For the first time ever, scientists watch an atom’s electrons moving in real time

An international team of scientists has used ultrashort flashes of laser light to directly observe the movement of an atom's outer electrons for the first time. Through a process called attosecond absorption spectroscopy, researchers were able to time the oscillations between simultaneously produced quantum states of valence electrons with great precision. These oscillations drive electron motion.

Reporter Mary Carmichael, will she do it? Newsweek and DTC Genomics!


" I don't even know if that was a hammer that got dropped on their heads. More like a piano."
-Anon Quote re: DTCG and Congressional hearings....

When Ms. Carmichael approached me to answer a burning question for her. She got an answer alright, more like a diatribe and then and answer.

In case you didn't know, Mary is a writer for Newsweek and is thinking about doing a DTC genetic test kit. In fact, she bought the kit and it is staring her in the face. FYI, she's not in New York, where such activity is illegal, she is in Boston, where it is encouraged......

She is taking opinions from just about everyone in the biz. And, yes, she has a comments section for all those Yahoos who feel left out.......

My recap here is what Newsweek wouldn't put in their print, but as you know.....I am more than happy to put here for my readers enjoyment......

Hi Mary,
You think you are set and ready to get, DTCG'd. Just hold on a second. I think you need to really think about what you can and can't learn from this sort of testing. Some say nothing, others say these little babies hold the secrets that the government is trying to keep from you, other say Google's overlords are plotting to steal your children's DNA.

I want to know, have you thought about it? What can you and what can't you learn? Since I have seen probably more patients with these types of tests than just about any clinician out there, I can tell you what the patients ask and what I tell them.

1. You will not learn what you will die from.
Yes, this is true. As a physician who has counseled and seen patients who have brought me their 23andMe, et.al., one thing is clear, patients ask about what this means they may die from.
This test won't tell you that, in fact most tests won't tell you that, whether ordered via Amazon or through your doctor. This test may show some scientifically linked risks for disease, but again, they won't tell you what you are going to die from.

As an aside, You will die from something. Everyone dies. Even those transhumanist singularity punks die. No amount of knock off stem cell clinics will help with that one. Even the G-Damn Buddha dies. In fact someone off'd him with rotten food....

2. You will not learn what diet is right for you.
Again, you are getting DTCG'd. But if you were getting some of the Nutrigenomics tests I would tell you the same thing, There is no magic diet currently based on 23andMe data or any other genetic data. We do know some people may benefit from some types of diets to lower cholesterol and lose weight, but the science to accurately predict genes and diet is not ready to bring to market, no matter what Proctor and Gamble tell you....

Second aside, Isn't funny how the GAO bashed these nutrigenomics companies in 2006 and they are still out there slinging there proton pills. Goes to show how much force the FDA or any other organization has to control commerce......I wonder what happens to the first batch who refuse to buy health insurance.....You can buy things that give you cancer or an erection, why not DTC tests? Properly regulated of course......

3. You will not learn if you are of the lost tribes of Israel.
True, your hot little hand will get a hold of a J Haplogroup analysis, but even the ancestry experts will tell you, this is a small window into heritage. Only 50% of the Cohanim have the Cohen Modal Haplotype. Is it a start? Yes, maybe a hint. But no SNP test offered by 23andMe will rule that out or in as J.E. Ekins et al stated. It requires extended STR testing.

Ok, my buddy, who shall remain nameless as he is at Camp in PA for his kids right now had a patient come to him adamant she was of the royal lineage of the Czar (Russia). She paid a bundle to have her mito DNA checked.....Guess what? She wasn't........

P.T. Barnum once said
"You can fool some of the people all of the time; you can fool all of the people some of the time, but you can never fool all of the people all of the time." But what he forgot to say is, some people are fools all of the time......

What will you learn?

Good Question Mary.

For all intents and purposes, the lab used by 23andMe is CLIA certified, which means its results for positive carrier tests are just as valid as those ordered by a doctor (in some instances). But remember, this test is better at ruling in than ruling out as it often misses carriers in genes such as CFTR for cystic fibrosis. So if they say you are NOT a carrier, don't trust the results. And if it say you are you can always double check with a doctor.

Mary, this is a medical test. And should be held to the same standards as other medical tests.

2. You may learn you carry a rare mutation putting you at significant increased risk of breast or ovarian cancer.
23andMe tests for 3 mutations in BRCA1 and BRCA2 which could put your risk of breast cancer as high as 85% over your life. Are you ready for what to do with those results if you had them?

Mary, this is a medical tests and I advise you to have some clinician back up when reviewing these results. Even if they are negative, that doesn't rule out a BRCA mutation. This test is confusing and should be regulated as a medical test.

3. You may learn you cannot metabolize medications properly.
23andMe tests for medication metabolism using the same genetic markers as found in other medical tests. Again, they use a CLIA lab, so you may be able to trust their poor metabolizer status. But are you taking Plavix Mary? Tamoxifen? Does it really matter for you now? Or ever?

The whole thing about Pharmacogenomovigilence is that ideally everyone would have a panel of these useful genotypes before dosing medications. But based on the soon to be available rapid turn around time here, we could do these in some labs overnight. The big question here is, is the DTCG test enough of a test to trust clinically?

I am not so certain as they miss certain SNPs and rare mutations that are important.
The Sherpa Says: Ok, Mary. You want it, you got. If you buy a test, you've got a guy just a few Acela Stops away who can help sort out the madness for you.......Clinically of course.....That is, if I haven't convinced you otherwise.....

Epic Carnivorous Plant Container Bog For Sale, This Thursday, August 5th, at Lord Whimsy's "Nature as Miniaturist" Lecture at Observatory



This Thursday August 5th at Observatory, Lord Whimsy, as part of his lecture "Nature as Miniaturist: An Illustrated Survey of the Bogs of Southern New Jersey" will be displaying the epic carnivorous plant-filled container bog seen above. Said bog is also, as it turns out, for sale; you can even take it home with you after Thursday's event if so inclined!

Full info follows, as found on Lord Whimsy's website; if you are interested, you can email Whimsy at email [at] lordwhimsy.com.

Mr. Bill Smith was kind enough to lend one of his container bogs (pictured above) for my Observatory talk this Thursday night in Brooklyn. He would like to inform you folks out in the netiverse that he is offering this three year-old bog garden for sale at the very reasonable price of $200--an excellent bargain, since purchasing these mature plants separately would cost considerably more.

The container is hollow resin, and can be left outside year-round without worry of cracking. The plants in the bog include: Purple Pitcher Plant (Sarracenia purpurea 'Jersey Girl'), Yellow Trumpet Pitcher (S. flava), Catesby's S. purpurea x S. flava hybrid pitcher plant (S. x Catesbei), Grass Pink Orchid (Calopogon tuberosus), 'Hamilton' dwarf cranberry, Spade leafed sundew (Drosera intermedia), and Thread leafed sundew (D. filiformis). A marvelous, mature grouping of classic North American bog plants, suitable for rooftop gardens and decks. No fertilizer necessary. Very low maintenance: just keep in full sun with regular waterings. Can be left outside year-round. All plants are cold hardy in zone 6b.

Interested parties may contact me (email [at] lordwhimsy.com) and claim their purchase after my lecture on Thursday evening.

Similar container bogs of all sizes can be had at Rarefind Nursery.

You can find out more about Lord Whimsy's presentation here. You can get directions to Observatory--which is next door to the Morbid Anatomy Library (more on that here)--by clicking here. You can find out more about Observatory here, join our mailing list by clicking here, and join us on Facebook by clicking here.

The Dangers and Pleasures of Curiosity, from Saint Augustine to the Renaissance

Augustine included curiositas in his catalog of vices, identifying it as one of the three forms of lust (concupiscentia) that are the beginning of all sin (lust of the flesh, lust of the eyes, and ambition of the world). The overly curious mind exhibits a “lust to find out and know,” not for any practical purpose but merely for the sake of knowing. Thanks to the “disease of curiosity” people go to watch freaks in circuses and charlatans in the piazzas. Augustine saw no essential difference between such perverse entertainments and the “empty longing and curiosity [that is] dignified by the names of learning and science.”

I just came across a nice meditation on the history of the debate of curiosity as value or vice on the website of Author William Eamon, author of Science and the Secrets of Nature and The Professor of Secrets: Mystery, Medicine, and Alchemy in Renaissance Italy:

The Disease Called Curiosity
Nowadays we think of curiosity as an emotion necessary for the advancement of knowledge, indeed as the well-spring of scientific discovery. It was not always so.

Saint Augustine, in the fourth century, stated the traditional medieval view of curiosity, and it wasn’t favorable. In the Confessions, the Bishop of Hippo made inquisitiveness in general the subject of a vicious polemic, thereby setting the tone for the debate over intellectual curiosity for centuries. Augustine included curiositas in his catalog of vices, identifying it as one of the three forms of lust (concupiscentia) that are the beginning of all sin (lust of the flesh, lust of the eyes, and ambition of the world). The overly curious mind exhibits a “lust to find out and know,” not for any practical purpose but merely for the sake of knowing. Thanks to the “disease of curiosity” people go to watch freaks in circuses and charlatans in the piazzas. Augustine saw no essential difference between such perverse entertainments and the “empty longing and curiosity [that is] dignified by the names of learning and science.”

No difference between gawking at freaks in a sideshow and making investigations in natural philosophy? That’s what the saint said: “From the same motive,” Augustine wrote, “men proceed to investigate the workings of nature, which is beyond our ken—things which it does no good to know and which men only want to know for the sake of knowing.” Augustine’s severe judgment of intellectual curiosity, linking it with the sin of pride, the black arts, and the Fall, became conventional in medieval thought. In the Renaissance, it gave rise to such memorable characters as Doctor Faustus, who bartered his soul to the devil to satisfy his insatiable curiosity and quest for power.

Yet gawking curiosity was the perpetuum mobile of Renaissance science. Early modern curiosity was insatiable, never content with a single experience or object. Whereas Augustine linked curiosity to sensual lust and human depravity, Renaissance natural philosophers saw it as being driven by wonder and the engine of discovery...

...Venice’s maritime empire and its rich craft tradition provided plentiful fuel for wonder and curiosity. The continual contact with exotic commodities, whether herbs from the New World, mechanical toys from Persia, or fake dragons and basilisks, fueled Renaissance curiosity. All that evoked curiosity and wonder became prized objects for collectors, who displayed rare and exotic natural and artifical objects in curiosity cabinets, like peacocks proudly displaying their colorful feathers—indeed, peacock feather, too, were prized objects for collectors.

Pharmacies displayed the curiosities of Renaissance culture. The cabinet of pharmacist Francesco Calzolari at Verona, pictured here, displayed dried herbs, minerals, preserved animals, birds and snakes, including a supposed unicorn horn.

Such objects would become the “curious” things of early modern science. Saint Paul’s admonition, Noli alta sapere, “Do not seek to know high things,” gave way in the Renaissance to Horace’s more hopeful Sapere aude, “Dare to know.”

The transformation of curiosity in the Renaissance was a precondition of modernity. Without curiosity, there can be no scientific discovery, and without discovery, there can be no new knowledge.

You can read this piece in its entirety--and find out more about William Eamon and his work-- by clicking here.

Image caption: Pharmacies displayed the curiosities of Renaissance culture. The cabinet of pharmacist Francesco Calzolari at Verona, pictured here, displayed dried herbs, minerals, preserved animals, birds and snakes, including a supposed unicorn horn.

1 in 200 men direct descendants of Genghis Khan | Gene Expression

473px-YuanEmperorAlbumGenghisPortraitIn 2003 a groundbreaking historical genetics paper reported results which indicated that a substantial proportion of men in the world are direct line descendants of Genghis Khan. By direct line, I mean that they carry Y chromosomes which seem to have come down from an individual who lived approximately 1,000 years ago. As Y chromosomes are only passed from father to son, that would mean that the Y is a record of one’s patrilineage. Genghis Khan died ~750 years ago, so assuming 25 years per generation, you get about 30 men between the present and that period. In more quantitative terms, ~10% of the men who reside within the borders of the Mongol Empire as it was at the death of Genghis Khan may carry his Y chromosome, and so ~0.5% of men in the world, about 16 million individuals alive today, do so. Since 2003 there have been other cases of “super-Y” lineages. For example the Manchu lineage and the Uí Néill lineage. The existence of these Y chromosomal lineages, which have burst upon the genetic landscape like explosive stars sweeping aside all other variation before them, indicates a periodic it “winner-take-all” dynamic in human genetics more reminiscent of hyper-polygynous mammals such as elephant seals. As we do not exhibit the sexual dimorphism which is the norm in such organisms, it goes to show the plasticity of outcome due to the flexibility of human cultural forms.

ResearchBlogging.orgJason Goldman of Thoughtful Animal reminded me of the 2003 paper a few days ago, so I thought it would be useful to review it again for new readers (as I know most of you have not been reading for 7 years!). To understand how one Y chromosomal lineage can have such a wide distribution across such a large proportion of the human race, here is a quote attributed to Genghis Khan:

The greatest joy for a man is to defeat his enemies, to drive them before him, to take from them all they possess, to see those they love in tears, to ride their horses, and to hold their wives and daughters in his arms.

You’re probably more familiar with the paraphrase in Conan the Barbarian.

The Genetic Legacy of the Mongols:

We have identified a Y-chromosomal lineage with several unusual features. It was found in 16 populations throughout a large region of Asia, stretching from the Pacific to the Caspian Sea, and was present at high frequency: ?8% of the men in this region carry it, and it thus makes up ?0.5% of the world total. The pattern of variation within the lineage suggested that it originated in Mongolia ?1,000 years ago. Such a rapid spread cannot have occurred by chance; it must have been a result of selection. The lineage is carried by likely male-line descendants of Genghis Khan, and we therefore propose that it has spread by a novel form of social selection resulting from their behavior.

What is social selection? In this context it’s pretty obvious, the Mongol Empire was the personal property of the “Golden Family,” the family of Genghis Khan. More precisely this came to consist of the descendants of Genghis Khan’s four sons by his first and primary wife, Jochi, Chagatai, Ogedei, and Tolui. Like descent from the gods in the mythology of the Classical World, or the House of David in medieval Christian monarchies, a line back to Genghis Khan became a necessary precondition for fitness to be a ruler in the centuries after the rise of the Mongol Empire across much of Asia.

To me the power and fury of the Mongol expansion, the awe and magnetism which Genghis Khan’s bloodline held for Asiatic societies in the wake of their world conquest, is attested to by the fact that descent from Genghis Khan became a mark of prestige even within Islamic societies. Timur claimed a relationship to Chagatai. His descendants in India, the Timurids, retained pride in their Genghiside heritage. In Russia among the Muslim Tatars and in Central Asia among the Uzbeks descent from Genghis Khan was a major calling card for any would-be warlord. This is peculiar in light of the fact that Genghis Khan, and his near descendants, were non-Muslims! Not only were they non-Muslims, but the Mongol assault on West Asian Muslims societies was particularly deleterious; it is generally assumed that Iran and Mesopotamia’s relatively productive irrigation system were wrecked during the Mongol conquests to the point where it took centuries for them to rebound to their previous levels of productivity. More symbolically, it was the Mongols who finally extinguished the Abbasid Caliphate.

In Muslim societies pride of place is given to Sayyids, descendants of Muhammad through his grandsons Hasan and Husain. Naturally this is often fictive, but that matters little. In fact in the Golden Horde, the northwestern region of the Mongol Empire which eventually gave rise to the Tatars who imposed the yoke on the Russians, non-Genghiside warlords produced fictive genealogies claiming descent from Muhammad as a way to negate the lineage advantage of their Genghiside rivals. But it is still shocking that there was even a question as to whether descent from Genghis Khan was more prestigious than descent from the prophet of Islam!

And the power of descent from Genghis Khan, the monopoly of the commanding heights which his male line descendants still felt to be theirs by right of their blood, obtained at the heart of his Empire, Mongolia, down to a very late period. The last of the great steppe polities, the Zunghar Empire, was defeated by the Manchus in part because it was led by a subset of the Oirat Mongols, a tribe whose leadership were not descended in the male line from the Golden Family, and so could not convince the Genghiside nobility of eastern Mongolia to align with them. From the perspective of moderns, who tend to conceive of historical patterns and forces in economic, or at least ideological, terms, this fixation on blood descent seems ridiculous. I suspect that many pre-modern people, who were accustomed to small family groups and kin networks in a way we are not, would find our own surprise rather perplexing.

So what did they find in the paper? First, they discovered that there was a particular Y chromosomal haplotype, a set of unique genetic markers, which was found across much of Asia. This haplotype seems to have expanded relatively recently, as was evident from small number of mutational steps connecting all of the local variants. Figure 1 illustrates the phylogenetic network:

stardd1

The shaded area represents the star-phylogeny. It’s characterized by a core haplotype, a nearby set of variants separated by one mutational step. This suggests that the genetic variant has risen rapidly in frequency before mutations had time to build up variation and generate a more complex topology. Observe the greater complexity of the network for other Y lineages. Here is the text which explains the factors behind the rise of the Genghis Khan haplotype:

This rise in frequency, if spread evenly over ~34 generations, would require an average increase by a factor of ~1.36 per generation and is thus comparable to the most extreme selective events observed in natural populations, such as the spread of melanic moths in 19th-century England in response to industrial pollution…We evaluated whether it could have occurred by chance. If the population growth rate is known, it is possible to test whether the observed frequency of a lineage is consistent with its level of variation, assuming neutrality…Using this method, we estimated the chance of finding the low degree of variation observed in the star cluster, with a current frequency of 8%, under neutral conditions. Even with the demographic model most likely to lead to rapid increase of the lineage, double exponential growth, the probability was <10?237; if the mutation rate were 10 times lower, the probability would still be <10?10. Thus, chance can be excluded: selection must have acted on this haplotype.

Could biological selection be responsible Although this possibility cannot be entirely ruled out, the small number of genes on the Y chromosome and their specialized functions provide few opportunities for selection…It is therefore necessary to look for alternative explanations. Increased reproductive fitness, transmitted socially from generation to generation, of males carrying the same Y chromosome would lead to the increase in frequency of their Y lineage, and this effect would be enhanced by the elimination of unrelated males….

A factor of 1.36 per generation is crazy high. In theory of course drift could do this, but in theory the molecules of gas in a room could all congeal to one corner. As noted in the text the Y chromosome is not rich in biologically useful genes. It may be that in the near future we’ll find something peculiar about the carriers of this particular haplotype, but until then, this map speaks for itself:

star2

The haplotype we’re focusing on clearly tracks the boundaries of the Mongol Empire as it was at the death of Genghis Khan. The main exception to this are the Hazara people of central Afghanistan, who importantly have a claim of paternal descent from Mongol soldiers who fled turmoil in Persia after the collapse of Mongol rule over that nation. Also, the shaded areas are regions where the population density was, and is, relatively low in relation to later societies which the Mongols conquered in East and West Asia. Finally, the shaded areas were under domination of Genghiside lineages for far longer than Yuan China or the Ilkhanate of Persia. In Mongolia, northeast China, and throughout Central Asia, Genghiside lineages were paramount down to the era of the “Great Game” between Russia and the British Empire.

The 2003 paper isn’t the last word. Here’s a table from a 2007 paper which surveyed groups which include many groups currently resident within the Russian Federation:

star3

Of interest in this table is the relatively higher frequency among the Kazakh sample than among the Kalmyks. The Kalmyks are a people who were a fragment of the aforementioned Zunghar Empire who took refuge in the Russian Empire. They make the claim to be the only indigenous people of Europe who are Buddhists (Kalmykia is to the west of the Urals and Volga). Though more closely related to the Mongols proper than the Turkic Kazakhs in culture and genes, they do not seem to carry the lineage of Genghis Khan, as was reputedly the case in the 18th century when the Genghiside led Mongol tribes fought them as arriviste interlopers. In contrast the Kazakhs have presumably mixed for centuries with the remnants of the Golden Horde. It is interesting to note that the 2007 Genghis Khan biopic Mongol had funding from the government of Kazakhstan, again attesting to the prestige which he still retains outside of Mongolia in Inner Asia.

Let’s jump back to the conclusion of the original paper:

…Several scenarios, which are not mutually exclusive, could explain its rapid spread: (1) all populations carrying star-cluster chromosomes could have descended from a common ancestral population in which it was present at high frequency; (2) many or most Mongols at the time of the Mongol empire could have carried these chromosomes; (3) it could have been restricted to Genghis Khan and his close male-line relatives, and this specific lineage could have spread as a result of their activities. Explanation 1 is unlikely because these populations do not share other Y haplotypes, and explanation 2 is difficult to reconcile with the high Y-haplotype diversity of modern Mongolians…The historically documented events accompanying the establishment of the Mongol empire would have contributed directly to the spread of this lineage by Genghis Khan and his relatives, but perhaps as important was the establishment of a long-lasting male dynasty. This scenario shows selection acting on a group of related men; group selection has been much discussed…and is distinguished by the property that the increased fitness of the group is not reducible to the increased fitness of the individuals. It is unclear whether this is the case here. Our findings nevertheless demonstrate a novel form of selection in human populations on the basis of social prestige. A founder effect of this magnitude will have influenced allele frequencies elsewhere in the genome: mitochondrial DNA lineages will not be affected, since males do not transmit their mitochondrial DNA, but, in the simplest models, the founder male will have been the ancestor of each autosomal sequence in 4% of the population and X-chromosomal sequence in 2.7%, with implications for the medical genetics of the region….

Garrett Hardin, pioneer of the “tragedy of the commons” model, also asserted that “nice guys finish last.” From what I know of the history it does not seem that Genghis Khan was any more evil or sociopathic than Julius Caesar, Charlemagne or Alexander the Great. What he had on his side was simply scale of success. So I don’t know if it truly is an example of nice guys finishing last. The biography gleaned from The Secret History of the Mongols doesn’t indicate the level of self-destructive sociopathy of Stalin or Ivan the Terrible. Rather, Genghis Khan was able to gather around himself a cadre of followers who were willing to stick with him through thick and thin.

In the life and legacy of the great Mongol warlord I suspect we see the patterns of male domination and power projection which were the norm after the decline of hunter-gatherers, and before the rise of the mass consumer society. During this period complex civilizations built on rents extracted from subsistence agriculturalists arose. These civilizations were dominated by powerful men, who could accrue to themselves massive surpluses, and translate those surpluses into reproductive advantage. This was not possible in the hunter-gatherer world where reproductive variance was constrained by the reality that allocation of resources was relatively equitable from person to person. But with agriculture and village society inequality shot up, and the winner-take-all dynamic came to the fore. And so the appearance on the scene genetically of super-Y lineages. Over the past 200 years the pendulum has started to shift back, thanks to the spread of Western values and normative monogamy, which dampens the potential unequal reproductive outcomes between the rich and the poor.

Addendum: Since my surname is Khan, I should admit that I am not a direct descendant of Genghis Khan through the male line. I’m R1a1a. In South Asia “Khan” was an honorific for Muslims.

Image Credit: National Palace Museum in Taipei

Citation: ZERJAL, T. (2003). The Genetic Legacy of the Mongols The American Journal of Human Genetics, 72 (3), 717-721 DOI: 10.1086/367774

Hundreds of New Views from Telescope Orbiting Mars

At the center of this view of an area of mid-latitude northern Mars, a fresh crater about 6 meters (20 feet) in diameter holds an exposure of bright material, blue in this false-color image. Image Credit: NASA/JPL-Caltech/University of Arizona - Larger image

The latest set of new images from the telescopic High Resolution Imaging Science Experiment Camera on NASA's Mars Reconnaissance Orbiter offers detailed views of diverse Martian landscapes.

Features as small as desks are revealed in the 314 observations made between June 6 and July 7, 2010, now available on the camera team's site and NASA's Planetary Data System.

The camera is one of six instruments on NASA's Mars Reconnaissance Orbiter, which reached Mars in 2006.

For More information visit http://www.jpl.nasa.gov/news/news.cfm?release=2010-256

Private Islands Top List of Best Hidden Beaches

paradise beachParadizo recently released it’s list of the best hidden beaches in the world and it’s no surprise that number of private island resorts made the list. Among the worlds best hidden beaches is The Mozambique Private Island Medjumbe in the Quirimbas Archipelago.  Medjumbe is a secluded private island that gives you the feeling that you’ve found your own hidden corner of the world. Abundant gardens, teeming wildlife and discrete beach villas abound in the ultimate private island hideaway.

Also on the list is the ultra exclusive Mustique the secret spot of pink sand and lazy, turquoise waves. Mustique’s villas are a treasure onto themselves, offering exclusive amenities beachside on this Caribbean private island catering to a lucky few, well-heeled travelers.

To read more about the World’s Best Hidden Private Beaches visit Paradizo