagged , | Comments Off