Academic and Govermental vs. Commerical Sequencing
on
Dog Genome Sequenced
·
· Score: 3, Informative
Sequencing that is done by the government and academic instutions generall is made availible to the public. I can't find the link right now, but one of the major funding organizations (NSF or NIH.. can't remember). Actually has it in writing that if you come up with a sequence and are funded by them, then you *must* put it in the database. I submitted a story to slashdot a while back about this, so if anyone can find it... be my guest.
Commercial sequencing, unfortunately, is another story. And because commerical science isn't funded by the government, they don't have those contracts that they must abide by. But they are a business, and if company X figures out how to make a protien that will give you a boner (at considerable expense), it is economically advantageous for them to keep that a secret so that company Y can't make boner drugs (piggybacking off the research that company X funded).
Nature needs to get some writers on their staff that are competent enough to write an article without omissions of important details. Venter's group did not just "sequence" the dog genome. They also annotated it to a certian degree. Annotation is the hard part, and thus this is a newsworthy achievement.
Annotation involves a great deal of wet lab work to actually use the sequences and produce ideas of what parts of the genome produce which protiens. Also, through methods such as ORF finding, CPG islands, Intron/Exon SNERP binding sites, and G/C content, mixed with some statistics, we can computationally detirmine where potential gene sites may lie.
One of the interesting things that Venters group did find is that there are nearly a million SNPs in the dog genome. Single Nucleotide Polymorphisms (SNPs) are responsible for the slight variation that can be found in closely related organisms. An example of this is the genetic differences between humans and chimpanzees being due to SNPs which are located in our developmental genes.
Website probably won't get slashdotted, it's actually housed at the university I go to (as it is a university program), and the evaluator of the IT story is actually one of my old professors.
From the manufacturer website: For that average commute of 20 miles and up to 24 miles per charge, the total cost per mile of the Tango is approximately 30% lower than that of a Honda Insight. This includes battery replacement, maintenance, and the cost of electricity at $.05 per kWh (as in the Northwest). The Honda Insight has an EPA rating of 56 mpg city and 57 highway.
Each concert is being released as a double CD. For shipping, and the price of the CD, my order came to about 19 bucks.
I know Pearl Jam is a band which is socially concious and tends to reach out on numerous occasions, but I see no problem with them keeping the extra money that this generates. The band keeps ticket prices low, which is admirable.
So for the fans that choose to add this cost to their concert-experience, just think of it as bringing the cost of the show more in-line with most of the other acts out there, and getting a free CD along with your concert.
I doubt that the record company has much to do with it for a few reasons.
1) In interviews, band members said they got the idea, and then Epic (Sony) wanted a piece of the action, to which the band agreed. And this is the reason you saw them in stores for the 2000 tour.
2) This time around, Epic didn't want in on the action, so the CD's are still being produced for the 2003 tour and are being sold on-line only, most likely with the band footing the overhead costs.
The first concert CD series was done by recording the shows, then mastering them on the road and then releasing them after the tour was over. The current CD series is done on-the-fly, with the concert-goer able to have the CD in their hands within 2 weeks of the show date.
For more info on the current approach to on-the-fly distribution, take a look at: Pearl Jam Recording Setup. You even get crappy 64kbps MP3's the day after the show if you can't wait for your CD in the mail!
Re:Privacy implications are nill
on
Twist on DNA Privacy
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· Score: 2, Interesting
It's only a matter of time before sequencing becomes inexpensive and extremely fast. There is one particular project that I have been watching for a while which can be described as: Nano-Pore Sequencing
The quick on this is that there are nano-scale pores on a membrane surface which allow DNA to pass through them, and can sequence the DNA in real time as it passes through. Once this technology is out there, you could have a seqencer in that would fit in your pocket, that can be hooked up to your computer to download the sequence into it.
Folks, I absolutely swear by the yellow engineering grid paper. For some reason, I am WAY more organized in my note taking when I do it on that.
Most of my school work is group presentations, writing papers, and using gcc to compile my CS projects. So my iBook 800mhz works well for me (but in retrospect, a tiBook 1ghz would have been a better choice for me)
I still find that I go home and use my desktop for extended periods of coding though, because the dual monitor setup is FAR easier to code on than any single screen system.
My reccomendations:
People doing more coding/scientific work: 15" or 17" airport equipped powerbook with a flat panel monitor for home.
People doing more papers/notetaking: Any PC or Mac laptop machine with wireless will work fine, don't worry so much about "cutting edge" because it costs more, and doesn't matter so much when all your doing is typing.
I have a second hand patton whole house air circulator, and god, do I love it. Turn it on during the day to blow all the hot air out of the house, and point it in the room at night to bring the cool air inside.
oh man... not true at all. I can't tell you how many CS courses I've had at 8:00am (this semester included).
On a bright note, most of my profs. seem to schedule their office hours right after class or before class... makes it much easier to get in to talk to them.
One of the mantra of proteomics is that structure equals function. So increasing protien function increases the exactness of what structure must be.
Creating a self replicating protien would require insertion of a encoding sequence of dna of the host. And the self replication would involve that protien doing something like functioning as a promoter for that sequence, thus requiring a portion of the structure of the protien be able to recognize a specific sequence of DNA.
Creating a malicous or beneficial protien indicates that it has a specific target (such as a specific receptor on the HIV protien coat). This also requires a specific structure to be able to recognize that.
The problem with computationally designing a protien that both self replicates and serves a malicious or beneficial purpose is that the computation involved increases exponentially when adding a new function to a protien.
This is because you may get a structure that works well for one of the two targets, but then you have to check it against the other target, and it may work horribly for that second one. So then you repeat the cycle until you find something that works well for both.
So while it is technically correct that they could do it, it's going to be a difficult thing to do by computational methods (and probably even harder by conventional methods).
While you are correct that bioinformatics involves a lot of string matching, you are trivalizing the scope, and the fruits of bioinformatics.
For example, doing an MSA on a set of strings is easy enough, and the computation involved in the algorithim to find the best alignment is slightly interesting. But the point of an MSA is not to parse the file, but to gain new knowledge from a bunch of data that was previously meaningless. And when we have thousands upon thousands of genetic sequences from various organisms, comparing them on a genetic level is definitely "new and exciting".
A Simple Example For those that know that Humans are 98.7% similar in DNA to a chimp, the question is really why are we so physically different. Well, bioinformatics, combined with lab research has provided insight into this.
We now know what makes us fundamentally different from the Chimps is that the SNPs that we have that make us 1.3% different are in key locations such as a genes which plays a role in developmentmental processes (and particullaraly the brain). For additional information on this, see: "Intra- and Interspecific variation in Primate Gene Expression Patterns; Science 4/13/02"
And in the 8/16/02 issue of Science, there was a short snippet on the discovery of a particular gene, FOXP2, that plays a role in speech and jaw development. They discuss that mutations in this gene have varied, and wide effects on the phenotypic expression in the organism. Now, lets apply what we know bioinformatics can apply, by asking the question. "What difference in the FOXP2 gene causes the differences between humans and chimpanzees in speech and jaw development".
There are SNP databases out there that have been constructed by analyzing the various known genetic sequences and if you search that database, you will notice there *is* a SNP in humans that is unique to humans.... now we have a really interesting argument to why humans can talk and other species can't. (http://www.geocities.com/asdut2002/FOXP2.html
Conclusion So the bottom line is that yes, bioinformatics allows us to do a lot of string comparisions, but the benefit of those comarisions are the real gem. And without computer scientists to construct algorithims, and IT professionals to develop world class database systems, this information just isn't useful.
PV = nRT Pressure × Volume = No. of moles × Universal Gas Constant × Absolute Temperature
First off, you will want to do this outside. All you need is a small amount of dry ice, water, and a plastic soda bottle (20oz, 1liter, or 2 liter are all fine). I would reccomend a 2 liter, because it's more impressive. Put enough dry ice in the bottle to barely cover the bottom of the empty 2 liter bottle. Then be ready for action, because you will want to put about an equal amount of water as dry ice in your bottle. After filling the bottle with water, the dry ice will start being convered to CO2 gas, and you will want to cap the bottle. Place it in the middle of a field or something and make sure everyone is well away from it.
You can take this time to explain that Dry Ice is a solid form of Carbon Dioxide, and when it is in a system with water, it undergoes sublimation (solid to gas, no liquid phase). And that it's gaseous volume is 800 times that of the solid volume. (so if you want to measure and get all scientific, you could).
Just about when you get done explaining this stuff, your experiment should alert you that it's ready. The pressure that the CO2 exerts on the closed volume system becomes too great, and the bottle gives and a rather loud sound is produced. Like everyone said, explosions are cool;)
So if we apply the science to it.
2 liters = (approx) 2000 cubic centimeters
2000cc/800 = 2.5cc of dry ice needed to fill the system with gas.
So lets say we put 5cc of ice, and 5 cc of water in.
5cc * 800 = 4000cc space needed for the gas to expand
system volume(2000cc) - water volume(5cc) = 1995cc
This would pretty much gaurantee an explosion. But for the kids, you might give them this information and see if they can come up with the minimum amount needed to make the bottle explode, make them draw upon some basic math skills:)
Exactly, but with the one exception that DNA transcription and translation into protiens is massively parallell and this process is MUCH more efficent in DNA than in computing.
And the even cooler part of it is that if they let the biotech people get away with it... then we have precedence when it starts happening in the computer world and goes to court!:)
This reminds me of a particular theory/joke that if a infinite number of monkeys typed for an infinite amount of time... they could come up with the complete soruce code for MS windows. Well this process that they are describing.
"Inserting pieces of DNA into cells to turn on genes randomly and then screen for the protein of interest"
Is basically analogous to having a copy of the source code and each time a monkey spits out a page, we look at it and see if it's a match to the page we are holding.
Then the conclusion is drawn that if we can get it by some other way than actually copying it from the original, then we can use it.
Another example of this technique is that lets say I have the complete specs for an algorithim for an encryption technique, lets call it CSS. And I decide to not copy it, but derive my own program from this knowledge that I have of the specs.... is that new program legal? Ask the courts... I still think that Jon kid is still in deep water for it.
1)I'm sure someone who has hands which are deformed, such as burn victims, will have altered fingerprints from that which are on file, and possibly no fingerprints at all.
2)What if someone has no hands... You can sign with your teeth, or feet... but you can't give a thumbprint with your toes!
Slashdot Mirror
Sequencing that is done by the government and academic instutions generall is made availible to the public. I can't find the link right now, but one of the major funding organizations (NSF or NIH.. can't remember). Actually has it in writing that if you come up with a sequence and are funded by them, then you *must* put it in the database. I submitted a story to slashdot a while back about this, so if anyone can find it... be my guest.
Commercial sequencing, unfortunately, is another story. And because commerical science isn't funded by the government, they don't have those contracts that they must abide by. But they are a business, and if company X figures out how to make a protien that will give you a boner (at considerable expense), it is economically advantageous for them to keep that a secret so that company Y can't make boner drugs (piggybacking off the research that company X funded).
Nature needs to get some writers on their staff that are competent enough to write an article without omissions of important details. Venter's group did not just "sequence" the dog genome. They also annotated it to a certian degree. Annotation is the hard part, and thus this is a newsworthy achievement.
7 0&ncid=753&e=4&u=/nm/20030925/sc_nm/science_dog_dc
Annotation involves a great deal of wet lab work to actually use the sequences and produce ideas of what parts of the genome produce which protiens. Also, through methods such as ORF finding, CPG islands, Intron/Exon SNERP binding sites, and G/C content, mixed with some statistics, we can computationally detirmine where potential gene sites may lie.
One of the interesting things that Venters group did find is that there are nearly a million SNPs in the dog genome. Single Nucleotide Polymorphisms (SNPs) are responsible for the slight variation that can be found in closely related organisms. An example of this is the genetic differences between humans and chimpanzees being due to SNPs which are located in our developmental genes.
Here is a better article on exactly what they did and what the importance of it is.
http://story.news.yahoo.com/news?tmpl=story&cid=5
Website probably won't get slashdotted, it's actually housed at the university I go to (as it is a university program), and the evaluator of the IT story is actually one of my old professors.
-Steve
Take a look at the link I added in there, they also address the cost of electric in California as well.
From the manufacturer website:
For that average commute of 20 miles and up to 24 miles per charge, the total cost per mile of the Tango is approximately 30% lower than that of a Honda Insight. This includes battery replacement, maintenance, and the cost of electricity at $.05 per kWh (as in the Northwest). The Honda Insight has an EPA rating of 56 mpg city and 57 highway.
Link To Reference Here
I know Pearl Jam is a band which is socially concious and tends to reach out on numerous occasions, but I see no problem with them keeping the extra money that this generates. The band keeps ticket prices low, which is admirable.
So for the fans that choose to add this cost to their concert-experience, just think of it as bringing the cost of the show more in-line with most of the other acts out there, and getting a free CD along with your concert.
I doubt that the record company has much to do with it for a few reasons.
The first concert CD series was done by recording the shows, then mastering them on the road and then releasing them after the tour was over. The current CD series is done on-the-fly, with the concert-goer able to have the CD in their hands within 2 weeks of the show date.
For more info on the current approach to on-the-fly distribution, take a look at: Pearl Jam Recording Setup. You even get crappy 64kbps MP3's the day after the show if you can't wait for your CD in the mail!
The quick on this is that there are nano-scale pores on a membrane surface which allow DNA to pass through them, and can sequence the DNA in real time as it passes through. Once this technology is out there, you could have a seqencer in that would fit in your pocket, that can be hooked up to your computer to download the sequence into it.
Steve
Folks, I absolutely swear by the yellow engineering grid paper. For some reason, I am WAY more organized in my note taking when I do it on that.
Most of my school work is group presentations, writing papers, and using gcc to compile my CS projects. So my iBook 800mhz works well for me (but in retrospect, a tiBook 1ghz would have been a better choice for me)
I still find that I go home and use my desktop for extended periods of coding though, because the dual monitor setup is FAR easier to code on than any single screen system.
My reccomendations:
People doing more coding/scientific work: 15" or 17" airport equipped powerbook with a flat panel monitor for home.
People doing more papers/notetaking: Any PC or Mac laptop machine with wireless will work fine, don't worry so much about "cutting edge" because it costs more, and doesn't matter so much when all your doing is typing.
I have a second hand patton whole house air circulator, and god, do I love it. Turn it on during the day to blow all the hot air out of the house, and point it in the room at night to bring the cool air inside.
link here from amazon
oh man... not true at all. I can't tell you how many CS courses I've had at 8:00am (this semester included).
On a bright note, most of my profs. seem to schedule their office hours right after class or before class... makes it much easier to get in to talk to them.
One of the mantra of proteomics is that structure equals function. So increasing protien function increases the exactness of what structure must be.
Creating a self replicating protien would require insertion of a encoding sequence of dna of the host. And the self replication would involve that protien doing something like functioning as a promoter for that sequence, thus requiring a portion of the structure of the protien be able to recognize a specific sequence of DNA.
Creating a malicous or beneficial protien indicates that it has a specific target (such as a specific receptor on the HIV protien coat). This also requires a specific structure to be able to recognize that.
The problem with computationally designing a protien that both self replicates and serves a malicious or beneficial purpose is that the computation involved increases exponentially when adding a new function to a protien.
This is because you may get a structure that works well for one of the two targets, but then you have to check it against the other target, and it may work horribly for that second one. So then you repeat the cycle until you find something that works well for both.
So while it is technically correct that they could do it, it's going to be a difficult thing to do by computational methods (and probably even harder by conventional methods).
Could we call this the "Laci Peterson Scientific Method"?
ya ya... I'm going to hell
1 gram of protein does not have the same caloric content as 1 gram of carbohydrate.
1 gram carbohydrate = 4.3 kcal
1 gram fat = 9.5 kcal
1 gram protein = 5.7 kcal
But you were right on the other part. It does take more energy to digest the protein, as it needs to be converted by the liver into a usable sugar.
SF
Ya ya, who cares. I'm a biology minor, and computer science major, and this article wasn't particullarly interesting to me even. ;)
a phb.htm
You wanna see something cool... how about DNA having a parity bit?? Take a peek....
http://www.academicpress.com/inscight/09112002/gr
While you are correct that bioinformatics involves a lot of string matching, you are trivalizing the scope, and the fruits of bioinformatics.
For example, doing an MSA on a set of strings is easy enough, and the computation involved in the algorithim to find the best alignment is slightly interesting. But the point of an MSA is not to parse the file, but to gain new knowledge from a bunch of data that was previously meaningless. And when we have thousands upon thousands of genetic sequences from various organisms, comparing them on a genetic level is definitely "new and exciting".
A Simple Example
For those that know that Humans are 98.7% similar in DNA to a chimp, the question is really why are we so physically different. Well, bioinformatics, combined with lab research has provided insight into this.
We now know what makes us fundamentally different from the Chimps is that the SNPs that we have that make us 1.3% different are in key locations such as a genes which plays a role in developmentmental processes (and particullaraly the brain). For additional information on this, see: "Intra- and Interspecific variation in Primate Gene Expression Patterns; Science 4/13/02"
And in the 8/16/02 issue of Science, there was a short snippet on the discovery of a particular gene, FOXP2, that plays a role in speech and jaw development. They discuss that mutations in this gene have varied, and wide effects on the phenotypic expression in the organism. Now, lets apply what we know bioinformatics can apply, by asking the question. "What difference in the FOXP2 gene causes the differences between humans and chimpanzees in speech and jaw development".
There are SNP databases out there that have been constructed by analyzing the various known genetic sequences and if you search that database, you will notice there *is* a SNP in humans that is unique to humans.... now we have a really interesting argument to why humans can talk and other species can't. (http://www.geocities.com/asdut2002/FOXP2.html
Conclusion
So the bottom line is that yes, bioinformatics allows us to do a lot of string comparisions, but the benefit of those comarisions are the real gem. And without computer scientists to construct algorithims, and IT professionals to develop world class database systems, this information just isn't useful.
When patent time comes, could the fu-fme be considered prior art? :)
Steve
I wasn't too impressed by his description and explination, so I found the page that had the real details, enjoy: http://www.osafoundation.org/our_product_desc.htm
Demonstration of the Ideal Gas Law:
;)
:)
;) http://caselaw.lp.findlaw.com/cacodes/pen/12301-12 316.html
PV = nRT
Pressure × Volume = No. of moles × Universal Gas Constant × Absolute Temperature
First off, you will want to do this outside. All you need is a small amount of dry ice, water, and a plastic soda bottle (20oz, 1liter, or 2 liter are all fine). I would reccomend a 2 liter, because it's more impressive. Put enough dry ice in the bottle to barely cover the bottom of the empty 2 liter bottle. Then be ready for action, because you will want to put about an equal amount of water as dry ice in your bottle. After filling the bottle with water, the dry ice will start being convered to CO2 gas, and you will want to cap the bottle. Place it in the middle of a field or something and make sure everyone is well away from it.
You can take this time to explain that Dry Ice is a solid form of Carbon Dioxide, and when it is in a system with water, it undergoes sublimation (solid to gas, no liquid phase). And that it's gaseous volume is 800 times that of the solid volume. (so if you want to measure and get all scientific, you could).
Just about when you get done explaining this stuff, your experiment should alert you that it's ready. The pressure that the CO2 exerts on the closed volume system becomes too great, and the bottle gives and a rather loud sound is produced. Like everyone said, explosions are cool
So if we apply the science to it.
2 liters = (approx) 2000 cubic centimeters
2000cc/800 = 2.5cc of dry ice needed to fill the system with gas.
So lets say we put 5cc of ice, and 5 cc of water in.
5cc * 800 = 4000cc space needed for the gas to expand
system volume(2000cc) - water volume(5cc) = 1995cc
This would pretty much gaurantee an explosion. But for the kids, you might give them this information and see if they can come up with the minimum amount needed to make the bottle explode, make them draw upon some basic math skills
Ok, now that I've gone though all this, check your state laws to see if this fun experiment is illegal, it is here in california
Now that he's being slashdotted (I get DNS not found) I'm sure that he won't be getting ranked by *anybody* for at least a few hours... heh
-Steve
steve
steve
Is basically analogous to having a copy of the source code and each time a monkey spits out a page, we look at it and see if it's a match to the page we are holding.
Then the conclusion is drawn that if we can get it by some other way than actually copying it from the original, then we can use it.
Another example of this technique is that lets say I have the complete specs for an algorithim for an encryption technique, lets call it CSS. And I decide to not copy it, but derive my own program from this knowledge that I have of the specs.... is that new program legal? Ask the courts... I still think that Jon kid is still in deep water for it.
steve
...that they are going to employ a beowouf cluster of audio experts?
2)What if someone has no hands... You can sign with your teeth, or feet... but you can't give a thumbprint with your toes!
OK.. enough rambling..
Steve
If he got slashdotted, would that be considered a 3 some... strike that.. half-a-million some?
Maybe next time I see a porn where some girl is in a "group situation"... I will just say she is getting slashdotted.
-steve