A call to all brown gene nerds!

Update II: Several people have emailed me and confirmed that they finally purchased a kit. A little over $100 seems to be a good price point for what is mostly recreational genetics. Tomorrow I will post on what you’ll see in your 23andMe account, and how you have to interpret it if you are brown.

Update: Sale is operative. Limit 5 per person!

Just thought I’d pass on word, tomorrow the 23andMe genotyping service is going to have a sale. The details:

When: April 11th, 12 AM PDT to 12 PM PDT (so 3 AM EDT to 3 PM EDT)

How much: $9/month for 12 months = $108 per year for their analytic service. The kit cost, $199, is waived for the sale.

What you get: Ancestry analysis, trait assessment, and disease risk estimates. I wouldn’t put too much stock in the last in terms of bang-for-buck if you are not adopted…though the last person I explained that to ended up finding over 50% probability of macular degeneration (not a 50% increased risk, a 50% probability of developing the disease!).

For nerds the big deal is that you can get your raw genotype for 1 million markers. There are several personal genetics projects which have been started by people pooling their data. I put up a simple tutorial for those curious, and have started my own African ancestry project. But for readers of this weblog, Harappa is the way to go. Zack has over 80 participants now. Below the fold I’ve placed a tree which shows the genetic relationships in terms of ancestral quanta. I’ve underlined myself (I’m right next to my parents, as you’d expect). Continue reading

Visualizing South Asian genetic variation (3-D)

About a month ago I put up my first post on this weblog. I argued that South Asians have been genetically undersampled, which is rather alarming considering that Indians, Pakistanis, Bangladeshis, Nepalis, Sri Lankans, etc., are 1/6th of humanity. The alarming part is that understanding population genetic structure is considered a prior condition of much medical genetic research. Without taking into account genetic relatedness one can not usefully establish correlations between particular variants and particular diseases or traits. For example, it is well known that South Asians have a high risk for diabetes, but the possible risk variation within this genetically diverse group has barely been addressed (there is some data which indicate that Bengalis and South Indians are at more risk than Punjabis). Continue reading

Do that Guju you do!

gujcluster.jpgThe 2009 paper Reconstructing Indian population history was a watershed in understanding the genomics of South Asians. Before this point the studies had been with unrepresentative samples, fewer markers, or, South Asians were only a sidelight. This paper put the focus on South Asians to elucidate the group’s population history (it still undersampled eastern South Asians, though this seems part of the plan because of their focus on two, not three, ancestral Indian components). If you want to know more about the paper, here is the ungated version. But in this post I want focus on an issue which you can find only in the supplements to the paper.

The HapMap project, which surveys genetic variation in world populations, has a set of Gujaratis, from Houston, Texas. This is currently the primary population of Indian origin you have to work with in the public data sets. There are other South Asian populations in the public domain, but their number of markers is far lower. So the Gujarati sample is very useful right now. But one thing that immediately jumps out at you is that there are in fact two Gujarati clusters. In the PCA plot I’ve extracted from the supplements you see the two largest components of genetic variation. PC 1, the x axis, separates whites from South Asians, and PC 2, separates one group of Gujaratis from everyone else. What’s going on here?

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The undersampled 1 billion (genetically that is)

nastruc1.pngTwo issues compel this post. One is practical. The other is more, shall I say, spiritual (or at least fun!). In regards to the first, a few weeks ago I reviewed a paper which reported that the efficacy of response to a particular leukemia treatment regime was dependent on the amount of Native American ancestry an individual had. One has to be specific here, because many people who are white or black American have significant Native American ancestry (Brett Favre’s paternal grandfather was Choctaw), and many people who identify as Native American may not have as much Native American ancestry as others. But for the purposes of this blog post, I want to bring to your attention the figure above, which I extracted from the paper. Its implications may pose a major problem in the future for South Asian biomedical research in the United States. Continue reading

Math nerd meets lottery ticket

Wired has a totally charming story of one man’s quest to understand and beat the confounding scratch-off lottery ticket:

Mohan Srivastava, a geological statistician living in Toronto, was working in his office in June 2003, waiting for some files to download onto his computer, when he discovered a couple of old lottery tickets buried under some paper on his desk. The tickets were cheap scratchers–a gag gift from his squash partner–and Srivastava found himself wondering if any of them were winners. He fished a coin out of a drawer and began scratching off the latex coating. “The first was a loser, and I felt pretty smug,” Srivastava says. “I thought, ‘This is exactly why I never play these dumb games.’”

The second ticket was a tic-tac-toe game. Its design was straightforward: On the right were eight tic-tac-toe boards, dense with different numbers. On the left was a box headlined “Your Numbers,” covered with a scratchable latex coating. The goal was to scrape off the latex and compare the numbers under it to the digits on the boards. If three of “Your Numbers” appeared on a board in a straight line, you’d won. Srivastava matched up each of his numbers with the digits on the boards, and much to his surprise, the ticket had a tic-tac-toe. Srivastava had won $3. “This is the smallest amount you can win, but I can’t tell you how excited it made me,” he says. “I felt like the king of the world.”

Delighted, he decided to take a lunchtime walk to the gas station to cash in his ticket. “On my way, I start looking at the tic-tac-toe game, and I begin to wonder how they make these things,” Srivastava says. “The tickets are clearly mass-produced, which means there must be some computer program that lays down the numbers. Of course, it would be really nice if the computer could just spit out random digits. But that’s not possible, since the lottery corporation needs to control the number of winning tickets. The game can’t be truly random. Instead, it has to generate the illusion of randomness while actually being carefully determined…”

Srivastava had been hooked by a different sort of lure–that spooky voice, whispering to him about a flaw in the game. At first, he tried to brush it aside. “Like everyone else, I assumed that the lottery was unbreakable,” he says. “There’s no way there could be a flaw, and there’s no way I just happened to discover the flaw on my walk home.”And yet, his inner voice refused to pipe down. “I remember telling myself that the Ontario Lottery is a multibillion-dollar-a- year business,” he says. “They must know what they’re doing, right?” [Link]

This story reiterated in my mind how important it is to have a good understanding of science and mathematics in modern society. Consider how many activities in your day are governed by a mathematical code or logical pattern of some kind. Every minute you spend on Facebook you are helping Facebook perfect and equation to predict what you might buy for example. Nerds are poised to inherit the future.

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Working the prefrontal cortex since the Gupta Empire

There were two stories relating to human cognition today that really had me thinking about the way we…think (how appropriate). The first involves the game of chess. You know, the game of kings invented so long ago in India:

Chess is commonly believed to have originated in North-West India during the Gupta empire, where its early form in the 6th century was known as caturanga (Sanskrit: four divisions [of the military] – infantry, cavalry, elephants, and chariotry, represented by the pieces that would evolve into the modern pawn, knight, bishop, and rook, respectively). The earliest evidence of Chess is found in the neighboring Sassanid Persia around 600 where the game is known under the name became chatrang. [Link]

Garry Kasparov, the former world chess champion (the current is India’s Viswanathan Anand) has penned a brilliant (absolute must-read) essay/review of the new book, Chess Metaphors: Artificial Intelligence and the Human Mind. The title of his essay could have easily been, “How I Learned to Stop Battling and Love the Computer.” It chronicles his victories over the machines, followed by his losses, followed finally by a type of brutally efficient partnership. Let the human worry about strategy and the machine about tactics.

…I narrowly defeated the supercomputer Deep Blue in a match. Then, in 1997, IBM redoubled its efforts–and doubled Deep Blue’s processing power–and I lost the rematch in an event that made headlines around the world. The result was met with astonishment and grief by those who took it as a symbol of mankind’s submission before the almighty computer. (“The Brain’s Last Stand” read the Newsweek headline.) Others shrugged their shoulders, surprised that humans could still compete at all against the enormous calculating power that, by 1997, sat on just about every desk in the first world.

It was the specialists–the chess players and the programmers and the artificial intelligence enthusiasts–who had a more nuanced appreciation of the result. Grandmasters had already begun to see the implications of the existence of machines that could play–if only, at this point, in a select few types of board configurations–with godlike perfection. The computer chess people were delighted with the conquest of one of the earliest and holiest grails of computer science, in many cases matching the mainstream media’s hyperbole. The 2003 book Deep Blue by Monty Newborn was blurbed as follows: “a rare, pivotal watershed beyond all other triumphs: Orville Wright’s first flight, NASA’s landing on the moon….” [Link]

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New Data from the World of Genetics: “There is no North-South divide”?

I’ve been meaning to link to the recent study in Nature, “Reconstructing Indian Population History” (subscription reqd.) all week, but have been too busy (note: a document full of supplementary information is freely available here, though you need to be able to understand the way they do statistical analysis to make sense of all the charts).

As this is genetics, one would expect some comments from Razib, and indeed, one is not disappointed: here are Razib Khan’s comments on the study (see also this follow up post, where Razib creates his own plots based on the study’s data). The study gives data that relates to quite a number of different things, but the takeaway points seem to be : (1) South Indian and North Indian populations are genetically fairly mixed, and are (1a) more closely related to each other than to any other genetic/ethnic group; (2) the “Ancestral South Indian” genetic type is projected to most closely resemble a nearly extinct tribe in the Andaman Islands, the Onge (which is not to say that the Onge are themselves the “origin” of the South Indian gene pool); and (3) caste groups in the same regions of India show surprisingly high genetic difference in some cases, suggesting that caste endogamy within individual regions is a rather ancient practice.

According to Razib at least, the biggest limitation of this study is the small sample size (in the low hundreds). It seems clear that all of the conclusions being drawn from this study would be on stronger ground if they could go back and multiply the number of samples by 10.

Finally, there is a good, not overly technical synopsis of the Nature study at the Times of India: here. The TOI focuses on point (1) more than the others:

`This paper rewrites history… there is no north-south divide,” Lalji Singh, former director of the Centre for Cellular and Molecular Biology (CCMB) and a co-author of the study, said at a press conference here on Thursday.

Senior CCMB scientist Kumarasamy Thangarajan said there was no truth to the Aryan-Dravidian theory as they came hundreds or thousands of years after the ancestral north and south Indians had settled in India.

It is probably a mistake to read too much into this study, or even to accept the co-author’s bald claim that “there is no North-South divide” (Razib points out that it’s not that there aren’t genetic differences between North and South Indians — there are — but they fall on a gradient, rather than a solid barrier). Still, the study might have implications for South Indian activists who articulate a separatist “Dravidian” agenda, as well as North Indian “Aryan Invasion” proponents, who fantasize that they are really European. The only people who are really genetically “pure” on the Indian subcontinent are, it appears, the Onge. Continue reading

Arthur C. Clarke, RIP (with excerpts from a novel)

Science fiction writer Arthur C. Clarke died earlier this week, at the age of 91. He was one of the best-known sci-fi writers of the 20th century, the author behind 2001: A Space Odyssey, among many others.

As is well-known, Clarke moved to Ceylon/Sri Lanka in 1956 — in large part for the year-around access to diving — and remained there until his death. The locale inspired at least one of Clarke’s novels, Fountains of Paradise:

Clarke lived in Sri Lanka from 1956 until his death in 2008, having emigrated there when it was still called Ceylon, first in Unawatuna on the south coast, and then in Colombo. Clarke held citizenship of both the UK and Sri Lanka. He was an avid scuba diver and a member of the Underwater Explorers Club. Living in Sri Lanka afforded him the opportunity to visit the ocean year-round. It also inspired the locale for his novel The Fountains of Paradise in which he described a space elevator. This, he believed, ultimately will be his legacy, more so than geostationary satellites, once space elevators make space shuttles obsolete. (link)

I first read The Fountains of Paradise many years ago, and I pulled it off the shelf this afternoon for a refresher. There is an intense opening, set in the classical period, 2000 years ago, involving a “Prince Kalidasa,” who does not seem to resemble the actual Kalidasa (who was not a prince, but a poet). And there are some rich descriptions of the island of Sri Lanka (named “Taprobane” — Tap-ROB-a-nee — by Clarke). Continue reading

Is happiness linked to race?

Earlier this week, an article in the Journal of Personality and Social Psychology detailed some provocative new findings:

Are you happy? Well don’t try to be happier; you might become less happy. That is the gist of a multi-cultural study published recently in the Journal of Personality and Social Psychology.

The study by University of Virginia psychology professor Shigehiro Oishi and colleagues at three other institutions found that, on average, European-Americans claim to be happy in general – more happy than Asian-Americans or Koreans or Japanese – but are more easily made less happy by negative events, and recover at a slower rate from negative events, than their counterparts in Asia or with an Asian ancestry. On the other hand, Koreans, Japanese, and to a lesser extent, Asian-Americans, are less happy in general, but recover their emotional equilibrium more readily after a setback than European-Americans.

“We found that the more positive events a person has, the more they feel the effects of a negative event,” Oishi said. “People seem to dwell on the negative thing when they have a large number of good events in their life. [Link]

So in a nutshell, what this article is saying is that “Whitey” is happier than me on a day-to-day basis (which is why he’s always whistling), but that I get over a bad day or a negative life event with greater ease than him. Could it be that since Asian families are likely to be newer to America (i.e. fewer generations removed from Asia) we are instilled with a certain sense of fatalism engrained within the family? When a grandparent or relative died in India and our parents couldn’t be there, we watched them deal with it and recover as best they could from afar. As another example, when we are the victims of racism we have to shake it off and keep going. A European American may not have to deal with some of these things. The study (and take it for what its worth) is essentially saying that Asian Americans have built up a greater immunity to bad news than European Americans.

“It is like the person who is used to flying first class and becomes very annoyed if there is a half-hour delay. But the person who flies economy class accepts the delay in stride…” [Link]
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Help Me Sing It, Ma Ma Se, Ma Ma Sa, Ma Ma Coo Sa

sooo much chocolate.jpg

When it comes to “hot fields of scientific research”, obviously desis are at the forefront of discovery and innovation; that’s not chauvinism, that’s just logic. Millions of brown people exist and a solid chunk of them are in science, so the odds are just stacked in our favor. But I digress. And there’s exciting stuff regarding Proteome Research to get to, so let’s get back on topic! [Via MSNBC]:

A small study links the type of bacteria living in people’s digestive system to a desire for chocolate. Everyone has a vast community of microbes in their guts. But people who crave daily chocolate show signs of having different colonies of bacteria than people who are immune to chocolate’s allure.
That may be the case for other foods, too. The idea could eventually lead to treating some types of obesity by changing the composition of the trillions of bacteria occupying the intestines and stomach, said Sunil Kochhar, co-author of the study. It appears Friday in the peer-reviewed Journal of Proteome Research.

This study isn’t biased at all:

Kochhar is in charge of metabolism research at the Nestle Research Center in Lausanne, Switzerland. The food conglomerate Nestle SA paid for the study. But this isn’t part of an effort to convert a few to the dark (or even milk) side of cocoa, Kocchar said.

Here’s my favorite part of the study:

In fact, the study was delayed because it took a year for the researchers to find 11 men who don’t eat chocolate.

BWAH! In your face, people who think chocolate craving = pre-menstrual misery and weakness. MEN! They couldn’t find eleven MEN who don’t indulge.

Kochhar compared the blood and urine of those 11 men, who he jokingly called “weird” for their indifference to chocolate, to 11 similar men who ate chocolate daily. They were all healthy, not obese, and were fed the same food for five days.
The researchers examined the byproducts of metabolism in their blood and urine and found that a dozen substances were significantly different between the two groups. For example, the amino acid glycine was higher in chocolate lovers, while taurine (an active ingredient in energy drinks) was higher in people who didn’t eat chocolate. Also chocolate lovers had lower levels of the bad cholesterol, LDL.

That does it. I’m having red wine and Cadbury for dinner tonight. What to do? It’s the healthy choice.

The levels of several of the specific substances that were different in the two groups are known to be linked to different types of bacteria, Kochhar said.

They’re still not sure if it’s the bacteria that wants to be startin something, gots to be startin something or if diet affected the bacteria blah blah chicken egg.

How gut bacteria affect people is a hot field of scientific research.

I think my tummy is always warm, but that is based on highly unscientific rubbing of it, while attempting to pat my head simultaneously.

Wots this? A reference to my bellowed alma mater? GO AGS! Continue reading