Usually we read about research that has uncovered single letter differences in the human genome, but in the current issue of Nature Genetics Stephen W Scherer & Charles Lee, in their study entitled, Detection of Large-Scale Variation in the Human Genomereport the discovery of huge segments, numbering into the hundreds of thousands of letters, of DNA that repeat or are missing. These segments contain genes, which means that some people have duplicate genes, and the researchers are postulating that these extra or missing genes could influence susceptability to disease.

This was first discovered in a study that used DNA microarrays to analyze DNA of patients with developmental disorders. A group of healthy people were chosen to be the control group, and it was within the control that they found either the missing or the repeating sequences. They found an average of 12 DNA segments that were missing or duplicated in the control group of 39 healthy people.

Scherer & Lee’s study fairly duplicates the work of Michael Wigler published in Science in July. In that study, Large-Scale Copy Number Polymorphism in the Human Genome they found that, on average, 11 stretches of DNA that had either missing or repeated sequences of more than 400,000 letters of genetic code.

Wigler’s study found that stretches of DNA contained genes associated with drug resistance in breast cancer, leukemia, and matters such as body weight.

Both of these studies of course supplement the work of the HapMap Project which is focusing primarily on single letter differences between populations and not such long sequences between populations.

Here is some supplementary data on large-scale copy number variations that were detected by Scherer & Lee. Here is some supplementary data on large-scale copy number variations near known polymorphic and disease loci such as Muscular Dystrophy, Duchenne (DMD) and Becker (BMD) Muscular Dystrophies, X-linked Mental Retardation, Squamous Cell Carcinoma, and Recessive Hereditary Megaloblastic Anemia 1. Here is a brief on the methods used in the study.

Posted by TangoMan at 11:38 PM

America is bad. You wanna know why? Because it puts so many people in prison: 715 per 100,000 population, the highest incarceration rate in the world.

For every 100,000 people, Sweden imprisons only 75 and Sudan only about 36. That’s because they’re more enlightened.

Also, America imprisons more people because it’s so violent, unlike peaceful and orderly societies like Japan. Or Haiti.

Prison Population Rates per 100,000 of the national population

United States	715
Japan	54
Haiti	53

Source: International Centre for Prison Studies, Kings College, London

In fact, the current US incarceration rate is a record high. That’s because crime is too.[1]“American prison population surpasses 2 million, the highest incarceration rate in the world”, Salt of the Earth: Your online resource for social justice, April 2003.

Violent crime, which is of most concern to people on the street, has fallen to its lowest levels since 1974, when data was first collected nationally.Unlike in Europe, where people are more civilized.[O]ver the last 25 years there appears to have been a general increase in crime in all European countries.Another reason that so many Americans are in prison is that American sentences are so long. That’s because Americans are vengeful. Europeans are enlightened, giving convicts shorter sentences so they have less trouble re-entering society.Laban Tall, “Cash for Good Causes”, UK Commentators, 2004 August 11.

In a British prison you never serve your full sentence – that would be too harsh. [Iorworth] Hoare was released early and by November 1975, when he should still have been inside, he was back in court for another attack on a woman.
….
He had been released early once, only to offend again and be convicted. Surely that would be an end of early release ? But to the probation officers and social workers of the Criminal Justice system he was still capable of redemption, of being reformed. Give him another chance. Sentenced to four years in November 1975, less that THREE years later he was back in court charged with assault and indecent assault – crimes again committed when he should have been in prison. This time he got four years.

We must assume he was let out early and avoided being convicted again until June 1983, almost a year after he should have finished his sentence. This time the charges were rape and indecent assault, the sentence seven years. Naturally he was released early, and only five years after sentence was attempting to rape a retired teacher.

This time the judge had had enough.

“Paramount in my mind is that every moment you are at liberty some woman is at risk and I believe it to be my duty to protect, so far as I am able, women from the risk you represent.

“This is the last in a long line of appalling offences committed against women and the only sentence I can pass is one of imprisonment for life.”

Life ? Fifteen years and he’s on day release.[/end sarcasm]
Let’s go back to the statistics. Despite an uptick in the past year, US “crime rates remain some of the lowest in a generation”. At the same time, the US incarceration rate has reached an all time high, at least four to five times the rate, depending on the country, seen in western Europe, which has seen a general increase in crime over the last 25 years.Peter Reydt, “Britain: prison overcrowding reaches breaking point”, World Socialist Website, 2004 February 26.

Under Prime Minister Tony Blair, the number of prisoners has risen by 24 percent. This is not due to rising crime rates, but to the readiness of the courts to resort to custodial sentencing for even minor crimes. First time burglars are twice as likely to go to jail now as they were eight years ago, whilst the number of adults serving sentences for less than 12 months is up 160 percent since 1999.
….
The increase has far overstepped all expectations. The projected figures for 2006 now expect the prison population in England and Wales to reach 87,200—9,500 more than planned for.
….
Such is the scale of overcrowding, that Home Secretary David Blunkett is said to be looking into increasing the use of electronic tagging. Some 3,500 people are currently on Home Detention Curfew.

The government’s criminal policy has been carried out under the banner of “tough on crime, tough on the causes of crime”. Committed to a right-wing big business agenda, the government has fulfilled the first pledge, but has done nothing to alleviate the social conditions that cause crime in the first place. Instead its own policies have contributed to the increase in the prison population through the rising levels of social inequality. Many inmates, for example, are in prison for petty offences, such as non-payment of fines, bills, etc. [Sure they are.]

The official attitude towards criminal policy, as with every other area of British social policy, increasingly mirrors that of the United States.Good for Britain.

In any criminal justice system, the safety of law-abiding citizens is the one priority that should supersede all others. Hell, it’s the very point of society. It’s the reason that the state has a monopoly on violence. We, as citizens, “outsource” self-defense to our police and military so the rest of us don’t have to worry about such things and can spend time on things we’d rather be doing and also because they can specialize and take advantage of economies of scale. This doesn’t preclude treating prisoners well, but to do so at the expense of the safety of society at large betrays the very purpose of civilization.Prison overcrowding has the most devastating impact on the well being of inmates. The annual report for England and Wales for 2002/2003 by the Chief Inspector of Prisons published earlier this year, graphically underscored this. Its main conclusion found that the explosion in prison numbers was directly related to a staggering rate of suicides and self-harm in English and Welsh prisons.Cry me a f*ckin’ river.

Hey, I’ve got an idea! BUILD MORE PRISONS, BITCH!

Now, before this post completely degenerates into right-wing bilespew, I’m going to point out how capitalism contributes to this state of affairs. Of the countries in western Europe, only Finland (17.1), Iceland (2.9), Norway (14.9) and Sweden (21.8) have population densities lower than the United States’ (32.0) (as measured in persons per square kilometer). Western Europe has an overall population density of 110.2. Of countries with a significant amount of rural territory (i.e. excluding San Marino, at 475.1; Malta, at 1,236.3 and Monaco, at 16,135.0[!]), Britain, at 249.5, is beaten only by Belgium (342.3) and the Netherlands (480.8), which is why God invented Australia. (Source: U.S. Bureau of the Census, International Data Base.)

When land is scarce, homes, offices and factories are gonna come up much higher on the priority list than prisons. I get that. I’m willing to cut western Europe a little slack on account of that.

But this clapped-out old nag of an anti-American high moral horse is long overdue his trip to the glue factory.

I understand that this post doe
sn’t address US drug policy, but this one does.

And on the matter of incarceration and race (via MilkandCookies), consider the words of noted African-American actor Samuel L. Jackson.Ninety-eight percent of the people in jail belong in jail. The other two percent probably did something somewhere, and it caught up with them. If you live your life a certain kind of way, you don’t have to worry about that kind of thing happening. Like with the police, I always gave them respect. Cops have a hard job; I understand that. Of course, some of ’em are kind of screwed up mentally in certain ways….They deserved to die and I hope they burn in hell!

[1]What the f*ck happened to Finland?

Posted by jeet at 06:11 PM

G. H. Hardy’s letter to science . He notes that: In a word, there is not the slightest foundation for the idea that a dominant character should show a tendency to spread over a whole population, or that a recessive should tend to die out. Reading a biography of Ramanujan a few years back I recall that Hardy was shocked about some of the naive and sloppy ideas espoused by the biologists of his day. For him, the Hardy-Weinberg Equation was so plainly obvious that he was reluctant to pursue the matter. The fact that scientists at the time were duped by what seem to be in hindsight (thanks in part to the Hardy-Weinberg Equation) supremely obvious fallacies should make us cautious about the ability of the public to digest the new bioscience with any level of clarity. We’ll know that psychology has really made it as a science capable of novel predictions when it stops making sense to our own intuitive understanding of human nature (The Theory Of Mind), graduating from the elaboration of the obvious to the exploration of the hidden structure of reality.

Posted by razib at 09:56 PM

A slight thought experiment, which I have alluded to before, but never been totally explicit about. Take a population, say 1,000 females of the black race and 1,000 males of the white race. Allow them to interact, isolated from the distractions of the outside world. In a few years, little brown children are born….

Moving into the world of ‘make believe,’ imagine that the phenotype ‘white’ is controlled by the same locus as the phenotype ‘black.’ One who expresses a black phenotype has the genotype BB while one who expresses the white genotype has the genotype bb. In the world of generation 1, blacks are jet black, while whites lack pigment at all (are albinos).

Assume that the density of melanin is proportional to the number copies of the B allele one carries. So, the density of melanin of blacks is 2x (1 copy of B is proportional to x), while for whites it is 0. In generation 2, all carry copies of both alleles. That is:

BB X bb = Bb, in that all matings were between a BB and bb individual in the parental generation.

Since density of melanin in the skin is proportional to the number of copies of B one carries, the generation 2 offspring are all ‘brown,’ fairer than their mothers, darker than their fathers.

So we live in a brown planet, right? Blacks and whites banished forever?

Not really. Assume random mating and Hardy-Weinberg proportions will quickly ensue (ignore random genetic drift and selection). That is, p2 + 2pq + q2. Since the allele frequencies are 50/50, about half of the population expresses the Bb phenotype, while 1/4 is homozygous for the black and white phenotypes (that is, p = .5 & q = .5, so, substitue into the equation above).

But let’s throw in a twist, rule: like mates with like whenever possible after generation 1. That is, people who express the black phenotype marry other blacks, browns prefer browns and whites only pair up with whites.

In generation 2, this is a moot point, only browns exist, ergo, browns pair up with browns. But, in generation 3 whites and blacks will reappear as homozygous offspring of their heterozygous parents. Since like mates with like, blacks and whites will pair up with each other in generation 3. Since they are homozygous, they will have black and white offspring only.

The browns also prefer each other. Because they are heterozygous they will give birth to mostly heterozygous offspring (1/2 within the population of the children of brown parents). But they will also give birth to white and black children (1/4 of each).

Iterate.

The process (assortive mating) clearly mitigates against the perpetuation of brown people. Perhaps a mild form of this happened in Brazil in the recent past?

I say this because a team of Brazilian researchers suggested that the lineages of Brazilian whites were highly confounded with non-white Brazilians. That is, though both groups were of distinct phenotype, their ancestry was far less pure than physique might have suggested.

Going back to the world of make believe, in generation x, where x >> 1, if the rule I state holds, you have a population that has been cleaved into two. Yet, aside from the color locus, the two populations are equally white and black, though you wouldn’t guess that from glancing at their butt cheeks.

No wonder such a simple idea like Mendelianism did not gain traction until well into the 20th century (see R. A. Fisher’s seminal paper that showed how continuous traits emerged out of Mendelian principles, resolving the ‘dispute’ between the Mendelians and the biometricians). Human beings are the products of millions of years of evolution. We have predispositions and tendencies, and our fine pattern detection sensors come preloaded with biases shaped by our past. Everyone understands genetics on the intuitive level in what it does, the principle of heredity is an atomic & foundational element of human nature. It is expected that a mother and father should birth offspring that resemble them, we do not attain this position via reason, rather our own cognitive modules come loaded with a few basic understandings, triggered and molded by our experience.

That being said, we do not have an instinctive understanding of Mendelianism. Humans know what genetics does, but have little grasp of how it does it. People speak in broad inclusive typologies of race, tribe or family, but these are ultimately fuzzy emergent concepts fixed upon the reality that we are all but a commune of genes and their protein slaves.

In the EEA family and tribe were restricted in space, and genes were exchanged at a tepid pace, from hillock to valley and hillock over the generations. Today, a man born in Ghana can become Secreatary General of the United Nations and wed a Swedish woman. Granted, the majority of the human race does not consist of mobile cosmopolitans, but mobile cosmopolitans are an influential segment of humanity. Additionally, in places like Latin America one can see the impact of hundreds of years of mixing between lineages, indigenous and foreign.

We are slowly stepping outside the land of make believe. Our intuition might not always lead us to the right path, and the principles that we could neglect because the sun always rose in the east must now be examined with greater care and attention.

Posted by razib at 08:38 PM

The Jewish magazine Forward has an article up titled A Skeleton in the Jewish Family Closet?. The genetic angle, the possible non-Levantine origin of the Levite male lineage (the article points to a Slavic source) is somewhat old news. Over the past few years several researchers have suggested a non-trivial level of intermarriage occurred between Jews and non-Jews in the areas in which they settled, while others, including Greg & Henry reject that position (here is a post where the study referenced in the article is linked to as well as a bunch of other Judaic-genetics) [1]. My personal opinion is that after the rise of Christianity the intogression of indigenous genes was the result of one generation of intermarriage with local women by immigrant Jewish men, but we all really have to wait and see, after all, a one-dimensional picture from only one lineage (NRY, mtDNA) tells us only so much.

The bigger point is that all these “Who is a Jew” arguments based on blood (the maternal descent rule), rather than the sum total of belief, experience, culture and yes, ancestry, is highly simplistic. When one makes faslifiable assertions one must be prepared to stumble upon evidence to the contrary. In the short term these genetic studies are grist for the mill of half Jews who take umbrage at the often patronizing attitude that “full Jews” display toward them. After all, who has more to lose, a half Jew demoted to a “quarter Jew” or a full Jew demoted to a half Jew? Whose the mischlinge now?

(thanks to “Xguy” for the link)

[1] Michael Hammer referred to in the article, posits that the Y lineage is actually Middle Eastern, and just happens to be of the same haplotype as the Eastern European line. This sounds like a weird assertion, until you realize that Hammer has argued for relatively minor introgression of “non-Jewish” ancestry in the modern Ashkenazi population, that is, his position must be viewed in light of his model.

Posted by razib at 10:24 AM

John B Whitfield writing in the August issue of Alcoholism: Clinical and Experimental Research and working with data from three studies conducted between 1980 and 1995 on volunteer adult male and female Australian twin subjects conclude that reported alcohol consumption was mainly affected by genetic factors and that genes that affect alcohol intake do affect alcohol dependence, but genetic effects unique to dependence are also significant; environmental effects are largely unique to either intake and dependence. Here is the abstract.

Nothing really earth shattering, but the genetic impulse towards addiction that is separate from the genes that code for alcohol consumption and addiction does open up some new avenues for research. Is there an addiction gene that predisposes one to addictive behavior?

The search for the actual gene sequences is being conducted by Dr. Howard J. Edenberg:

There are 7 human alcohol dehydrogenase genes that evolved from a common precursor, but now differ in the tissues in which they are expressed. We are now mapping cis-acting elements in the distal 5′ regions of these genes, and examined their effects in transient transfection assays. We are looking for tissue-specific elements that regulate these genes, and the transcription factors that control them. Posted by TangoMan at 08:32 PM

We’re all familiar with the concepts of darwinian selection but let’s for a moment consider the conseqences of a world in which we turn the model on it’s head. What happens when mate selection becomes a information blind (or almost so) process? No, I’m not referencing arranged marriages because in that practice the families act as the agents in the information exchange process and are making rational (one hopes) decisions on behalf of their sons and daughters. Rather, I’m referring to the Kyrgyz practice of Bride Kidnapping:

Petr and Fatima arrive as a wedding is about to begin. Women are busy making traditional Kyrgyz bread for the occasion, and men sit in chairs outside, talking and sipping tea. The groom confesses he has had some difficulty finding a bride, but he is hopeful that “this one will stay.”

When the bride does arrive, she is dragged into the groom’s house, struggling and crying. Her name is Norkuz, and it turns out she has been kidnapped from her home about a mile away.

[ . . . . . ]

As the women of the groom’s family surround Norkuz and hold down both of her hands, they are at once forceful and comforting, informing her that they, too, were kidnapped. The kidnappers insist that they negotiated the abduction with Norkuz’s brother, but her sister, a lawyer from Osh, arrives to protest that her sister is being forced to marry a stranger. Ideally in Kyrgyz circles, a bride’s family gets a price for their daughter, but Norkuz is 25 — considered late to marry — and the women remind her she is lucky she was kidnapped at all.

Within the space of an hour, Norkuz struggles less, looking exhausted but laughing along with the women who have placed a scarf on her head. Tradition dicates that once the bride accepts the ceremonial scarf, the matter is settled and the wedding can commence. Norkuz relents.

[ . . . . . ]

Petr learns that the origins of this strange custom are murky: “Some say Kyrgyz men used to snatch their brides on horseback. Now they use cars, and if a villager doesn’t have a car, he hires a taxi for the day.”

Petr and Fatima speak with a taxi driver in Osh who says he helped kidnap a girl earlier that same day. During Soviet times, bride kidnapping was banned, but in the past decade, the old tradition has revived, especially in rural areas.

Jumankul, 19, is under pressure from his parents to marry and bring home a wife who can help work on the family farm. Jumankul tells Petr and Fatima that he’s seen a girl in Osh whom he likes and plans to drive to the city in a few hours to kidnap her.

“We can’t afford her hand,” says Jumankul’s father. “They wanted too much money.”

The family has hired a taxi to drive Jumankul to Osh where he and his friends plan to find and kidnap the girl he has seen at a bazaar. But when they get to Osh, Jumankul can’t find the girl. The group drops by a vodka stand to try to find out where she lives, but the girl working there suspects a kidnapping and refuses to tell Jumankul’s brother, Ulan, the address of the girl. “Find it yourself,” she tells him.

Not wanting to return home empty-handed, Jumankul and his friends decide to change plans and kidnap the girl in the vodka bar.

Her name is Ainagul, and by the time Petr and Fatima return to Jumankul’s village outside of Osh, she has been resisting a room full of women for more than ten hours. Though Jumankul’s older brother claims her family has already agreed to the kidnapping, Ainagul stands in a corner of the room, crying, and continuing to fend off the women who take turns trying to put the wedding scarf on her head.

“It’ll be over soon,” Jumankul’s brother, Ulan, tells Petr. “You’ll see.”

But Ainagul puts up a strong fight, and the women tire of trying to convince her. After the oldest woman in the village makes a final attempt, telling Ainagul to stay or she will be unhappy, the women give up. Her ordeal over, Ainagul is free to go.

Once she has left, the women sit outside Jumankul’s home and curse the departed girl. They say that her child will be a drunk and that her mother-in-law will be cruel. Jumankul, too, is upset and worries that he will never find a bride who will stay.

The information void here is startling. The initiation of the process is made by a would-be groom who stalks an unsuspecting bride. Her fate is determined only be her resistance or acquiescence to a process of duress all while she is in an almost complete information vacuum.

Not to be outdone by such revolutionary disregard for darwinian selection processes the British are doing their best to even the cultural playing field:

A BOSS had her job ad banned – because it asked for “hard-working” staff.

Beryl King was told by a Jobcentre that it discriminated against people who were not industrious.

Yesterday Beryl, 57 – who was after warehouse workers – said: “I couldn’t believe my ears. Has our world gone mad?

“I’ve been running my business for 27 years and it’s getting harder to find people who want to do a fair day’s work for a fair day’s pay.

“How long before someone says you can’t pay people for working because it discriminates against those on benefit who are paid for not working?”

Beryl, who owns two job agencies in Totton, Hants, offered £5.42 an hour for “warehouse packers who must be hard-working and reliable”. She added: “We wouldn’t dream of discriminating on grounds of race, sex or age.

“However, this is taking it too far. The ability to work hard is a talent in the same way as is the ability to type. If I advertise for a typist am I discriminating against people who can’t type?”

The Southampton Jobcentre is investigating. A spokesman said: “Words such as ‘hardworking’ can be accepted if used with a clear job description.”

Last month, optician Pauline Millican told how a Liverpool Jobcentre axed her request for a £5-an-hour hard-working receptionist on similar grounds to Beryl’s.

The drive towards the lowest common denominator continues unabated, for men unable to find brides and for lazy slobs alike. Welcome to the Lowest Common Denominator World. For those who are mathematically inclined, and who wish to use this talent before it too is discriminated against, you may appreciate the significance of this mindset by considering this equivalence:

Information = discrimination.

Posted by TangoMan at 05:39 PM

or, Are the Chinese a bunch of prudes or what?

I bring this up because, not only does the sexual morality of modern Britons dismay Laban (a proud Briton though he may be, I doubt he’ll dispute the assertion), but the survey “cited” by the article (I put “cited” between scare quotes because the article fails to give either its title or author) suggests an alternative explanation for what godless describes as (and I’m paraphrasing here) “East Asian guys’ tendency to have a hard time in the female department.” (My Lord, my Lord, why hast thou forsaken me!)[J]ust 17% of Chinese and 30% of French[!] would consider it normal to have had a number of lovers in the double digits.
….
[Of the peoples surveyed] the Chinese were the most moral, with 70% believing in monogamy.[self-deception]Maybe we’re not failing to get laid, maybe we just don’t wanna! Didja ever consider that![/self-deception]

You can find the whole article on those slutty, slutty limeys here.

I wonder how much of an increase in traffic we’re going to see from searches for “christina aguilera + slutty”.

Posted by jeet at 02:00 PM

Just got this in the mail today:

I have put our Ashkenazi manuscript back up on my website together with some quotes from the editor rejecting it. Meanwhile you are free to tell folks about it.

http://harpend.dsl.xmission.com/Documents/Ashkenazi.IQ.pdf

Best, Henry

Enjoy.

Those readers with blogs should link, would be interesting to see Greg & Henry’s work getting attention our tiny corner of the blogosphere.

Posted by razib at 05:19 PM

New ACT data out. Surprise, surprise regarding rank order, etc.

What is interesting is the stability of the mean score.

If you look at a little longer time period, the stability of mean scores is uncanny1:

National Average ACT Composite Score, 1994–2004 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 20.8 20.8 20.9 21.0 21.0 21.0 21.0 21.0 20.8 20.8 20.9

Now, we know the SAT is highly g-loaded, and the ACT cannot be too far behind (see how high they correlate). So, combine this with J. P. Rushton’s work, and I pose to you that the Flynn Effect is just psychometric slight-of-hand, i.e., while IQ scores appear to the naked eye to be going up, mean “intelligence” is rather steady.

1. The rescaling was in the early 1990s, and I do not believe that any of the scores were computed under the old scaling. Posted by A. Beaujean at 09:47 PM