At the Earth's Core

September 8, 2012, 5:40 am

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Some days ago the Integrated Ocean Drilling Program announced a new "record" of the scientific vessel "Chikyu" (Japanese for "earth") - the at time deepest (scientific) borehole with 2.300 meters below the seafloor was completed in the 1.180 meters deep, blue sea off Shimokita-Peninsula. The longest rig ever done from board of the Chikyu was 7.740 meters long, however in the open sea the greatest problem is not the water, but drilling in the ground. 

Since old times people - especially geologists - were interested to know about the interior of Earth. The Italian poet Dante Alighieri (1265-1321) imagined an allegoric center of the Earth: a frozen wasteland, not reached by the divine light, where Lucifer is entrapped in eternal ice.

Fig.1. Illustration to Dante's "The Divine Comedy" from the "Codice Urbinate Latino 365" (1480) showing the frozen center of Earth.

The French Sci-Fi author Jules Gabriel Verne (1828 - 1905) based an imaginary "Lost World" in "A Journey to the Center of the Earth" (1864) on more scientific ground. In his novel Verne uses the hollow conduit of an Icelandic volcano to venture inside earth, an idea supported by the geologic models of volcanoes proposed at the time - a single or a series of magma chamber(s) with conduits connecting them to the surface. Geologists assumed that during an eruption the magma reservoir becomes empty and large voids and caverns were left behind. 

Fig.2. This schema, published in the book by German professor of geophysics August Sieberg "Einführung in die Erdbeben- und Vulkankunde Süditaliens" (1914), shows the anatomy of a stratovolcano, with a main conduit, various lateral dikes and a large sill connected to the magma reservoir. In contrast to the sketch, the conduits for magma are in reality only a few meters wide - too small for travel the Center of the Earth.

Verne's vision inspired the wonderful U.S. movie of 1959 "Journey to the Center of the Earth" and was reused in the mediocre "At The Earth´s Core" (1976), even if the last movie was based on the novel "At the Earth's Core*" (1914) by Edgar Rice Burroughs (*considering the display of the "Mole"-vehicle, the supposed cavern with the mythical land of "Pellucidar" is situated in the transition zone of Outer Core - Lower Mantle).



Also the first movie featuring "Superman" touches the subject of a deep-earth civilisation. In "Superman and the Mole Men" (1951) the Mole Men invade earth's surface from the deepest oil well of the world (more than 6 miles/ 9 kilometers deep!).
In fact the deepest boreholes in the real world stopped at more than 12 kilometers - however that's just 0,2% of the radius of earth.
In May 1970, to celebrate the birthday of Lenin, the former Soviet Union initiated the secret project "SG-3" on the Kola-Peninsula. The drilling project planned to study the Mohorovičić discontinuity, situated at 15 kilometers below the surface of the continents. The project was continued until 1989, when technical and especially financial problems, stopped the drill at 12.261 meters forever.
The United States initiated a similar ambitious project, but decided to drill the thinner oceanic crust (5-10 kilometers thick). Project Mohole started in 1961 and was abandoned in 1966, after recovering 170 meters long cores from the ocean floor in 3.500 meters depth. Modern commercial boreholes reach depths of 2.000-3.000 meters.
 
"Gentleman, the truth is that all our theories are just that, theories. None of us has the least idea of how the earth was really formed. Because the distance between the earths crust and its core is over 6.500 kilometres, and no men has ever descended to a depth of more than 3 miles. So it's obvious, we will never have a glimmer of true knowledge, until we are able to reach a depth of at least a 100 leagues.
- What's your opinion Professor Lindenbrook?
- Well gentlemen, at one point at least I agree with Professor Christophe, the materials of the geologists are not charts, chalk and chatter, but the earth itself. We should never know the truth, until we are able to make that journey, and see for ourselves."
Dialogue from the movie adaption "The Fabulous Journey to the Center of the Earth" / "Where Time Began" (1976), a Spanish version of Jules Gabriel Verne's novel.

Bibliography:

CARLSON, D.H.; PLUMMER, C.C. & HAMMERSLEY, L. (2009): Physical Geology - Earth Revealed. McGraw-Hill Publ, 9th ed.: 645
SCHICK, R. (2002): The Little Book of Earthquakes andVolcanoes. Springer/Copernicus Books, New York: 164

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Neil Gaiman: "Make good art"

September 9, 2012, 2:07 am

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Watch this video. Watch it now. It goes alongside that of the late Steve Jobs talking at Stanford but this time it is Neil Gaiman. And this time it is at Philadelphia University of Arts in 2012. Listen to the author build upon the motto: "Make good art". He fills the 19 minutes with dozens of worthwhile, distilled quanta of advice for young journalists and writers. But where is the talk: "Make good science"? Where are the role models for young researchers? Why are they not being recorded giving commencement addresses on doing good science? In the meantime until they step forward, Neil's advice may be quite easily transferred to the fields of science.

About okra

September 9, 2012, 4:14 am

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Yesterday's trip to our local farmer's market held no real surprises: peppers were rebounding, tomatoes, except maybe cherry tomatoes, were shot, fall crops were coming into season, and people had a lot of okra for sale, and sadly, most of it was not worth buying.  The reason for this is simple; it was all too mature.  There are a number of fruits that we usually eat as vegetables that are only edible when immature.  The mature fruits are inedible.  Okra matures into a hard, dry capsular fruit that splits open along 5 seams to release its seeds.  As long as the young fruits are elongating, they are soft enough to consume, but once they reach their mature length, they become fibrous very quickly, and okra grows rather quickly so you must pick any pods more than an inch long once a week.  This is the zucchini lesson all over again.  Pick them young!  But vendor after vendor had great big old things as if large size were a virtue.  Hmm, no image of okra in the files, especially a mature fruit, but here's a nice image of an okra flower.  The flower is a dead give-away that okra belongs in the mallow/hibiscus family.

The season and okra in combination remind TPP of one more thing: my suggestion that team mascots be plant names.  Let's add to the ranks of forward looking universities and colleges by introducing the Delta State Fighting Okras!  Yea, go Okras!  Fear the Okra!  Got to get one of those t-shirts!  If the pods start to sprout arms, they're too old to eat.

British Health Minister believes in magic water

September 9, 2012, 7:13 am

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Well, this is one way to save money on health care.  The new British Minister of Health, Jeremy Hunt, is a firm believer in homeopathy, which treats disease using magic water solutions that contain - well, only water.

Just a few days ago, British prime minister David Cameron shuffled his cabinet, moving Hunt from Minister of Culture to his new position in charge of health.  Within hours, Tom Chivers, a science editor at the Telegraph, reported on Hunt's belief in homeopathy:

"The man put in charge of the nation's health policy is on record as supporting spending public money on magic water to cure disease." 

He went on to add:

"This is not unlike putting someone who thinks the Second World War began in 1986 in charge of the Department of Education."

Not surprisingly, Chivers' blog post was flooded with hundreds of comments, many of them from upset defenders of homeopathy.  Most of their arguments boiled down to "I think it works for me, so there."

Homeopathy is one of the most absurd, wildly implausible forms of quack medicine. I've written about it many times (for example, about the bogus flu pills sold as oscillococcinum,
about NCCAM's embarrassing funding of studies of homeopathy, and about how homeopaths offer strychnine to cure children's colds), so I'll try not to repeat myself.  Homeopathy is founded on two basic notinos, both of them dead wrong:

1. Infinitely diluted substances are more potent than substances at higher concentrations, and
2. "Like cures like," meaning that if a substance causes a symptom, you can use that substance to cure the symptom.  

Thus caffeine can be used to help you sleep, and poison ivy can cure itching.  No, I'm not making this up; homeopaths really believe this stuff.

Homeopathy is simply magical thinking.  There has never been a shred of scientific evidence to support it, and the British Medical Association declared in 2010 that homeopathy is witchcraft.  After pressure from science bloggers, NIH's NCCAM has corrected its website to state that

"it is not possible to explain in scientific terms how a remedy containing little or no active ingredient can have any effect."

But homeopaths make a lot of money selling homeopathic potions, and through clever marketing they keep themselves in business.  Now they have a new ally, the UK Minister of Health. Andy Coghlan, writing in The New Scientist, called him "the new minister for magic."  Brilliant!  As Coghlan pointed out, magic is much cheaper than real medicine:

"Think of the savings if all those expensive proven treatments and drugs are phased out, and patients are offered cheap little vials of water instead."

We're desperately looking for ways to control health care costs here in the U.S. as well.  The UK Minister of Magic may have a solution for us.  I wonder, though, if it works for muggles?

Pricing conundrum

September 10, 2012, 5:00 am

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Before I went to Riva del Garda for this year's AMLaP, I picked up a travel guide on my Kindle. (If only such things had existed the years I backpacked in Eurasia. My strongest memories are of how much my backpack weighed. Too many books.)

Oddly, the Lonely Planet Italian Lakes Region guide is the exact same price as the whole Italy guide. These local guides tend to be glorified excerpts of the country book, and since they both weigh the same...

2012 Nobel Prizes

September 10, 2012, 6:50 am

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Predicting the Nobel Prizes gets easier every year ((I said predicting, not getting your predictions right) since there’s very little you can add in the previous year’s list, although there are a few changes; the Plucky Palladists can now happily be struck off the list. As before, I am dividing categories into ‘easy’, and ‘difficult’ and assigning pros and cons to every prediction. This is a revised and updated version of my list from last year. Paul has already kicked off the predictions.

The easy ones are those regarding discoveries whose importance is (now) ‘obvious’; these discoveries inevitably make it to lists everywhere each year and the palladists clearly fell into this category. The difficult predictions would either be discoveries which have been predicted by few others or ones that that are ‘non-obvious’. But what exactly is a discovery of ‘non-obvious’ importance? Well, one of the criteria in my mind for a ‘non-obvious’ Nobel Prize is one that is awarded to an individual for general achievements in a field rather than for specific discoveries, much like the lifetime achievement Academy Awards given out to men and women with canes. Such predictions are somewhat harder to make simply because fields are honored by prizes much less frequently than specific discoveries.

When predicting the Nobel prize it’s also prudent to be cognizant of discoveries whose recognition makes you go “Of course! That’s obvious”. Prizes for the charge-coupled device (CCD) (2009) integrated chip (2000) and in-vitro fertilization (2010) fall into this category.

Anyway, here's the N-list for chemistry:

Single-molecule spectroscopy (Easy)
Pros: The field has obviously matured and is now a powerful tool for exploring everything from nanoparticles to DNA. It’s been touted as a candidate for years. The frontrunners seem to be W E Moerner and M Orrit, although Richard Zare has also been floated often.
Cons: The only con I can think of is that the field might yet be too new for a prize.

Lithium-ion batteries (Moderately easy): Used in almost every kind of consumer electronics, lithium-ion batteries are also touted as the best battery alternative to fossil fuels. A great account is provided in Seth Fletcher’s “Bottled Lightning”. From what I have read in that book and other sources, John Goodenough, Stanley Whittingham and Akira Yoshino seem to be the top candidates, although others have also made important contributions and it may be hard to divide up the credit.

Computational chemistry and biochemistry (Difficult):

Pros: Computational chemistry as a field has not been recognized since 1998 so the time seems due. One obvious candidate would be Martin Karplus. Another would be Norman Allinger, the pioneer of molecular mechanics.

Cons: This would definitely be a lifetime achievement award. Karplus did do the first MD simulation of a protein ever but that by itself wouldn’t command a Nobel Prize. The other question is regarding what field exactly the prize would honor. If it’s specifically applications to biochemistry, then Karplus alone would probably suffice. But if the prize is for computational methods and applications in general, then others would also have to be considered, most notably Allinger but perhaps also Ken Houk who has been foremost in applying such methods to organic chemistry. Another interesting candidate is David Baker whose program Rosetta has really produced some fantastic results in predicting protein structure and folding. It even spawned a cool game. But the field is probably too new for a prize and would have to be further validated; at some point I do see a prize for biomolecular simulation.

Chemical genetics (Easy)
Another favorite for years, with Stuart Schreiber and Peter Schultz being touted as leading candidates.Pros: The general field has had a significant impact on basic and applied scienceCons: This again would be more of a lifetime achievement award which is rare. Plus, there are several individuals in recent years (Cravatt, Bertozzi, Shokat) who have contributed to the field. It may make some sense to award Schreiber a ‘pioneer’ award for raising ‘awareness’ but that’s sure going to make at least some people unhappy. Also, a prize for chemical biology might be yet another one whose time has just passed).

Electron transfer in biological systems (Easy)
Pros: Another field which has matured and has been well-validated. Gray and Bard seem to be leading candidates.

NMR (Difficult): It’s been a while since Kurt Wuthrich won the prize for NMR. But it’s been even longer since a prize was awarded for methodological developments in the field (Richard Ernst). I don’t know enough about the field to know who the top contenders would be, but Ad Bax and Alexander Pines seem to have really made pioneering contributions. Pines especially helped launch the field of solid-state NMR which as a field certainly seems to deserve a Nobel at some point.

Among other fields, I don’t really see a prize for the long lionized birth pill and Carl Djerassi; although we might yet be surprised, the time just seems to have passed. Then there are fields which seem too immature for the prize; among these are molecular machines (Stoddart et al.) and solar cells (Gratzel). One promising candidate is Krzysztof Matyjaszewski whose work in ATRP has had a pronounced impact on the way polymers are made; this would neatly fit into the Nobel Prize’s requirement for work that is both fundamental and has “benefited humanity”.

MEDICINE/CHEMISTRY:

Nuclear receptors (Easy)

Pros: The importance of these proteins is unquestioned. I worked a little on NRs during my postdoc and remember being awed by the sheer diversity and ubiquity of these molecules in mediating key physiological functions. In addition they are already robust drug targets, with drugs like tamoxifen that hit the estrogen receptor making hundreds of millions of dollars. Most predictors seem to converge on the names of Chambon, Jensen and Evans and this prediction is definitely at the top of my list.

Chaperones: (Easy)

Arthur Horwich and Franz-Ulrich Hartl just won this year’s Lasker Award for their discovery of chaperones. Their names have been high on the list for some time now.

Pros: Clearly important. Chaperones are not only important for studying protein folding on a basic level but in the last few years the malfunctioning of chaperones such as heat-shock proteins has been shown to be very relevant to diseases like cancer.

Cons: Too early? Probably not.

Statins (Difficult)

Akira Endo’s name does not seem to have been discussed much. Endo discovered the first statin. Although this particular compound was not a blockbuster drug, since then statins have revolutionized the treatment of heart disease.

Pros: The “importance” as described in Nobel’s will is obvious since statins have become the best-selling drugs in history. It also might be a nice statement to award the prize to the discovery of a drug for a change. Who knows, it might even boost the image of a much maligned pharmaceutical industry...
Cons: The committee is not really known for awarding actual drug discovery. Precedents like Alexander Fleming (antibiotics), James Black (beta blockers, antiulcer drugs) and Gertrude Elion (immunosuppresants, anticancer agents) exist but are far and few in between. On the other hand this fact might make a prize for drug discovery overdue.

Drug delivery (Difficult): A lot of people are pointing to Robert Langer for his undoubtedly prolific and key contributions to drug delivery. The field as a whole has not been recognized yet so the time may be ripe; from my own understanding of his contributions, Langer seems to me more of an all-rounder, although it may not be too late to single out some of his earlier discoveries, such as the first demonstration of the delivery of high molecular weight polymer drugs.

Cancer genetics (Easy): Clearly a very important and cutting-edge field. We still don’t know how much of an impact genomic approaches will ultimately have on cancer therapy since the paradigm is clearly evolving, but any history of the field will have to include Robert Weinberg and Bert Vogelstein. Vogelstein discovered p53, the “guardian of the genome” while Weinberg discovered the first oncogenes. In addition both men have also been prominent influences on the field as a whole. Given both the pure and applied importance of their work, their discoveries should fit the Nobel committee’s preferences like a glove.

Genomics (Difficult)

A lot of people say that Venter should get the prize, but it’s not clear exactly for what. Not for the human genome, which others would deserve too. If a prize was to be given out for synthetic biology, it’s almost certainly premature. Venter’s synthetic organisms from last year may rule the world, but for now we humans still prevail. On the other hand, a possible prize for genomics may rope in people like Carruthers and Hood who pioneered methods for DNA synthesis.

DNA fingerprinting (Easy):Now this seems to me to be very much a field from the “obvious” category. The impact of DNA fingerprinting and Western and Southern Blots on pure and applied science- everything from discovering new drugs to hunting down serial killers (and exonerating wrongly convicted ones; for instance check out this great article by Carmen Drahl in C&EN)- is at least as big as the prizeworthy PCR. I think the committee would be doing itself a favor by honoring Jeffreys, Stark, Burnette and Southern. And while we are on DNA, I think it’s also worth throwing in Marvin Caruthers whose technique for DNA synthesis really transformed the field. In fact it would be nice to award a dual kind of prize for DNA- for both synthesis and diagnosis.
Cons: Picking three might be tricky.

Stem Cells (Easy)

This seems to be yet another favorite. McCulloch and Till are often listed. Unfortunately McCullough died earlier this year so it would be a little unfair to award just Till. However such a thing is not unprecedented. For example, the psychologist Daniel Kahneman shared the 2002 Economics Nobel Prize with Vernon L. Smith. Left out was his long-time collaborator Amos Tversky who had died in the 90s; it’s pretty much regarded as a given that Tversky would have shared the prize had he been alive.

Pros: Surely one of the most important biological discoveries of the last 50 years, promising fascinating advances in human health and disease.

Cons: Politically controversial (although we hope the committee can rise above this). Plus, a 2007 Nobel was awarded for work on embryonic stem cells using gene targeting strategies so there’s a recent precedent.

Membrane vesicle trafficking (Easy)

Pros: Clearly important. The last trafficking/transport prize was given out in 1999 (Blobel) so another one is due and Rothman and Schekman seem to be the most likely canidates. Plus, they have already won the Lasker Award which in the past has been a good indicator of the Nobel.

GPCR structures (Difficult)

When the latest GPCR structure (the first one of a GPCR bound to a G protein) came out I remember remarking that Kobilka, Stevens and Palczewski are probably up for a Nobel Prize sometime. In the last two years I have become convinced that they deserve it. Palczewski solved the first structure of rhodopsin and Stevens and Kobilka have been churning out structure after important structure over the last decade, including the first structure of an active receptor along with several medicinally important ones including the dopamine D3 and CXCR4 receptors. Kobilka topped it off early this year with another tour-de-force, the structure of the beta adrenergic receptor bound to its G-protein. The implications of these structures are far-reaching but the results are already being used by both pure and applied scientists to better understand GPCR function and design GPCR-targeting drugs.

Pros: GPCR’s are clearly important for basic and applied science, especially drug discovery where 30% of drugs already target these proteins.

Cons: Perhaps too early.

PHYSICS

I think it’s high time Anton Zeilinger, John Clauser and Alain Aspect got it for bringing the unbelievably weird phenomenon of quantum entanglement to the masses. Zeilinger’s book “Dance of the Photons” presents an informative and revealing account of this work

I have also always wondered whether non-linear dynamics and chaos deserves a prize. The proliferation and importance of the field certainly seems to warrant one; the problem is that there are way too many deserving recipients (and Mandelbrot is dead). Among the pioneers, Feigenbaum, May and Yorke come to mind easily.

Subliminal Placebo: You Didn't See It, but It's Working

September 10, 2012, 7:01 am

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The latest additions to the placebo effect family might be the rudest. First there was placebo, which uses your body's own tools to make you feel better after you try a treatment you imagine will help you. Then there was nocebo, placebo's evil twin: it makes you feel worse only because you think you will. Now researchers have discovered that placebo and nocebo effects can be triggered subliminally, which is like finding out that the good and evil twins have both been living in your basement without you knowing it.

Usually, placebo and nocebo look like cases of our own expectations manipulating us. Someone swallows his favorite headache remedy or visits a doctor, and his body, expecting to feel better, ramps up production of its own pain-relief molecules. Someone else steps onboard a plane and begins to feel nauseous, simply because her body has learned that airplanes mean queasiness. If we were more ignorant of our circumstances, the effects wouldn't be there.

But there seem to be some cues we can take in subliminally, without noticing them. So researchers led by Karin Jensen at Harvard Medical School wondered whether visual signals that are too brief to reach our consciousness—but perhaps not too brief for certain areas of our brains to snag as they pass—can trigger placebo and nocebo effects too.

For their visual signals, the team chose photos of male faces. "We know from previous studies that faces can be detected and processed very quickly in the brain," Jensen says. Their models came from a set of photos created for use in psychology experiments.

The researchers carried out two experiments, the first of which was a classic test of placebo and nocebo. Subjects were shown pictures of two expressionless male faces over and over. Each time they saw face A, they felt a painfully hot sensation on the forearm. Face B was paired with heat that was milder, but still uncomfortable. (The A and B models alternated between different subjects—just in case one man's face really was more painful to look at.) During the conditioning part of the experiment, subjects saw each face 25 times. This taught them to expect higher pain with face A and lower pain with face B.

Then came a second series where subjects saw the same two faces as before, with a few new ones mixed in as controls. With each face they saw, subjects rated the pain they felt from the heat instrument on a 100-point scale. The twist was that in this part of the experiment, the heat level was exactly the same every time. But subjects consistently reported high pain for face A and low pain for face B. When they saw a new face, subjects reported an intermediate level of pain (which corresponded to what they were actually feeling).

This first experiment showed the researchers that pairing faces with painful heat stimuli could create both a placebo effect (when subjects rated moderate heat as less painful because they saw face B) and a nocebo effect (when subjects found moderate heat more painful, thanks to face A). So they moved on to the second experiment. In this round, the visual signals would be "nonconscious,"or subliminal.

A new group of subjects went through the same conditioning sequence as before. Then they were given a testing sequence using face A, face B, and the new (control) faces, all paired with the same moderate heat on the arm. But the faces in this sequence flashed on the screen for just 12 milliseconds, compared to 100 milliseconds in the earlier experiment.

12 milliseconds is fast. Too fast, in fact, for subjects to consciously process the faces zipping by. They reported that they couldn't tell who was who (and a separate experiment confirmed that people can't recognize faces shown this quickly).

But, as the researchers report this week in PNAS, the pain scores still matched the faces subjects said they couldn't see. Face A got significantly higher pain scores than face B, with the control faces scoring in the middle—and don't forget that, once again, subjects were actually feeling the same degree of heat every time.

Even though the pictures flashed too briefly to enter conscious awareness, they seem to have snuck in through the brain's back door. These visual cues made subjects experience more or less pain than they should have, even though they had no idea what they'd seen.

There were only 20 subjects in each experiment; it would take further studies to show how consistent or how powerful the subliminal placebo and nocebo effects are. But the fact that they found an effect at all is exciting news to the researchers. "To the best of my knowledge, there has not been an experiment [previously] where placebo/nocebo effects have been activated by nonconscious cues," Jensen says.

The common assumption, Jensen says, is that placebo and nocebo rely on the signals we're paying attention to (pills, needles, drug commercials) and the results we expect (relief, discomfort, alarming side effects). But this study "proves that we don't need to be aware of the cue to elicit a conditioned response," Jensen says.

Don't expect to start seeing mysterious images flashing at you in the doctor's office. The subjects in Jensen's study had to be trained to associate photos of faces with high or low pain. And even if there were another kind of image that automatically produced a placebo effect in a wide audience (teddy bears? puppies?), our brains might not be able to recognize it as quickly as a human face.

But the idea that placebo and nocebo effects can be triggered by cues patients don't even notice could be important for healthcare, Jensen says. Certain conditions such as asthma, depression, and irritable bowel syndrome are known to respond well to placebos. Maybe doctors' offices and hospitals in the future will tailor everything patients see—from the posters on the wall to the instruments on the counter to the fish swimming in the lobby aquarium—to encourage placebo and avoid nocebo. Or maybe we'll be able to use the same tricks at home to keep ourselves feeling our best. Let's kick those weird placebo relatives out of the basement and put them to work.

Karin B. Jensen, Ted J. Kaptchuk, Irving Kirsch, Jacqueline Raicek, Kara M. Lindstrom, Chantal Berna, Randy L. Gollub, Martin Ingvar, & and Jian Kong (2012). Nonconscious activation of placebo and nocebo pain responses PNAS : 10.1073/pnas.1202056109

Image: freya.gefn/Flickr

No ornamental sweet potatoes!

September 10, 2012, 8:16 am

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OK, this is seriously annoying.  Every year for years now TPP has liberated some ornamental sweet potatoes from one of many planters on campus to use for a laboratory specimen on starchy staples.  And this year there are none!  Why just a couple of years ago all of the bayberry bushes on campus were victims of new buildings or new landscaping with nary a thought of where my students were going to get bayberries so that they could extract the wax.  TPP has this crazy notion that everything, everything, on campus is here to help me do my job, and wouldn't it be nice if before removing a plant or changing your ideas about ornamentals you checked with someone, the SOMEONE, who uses them?  You see, and this comes as a surprise to most of our administrators, the campus and its lovely landscaping is not just something pretty to fill in the spaces between buildings.  No question this is a valid function, but the campus is my classroom and good manners dictates that you check with the instructor before removing something from my classroom!  Got that?  And while you're at it, keep the squirrels from eating all the native pecans too. 

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Titles in evolutionary biology

September 10, 2012, 10:17 am

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These are the new papers for the last couple of weeks that I would like to read but will probably never get to. Gone are the days of the polymaths already, and now this!

• Systematic underestimation of the age of selected alleles
• Predatory Fish Select for Coordinated Collective Motion in Virtual Prey
• Rapid evolution of Wolbachia incompatibility types
• Avoidance of roads and selection for recent cutovers by threatened caribou: fitness-rewarding or maladaptive behaviour?
• Weak Selection and Protein Evolution
• Patterns of Neutral Diversity Under General Models of Selective Sweeps
• Selective Sweeps in Multilocus Models of Quantitative Traits
• Distinct evolutionary patterns of morphometric sperm traits in passerine birds
• A selective force favoring increased G+C content in bacterial genes
• Evolutionary Dynamics of Strategic Behavior in a Collective-Risk Dilemma
• Evolution of Stress Response in the Face of Unreliable Environmental Signals
• Network Context and Selection in the Evolution to Enzyme Specificity
• Clade Age and Species Richness Are Decoupled Across the Eukaryotic Tree of Life
• Evolutionary medicine: its scope, interest and potential*
• The role of ‘soaking’ in spiteful toxin production in Pseudomonas aeruginosa
• On the evolutionary origins of the egalitarian syndrome
• Clade Age and Species Richness Are Decoupled Across the Eukaryotic Tree of Life

* Because I am meeting with Stephen Stearns when he visits MSU this Thursday, I will take an actual look at this review article. Paul Ewald was here last week, and we had a good talk about selection in pathogens and human disease. I also met with Randolph Nesse last semester, so evolutionary medicine has been in focus a lot lately.

Habemus papers (about the new boson)

September 10, 2012, 11:30 am

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posted by @ulaulaman thanks to @tanzmax @spimpompam #Higgs #boson #newboson #LHC #CMS #ATLAS #CERN

Finally Physics Letters B published the two papers by ATLAS and CMS about the discovery of the new boson at LHC (via tanzmax):

A search for the Standard Model Higgs boson in proton–proton collisions with the ATLAS detector at the LHC is presented. The datasets used correspond to integrated luminosities of approximately $4.8 \, fb^{−1}$ collected at $\sqrt{s} = 7$ TeV in 2011 and $5.8 \, fb^{−1}$ at $\sqrt{s} = 8$ TeV in 2012. Individual searches in the channels $H \rightarrow ZZ^{(*)} \rightarrow 4l$, $H \rightarrow \gamma \gamma$ and $H \rightarrow WW^{(*)} \rightarrow e \nu \mu \nu$ in the 8 TeV data are combined with previously published results of searches for $H \rightarrow ZZ^{(*)}$, $WW^{(*)}$, $b \bar{b}$ and $\tau^+ \tau^-$ in the 7 TeV data and results from improved analyses of the $H \rightarrow ZZ^{(*)} \rightarrow 4l$ and $H \rightarrow \gamma \gamma$ channels in the 7 TeV data. Clear evidence for the production of a neutral boson with a measured mass of 126.0 ± 0.4 (stat) ± 0.4 (sys) GeV is presented. This observation, which has a significance of 5.9 standard deviations, corresponding to a background fluctuation probability of 1.7 × 10⁻⁹, is compatible with the production and decay of the Standard Model Higgs boson.

Aad, G., Abajyan, T., Abbott, B., Abdallah, J., Abdel Khalek, S., Abdelalim, A.A., Abdinov, O., Aben, R., Abi, B., Abolins, M. & (2012). Observation of a new particle in the search for the Standard Model Higgs boson with the ATLAS detector at the LHC, Physics Letters B, 716 (1) 29. DOI: 10.1016/j.physletb.2012.08.020

Results are presented from searches for the standard model Higgs boson in proton–proton collisions at $\sqrt{s} =$ 7 and 8 TeV in the Compact Muon Solenoid experiment at the LHC, using data samples corresponding to integrated luminosities of up to $5.1 fb^{−1}$ at 7 TeV and $5.3 fb^{−1}$ at 8 TeV. The search is performed in five decay modes: $\gamma \gamma$, $ZZ$, $W^+ W^−$, $\tau^+ \tau^-$, and $b \bar{b}$. An excess of events is observed above the expected background, with a local significance of 5.0 standard deviations, at a mass near 125 GeV, signalling the production of a new particle. The expected significance for a standard model Higgs boson of that mass is 5.8 standard deviations. The excess is most significant in the two decay modes with the best mass resolution, $\gamma \gamma$ and $ZZ$; a fit to these signals gives a mass of 125.3 ± 0.4 (stat.) ± 0.5 (syst.) GeV. The decay to two photons indicates that the new particle is a boson with spin different from one.

Chatrchyan, S., Khachatryan, V., Sirunyan, A.M., Tumasyan, A., Adam, W., Aguilo, E., Bergauer, T., Dragicevic, M., Erö, J., Fabjan, C. & (2012). Observation of a new boson at a mass of 125 GeV with the CMS experiment at the LHC, Physics Letters B, 716 (1) 61. DOI: 10.1016/j.physletb.2012.08.021

To the previous papers, I add also the following (via spimpompam), that it could be interesting to read:

Following recent ATLAS and CMS publications we interpret the results of their Higgs searches in terms of Standard Model operators. For a Higgs mass of 125 GeV we determine several Higgs couplings from 2011 data and extrapolate the results towards different scenarios of LHC running. Even though our analysis is limited by low statistics we already derive meaningful constraints on modified Higgs sectors.

Klute, M., Lafaye, R., Plehn, T., Rauch, M. & Zerwas, D. (2012). Measuring Higgs Couplings from LHC Data, Physical Review Letters, 109 (10) DOI: 10.1103/PhysRevLett.109.101801 (arXiv)

Biotechnology. Misunderstood.

September 10, 2012, 12:11 pm

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David Kroll, veteran science blogger, educator and Director of Science Communications at the NC Museum of Natural History is having a hard time convincing someone of the importance of biotechnology and of communicating it to the public. As a scientist working at a biotech company myself, this seemed to be of particular interest to me and it also turned out to be particularly disconcerting. In this case David's correspondent happens to be Ms. Laura Combs, a former state environmental agency employee writing at a blog that seems to discuss diverse topics connected with medicine and the environment. Unfortunately that's not precluded her from inventing some rather strange ideas about the definitions and scope of biotechnology.

Ms. Combs seems to be an engaged citizen who genuinely appreciates the work done by the NCMNS, and that makes her response even more perplexing. The incident started innocently enough with the NCMNS organizing a 'Biotechnology Day' that showcased biotechnology research for the public. I believe this is an exceedingly important endeavor that should be encouraged, especially in the face of the growing importance of biotechnology and genomics in our lives. The presentations were split evenly between people from industry, academia and the agricultural sector; again, an entirely fair split since these three sectors are where the majority of biotech research takes place. 

Unfortunately the inclusion of industry in the museum's events sparked a backlash from Ms. Combs, which resulted in a lengthy correspondence with David and others at the museum. What left me the most nonplussed was Ms. Combs's definition of biotechnology as something antagonistic to the natural world and generally malevolent to humanity. Biotechnology, according to Ms. Combs, was not compatible with the "natural science" that the museum claimed to promote. Leaving aside the fact that the public dissemination of science should include all of science and not just "natural" science, unfortunately this seems to be a common foundational misunderstanding on the part of biotech opponents and it seems to ignore a lot of things, including a starting point in Darwin's great work "The Origin of Species".

Darwin kicked off his thoughts on natural selection in the first chapter of his book by reminding us of the artificial selection done on domestic animals and agricultural plants for hundreds of centuries. Yes, all these people who were practicing artificial selection were doing 'biotechnology' even if they had no knowledge of genes. But the overarching point that Darwin was getting at was that nature also practices biotechnology in the form of natural selection, and has in fact been doing so since the origin of life. This is probably the biggest mistake that biotech opponents make, to think of biotech as a wholly human invention. All of natural selection that involves the selective retention and manipulation of genes and phenotypes is biotechnology. In addition as David notes in his detailed reply, horizontal genetic transfer has been one of the key driving forces of evolution. Again, biotechnology. And perhaps Ms. Combs would like to know that about 8% of our genome consists of genes from retroviruses that were inserted during evolution. Thus, viruses were doing biotech with us long before we started doing biotech with them. The fact is that gene transfer and manipulation have been natural processes that we have very recently started to exploit. That also leads directly to Ms. Combs's criticism about GM foods. She is right in insisting that presentations regarding the benefits of GM foods need to be balanced with their possible side-effects, but she also seems to fall prey to a more basic and flawed belief that GM foods are fundamentally a new, man-made creature in the list of biological species. They are not. Nature has been trying out GM foods for millennia.

As a biotechnology scientist myself I was particularly distressed by the response, since I happen to study a particular form of biotechnology in my research that would not follow Ms. Combs's definition. My company uses the specific base pairing properties of DNA - one of its most amazing and fundamental features - to make drugs for cancer, psoriasis and other disorders. My research which has been pioneered by an academic lab has nothing to do with GM foods, I don't work for Big Pharma, and I am not manipulating anyone's genes. I am using entirely natural processes to help me find drugs for diseases which very palpably affect millions of people every year. In my case, nature is the entity that's allowing me to do biotechnology and I find this fact fascinating. I find it hard to see how Ms. Combs could be against the kind of research I am doing, but the major point as pointed out David is that biotech goes far beyond GM and into many areas of science like detergent manufacture, biodefense and health supplements. What I am doing is just one of its myriad manifestations.

Unfortunately, this kind of valid debate about the definition or pros and cons of biotechnology is undermined by Ms. Combs insinuations about the penalties paid by Big Pharma and their unethical practices. Ms. Combs seems to erect a classic straw man and points out the huge fines paid by Monsanto, Pfizer, Bayer and others for false labeling, bribes to doctors and other transgressions - and nobody's supporting these practices - but what on earth do these fines have to do with the scientific evidence for or against GM foods? This listing of pharmaceutical evils is completely tangential to the science of GM foods and smells suspiciously of guilt-by-association. In her emphasis on including equal time for critics of biotech, she also suggests the name of people who seem to be bonafide supporters of the vaccine-autism link. It's one thing to have a balanced debate, quite another to give voice to critics whose arguments are chiefly fueled by emotion and incomplete evidence rather than reason. 

Finally, she is not impressed by the inclusion of academic presentations in the museum's events because she says that universities "receive significant funds from industry to support biotechnology research". That part is especially amusing since the biotechnology revolution was launched almost entirely by academic scientists like Fred Sanger, Paul Berg and Hamilton Smith as an offshoot of basic, curiosity-driven research about the natural world. And a moment's research would have convinced Ms. Combs that the scientific underpinnings of biotechnology have been almost entirely taxpayer funded...by taxpayers like herself.

I am not singling out Ms. Combs for her objections and I do respect her general support of the museum and her regular visits to it. But she seems to have started a minor campaign on her blog to discredit the museum's attempts to help the public to understand biotechnology. This is disappointing. David has responded in as much detail as possible to her emails, and anyone who knows him would be aware of the tremendous and admirable work he has done for years in support of the public understanding of science; it would sound ludicrous for those of us who know his work to hear the allegation that he does not appreciate the merits of a balanced scientific debate. 

What I would like to say to Ms. Combs is this; biotechnology has been with us since the origins of life, and recombinant DNA is only the latest incarnation of a process that started billions of years ago. To say that biotechnology is at odds with the natural world is to completely ignore the biotechnology that nature has always practiced and to proclaim that man is not a part of nature. But more importantly, whether you like it or not, biotechnology and genomics are poised to enter the public discourse in ways that we can't even imagine yet. Genomic medicine is on the threshold of impacting public health and policy in a big way, and it promises to create new drugs for major disease and new diagnostics that will allow us to detect diseases like cancer earlier. Like other scientific developments, discoveries in the next few decades will make us confront novel social and moral issues. It's all biotechnology, knowledge that's based on the fundamental workings of the biological universe, and it will be upon us very soon. And as recent progress demonstrates, it will inevitably be developed by both academia and industry. 

Would it have unintended consequences? Of course it would, like every other technology. But that is precisely the reason to publicize it as widely as possible, to make sure that the public is aware of the most cutting-edge research in the field. If you are suspicious of biotechnology, then you should be the first one to make sure that museums all around the country organize biotechnology days to discuss, debate and present. About the worst thing you can do about a topic which you don't trust is to advocate that it should not be discussed in a public forum.

When did moralising gods emerge?

September 10, 2012, 3:06 pm

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Looking at societies cross the world, you're stuck by the enormous variety of mystical beliefs out there - to the point where, infamously, even trying to come up with a definition of religion that everyone agrees on is pretty much impossible.

Yet there are common themes. Many societies do believe in some kind of chief god, and many of those believe that this god is some kind of parent or leader figure - one that takes an interest in his people, and punishes bad behaviour.

So the question is, do societies vary in some systematic way? Is it, as some people have claimed, that complex societies lead to the development of moralising gods?

Hervey Peoples and Frank Marlowe, at the University of Cambridge, have set out to test this statistically - no mean feat.

They used a something called the "Standard Cross-Cultural Sample", which was created in 1980 and which provides an unbiased sample of the worlds societies - representing every region, language family, and cultural area. They're predominantly pre-industrial.

They categorised each society according to whether they believed in an active High God (a single, all-powerful creator active in human affairs and supportive of human morality), a High God that is inactive or remote, or no belief in any High God.

Belief in an active High God was significantly greater in societies that were larger, more stratified (i.e. less equality) and societies engaged in intensive agriculture. Now, all of these things go together - you need intensive agriculture to support a large society, and large agricultural societies have the surpluses and politics that facilitate stratification.

All of this fits nicely with the hypothesis that moralising gods are an invention of large, structured societies. But what about pastoralists?

The thing about pastoralists is that they are vulnerable to the environment - herds could scatter or be devastated by drought. Lifestyles based on foraging and low-intensity agriculture are vulnerable to the same things, although it it easier for such groups to relocate.

Even more important, I think, is that pastoralists have a source of transportable wealth - their cattle. That means that they are vulnerable to attack from other pastoralists (and, indeed, can gain from attacking other groups). And that in turn means that their groups must be cohesive and well-organised to survive.

In other words, they have a very great incentive to punish free-riders and cheats. If a forager goes off the rails, no-one really suffers except him. For a pastoralist group, however, sticking together is all important.

At first blush, all of this is in line with other research that links the emergence of complex societies to the invention of moralising gods. However, that's not quite the case.

The previous research showed that 'world religions' are linked to altruism towards anonymous strangers. In practice, that means breaking down inter-group barriers.

This new research seems to show that moralising powerful gods are linked to stronger group cohesion.

Now, those two results are actually in conflict. But they do reinforce the fact that religious beliefs do not act in a straightforward way.

It seems likely that their effects are quite context dependent - a conclusion, of course, that's borne out by a lot of other research!

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Peoples HC, & Marlowe FW (2012). Subsistence and the evolution of religion. Human nature (Hawthorne, N.Y.), 23 (3), 253-69 PMID: 22837060

This article by Tom Rees was first published on Epiphenom. It is licensed under Creative Commons.

Multilayer interference iridescence or shiny!

September 11, 2012, 4:11 am

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Wow!  Those are some shiny fruits!  Quite a few shiny, colorful things actually lack pigments and their apparent color is due to iridescence, the way then bend and reflect light.  Supposedly these fruits (Pollia condenstata) are the shiniest of all such biological materials.  Now of course plants make attractive fruits to lure seed dispersers, in this case most likely birds, and the birds seek such displays to get a nutritive reward and everyone goes away happy.  However these really, really attractive fruits are deceptive providing no reward at all, so any bird that eats these fruits disperses the seeds and considering some effort was involved bascially gets cheated.  This works because such fruits mimic a similar rewarding plant, in this case possibly a species of Psychotria (right) that has bright blue rewarding fruits.  You don't get fruits colored like this in the temperate zone.

What would surprise you?

September 11, 2012, 5:58 am

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How often do you go "shiiiiiiiiiiit, so that's how it is!?!" What would really shock you? "FUCK! I never thought that would be the case..."

Probably not that often. But those moments are so great, and as a scientist, I'd say we sort of live for them.

I was thinking about this in terms of working in evolution. What would be a really big moment that I could say advanced my understanding of how living things evolve? Most papers I read anymore are incremental advances. Actually, all of them are. When I first started learning about evolution, I was in near-constant shock/revelational mode. It was pure delight to discover what we know about evolution. But now that I know most of it, nothing much surprises me anymore. Which is a shame.

So it got me thinking about where I could search for such moments. Something akin to learning that the Earth is not the center of the universe, or that everything is made of atoms. Or that there were dinosaurs, and that we evolved. The rest seems to be details. Important details, but not revelational.

I do various things in evolution, but my overarching focus is the origin of evolutionary novelty (but I like speciation, too). How do new things come into existence? The first eyes, first brain, first blood. People will then say that those things are derived from previous structures. Eyes from simpler photoreceptors, brains from simple nervous systems, blood cells from other cells. And these systems derived from yet simpler cells, but along the way, something new happened at least at some points that enabled these new systems/structures to form. New proteins were added to the mix, encoded by new genes. So where did these new genes come from? Well, they were derived from other genes, by duplication and neofunctionalization: a new gene is a copy and a refashioning of an old gene. So far so good. Then where did the first gene come from? Sorry, I don't work on origin-of-life stuff.

Is that it? Not quite. There are some major transitions in evolution to be explained. Unicellularity to multicellularity, cellular differentiation, asexual to sexual reproduction, and stuff like that.

But then, I am still left with this feeling at times that there is really nothing that would really upset my world-view (of evolution) much anymore. Still nothing revelational in sight. I hope I'm wrong.

In serach of the ETs with the distributed computing

September 11, 2012, 11:47 am

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published by @ulaulaman about #SETI #astronomy #distributed_computing

One of the most intriguing question of the mankind is if we are alone in the universe, if in a some little part of the cosmos it exists intelligent life. Starting from this quest, a lot of science fiction writers gave us some good sci fi novels. For example The Voyage of the Space Beagle by Alfred Elton van Vogt, inspired by the journey of Charles Darwin on the Beagle. In this novel, during the search of alien life, the spaceship Argus found not only vestiges of vanished civilizations, but also interacted with real aliens.
But the research for other cosmic intelligences beyond the limits of our Solar System has also fascinated, for many reasons, the scientists themselves. It is famous the dinner (or maybe it was a lunch) where Enrico Fermi explained his equally famous paradox from which Frank Drake drew inspiration for his famous equation. And Drake became one of the founders of the SETI project⁽⁵⁾, Search for extraterrestrial intelligence, a project that involved a lot of researchers around the world. This kind of research, which may seem absurd as to get the ghostbuster, is based, first, on the assumption that

(...) an alien civilization wishing to make contact with other races would broadcast a signal that is easily detectable and easily distinguishable from natural sources of radio emission. One way to achieve these goals is to send a narrowband signal. By concentrating the signal power in a very narrow frequency band, the signal will stand out among the natural broadband sources of noise.⁽¹⁾

At the beginning SETI focused its activity on listening to radio signals from space. The type of signal that should be detected presents some problems: first, the frequency stability, caused by the acceleration of the transmitter and receiver⁽¹⁾, which for example they are influenced by the speed of rotation (around the axis, around the star). Solving this problem is not in principle impossible: certainly we know very well the properties of our planet in order to perform this kind of correction, but it is not the same thing for an alien planet. In this last case, the story is certainly very different, especially if the planet is completely unknown

An alien civilization narrowly beaming signals at the earth could correct the outgoing signal for the transmitter's motions, but a civilization transmitting an omnidirectional beacon could not make such an adjustment.⁽¹⁾

One way to remedy is to use the Doppler effect⁽¹⁾, but this means making a lot of calculations, and answering to a lot of questions about the characteristics of the signal itself:

at what frequency will it be transmitted? What is its bandwidth? Will it be pulsed? If so at what period? Fully investigating a wide range of these parameters requires proportionally larger computing power.⁽¹⁾

And we don't forget that we have to understand if the detected signal with a presumed extraterrestrial origin is not, in reality, of cosmic origin (i.e. produced by a star or a galaxy or some other not artificial object traveling in space).
All these calculations are extremely complex and require a much greater computing power than supercomputers. It is for this reason that in 1995, David Gedye, a project manager at Starwave Corp., proposed to use the distributed computing in order to create a virtual supercomputer: the birth SETI@home⁽²⁾.
The first step in the construction of the project is to find a good radio telescope. The ideal candidate was the telescope in Arecibo, Puerto Rico, administrated by Cornell University and the National Science Foundation⁽²⁾. This choice, however, had a small problem: the time of use. SETI could not have the exclusive use of the telescope, because it was already being used for various astronomical and meteorological researches. The problem was solved in 1997 by Berkeley's SERENDIP project, who developed a technique to use a second antenna⁽²⁾.

Now the SETI@home client could be distributed on-line:

The SETI@home client program, written in C++, consists of a platform-independent framework for distributed computing (6,423 lines of code), components with platform-specific implementations (such as the graphics library, with 2,058 lines in the Unix version), SETI-specific data analysis code (6,572 lines), and SETI-specific graphics code (2,247 lines).
The client has been ported to 175 different platforms. The GNU tools, including gcc and autoconf, greatly facilitate this task. The Macintosh, SPARC/Solaris, and Windows versions are all maintained directly by SETI researchers; all other porting is done by volunteers.
The client can run as a background process as either a GUI application or as a screensaver. To support these different modes on multiple platforms, the system employs an architecture in which one thread handles communication and data processing, a second thread handles GUI interactions, and a third thread (perhaps in a separate address space) renders graphics based on a shared-memory data structure.⁽²⁾

Today, thanks to Kepler, the SETI's search could be considerably improved, not only using new devices for sky observation, but also simplifying calculations, for example obtaining the corrections to radio signals from Kepler's data. An examnple of this approach was proposed by Rampadarath, Morgan, Tingay and Trott that described the first SETI experiment with the Very Long Baseline Interferometry (VLBI) using data about Gliese 581⁽³⁾.
VLB allows,

(...) by the combination (via a correlator) of signals from multiple radio telescopes, the emulation of a telescope the size of the maximum telescope separation, which is generally hundreds to thousands of kilometres.⁽³⁾

Although they not found any radio signal of intelligent life, as expected, the paper⁽³⁾ aims to show that the VLB can be used for the SETI project.
All of this, however, including the possible use of the Square Kilometre Array, is part of the so-called passive SETI: in other words, listening for signals from space and searching for possible signals from extraterrestrial intelligence. In recent years there has also discussed to the so-called active SETI (and partly sending music, for example, or images with satellites is part of this second type of project), or sending radio signals in space, only to respond to a possible alien message.

The main objection against the idea of transmitting messages from Earth always was, and still is, that, while passive SETI is surely not dangerous for us, active SETI may be, since ETs could be malevolent. The first to raise the problem was Martin Ryle in 1967, when the first pulsar was discovered and its regular pulsating signal was believed for a while an alien message. More recently, in 2010, also Stephen Hawking issued a similar warning, then followed by John Billingham and James Benford. But people sharing this concern are surely many more than two couple of distinguished scientists.⁽⁴⁾

We can replicate in many ways to these concerns. The strongest is certainly remember that we are sending messages, however unintentional, in space, thanks to satellite broadcasts. This observation has indeed shifted the focus towards an intentional message, such that it could contain information on humans.
Another quite famous reply was signed by Iosif Shklovsky Samuilovich

What would happened if all the civilizations of the galaxy is healing it only to receive, and not to send interstellar radio signals?⁽⁶⁾

Of course, given the set of doubts regarding an active SETI, we must determine whether the possible dangers of this project are greater or less than their benefits.

Paolo Musso⁽⁴⁾, which certainly does not exclude the possibility of encountering a hostile alien civilization, defines four types of hostile reactions to our message: a dangerous discovery, a dangerous signal; malicious content; a dangerous reaction.
A dangerous discovery implies a cultural shock, or the arrival of a series of disruptive informations to our culture, but, first of all, our culture is not so unique, in particular outside the scientific domain, where instead scientists can take a regular synthesis in each areas.
The dangerous signal is definitely a curious situation: it suggests the possibility that the alien signal that follows as a response contains a viral code, but this implies a thorough knowledge of our operating systems.
The malicious content is not unlike the dangerous discovery, but it focuses not so much on what might be called a war of civilizations, but worries about the literal meaning of the communication, which could destabilize our society. According to Musso, however, the active SETI could reduce or even remove this risk.
The dangerous reaction is instead the good old alien invasion. This is probably the most imaginative fear, because there are many variables to consider in this situation: for example, the Fermi paradox, or, more importantly, the possibility of interstellar travels, not only for our planet, but also for the extraterrestrial people.
This is probably a good time to take seriously the idea of ​​an active SETI, after a series of experiments already made in the past, such as the Arecibo message, but of course, looking at what has been done, the SETI project is definitely, including SETI@home, one of the best ideas we've ever had.

The only radio contact with a superior civilization deeply and radically changed our lives.⁽⁶⁾

NASA's Commission on the study of long-distance, 1960

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(1) Eric Korpela, Dan Werthimer, David Anderson, Jeff Cobb, Matt Lebofsky (2001). SETI@home-massively distributed computing for SETI Computing in Science & Engineering, 3 (1), 78-83 DOI: 10.1109/5992.895191
(2) David P. Anderson, Jeff Cobb, Eric Korpela, Matt Lebofsky, Dan Werthimer (2002). SETI@home: an experiment in public-resource computing Communications of the ACM, 45 (11), 56-61 DOI: 10.1145/581571.581573
(3) H. Rampadarath, J. S. Morgan, S. J. Tingay, C. M. Trott (2012). The first very long baseline interferometric SETI experiment The Astronomical Journal, 144 (2) DOI: 10.1088/0004-6256/144/2/38
(4) Paolo Musso (2012). The problem of active SETI: An overview Acta Astronautica, 78, 43-54 DOI: 10.1016/j.actaastro.2011.12.019
(5) The paper that we could consider the first step of the SETI project was:
Giuseppe Cocconi, Philip Morrison (1959). Searching for Interstellar Communications Nature, 184 (4690), 844-846 DOI: 10.1038/184844a0
tending with these inspired words:

the probability of success is difficult to estimate; but if we never search the chance of success is zero

You can read a scanned version of the paper on coseti.org (images) and on iaragroup.org (pdf) or an incomplete html version on bigear.org
(6) Quotes are extracted from the italian versions of The listeners by James Gunn. I didn't find the original quotations so I translate them from italian.

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Stabbing kids with needles: malpractice, or just a very bad idea?

September 12, 2012, 5:39 am

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Yesterday's Washington Post featured a terribly researched article titled "Kids and needles is sometimes a good match: Acupuncture can help with pain."

Imagine: a one-year-old boy arrives at an emergency room in New York at 3 a.m. with an asthma attack.  He is slow to respond to a nebulizer treatment.  Enter Dr. Stephen Cowan, who decides to use acupuncture.  That's right, he stabs a one-year-old baby with multiple needles to treat asthma.  According to Dr. Cowan, the boy "reacted calmly" and improved.  The article doesn't provide any more details.

This is appalling.  Sticking needles into a baby has never been shown to have any effectiveness at treating asthma, and we do have treatments that work.  In all likelihood, the nebulizer did work, in the case that Dr. Cowan related to the reporter, but Dr. Cowan mistakenly credits his acupuncture treatment.

Stephen Cowan is a aggressively self-promoting doctor, who claims on his website that he can treat both autism and ADHD with acupuncture and other forms of Chinese Medicine.  He also describes how he convinces children to let him stick needles into them.  He states his belief in mystical "vital energy" or qi, one of the wacky pseudoscientific notions at the core of acupuncture beliefs.  His claims are little more than a modern, mystical version of the claims made by 19th-century snake oil salesman.

The Washington Post story also revealed that Children's National Medical Center in Washington, D.C. recently treated a 17-year-old girl with pancreatitis by stabbing needles into her stomach and other places.  There is no evidence that this works, but the girl's doctor believes it does.  The girl reportedly wasn't harmed, fortunately.

The doctor at Children's Hospital, Jennifer Anderson, is an anesthesiologist who is also an acupuncturist.  In the story, she said "I often treat patients with chronic issues" with acupuncture.  This is frightening: a doctor at a major medical center is telling children, most of whom are too young to even think of questioning the wisdom of a doctor, that sticking them with needles will help their pain.  Dr. Anderson admitted that "she often does two to three treatments a week at first on a child."  So she admits to stabbing many sharp needles into children and telling them that the treatments will help their pain.  She argues that the children report that this is "helpful."

This is perilously close to child abuse.  Children want to please adults, and if an adult tells them something is good for them, especially if an authority figure tells them, they are extremely unlikely to disagree. They'll just swallow the medicine, or endure the treatment, and then tell the adult what she wants to hear.  Dr. Anderson seems unaware of this.  And Children's National Medical Center, a generally outstanding hospital, should be seriously concerned that one of its anesthesiologists is practicing quack medicine on children, who are perhaps the most vulnerable of all patients.

Let's be clear: acupuncture is based on nonsense.  Scientists have gone to great pains to study it, and the conclusion can be stated simply: acupuncture does not work.  (And yes, I know about the latest meta-analysis claiming that acupuncture works.  Dr. Steven Novella has already explained why that analysis is "completely useless.")  If acupuncture were a drug being tested by a pharmaceutical company, it would have been abandoned long ago.  Its proponents are no better than any big pharma company that pushes a drug that it knows to be ineffective.

Acupuncture is worse than ineffective: because it's an invasive procedure, there is a small but real risk of harm.  As I wrote last year in The Atlantic, acupuncturist sometimes cause infections, which can lead to rare but serious complications.  Acupuncturists protest (often) that they use sterile needles, but this very protest reveals their ignorance: most infections are caused by bacteria already present on the skin, which enter through the puncture wound.

Parents: don't let an acupuncturist stick needles into your kids.  Read the science first, and avoid - no, run screaming from - any practitioner who claims that he can adjust the "qi" in your child.

Strange thing to do - justify your own replacement

September 12, 2012, 9:35 am

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My colleagues, a few of my colleagues at least, have noticed that TPPs retirement from academic servitude in a couple of years will leave a pretty large gap in organismal botany; it'd be gutted actually.  So with positions so hard to come by, replacements so long delayed, justifications must be put into the queue with considerable lead time.  Thus TPP finds himself writing a justification for his own position, and this is proving a very strange thing to do.  A justification needs to be strong, but then it begins to sound like arguing for your own significance, your own importance, your indispensability.  And this list of what you actually do do does begin to look like a considerable undertaking should it be suddenly handed to another person in toto, and someone needs to do it all, although it was indeed acquired gradually, or in fits and starts over the years.  Let's see, this position requires someone with a broad and encyclopedic knowledge of plants.  Check. This person should contribute to the scholarship of the school, perhaps with a distinguished publication record extending over years (37 years and counting).  This person should be an excellent teacher.  Well, duh, and maybe receive both the university's and the botanical society's highest honors and awards for teaching.  Check.  This person should play well with others.  Hmm, well, ...  OK, maybe that one can slide.  This person should be capable of making excellent, award-winning chili, and not some slop with beans and corn, or even worse, macaroni, in it.  Whoa!  Maybe this is starting to sound too much like the current occupant even leaving out the part about being a fashion icon in biology. 

The invisible universe

September 12, 2012, 9:51 am

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posted by @ulaulaman about #x-ray #astronomy #riccardogiacconi #universe #exhibition #milano

Today will be open in Milano an exhibition about the x-ray astronomy in order to celebrate the discover of the first cosmic x-ray source in 1962. And today I try to resume the story of this research.
The beginning of this branch of the astronomy is in 1946 when Bruno Rossi, who has worked with Enrico Fermi during Manhattan project, started to deal with physics of cosmic rays while teaching at MIT about X-ray. In 1958, with the birth of the American Science & Enginnering (AS&E), Bruno Rossi joined it as chairman of the board of directors and scientific advisor and a year later he called to work even Riccardo Giacconi. One of the first experimental successes includes the launch of the first rocket equipped with detectors for X-rays in 1962. The team of this project as well as Giacconi included, Herb Gursky, Frank Paolini, and Bruno Rossi. With this mission, it was reported the first cosmic X-ray source outside the sun, Scorpius X-1 in the constellation Scorpius.^{(1, 2)}
The uniqueness of the observations of Scorpius X-1 is due mainly to its properties. In fact, while the X-radiation from the sun has an intensity that is approximately 10^-6 times than visible light, Scorpius X-1 has a X-brightness that is 10³ times higher than its same brightness in the visible light. It was subsequently discovered that its intrinsic brightness is 10³ times that of the Sun!⁽¹⁾
There was therefore in front of the discovery of new celestial objects, which had X-rays produced in different physical processes compared to the processes made in the laboratories of the Earth, since their efficiency (99.9%) was unmatched!⁽¹⁾
1960s were, therefore, rich for X-rockets into space, but for the very first X-satellite was launched only in 1970 thanks to a new group leaded by Giacconi⁽¹⁾:
The X-ray astronomy achieved great success with the launch of the first satellite dedicated to X-rays, Uhuru, launched in 1970, with it performed an initial mapping of the X-ray sources in space. It was discovered that the universe is full of objects that emit X-rays, from the black holes to the pulsars, to the binary stars. In fact after this mission, the X-ray astronomy assumes an important role between the international scientific community. It soon became clear that, in order to better understand the secrets of the sky, instead of simply detecting the X-rays, it would be useful to make observations with a telescope sensitive to X-rays. The development of this telescope began with the entry into AS&E team of Giuseppe Vaiana, who leaded the program about the solar X-ray astronomy and the construction of the first telescope. In 1973, Skylab was launched, the U.S. space laboratory directed by Vaiana, that, in addition to various scientific experiments, carried on the observation of the Sun and the corona in X-rays. In 1978 it was sent into orbit the Einstein Observatory, the first X-ray space telescope. The important discoveries of the ROSAT and Chandra followed.⁽²⁾
One of the successive results of astronomy X, always signed Giacconi, in this case with Ethan Schreier, was the discovery of an X-ray source around Cen X-3⁽¹⁾.

Very important discoveries of Uhuru, however, were mainly those concerning the existence of neutron stars and binary systems consisting of a visible star and an unseen companion, a black hole⁽¹⁾!

Illustration of Hercules Hercules X-1 by R. Plourde

Illustration of Cygnus X-1 by L. Cohen

An equally important observation with strong implications for cosmology, however, was the recognition of an intergalattic emission between clusters of galaxies:

This emission is not simply due to the sum of the emission from individual galaxies, but originates in a thin gas which pervades the space between galaxies. This gas was heated in the past during the gravitational contraction of the cluster to a temperature of millions of degrees and contains as much mass as that in the galaxies themselves.⁽¹⁾

In the last 50 years the X-ray astronomy has opened the door to a universe otherwise invisible with the usual tools, those that work with the visible light. Therefore its importance has been and continues to be crucial in astronomical research:

The reason is that this radiation reveals the existence of astrophysical processes where matter has been heated to temperatures of millions of degrees or in which particles have been accelerated to relativistic energies. The x-ray photons are particularly suited to study these processes because they are numerous, because they penetrate cosmological distances, and because they can be focused by special telescopes. This last property significantly distinguishes x-ray from -ray astronomy. However, in a more fundamental way, high energy astronomy has great importance in the study of the Universe because high energy phenomena play a crucial role in the dynamics of the Universe.⁽¹⁾

The Sun

M31

Crab Nebula

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The exhibition was a combination between scientific posters, models of satellites, and some artistic interpretations of the Universe given by the students of the local Academy of Fine Arts. In the following slideshow I present a little preview of these operas:

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(1) Giacconi, R. (2003). Nobel Lecture: The dawn of x-ray astronomy, Reviews of Modern Physics, 75 (3) 1010. DOI: 10.1103/RevModPhys.75.995 (pdf)
(2) Translation from it.wiki

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Riccardo Giacconi winned Nobel Prize in Physics in 2002

for pioneering contributions to astrophysics, which have led to the discovery of cosmic X-ray sources

Sex Makes Everything Less Disgusting

September 13, 2012, 3:07 am

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Our biological drive to do it conflicts pretty directly with our biological drive not to get involved with other people's bodily fluids. How do we ignore the obvious grossness of sex for long enough to propagate the species? Maybe, researchers say, by turning off our disgust reflex whenever we get turned on.

Earlier studies have asked this question in a variety of ways. For example, by asking men to "self-stimulate" and then quizzing them on what sex acts or partners they'd be open to. Or by showing men erotic slideshows and then having them stick their hands into cold pea soup or buckets of condoms. Psychology researchers Charmaine Borg and Peter J. de Jong at the University of Groningen in the Netherlands—perhaps feeling less pessimistic than others about their ability to arouse a group of female subjects—decided to study the question in women instead.

The researchers gathered 90 female university students. Rather than just answering questions about distasteful things, these subjects were going to be challenged with some actual gross tasks to see how many they would do.

But first the researchers had to turn their subjects on. Well, a third of them, anyway. One group of women watched a film described as "female friendly erotica." A second group watched a movie that was meant to be non-sexually arousing—that is, heart-pounding but not steamy. These women saw footage of sky diving and mountain climbing. The third group saw a movie about a train ride, meant to not cause any feelings at all. The movies had been previously tested with a separate group to make sure they elicited the right emotions.

As the women watched their steamy, exciting, or boring movies, they were periodically interrupted by an experimenter who showed up and gave them disgusting tasks to do. There were a total of 16 challenges, ranging from picking up apparently soiled toilet paper to sticking a needle in a cow eye. The subjects didn't have to go through with any task they didn't want to, but they did have to rate how disgusting they found each one.

Out of the 16 gross-out tasks, 5 were classified as sex-related. These included touching some "used" condoms, handling "used" women's underwear, and reading aloud a sexual phrase about, um, a dog. (The researchers made liberal use of Halloween-style tools and props, including blood-colored ink, fake feces, coconut milk in the underwear, and one plastic bug. And one real worm, which they rereleased outside when the study was over.)

The groups who watched the train movie and the sky-diving movie didn't differ in their willingness to do the gross tasks, or in how disgusting they rated those tasks. But the women who watched the erotic film rated the sex-related tasks as significantly less disgusting than the other groups. They seemed to find the rest of the tasks less gross too, though the result wasn't quite significant. And overall, the erotica group completed more challenges of both kinds. The turned-on subjects completed 85% of the non-sexy tasks, for example, compared to about 66% in the other two groups.

Charmaine Borg says she was surprised to see that sexual arousal, but not general arousal (the sky-diving kind), "makes us approach stimuli that are in general so disgusting." The way subjects perceived disgusting things seemed to change when they were sexually aroused.

The study focused on a small group of young, heterosexual, dysfunction-free women. It was limited to one method of turning those subjects on (the erotic film) and an odd handful of gross, somewhat sex-related tasks. And the study relied on subjects' own ratings of their arousal and repulsion. But if it proves to be generally true that sexual arousal squelches disgust, it would explain how we manage to reproduce despite our usual instincts—which presumably evolved to keep us safe from disease-carrying stuff.

Borg is more interested, though, in women whose bodies don't let them have sex. She wonders if sexual disorders such as dyspareunia (painful intercourse) or vaginismus (involuntary clenching of the muscles around the vagina, making intercourse difficult or impossible) are rooted in problems overcoming disgust.

"Studies from our lab with women afflicted with vaginismus have shown that they experience disgust responses towards erotic stimulation," Borg says. "Sex-related stimuli appeared to elicit disgust rather than arousal." Since our usual response to disgust is to keep far away from what's causing it, she says the problem could be self-perpetuating as women start avoiding sex altogether.

Borg says her results so far are "very exciting." By carrying on her experiments in the condom-filled, fake-blood-soaked laboratory, she helps to hope women overcome their difficulties and get down to whatever business they want.


Charmaine Borg, & Peter J. de Jong (2012). Feelings of Disgust and Disgust-Induced Avoidance Weaken following Induced Sexual Arousal in Women. PLOS ONE : 10.1371/journal.pone.0044111

Image: Feggy Art/Flickr (Related note: I cannot BELIEVE I lived this long without knowing that England has both a name for making horrible faces—"gurning"—and competitions for it.)

Cost of chocolate

September 13, 2012, 4:33 am

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The time-honored, although not honorable, practice is to get someone hooked on an addictive substance by basically giving it to them free, and then once the addiction hook is set, reel them in and charge them a fortune to maintain their habit or die trying.  In general chocolate doesn't seem to fit this scenario, but like its close cousin caffeine, theobromine is an addictive stimulant.  A local chocolate maker has a semi-sweet dark chocolate containing finely ground coffee beans.  A couple of pieces of this delectable stuff gives you a real buzz, and you wonder if there should be age restrictions for buying it!  At another level, such things as chocolate come from crops in distant places, foreign countries with tropical climates, and chocolate is just taken for granted along with its affordability, so what would you pay to insure that cacao (image - cacao tree with ripe fruit) as a crop is protected and sustainable?  Well, there is a protection strategy and a price tag (visiting this link will be a good time to try out your scratch and sniff monitor).  On a world-wide basis $2 million annually is probably not too much, but you know, a couple of million here, a couple of million there, multiplied by all those other commodities people would still like to have and pretty soon you're talking real money.  Unfortunately the human race has borrowed against the future using natural resources without really paying the price for their conservation, maintenance, and sustainability.  This cost, these costs, are now going to come home to roost over the next few decades.  The free lunch is over, and things like chocolate may become pricier, a luxury.  Pay up, or go cold turkey.  HT to Agricultural Biodiversity.