Supercomputers and the mystery of IQ

This article appeared today in the South China Morning Post, one of the leading newspapers in HK. I fixed a couple of typos in what appears below, but can neither confirm nor deny the accuracy of the entire article ;-)

Scientists seek to unravel the mystery of IQ: Hong Kong supercomputers will power unique genetic study of students

Fiona Tam
Updated on Dec 04, 2010

Some of the world's fastest supercomputers are being set up in Hong Kong to address the age-old mystery of human intelligence.

The study of intelligence quotient (IQ) is being conducted by BGI Hong Kong, [formerly] known as the Beijing Genomics Institute. It will survey DNA samples from 1,000 child prodigies from China's best high schools, comparing them with samples from 1,000 children of average intelligence, searching for genetic variations.

The study will examine protein coding genes of the extremely smart children, many of whom are expected to enroll at Harvard, Yale or Cambridge. The results will be correlated with each youngster's school test scores, in hopes of learning how specific genetic variations affect intelligence.

The study, which started in 2009 in Shenzhen, is moving to a new facility in Tai Po. By the end of this month, 115 of the world's fastest sequencers - the HiSeq 2000 - will have relocated to the city. They will be able to sequence the equivalent of 1,000 human genomes a day, and soon surpass the entire sequencing output of the United States to become the world's largest sequencing centre.

The study by BGI, which receives strong financial backing from the Shenzhen and mainland governments, will be the largest-scale examination of its kind. Ethical and privacy concerns have hindered such work in America and Europe.

In fact, ethical concerns haunt this entire subject. Ever since Nazi Germany misused science to support its murderous racist and anti-Semitic theories, Western societies have been extremely sensitive about linking genetics to IQ. Nevertheless, much scientific research suggests that IQ is strongly affected by heredity, although environment, education and nutrition also play a significant role.

According to Professor Steve Hsu, who comes to the study from the University of Oregon, scientists have identified several candidate genes that may relate to IQ, although researchers are not yet sure. He said about 50 per cent of humans' IQ is substantially [heritable]. "Scientists believe there are many genes that affect IQ, but none of them has been definitively discovered so far," he said. "Although there are some candidates in published work, so far the results have not been replicated." So-called IQ genes are those that influence cognitive capabilities, including verbal and spatial abilities, perceptual speed, memory and math skills.

The BGI study, however, did not begin by focusing on suspected IQ genes nor on candidate areas. Instead, geneticists from BGI, together with researchers from Harvard, Oregon and San Diego, are surveying markers across complete sets of genomes, using a method called GWAS (Genome Wide Association Study).

The GWAS method has proved particularly useful in finding genetic variations that contribute to complex diseases such as asthma, cancer, diabetes, heart disease and mental illnesses. Researchers first obtain DNA samples from each child by rubbing a swab inside his or her mouth to collect cells. DNA is extracted from the cells and spread on tiny gene chips, which can be later read and automatically surveyed by sequencers in the laboratory.

Specialists known as bioinformaticians will then build a genetic model and calculate the differences in genetic variations between the two groups of youngsters using supercomputers. When variations of brain-related genomes are found to be significantly more frequent in smart children than average ones, these variations will be associated with intelligence. Researchers will use these variations to identify the genetic differences that determine IQ.

Hsu said: "Typical genotyping [or analysis] scans the markers of genetic variation, known as single-nucleotide polymorphism[s], or SNPs. However, scanning the SNPs only gives researchers a crude picture. BGI's sequencing capacity enables us to scan the whole genome rather than just the SNPs." Hsu, a theoretical physicist, is helping the team improve its model design and calculations.

Yin Ye, BGI's vice-president, said researchers have already made some discoveries about IQ genes, but "it's too early to make public our results". While reluctant to give further details about the experiment, he took pains to say the study was essentially focused on studying students' aptitudes and suggesting occupations that would make the best use of their capabilities.

Hsu said the genetic basis for intelligence and other characteristics or traits - known as phenotypes - was likely to be discovered in the next five or ten years.

"Even if our planned study fails," Hsu said, "it's clear on the basis of trends in cost and capacity of sequencing [that] massive GWAS involving 100,000 or 1,000,000 individuals are right around the corner."

The idea of probing the genetic basis for human intelligence came after Beijing high school student Zhao Bowen, 17, who came to BGI on a summer internship last year to work on cucumbers, solved an assignment within a few hours that scientists expected to take him weeks.

Zhao is working as a full-time researcher now, and he will study the genes of 1,000 of his best-performing schoolmates from the affiliated high school of China's prestigious Renmin University, where some of the smartest children from across the country have been sent. It's a collaboration project between the institute and the high school.

Liu Pengzhi , principal of the affiliated high school, told parents in a forum that prodigies accounted for 1 to 3 per cent of the population, and the school was working closely with BGI to develop talented children, in addition to the high school's own experimental classes for nurturing prodigies.