I don't know the details, but my understanding is that they're technically patenting the assay, not the DNA sequence, per se. I'd love to be corrected on that.
Someone please mod the parent higher. It's good to see someone who seems to know what's going on.
The grandparent message is correct that the $1000 genome will not tell you about BRCA 1/2 or other "patented" genes. In fact, I'd have a hard time believing this tells users much about many diseases. The truth of the matter is that most genetic disease are caused by several mutations which may elevate risk. Mendelian traits -- those caused by a single mutation -- are quite rare and you're likely to know if you have one. Conditions like lupus, diabetes, heart disease, and numerous others are caused by a combination of LOTS of genes and unknown environmental factors. To give you an idea of the relative importance of the two, the identical twin of someone with lupus has something like a 25% risk of developing the disease (don't impale me if I got the number wrong, 25% is in the neighborhood). To confound matters, mutations outside of genes in parts of the genome formerly referred to as junk DNA play an ill-defined, yet important role in many (or perhaps most) complex genetic diseases. Discovering you have a rare mutation in some seemingly random spot isn't all that helpful, even if it's going to cause you to drop dead some day.
Mapping disease risk mutations is a very rich area of research. Here's a taste: some people suspect that mutations operating in pairs or general n-tuples may cause disease in specific combinations. The drag here is that when these mutations are tested individually, they may show little or no statistical association. To test even all pairs is intractable (NP complete for you CS types) and doing so introduces a statistical nightmare with lots of semi-independent tests inflating the false positive rate.
I'd suggest you save your money for a few years unless you just really want to know about ancestry, which is relatively easy to determine from many fewer SNPs than these companies are offering. I don't recall the details, but I suspect something like this plus freely available software should do the trick. You just need to find a lab with a hyb oven and a microarray scanner and a statistician to do the analysis.
Good thoughts, but I think you've focussed on the wrong market.
Steve Jobs said that Intel delivers more power per watt. Let's think about that. Laptops have outpaced desktops for the first time. If Intel can deliver longer battery life than a cooled off G5, most users are going to respond to that. Let's face it. When I'm on a plane, I'm the only one compiling anything or doing monte carlo runs or pretty much anything else CPU intensive.
If I'm my boss (who's considering the switch), am I going to be impressed with benchmarks or how long I can stare at a grant application in Word?
That said, I'm really ticked off that the dev box for sale is 32-bit. hope we end up with something with a bigger address space without resorting to segmentation, which seems rather impossible. I was also anticipating a switch to dual-core G4s for my next PowerBook purchase. I'll just have to make the current one last a little longer now...
What? no, that's not right.
It uses the FreeBSD userland utilities, but not the kernel. You can't just compile them together. I mean, it's possible to take parts related to one, like the XYZ bootloader and use it to start the ZYX kernel, you can't just plug in modules or code. The ABIs and APIs are different.
In this case, MacOS doesn't even do that. They just use a lot of the user utilities and such.
If it's as good as they tout, it's probably not classified as fair trade coffee. But at nearly 10 bucks a pound, it damn well better provide fair compensation for the farmers. In general, good plantations aren't fair trade, as they can support themselves on the world market on the merits of their cups.
In short, the farmers here are likely getting fair compensation.
Amen brother-
I can take the engine in my 73 Super Beetle out in under half an hour. Half an hour to take out my engine. It's held on by (literally) four bolts. That's pretty awesome.
Wanna mod anything in an aircooled vw? no problem. You're only limited by space and your imaginiation. It's super cheap for parts, and easy to get started.
Assuming they could, as dr. D pointed out, make it past the problems of knowing, well very little, about developmental biology (a fetus can't sign a waiver to draw blood for study... research irb's would just laugh at the thought), would this thing get a soul? Is this a property of a body given at birth or something assigned at conception?
Any of you (prolly one) theologists out there please give a serious response. I'm really interested in this.
"This song is about eating meat. [...] Some of you vegetarians might be wondering why you should have to listen to a song about not eating meat. Don't just sit there with the attitude 'I'm not a meateater, I'm OK' go out and convince a meateater to give it up, there's plenty of fucking reasons!"
-Citizen Fish
s/eat.* meat/getting screwed by hollywood/
you have an answer.
I'm not too sure about this particular project, but obviously things like protein folding are out of the question. However, I can certainly imagine (and have actually implemented) algorithms for different medical research problems small enough to run in the background with a nice level of 19 and still crunch out a few thousand a minute.
There are great things to be learned from simulation. Implementation is a small detail. A devoted enough company will make it feasable for average users to do this kind of thing.
[Insert plug for my project]
Anyone interested in donating a few CPU cycles a month to a genetics project?
I was fairly impressed by this until the author lost all credibility as far as I'm concerned:
Chromosome 21 is the smallest human chromosome comprising less than 1.5% of the entire human genetic code.
False: the numbers of autosomal (ie, not x or y) chromosomes are assigned based on size from largest to smallest. Chromosomes 22 and y are smaller, the latter of which is the smallest in the genome. I'd expect more from the BBC.
-jeff kilpatrick Programmer, Oklahoma Medical Research Foundation, Lupus Genetics Study
Another project using linux for analysis
on
Linux on the Brain
·
· Score: 1
On a bit of a related note, I'd just like to point out another a genetics study using Linux for it's main number crunching. At the Oklahoma Medical Research Foundation, we have a dual Xeon box running through numbers to find linkage for the gene(s) causing the autoimmuno disease lupus. Since it's been deployed, our average analysis time has but cut to a fraction and our uptime beats the heck out of our NT domain master... The only problems we've had (aside from porting everything from OpenVMS) have to do with poor NT integration (likely non-RFC compliant dhcp serving us) and a lack of personell to run it! Just something that I thought I'd mention
I see two ways of looking at this, in terms of property. The most direct way of looking at things is to say that the state owns the schools, and the lines leading to the dorms. Therefore, they should have the right to restrict access to the internet. However, this isn't like some parents burdening their kids with NetNanny; these are public institutions. By installing a "filter" to close off access to certain sites, which may be vital in expressing opinions held by the students, this legislation would restrict free speech in schools. Further, who is to say what is educational in the first place?
What? Show me a single self-respecting woman who would respond to this in a positive way! Allow me to sum up roblimo's wife, as he described her: She's there to hug him at his will, but leaves him alone otherwise. She cooks his meals. She rubs his shoulders. She runs bath water for him. She's no supermodel. She has big breasts (or so I assume, since he made a big deal out of it in the Teenagers Take Heart: It Gets Better section She redocorates too much, and roblimo doesn't like what she does
If I were his wife, I'd be pretty pissed right now, or have no self-esteem to start with. For her sake, I hope she doesn't see the article. As for tactics on how to pick up chix: Don't bother. Treat females with the same respect you give other humans. (For some of you, it may require a bit more.) A novel concept: stay honest and try to show interest in things without microprocessors. (There is an entire world out there, and more beyond that!) To sum up, be true. Don't lie, don't embellish. If you're looking for someone to love and respect you, you have to be prepared to do the same. -noop
The/.ing of a server is not cool for those who have to deal with it, but let's keep mirrors out of this. They do get the stuff early. case in point: the University of Oklahoma mirror, for example, got it. This may seem trivial, but I'm on that network and I know how bogged down and slow it is!
It may be true that only 50% of Americans have the resources and equipment required to take part in the exchange of eMail, but the fact that all this has happened, for all intents and purposes, in the current decade should say enough. With the exponential growth of usage of the internet by home users, it appears to be just a matter of time until almost only the (although notably sizeable) impoverished population of this country is still without the means of digital communication.
Slashdot Mirror
Voting security research is happening in Houston at Rice. Get in contact with Dan Wallach in the Computer Science department.
I don't know the details, but my understanding is that they're technically patenting the assay, not the DNA sequence, per se. I'd love to be corrected on that.
Someone please mod the parent higher. It's good to see someone who seems to know what's going on.
The grandparent message is correct that the $1000 genome will not tell you about BRCA 1/2 or other "patented" genes. In fact, I'd have a hard time believing this tells users much about many diseases. The truth of the matter is that most genetic disease are caused by several mutations which may elevate risk. Mendelian traits -- those caused by a single mutation -- are quite rare and you're likely to know if you have one. Conditions like lupus, diabetes, heart disease, and numerous others are caused by a combination of LOTS of genes and unknown environmental factors. To give you an idea of the relative importance of the two, the identical twin of someone with lupus has something like a 25% risk of developing the disease (don't impale me if I got the number wrong, 25% is in the neighborhood). To confound matters, mutations outside of genes in parts of the genome formerly referred to as junk DNA play an ill-defined, yet important role in many (or perhaps most) complex genetic diseases. Discovering you have a rare mutation in some seemingly random spot isn't all that helpful, even if it's going to cause you to drop dead some day.
Mapping disease risk mutations is a very rich area of research. Here's a taste: some people suspect that mutations operating in pairs or general n-tuples may cause disease in specific combinations. The drag here is that when these mutations are tested individually, they may show little or no statistical association. To test even all pairs is intractable (NP complete for you CS types) and doing so introduces a statistical nightmare with lots of semi-independent tests inflating the false positive rate.
I'd suggest you save your money for a few years unless you just really want to know about ancestry, which is relatively easy to determine from many fewer SNPs than these companies are offering. I don't recall the details, but I suspect something like this plus freely available software should do the trick. You just need to find a lab with a hyb oven and a microarray scanner and a statistician to do the analysis.
Good thoughts, but I think you've focussed on the wrong market.
Steve Jobs said that Intel delivers more power per watt. Let's think about that. Laptops have outpaced desktops for the first time. If Intel can deliver longer battery life than a cooled off G5, most users are going to respond to that. Let's face it. When I'm on a plane, I'm the only one compiling anything or doing monte carlo runs or pretty much anything else CPU intensive.
If I'm my boss (who's considering the switch), am I going to be impressed with benchmarks or how long I can stare at a grant application in Word?
That said, I'm really ticked off that the dev box for sale is 32-bit. hope we end up with something with a bigger address space without resorting to segmentation, which seems rather impossible. I was also anticipating a switch to dual-core G4s for my next PowerBook purchase. I'll just have to make the current one last a little longer now...
What? no, that's not right.
It uses the FreeBSD userland utilities, but not the kernel. You can't just compile them together. I mean, it's possible to take parts related to one, like the XYZ bootloader and use it to start the ZYX kernel, you can't just plug in modules or code. The ABIs and APIs are different.
In this case, MacOS doesn't even do that. They just use a lot of the user utilities and such.
If it's as good as they tout, it's probably not classified as fair trade coffee. But at nearly 10 bucks a pound, it damn well better provide fair compensation for the farmers.
In general, good plantations aren't fair trade, as they can support themselves on the world market on the merits of their cups.
In short, the farmers here are likely getting fair compensation.
-- your friendly neighborhood home coffee roaster
Amen brother-
I can take the engine in my 73 Super Beetle out in under half an hour. Half an hour to take out my engine. It's held on by (literally) four bolts. That's pretty awesome.
Wanna mod anything in an aircooled vw? no problem. You're only limited by space and your imaginiation. It's super cheap for parts, and easy to get started.
Ye non-believers can skip this one.
Assuming they could, as dr. D pointed out, make it past the problems of knowing, well very little, about developmental biology (a fetus can't sign a waiver to draw blood for study... research irb's would just laugh at the thought), would this thing get a soul? Is this a property of a body given at birth or something assigned at conception?
Any of you (prolly one) theologists out there please give a serious response. I'm really interested in this.
"This song is about eating meat. [...] Some of you vegetarians might be wondering why you should have to listen to a song about not eating meat. Don't just sit there with the attitude 'I'm not a meateater, I'm OK' go out and convince a meateater to give it up, there's plenty of fucking reasons!"
-Citizen Fish
s/eat.* meat/getting screwed by hollywood/
you have an answer.
Well come on...
Propagandhi (vegan punk) + label owned by fat mike = hipocracy all over.
I'm not too sure about this particular project, but obviously things like protein folding are out of the question. However, I can certainly imagine (and have actually implemented) algorithms for different medical research problems small enough to run in the background with a nice level of 19 and still crunch out a few thousand a minute.
There are great things to be learned from simulation. Implementation is a small detail. A devoted enough company will make it feasable for average users to do this kind of thing.
[Insert plug for my project]
Anyone interested in donating a few CPU cycles a month to a genetics project?
Come on. Let's face the fact that TVT has always been jerky anyway. I hardly think they're representative of the rest of the indie labels.
I'm all for their cheap comps and like a lot of the music, but don't buy from Fat to stick it to the riaa. check the list; they're on it!
you may be right about that, but 21 would still be much larger than Y.
-jk
I'd expect more from the BBC.
-jeff kilpatrick
Programmer, Oklahoma Medical Research Foundation, Lupus Genetics Study
On a bit of a related note, I'd just like to point out another a genetics study using Linux for it's main number crunching. At the Oklahoma Medical Research Foundation, we have a dual Xeon box running through numbers to find linkage for the gene(s) causing the autoimmuno disease lupus. Since it's been deployed, our average analysis time has but cut to a fraction and our uptime beats the heck out of our NT domain master... The only problems we've had (aside from porting everything from OpenVMS) have to do with poor NT integration (likely non-RFC compliant dhcp serving us) and a lack of personell to run it! Just something that I thought I'd mention
I see two ways of looking at this, in terms of property. The most direct way of looking at things is to say that the state owns the schools, and the lines leading to the dorms. Therefore, they should have the right to restrict access to the internet. However, this isn't like some parents burdening their kids with NetNanny; these are public institutions. By installing a "filter" to close off access to certain sites, which may be vital in expressing opinions held by the students, this legislation would restrict free speech in schools. Further, who is to say what is educational in the first place?
Looks like the fbcom-* modules are what you're looking for. You may want to have a look at /usr/src/linux/include/linux/fb.h.
-jeffy
What?
Show me a single self-respecting woman who would respond to this in a positive way!
Allow me to sum up roblimo's wife, as he described her:
She's there to hug him at his will, but leaves him alone otherwise.
She cooks his meals.
She rubs his shoulders.
She runs bath water for him.
She's no supermodel.
She has big breasts (or so I assume, since he made a big deal out of it in the Teenagers Take Heart: It Gets Better section
She redocorates too much, and roblimo doesn't like what she does
If I were his wife, I'd be pretty pissed right now, or have no self-esteem to start with. For her sake, I hope she doesn't see the article.
As for tactics on how to pick up chix:
Don't bother. Treat females with the same respect you give other humans. (For some of you, it may require a bit more.)
A novel concept: stay honest and try to show interest in things without microprocessors. (There is an entire world out there, and more beyond that!)
To sum up, be true. Don't lie, don't embellish. If you're looking for someone to love and respect you, you have to be prepared to do the same.
-noop
The /.ing of a server is not cool for those who have to deal with it, but let's keep mirrors out of this. They do get the stuff early. case in point: the University of Oklahoma mirror, for example, got it. This may seem trivial, but I'm on that network and I know how bogged down and slow it is!
It may be true that only 50% of Americans have the resources and equipment required to take part in the exchange of eMail, but the fact that all this has happened, for all intents and purposes, in the current decade should say enough. With the exponential growth of usage of the internet by home users, it appears to be just a matter of time until almost only the (although notably sizeable) impoverished population of this country is still without the means of digital communication.