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!


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 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.

Monday, March 12, 2012

Otter who raised orphaned pups, inspired law dies

The main reason for this post was more about Otters in Sri Lanka. I know there are Otters (Diya Balla) in Sri Lanka. They are supposed to be found around lagoons and mangroves. If you talk to old timers who live near the Negombo and Rathgama/Dodanduwa Lagoons will say that Otters were quite common when they were growing up. That said, Shirmp Trap (Isso Kotu) owners detested the otters as they would enter the trap and eat the shrimp and get away.

I have yet to see an Otter (other than the ones in Otters) in Sri Lanka. Not even a photograph, even though I have lived on the banks of Negombo and Rathgama/Dodanduwa Lagoons for the last couple of years. Not even a photograph, Sad.

Does anyone have photos of Otters of Sri Lanka. Do you want to provide a link or I could post it with credit to you.

Anyway here is a good story.
The California sea otter, who died Saturday in Monterey, not only raised more than a dozen orphaned otter pups, but also inspired important legislation and changed the way scientists handle abandoned otter babies.

And she did it all while battling a chronic neurological illness.

All that changed with Toola. She arrived at the aquarium in July 2001 after someone found her floundering and pregnant on Pismo Beach. Aquarium veterinarians discovered she had toxoplasmosis, a parasite spread by cat feces and a common threat to sea otters.The pathogen had infected her brain, leaving her with frequent seizures and an almost certain death sentence. Aquarium staff were able to control her convulsions with twice-daily doses of Phenobarbital, but she would never be released back to the wild.

A month or two after arriving at the aquarium, Toola gave birth to a stillborn pup. That's when Toola's motherhood miracle happened.
Toola didn't hesitate. She nursed the orphaned p like he was her own, taught him to open clamshells with rocks, how to eat a crab without getting pinched, and other tricks of sea otter life.
That pup, raised by Toola instead of humans, was able to return to the Pacific, where he's now king of a pack at Elkhorn Slough and has fathered countless pups himself.
Toola went on to foster 12 more pups, each for five months or so. Of the 13, two are still at the aquarium, too young for release; five are cavorting around the coastline making babies of their own; and six are unaccounted for, either dead or having shaken off their tracking tags.
Toola's most recent foster child was a male whom she was cuddling as recently as Friday. Late in the day, staff noticed she was listless and refusing food, and early Saturday she died naturally at the aquarium, surrounded by staff and her otter friends. She was 15 or 16.
Complete article here.

Wild Boar in NY State: Open Season

Wild boar in New York. Hopefully some enterprising Sri Lankan will start supplying the NY Metro and New Jersey Sri Lankan population with Wild Boar.
Anyway here are excerpts from the article.
First the most important statement:
In New York, the state’s ordinarily strict hunting rules have b..een relaxed for feral swine. The Department of Environmental Conservation’s Web site advises those with small game licenses to “shoot and keep feral swine at any time and in any number.”

PERU, N.Y. — They roam by night, picking cornstalks clean, making off with apple crops. They have almost no natural predators, but they have razor-sharp tusks and a seemingly bottomless appetite for plants and animals. Their population can triple in one year.
They are feral pigs, and while they have long plagued parts of the S
outhern and Western United States, now they have become a problem in the peaceful Champlain Valley of New York, an agricultural heartland on the edge of the Adirondacks.
They carry disease and can be aggressive toward people. They have even inspired a new television series, “Hogs Gone Wild,” about efforts to hunt them from Hawaii to Alabama. Perhaps most worrisome is their reputation as eating machines: the pigs devour ground-nesting birds and reptiles, fawns and domestic livestock, native vegetation and crops. Feral pigs have already proliferated in parts of western New York.
Complete Article here

Tuesday, March 6, 2012

Pariah Dog and Sinhala Hound

This post is mainly a extraction from Wikis for Sinhala Hound and Pariah Dogs and Indian pariah dog

I dont know why its Sinhala Hound and not Sri Lankan Hound.

The Indian pariah dog is a purebred dog category of pariah dog. The Indian Native Dog (INDog) is an ancient autochthonous (landrace) type of dog that is found all over South Asia. The Indian Native Dog and is nowadays referred to as the INDog by experts and enthusiasts. The term "Pariah Dog" is not derogatory in the canine context and refers to a class of primitive dogs of a specific appearance known as the "long-term pariah morph." The United Kennel Club (United States) recognizes purebred dogs bred for chasing large game in the Sighthound & Pariah Group. Included in this group are breeds that are either of early origin or modern reconstructions of early breeds or types.

Where not mixed with the blood of European dogs or other breeds and types, it is remarkably uniform in appearance all across the entire country...The type represents one of the few remaining examples of mankind's original domestic dog and its physical features are the same as those of the dogs whose fossil remains have been found in various parts of the world, from very early remains in Israel and China to later ones such as those found in the volcanic lava at Pompeii, near Naples in Italy. In India these were the hunting partners and companion animals of the aboriginal peoples of India...they are still found with the aboriginal communities who live in forested areas. Since these dogs have never been selectively bred, their appearance, physical features and mental characteristics are created by the process of natural selection alone.

INDogs are extremely alert and social. They make excellent watch dogs due to their territorial instincts. Their ruralevolution, close to forests where predators were common has made them extremely cautious and this caution is not to be mistaken for lack of courage. They bark at the slightest doubt or provocation and hence can be very noisy.

Other articles:

Saturday, March 3, 2012

Jazzfied Carnatic Music: from Shankar Tucker

I think I got introduced to this from Brown Pundits, maybe a Nandalal Rasiah post.

So whats with Carnatic Music. I remember my Uncle (Periappa) listening to this kind of music, while my cousin Robin was listening to Deep Purples Fireball (my Intro to rock, and still a great favorite). I too am starting to get what my Uncle Periappa heard. Deep music, just like the Blues of America. Then to sing the Blues you have to hurt and we dont have that in Sri Lanka.

So in Sri Lanka we will have the rhythm, beat and happiness (think papare), but never the depth and sadness of song as in the Blues. So what I am trying to say is maybe its really hard to be to be really sad, down and out and sing the blues in Sri Lanka.

Anyways here is the Jazzfied Carnatic Music from Shankar Tucker

Friday, March 2, 2012

Poisoning vs. Road Traffic Injuries as a Cause of Death in Rural Sri Lanka

Nice article by Michael Eddleston et al in PlosOne which says Poisoning bigger cause of Death than Road accidents in Rural (North Western Province) Sri Lanka.

Here is breakdown of the numbers of the biggest causes of death. Obviously most of the poisoning cases are self inflicted and the road deaths accidental. You can access and read the whole article here.

NY Times: Fidelity Ad: Investment Opportunities in Water

Back to Water as valuable resource of Sri Lanka.

Todays NY Times had a advertisement from Fidelity Investments about investment opportunities in Water. Fidelity Investments is is one of the largest US mutual fund companies with nearly $3.3 trillion in assets under administration and $1.5 trillion of assets under management.

Anyway here is the wording in the ad.

It takes 35 gallons of water to make one cup of coffee. Why? Because of all the water used to cultivate coffee beans. Similarly, it can take about 635 gallons to make one hamburger because of all the water required to grow feed for the cows.
The need for clean fresh water is increasing rapidly, too, as populations rise and standards of living improve around the world. In some places -- such as central California, the North China Plains, and parts of India -- the demand for water is already outstripping the local supply.

Because global water consumption is expected to increase by 40% over the next 20 years, water shortages may get more acute and widespread, spurring more reliance on desalination technologies, water reuse, and conservation. The results could have massive economic, ecological, and geopolitical consequences, creating investing opportunities in places you may never have considered.
This advertisement should be read in context of the following posts.