Tuesday, November 6, 2012

America Gone Wild: Is Sri Lanka going Wild

Article in the Wall Street Journal details the resurgence of wild life and forests in the US.
Today, the eastern third of the country has the largest forest in the contiguous U.S., as well as two-thirds of its people. Since the 19th century, forests have grown back to cover 60% of the land within this area. In New England, an astonishing 86.7% of the land that was forested in 1630 had been reforested by 2007, according to the U.S. Forest Service.

Sterilize them? Kill them? For every option and every creature there is a constituency. We have bird lovers against cat lovers; people who would save beavers from cruel traps and people who would save yards and roads from beaver flooding; Bambi saviors versus forest and garden protectors.

Some towns are becoming more tolerant of hunters than of deer, noting that while guns kill 31,000 Americans a year, hunters kill only about 100, mostly each other. Deer, on the other hand, kill upward of 250 people a year—drivers and passengers—and hospitalize 30,000 more. Some communities screen hunters, allowing them to use only bows and arrows and shotguns that have limited ranges.
Just a few days ago we had Elephants  come into our property at Eluvankulam. They ate the tender crown of the coconut Trees and just walked over the vegetable plots, destroying bean plants, squash  and the remaining papaya plants (they didn't do well to start with).  This is the second time elephants have encroached since the rainy season started. The traditional thinking is that elephants
encroach onto plantations during the dry season when forests and grass lands have marginal greenery,  but this is occurring when its green all over.
So what is happening, to quote from the WSJ article
Why? Our habitat is better than theirs. We offer plenty of food, water, shelter and protection. We plant grass, trees, shrubs and gardens, put out birdseed, mulch and garbage.
Sprawl supports a lot more critters than a people-free forest does. For many species, sprawl's biological carrying capacity—the population limit the food and habitat can
From one of the comments on the WSJ article which highlights there been no correct answers.

Friends of mine,  who have spent time in Spain, in the past several years, tell me that wind farms are devastating to wild life. They say that there is isn't a rabbit, squirrel or deer to be seen in Spain. They didn't know if the animals were hiding somewhere, but they certainly weren't visible. Thinking is that the vibrations from the wind turbines discourage the reproduction of the animals.

Tuesday, October 2, 2012

Dioxin causes Kidney Disease: Alternative Explanation to Arsenic

The increased incidence of kidney disease in the North Western Province is true.  That said is Arsenic the true cause as Nalin de Silva makes it out to be.  Could dioxins  which can be contaminants in Agrochemicals be more likely the cause of kidney disease in the NWP.

Agent Orange in Vietnam was contaminated by a Dioxin where even "vanishingly small" quantities in the diet caused adverse health effects.

From ScienceDaily (Sep. 26, 2012)
  • Writing in the journal PLoS ONE, biologist Michael Skinner and members of his lab say dioxin administered to pregnant rats resulted in a variety of reproductive problems and disease in subsequent generations. The first generation of rats had prostate disease, polycystic ovarian disease and fewer ovarian follicles, the structures that contain eggs. To the surprise of Skinner and his colleagues, the third generation had even more dramatic incidences of ovarian disease and, in males, kidney disease.
  • "Therefore, it is not just the individuals exposed, but potentially the great-grandchildren that may experience increased adult-onset disease susceptibility," says Skinner.
  • Skinner is a professor of reproductive biology and environmental epigenetics -- the process in which environmental factors affect how genes are turned on and off in the offspring of an exposed animal, even though its DNA sequences remain unchanged. In this year alone, Skinner and colleagues have published studies finding epigenetic diseases promoted by jet fuel and other hydrocarbon mixtures, plastics, pesticides and fungicides, as well as dioxin.
  • The field of epigenetics opens new ground in the study of how diseases and reproductive problems develop. While toxicologists generally focus on animals exposed to a compound, work in Skinner's lab further demonstrates that diseases can also stem from older, ancestral exposures that are then mediated through epigenetic changes in sperm.

Mohan Manikkam, Rebecca Tracey, Carlos Guerrero-Bosagna, Michael K. Skinner. Dioxin (TCDD) Induces Epigenetic Transgenerational Inheritance of Adult Onset Disease and Sperm Epimutations. PLoS ONE, 2012; 7 (9): e46249 DOI: 10.1371/journal.pone.0046249

Monday, April 23, 2012

UNHRC to Investigate plight of US Native Americans

 I guess there are some in Sri Lanka who will be happy to hear this. from the Guardian via finance blog Naked Capitalism
The UN human rights inquiry will focus on the living conditions of the 2.7 million Native Americans living in the US

The human rights inquiry led by James Anaya, the UN special rapporteur on indigenous peoples, is scheduled to begin on Monday.

Many of the country's estimated 2.7 million Native Americans live in federally recognised tribal areas which are plagued with unemployment, alcoholism, high suicide rates, incest and other social problems.

The UN mission is potentially contentious, with some US conservatives likely to object to international interference in domestic matters. Since being appointed as rapporteur in 2008, Anaya has focused on natives of Central and South America.

A UN statement said: "This will be the first mission to the US by an independent expert designated by the UN human rights council to report on the rights of the indigenous peoples."

Anaya, a University of Arizona professor of human rights, said: "I will examine the situation of the American Indian/Native American, Alaska Native and Hawaiian peoples against the background of the United States' endorsement of the UN declaration on the rights of indigenous peoples."

The US signed up in 2010 to the declaration, which establishes minimum basic rights for indigenous people globally.

Anaya said: "My visit aims at assessing how the standards of the declaration are reflected in US law and policy, and identifying needed reforms and good practices."

Apart from social issues, US Native Americans are involved in near continuous disputes over sovereignty and land rights. Although they were given power over large areas, most of it in the west, their rights are repeatedly challenged by state governments.

Most Americans have little contact with those living in the 500-plus tribal areas, except as tourists on trips to casinos allowed on land outside federal jurisdiction or to view spectacular landscapes.

Anaya is originally from New Mexico and is well versed in Native American issues.

He will visit Washington DC, Arizona, Alaska, Oregon, Oklahoma and South Dakota, and will conclude his trip with a press conference on 4 May. He will present his findings to the next session of the UN human rights council.

Anaya's past record shows a deep sympathy with Native Americans' plight. In one development dispute, he told the council that the desecration of sacred sites was an urgent human rights issue.

The Tucson Sentinel reported in 2011 that he had testified to Congress on the need for the US to pass legislation that abides by the declaration.

Also in 2011, he wrote to the Canadian government requesting information about the poor living conditions of aboriginal groups in the country.

Disable your Cell Phone if Stolen: IMEI Number

*#06# into Keypad to get IMEI number.  If phone gets lost or stolen the phone let the company know IMEI number. Does Dialog Mobitel etc support "blacklist IMEI number" of lost phone.

The International Mobile Equipment Identity or IMEI  is a number, usually unique,[1][2] to identify GSM, WCDMA, and iDEN mobile phones, as well as some satellite phones. It is usually found printed inside the battery compartment of the phone. It can also be displayed on the screen of the phone by entering *#06# into the keypad on most phones.

The IMEI number is used by the GSM network to identify valid devices and therefore can be used for stopping a stolen phone from accessing the network in that country. For example, if a mobile phone is stolen, the owner can call his or her network provider and instruct them to "blacklist" the phone using its IMEI number. This renders the phone useless on that network and sometimes other networks too, whether or not the phone's SIM is changed.


Sunday, April 22, 2012

'Eggless' chick laid by hen in Sri Lanka

from the BBC via finance blog Naked Capitalism

Only in Sri Lanka
A Sri Lanka hen has given birth to a chick without an egg, in a new twist on the age-old question of whether the chicken or the egg came first. Instead of passing out of the hen's body and being incubated outside, the egg was incubated in the hen for 21 days and then hatched inside the hen.
The chick is fully formed and healthy, although the mother has died.
The government veterinary officer in the area said he had never seen anything like it before.
PR Yapa, the chief veterinary officer of Welimada, where it took place, examined the hen's carcass.
He found that the fertilised egg had developed within the hen's reproductive system, but stayed inside the hen's body until it hatched.
A post-mortem conducted on the hen's body concluded that it died of internal wounds.
The BBC's Charles Haviland in Colombo says that the story has made headlines in Sri Lanka, with the Sri Lankan Daily Mirror's concluding: "The chicken came first; not the egg."

Friday, April 20, 2012

Agni Putri: Tessy Thomas Project Director of the Agni-V missile

Tessy Thomas is the first woman scientist to head a missile project in India. An expert of solid system propellants which is used in Agni missile, Dr. Tessy Thomas earlier has worked as Assistant Project Director in the successful launch of India's longest range nuclear capable Agni III Inter Ballistic missile

The tranquil backwaters of Alappuzha, advertised as the perfect setting to lazily watch houseboats that glide past, is the home town of DRDO project director Tessy Thomas, who guided a team of scientists to successfully test Agni-V, the fiercest weapon in India's armour.

Other Indian Nuclear Program Notables
Excerpt from IndiaTimes
A rare woman in a male bastion, the 48-year-old was hooked on to science and mathematics from school days, especially wonder-struck at the rocket launches from Thumba on the outskirts of Thiruvananthapuram.

"The world of missiles opened up for me after I happened to be picked as one of 10 youngsters from around the country for a DRDO programme in 1985," Thomas told ET in a telephone interview, while awaiting a flight from Bhubaneswar after being the toast of the nation earlier in the day.

Right after she landed in DRDO, everything just happened, she says. And that includes a stint as faculty for guided missiles for DRDO in Pune, and having former President APJ Abdul Kalam as her director.

Her own career went ballistic, when she headed the Agni-IV team as project director for vehicles and mission, and was project director (mission) for the more sophisticated Agni V launch.

What does she have to say about a country which has women defence mission directors and, at the same time, rampant female infanticide? "Science shows no gender discrimination, and in that sense offers hope to a society where discrimination is practised.

Here in DRDO, we have a good example of a number of women scientists, who try and balance work and family," she says. Her husband Saroj Kumar Patel is a naval officer based in Mumbai, and son Tejas - named after India's light combat jet - is completing his engineering in Vellore.

Thomas would ideally like to unwind with a game of badminton and some cooking, but "that hasn't happened over the past two years", thanks to the latest editions of the Agni missile programme.

Now that Agni-V has been successfully test launched, would she care more for the trajectory of the shuttle cock? "Well, I now have my sights on the multiple independent re-entry vehicle," says the multi-tasking scientist.

Back home in Alappuzha, where her mother stays, the land phone rings incessantly after Tessy Thomas' contribution to India's pride at Wheeler Island. Yet, she may not get time to relax and have a backwater cruise one of these days.

Bob Marleys father

Norval Sinclair Marley was Robert Nesta "Bob" Marley's father. Norval Marley was born in Jamaica to Albert Thomas Marley, an English man from Sussex, and Ellen Broomfield a coloured Jamaican. The Marleys considered themselves as descendants of Syrian Jews who had emigrated to England and from there to Jamaica.

Norval Marley in his later life was an overseer in Jamaican plantations. One of his lovers was 18-year-old gospel singer Cedella Booker. Their son, Robert Nesta Marley, was born in 1945 and spent his formative years living in considerable poverty in the slums of Jamaica. Norval Marley did not stay long after Bob Marley but gave some financial support. When Bob Marley was 28 and his mother 28 Norval Marley died. Mother and son then moved to Kingston and settled in a corrugated-iron shack in a street with open sewers in the Trenchtown area, one of the roughest parts of the capital.

Excerpts from the Daily Mail Article
In the Kingston slums, Marley was confronted in the starkest terms with the reality of his mixed parentage.
He was taunted mercilessly by his peers for standing out from the crowd. Indeed, he longed so much to fit in that, as his 65-year-old widow Rita has recently revealed, he used to black his face with boot polish. She says he even married her when he was 21 and she 19 —because, unlike him, she was completely black.
But family and friends, speaking out for the first time in the new film, reveal that because Bob was so single-minded about his career those close to him were often neglected.
His daughter Cedella, named after Bob’s mother, seems during conversations in the film to be quite bewildered at having to share her father with so many fans across the globe — not to mention his ten other children, many of them  illegitimate and the result of the many affairs he conducted during his marriage.
Marley had at least seven mistresses, including 1976 Jamaican Miss World Cindy Breakspeare.
The women themselves say he was so shy that they made all the  running. Several even fell pregnant by him at the same time: this year, three of his sons by different women will all turn 40.
His daughter Cedella is 44, a successful businesswoman with three children who lives in Miami.

Eating Meat helped Humans have a shorter Breast Feeding period

New research appears to explain that eating meat was why humans breast feed less than great apes.
Below excerpt from the  Daily Mail
The research compared 67 species of mammals, including humans, apes, mice and killer whales, and found a clear correlation between eating meat and earlier weaning.
The research compared 67 species of mammals, including humans, apes, mice and killer whales, and found a clear correlation between eating meat and earlier weaning.
They found young of all species stop suckling when their brains have developed to a particular stage, but that carnivores reached this point more quickly than herbivores or omnivores. 
Eating meat enabled the breast-feeding periods and thereby the time between births to be shortened,' said Elia Psouni, lead author of the study. 'This must have had a crucial impact on human evolution.'
Among natural fertility societies, the average duration of breast-feeding is 2 years and 4 months. This is not much in relation to the maximum lifespan of our species, around 120 years.
It is even less if compared to our closest relatives: female chimpanzees suckle their young for 4 to 5 years, whereas the maximum lifespan for chimpanzees is only 60 years.
Below excerpts from the  Psouni, Elia et al abstract at PLoS

Our large brain, long life span and high fertility are key elements of human evolutionary success and are often thought to have evolved in interplay with tool use, carnivory and hunting. 
Crucially, carnivory predicted the time point of early weaning in humans with remarkable precision, yielding a prediction error of less than 5% with a sample of forty-six human natural fertility societies as reference. Hence, carnivory appears to provide both a necessary and sufficient explanation as to why humans wean so much earlier than the great apes.
While early weaning is regarded as essentially differentiating the genus Homo from the great apes, its timing seems to be determined by the same limited set of factors in humans as in mammals in general, despite some 90 million years of evolution.
Our analysis emphasizes the high degree of similarity of relative time scales in mammalian development and life history across 67 genera from 12 mammalian orders and shows that the impact of carnivory on time to weaning in humans is quantifiable, and critical.
Since early weaning yields shorter interbirth intervals and higher rates of reproduction, with profound effects on population dynamics, our findings highlight the emergence of carnivory as a process fundamentally determining human evolution.

Thursday, April 19, 2012

Ibogaine to Treat Heroin and Cocaine Addiction

Ibogaine appears to be successful in  treating Heroin, Cocaine and other Addiction.

The drug, derived from the root of a central African plant called iboga, had been used for centuries by the Bwiti people of Gabon and Cameroon, as part of a tribal initiation ceremony.  The total alkaloid extract of the Tabernanthe iboga plant, which also contains all the other iboga alkaloids and thus has only about one-fifth the potency by weight as standardized ibogaine hydrochloride.
Currently, pure crystalline ibogaine hydrochloride is the most standardized formulation. It is typically produced by the semi-synthesis from voacangine in commercial laboratories.  There is also a synthetic derivative of ibogaine, 18-methoxycoronaridine.

Excerpts from BBC Article
In 1962 a young heroin addict called Howard Lotsof took iboga to get high, but when the hallucinogenic effects wore off, he realised he no longer had the compulsion to take heroin. He became convinced that he had found the solution to addiction and dedicated much of his life to promoting ibogaine as a treatment.

Howard Lotsof's early campaign had little success and ibogaine was banned in the US, along with LSD and psilocybin mushrooms, in 1967.

They began working together and in 1995 secured full approval from the US Food and Drug Administration (FDA) to investigate its potential in humans. But these tests cost millions of dollars, and Mash applied for five separate public grants but each one was declined.

Usually, this money would come from big pharmaceutical companies but drugs like ibogaine offer little potential for profit. It only has to be taken once, unlike conventional treatments for heroin addiction such as methadone which is a substitute and addictive itself.

"One very cynical reason they are not being developed is that there is no patent on these drugs anymore so there is no pharmaceutical company involvement," says Ben Sessa.
Pharmaceutical companies make money by patenting new chemicals but ibogaine is a naturally occurring substance and is difficult to secure a patent on.

Awesome photo of Lightning Strike

This was a photo caught by Phil McGrew from his office window in San Francisco.  The camera lens was was set up to a long exposure and as he says "I shot this from my office window because I was too chicken to get my new camera wet (or worse)".

Phil says on Flickr, "This shot has been on my list since moving to San Francisco. Unfortunately, I've only seen lightning 3 times in the 2 years I've lived here. Tonight, I got lightning in 3 separate 20 second exposures. This is a single exposure."

Friday, April 13, 2012

Porn Bigger Than CNN

Sunny Leone Indian Porn Star
Xvideos, the largest porn site on the web with 4.4 billion page views per month, is three times the size of CNN or ESPN, and twice the size of Reddit. LiveJasmin isn’t much smaller. YouPorn, Tube8, and Pornhub — they’re all vast, vast sites that dwarf almost everything except the Googles and Facebooks of the internet.

Four billion page views sure sounds like a lot, but it’s only when you factor in what those porn surfers are actually doing that the size and scale of adult websites truly comes into focus.

For a news site like Engadget or ExtremeTech, an average visit is usually between three and six minutes; enough time to read one or two stories. The average time spent on a porn site, however, is between 15 and 20 minutes.

To put that 800Gbps figure into perspective, the internet only handles around half an exabyte of traffic every day, which equates to around 50Tbps — in other words, a single porn site accounts for almost 2% of the internet’s total traffic.

Via Naked Capitalism to how big are porn sites

Best Wishes for Sri Lankan New Year

Best wishes for the Sri Lankan New Year, Not Sinhala/Tamil New Year.
Like Chinese New Year, not Hakka or Cantonese New Year.
The YouTube below is from Sunil Shantha singing in Sinhalese and beautiful art work.
Wish I knew enough Tamil  to pick an equivalent.

My young years from age 5 to 12 were growing up in Koralaewella (98 Vinitha), Moratuwa.  My father ( a Tamil)  built three Swings on the trees in the garden.  The easy swing was wide and the top end of swing 5 feet off the ground, that held three kids. The top of the best swing was 12 feet off the ground, and my sisters and me  could get it to a good sixty degrees off the ground. Then how many Colombo School students knew how to get swing moving without a push and getting it moving to sixty degrees off the ground. It was much more "cool" to know how to play cricket or rugby even then.

How many Colombo (Kandy, Galle etc) school boys or girls wanted to be Avurudu Kumara/Kumari even in the 70's  Among the Diaspora Sinhalese or Tamil, its only recent immigrants who want their children to compete in the local Avurudu Kumari.  As a good friend said  "There was a time that rural people of Sri Lanka were conservative enough to keep the beauty of the village and village life intact.  We lost this little by little, but still could find a remote village to go to and enjoy the village life even in the 80's".

Just as much as my friend , I too have lived many years in other countries and we would love to see  the "old ways".  Maybe we should emulate  "the colonial masters, English in particular, who go to great pains to preserve their country side".  
Simple things, beautiful life which we are loosing.

Other  Avurudu videos

Thursday, April 5, 2012

Indian Man Plants 1,360 Acre Forest over 30 years

Maybe we all should do something like this even if its 10 perch plot.
Jadav “Molai” Payeng started his project 30 years ago when he was still a teenager. Then, in 1979, flood waters washed a large number of snakes ashore on the local sandbar in Jorhat, some 350 km from Guwahati. When the waters receded, Payneg (who was 16 at the time) noticed the reptiles had died due to a lack of forestry.
“The snakes died in the heat, without any tree cover. I sat down and wept over their lifeless forms. It was carnage. I alerted the forest department and asked them if they could grow trees there. They said nothing would grow there. Instead, they asked me to try growing bamboo. It was painful, but I did it. There was nobody to help me. Nobody was interested,” said Payeng, who is now 47, to the The Times of India.
Payeng chose to live on the sandbar, starting a life of isolation as he began work to create a new forest. Planting the seeds by hand, watering the plants in the morning and evening, and pruning them when required, he cultivated a huge natural reserve. After a few years, the sandbar was transformed into a bamboo thicket.
“I then decided to grow proper trees. I collected and planted them. I also transported red ants from my village, and was stung many times. Red ants change the soil’s properties . That was an experience,” Payeng recalled.
Over the years, the reserve has seen a huge variety of flora and fauna blossom on the sandbar, including endangered animals like the one-horned rhino and Royal Bengal tiger. “After 12 years, we’ve seen vultures. Migratory birds, too, have started flocking here. Deer and cattle have attracted predators,” claims Payeng . Unfortunately, locals reportedly killed a rhino which was seen in his forest, something that Payeng clearly disapproves of.  ”Nature has made a food chain; why can’t we stick to it? Who would protect these animals if we, as superior beings, start hunting them?”
Read more: Indian Man Single-Handedly Plants 1,360 Acre Forest | Inhabitat - Sustainable Design Innovation, Eco Architecture, Green Building

Wednesday, April 4, 2012

Marriage and fatherhood have both been shown to decrease testosterone levels

Excerpt of an Article in Zero Hedge (a Financial blog)

Newsweek reported in 2009:
Monkeys that see sexually active females register as much as a 400 percent jump in testosterone (nature’s own performance-enhancing drug) promoting lean muscle and quick recovery times, according to the Yerkes Center for Primate Research at Emory University. In humans, German researchershave found that just having an erection is enough to spur testosterone levels. it makes no difference whether a man is watching sex on a screen or having it in real life, his testosterone levels will go up. Just having an erection, in fact, is enough to spur production.

Such findings, along with work that shows family life to be a drain on testosterone levels, prompted Rutgers University sex researcher Helen Fisher to advise this month that males in the “captivity situation”-her term for married with kids-”go on the Internet and look at porn” as a kind of hormone-replacement therapy. “[Porn] drives up dopamine levels, which drives up your testosterone,” she tells NEWSWEEK, while kissing your wife or hugging your kids drives it down.
Indeed, marriage and fatherhood have both been shown to decrease testosterone levels.

Other stuff to Boost Testosterone Levels.

Monday, April 2, 2012

US Supreme Court: Strip-Searches for Any Offense

Wonder how this can be interpreted when there is reasonable suspicion of suicide vests, grenades on dead enemy (citizen, terrorist insurgent or whatever).  David Blacker can you weigh in.

officials may strip-search people arrested for any offense, however minor, before admitting them to jails even if the officials have no reason to suspect the presence of contraband. 
According to a supporting brief filed by the American Bar Association, international human rights treaties also ban the procedures.
A nun was strip-searched, he wrote, after an arrest for trespassing during an antiwar demonstration. So were victims of sexual assaults and women who were menstruating.
Justice Kennedy responded that “people detained for minor offenses can turn out to be the most devious and dangerous criminals.” He noted that Timothy McVeigh, later put to death for his role in the 1995 Oklahoma City bombing, was first arrested for driving without a license plate. “One of the terrorists involved in the Sept. 11 attacks was stopped and ticketed for speeding just two days before hijacking Flight 93,” Justice Kennedy added.

via NY Times:  http://www.nytimes.com/2012/04/03/us/justices-approve-strip-searches-for-any-offense.html?

Wednesday, March 28, 2012

Birth Control For Men: Great for Casanovas

Apparently an  inexpensive procedure developed in India, excerpts below.
My opinion is great  for Casanovas, who can run around.  Ultimately the decision should be left to the woman.
The procedure called RISUG in India (reversible inhibition of sperm under guidance) takes about 15 minutes with a doctor, is effective after about three days, and lasts for 10 or more years. A doctor applies some local anesthetic, makes a small pinhole in the base of the scrotum, reaches in with a pair of very thin forceps, and pulls out the small white vas deferens tube. Then, the doctor injects the polymer gel (called Vasalgel here in the US), pushes the vas deferens back inside, repeats the process for the other vas deferens, puts a Band-Aid over the small hole, and the man is on his way. If this all sounds incredibly simple and inexpensive, that’s because it is. The chemicals themselves cost less than the syringe used to administer them. But the science of what happens next is the really fascinating part.
The two common chemicals — styrene maleic anhydride and dimethyl sulfoxide — form a polymer that thickens over the next 72 hours, much like a pliable epoxy, but the purpose of these chemicals isn’t to harden and block the vas deferens. Instead, the polymer lines the wall of the vas deferens and allows sperm to flow freely down the middle (this prevents any pressure buildup),  and because of the polymer’s pattern of negative/positive polarization, the sperm are torn apart through the polyelectrolytic effect. On a molecular level, it’s what super villains envision will happen when they stick the good guy between two huge magnets and flip the switch. ...
To reverse the procedure
With one little injection, this non-toxic jelly will sit there for 10+ years without you having to do anything else to not have babies. Set it and forget it. Oh, and when you do decide you want those babies, it only takes one other injection of water and baking soda to flush out the gel, and within two to three months, you’ve got all your healthy sperm again.
via Brown Pundits, complete article here

Monday, March 26, 2012

My DNA 01: Heroin Addiction, Smoking etc

Got my DNA results from 23andMe, very quick in almost 3 weeks.
First off,  the 23andMe autosomal, Y-DNA, mtDNA and mitochondrial data can be downloaded here.

So until I get Zacks analysis of ancestral groups, here are a very few of the large amount of health and trait indicators I got with my DNA results analysis.  Please Note most of this type of research has been done on people with European ancestry, and applicability to South Asians is yet to be determined.
rsid       chromosome position  genotype       Trait
rs1799971     6       154402490    AG       Heroin Addiction
rs17822931   16        46815699    TT       Ear Wax Type
rs762551     15        72828970    AA       Caffeine Metabolism
rs1051730    15        76681394    AG       Smoking Behavior

Heroin Addiction: rs1799971  AG: Substantially higher odds
This study of 139 heroin addicts (primarily Swedes) and 170 non-addicts found that people with at least one G at rs1799971 have almost 2.9 times the odds of being a heroin addict. .
I was dead scared of the horse because of all the stuff I had read about teeth falling out etc. Good thing I am no longer a young adult and that I read all the warnings when i was a young adult.
  • Zhang H et al. (2006) . “Association between two mu-opioid receptor gene (OPRM1) haplotype blocks and drug or alcohol dependence.” Hum Mol Genet 15(6):807-19.
  • Bart G et al. (2004) . “Substantial attributable risk related to a functional mu-opioid receptor gene polymorphism in association with heroin addiction in central Sweden.” Mol Psychiatry 9(6):547-9.
Ear Wax: rs17822931  TT: Dry Ear wax
Earwax type is highly heritable. This means that this trait is controlled almost entirely by your genes-environmental factors play little or no role. Because of this, simply knowing your genotype is enough to know your earwax type.
I have dry earwax and body sweat does not smell all that much (according to others) even though I sweat profusely (overweight). The sweat does tend to smell when I eat steak over two three days (this happens only during Christmas/Year end) and when I eat Ethiopian/Indian food. I think this because of larger amounts of Fenugreek (sinhala uluhal) in Berbere and Indian curry powder.  I guess that is Environment overshadowing Genes.
Caffeine Metabolism: rs762551  AA: Substantially higher odds
The form of the SNP rs762551 a person has determines how fast CYP1A2 metabolizes caffeine. In this study, people with the slower version of the CYP1A2 enzyme who also drank at least two to three cups of coffee per day had a significantly increased risk of a non-fatal heart attack. The study found that fast metabolizers, on the other hand, may have actually reduced their heart attack risk by drinking coffee.
I drink more than 6 cups of black coffee at work (US), specially because its free. Drink the stuff even before I go to sleep. 
Smoking Behavior: rs1051730  AG: More on Average if Smoker
Genes vs. Environment: Not all smokers are created equal—some light up just a few times a day, while others go through multiple packs. There are many social and environmental factors that affect whether people start smoking, but once they do, research based on Dutch Twins has shown that genetic factors play a large part in how dependent on nicotine they'll become and how much they'll smoke.
I used to smoke almost 3 packs (20 packs) as a teenager and young adult. Then stopped for about 13 years, started again and was smoking about 30 cigarettes. The only reason it was not more was cost and restrictions in ability to smoke in many locations. Stopped again and its been more than 6 years with the main motivation for stopping being cost and that I am a little too old to be bumming cigarettes.
  • Lerman C., Berrettini W. Elucidating the role of genetic factors in smoking behavior and nicotine dependence. Am. J. Med. Genet. B Neuropsychiatr. Genet. 2003;118B:48-54.
Also see
Sinhalese and Tamil DNA Admixture Analyis
Vijaya Kuveni: Paradigm for M mtDNA in South Asia

Sunday, March 25, 2012

Private Power Generation in Sri Lanka

There was a Jack Point post on CEB (Ceylon Electricity Board) losses and payments to private Power. I was skeptical that the percentage of private power was that significant. N pointed out a link to on the CEB losses were correct.  I was now curious, how much of private thermal power generation was there in Sri Lank.

I dont have an issue with the private hydro power, but private Thermal can be issue specially if foreign owned (if foreign owned then SL e would be twice f#%&*d, once while paying for imported oil, second when profits get repatriated.)

First off tried to get a list of Thermal Power Stations and then find out ownership.  . There were two sources, the Power Stations Wiki  and policy analysis report, but the two reports were slightly different.   Then came across the CEB 2008 report, which had a wealth of information. Kudos to the CEB for a really great report, unhappily no reports online after 2008. Based on the information (pg 14 &21), provided, below is the list of Private and CEB Thermal Power generation plants. There are 10 Private and 6 CEB Thermal Power Plants.   Total capacity all Thermal power plants were 1270 MW, with Private and CEB sharing 57% and 43% respectively.  Total generated power in 2008 was 5770 GWh with Private and CEB sharing 64% and 36% respectively. (Table below is sortable, click on header to sort).
The whole private thermal power ownership is a maze.  Here is some of what I managed to tease out before I gave up.
ACE Power: DEG (German Investment and Development Organisation ) 26% and Aitken Spence Power
AES Power: AES Corporation (also has Indian Arm) and Hayleys  (see here)
Agrico Pvt: .  Maybe part of US based Aggreko (see here and here)
West Coast Power:  As Tharindu de Silva says Yugadanavi is the name of the power plant, owned by  Lakdhanavi  but the foreign loan lending counties wanted the government guarantee for the loan. (Other link here )
There is also  Report on Electricity Tariff Rates in South Asia  and to me the two take home points were that
  • a) GDP 2005/per unit in Sri Lanka (9.5) was better than India (5.1). I dont know what percentage of electricity in India is consumed by Industry compared to household. I suspect in  India Industry usage is probably greater than in Sri Lanka (1%). 
  • Tariff rates were the highest in South Asia. 

Tuesday, March 20, 2012

How the Dongfeng ‘Hummer’ got built

AM General tried to sell the HMMWV to the People’s Liberation Army (PLA) in the late 1980′s.
The PLA however had no interest in the vehicle by that time, they thought it too big and heavy. AM General left one HMMWV in China, hoping the Chinese would change their mind.

They did after the first Gulf War in 1991 when the HMMWV was on every TV screen in the world, seen as a winning vehicle that could cross every desert. The HMMWV that was rotting away somewhere in China was cleaned up and taken apart to the last bit. In the mid ’90′s, Chinese oil companies bought several civilian HMMWV’s, officially for oil exploration but the vehicles actually ended up in PLA’s laboratories and were taken apart as well.

The PLA now wanted a HMMWV, and in the early 2000′s, two Chinese companies bid for the order. Each made its own HMMWV prototype based on knowledge gained by reverse engineering the American HMMWV’s. One company was Dongfeng, the other one the Shenyang Aircraft Corporation (SAC). Dongfeng won the order and the EQ2050 was born. I’ll get back on SAC’s prototype in a later article.
Now things get a bit murky. Dongfeng had to deliver, but it didn’t have parts to mass produce. AM General had plenty. So Dongfeng bought the parts from AM General and started production at around 2004. The first 100 or so EQ2050 were made with the American parts. In the meantime, Dongfeng set up their own parts operation and soon it was able to make the EQ2050 without American parts, and so it still does.
Except for one vital thing: the engine. It is a Cummins diesel made by Dongfeng in China under license from Cummins USA. Dongfeng also imports a GM V8 diesel, but that engine is only used in the civilian version of the Dongfeng EQ2050 which nobody can buy. I’ll get back to that in a moment.

Some other reports say that AM General licensed the HMMWV’s design to Dongfeng. This is not true. AM General was happy to sell parts to Dongfeng, the very company that copied their own car. Its all bout the money indeed. The only thing licensed is the engine, licensed by Cummins.

Back now to the civilian version. There is an arms embargo against China since 1989 when a student party on Tiananmen Square got messy. The US takes part in this embargo. That means US companies are not allowed to sell military goods to China. This is not only about finished military goods, like a tank, but also for everything that can be used to make a tank, like the gun, the armor – or the engine.

This was a problem for both AM General and Cummins. The HMMWV was clearly a military vehicle and so was the Dongfeng EQ2050. There is however an exception in the embargo. When something can be used both in a military and civilian way, it can be sold to China. Let’s say binoculars. They can be used by the army but also by civilians spotting birds. These goods are called ‘dual use goods’.

The American companies and Dongfeng talked things trough and arrived at a simple answer: Dongfeng was to make a civilian version of the EQ2050, right next the the military version. Dongfeng promised to do so, and the Americans started selling parts and engines, approved by the American government. Dongfeng showed a civilian EQ2050 on several autoshows but nobody can actually buy it and nobody ever will.
Today it doesn’t really matter anymore anyway, Dongfeng can make the parts from AM General by itself and the Cummins engines are now also used in very civilian trucks. But it was a nice trick – most likely with the full knowledge of all involved. Plausible deniability is everything!

from CarNewsChina.com

In My Mother's House: Civil War in Sri Lanka By Sharika Thiranagama

Google Books Preview: Has the Foreword (by Gananath Obeyesekere), Introduction and Acknowledgements. Amazon: Books: USD 23 to 60

Background of Sharika Thiranagama:
Sharika Thiranagama
Normally the parents are not that relevant for the background of an author. In this case it does play a large factor.  Daughter of Dayapala Thirangama. and Dr. Ranjani Thiranagama.  Dayapala Thirangama was a left oriented political activist (I dont know if he was ever affiliated with the JVP) and still writes to Groundviews (List of Dayapala Thirangama's articles at Groundviews).  Ranjani Thiranagama (nee Rajasingham), onetime LTTE member,  head of the Department of Anatomy, University of Jaffna and allegedly shot dead at the age of 35 by Tamil Tigers cadres after she criticized them for their atrocities. Ranjani Thiranagama was a co author of Broken Palmyra

Sharika Thiranagama:
Assistant Professor, Department of Anthropology, Stanford
Anyway excerpts from Introduction and Acknowledgements.
Diasporic Tamils in Australia, Canada, and the United Kingdom mounted campaigns calling for the end of bombing by the Sri Lankan government. Increasingly, the LTTE abroad took over the management of those campaigns, and turned them into massed displays of LTTE flags and demands for the LTTE to be recognized and rescued by foreign governments. The gulf between internally displaced Sri Lankan Tamils in Sri Lanka and those in the diaspora who rallied around the LTTE was all too apparent to those of us who had done fieldwork in Sri Lanka. The, support of expatriate Tamils for an increasingly delegitimized and violent LTTE meant that the protests became ineffective and the international community did not hold the Sri Lankan state to account and make it halt its use of heavy weaponry.

described through bombing  forced displacement, rape, recruitment, and so on, events that "happened" "to one," was also, as people frequently described as something that "happened inside one" One common way of describing the war by Tamils in Sri Lanka was to tell me of the fear that they felt toward other Tamils, unsure of who was LTTE and who was not. "There is no trust (nambikkai) among Tamils any more" was a frequent phrase. LTTE's often forcible recruitment of ordinary Tamils from families, and its widespread intelligence network and seeming pervasive presence in the Tamil community had led to a situation where networks of trust among Tamils were shrinking. The battlefields of the war were not only the frontlines where LTTK. cadres and Sri Lankan soldiers died, but were also the internal lives of Tamil communities and families.

Because the conflict has centered on the relationship between the Sri Lankan state ( as "acting for" the Sinhalese majority community) and Sri Lankan Tamils, representations of the ethnic conflict have often neglected the perspectives of Sri Lankan Muslims whose lives have also been indelibly marked by ongoing war. The Northern Muslims I worked with were all forcibly expelled from the north by the LTTE and have lived as collectively displaced people ever since. However, the north became a mono-cultural— if not mono-religious given the large proportion of Christian Tamils— Tamil region only after the expulsion of Muslims. Muslims remain, I argue, the unspoken void of the Tamil nationalist project- The breakdown of Tamil and Muslim relations in violence in the east, and in forcible eviction in the north, has been the major fissure of the 1990s war. Any possible peaceful future in northern and eastern Sri Lanka has to contend with Tamil-Muslim relations (McGilvray 2008).

Furthermore, that this book is about northern Tamils and Muslims is to highlight another contested assumption of pan-regional Tamil and Muslim Identity The pan-regional Tamil identity enshrined at the heart of contemporary Sri Lankan Tamil nationalism is historically problematic and regionally contested—most evidently in the schism in the LTTE on regional (north versus east) lines in 2004. Sivathamby (1984) identities three distinct Sri Lankan Tamil regions: the "North," " East," and "Vanni" districts of the North Central province. This regionalization is also important for Sri Lankan Muslims, who can also be subdivided regionally into "Eastern," "Northern" and "Southwest" blocs, though Muslim dispersal across the island, especially in highland Randy, makes the southwest bloc more permeable. Northern and eastern Tamils and Muslims differ in the ways they reckon caste, mosque membership, folk dialects, and family structure (Pfaffcnbergcr 1982; McGil-vray 1982, 1998). Despite national ethnic identities, at a local level northern Tamils and northern Muslims are more alike in social and familial structures, as Tamils and Muslims are in the east.

Jaffna has not stood still for over two hundred years, if ever. For Jaffna Tamils, becoming displaced (idam peyrntha) with little control over ones movement was played out against a longer history of migration as a means of economic and social mobility. The Jaffna peninsula is notable for consistently high rates of out-migration throughout the colonial and post colonial period. Economically marginal to the emerging Sri Lankan plantation economy, and overpopulated (Arasaratnam 1994), the area remained largely rural and underdeveloped, while its highly educated young men and (later) women became salaried labor within the colonial administration in the rest of the island and in the wider British empire of South and South-East Asia (Bastin 1997)" and to a lesser extent Africa. The economy was heavily dependent on remittances, with over 600,000 rupees remitted from outside the island in 1903 (Bastin 1997). By the twentieth century "a sprit of migration mostly by middleclass Tamils, became built into Tamil cultural aspirations" (McDowell 1996: 69). Within the island, Colombo, the capital city, was the favored site of internal migration flows from Jatfna for those seeking salaried work, the flow between Jatfna and Colombo being one of the most consistent migratory flows into Colombo throughout the twentieth century (Don Arachchige 1994: 30). Thus what I describe is not a largely sedentary group of people. Jaffna Tamils to whom movement was unknown, but a people for whom the possibility for chosen migration was always valued. In contrast, until their eviction in Northern Muslims were far more sedentary and less migratory.

Kumaraguru Kugamoorthy, my favorite uncle, a journalist who helped so many And who I remember for his kindness, his big smiles, explosive laughter, and his many stories, disappeared in Colombo on September 13, 1990, falsely accused as an LTTE supporter and taken into an army camp. We have never heard from him again. He leaves behind Thenmoli, his widow who searched for him for years, and Manoujitha, his daughter born in Jaffna days before he disappeared in Colombo, who has never seen him. Their lives are the lives of so many in Sri Lanka—for whom this book is ultimately written.

Monday, March 19, 2012

Scientist Politicians in Singapore and China

Tony Tan, who has a Ph.D. in applied mathematics. Tan won the very close election and joined the government of Prime Minister Lee Hsien Loong, who also has a degree in mathematics.

President Hu Jintao was trained as a hydraulic engineer and Premier Wen Jiabao as a geo=mechanical engineer. In fact, eight out of the nine top government officials in China have scientific backgrounds.

German Chancellor Angela Merkel has a doctorate in physical chemistry, and, going back a bit, Margaret Thatcher earned a degree in chemistry.

Complete NY Times:Why Don’t Americans Elect Scientists?   article here

Wet or Dry Ear wax and Armpit Odor

Excerpt from a Nature Genetics Article.
They write that earwax type and armpit odor are correlated, since populations with dry earwax, such as those of East Asia, tend to sweat less and have little or no body odor, whereas the wet earwax populations of Africa and Europe sweat more and so may have greater body odor.
They show that a SNP, 538G right arrow A (rs17822931), in the ABCC11 gene is responsible for determination of earwax type. The AA genotype corresponds to dry earwax, and GA and GG to wet type. A 27-bp deletion in ABCC11 exon 29 was also found in a few individuals of Asian ancestry.
I think the excerpt of article is self explanatory. When I have my autosomal DNA, I too will check for rsID rs17822931 and see the genotype. I already know my ear wax type. (Please see here on reading rsID from a typical autosomal file).

According to the ALFRED database, This SNP is the first example of DNA polymorphism determining a visible genetic trait.

From:  Gene Expression: Wet or Dry Ear Wax 
Original articleNature Genetics 38, 324 - 330 (2006) A SNP in the ABCC11 gene is the determinant of human earwax type Koh-ichiro Yoshiura et al
Other related articles:  The impact of natural selection on an ABCC11 SNP determining earwax type Ohashi J et al 2011  (A blog post discussing article)

Friday, March 16, 2012

A real Interactive Travelogue Blog srilankafor.91days

For those who follow kottu, I am sure you have seen the posts of  srilankafor.91days.
But then have you ever got to this point, the srilankafor.91days Interactive Index.

Kirigalpoththa and Lanka Reviewed please note.

Airlines: Passenger and Baggage Weight and Seating in a Bus

Excerpts of a article I just read.
I am writing this at an airport. A slight Asian woman has checked in with, I would guess, about 40 kilograms (88 pounds) of suitcases and boxes. She pays extra for exceeding the weight allowance. A man who must weigh at least 40 kilos more than she does, but whose baggage is under the limit, pays nothing. Yet, in terms of the airplane's fuel consumption, it is all the same whether the extra weight is baggage or body fat.

Another way to achieve the same objective would be to set a standard weight for passengers and luggage, and then ask people to get on the scales with their luggage. That would have the advantage of avoiding embarrassment for those who do not wish to reveal their weight.
I kind of like the solution of total passenger and baggage weight standard. That said, what about space taken up in in the seat.  I am acutely aware of this when traveling in a Bus in Sri Lanka.  Being a short 88 kilo (190 lb) guy who is more wide than tall, this becomes a issue unless its the skinny variety of the Sri Lankan (endangered by the day) seated next to me.  The choices are that
a) You paste against each other and become sweaty regardless of how well it is air conditioned
b) Have half of the posterior off the seat.

Neither choice is all that great if you have to travel for a hour or two, specially if you have personal space issues (Read the wiki to see how personal space comfort changes with country/culture).  I get around this when traveling long distances by buying two tickets, one for myself and one for my baggage (and I dont mean the human kind) and use up two seats. It needs a bit of thick skin, specially when the bus is packed to the roof and someone asks pointing to the seat occupied by the bag.  I rationalize it out by observing that the Intercity/Air Con buses regularly get tourists to buy tickets for their baggage placed on a seat. 

Anyway read more of the article Weigh more, pay more that started off this post.

Story at Caravan: The Defeated

The Defeated a Story/Report at Caravan. The author, whose name has been withheld for security reasons, is a journalist in India.
Swarna’s hardest moment in the LTTE was the haircut. After a 10-day training at the Siruthai Puligal facility, all 20 girls of her batch were asked to form a line under the harsh sun. One by one, their heads were shaved. Symbolically, they were being sheared of their femininity, lest it cripple their readiness for war. Practically, it did what easily identifiable smocks in rehab facilities do: it prevented recruits, especially minors, from escaping back to their normal lives. Swarna went through the haircut ritual for the eight years that she was a fighter. Each time she bowed her head under the razor, it brought on a fatalistic impulse. She remembered that she had no identity but that of a combatant, no freedom to run if she ever let herself feel fear. Running her hand over her prickly scalp, Swarna felt like a part of something larger. It was a por (war), but she believed it was a porattam (a revolutionary struggle). In recognition of her commitment, she was one of the few batches of girls that were taught satellite technology, and she became a navigator for GPS-dependent weaponry.
Did not agree with this line, which is incorrect.
Next came a republican constitution that said the Sinhalese were the original inhabitants of the island, and that their greatest duty was to protect Buddhism.
The constitution absolutely does not say "Sinhalese were the original inhabitants".  Does not even mention Sinhalese.
Neither does it say "greatest duty was to protect Buddhism"; what it says
The Republic of Sri Lanka shall give to Buddhism the foremost place and accordingly it shall be the duty of the State to protect and foster the Buddha Sasana, while assuring to all religions the rights granted by Articles 10 and 14(1)(e)
You can check it yourself by reading the Sri Lanka Constitution (you can get the complete constitution as pdf here)

Wednesday, March 14, 2012

Sri Lankan Population DNA Genetics 01

This is a first article on Sri Lankan Genetics. The data and and analysis is from HarappaDNA project run by Zack Ajmal.
a) Please read the previous blog post to understand the jargon and for a simple introduction to genetics.
b) There isnt enough of Sri Lankan data. If you live in the US/Canada and specially over the age of 40 please consider getting your autosomal DNA tested. Its $99 (and I think a $9/month compulsory 12 month subscription) for the autosomal test at 23andMe. I have already had my Y-DNA and mtDNA tested at FTDNA a few years back and have just sent in the saliva sample for the autosomal test. The autosomal results should be available in about two months and I will publish the results online.
Anyway here we go. What I have presented is a a subset of the data and analysis reported by Zack on HarappaDNA in Jan 2012 . This particular data set has 220 South Asian participants. All I have done is extracted a a total of 17 individuals, 6 Sri Lankan participants, some nearby South Indian participants and one Sindhi as a North-West Indian Comparison.

The Sri Lankan contingent of 6 as follows
  • Sri Lankan (ethnicity unknown)
  • Sinhalese Govigama
  • Sri Lankan Vellala (2 individuals)
  • Sri Lankan Vellala 1/2 and Telugu (1/2)
  • Sri Lankan (1/2) and German (1/2)
Note: Charts and Tables are interactive. Click on Legend or Column headers to Sort. (In brackets number of individuals in Group)

First an explanation of the Components/Legend.
  • S. Asian = South Asian and is roughly equivalent to the Ancestral North Indian (ANI) + Ancestral South Indian (ASI) of Reich et al. (more on that later)
  • Onge= The Onge are Andaman Islanders, who have no ANI component
  • E. Asian=Represents the component of Chinese etc component.
  • SW Asian= Its a bit of misnomer, It repesents NW Asian, Such as Iranian etc.
  • The Harappa analysis is an extended analysis of the Reich et al paper, but separates the ANI and ASI into S Asian and SW Asian components.
Reich et al abstract.(David Reichs other publications)
provide strong evidence for two ancient populations, genetically divergent, that are ancestral to most Indians today. One, the ‘Ancestral North Indians' (ANI), is genetically close to Middle Easterners, Central Asians, and Europeans, whereas the other, the ‘Ancestral South Indians' (ASI), is as distinct from ANI and East Asians as they are from each other By introducing methods that can estimate ancestry without accurate ancestral populations, we show that ANI ancestry ranges from 39–71% in most Indian groups, and is higher in traditionally upper caste and Indo-European speakers. Groups with only ASI ancestry may no longer exist in mainland India. However, the indigenous Andaman Islanders are unique in being ASI-related groups without ANI ancestry. Allele frequency differences between groups in India are larger than in Europe, reflecting strong founder effects whose signatures have been maintained for thousands of years owing to endogamy.
Figure 4. A model relating the history of Indian and non-Indian groups. Modeling the Pathan, Vaish, Meghawal and Bhil as mixtures of ANI and ASI, and relating them to non-Indians by the phylogenetic tree (YRI,(CEU,ANI),(ASI, Onge))), provides an excellent fit to the data. While the model is precise about tree topology and ordering of splits, it provides no information about population size changes or the timings of events. We estimate genetic drift on each lineage in the sense of variance in allele frequencies, which we rescale to be comparable to FST (standard errors are typically ±0.001 but are not shown).

So a couple of Initial observations. I'll revisit the charts and tables again if there is sufficient interest.
  • Regardless of how the data is sorted, by Onge or S Asian or European the Sri Lankan contingent groups together (except for the 1/2 German).
  • The Sri Lankan participants have a Y-DNA haplogroup of H. To quote from the Wiki Y-DNA H haplo group "seems to represent the main Y-haplogroup of the indigenous paleolithic inhabitants of India, because it is the most frequent Y-haplogroup of tribal populations (25-35%). H-M69 presence in upper castes is quite rare (ca. 10%) . Maybe the Sri Lankans are the Ravana's.
  • The mtDNA of one of the Sri Lankan participant (Sinhalese) is W3a. The Wiki quote for W Y-DNA haplo group is "Haplogroup W appears in Europe, West and South Asia. It is everywhere found as minority clade, with the highest concentration being in Northern Pakistan . A related unnamed N* clade is found among Australian Aborigines".
  • The mtDNa for the two Sri Lankan Tamils is M36. The Wiki quote for the M mtDNA haplo group is, "There is an ongoing debate concerning geographical origins of Haplogroup M and its sibling haplogroup N. Both these lineages are thought to have been the main surviving lineages involved in the out of Africa migration (or migrations) because all indigenous lineages found outside Africa belong to either haplogroup M or haplogroup N".
I need to find out What are the Y-DNa and mtDNA of the Onge Participants.
Reich et al quote.
These genomic analyses revealed two ancestral populations. "Different Indian groups have inherited forty to eighty percent of their ancestry from a population that we call the Ancestral North Indians who are related to western Eurasians, and the rest from the Ancestral South Indians, who are not related to any group outside India," said co-author David Reich
The one exception to the finding that all Indian groups are mixed is the indigenous people of the Andaman Islands, an archipelago in the Indian Ocean with a census of only a few hundred today. The Andamanese appear to be related exclusively to the Ancestral South Indian lineage and therefore lack Ancestral North Indian ancestry.

Reich et al divergence.
4,000 gens (100,000 yrs) ago Split of West African and Eurasian ancestors
2,000 gens (50,000 yrs) ago: Split of ANI and ASI ancestors
1,700 gens (42,500 yrs) ago: Split of Asian populations (‘proto-East Asia', ASI, and Onge)
600 gens (15,000 yrs) ago: Gene flow from ‘proto-East Asia' into the ancestral population of ANI and West Eurasians, so that the proto-West Eurasian/ANI mixture proportion is mP. Most of our simulations assume mP=100% (no gene flow), but we vary this parameter to test the robustness of our procedure if the ancestors of ANI and West Eurasians were mixed.
400 gens (10,000 yrs)ago: Split of CEU and Adygei
200 gens (5,000 yrs) ago: Age of the ancient mixture event that formed the Indian Cline.

Basic Primer on Population DNA Genetics

Basically a primer meant to help understand a few blog posts on Sri Lankan Population Genetics I plan to be writing in the near future. Click here for the Latest list of  Sri Lankan Population Genetics Posts.

The genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus , in RNA . The genome includes both the genes and the non-coding sequences of the DNA/RNA. The haploid human genome (23 chromosomes ) is estimated to be about 3.2 billion base pairs long and has about 20,000–25,000 distinct genes.

The gene is the molecular unit stretches of DNA and RNA which are the heredity of a living organism. A modern working definition of a gene is " a locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions, and or other functional sequence region . Each gene has a specific location ( locus ) on a chromosome and may come in several forms (alleles). In simpler language the DNA that gives Brown Hair, the DNA that gives Black hair are both alleles of the hair color gene (more info here). A more detailed non technical introduction to the genomes and genes, is Introduction to genetics).

Genotype vs. Phenotype:
Very important concept. Even if the genes are identical (genotype) the outward expression / looks (phenotype) could be different. Example would be identical twin, who have the same genes will have differences and fingerprints will be different. Another example would be children of short parents (and also have the sort genes) could be taller because of better nutrition.

The opposite is also true in that just because outward appearance is similar (phenotype) the genes (genotype) do not have to be similar. Example: Africans and Papua New Guineans though superficially similar are about the furthest apart genetically.
Papua New Guinean

What Kind of Genetic Tests: (see here for more non technical info)
Humans have 22 pairs autosomal non sex related chromosomes. The other is a pair of X and Y, XX in the case of a female, XY in the case of a male. These are the tests currently available.
  • Y-DNA; This test is only for males (X-Chromosome) and gives your direct male ancestry. i.e. the genes that were passed down from, your fathers, fathers, father etc. Currently about 67 markers are tested.
  • mt-DNA: Males and Females can be tested. This gives the genes in the mitochondrial cells that were passed from your mothers, mothers, mother etc.
  • Autosomal: Males and Females can be tested. This tests the 22 pairs of autosomal non sex related chromosomes. Currently about 0.024% of about 3 billion base pairs are tested.
Assume there is genome that is Pure Sri Lankan and Pure European. Three generations ago the maternal great grand mother (DF=Direct Female) and Paternal great grandfather (DM=Direct Male) were Pure Sri Lankan. The maternal sides daughters and paternal side sons always marry Pure European.
When the Person gets tested the Y-DNA and mt-DNA test will show that they are Pure Sri Lankan. However the autosomal test will show 25% Sri Lankan and 75% European. That because 3 generations there were 8 great grand parents (2number generations=23=8). 2 were Sri Lankan (2/8=25%) and 6 were European (6/8=75%).

Testing and Results
I have almost no clue as to the steps between sending your saliva and getting your genome data. There is DNA amplification, get more copies of the same DNA from the small sample sent. Then probably analysis thru machines like the Illumina which are like 10th generation HPLC's ( High Pressure Liquid Chromatograph ).
Depending on the kind of machine (chip), then different parts of the genome (~0.024% of 32 billion base pairs) gets tested. That means when comparison and analysis of results from different machines needs to be done, then the common tested locations need to be extracted before analysis can be done. Say for example you got your autosomal tests done at FTDNA and you are submitting the results to a research group that has mainly 23andMe results. Then the researcher will have to extract the data common to both FTDNA and 23andMe before any analysis can be done.

Anyway once the analysis is done you will get a whole lot of results, ranging from heath to ancestry. Other than that you also get approx 5mb data file in text format.
What Can be done with the Raw DNA data
a) There is SNPTips a free Firefox extension that will automatically match your genotype SNP's with others.
b) You could analyse it at http://snpinfo.niehs.nih.gov/snpfunc.htm. Use rsid from example above and then paste into SNP Function Prediction or SNP Information in DNA Sequence see results. For SNP Function Prediction you need to click some of the boxes like "Based on Genotype Data from dbSNP" say Asian. I have no clue as to what the results mean, its going to be a learning curve.
d) Do more research yourself or participate (anonymously if you wish) in many of the projects, such as HarrapaDNA (for South Asian analysis), Dodecad Ancestry Project and Eurogenes Ancestry Project.

Data and Analysis
This section focuses on general outline of data preparation and analysis of the raw autosomal data.
The 5 mb raw autosomal data (from 23andMe) will look like below.
rsid       chromosome position genotype
rs3094315  1          742429    AG
rs12562034 1          758311    AG
rs3934834  1          995669    CC
rs9442372  1          1008567   AG
rs3737728  1          1011278   AG
rsid or SNP: Typically only 0.024% (still thousands) of SNP are tested at locations (positions) known for genetic diversity (there are about 3 billion base pairs).
chromosome: The chromosome number of the 22 pairs autosomal non sex related chromosomes.
position: Position (also called locus or marker) of the place tested..
genotype: The base pair (or alleles), one from each strand in double helix. Each will be one of the four bases that make the DNA A (adenine) , G (guanine), and T (thymine).

To do analysis and comparison for genetic affinities. (See here for an in depth description of using ADMIXTURE at Razib Khan's Gene Expression and Anderson et al (2010) Data Control..(complete pdf).
Note: There is a software program ADMIXTURE and admixture the process of mixing of genes.

  1. Your raw data is combined with thousands of other genomes, some available freely from studies and others handed over by people who have got their genome test.
  2. Software like plink is used to do genome association analysis. Additionally it is used to create standard file formats that are used as inputs to other genome analysis software such as ADMIXTURE
  3. ADMIXTURE's input is binary PLINK (.bed) or ordinary PLINK (.ped and .map). The plink .ped file contains the genotype information (which SNP variants are where) and the .map file is essentially a list of the SNP names.
  4. To use ADMIXTURE, you need an idea of K, your belief of the number of ancestral populations.
  5. You can run ADMIXTURE in regular mode or supervised mode. Supervised mode is essentially anchoring ouptut to some reference populations. The reference population can either be autosomal data of real individuals or zombies. Zombies are recreated data to reference a hypothetical genetically pure indidividual or population (genomes created using the --simulate option of plink from allele frequencies) .
Important Caveats
  • Admixture analysis cannot distinguish between recent and ancient gene flow or directionality of flow
  • It is important to recognize that regions of highest haplo group frequency are not necessarily representative of origin. An obvious example is haplo group C, which displays its highest frequency in Polynesia (Kayser et al. 2000), but Polynesia is one of the last regions known to be colonized by modern humans (Sengupta et al, 2005).
  • Linguistic and Cultural (possible proxies for "Race") groups may not be the not the same as the genetic grouping.