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After years of bitter rivalry, Francis Collins, then the director of the US National Human Genome Research Institute and Craig Venter together made the announcement from the East Room of the White House.
Then-president Bill Clinton predicted that the feat, which cost billions of dollars and took more than a decade, would “revolutionize the diagnosis, prevention and treatment of most, if not all, human diseases.”
We’re clearly not there yet. So what exactly have we gained from knowing the sequence of 3 billion base pairs?
Collins, Venter and two heavyweights in cancer genetics — Robert Weinberg and Todd Golub — each tackle that question in editorials published today in Nature.
Collins, now head of the National Institutes of Health, writes that although the decoding of the genome has led to many scientific advances — notably, a better understanding of how species, including humans, evolve — its progress in the clinic has been much more modest. Genetic tests can predict, for example, whether someone will develop certain types of breast cancers, or respond well to hepatitis C treatment. But studies comparing genomes of sick and healthy people have failed to find genetic causes for common diseases.
Venter’s view of clinical genetics is similarly sobering. He points out that although human genome sequencing costs continue to plummet — from $300 million in 2003 to less than $5,000 today — researchers don’t know how to interpret most of that glut of data. The key, Venter says, is to match an individual’s genomic readout with rigorously characterized clinical symptoms, family medical histories and lifetime environmental exposures.
Bottom line: The decoded genome may very well hold answers to the mysteries of many diseases — but only if we can figure out how to interpret it.
Anyone who reads my blog knows how I feel about this “debate”. In fact, the answer to whether genetics is helping us understand disease, and health, is so ridiculously, obviously YES that the question seems not worth asking. But BMJ asked it, and managed to find two experts with opposing answers.
David Weatherall, a professor at the, ahem, Weatherall Institute of Molecular Medicine at the University of Oxford, agrees with me. He points out that genetic science has (among other things): found the cause of many single-gene disorders, such as cystic fibrosis and Huntington’s; uncovered how cholesterol metabolism works, leading to new drug treatments; and has shown us how acquired mutations (from, say, cigarette smoke) can cause cancer.
On the other side is James Le Fanu, a general practitioner and book author from London. He agrees that now, 10 years since figuring out the sequence of the human genome, geneticists generate “billions of bytes of biological data each week” and have published “fascinating insights”. He just doesn’t think they matter much in the clinic: “And yet for all this cornucopia of new facts and knowledge, its influence on everyday medical practice remains scarcely detectable.”
He gives two possible explanations for this slow start: A) genetics may not be all that important to disease; and B) we don’t understand even the basic function of a gene, let alone how they work together to create disease.
I have two objections to Le Fanu’s argument. The first is that 10 years is not a long time! Yes, this is extremely complicated science, which is why I often marvel at just how much has been learned about our genome in only 10 years.
The second problem is that Le Fanu made a negative argument, rather than a positive one. He says we shouldn’t bother spending money on genetics to understand medicine. OK, so what should we study, then? He ends his commentary with this doozy: “The current dominance of medical genetics threatens to bury the true spirit of intellectual inquiry under an avalanche of undigested (and indigestible) facts.” On the contrary, I think what he’s advocating — giving up on a young and extremely productive field — is a much better example of “burying intellectual inquiry.” Well, since we don’t understand a lot of this stuff, let’s not even bother trying to.
Of course genetics is not everything, and of course, the more we find out, the more that remains a mystery. But isn’t that what science is all about?
I love holidays, mostly because they give me an excuse to bake cutesy things. And aren’t these lemon meringue cupcakes just darling? Here’s how I did it:
Yesterday I posted about the future of robotic surgery. Surgery seems somewhat conducive to robotic aide — a lot of it is precise, mechanical movements, after all. Machines can do things that people can’t, like see deep inside an intestinal tract, or rotate a tiny screw for a hip joint exactly one degree counterclockwise (I’m making that up, but you get what I mean). And the bots don’t actually replace the supremely skilled human, they’re just a really useful tool.
Journalism, in contrast, is not at all mechanical. Every story requires different background reading, different sources. Every interview is structured a bit differently, and changes depending on what the interviewee says. New things happen every day, which may change the facts of the story. Journalism is fundamentally about things that only a human mind can deal with: facts, ideas, analysis. At least I like to think so.
That’s why I was stunned to read about a robot journalist:
Researchers at the Intelligent Systems Informatics Lab (ISI) at Tokyo University have developed a journalist robot that can autonomously explore its environment and report what it finds. The robot detects changes in its surroundings, decides if they are relevant, and then takes pictures with its on board camera. It can query nearby people for information, and it uses internet searches to further round out its understanding. If something appears newsworthy, the robot will even write a short article and publish it to the web.
This story got a lot of play on my Twitter feed yesterday, especially from cynical/frightened/dismissive journos. But I see this bot as filling the same role that the surgery-bot does: a tool to help a skilled human.
Let’s say I was writing a profile about some fabulous biologist. I visit her lab for a personal interview and to meet her team. While I’m busy with all that good stuff, my bot could be roaming around the various lab rooms, taking high-res pictures, video, making measurements, asking lab techs a series of simple questions (that I’ve crafted ahead of time) and recording their answers. When I get home, in addition to my own scribbles and tape recordings from the interviews, I’ll have all of this great extra stuff from my bot. It’d be an enormously useful resource!
Now, where can I order one?
Credit: Emily Singer, Technology Review
Most people have heard of the robots that allow surgeons to see inside the body in 3D, and make super-precise and super-small movements, all without cutting more than a 1-inch incision. (Check out the website of the da Vinci robotic system, for instance.)
But, as Emily Singer reports in an interesting Technology Review feature (with slide show, and video!), a lot of surgeons are disillusioned with the flashy, clunky and expensive technology:
The group had varying concerns–if and when the robot will outperform traditional laparoscopy; the learning curve associated with the technology; whether it allows less experienced surgeons to perform more complex surgeries. But everyone agreed on two points. The technology isn’t advancing fast enough or dropping in price quickly enough. “The system is very expensive because only one company makes it now,” says [Hiep] Nguyen. “We need more competition to drive down price.”
da Vinci, apparently, is the only game in town. Sounds like a good project for industrious biomedical engineers!
The brain can only adapt to new experiences during these windows of plasticity. But researchers may have found a way to reopen the windows, according to a paper published late last month in Science.
The visual system is the best platform to study plasticity. For example, if you shut one eye of a mouse during a ‘critical period’ of development, around the 28th day of its life, its brain will rewire so that it only processes light from the other eye. In the 1970s, scientists Tortsen Wiesel and David Hubel were the first to demonstrate this phenomenon in a one-week-old kitten. This critical period also exists in people.
A decade ago, scientists discovered that plasticity can be induced or delayed by drugs that mimic inhibitory interneurons — cells that dampen nerve impulses.
In the new study, the researchers transplanted fetal interneurons into the brains of young mice and shut one of the animals’ eyes during the normal critical period. After the window closed, the researchers opened the eye and, as expected, the mouse could not see from it.
Amazingly, though, a few days later the animals went through an unexpected second critical period. The blind eye linked up with other brain cells, and began feeding the brain visual information. The interneurons, it seems, had somehow reopened the critical window.
Who needs fingerprints? Police may be able to place suspects at a crime scene based on the precise composition of bacteria living on their skin. From the Philadelphia Inquirer:
By sequencing fragments of bacterial DNA, researchers found that the bacteria on a keyboard or mouse could be readily matched with the microbes on the skin of the person who used it.
They also found that bacteria swabbed from a person’s skin maintained a fairly stable composition for up to two weeks at room temperature – potentially allowing the identification of a suspect long after he flees the scene.
Carl Zimmer has a knack for writing about things I’ve always wondered about, but never bothered to look up myself.
Like, I wonder why leaves turn colors? I wonder what dogs think about? I wonder how museum-artist types know how to draw accurate pictures of dinosaurs or human ancestors that they’ve never seen in the flesh?
The answer to that last one, as Carl writes in his latest column at the New York Times, is that artists do the best they can with the known scientific facts, and take a bit of creative license with characteristics that are less certain.
For instance, take illustrator Nuka Godtfredsen, who drew the image of Inuk, the 4,000-year-old paleo-Eskimo that made the cover of Nature last month:
tkt
He studied photographs of Chukchi people to give Inuk a face. He also took note of the fact that, despite Inuk’s genetic propensity for baldness, the tufts of his hair were up to eight inches long. As a compromise, he gave Inuk a receding hairline and a mullet.
Publisher Elsevier plans to make some sweeping changes to Medical Hypotheses, a ‘scientific’ journal that’s not peer-reviewed. From Nature News:
The journal’s publisher Elsevier is seeking major changes to Medical Hypotheses in the wake of a furious row over the publication last year of a paper claiming that there is no proof that HIV causes AIDS. A key part of these changes will be to implement peer review in place of the current editorial review.
Elsevier also says there will be “especially careful review” of potentially controversial articles.
But Charlton [the editor] claims that this “would utterly destroy Medical Hypotheses”, and he insists that he will neither resign nor assist with the proposed reforms, as demanded by Elsevier.
“Elsevier plan to continue a zombie Medical Hypotheses — i.e. still moving around, but dead inside,” he told Nature. “I have requested that they do the honest thing and kill the journal outright. I would rather Medical Hypotheses existed in its pure form for 35 years than that it has a dwindling and corrupt afterlife.”
I’m surprisingly torn by what’s going on here. This journal publishes some abhorrent articles (ie HIV denialism, autism-vaccine crap). Still… it is just about the only place in the scientific literature where scientists can go out on a limb and make a grand-scale hypothesis. Throw an idea out there, for the record, and let other scientists think about it. Kind of old school and romantic, no? And it’s not like scientists don’t understand that the journal is a joke, right?
Yep, those green fellas are sperm, fruitfly sperm to be precise, swimming in a female’s reproductive tract. From Nature News:
When the sperm of different male insects meet inside a female, they use everything from wrestling to chemical warfare to try and fertilize as large a share of her eggs as possible, according to two studies published this week. The studies also show that females don’t just let the battle take its course, but manipulate it to their own ends.
