That's why the patent applications won't cover the organism itself. They'll cover methods for producing the organism on a large scale (no small challegene for some bacteria) and methods of use to cure MRSA infections. None of these things were 'found in a rock pool'; they're exactly what patents are intended to protect and promote. More power to them, you'd be thankful if your leg were being eaten alive by MRSA.
Repeat after me: The concept of IP isn't bad, abuse of the USPTO is the problem. -j
Yup, before Bayh-Dole universities and non-profits weren't allowed to patent inventions that came out of federally-funded research. There are two schools of thought on this amd I'm fairly sure where the slashdot crowd will come out:
1) This is a good thing, it fosters research and brings money back to the University creating a cycle of innovate-to-profit.
2) The entire idea of allowing someone else to lock up knowledge invented on the public dime is repulsive and even if it HAS icreased tech-transfer rates and numbers of patents filed (and I've yet to figure out why that, in and of itself, is a goal) this is certainly no direct measure of increased INNOVATION.
Personally I think it was a terrible thing. It let the federal and state governments cut funding to major universities virtually in lock-step w/ the amount of cash those universities were bringing in with tech-transfer revenue. This creates a desperate cycle of invention-for-survival and patents and tech-transfers for cash, NOT for science.
The court's job is not one of judicial activism (unless Bush has his way). Its only reason to exist is to ensure Congress passes laws in accordance w/ Consitutional mandates. Sadly, they did. -j
If Lessig would fare better here than during the Eldred vs. Ashcroft debacle.
Calling Eldred v. Ashcroft a 'debacle' is unfair to Lessig. One can make a perfectly coherent argument that the Supremes were correct in judging that the Bono act doesn't violate the copyright clause in the Constitution. It is limited, even if infinitisimally so from an economic standpoint.
That Lessig felt arguing the case before the Supremes was his only rememedy against bad legislative policy says more about the U.S. citizenry's ability to participate in the creation of the laws that govern them than anything else.
Eldred v. Ashcroft wasn't a debacle; it was prudent case law and the 7-2 judgement reflects this support across the political spectrum on the bench. The debacle sits firmly in the halls of Congress and we should concentrate our judgement there.
Simple solution -- things that have wide effect on public welfare should be funded by the government directly, not by forcing citizens to do it in a convoluted and humiliating ways through monopolies.
I'll bite. In your model, who decides what sicknesses get priority in the research queue? Do you believe that our federal cash flows, in the absence of massive increases in taxation, can support the level of parallel development currently taken on by the pharmaceutical industry we all so love to demonize?
I don't think your model would work. No country in the world relies chiefly on public funding for medical research; the vast majority rely on public funds for basic research and massive private investment (accompanied by massive private returns) for applied research. This is why the founders included patents and copyright in the Constitution.
Perhaps, but they are groups of people lacking the accountability present in the personal actions of a single citizen. When Union Carbide, through negligence and plain stupidity, killed thousands in Bhopal no one went to jail. No one stood in court accused of a crime and was convicted by a jury of their peers.
Instead, they paid a fine; the usual way corporations cleanse themselves of guilt. If, in Santa Clara County v. Southern Pacific, we decided companies were the equal to individual citizens, legally, why did we not also decide that they must face the same consequences?
I'm not sure about you but I don't trust an entity that has all the rights but faces none of the consequences, corporate or otherwise.
This is the world of Ayn Rand. These are the evils of capitalism. The combination of a patent system run amok and technologies which involve human DNA have given us a glimpse into just how evil capitalism can become
Sure. Because a company should spend $500M over ten years developing a drug to save millions of lives without assurance of recouping that cost through limited, government-granted monopolies in the market.
I'm not sure what you're semi-coherent rambling is attempting to suggest but the patent system, at least in biotech, has taken a great leap towards sensibility in this regulation. We should applaud the USPTO when they deserve it and decry them when they do not.
2. The liver produces complex proteins from
amino acids. It wouldn't be uncommon for the
transplanted liver to produce IgE
(immunoglobulin E) which, if I remember
correctly, is what causes the reaction that
causes anaphylactic shock (fancy term for
bad allergic reaction).
You remember correctly but it would indeed be strange for the liver to produce IgE. IgE is released by only mast cells, immunge cells that are not normally circulatory but that settle in tissues and do their thing in situ.
They're usually found resting in connective tissues but I can imagine a liver transplant would move a few along for the ride (and it doesn't take much IgE to do a lot of harm; it's powerful stuff). They do, however, have a limited life span (though I don't remember what it is). If only he'd waited to eat those nuts...
many authors have only
written one good work in their lives (e.g. Steinbeck)
<resists urge for literary bitch fest>
I do believe you've just likened John Steinbeck to Billy Ray Cyrus. Just because you have only ever read Grapes of Wrath does not mean it was Steinbeck's Achy Breaky Heart.
You made such a good point; it's a shame to screw it up by insulting one of America's great writers.
-j
I'm not sure from whence came all your 'hences' but the sixty four combinations of ACTG only translate into 20 (some argue a few more) amino acids and start/stop signals. The system is highly redundant to lessen the impact of single-base polymorphsims (i.e. if a codon is CCA and the second C is copied as an A accidentally the same amino acid still can be produced in the end-result protein chain).
So hence... it's not 64bit computation. It's ~23bit computation... but all those other buzzwords are fun too.:) -j
I suggested that consumers pay 1 cent per commercial skipped (which is about the same as what advertisers pay). That would be equivalent to $10/thousand commercials skipped. I think that's reasonable.
And I agree. From the majority of comments in this forum one would have to assume we believe that the $40 - $100/mo we pay our cable companies (in my case including fast, efficient broadband access) is enough to pay for all the content we view -- advertisers be damned.
Not so. The comment referenced above is the first really intelligent thing I've heard out of the cable industry (or someone close to it) since this whole debate started. The cable industry depends on ads; because of this, it's understandable that they freak out when users begin using technologies that obviate ads.
So what's the answer here? Wean the cable giants from their dependance on advertising revenue. 1 cent per ad skipped is completely reasonable. Figure four ads per commercial break, five breaks per hour, twenty ads per hour long show. Would you pay twenty cents to see Jennifer Garner's uninterrupted well-dressed self in Alias for an hour? I sure as hell would.:)__
We can rant and rave all we want but this guy is offering solutions. Do him the favor of listening to him and writing to the cable companies to voice your support for common-sense middle-ground approaches.
This, even though the largest corporations possess monitary power far and above that of the vast, vast majority of the rest of the citizenry and in some cases span hundreds of countries in their global operations.
Laws like the current campaign finance reform attempt wouldn't be necessary if we didn't have to try and stop Smith, Smith and Nobody from donating millions of dollars to pet issues that in many cases don't even directly impact American citizens each and every election cycle.
Until we sit up and realize the danger inherent in assigning 'natural person' status and the rights that go along with that status to entities who's sole reason for existence is profit-making (with zero social responsibility) we'll continue struggling with legal ways in which to make these distinctions and we will always fail.
The current law deserves to be shot down. A citizen should be able to spend as much as he or she wishes to spend and say whatever they wish in the forum of their choice. The problem is that we've given this same power to souless corporate entities who've proven over and over again a bald-faced willingness for abuse.
Meaningful dialog on campaign finance reform is doomed to failure as long as we consider human beings and corporations as equals under the law.
-j
Actually, corporate entities are legally afforded many if not all of the same protections afforded individual citizens. Read up on Santa Clara County v. Southern Pacific Railroad (1886) here.
For biotech patents on genes or proteins the USPTO requires you include a 'sequence listing' describing the sequence of the gene(s) or protein(s) you're patenting. This must be submitted in a very structured format that increases the vertical length of the submitted content by a great deal, especially for long sequences (so I imagine this 140k page application was a small app with a giant sequence listing trying to keep the claims as biologically broad as possible).
The PTO has finally gotten wise to the act of including everything but the kitchen sink in a patent listing (as was the industry's habit a few years ago) and now charges on a per-page basis for patent submissions. This ensures that if a company files a 140k page patent, they really mean it and are willing to pay for it.
One of the FEW good ideas out of the USPTO in a long time; let's hope there are others. -j
In the short term, you're right. Intellectual property protections will, as usual, deny the third world the ability to afford these medications (unless they take steps to ignore the patent and make the drugs anyway).
But patents are temporary. Eventually this knowledge can be worked into an affordable, open treatment as soon as science/pharma moves on to bigger and better things.
It might take fifty years but the sequence of the genome is the first step in a long road to curing humanity's availability to the malaria parasite.
McCullagh is a journalist. As such, he's not supposed to be your friend. Nor is he supposed to be that of Ms. Rosen. That's kind of the point.
Like it or not, Declan's made great points in both of the articles mentioned above. Disorganized 'geektivism' hurts our causes. The legal verbage in the DMCA doesn't apply to academics publishing research.
The problem in both of these cases is one of education. Geeks need to learn how to be activists. They need poise, patience and funding. Researchers and educational institutions need to know their rights and be prepared to stand up for them if/when challenged (which USED to be academe's place in society).
Personally, I think Declan's right-on and I applaud him for trying to bring even-handed journalism into this debate. -j
Thanks for that unfortunately worded reply. I don't think I ever claimed to be a statistician and though you made and interesting point (the power analysis) I can point out issues w/ your thoughts as well.
First, I never implied the sample size was 54 in total; I said 'two sample populations of 54 people' for, yes, 108 in total. Thanks for the credit.
In addition the linear distance between the means, which you claim is 'significant', cannot be considered without regard to the deviation of that mean, which wasn't in the article but is most certainly at least in the paper.
My main point, which you seem to have missed, was simply that using such small sample sizes in a situation with many, many factors leaves much to be desired where statistical relavance is concerned. I would imagine that if all 108 samples had complete, detailed life histories that we could find any number of variables with high correlation, many of which MIGHT have something to do with Alzheimers, and many not. That these researchers choose to publish about caffeine probably said more about the contents of their patient histories than anything else.
Do you always talk down to your peers this way? Does it get you anywhere? -j
I wouldn't get too excited - the fact that small-sample studies this like manage to get published amazes me. They're using two sample populations of 54 people for a disease state who's incidence, from what we currently understand, is probably affected by DOZENS of parameters over a span of decades.
Even the most basic course in statistics won't let you put much trust in these results. You could probably show a correlation in the same small population for tv viewing habits or propensity for wearing tinfoil hats. -j
Palladium won't run unauthorized programs, so viruses can't trash protected parts of your system.
By this they mean one of two things. Either it simply WONT run anything 'unauthorized' which brings up:
will an independant developer have to jump through hoops to 'certify' every exe you compile to run on your own machine?
will we have to go through another damn 'trusted' certifying agency a la SSL certs? Perhaps MS will be the last word?
Alternatively the OS might run things as long as the user tells the OS a particular binary is authorized. In this case I give it a good five minutes until some newbie tells the OS the latest email worm is an 'authorized' exe because they're looking to see that promised video of Brittany Spears some stranger w/ poor english apparently sent them out of the goodness of his heart. -j
Re:More to biology than genomics!
on
Bioperl 1.0 Release
·
· Score: 4, Informative
they don't encompass any of us
The content of Bioperl is driven far more by the interests of the bioperl community than by some malfeasant desire to exclude ecologists. What started out as a codebase dealing mostly with parsing sequence files and results from sequence-analysis applications is slowly branching out to include code for analysis of phylogenetic trees, etc.
If bioperl doesn't meet your needs the community as a whole needs to hear from you! Let the mailing list know what interests you or, even better, start contributing code!
The Bio* namespace can help address your problems only if you share them with the community!:)
IAB (I'm a bioinformaticist). You're partly correct. Introns (the 'junk' inbetween the exonic regions in DNA and freshly transcribed mRNA) do tend towards non-random sequence. You can use a variety of metrics to make guesses as to where introns and exons begin and end within a gene's coding region based on sequence entropy, on GC/AT frequency, on neural nets or hidden markov models trained on known examples, etc.
These metrics, however, are only useful once one knows something about where a 'gene' starts and ends. The real problem here is that some of the assumptions we've made historically about gene structure has potentially led us astray. Yes, the chromosomes are full of junk DNA but no, it's nothing near random for the most part and is full of 'repetitive' elements (short segments that repeat endlessly, query Genbank for 'ALU Repeat' and see how many sequences you find) that make any sort of pattern matching a tough sell genome-wide. There are also plenty of 'psueudogenes' interspersed throughout the genome, leftovers from a bygone era. It's the question of which of these pseudogenes might actually still BE transcribed that only mRNA expression analysis can provide. Hopkins is definitely on the right track w/ something like SAGE (though it's not exactly high-throughput, hence our man's need for extrapolation to genome-wide numbers).
The paper should be an interesting read to say the least. -j
Re:You are not a walking patent, no
on
Squatting On Life
·
· Score: 1
No, you'll actually find that companies are patenting particular sequences without knowing what they do.
True, but remember that being granted a patent is a lot less important than being able to adequately enforce that patent in a court of law. None of these 'sequence only' patents have yet come up in court cases. Should they do so, there is a feeling in the industry that they would easily be overturned. The fact that the USPTO granted these sequence-only composition of matter patents is difficult to support, agreed. But the really important question is not the fact that the USPTO is willing to grant them, the real question is whether the courts are willing to overturn them. That we just don't know.
And keep in mind that there is a large difference between the two major patent types. These sequence only composition of matter patents are bunk, truly, as everyone here has noticed: prior art exists in us all. However, the second type, methods of use is a different beast all-together. Here a researcher is saying 'Hey, I found that this gene is significantly up-regulated during late state Alzheimer's diseases. This makes it a GREAT candidate for a therapeutic, and if it comes to pass that the drug cures Alzheimers, I want protection for my rights to discovery'. Can anyone really argue with that? Getting a drug through FDA approval can cost billions, why the hell would a drug company do this without the promise of protection of profits?
Answer: they wouldn't.
------------------------------------------------ ---------------
James C. Diggans
jdiggans@excelsior-web.com
Slashdot Mirror
That's why the patent applications won't cover the organism itself. They'll cover methods for producing the organism on a large scale (no small challegene for some bacteria) and methods of use to cure MRSA infections. None of these things were 'found in a rock pool'; they're exactly what patents are intended to protect and promote. More power to them, you'd be thankful if your leg were being eaten alive by MRSA.
Repeat after me: The concept of IP isn't bad, abuse of the USPTO is the problem.
-j
Yup, before Bayh-Dole universities and non-profits weren't allowed to patent inventions that came out of federally-funded research. There are two schools of thought on this amd I'm fairly sure where the slashdot crowd will come out:
1) This is a good thing, it fosters research and brings money back to the University creating a cycle of innovate-to-profit.
2) The entire idea of allowing someone else to lock up knowledge invented on the public dime is repulsive and even if it HAS icreased tech-transfer rates and numbers of patents filed (and I've yet to figure out why that, in and of itself, is a goal) this is certainly no direct measure of increased INNOVATION.
Personally I think it was a terrible thing. It let the federal and state governments cut funding to major universities virtually in lock-step w/ the amount of cash those universities were bringing in with tech-transfer revenue. This creates a desperate cycle of invention-for-survival and patents and tech-transfers for cash, NOT for science.
Ick.
-j
The court's job is not one of judicial activism (unless Bush has his way). Its only reason to exist is to ensure Congress passes laws in accordance w/ Consitutional mandates. Sadly, they did.
-j
Just another waste of taxpayer money trying to prove that God doesn't exist.
Looking for a state-sponsored theocracy? Try the administration of George W. Bush and his Helpful Friend, John Ashcroft!
Scaring the bejeezus out of center-left citizens since January, 2000. :P
-j
If Lessig would fare better here than during the Eldred vs. Ashcroft debacle.
Calling Eldred v. Ashcroft a 'debacle' is unfair to Lessig. One can make a perfectly coherent argument that the Supremes were correct in judging that the Bono act doesn't violate the copyright clause in the Constitution. It is limited, even if infinitisimally so from an economic standpoint.
That Lessig felt arguing the case before the Supremes was his only rememedy against bad legislative policy says more about the U.S. citizenry's ability to participate in the creation of the laws that govern them than anything else.
Eldred v. Ashcroft wasn't a debacle; it was prudent case law and the 7-2 judgement reflects this support across the political spectrum on the bench. The debacle sits firmly in the halls of Congress and we should concentrate our judgement there.
-jSimple solution -- things that have wide effect on public welfare should be funded by the government directly, not by forcing citizens to do it in a convoluted and humiliating ways through monopolies.
I'll bite. In your model, who decides what sicknesses get priority in the research queue? Do you believe that our federal cash flows, in the absence of massive increases in taxation, can support the level of parallel development currently taken on by the pharmaceutical industry we all so love to demonize?
I don't think your model would work. No country in the world relies chiefly on public funding for medical research; the vast majority rely on public funds for basic research and massive private investment (accompanied by massive private returns) for applied research. This is why the founders included patents and copyright in the Constitution.
-jPerhaps, but they are groups of people lacking the accountability present in the personal actions of a single citizen. When Union Carbide, through negligence and plain stupidity, killed thousands in Bhopal no one went to jail. No one stood in court accused of a crime and was convicted by a jury of their peers.
Instead, they paid a fine; the usual way corporations cleanse themselves of guilt. If, in Santa Clara County v. Southern Pacific, we decided companies were the equal to individual citizens, legally, why did we not also decide that they must face the same consequences?
I'm not sure about you but I don't trust an entity that has all the rights but faces none of the consequences, corporate or otherwise.
-jThis is the world of Ayn Rand. These are the evils of capitalism. The combination of a patent system run amok and technologies which involve human DNA have given us a glimpse into just how evil capitalism can become
Sure. Because a company should spend $500M over ten years developing a drug to save millions of lives without assurance of recouping that cost through limited, government-granted monopolies in the market.
I'm not sure what you're semi-coherent rambling is attempting to suggest but the patent system, at least in biotech, has taken a great leap towards sensibility in this regulation. We should applaud the USPTO when they deserve it and decry them when they do not.
-j2. The liver produces complex proteins from amino acids. It wouldn't be uncommon for the transplanted liver to produce IgE (immunoglobulin E) which, if I remember correctly, is what causes the reaction that causes anaphylactic shock (fancy term for bad allergic reaction).
You remember correctly but it would indeed be strange for the liver to produce IgE. IgE is released by only mast cells, immunge cells that are not normally circulatory but that settle in tissues and do their thing in situ.
They're usually found resting in connective tissues but I can imagine a liver transplant would move a few along for the ride (and it doesn't take much IgE to do a lot of harm; it's powerful stuff). They do, however, have a limited life span (though I don't remember what it is). If only he'd waited to eat those nuts ...
-j<resists urge for literary bitch fest>
I do believe you've just likened John Steinbeck to Billy Ray Cyrus. Just because you have only ever read Grapes of Wrath does not mean it was Steinbeck's Achy Breaky Heart.
You made such a good point; it's a shame to screw it up by insulting one of America's great writers.
-j
I'm not sure from whence came all your 'hences' but the sixty four combinations of ACTG only translate into 20 (some argue a few more) amino acids and start/stop signals. The system is highly redundant to lessen the impact of single-base polymorphsims (i.e. if a codon is CCA and the second C is copied as an A accidentally the same amino acid still can be produced in the end-result protein chain).
... it's not 64bit computation. It's ~23bit computation ... but all those other buzzwords are fun too. :)
So hence
-j
And I agree. From the majority of comments in this forum one would have to assume we believe that the $40 - $100/mo we pay our cable companies (in my case including fast, efficient broadband access) is enough to pay for all the content we view -- advertisers be damned. Not so. The comment referenced above is the first really intelligent thing I've heard out of the cable industry (or someone close to it) since this whole debate started. The cable industry depends on ads; because of this, it's understandable that they freak out when users begin using technologies that obviate ads.
So what's the answer here? Wean the cable giants from their dependance on advertising revenue. 1 cent per ad skipped is completely reasonable. Figure four ads per commercial break, five breaks per hour, twenty ads per hour long show. Would you pay twenty cents to see Jennifer Garner's uninterrupted well-dressed self in Alias for an hour? I sure as hell would. :)__
We can rant and rave all we want but this guy is offering solutions. Do him the favor of listening to him and writing to the cable companies to voice your support for common-sense middle-ground approaches.
-j
The problem here is that ever since Santa Clara County v. Southern Pacific Railroad corporations have been considered, legally, as a 'natural person'.
This, even though the largest corporations possess monitary power far and above that of the vast, vast majority of the rest of the citizenry and in some cases span hundreds of countries in their global operations.
Laws like the current campaign finance reform attempt wouldn't be necessary if we didn't have to try and stop Smith, Smith and Nobody from donating millions of dollars to pet issues that in many cases don't even directly impact American citizens each and every election cycle.
Until we sit up and realize the danger inherent in assigning 'natural person' status and the rights that go along with that status to entities who's sole reason for existence is profit-making (with zero social responsibility) we'll continue struggling with legal ways in which to make these distinctions and we will always fail.
The current law deserves to be shot down. A citizen should be able to spend as much as he or she wishes to spend and say whatever they wish in the forum of their choice. The problem is that we've given this same power to souless corporate entities who've proven over and over again a bald-faced willingness for abuse.
Meaningful dialog on campaign finance reform is doomed to failure as long as we consider human beings and corporations as equals under the law.
-j
FIVE asses. Not three. Monkeys with only three asses are genetically inferior.
(if you don't watch South Park don't bother modding)
-j
-j
Actually, corporate entities are legally afforded many if not all of the same protections afforded individual citizens. Read up on Santa Clara County v. Southern Pacific Railroad (1886) here.
For biotech patents on genes or proteins the USPTO requires you include a 'sequence listing' describing the sequence of the gene(s) or protein(s) you're patenting. This must be submitted in a very structured format that increases the vertical length of the submitted content by a great deal, especially for long sequences (so I imagine this 140k page application was a small app with a giant sequence listing trying to keep the claims as biologically broad as possible).
The PTO has finally gotten wise to the act of including everything but the kitchen sink in a patent listing (as was the industry's habit a few years ago) and now charges on a per-page basis for patent submissions. This ensures that if a company files a 140k page patent, they really mean it and are willing to pay for it.
One of the FEW good ideas out of the USPTO in a long time; let's hope there are others.
-j
In the short term, you're right. Intellectual property protections will, as usual, deny the third world the ability to afford these medications (unless they take steps to ignore the patent and make the drugs anyway).
But patents are temporary. Eventually this knowledge can be worked into an affordable, open treatment as soon as science/pharma moves on to bigger and better things.
It might take fifty years but the sequence of the genome is the first step in a long road to curing humanity's availability to the malaria parasite.
McCullagh is a journalist. As such, he's not supposed to be your friend. Nor is he supposed to be that of Ms. Rosen. That's kind of the point.
Like it or not, Declan's made great points in both of the articles mentioned above. Disorganized 'geektivism' hurts our causes. The legal verbage in the DMCA doesn't apply to academics publishing research.
The problem in both of these cases is one of education. Geeks need to learn how to be activists. They need poise, patience and funding. Researchers and educational institutions need to know their rights and be prepared to stand up for them if/when challenged (which USED to be academe's place in society).
Personally, I think Declan's right-on and I applaud him for trying to bring even-handed journalism into this debate.
-j
Thanks for that unfortunately worded reply. I don't think I ever claimed to be a statistician and though you made and interesting point (the power analysis) I can point out issues w/ your thoughts as well.
First, I never implied the sample size was 54 in total; I said 'two sample populations of 54 people' for, yes, 108 in total. Thanks for the credit.
In addition the linear distance between the means, which you claim is 'significant', cannot be considered without regard to the deviation of that mean, which wasn't in the article but is most certainly at least in the paper.
My main point, which you seem to have missed, was simply that using such small sample sizes in a situation with many, many factors leaves much to be desired where statistical relavance is concerned. I would imagine that if all 108 samples had complete, detailed life histories that we could find any number of variables with high correlation, many of which MIGHT have something to do with Alzheimers, and many not. That these researchers choose to publish about caffeine probably said more about the contents of their patient histories than anything else.
Do you always talk down to your peers this way? Does it get you anywhere?
-j
I wouldn't get too excited - the fact that small-sample studies this like manage to get published amazes me. They're using two sample populations of 54 people for a disease state who's incidence, from what we currently understand, is probably affected by DOZENS of parameters over a span of decades.
Even the most basic course in statistics won't let you put much trust in these results. You could probably show a correlation in the same small population for tv viewing habits or propensity for wearing tinfoil hats.
-j
By this they mean one of two things. Either it simply WONT run anything 'unauthorized' which brings up:
- will an independant developer have to jump through hoops to 'certify' every exe you compile to run on your own machine?
- will we have to go through another damn 'trusted' certifying agency a la SSL certs? Perhaps MS will be the last word?
Alternatively the OS might run things as long as the user tells the OS a particular binary is authorized. In this case I give it a good five minutes until some newbie tells the OS the latest email worm is an 'authorized' exe because they're looking to see that promised video of Brittany Spears some stranger w/ poor english apparently sent them out of the goodness of his heart.-j
The content of Bioperl is driven far more by the interests of the bioperl community than by some malfeasant desire to exclude ecologists. What started out as a codebase dealing mostly with parsing sequence files and results from sequence-analysis applications is slowly branching out to include code for analysis of phylogenetic trees, etc.
If bioperl doesn't meet your needs the community as a whole needs to hear from you! Let the mailing list know what interests you or, even better, start contributing code!
The Bio* namespace can help address your problems only if you share them with the community! :)
-j
IAB (I'm a bioinformaticist). You're partly correct. Introns (the 'junk' inbetween the exonic regions in DNA and freshly transcribed mRNA) do tend towards non-random sequence. You can use a variety of metrics to make guesses as to where introns and exons begin and end within a gene's coding region based on sequence entropy, on GC/AT frequency, on neural nets or hidden markov models trained on known examples, etc.
These metrics, however, are only useful once one knows something about where a 'gene' starts and ends. The real problem here is that some of the assumptions we've made historically about gene structure has potentially led us astray. Yes, the chromosomes are full of junk DNA but no, it's nothing near random for the most part and is full of 'repetitive' elements (short segments that repeat endlessly, query Genbank for 'ALU Repeat' and see how many sequences you find) that make any sort of pattern matching a tough sell genome-wide. There are also plenty of 'psueudogenes' interspersed throughout the genome, leftovers from a bygone era. It's the question of which of these pseudogenes might actually still BE transcribed that only mRNA expression analysis can provide. Hopkins is definitely on the right track w/ something like SAGE (though it's not exactly high-throughput, hence our man's need for extrapolation to genome-wide numbers).
The paper should be an interesting read to say the least.
-j
True, but remember that being granted a patent is a lot less important than being able to adequately enforce that patent in a court of law. None of these 'sequence only' patents have yet come up in court cases. Should they do so, there is a feeling in the industry that they would easily be overturned. The fact that the USPTO granted these sequence-only composition of matter patents is difficult to support, agreed. But the really important question is not the fact that the USPTO is willing to grant them, the real question is whether the courts are willing to overturn them. That we just don't know.
And keep in mind that there is a large difference between the two major patent types. These sequence only composition of matter patents are bunk, truly, as everyone here has noticed: prior art exists in us all. However, the second type, methods of use is a different beast all-together. Here a researcher is saying 'Hey, I found that this gene is significantly up-regulated during late state Alzheimer's diseases. This makes it a GREAT candidate for a therapeutic, and if it comes to pass that the drug cures Alzheimers, I want protection for my rights to discovery'. Can anyone really argue with that? Getting a drug through FDA approval can cost billions, why the hell would a drug company do this without the promise of protection of profits?
Answer: they wouldn't.- ---------------
-----------------------------------------------
James C. Diggans
jdiggans@excelsior-web.com