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Monday, June 4, 2007 | Science : Genetics | print version Print | Comments

Document 6 Billion Bits of Data About Me, Me, Me!

by Amy Harmon, NYTimes.com

Thanks to ranjani for the link.

Reposted from:
http://www.nytimes.com/2007/06/03/weekinreview/03harm.html

JAMES D. WATSON, who helped crack the DNA code half a century ago, last week became the first person handed the full text of his own DNA on a small computer disk. But he won't be the last.

genome
DOUBLE HELIX DAY James D. Watson (is there a gene for left-handedness?) last year in Cold Spring Harbor, N.Y.

Soon enough, scientists say, we will all be able to decipher our own genomes — the six billion letters of genetic code containing the complete inventory of the traits we inherited from our parents — for as little as $1,000.

Just what we will do with the essence of who we are once we bottle it, however, is likely to be as much a social experiment as a scientific one.

As thousands of people decode their DNA over the next few years, they are likely to find themselves facing a genetic mirror whose reflection changes on an almost daily basis.

The more genomes that scientists have to work with, the more they can learn about them. So staying on top of your own health outlook may begin to resemble checking the performance of your stock portfolio. One day you find you have a gene that puts you at risk for diabetes; the next it's one that may make you live longer.

genome"Nobody quite knows how to manage expectations in such a rapidly changing and deeply personal field," said George M. Church, a Harvard Medical School geneticist who directs the Personal Genome Project. "The picture is getting more and more complete, but along the way there's going to be a lot of, 'You told us this last week and now you're telling us this!' "

By the end of the summer, Dr. Church's research project promises to deliver sequences to its first 10 volunteers. Unlike Dr. Watson, whose complete genome cost $1 million, the project's volunteers will receive the one percent of their genome currently deemed most useful at a cost of $1,000.

One start-up company, 23andme, recently announced plans to provide affordable chunks of their DNA to individual consumers, along with tools to help them keep track of and understand their genetic information.

And technology companies like Illumina, Applied Biosystems and 454 Life Sciences, which solicited Dr. Watson's DNA to prove its abilities, say the price of a complete human genome has already dropped to $100,000. They are competing for a $10 million "X prize" to sequence 100 human genomes within 10 days. (Dr. Watson's took about two months.)

Those who have signed up to be sequenced as part of the competition include Paul Allen, co-founder of Microsoft; the astrophysicist Stephen Hawking; the television interviewer Larry King; and the financier Michael Milken.

"It's the start of an era of comparative individual genomics," said J. Craig Venter, who as president of the Celera Corporation sequenced much of his own genome in 2000 and recently completed it. "Hopefully we'll have tens of thousands to compare in the next year or two."

Dr. Venter said he consulted his genetic profile every time a new announcement of a gene discovery came out. Just last month, having read a report in this newspaper about a gene that raises the risk of heart disease, he found that he indeed carried the mutation.

He might have guessed that from his family history, but knowing his individual risk, rather than a statistical average, is a stronger motivator to change, Dr. Venter said. Because of another risk gene he carries for heart disease, he altered his diet and has been taking a cholesterol-lowering drug for several years.

"Now we can do something to alter what might have been our genetic destiny," he added.

Beyond heart disease, there are a growing number of genes already known to influence predispositions to common diseases like breast and colon cancer, depression and dementia.

There are other reasons to unravel your genome. Embracers of nature over nurture may sift through their 20,000 genes to find an explanation for personality traits thought to have a partial genetic basis — like early rising, risk-taking, shyness and addiction.

And the curiosity is unlikely to be restricted to our own genetic code. A generation of personally motivated amateur geneticists may seek out others who have similar traits and similar quirks in their genetic code, hoping to deduce a connection.

Friends and families, too, may begin to compare notes.

"You can imagine a family who won't let someone marry their daughter until they examined her prospective husband's genome," Dr. Watson suggested at a news conference on Thursday. "You'll want to know what your mate is going to have."

The mate, of course, may not want to know himself. Dr. Watson told the company that sequenced his genome not to reveal to him the status of one gene known to predispose people to Alzheimer's disease. "Who wants to know that?" he said.

But Dr. Watson, 79, may yet learn that his genome contains Alzheimer's risk genes that may be discovered tomorrow or next month or next year. On the other hand, he may find that he carries genes that offset the risk. Or both.

Moreover, because the way genes influence health and behavior depends heavily on their interaction with the environment, what our genome can tell us may change depending on lifestyle choices.

People who learn they carry a higher genetic risk of Type II diabetes, for instance, may see that risk increase if they start to gain weight. A gene that makes it difficult for some people to sweat in extreme heat might not matter to you if you live in Seattle. But if you are thinking of moving to Miami, knowing it exists in your genome could prove useful.

The lack of established medical authorities to interpret or filter such information could cause deep discomfort, some experts caution. And the technology is quickly outpacing social debate over how it should be handled.

"Some people are going to have information that they don't know what to do with," said Angela Trepanier, president elect of the National Society of Genetic Counselors. "And that can do more harm than good."

Still, the early boosters of the personal genome say the best bet for improving individual health care is not only to embrace genetic knowledge about ourselves, but to share it with others.

If hundreds of thousands of people make their genomes public — along with personal information about their ancestry, their health history, what they look like, what they do and where they live — they argue, scientists will finally be able to draw meaningful correlations between variations in DNA sequence and any trait that has even a partial genetic basis, from what drugs we should take to what foods we like to eat.

As that happens, everyone with a sequenced genome will learn how the new findings affect them.

"Let's sequence prominent Texans," Dr. Watson said at the press conference in Houston last week. "What we really want now is a lot of data."

Until then, even Dr. Watson, who posted his genome on the Internet last week, has to wait. At a ceremony marking the occasion, he stared at the disk containing his genome for a few seconds, then stuck it in his pocket.

Comments 1 - 15 of 15 |

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1. Comment #47524 by Zaphod on June 4, 2007 at 9:19 pm

 avatarYes I read about this before. Very interesting stuff.

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2. Comment #47616 by sgr79 on June 5, 2007 at 4:34 am

 avatarKewl!

...Though it makes my head spin once the possibilities presented here are combined with advances in fertililty procedures and cloning...

Although I don't feel that designer babies are the way to go should that become a real choice in the future, I do agree that genetic analysis is a great diagnostic tool.

Quick question: if we do wind up going the route of designer babies, how does that impact concepts of evolution? Would we be self-evolving? Which also makes me wonder what category genetic engineering falls into?

Okay, morning here, time to pour my first cup of coffee and get to work!

Other Comments by sgr79

3. Comment #47622 by CJ22 on June 5, 2007 at 4:58 am

 avatarNo doubt the wingnuts will be frothing: "What's next, designer babies??!!!???!?" (yes, with that many exclamation marks).

Personally I've never been quite sure what is wrong with the concept of doing the best one can to elliminate abnormalities and propensities for disease. Clearly there are issues with gender balance, but nothing beyond the wit of man to solve.

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4. Comment #47638 by CJ on June 5, 2007 at 5:42 am

 avatar
Personally I've never been quite sure what is wrong with the concept of doing the best one can to elliminate abnormalities and propensities for disease.
While I basically agree with this there is a huge element of luck involved. For example cystic fibrosis, a genetically inherited illness, is caused when both the mother and father carry the gene for it and both pass it on to a child. But if one parent passes the gene on the illness is not carried forward, so it would appear simple to engineer out the effected gene. However possession of a single gene gives immunity from typhoid. There was also an old wife's tale that salty babies don't live more than a couple of years. Well it transpires that children with cystic fibrosis have excessively salty sweat.

There is a similar situation with sickle cell anaemia and malaria where a single gene gives protection from the malaria parasite.

The genetic code of all creatures is the result of natural selection not design as we continually have to state. Sorry if I'm preaching to the choir here. This means that there is a lattice work of support within our genome. Modifying this evolved lattice could, in my opinion probably would, result in unforeseen effects. The catch 22 is that to find out which elements of the lattice do what you have to modify the lattice but by attempting that modification you risk unwanted results. These unpredictable results may be acceptable if say mice are the subject but could we ever continue the experimentation into the human genome? I think that would be a very serious ethical question.


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5. Comment #47650 by rokort on June 5, 2007 at 6:33 am

 avatarOn the risk of sounding pedantic i would like to add a note here: It can take thousands of manhours to have only a faint idea of the function or regulation of just one (1) protein or gene. So "deciphering" a genome is not exactly describing what happens how, when and where in an organism. It's like deciphering what letters make up a very very heavy and big book, but having absolutely no idea what language it's written in, how to combine letters into words, which words are to be put where, or what they mean by themselves or when written up in a sentence.

Thought deciphering a genome for a couple of bucks and in no-time is a tremendous feat, it's gonna take some more time and effort before we can translate this towards understanding genetic abnormalities in detail, let alone treat them.

But well, you know, Rome wasn't built in one day either...

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6. Comment #47656 by CJ22 on June 5, 2007 at 7:19 am

 avatarYeah, all granted. I meant 'in principle' of course. There are those that think even if we could do it safely, reliably and in full knowledge of the consequences, it's still a bad idea. Those coming at it from one side feel it's against God's plan, those coming from the other side think it's 'messing around with nature' (a nonesense phrase if ever there was one) or something equally vague and budhist.

I imagine a heavily-improved humanity living in the year 3000 (with their 300-year lifespans, wet-wired network connectivity, long-term views of life and eyes on a horizon that makes today's petty Gods look like hicks) shaking their heads in wonder at how ready we are to attach policies to our baseless superstitions.

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7. Comment #47657 by Bonzai on June 5, 2007 at 7:30 am

This is fascinating yet creepy. It is a step closer to the nightmarish scenario where everyone will get pinned down and classified like specimens. Soon we will be all literally like open books. Strong privacy legislations must be put in place to regulate and restrict the use and access to such data.

Someone pointed out the difficulty in decoding the genome, this is no doubt true. But incomplete information and insufficient knowledge has not stopped dubious "science" from being used as tools of repression. In fact, the less mature the science is the more likely it is to be hijacked by various agendas. A little knowledge is a dangerous thing, as the old saying goes. This is especially true for something so ill understood, yet so over hyped and and sounding so intoxicatingly promising like applied genetics. We just have to look at the sorry history of "scientific" racism and eugenics.

It is legitimate and pertinent to ask whether our society is ethically mature enough to handle the implications of biotechnology. I am not optimistic in witnessing the barbarity that goes on around us on a daily basis. One doesn't have to be motivated by religion to advocate caution.

Sorry to rain on your parade.

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8. Comment #47660 by paulcaira on June 5, 2007 at 7:44 am

At the risk of sounding even more pedantic, 6 billion characters of a 4-base code, is 6 billion characters in base 4 (this pun of 4-bases in base 4 has really only just occurred to me) which is 12 billion bits (as in binary digits), not 6 billion, as each base 4 digit needs to be replaced by 2 binary digits.

(Well I told you it was pedantic)

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9. Comment #47665 by Bonzai on June 5, 2007 at 8:18 am

Comment #47622 by CJ22

Personally I've never been quite sure what is wrong with the concept of doing the best one can to elliminate abnormalities and propensities for disease.


"Abnormalities" is a loaded word and to some degree it is a socially constructed notion that reflects the prejudice of society. Desirability of various traits are often just cultural preferences, lacking in any objective basis. I am sure somewhere there are prospective parents already thinking of the technological possibility of screening for "gay fetuses" in order to abort them.



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10. Comment #47675 by Donald on June 5, 2007 at 8:57 am

At the risk of sounding even more pedantic, 6 billion characters of a 4-base code, is 6 billion characters in base 4 (this pun of 4-bases in base 4 has really only just occurred to me) which is 12 billion bits (as in binary digits), not 6 billion, as each base 4 digit needs to be replaced by 2 binary digits.

The human genone has about 3 billion "characters in base 4", not 6 billion, so the "6 billion bits" in the title is ok.

Other Comments by Donald

11. Comment #47732 by Big T on June 5, 2007 at 11:23 am

I'm not real knowledgeable about science, and I haven't read the book, but I believe E.O. Wilson in his book 'Consilience' wrote that Homo sapiens is about to decommission the force (natural selection) that shaped the species. To some extent, of course, we have already done that. The late science fiction writer Robert Heinlein once had a character of his say "The real cure for hemophiliacs is to let them bleed to death before they breed more hemophiliacs." That, of course, if not done. Anyway, like it or not, our species has already begun to decommission natural selection and, unless we blow ourselves up in the near future, will continue to do so. For a positive take on what the future (including genetic engineering) might hold, there is a fascinating website called "The Hedonistic Imperative" that is worth checking out. Be warned, though, it is not a site for unintelligent or uneducated people. The author is brilliant and it takes work to understand what he's saying.

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12. Comment #47823 by sgr79 on June 5, 2007 at 4:04 pm

 avatarRobert Heinlein also wrote a book where an old man who is about to die gets his brain transplanted in his sexy secretary's body, and it turns out that her body has some memory of her thoughts (spirit?) even though her brain is no longer there...sorry, can't remember the title :P

Anyhoo, another version of screwing with evolution!

Other Comments by sgr79

13. Comment #47912 by Luthien on June 6, 2007 at 3:07 am

 avatar
"Some people are going to have information that they don't know what to do with," said Angela Trepanier, president elect of the National Society of Genetic Counselors. "And that can do more harm than good."


Yes Ms Trepanier, but it's better than a hole in the head ;-)

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14. Comment #47927 by epeeist on June 6, 2007 at 4:09 am

 avatarComment #47732 by Big T

I'm not real knowledgeable about science, and I haven't read the book, but I believe E.O. Wilson in his book 'Consilience' wrote that Homo sapiens is about to decommission the force (natural selection) that shaped the species.

The renegade Jesuit Teilhard de Chardin has some interesting views on this that almost got him excommunicated.

Atheists will presumably not accept his ideas in their entirety (or possibly at all) and they will infuriate the bible literalists. Worth a read though.

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15. Comment #48896 by elastigirl on June 9, 2007 at 11:48 am

I think that the pace of natural evolution has progressively slowed down over the history of human civilization. You have to see that we've hit a point where much greater numbers of people actually survive through childhood and go on to reproduce because our medicine and our technology in general has gotten better.

Things that used to kill you don't kill you anymore, and people reproduce who never would have reproduced before. Death and attrition are the driving forces behind evolution, and so, having reached the point of near-universal ability to produce offspring, natural evolution seems to have slowed to a crawl. Not to say that modern medicine is a bad thing, though. Modern medicine levels the playing field and makes everyone fit for survival, and is in itself a force of evolution.

Anyhow, I think it would be foolish for us to go tinkering with our genetic code with the purpose of removing faulty code. We already have evidence, like the previously mentioned example of the cystic fibrosis gene granting immunity to typhoid, that indicates that some benefits are inextricably tied to drawbacks. And I think that this pattern is more prevalent than we currently know. If we set out with the purpose of eliminating defects, we will inadvertently eliminate strengths in the process.

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