Do Humans Pick Friends Who Have Similar Genetic Makeup?

Nicholas A. Christakis and James H. Fowler, in a recent paper titled “Friendship and Natural Selection,” make an interesting hypothesis: that we select friends who have similar genetic makeup as ourselves. The dataset used was the famous Framingham Heart Study. From their abstract:

More than any other species, humans form social ties to individuals who are neither kin nor mates, and these ties tend to be with similar people. Here, we show that this similarity extends to genotypes. Across the whole genome, friends’ genotypes at the SNP level tend to be positively correlated (homophilic); however, certain genotypes are negatively correlated (heterophilic). A focused gene set analysis suggests that some of the overall correlation can be explained by specific systems; for example, an olfactory gene set is homophilic and an immune system gene set is heterophilic. Finally, homophilic genotypes exhibit significantly higher measures of positive selection, suggesting that, on average, they may yield a synergistic fitness advantage that has been helping to drive recent human evolution.

So the interesting question is why would this happen? The arXiv blog goes into possible explanations:

Perhaps the genetic links are simply a reflection of this common background. Not so, say Christakis and Fowler. The correlation they have found exists only between friends but not between strangers. If this was a reflection of their common ancestry, then the genomes of strangers should be correlated just as strongly. “Pairs of (strictly unrelated) friends generally tend to be more genetically homophilic than pairs of strangers from the same population,” they point out.

There are certainly other processes that could lead to friends having similar genomes. One idea that dates back some 30 years is that a person’s genes causes them to seek out circumstances that are compatible with their phenotype. If that’s the case, then people with similar genes should end up in similar environments.

Personally, I don’t buy this:

There may be another mechanism at work. One idea is that humans can somehow identify people with similar genetic make up, perhaps with some kind of pheromone detector. Indeed, Christakis and Fowler say that some of the genes they found in common are related to olfaction, a discovery they describe as “intriguing and supportive”.

While interesting, I’m not entirely convinced of the overall findings and would be curious to see this study expand. What do you think?

On Compatibility Genes: Can You Smell the Perfect Partner?

The Guardian on whether humans have the ability to smell out suitable partners/mates, based on an upcoming book by Daniel M. Davis, The Compatibility Gene: How Our Bodies Fight Disease, Attract Others, and Define Our Selves:

The basis for this notion is the so-called smelly T-shirt experiment, first performed by a Swiss zoologist called Claus Wedekind in 1994. He analysed a particular bit of the DNA of a group of students, looking specifically at the major histocompatibility genes (MHC). The students were then split into 49 females and 44 males. The men were asked to wear plain cotton T-shirts for two nights while avoiding anything – alcohol, cologne etc – that might alter their natural odour. After two days the shirts were placed in cardboard boxes with holes in them, and the women were asked to rank the boxes by smell using three criteria: intensity, pleasantness and sexiness.

Wedekind’s results appeared to show that the women preferred the T-shirts worn by men with different compatibility genes from themselves, raising the possibility that we unconsciously select mates who would put our offspring at some genetic advantage. The experiment was controversial, but it did alter scientific thinking about compatibility genes. And while the mechanism behind this phenomenon is poorly understood, that hasn’t stopped dating agencies from employing MHC typing as a matchmaking tool.

Of course, there are labs out there taking advantage of this science:

One lab offering such testing to online agencies (you can’t smell potential partners over the internet; not yet), a Swiss company called GenePartner, claims: “With genetically compatible people we feel that rare sensation of perfect chemistry.”

But take all this with a big grain of salt, as the research is still preliminary and no one really understands how all this works:

It is not completely understood how all this works at the molecular level, but it is at this forefront that Davis toils. “My research is in developing microscopes that look with better resolution at immune cells and how they interact with other cells,” he says. This interaction is “reminiscent of the way neurons communicate” in the brain, raising the possibility that your compatibility genes are responsible for more than just fighting infection, and could even influence how your brain functions. I confess to Davis that I don’t really understand this part. “None of us do,” he says. “I just happened to write a book about it.”

But how does the smelling thing work – if it works? It has been shown that mice can, and do, detect compatibility genes by smell, and that stickleback fish also choose mates by their odour, but in humans, Davis admits, the jury is out. “How it works on the olfactory level is basically not understood at all,” he says.

I think the more interesting point from Davis’s research is this: since each human responds slightly differently to any particular disease, in the not-too-distant future vaccines and other medications may be tailored to match our compatibility genes.

On Genetic Advantages, Doping, and Sports

Malcolm Gladwell, in my opinion, has published the best piece he’s written this year in “Man and Superman.” The central question he posits: do genetic advantages make sports (in particular, cycling) unfair compared to those who choose to dope? Paraphrased: what qualifies as a sporting chance in athletic competitions? He goes through a brief comparison of elite athletes in skiing, long-distance running, but his primary focus is on cycling.

When Hamilton joined Armstrong on the U.S. Postal Service racing team, he was forced to relearn the sport, to leave behind, as he puts it, the romantic world “where I used to climb on my bike and simply hope I had a good day.” The makeover began with his weight. When Michele Ferrari, the key Postal Service adviser, first saw Hamilton, he told him he was too fat, and in cycling terms he was. Riding a bicycle quickly is a function of the power you apply to the pedals divided by the weight you are carrying, and it’s easier to reduce the weight than to increase the power. Hamilton says he would come home from a workout, after burning thousands of calories, drink a large bottle of seltzer water, take two or three sleeping pills—and hope to sleep through dinner and, ideally, breakfast the following morning. At dinner with friends, Hamilton would take a large bite, fake a sneeze, spit the food into a napkin, and then run off to the bathroom to dispose of it. He knew that he was getting into shape, he says, when his skin got thin and papery, when it hurt to sit down on a wooden chair because his buttocks had disappeared, and when his jersey sleeve was so loose around his biceps that it flapped in the wind. At the most basic level, cycling was about physical transformation: it was about taking the body that nature had given you and forcibly changing it.

“Lance and Ferrari showed me there were more variables than I’d ever imagined, and they all mattered: wattages, cadence, intervals, zones, joules, lactic acid, and, of course, hematocrit,” Hamilton writes. “Each ride was a math problem: a precisely mapped set of numbers for us to hit. . . . It’s one thing to go ride for six hours. It’s another to ride for six hours following a program of wattages and cadences, especially when those wattages and cadences are set to push you to the ragged edge of your abilities.”

Hematocrit, the last of those variables, was the number they cared about most. It refers to the percentage of the body’s blood that is made up of oxygen-carrying red blood cells. The higher the hematocrit, the more endurance you have. (Mäntyranta had a very high hematocrit.) The paradox of endurance sports is that an athlete can never work as hard as he wants, because if he pushes himself too far his hematocrit will fall. Hamilton had a natural hematocrit of forty-two per cent—which is on the low end of normal. By the third week of the Tour de France, he would be at thirty-six per cent, which meant a six-per-cent decrease in his power—in the force he could apply to his pedals. In a sport where power differentials of a tenth of a per cent can be decisive, this “qualifies as a deal breaker.”

A must-read if you’re at all interested in sports, genetics, and the doping as cheating debate.

This sentence in the concluding paragraph is telling:

It is a vision of sports in which the object of competition is to use science, intelligence, and sheer will to conquer natural difference. 

Malcolm Gladwell Responds to Critics of the 10,000-Hour Rule

Malcolm Gladwell came into mainstream prominence with his explanation of the 10,000 hour rule. While Malcolm Gladwell didn’t invent the rule, he instantly popularized it via his best-selling book Outliers. The principle actually dates to a 1993 study (“The Role of Deliberate Practice in the Acquisition of Expert Performance”; PDF link), though in that paper the authors called it the 10-year rule.

In the latest piece for The New Yorker, Gladwell is back in the spotlight, but this time he is on the defensive. Here, he eviscerates the simplification of the 10,000 hour rule:

No one succeeds at a high level without innate talent, I wrote: “achievement is talent plus preparation.” But the ten-thousand-hour research reminds us that “the closer psychologists look at the careers of the gifted, the smaller the role innate talent seems to play and the bigger the role preparation seems to play.” In cognitively demanding fields, there are no naturals. Nobody walks into an operating room, straight out of a surgical rotation, and does world-class neurosurgery. And second—and more crucially for the theme of Outliers—the amount of practice necessary for exceptional performance is so extensive that people who end up on top need help. They invariably have access to lucky breaks or privileges or conditions that make all those years of practice possible. As examples, I focussed on the countless hours the Beatles spent playing strip clubs in Hamburg and the privileged, early access Bill Gates and Bill Joy got to computers in the nineteen-seventies. “He has talent by the truckload,” I wrote of Joy. “But that’s not the only consideration. It never is.”

Malcolm Gladwell goes on to reference David Epstein’s new book, The Sports Gene: Inside the Science of Extraordinary Athletic Performance:

I think that it is also a mistake to assume that the ten-thousand-hour idea applies to every domain. For instance, Epstein uses as his main counterexample the high jumper Donald Thomas, who reached world-class level after no more than a few months of the most rudimentary practice. He then quotes academic papers making similar observations about other sports—like one that showed that people could make the Australian winter Olympic team in skeleton after no more than a few hundred practice runs. Skeleton, in case you are curious, is a sport in which a person pushes a sled as fast as she can along a track, jumps on, and then steers the sled down a hill. Some of the other domains that Epstein says do not fit the ten-thousand-hour model are darts, wrestling, and sprinting. “We’ve tested over ten thousand boys,” Epstein quotes one South African researcher as saying, “and I’ve never seen a boy who was slow become fast.

It appears Gladwell is accepting of the challengers:

It does not invalidate the ten-thousand-hour principle, however, to point out that in instances where there are not a long list of situations and scenarios and possibilities to master—like jumping really high, running as fast as you can in a straight line, or directing a sharp object at a large, round piece of cork—expertise can be attained a whole lot more quickly [than 10,000 hours]

Malcolm Gladwell’s elaboration is important: it’s not just about taking in the time to practice, it’s also the efficacy of practice that matters. Preparation beats innate talent, but there is a limit.

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Further reading:

1) “Your Genes Don’t Fit: Why 10,000 Hours of Practice Won’t Make You an Expert”

2) “The Sports Gene and the New Science of Athletic Excellence

The Sports Gene and the New Science of Athletic Excellence

Katie Drummond interviews David Epstein, the author of the recently released The Sports Gene: Inside the Science of Extraordinary Athletic Performance.

The context is fascinating: whether you’re a gym rat or just starting out with an exercise routine, you typically follow the advice you read in magazines, from friends/coworkers, or personal trainers. But in the future, however, you might be able to develop a training plan that has nothing to do with external edicts, generalized principles, or even trial and error. Instead, you’d be training according to your own genetic athletic profile — a sequence of genes that determine what kind of exercise, done for how long and how often, your body will best respond to.

According to Drummond,

Epstein offers a fascinating look at how genetic research is already transforming sports science. Along the way, he digs into controversial questions about gender and race, examines the latest in genetic testing that purports to spot athletic traits, and unravels how some of the world’s best athletes — from Usain Bolt to Michael Jordan — attained the pinnacle of sporting success.

On to the interview questions:

Q: You don’t shy away from controversial topics in the book, including gender and ethnic differences where athletic ability is concerned. You also mention how scientific progress has been hindered because of concerns about sexism or racism creeping into cultural discussions about findings. To what extent, do you think, have those fears held back research on genetics and athleticism?

A: You know, when I went into the book I figured that scientists worked in bubbles to some extent, and that they didn’t decide what to publish based on any external force. In a sense, that they published their data so long as they maintained academic rigor. But in this field, that hasn’t been the case at all: scientists have literally told me that they have data, really great data, that they won’t publish because of how it might be perceived or construed by the public.

The primary instance of this is related to race. Namely, scientists are concerned that data suggesting that black people are predisposed to some athletic superiority will get wound up into this bigoted misconception that athletic ability means someone lacks intellect. That might sound ridiculous, but it’s been a prejudice for some time, and it has really reached deeply into the psyches of some scientists. Where gender is concerned, I had one researcher who has published a huge amount on sex and gender differences tell me that he didn’t publish any findings until he got tenure, because it just threatened to be too controversial. From my perspective, the best way to move the field forward and to help athletes is to collect sound data and then publish it — I was disappointed to see that this hasn’t happened.

Q: As you point out, the relationship between athletics and genetics is really complicated. But where do you see research going in the future, and what will it mean for athletes — elite or otherwise?

A: It is complicated, but we’re already seeing genetic tests trickling out that can hint at different aspects of someone’s athletic ability. Namely we’re seeing gene tests that relate to injury risk — one example is a test for the ApoE gene, which helps determine your vulnerability to brain damage from the hits you take during boxing or playing football, for example. That test is already out there, and it might really make a difference for athletes, how they compete, and what kind of medical treatment they get.

Where research is concerned, the most progress we’re seeing now is in studies that look at genes related to responses to endurance training — genetic pathways that determine who responds well to cardiovascular exercise, and who doesn’t. That has obvious appeal for athletes, or even people who wish they were athletes: the takeaway is that just because you don’t seem to have this innate, amazing talent, you might have an underlying predisposition to respond much better than you’d expect. The idea of figuring out someone’s training routine based on what they do and don’t respond to is really appealing, and I’d say we’re maybe five or ten years away from getting into that.

And it might also play an important role in personalized medicine: if someone with heart problems can respond well to aerobic activity, then maybe we can prescribe an exercise program instead of medicating them.

Fascinating. I’ve placed The Sports Gene in my to-read queue.

On Patent Law, Life, and Nature

Did you know that genes are patentable? Because I hadn’t until I read Michael Specter’s New Yorker piece summarizing patent law as it applies to life:

Traditionally, patents have applied solely to inventions, granted as a reward for ingenuity and to encourage innovation. Naturally occurring substances, like DNA, were exempt from such laws. Then, in 1980, Ananda Mohan Chakrabarty, a scientist working for General Electric, filed an application for a patent on a bacterium that he had modified genetically so that it could consume oil. The Patent and Trademark Office rejected Chakrabarty’s application on the ground that the bacterium was a product of nature. Chakrabarty sued, arguing that, by altering the organism, it was his ingenuity that made the bacterium valuable. The case ended up before the Supreme Court, which, by a vote of five to four, ruled in favor of the engineer. “The fact that micro-organisms are alive is without legal significance for the purpose of patent law,” the Court wrote. Chakrabarty’s creation became the first life-form to receive a patent.

Since then, genes considered to have been “isolated from their natural state and purified” have been eligible for patent protection. The first such patents were issued for DNA that had been altered to produce specific proteins, such as the insulin used daily by millions of diabetics. Those patents were rarely controversial. Over the years, however, patents have also been granted to people who have identified genes with mutations that are likely to increase the risk of a disease. Any scientist who wants to conduct research on such a gene—even on a small sequence of its DNA—has to pay license fees. The practical effect has been chilling. According to public-health officials and academic leaders, it has stymied research into many types of disease.

This seems particularly outrageous:

A patent on a product of Nature would authorize the patent holder to exclude everyone from observing, characterizing or analyzing, by any means whatsoever, the product of Nature.

In the end, this is big business (but with a cost):

Moreover, when a company patents a gene, it also patents the rights to what that gene (or any fragment of its DNA) might tell us about our health, including our chances of living or dying. A woman who inherits a harmful version of either of the genes that Myriad has under patent, for example, is five times more likely to develop breast cancer than a woman who does not. She is also at significantly greater risk of developing ovarian cancer. Women who want to know whether they possess those harmful mutations have just one way of finding out: by taking a three-thousand-dollar blood test offered by Myriad Genetics.

Terrifying.

On Milk, Lactose Intolerance, and Mutations

Benjamin Phelan writes about the “most spectacular mutation” in human history in this Slate piece. He begins:

To repurpose a handy metaphor, let’s call two of the first Homo sapiens Adam and Eve. By the time they welcomed their firstborn, that rascal Cain, into the world, 2 million centuries of evolution had established how his infancy would play out. For the first few years of his life, he would take his nourishment from Eve’s breast. Once he reached about 4 or 5 years old, his body would begin to slow its production of lactase, the enzyme that allows mammals to digest the lactose in milk. Thereafter, nursing or drinking another animal’s milk would have given the little hell-raiser stomach cramps and potentially life-threatening diarrhea; in the absence of lactase, lactose simply rots in the guts. With Cain weaned, Abel could claim more of his mother’s attention and all of her milk. This kept a lid on sibling rivalry—though it didn’t quell the animus between these particular sibs—while allowing women to bear more young. The pattern was the same for all mammals: At the end of infancy, we became lactose-intolerant for life.

Two hundred thousand years later, around 10,000 B.C., this began to change. A genetic mutation appeared, somewhere near modern-day Turkey, that jammed the lactase-production gene permanently in the “on” position. The original mutant was probably a male who passed the gene on to his children. People carrying the mutation could drink milk their entire lives. Genomic analyses have shown that within a few thousand years, at a rate that evolutionary biologists had thought impossibly rapid, this mutation spread throughout Eurasia, to Great Britain, Scandinavia, the Mediterranean, India and all points in between, stopping only at the Himalayas. Independently, other mutations for lactose tolerance arose in Africa and the Middle East, though not in the Americas, Australia, or the Far East.

In an evolutionary eye-blink, 80 percent of Europeans became milk-drinkers; in some populations, the proportion is close to 100 percent. (Though globally, lactose intolerance is the norm; around two-thirds of humans cannot drink milk in adulthood.) The speed of this transformation is one of the weirder mysteries in the story of human evolution, more so because it’s not clear why anybody needed the mutation to begin with. Through their cleverness, our lactose-intolerant forebears had already found a way to consume dairy without getting sick, irrespective of genetics.

Why do humans keep drinking milk? And why is it such a mystery why the lactose-tolerance mutation has propagated?

Analysis of potsherds from Eurasia and parts of Africa have shown that humans were fermenting the lactose out of dairy for thousands of years before lactose tolerance was widespread. Here is the heart of the mystery: If we could consume dairy by simply letting it sit around for a few hours or days, it doesn’t appear to make much sense for evolution to have propagated the lactose-tolerance mutation at all, much less as vigorously as it did. Culture had already found a way around our biology. Various ideas are being kicked around to explain why natural selection promoted milk-drinking, but evolutionary biologists are still puzzled.

Fascinating.

In 3,000 Years, Someone Alive Today Will Be the Common Ancestor of All Humanity

Dr. Yan Wong explains why everyone alive in the Holy Land at the time of Jesus would have been able to claim David for an ancestor. He provides a simple mathematical explanation (exponential growth) and makes a couple of assumptions (that any two people in any one country probably won’t need to go back many generations before finding a common ancestor due to inbreeding), and then he extrapolates to the future:

What about the wider ramifications? A single immigrant who breeds into a population has roughly 80% chance of becoming a common ancestor. A single interbreeding event in the distant past will probably, therefore, graft the immigrant’s family tree onto that of the native population. That makes it very likely that King David is the direct ancestor of the populations of many other countries too.

How far do we have to go back to find the most recent common ancestor of all humans alive today? Again, estimates are remarkably short. Even taking account of distant isolation and local inbreeding, the quoted figures are 100 or so generations in the past: a mere 3,000 years ago.

And one can, of course, project this model into the future, too. The maths tells us that in 3,000 years someone alive today will be the common ancestor of all humanity.

A few thousand years after that, 80% of us (those who leave children who in turn leave children, and so on) will be ancestors of all humanity. What an inheritance!

Have you ever traced your family genealogy?

Why Supermarket Tomatoes Taste Like Cardboard

It’s no secret that the mass-produced tomatoes we buy at a typical grocery store tend to taste like cardboard. Now researchers have discovered one reason why: a genetic mutation, common in store-bought tomatoes, that reduces the amount of sugar and other tasty compounds in the fruit.

Mass-produced tomato varieties carrying this genetic change are light green all over before they ripen. Tomatoes without the mutation — including heirloom and most small-farm tomatoes — have dark-green tops before they ripen. There is also a significant difference in flavor between the two types of tomatoes, but researchers had not previously known the two traits had the same root cause.

The study authors set out to pin down the genetic change that makes tomatoes lose their dark-green top. They focused their attention on two genes — GLK1 and GLK2 — both known to be crucial for harvesting energy from sunlight in plant leaves.

They found that GLK2 is active in fruit as well as leaves — but that in uniformly colored tomatoes, it is inactivated.

Adding back an active GLK2 gene to bland, commercial-style tomatoes through genetic engineering created tomatoes that had the heirloom-style dark-green hue. The darker green comes from greater numbers of structures called chloroplasts that harvest energy from sunlight.

The harvested energy is stored as starches, which are converted to sugars when the tomatoes ripen.

The vast majority — 70% to 80% — of the sugar in tomatoes travels to the fruit from the leaves of the plant. But the remaining amount of sugar is produced in the fruit. This contribution is largely wiped out in uniform, commercial-style tomatoes — and thus they won’t be as sweet.

For the science nerds, here is the paper’s abstract:

Modern tomato (Solanum lycopersicum) varieties are bred for uniform ripening (u) light green fruit phenotypes to facilitate harvests of evenly ripened fruit. U encodes a Golden 2-like (GLK) transcription factor,SlGLK2, which determines chlorophyll accumulation and distribution in developing fruit. In tomato, two GLKs—SlGLK1 and SlGLK2—are expressed in leaves, but only SlGLK2 is expressed in fruit. Expressing GLKsincreased the chlorophyll content of fruit, whereas SlGLK2 suppression recapitulated the u mutant phenotype. GLK overexpression enhanced fruit photosynthesis gene expression and chloroplast development, leading to elevated carbohydrates and carotenoids in ripe fruit. SlGLK2 influences photosynthesis in developing fruit, contributing to mature fruit characteristics and suggesting that selection of u inadvertently compromised ripe fruit quality in exchange for desirable production traits.

It’s no wonder that tomatoes you can grow in your backyard taste that much better.

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(via Los Angeles Times)