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Topics - Kai

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Techmology and Scientism / Hey, yet ANOTHER peer review fail.
« on: February 04, 2012, 06:38:22 pm »
I really can't summarize it any better than other people have.

Overview by Greg Fish

More in depth look by PZ Myers

Another investigation and summary over at Ars Technica

Quote from: From the Ars Technica link
The theory in question springs from the brain of one Erik Andrulis, a CWRU faculty member who has a number of earlier papers on fairly standard biochemistry. The new paper was accepted by an open access journal called Life, meaning that you can freely download a copy of its 105 pages if you're so inclined. Apparently, the journal is peer-reviewed, which is a bit of a surprise; even accepting that the paper makes a purely theoretical proposal, it is nothing like science as I've ever seen it practiced.

The basic idea is that everything, from subatomic particles to living systems, is based on helical systems the author calls "gyres," which transform matter, energy, and information. These transformations then determine the properties of various natural systems, living and otherwise. What are these gyres? It's really hard to say; even Andrulis admits that they're just "a straightforward and non-mathematical core model" (although he seems to think that's a good thing). Just about everything can be derived from this core model; the author cites "major phenomena including, but not limited to, quantum gravity, phase transitions of water, why living systems are predominantly CHNOPS (carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur), homochirality of sugars and amino acids, homeoviscous adaptation, triplet code, and DNA mutations."

He's serious about the "not limited to" part; one of the sections describes how gyres could cause the Moon to form.

Is this a viable theory of everything? The word "boson," the particle that carries forces, isn't in the text at all. "Quark" appears once—in the title of one of the 800 references. The only subatomic particle Andrulis describes is the electron; he skips from there straight up to oxygen. Enormous gaps exist everywhere one looks.

The theory is supposed to be testable, but the word "test" only shows up in the text twice. In both cases, Andrulis simply claims his theory is testable in specific areas of study. He does not indicate what those tests might be, nor what results would be predicted based on his gyres.

ETA: You can download the full text here: I'm not going to start reading it till I've had something to eat, and then I will dive in. Expect an investigation like the AIDS paper.

Techmology and Scientism / 'Man vs MRSA'
« on: February 02, 2012, 08:30:30 pm »
Methicilin-Resistant Strephlococcus aureus (AKA MRSA) is becoming a huge problem in some parts of the country. You have probably heard of staph infections before, which occur when wounds are not properly sterilized. That's because S. aureus is all over our skin, it's a commensalist organism that usually doesn't cause us problems. And like most bacteria, a good sulfactant such as soap kills them without issue. And up until recently, antibiotics worked in most cases when they ended up inside people.

However, and like many pathogenic organisms these days, they are becoming resistant. In MRSA infections, there isn't much treatment that works because, as I said, it's resistant to antibiotics and /all over your skin/. If you get one MRSA infection, chances are that a second staph infection will also be MRSA.

So the current work is towards a vaccine.

The heretical approach was inspired, in part, by a patient. As part of an ongoing project to root out the causes of recurring infections, in 2009 two of Daum's team members went to the home of a toddler who had recently been in the emergency department. But the girl wasn't there; she was in the hospital's intensive-care unit with a new infection. When Daum tracked her down, he noticed something odd in her records. She had had unusually frequent abscesses and repeated bouts of pneumonia.

Acting on a hunch, Daum teamed up with Steven Holland, chief of the clinical infectious diseases laboratory at the National Institute of Allergy and Infectious Diseases in Bethesda, Maryland, to carry out a detailed genetic analysis. Daum's hunch was right: the girl had a mutation that Holland had recently linked to a rare immunodeficiency called Job's syndrome7. People with the syndrome have persistent, smouldering S. aureus infections, owing to an inability to make a type of lymphocyte, or immune cell, called a TH17 cell.

These cells, which make a proinflammatory protein called interleukin-17, have become a hot topic in vaccine research. They are produced by a different branch of the immune system from the one that makes antibodies, yet they still seem to be involved in the body's memory of exposures to pathogens.

Daum believes that TH17 cells are the key to an S. aureus vaccine. “It looks like T cells are very important in staphylococcal immunity,” he says. Spellberg demonstrated in 2009 that a vaccine that stimulated production of interleukin 17 could protect mice against infections of S. aureus and Candida albicans8. (That vaccine is now being developed by NovaDigm Therapeutics as NDV3.)

Techmology and Scientism / 'Massage's Mystery Mechanism Unmasked'
« on: February 02, 2012, 07:55:26 pm »

Mark Tarnopolsky, a neurometabolic researcher at McMaster University in Hamilton, Canada, was one of those physicians—until he suffered a severe hamstring injury in a waterskiing accident 4 years ago. Massage therapy was part of his rehabilitation regimen, and it was so effective at easing his pain that he became determined to track down the mechanism that made him feel so good. "I thought there has to be a physiologic basis for this," he says. "And being a cellular scientist, my interest's in the cellular basis."

So Tarnopolsky and colleagues—including the coordinator of his rehab program—recruited 11 young men willing to exercise in the name of science. The subjects underwent a grueling upright cycling session that left their muscles damaged and sore. Ten minutes after their workout, a massage therapist massaged one of their legs. Meanwhile, the researchers took tissue samples from the volunteers' quadriceps muscles—once before the workout, once 10 minutes after the massage, and once 3 hours after the workout—and compared the genetic profiles of each sample.

The researchers detected more indicators of cell repair and inflammation in the post-workout samples than in the pre-workout samples. That didn't surprise them because scientists know that exercise activates genes associated with repair and inflammation. What did shock them were the clear differences between the massaged legs and the unmassaged ones after exercise. The massaged legs had 30% more PGC-1alpha, a gene that helps muscle cells build mitochondria, the "engines" that turn a cell's food into energy. They also had three times less NFkB, which turns on genes associated with inflammation.

The results, published online today in Science Translational Medicine, suggest that massage suppresses the inflammation that follows exercise while promoting faster healing. "Basically, you can have your cake and eat it too," Tarnopolsky says. He adds that the study found no evidence to support often-repeated claims that massage removes lactic acid, a byproduct of exertion long blamed for muscle soreness, or waste products from tired muscles.

This is really cool research with physiological evidence supporting the use of massage therapy after muscle injury or even heavy exercise. And out with this lactic acid crap that people blame for muscle soreness. It's a byproduct of anaerobic metabolism, and it only sticks with you short term. The soreness is actual injury to the muscle tissue, which is then strengthened during repair.

Principia Discussion / The original Principia Discordia.
« on: February 01, 2012, 10:25:55 pm »
Quote from: pg 00075 Principia Discordia 4th ed.
This being the 4th Edition, March 1970, San Francisco; a revision of the 3rd Edition of 500 copies, whomped together in Tampa 1969; which revised the 2nd Edition of 100 copies from Los Angeles 1969; which was a revision of PRINCIPIA DISCORDIA or HOW THE WEST WAS LOST published in New Orleans in 1965 in five copies, which were mostly lost.

Has anyone ever heard what happened to these earlier editions and if any copies survive? La Wik mentions

In 1978, a copy of a work from Kerry Thornley titled "THE PRINCIPIA DISCORDIA or HOW THE WEST WAS LOST" was placed in the HSCA JFK collections as document 010857 [1]. A scan of this document has been identified as the first edition and uploaded to The record identifier can be found by searching for Thornley and Discordian on

However, I can't find it on 23ae. I'm interested, because of historical significance as an artifact, and to compare the first with the latest editions and see if any parts have mutated.

Techmology and Scientism / Well, 3700 mi a start, I guess.
« on: January 31, 2012, 11:52:20 pm »
At least it's beyond low earth orbit.

WASHINGTON -- There's no firm date yet, but sometime in early 2014 NASA intends to take its first major step toward rebuilding its human spaceflight program.

The milestone is the maiden test flight of its Orion spacecraft, a launch that has come into sharper relief in the three months since NASA and manufacturer Lockheed Martin announced it.

As planned, an unmanned Orion capsule will begin its journey at Cape Canaveral and take two loops around Earth before splashing down in the Pacific Ocean. What's now clear is that the capsule will be sent far beyond the lower Earth orbit of the International Space Station.

At its peak, Orion's orbit is expected to extend nearly 3,700 miles from Earth -- the farthest a NASA spacecraft built for humans has gone since the early 1970s.

That distance is "significantly higher than human spaceflight has gone since Apollo," said Larry Price, Orion deputy program manager at Lockheed Martin. "The reason for that is so we can get a high-energy entry so we can stress the heat shield."

The test will determine whether Orion can survive the re-entry into Earth's atmosphere -- where temperatures are expected to reach 4,000 degrees -- in preparation for a human flight in 2021. NASA hopes that Orion eventually can carry astronauts back to the moon or to nearby asteroids.

Besides the heat shield, the practice flight is designed to test 10 systems whose failure could be disastrous, including the capsule's flight software and parachutes. Like its Apollo-era predecessors, the four-person Orion capsule is designed to land in water.

The test also gives NASA, and Lockheed Martin, a chance to showcase part of the agency's new exploration program, details of which were agreed to last fall after a year of negotiation among the White House, Congress and industry.

The timetable for NASA's new exploration program envisions a first manned flight of Orion in 2021 aboard a new rocket -- still under development -- that NASA expects to be the most powerful ever. An unmanned test flight of that rocket, being built by Lockheed Martin rivals Boeing and ATK, is planned for 2017.

I was hoping we wouldn't have to wait 10 years, but I guess that's better than the alternative (which is never).

Principia Discussion / Why Pastafarianism didn't persist.
« on: January 31, 2012, 08:54:43 pm »
I'm currently having a conversation with someone about Church of the Flying Spaggetti Monster (AKA Pastafarianism). I was posing that, unlike she had proposed, Pastafarianism and Discordianism (or CotSG) are not really that similar.

My argument was that, while the latter irreligions were "religion masking joke masking substance", the latter was a joke through and through. People who use the parody tend not to self identify under that label, which is at best a ploy by atheists to counteract the teaching of creationism in schools.

Compare this with the more "traditional" irreligions of Discordianism and Church of the Subgenius. The former is a radical westernization of zen and taoism, the later a radical subversion of religion in general. And I pointed out that in 10 years, hardly anyone will remember the flying spagetti monster, but there will still be Discordians.

Now, why is that?

It seems to me that these "one-liner" irreligions have essentially no substance. As Nigel said previously, Discordianism is a complete system, a complete metamap through which to go about exploring reality. It provides an entire, absurdist groundplan from which to view the universe. The "substance obscured by the joke" is actually rather deep and useful. And this substance, and the history of human creativity surrounding this substance, allows a social cohesiveness despite the fact that it is a joke (and that "Discordians stick apart"). For example, this forum wouldn't still be around 10+ years after it got started if there wasn't some essential substance beneath the joke.

There is no social cohesion in Pastafarianism beyond the original goal to push creationism out of public schools. I would argue that there is actually NO Pastafarianism in the first place, because no one actually identifies as one. The lack of substance means that social groups tend to quickly fall apart. Look at the Church of Google for the same reason. It's the difference between laughing at a joke and forgetting it, and laughing at a joke only later to go "oh, there are a whole bunch of hidden gems there".

I know people here have been to some of these parody religion forums, and I hope you will comment.

My other thought is when you cling to a joke which has no substance as if it did, you start taking yourself too seriously. And if the backers of the parody aren't high enough in numbers, the social structure tends to fall apart quickly when under attack. There's no reason to cling together, as it was at the Church of Google forums.

Techmology and Scientism / A Parade of Badass Scientists.
« on: January 23, 2012, 04:31:07 pm »
Starting with William Dampier.

He was, as you can see here, a large nosed, lean, keen-eyed man whose image still hangs in Great Britain's national portrait gallery, alongside kings, writers, warriors and other great personages. Which is odd, because he was a pirate.

Not a gentleman pirate. William Dampier was a doubloon-stealing, knife-flashing, boat-nabbing outlaw who preyed on Spanish frigates, who pillaged, robbed and behaved very, very badly.

But he was also a great naturalist, one of the 17th century's best; a man who collected plants and animals and wrote about them during short breaks between piratical adventures.

Some of the stories include: stealing food from a Vietnamese funeral and barely escaping with his life; fashioning a bamboo container to waterproof his journals while running/swimming through the jungle; and that Darwin called him "old Dampier", as if the pirate was his pal over a century later.

The new biography is now on my 2012 reading list.

Techmology and Scientism / Thingiverse.
« on: January 15, 2012, 03:24:58 pm »
(Ed Yong is apparently my muse, because I'm on a roll today.)

Thingiverse, founded in 2008, is a design library from the folks at MakerBot Industries, the Brooklyn-based company that is designing and building open-source 3D printers. On Thingiverse, people can download the plans for obsjects, tweak them, and share their improved versions. As CEO Bre Pettis explained, "You just download this digital design or you create one yourself, and the thing is made right there for you. ... Up until now, you've been able to download books, you've been able to download movies, you can download music. Well, now you can download things. And, once you download the digital design, you can just crank up your MakerBot, fire it up, and print it out."

And there are pictures of makerbot made items with designs downloaded from Thingiverse at the link.

...birds are dinosaurs.

And while their simple answer seems to be "anything with feathers is not a dinosaur" (which is a near-idiotic just so story), the article reveals the real problem.

Ultimately, though, many of Feduccia’s objections boil down to a rejection of a methodology known as cladistics. This method of determining relationships among organisms is based on the analysis of shared derived characteristics—specialized features found in two organisms or lineages and their most recent common ancestor. Researchers look for numerous traits, record whether the traits in question are present or absent, and then insert that mass of data into a computer program that produces a hypothesis about the relationships among the various organisms included in the study. The point is not to find direct ancestors and descendants, but to figure out who is most closely related to whom. The method is not perfect—which organisms are included, the choice of traits for comparison and the way those traits are scored all affect the outcome. Still, this process has the benefit of requiring researchers to show their work. Each evolutionary tree resulting from such methods is a hypothesis that will be tested according to new evidence and analyses. If someone disagrees with a particular result, they can sift through the collected data to see if an inappropriate trait was included, an essential organism was left out, or if there was some other problem. Cladistics is useful not because it results in a perfect reflection of nature each time, but because it allows researchers to effectively examine, test and improve ideas about relationships.

They're using phenetics, something I thought was long dead in studies of morphology (though not in DNA sequences). Of course, the biggest problem with their methods is just that; Phenetics was never meant to find the evolutionary relationships of organisms. Sokal and Sneeth, who came up with the method, outright rejected that anyone should try to find evolutionary relationships because they were almost always too obscured to confidently reconstruct. Most systematists, such as myself, reject this idea, because it strikes us as solipsism. We know there are evolutionary relationships, and so we use specially shared characters (characters shared between species that are shared by no other species) to infer the relationships. As we find more characters, more information, we refine those relationships. Characters that are more widely shared, more general, are not useful because they don't tell us about common ancestry.

So, these birds-as-dinosaurs denialists ignore all evidence that doesn't support their claim that there is some unknown ancestor of birds that was not a dinosaur, and use methods to devise actual relationships that were never meant to find actual relationships. Pseudoscience is alive and well in systematics, as it is in some small amount in every field of science.

Techmology and Scientism / Worst (Best?) Scientific Presentation Ever.
« on: January 15, 2012, 02:50:23 pm »

But the mere public showing of his erection from the podium was not sufficient. He paused, and seemed to ponder his next move. The sense of drama in the room was palpable. He then said, with gravity, ‘I’d like to give some of the audience the opportunity to confirm the degree of tumescence’. With his pants at his knees, he waddled down the stairs, approaching (to their horror) the urologists and their partners in the front row. As he approached them, erection waggling before him, four or five of the women in the front rows threw their arms up in the air, seemingly in unison, and screamed loudly. The scientific merits of the presentation had been overwhelmed, for them, by the novel and unusual mode of demonstrating the results.

 :lulz: And you thought professional meetings are quiet, boring affairs.  :lulz:

Apple Talk / ATTN: PHOX.
« on: January 07, 2012, 07:54:19 pm »

Techmology and Scientism / Cockroaches with jet packs.
« on: January 07, 2012, 07:03:19 pm »
Title says it all. Some researchers wanted to test the stride reaction time of an insect to find out just how stable having six legs in tripodal alternation really is. So they strapped some jet packs to roaches and fired them off in front of a high speed camera, and the roaches barely broke stride.

Also, another jetroach video.

And the best part is, the paper is open access so we can ALL read it.

The most interesting thing about this find is how different these vent ecosystems are from the ones in the Atlantic and Pacific oceans. For one, there are no tube worms, and all the rest of the species are different as well. I'm very curious about these octopuses.

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