IBM Researchers Working Toward Cheap, Fast DNA Reader 90
nk497 writes "IBM scientists are working on ambitious research where nano-sized holes will be drilled into computer chips and DNA passed through to create a 'genetic code reader.' A DNA molecule would be passed through a hole just three nanometers wide, while an electrical sensor 'reads' the DNA. The challenge of the silicon-based 'DNA Transistor' would be to slow and control the motion of the DNA through the hole so the reader could decode what is inside it. IBM claimed that if the project was successful it could make personalised genome analysis as cheap as $100 to $1,000, and compared it to the first-ever sequencing done for the Human Genome Project, which cost $3 billion."
Amazing! (Score:2, Interesting)
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Just watch a few episodes of Judge Judy or Cops. You'll see all sorts of characters that "write" with arbitrary strands of DNA ;)
Re:Amazing! (Score:5, Informative)
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...and to verify that we aligned the initial sequences (that we use as guides) correctly in the first place ;)
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If by longer reads you mean read the whole thing at once, then yes. The removal of shotgun sequencing techniques would remove much of the cost I would think.
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they aren't reading the whole thing at once - mostly because it isn't practical. Think about the shapes involved, and then try to imagine fitting the whole thing through a hole that is purposefully barely large enough for the dna to squeeze through. They are however reading much much larger fragments. How large? no idea, haven't found anything that quantifies it. Wouldn't be surprised if it was in the 10s of thousands of base pairs, though.
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Not to my exact needs though:
What I want is a DNA writer that will write realtime. It will look a lot like an old typewriter, but will have only 5 keys, ATCG and U. You push the buttons in the sequence that you want (the keys will actually clack), and then hit the return bar, but instead of the roller sliding over, it will instantly shoot out an eppendorf tube full of that sequence on the side with a nice "ding."
I've asked Santa for one every year, but the one at the mall just said what my parents have be
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Nanosprockets! DNA is just tiny, tiny tractor-paper.
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All you'll have to do is unpop the write protect tab on the side of the reader. Simple.
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Re:The implications are huge (Score:4, Funny)
Re:Cynicism (Score:4, Insightful)
Why is it that multibillion dollar companies are constantly researching exciting new tech that makes it more and more impossible for us to remain annonymous? Just once, I want to see IBM or somebody backing Tor or Freenet or something similar.
Please remember that IBM is, like most corporations, a for-profit entity. Which means that the vast majority of their research is going to be aimed at projects that will allow them to make a buck.
In short - Tor and Freenet don't spend gazillions of dollars on technologies, while governments do.
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And if they DID back Tor, would you trust it?
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You look at this as a potential privacy invasion, which I supose that it is technically, although it is way overkill for mere identification purposes. I look at this and see the possibilities for huge medical breakthroughs. Having one human DNA sequenced is neat, but it isn't really enough to tell us much about what our DNA does. To really discover or rule out genetic causes of disease, we'll need tens of thousands of sequenced genomes that we can cross reference and compare; something that is within the
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At $100 for a reader, who is to say they cant screen job applicants to see if they will have future medical issues and deny them a job (and health insurance).
Who is to say medical insurance wouldnt require such a test, to flag any possible "pre-existing conditions"
Gattaca [imdb.com], here we come
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Wait. A modified "clone"? With--say--only 50% of my DNA included? Isn't that what they call a "normal child"!
So just what is it that you're volunteering for here, and are you sure it's legal in this state? Tell you what. Bend over, pick up that pencil I just dropped, and let me see if I might be willing to let you "access" my "source code". :)
Re:Cynicism (Score:5, Insightful)
If you think that fast and cheap DNA reading applies only (or even mostly) to monitoring of individuals, you do not have a real grasp of the scope and applicability of DNA sequencing.
There are enormous resources in scientific research that goes toward generating datasets. Sequencing of humans is a significant part of it, but most of that applies to medicinal uses, such as cancer genotyping (which uses sequencing to identify specifically the genotypic characteristics of a particular tumor colony so it can be treated much more effectively than just trying to guess by looking at it "from the outside"). Also, a huge new area in medicine is going to be "personalized" medicine. Medicine that's actually tailored to the specific genetic traits that YOU have, so that the chances of side-effects are reduced and effectiveness is increased.
Then there are the thousands of researchers that need to collect sequence datasets on organisms that have NOTHING to do with humans. A big chunk of this is plant genetics: crop stress tolerance (e.g. make wheat grow more reliably in colder or dryer climates, or resist disease better), natural product optimization (e.g. make canola plants produce 10% more of the kinds of oils you care about, and less of the crap you don't). Another big chunk of this research is basic science: figuring out the specific details of how evolution has progressed, or to identify the core biological processes that make organisms tick. That's core evolutionary biology and biomechanics research.
Then there's the people trying to do constructive genomics: actually build organisms that do specific things. Like modifying yeast to produce some complex bioproduct that requires a network of potentially hundreds of genes. Or creating organisms that filter waste from water. Or building algae variants that run on sunlight and produce oil.
All of these things could desperately use robust, cheap, accessible sequencing platforms. Genetic sequencing is not all about your privacy. It's a platform which has the scope to save scientists and researchers millions, and put that towards more research and better results than towards trying to scrape out a few bases from a tissue sample.
IBM is trying big time to get into the life sciences (that's wrong actually, they actually already HAVE products they market to the life sciences, like systems for large-scale data processing). It is worth billions to them, and they want to tap it.
-Laxitive
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Re:Cynicism (Score:4, Insightful)
I completely agree that the technology can be used for awesome and amazing things. I just have a feeling that most of the things it's going to be used for are things that aren't going to benefit humanity in such lofty ways.
That second part is true of every single technology ever invented. The first sharpened stick man ever made may have been used to kill food, but the second one was probably used to kill another dude and steal his woman.
Tor isn't a holy technology that can only be used in good ways either. I'm guessing 5 seconds after it was finished, someone said something like "Think of the children! This will be used to transmit child porn." You probably scoff at that objection and, and rightfully so, but that's exactly our reaction to your objection to the DNA reader.
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'If you think that fast and cheap DNA reading applies only (or even mostly) to monitoring of individuals, you do not have a real grasp of the scope and applicability of DNA sequencing.'
Indeed. For a great summary of what some of the people who really do grasp it think, check out the answers to Nature Genetics' question of the year in 2007 - 'What would you do if it became possible to sequence the equivalent of a full human genome for only $1,000?':
http://www.nature.com/ng/qoty/index.html [nature.com]
Right now, commercia
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For most extant species on the planet, we don't even know how many chromosomes they have, let alone having sequenced them. This will speed things up enormously.
The world is about information. (Score:2, Interesting)
You could argue that the entire purpose of mankind is to acquire, and then use to his benefit, information. This has been the ongoing work of mankind since the dawn of mankind. Our appetite for information is insatiable, as the ways to benefit from information seem endless.
Consequently, privacy is doomed.
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'You could argue that the entire purpose of mankind is to acquire, and then use to his benefit, information. This has been the ongoing work of mankind since the dawn of mankind.'
Better hope we don't finish it any time soon, then:
http://lucis.net/stuff/clarke/9billion_clarke.html [lucis.net]
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Why is it that multibillion dollar companies are constantly researching exciting new tech that makes it more and more impossible for us to remain annonymous?
Look at it this way, with so many more people's genomes sequenced, there will be that much more data to sort through to find yours. Security through obscurity!
Anyway, DNA is useful, they're developing it for other uses, it's not IBM's fault your ancestors foolishly chose to make everyone have unique DNA that can be used to identify you.
(Yes, this was a joke, but I prefer to believe dyingtolive was also joking.)
From The YouTube Title (Score:1, Interesting)
If you can read DNA through a fabricated chip, possible next step is fabricating microcircuits from transistors scaffolded on DNA.
Yours In Belarus,
Kilgore Trout
Other uses (Score:2, Insightful)
âoeUltimately it could improve the quality of medical care by identifying patients who will gain the greatest benefit from a particular medicine and those who are at most at risk of adverse reaction,â he added.
Insurance companies will use it to deny health insurance outright or label any diseases that this thing finds as "pre-existing conditions".
Travelers to the US will have to stick their fingers and give a DNA sample along with their finger prints and photo.
Government will use for the "war on [insert buzzword here]"
Genetic propensity for mental illness, well, we'll have to keep an eye on you! Especially, if there is some sort of genetic predisposition towards pedophilia - think of the children!
Have to take thi
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Insurance companies will use it to deny health insurance outright or label any diseases that this thing finds as "pre-existing conditions".
There is already a law banning them from doing this.
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Insurance companies will use it to deny health insurance outright or label any diseases that this thing finds as "pre-existing conditions".
There is already a law banning them from doing this.
Yeah, so? If they do it, exactly how do you prove it? And even then if you do prove it by some miracle , all the insurance has to do is say, "Oops, it was an error. We are investigating and we'll correct the problem." They pay a small fine and on they go.
Re:Other uses (Score:4, Insightful)
You prove it by the piece of paper that tells you your health benefits was denied because of a pre-existing condition. Your records will show if you've had treatment for it or not. It's not a conspiracy/finger pointing kind of thing. Proof is easily come by.
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Challenge accepted. [wikipedia.org]
Re:Other uses (Score:4, Interesting)
Well, since you are being a complete nay-sayer to further your own agenda, allow me to respond with some other potential uses of this technology:
Law enforcement will use it to help solve crime.
The innocence project will use it to get wrongfully convicted people out of prison/off death row.
Businesses and private individuals will be able to use it to enhance the security of their homes/offices/factories/etc.
Adopted children will be able to use it to figure out who their biological parents are.
The child support system will be able to use it to weed out those who aren't parents and confirm those who are.
The point I'm trying to make is that technology isn't inherently good or evil. It's what we do with it that matters. I find it disturbing that you couldn't name a single positive use for this technology.
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>Insurance companies will use it to deny health insurance outright or label any diseases that this thing finds as "pre-existing conditions".
Sounds like all the more reason to support healthcare reform and to shut people up who equate it with Nazi Germany, or whatever the right complains about in public.
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Have to take this DNA test as part of our drug screening. Predisposition towards alcoholism or any other disease or disorder that will send our health care costs through the roof? Well, you don't have the necessary "skills" for this job. Sorry, best of luck finding another job. (Yeah, good luck in proving that we violated the ADA or EEOC!)
nothing but good (TM) can come of this!
Incredibly short sighted. I sequence DNA all the time, it's a valuable tool for biomedical research. If sequencing my samples took a matter of hours instead of days, that would really speed thing up. My research is on neural stem cells. I may be an idiot, but I think my research could eventually lead to some findings that would be useful to many people. Shortening the amount of time it will take me to find stuff is, in my opinion, a good thing, and not just for me. The same is true for most biologists
Say goodbye to fingerprint scanners on laptops (Score:1)
Say hello to DNA code readers.
"Please insert your DNA in the hole for authentication"
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Perhaps this will usher in a golden age of sperm-jacking and blood-letting?
Hasn't the Internet already brought a golden age of sperm-jacking?
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Challenge (Score:3, Interesting)
Well I would imagine that slowing and controlling the motion of the DNA wouldn't be all that difficult. DNA has a net negative charge due to the backbone. However, how the EM fields they'd use to manipulate it would interact with the circuitry of the reader I do not know. That might be the real challenge.
I Smell Synergy! (Score:4, Insightful)
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I really dont understand the fuss, given that even some Nazi SS officers/scientist were honored by the US later on.
Wernher von Braun and his team of rocket scientist were among them. He was an SS officer and used slave labor in manufacturing
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No reason why not, since the genetic payload of most viruses is quite small, even allowing for the open reading frame. But I suspect the technology will be used primarily for less benign purposes.
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Think along the lines of going to a doctors office, and getting a shot specifically designed on the spot to wipe out all of your specific diseases.
Another technology is ahead so far (Score:5, Informative)
The New York Times published an article in August about a technology that decoded a human genome for less than $50,000 [nytimes.com]. The inventor speculates that the technology will be able to decode a genome for just $1,000 in 2-3 years.
That being said it will be amazing to see the IBM project succeed. Either way the cost of decoding a genome is dropping so quickly it puts Moore's Law to shame.
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From the article: Dr. Quake's DNA sequencing machine, about the size of a refrigerator, works by splitting the double helix of DNA into single strands and breaking the strands into small fragments that on average are 32 DNA units in length.
That's not terribly different than what happens now; we cut things into chunks of X units (say, 400 base pairs), and then use all sorts of tools to guess how to put it all back together. The major problem being something elsewhere mentioned in that article: A computer
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I don't see what Moore's Law has to do with this. Moore's Law is about the number of transistors doubling every 18 months. It has nothing to do with costs.
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To echo "Dog Day Afternoon" (Score:1)
GATTACA! GATTACA! GATTACA!
And The First DNA sequence to be read... (Score:2)
G A T T A C A
-S
Summary is wrong (Score:3, Funny)
It cost a lot more than that. I mean first we had to evolve from amoeba and create a civilization.
Re:Summary is wrong (Score:4, Insightful)
And it cost $15 billion for the first person to drive into Boston after the Big Dig. [wikipedia.org] That's creative accounting. [wikipedia.org]
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The biggest problem with this sentence is its misplaced prepositional phrase. The Human Genome Project probably cost $3B up to some point, but the sentence may imply that the first sequencing cost $3B. There was a recent article [nytimes.com] in the NY Times discussing this problem.
Other "fast readers" we need (Score:1)
A reader for all sorts of diseases, especially communicable ones. It'd cut costs in countries with relatively modern health systems by wasting less of medical professionals' time, and since it'd likely be small (and hopefully very cheap) it'd help countries with very poor or non-existent health care systems. Would also be very helpful during/before epidemics break out. I know some of these exist for specific diseases, but we need ones that can test for thousands at once.
A reader specifically for STDs. Would
It's about time. (Score:3, Insightful)
It's about time someone did this. People have been talking about real nanotechnology for about two decades. Most of what's now called "nanotechnology" is surface chemistry of finely divided powders, or simple self-assembling structures like carbon nanotubes. Real nanotechnology, useful mechanisms made of deliberately placed individual atoms, hasn't been happening much. A DNA reader is one of the few applications where building a very small number of devices at the atomic scale is useful. You don't need self-replicating assemblers turning out vast numbers of nanomachines. Small numbers of devices can be created, slowly, with STM-type devices.
At least readers are safe. DNA writers are going to be an issue.
Hmmm... (Score:2)
Similar projects already exists... (Score:1)
http://www.nytimes.com/2008/02/09/business/09genome.html [nytimes.com]
``There, Pacific Biosciences has been developing a DNA sequencing machine that within a few years might be able to unravel an individual's entire genome in minutes, for less than $1,000."
Pacific Biosciences (Score:1)
There is a private company called Pacific Biosciences that is doing something very similar, single DNA molecule sequencing. They managed to get reads from a single DNA molecule, and this was sort of the hot topic at a few computational biolgoy conferences I went to last year. It's not clear who is going to win this race, but I think a lot of people think this is the future of DNA sequencing.
How to solve the DNA migration rate problem! (Score:1)
In the current system, if the strand moves to slowly between reads, a base will be scanned twice. If the strand moves too quickly, some bases may be skipped altogether. You could slow down the rate of strand passage rela