Use of CPUs from cloud-based providers is not as efficient for computations as using multiple GPUs linked together on a custom built setup.
This assumes that GPUs are actually suitable for the task at hand. I work in a very different branch of the computational sciences, but I can testify that GPUs are near-useless for most of what we do. If a "systems analyst" gave us advice like yours, I'd be furious.
How much time/money did they spend optimizing the software?
That's a good question - I think it was not insignificant. And I agree that optimization by hand is often a terribly inefficient solution. However, I think this blog post by Scott Aaronson makes a good counter-argument:
Some people might claim it’s “unfair” to optimize the classical simulated annealing code to take advantage of the quirks of the D-Wave problem. But think about it this way: D-Wave has spent ~$100 million, and hundreds of person-years, optimizing the hell out of a special-purpose annealing device, with the sole aim of solving this one problem that D-Wave itself defined. So if we’re serious about comparing the results to a classical computer, isn’t it reasonable to have one professor and a few postdocs spend a few months optimizing the classical code as well?
Now, it's possible this is unfair to the D-Wave computer: it is totally unclear to me how the different algorithms scale, and whether the D-Wave device is actually more versatile than this implies. However, the evidence for this has yet to be presented.
I am pretty sure that this 7-month-old arXiv preprint corresponds to the Nature Communications paper. The titles and author lists are identical, but the abstract deviates, so who knows what changes it went through in revision (I don't have access to the official paper either, even at the university where I work). But presumably it covers the same ground, and it looks like all of the figures from the official are in the preprint.
there has been a fair amount of algorithm development done for quantum computers even though they are barely out of the concept stage
As the AC above me notes, most of those algorithms won't run on this particular computer. Building a more general-purpose quantum computer is vastly more difficult - this is not even remotely my field of expertise, but from what I've read it has something to do with error-correction. D-Wave is essentially taking a huge shortcut to end up with a vastly less powerful (but probably still unique) technology. It's possible that this will turn out to have been a wise course; the best-case scenario is that their system is successful enough within its limited domain to promote more aggressive development of a more conventional machine - either by an expanded D-Wave or someone else with deep enough pockets.
No, I mean the 439 benchmark just recently that absolutely destroyed classic computers. Mere seconds compared to over half an hour quicker.
That was a terrible benchmark. They measured performance against possibly the most inefficient algorithm possible (using a third-party implementation) - not even remotely doing the same type of computations. That was where the "3600-fold" improvement came from. Some other computer scientists spent a bit of time optimizing an algorithm (also annealing, I think) for conventional computers in response, with the eventual result that their implementation was faster than the D-Wave. Which makes the entire effort sound like $10 million to avoid writing better software in the first place.
It vaguely reminds me of all of the GPU benchmarks I've seen where single-precision floating-point performance on the GPU is compared to double-precision performance on the CPU. Except orders of magnitude worse.
The comparison is between conventional storage in ASCII format, versus storing information in DNA. Whether ASCII is an optimally fast and error free on a purely objective scale, among other forms of conventional digital electronic storage, is irrelevant to the question I was answering.
Relative to genome sequencing, hell yes it is! For the original sequencing, a relatively high error rate isn't a huge deal because there is massive redundancy in the fragment reads, which is also required to actually assemble all those bits and pieces. But you can see why it's even more inefficient this way...
Re:Digital DNA storage anyone ?
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The DNA Data Deluge
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· Score: 4, Informative
why aren't they storing it in digital DNA format
Because they need to be able to read it back quickly, and error-free. Add to that, it's actually quite expensive to synthesize that much DNA; hard drives are relatively cheap by comparison.
"A collaborator of Rienhoff is now engineering a mouse that shares Bea’s gene variant" That sounds far beyond the capabilities of our current technology. How the heck would they do that?
Genome editing has gotten a lot better; here is a recent example, but I'm sure this isn't the only way to do it. Of course deliberately generating mutant mice is one thing; genetically manipulating live humans to make them healthy is much more difficult. (Hint: there's a lot of attrition in these mouse studies!)
Some arguments have held that not only the existence of the moon
One of my favorite ruminations of this sort is in AE Van Vogt's "The Voyage of the Space Beagle". At one point the titular intergalactic ship lands on a remote planet on the rim of the galaxy, which has only a single rocky planet with no moon. A highly advanced civilization once lived there but died out - because they had no moon, no nearby rocky planets, and no stars with planets within hundreds of light years. So they had no "stepping stones" to develop interplanetary travel, and never made it to interstellar travel. Humans, on the other hand, were able to mount a manned mission to another body within 70 years of developing flight - just because it's so damn convenient. And Mars provides a convenient (if vastly more difficult) next step.
Modern enthusiasm for advances in technology seems to be limited mostly to whatever the latest smartphone is. Also, the people clamouring for those more advanced smartphones also typically have no clue whatsoever about the actual tech specs of them and are typically just being led around by the nose by marketing.
Or, alternately, modern enthusiasm for technology is directed towards products that can be profitably mass-produced and are within the financial means of the average middle-class consumer. The Concorde was both expensive and money-losing, and the side effects (sonic boom) were more than most people wanted to deal with. (Although I sometimes wish we could use the same logic to ban Bluetooth headsets.)
Unfortunately there are lots of technologies like this, where the know-how and manufacturing capability exists, but the economics and other practical aspects make it unsustainable. I don't think it reflects negatively on modern consumers that they aren't willing to support huge, expensive projects like this, or the International Space Station, etc., simply because technology enthusiasts think they look cool. Having been on intercontinental flights in both directions in the last year, I would love if I could cut the flight times in half. But neither my budget nor my employer's budget would allow me to take the Concorde if it were still in flight, so I don't know why I should be excited about that idea, any more than I'm excited by the availability of fully-reclining seats.
She did work in the same field and is listed on other patents, but she doesn't appear to have any relationship to the patents involved in the court case.
From Wikipedia: "While on the faculty at Berkeley, King demonstrated in 1990 that a single gene on chromosome 17, later known as BRCA1, was responsible for many breast and ovarian cancers—as many as 5-10% of all cases of breast cancer may be hereditary."
The patent is on uses of the sequence, which was what the now-overturned patent covers. Back in the old days, identification of genes was done not through sequencing (the Human Genome Project had just started), but by analysis of how different genotypes were inherited - the relative locations of genes could be determined based on how they segregated during cellular reproduction. As a result, many genes were identified and their approximate chromosomal positions were mapped in multiple organisms, long before the actual sequences had been isolated. This information alone wouldn't be sufficient for a genetic test for breast cancer susceptibility, but neither would the patent holders have been able to sequence the gene in 1994 without King showing them where to look for it.
Just to add to my previous arguments: in my opinion, the reason cDNA shouldn't be patentable is that it doesn't even come close to the threshold of "non-obvious". Especially in an era where whole cell mRNA extracts can be sequenced in bulk and gene synthesis is getting cheaper all the time, giving these patent protection is just a terrible idea, but I would argue that most such patents shouldn't even have passed the test when they were first issued. To anyone skilled in the art, making a cDNA is a bloody obvious thing to do. (Changing the activity of an existing gene/protein so it does something truly novel, on the other hand, I think is not so obvious.)
Yes, the cDNA is 'created' using an artificial process, like copying a book with a photocopier.
Maybe, if it's a photocopier that also translates the book into another language. And in that case, even if the book was public domain, the translation would not be. (Although it would be covered under copyright, not patent, but for something like DNA the distinction is difficult to make.)
Again, I am playing devil's advocate here - I was merely trying to disabuse the parent poster of the notion that any method or product which might vaguely resemble something natural is automatically excluded from patentability. I would strongly prefer that cDNA not have patent protection, but the arguments being given were poorly chosen, and could be used to exclude just about any biological product from being patented based on the presumption that it might occur naturally (by accident).
I'm not enough of a virologist to say "Retroviruses accidentally reverse transcribe human mRNAs often when we get a retroviral infection," but I'm willing to bet money they do.
It's quite possible, but largely irrelevant - you would first have to prove that a specific cDNA under question did actually occur naturally. And in any case, a controlled process that produces large amounts of a cDNA is very different from a freak accident like this. Technically speaking, it's also possible that many patented synthetic molecules do actually occur in nature due to biological or spontaneous chemical processes. That doesn't make them unpatentable.
Either way, the sequences of cDNA are fundamentally natural. All of the cDNA sequence is found in the genomic sequence. I can't retype a popular book on a typewriter, exclude a boring chapter or two, and claim it's novel and claim exclusive rights to it based on the fact that no one had previously typed it out on a typewriter. Transcribing and editing is all cDNA is.
cDNA is a chemically synthesized product. So is (for instance) an impotence drug. To a chemist there is very little distinction, other than you're using polymerases for the first product, and probably some sort of weird metal catalyst for the second.
If some biotech company comes up with a completely novel protein designed by a computer, they should be able to COPYRIGHT it. That's creating something, not simply copying something that's natural.
I'm confused, what does copyright have to do with this?
nor should you be able to modify an existing virus and patent that
Why not? If I take a naturally occurring biological entity and modify it to do something completely different and unnatural, how is that not a patentable invention? You are basically demanding that everyone performing any kind of molecular bioengineering start completely from scratch and completely avoid anything that vaguely resembles something natural. We'd also have to avoid using traditional amino acids or nucleic acids, because those are naturally synthesized, which means we couldn't use existing biological systems to replicate our products. This is just insane; it may be an interesting research question but everything we do builds upon prior knowledge, and you are asking that we throw all that out.
reverse transcriptase is a naturally occouring enzyme, and viruses make cDNA all the time, and your cells remove introns all the time, so there is absofuckinglutely nothing patentable about cDNA
But the cDNAs that people would like to patent is not simply endogenously present - it has to be created using an entirely artificial process. And reverse transcriptase isn't a naturally occurring enzyme in humans, or at least not the kind that's used to make cDNA*. And our cells remove introns only to make mRNA, not cDNA. So it's a little deceptive to say that cDNA is a natural product and therefore not patentable. If your rather simplistic argument were valid, a vast number of forms of gene manipulation and genetic engineering would become unpatentable, because organisms undergo gene manipulation all the time. (The most extreme example is probably horizontal gene transfer, but there are plenty of other weird things going on, many involving viruses.)
Now, my personal preference (as both a scientist and a consumer) is for as few patents as possible on any genetic material, and I was relieved to see Myriad get slapped down by all nine justices. But what I prefer isn't always in line with what current case law decrees is allowable, and I wouldn't call the Supreme Court incompetent just because they didn't reach the conclusion I personally favor.
(* In fact, the polymerases used in molecular biology labs are often heavily engineered for greater stability and control, and of course they're not endogenously produced but rather purified from a [heavily modified] recombinant organism expressing the protein on a [human-designed] plasmid, so the connection to the naturally occurring proteins is tenuous.)
The press release makes some very grand-sounding claims about replacing synchrotrons and free-electron lasers. I'm not an expert in the accelerator field but I've used these systems, and I have some idea of what the actual output needs to be in order to be useful for biologists. Specifically, it's not just the electron energies that matter, but the photon flux per unit of area. The figures for modern synchrotrons are on the order of 10^11 - 10^13 with a spot size of 100 microns or less - the very best will focus down to just a few microns. From what I can understand of the paper, they're talking about several orders of magnitude fewer photons over much larger areas. (If someone who understands this stuff better can confirm whether or not I'm reading it correctly, I'd be grateful.) The only hard free-electron laser in the US, the LCLS at Stanford, is orders of magnitude brighter than synchrotrons, and compressed into pulses on the order of tens of femtoseconds long.
It would be great if someone could build a high-intensity hard X-ray source at every big research university. But it's not the first time such claims have been made; there is (or was) a company called Lyncean that tried to build a tabletop synchrotron in the previous decade, and made similar predictions about its utility for biology. Their technology worked perfectly well from a theoretical standpoint - but it was several orders of magnitude too weak to be competitive with existing synchrotron beamlines, and too expensive to be competitive with existing laboratory X-ray sources.
(Of course this is pretty much standard stuff from university PR departments, which would always like you to believe that they're on the brink of curing caner or revolutionizing some widely used method. The actual Nature Communications article is much more sober.)
Or maybe you assume every KKK member is a blood crazed fanatic. There are plenty of groups around the world that peacefully avoid integration
The KKK, however, is not one of those groups. Or at least they weren't in their heyday (the group is now a pathetic shadow of what it was in the early 20th century) - in fact, they were a classic example of what we now call "domestic terrorism".
Have the Chinese done anything of interest with their supercomputers yet?
Not in the area of biology/biochemistry, as far as I know. Basically all of the high-performance codes used for that purpose are written in the usual handful of countries (US/EU/Japan) and/or work just as well on distributed systems, and all of the really cutting-edge work I've seen has been done in the same countries. The big advantage that the Chinese have is cheaper labor (although getting steadily less so) and large amounts of money to through around (without any accountability), but I haven't seen any results that couldn't have been obtained just as easily by Western nations. (Whereas I've seen many cases where the reverse is true, because the Western world still has technology and expertise in many fields far beyond anything in China.)
there are some things supercomputers can do well, but the same effect can be reached with distributed computing, which, in addition, makes the individual CPUs useful for a range of other things. Basically, building supercomputers is pretty stupid and a waste of money, time and effort.
That's a bit of an overstatement. There are plenty of simulations that really do benefit from a monolithic supercomputer rather than a distributed system, such as protein dynamics, global climate, etc. And the level of detail which can be attained (without approximations which diminish accuracy) increases with the size of computer.
I do think however that it's reasonable to question what the real-world impact of such systems is, and whether there are better approaches. My field is life sciences, where the applications are indeed limited. In the molecular dynamics field, for instance, specialized hardware is potentially superior for both performance and efficiency (although this has some tradeoffs too). For genomics a supercomputer is completely unnecessary, and cloud computing is quite adequate. Ditto for most other analyses of experimental data, protein design, and so on.
Furthermore, the economic impact of supercomputer simulations tends to be greatly overstated. A common example is studies of drug binding to proteins - supercomputer centers love to put out press releases about how "new simulations tell us how to cure cancer/AIDS/Alzheimer's". But anyone familiar with pharmaceutical development will tell you that lack of supercomputers is by far the least of the problems faced by the field. Simulations aren't a magical substitute for actual benchwork, unfortunately - and clinical studies are vastly more expensive than supercomputers.
The main reason why having the biggest supercomputer is a status symbol is that it's traditionally tied to nuclear weapons research, and therefore the importance to the country in general is inflated by the politicians, the media, and of course the people who build and use supercomputers. A secondary reason is that it indicates the overall level of technical competence of a country, although as noted China is still using Intel CPUs. (This is not a trend specific to supercomputing; the Beijing Genomics Institute famously uses equipment entirely designed and built in the US and UK for sequencing.)
You seriously think the academics were more concerned about prestige than lined pockets?
You haven't met many academic scientists, have you? A long-term job at a major research institution pays enough for a comfortable, secure, upper-middle-class 1st-world lifestyle (and equally comfortable retirement), and most scientists are entirely content with that as long as their job description basically involves geeking out over obscure theory for days on end. If they wanted to line their pockets there are far better ways to do this - the people who really care about money figure out very early that staying in academia is not the most efficient way to get rich. (One of the scientists who used to work on the project I'm on ended up at Goldman Sachs.) But some academics will do pretty nearly anything short of murder for a Nobel prize if they smell an opportunity.
we are corrupt moslem third world-ers, that might be better off to just die already or to pay you for everything for eternity forgetting we already past the colonialism and whatnot for decades already
You are misrepresenting my opinion and putting words into my mouth. If you're going to attribute such views to me when I'm attempting to discuss the issue in good faith from a disinterested perspective, why should I believe anything you say about the motivations of the Indonesian (or Saudi) government?
it's very clear that patents and IP rights generally are behind the whole problem
I wouldn't be so sure in this case. The Saudi official who has been complaining the loudest admitted (to a journalist who actually bothered to ask pointed questions) that the Dutch claim hasn't actually held up research in Saudi Arabia. He also admitted that the most bothersome aspect of this mess wasn't the lack of access, it was the fact that the Dutch were even claiming commercial rights that should have belonged exclusively to Saudi Arabia. (And I agree to the extent that the Dutch are behaving somewhat unethically here.)
As I've pointed out elsewhere in this thread, an MTA of some sort is standard practice, and in this case, where the material is a known human pathogen, some legal documentation and waiver of liability is absolutely essential. Even more so when the sample is being distributed internationally. Any researcher who would send a virus like this to a lab in another country without some kind of legally binding agreement should be fired for incompetence. Whether IP rights are involved or not does not affect this.
I think it's only a matter of time before biotech patents really do start to inhibit potentially life-saving research; I've seen it argued that personal genomics research is essentially violating gene patents in bulk, because that's the only way they can do any research at all! If our ability to get diagnostics from genome sequencing were held up by patents, or (more likely) if the $1000 genome became a $10,000 genome again because of all of the licensing fees, that would be genuinely tragic. But I think this case is simply a multi-national spat over IP rights; it has nothing to do with actually curing the disease.
The only problem is that if someone makes money off this, the House of Saud might not get a cut. No one is preventing their government (or anyone else) from researching a cure; it's simply another excuse to bash Western pharmaceutical companies, as if any more excuses were needed.
The Indonesians, and the Saudis, want to put the lives of their "throw-away" citizens (third-worlders, Muslims, riff-raff, you know) ahead of the profits curing only those who can afford the cure and sucking off funds of charities to pay the margins their patents etc. add on, may provide them.
I was going to respond to this, but another comment already made my point. The Indonesians and Saudis are grandstanding, because everyone hates Western pharmaceutical companies (I don't like them either) and they make easy targets. There is still nothing stopping them from making their own cures if they so desire. I think Erasmus University is being pretty stupid about this (and probably unethical as well), but most of the controversy is being manufactured by corrupt third-world governments. As usual.
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Use of CPUs from cloud-based providers is not as efficient for computations as using multiple GPUs linked together on a custom built setup.
This assumes that GPUs are actually suitable for the task at hand. I work in a very different branch of the computational sciences, but I can testify that GPUs are near-useless for most of what we do. If a "systems analyst" gave us advice like yours, I'd be furious.
How much time/money did they spend optimizing the software?
That's a good question - I think it was not insignificant. And I agree that optimization by hand is often a terribly inefficient solution. However, I think this blog post by Scott Aaronson makes a good counter-argument:
Now, it's possible this is unfair to the D-Wave computer: it is totally unclear to me how the different algorithms scale, and whether the D-Wave device is actually more versatile than this implies. However, the evidence for this has yet to be presented.
I am pretty sure that this 7-month-old arXiv preprint corresponds to the Nature Communications paper. The titles and author lists are identical, but the abstract deviates, so who knows what changes it went through in revision (I don't have access to the official paper either, even at the university where I work). But presumably it covers the same ground, and it looks like all of the figures from the official are in the preprint.
(Yo, fuck Nature Publishing Group.)
there has been a fair amount of algorithm development done for quantum computers even though they are barely out of the concept stage
As the AC above me notes, most of those algorithms won't run on this particular computer. Building a more general-purpose quantum computer is vastly more difficult - this is not even remotely my field of expertise, but from what I've read it has something to do with error-correction. D-Wave is essentially taking a huge shortcut to end up with a vastly less powerful (but probably still unique) technology. It's possible that this will turn out to have been a wise course; the best-case scenario is that their system is successful enough within its limited domain to promote more aggressive development of a more conventional machine - either by an expanded D-Wave or someone else with deep enough pockets.
No, I mean the 439 benchmark just recently that absolutely destroyed classic computers. Mere seconds compared to over half an hour quicker.
That was a terrible benchmark. They measured performance against possibly the most inefficient algorithm possible (using a third-party implementation) - not even remotely doing the same type of computations. That was where the "3600-fold" improvement came from. Some other computer scientists spent a bit of time optimizing an algorithm (also annealing, I think) for conventional computers in response, with the eventual result that their implementation was faster than the D-Wave. Which makes the entire effort sound like $10 million to avoid writing better software in the first place.
It vaguely reminds me of all of the GPU benchmarks I've seen where single-precision floating-point performance on the GPU is compared to double-precision performance on the CPU. Except orders of magnitude worse.
The comparison is between conventional storage in ASCII format, versus storing information in DNA. Whether ASCII is an optimally fast and error free on a purely objective scale, among other forms of conventional digital electronic storage, is irrelevant to the question I was answering.
ASCII is fast and error correcting now?
Relative to genome sequencing, hell yes it is! For the original sequencing, a relatively high error rate isn't a huge deal because there is massive redundancy in the fragment reads, which is also required to actually assemble all those bits and pieces. But you can see why it's even more inefficient this way...
why aren't they storing it in digital DNA format
Because they need to be able to read it back quickly, and error-free. Add to that, it's actually quite expensive to synthesize that much DNA; hard drives are relatively cheap by comparison.
"A collaborator of Rienhoff is now engineering a mouse that shares Bea’s gene variant"
That sounds far beyond the capabilities of our current technology. How the heck would they do that?
Genome editing has gotten a lot better; here is a recent example, but I'm sure this isn't the only way to do it. Of course deliberately generating mutant mice is one thing; genetically manipulating live humans to make them healthy is much more difficult. (Hint: there's a lot of attrition in these mouse studies!)
Some arguments have held that not only the existence of the moon
One of my favorite ruminations of this sort is in AE Van Vogt's "The Voyage of the Space Beagle". At one point the titular intergalactic ship lands on a remote planet on the rim of the galaxy, which has only a single rocky planet with no moon. A highly advanced civilization once lived there but died out - because they had no moon, no nearby rocky planets, and no stars with planets within hundreds of light years. So they had no "stepping stones" to develop interplanetary travel, and never made it to interstellar travel. Humans, on the other hand, were able to mount a manned mission to another body within 70 years of developing flight - just because it's so damn convenient. And Mars provides a convenient (if vastly more difficult) next step.
Modern enthusiasm for advances in technology seems to be limited mostly to whatever the latest smartphone is. Also, the people clamouring for those more advanced smartphones also typically have no clue whatsoever about the actual tech specs of them and are typically just being led around by the nose by marketing.
Or, alternately, modern enthusiasm for technology is directed towards products that can be profitably mass-produced and are within the financial means of the average middle-class consumer. The Concorde was both expensive and money-losing, and the side effects (sonic boom) were more than most people wanted to deal with. (Although I sometimes wish we could use the same logic to ban Bluetooth headsets.)
Unfortunately there are lots of technologies like this, where the know-how and manufacturing capability exists, but the economics and other practical aspects make it unsustainable. I don't think it reflects negatively on modern consumers that they aren't willing to support huge, expensive projects like this, or the International Space Station, etc., simply because technology enthusiasts think they look cool. Having been on intercontinental flights in both directions in the last year, I would love if I could cut the flight times in half. But neither my budget nor my employer's budget would allow me to take the Concorde if it were still in flight, so I don't know why I should be excited about that idea, any more than I'm excited by the availability of fully-reclining seats.
She did work in the same field and is listed on other patents, but she doesn't appear to have any relationship to the patents involved in the court case.
From Wikipedia: "While on the faculty at Berkeley, King demonstrated in 1990 that a single gene on chromosome 17, later known as BRCA1, was responsible for many breast and ovarian cancers—as many as 5-10% of all cases of breast cancer may be hereditary."
The patent is on uses of the sequence, which was what the now-overturned patent covers. Back in the old days, identification of genes was done not through sequencing (the Human Genome Project had just started), but by analysis of how different genotypes were inherited - the relative locations of genes could be determined based on how they segregated during cellular reproduction. As a result, many genes were identified and their approximate chromosomal positions were mapped in multiple organisms, long before the actual sequences had been isolated. This information alone wouldn't be sufficient for a genetic test for breast cancer susceptibility, but neither would the patent holders have been able to sequence the gene in 1994 without King showing them where to look for it.
Just to add to my previous arguments: in my opinion, the reason cDNA shouldn't be patentable is that it doesn't even come close to the threshold of "non-obvious". Especially in an era where whole cell mRNA extracts can be sequenced in bulk and gene synthesis is getting cheaper all the time, giving these patent protection is just a terrible idea, but I would argue that most such patents shouldn't even have passed the test when they were first issued. To anyone skilled in the art, making a cDNA is a bloody obvious thing to do. (Changing the activity of an existing gene/protein so it does something truly novel, on the other hand, I think is not so obvious.)
Yes, the cDNA is 'created' using an artificial process, like copying a book with a photocopier.
Maybe, if it's a photocopier that also translates the book into another language. And in that case, even if the book was public domain, the translation would not be. (Although it would be covered under copyright, not patent, but for something like DNA the distinction is difficult to make.)
Again, I am playing devil's advocate here - I was merely trying to disabuse the parent poster of the notion that any method or product which might vaguely resemble something natural is automatically excluded from patentability. I would strongly prefer that cDNA not have patent protection, but the arguments being given were poorly chosen, and could be used to exclude just about any biological product from being patented based on the presumption that it might occur naturally (by accident).
I'm not enough of a virologist to say "Retroviruses accidentally reverse transcribe human mRNAs often when we get a retroviral infection," but I'm willing to bet money they do.
It's quite possible, but largely irrelevant - you would first have to prove that a specific cDNA under question did actually occur naturally. And in any case, a controlled process that produces large amounts of a cDNA is very different from a freak accident like this. Technically speaking, it's also possible that many patented synthetic molecules do actually occur in nature due to biological or spontaneous chemical processes. That doesn't make them unpatentable.
Either way, the sequences of cDNA are fundamentally natural. All of the cDNA sequence is found in the genomic sequence. I can't retype a popular book on a typewriter, exclude a boring chapter or two, and claim it's novel and claim exclusive rights to it based on the fact that no one had previously typed it out on a typewriter. Transcribing and editing is all cDNA is.
cDNA is a chemically synthesized product. So is (for instance) an impotence drug. To a chemist there is very little distinction, other than you're using polymerases for the first product, and probably some sort of weird metal catalyst for the second.
If some biotech company comes up with a completely novel protein designed by a computer, they should be able to COPYRIGHT it. That's creating something, not simply copying something that's natural.
I'm confused, what does copyright have to do with this?
nor should you be able to modify an existing virus and patent that
Why not? If I take a naturally occurring biological entity and modify it to do something completely different and unnatural, how is that not a patentable invention? You are basically demanding that everyone performing any kind of molecular bioengineering start completely from scratch and completely avoid anything that vaguely resembles something natural. We'd also have to avoid using traditional amino acids or nucleic acids, because those are naturally synthesized, which means we couldn't use existing biological systems to replicate our products. This is just insane; it may be an interesting research question but everything we do builds upon prior knowledge, and you are asking that we throw all that out.
reverse transcriptase is a naturally occouring enzyme, and viruses make cDNA all the time, and your cells remove introns all the time, so there is absofuckinglutely nothing patentable about cDNA
But the cDNAs that people would like to patent is not simply endogenously present - it has to be created using an entirely artificial process. And reverse transcriptase isn't a naturally occurring enzyme in humans, or at least not the kind that's used to make cDNA*. And our cells remove introns only to make mRNA, not cDNA. So it's a little deceptive to say that cDNA is a natural product and therefore not patentable. If your rather simplistic argument were valid, a vast number of forms of gene manipulation and genetic engineering would become unpatentable, because organisms undergo gene manipulation all the time. (The most extreme example is probably horizontal gene transfer, but there are plenty of other weird things going on, many involving viruses.)
Now, my personal preference (as both a scientist and a consumer) is for as few patents as possible on any genetic material, and I was relieved to see Myriad get slapped down by all nine justices. But what I prefer isn't always in line with what current case law decrees is allowable, and I wouldn't call the Supreme Court incompetent just because they didn't reach the conclusion I personally favor.
(* In fact, the polymerases used in molecular biology labs are often heavily engineered for greater stability and control, and of course they're not endogenously produced but rather purified from a [heavily modified] recombinant organism expressing the protein on a [human-designed] plasmid, so the connection to the naturally occurring proteins is tenuous.)
The press release makes some very grand-sounding claims about replacing synchrotrons and free-electron lasers. I'm not an expert in the accelerator field but I've used these systems, and I have some idea of what the actual output needs to be in order to be useful for biologists. Specifically, it's not just the electron energies that matter, but the photon flux per unit of area. The figures for modern synchrotrons are on the order of 10^11 - 10^13 with a spot size of 100 microns or less - the very best will focus down to just a few microns. From what I can understand of the paper, they're talking about several orders of magnitude fewer photons over much larger areas. (If someone who understands this stuff better can confirm whether or not I'm reading it correctly, I'd be grateful.) The only hard free-electron laser in the US, the LCLS at Stanford, is orders of magnitude brighter than synchrotrons, and compressed into pulses on the order of tens of femtoseconds long.
It would be great if someone could build a high-intensity hard X-ray source at every big research university. But it's not the first time such claims have been made; there is (or was) a company called Lyncean that tried to build a tabletop synchrotron in the previous decade, and made similar predictions about its utility for biology. Their technology worked perfectly well from a theoretical standpoint - but it was several orders of magnitude too weak to be competitive with existing synchrotron beamlines, and too expensive to be competitive with existing laboratory X-ray sources.
(Of course this is pretty much standard stuff from university PR departments, which would always like you to believe that they're on the brink of curing caner or revolutionizing some widely used method. The actual Nature Communications article is much more sober.)
Or maybe you assume every KKK member is a blood crazed fanatic. There are plenty of groups around the world that peacefully avoid integration
The KKK, however, is not one of those groups. Or at least they weren't in their heyday (the group is now a pathetic shadow of what it was in the early 20th century) - in fact, they were a classic example of what we now call "domestic terrorism".
Have the Chinese done anything of interest with their supercomputers yet?
Not in the area of biology/biochemistry, as far as I know. Basically all of the high-performance codes used for that purpose are written in the usual handful of countries (US/EU/Japan) and/or work just as well on distributed systems, and all of the really cutting-edge work I've seen has been done in the same countries. The big advantage that the Chinese have is cheaper labor (although getting steadily less so) and large amounts of money to through around (without any accountability), but I haven't seen any results that couldn't have been obtained just as easily by Western nations. (Whereas I've seen many cases where the reverse is true, because the Western world still has technology and expertise in many fields far beyond anything in China.)
there are some things supercomputers can do well, but the same effect can be reached with distributed computing, which, in addition, makes the individual CPUs useful for a range of other things. Basically, building supercomputers is pretty stupid and a waste of money, time and effort.
That's a bit of an overstatement. There are plenty of simulations that really do benefit from a monolithic supercomputer rather than a distributed system, such as protein dynamics, global climate, etc. And the level of detail which can be attained (without approximations which diminish accuracy) increases with the size of computer.
I do think however that it's reasonable to question what the real-world impact of such systems is, and whether there are better approaches. My field is life sciences, where the applications are indeed limited. In the molecular dynamics field, for instance, specialized hardware is potentially superior for both performance and efficiency (although this has some tradeoffs too). For genomics a supercomputer is completely unnecessary, and cloud computing is quite adequate. Ditto for most other analyses of experimental data, protein design, and so on.
Furthermore, the economic impact of supercomputer simulations tends to be greatly overstated. A common example is studies of drug binding to proteins - supercomputer centers love to put out press releases about how "new simulations tell us how to cure cancer/AIDS/Alzheimer's". But anyone familiar with pharmaceutical development will tell you that lack of supercomputers is by far the least of the problems faced by the field. Simulations aren't a magical substitute for actual benchwork, unfortunately - and clinical studies are vastly more expensive than supercomputers.
The main reason why having the biggest supercomputer is a status symbol is that it's traditionally tied to nuclear weapons research, and therefore the importance to the country in general is inflated by the politicians, the media, and of course the people who build and use supercomputers. A secondary reason is that it indicates the overall level of technical competence of a country, although as noted China is still using Intel CPUs. (This is not a trend specific to supercomputing; the Beijing Genomics Institute famously uses equipment entirely designed and built in the US and UK for sequencing.)
You seriously think the academics were more concerned about prestige than lined pockets?
You haven't met many academic scientists, have you? A long-term job at a major research institution pays enough for a comfortable, secure, upper-middle-class 1st-world lifestyle (and equally comfortable retirement), and most scientists are entirely content with that as long as their job description basically involves geeking out over obscure theory for days on end. If they wanted to line their pockets there are far better ways to do this - the people who really care about money figure out very early that staying in academia is not the most efficient way to get rich. (One of the scientists who used to work on the project I'm on ended up at Goldman Sachs.) But some academics will do pretty nearly anything short of murder for a Nobel prize if they smell an opportunity.
we are corrupt moslem third world-ers, that might be better off to just die already or to pay you for everything for eternity forgetting we already past the colonialism and whatnot for decades already
You are misrepresenting my opinion and putting words into my mouth. If you're going to attribute such views to me when I'm attempting to discuss the issue in good faith from a disinterested perspective, why should I believe anything you say about the motivations of the Indonesian (or Saudi) government?
it's very clear that patents and IP rights generally are behind the whole problem
I wouldn't be so sure in this case. The Saudi official who has been complaining the loudest admitted (to a journalist who actually bothered to ask pointed questions) that the Dutch claim hasn't actually held up research in Saudi Arabia. He also admitted that the most bothersome aspect of this mess wasn't the lack of access, it was the fact that the Dutch were even claiming commercial rights that should have belonged exclusively to Saudi Arabia. (And I agree to the extent that the Dutch are behaving somewhat unethically here.)
As I've pointed out elsewhere in this thread, an MTA of some sort is standard practice, and in this case, where the material is a known human pathogen, some legal documentation and waiver of liability is absolutely essential. Even more so when the sample is being distributed internationally. Any researcher who would send a virus like this to a lab in another country without some kind of legally binding agreement should be fired for incompetence. Whether IP rights are involved or not does not affect this.
I think it's only a matter of time before biotech patents really do start to inhibit potentially life-saving research; I've seen it argued that personal genomics research is essentially violating gene patents in bulk, because that's the only way they can do any research at all! If our ability to get diagnostics from genome sequencing were held up by patents, or (more likely) if the $1000 genome became a $10,000 genome again because of all of the licensing fees, that would be genuinely tragic. But I think this case is simply a multi-national spat over IP rights; it has nothing to do with actually curing the disease.
So where is the problem?
The only problem is that if someone makes money off this, the House of Saud might not get a cut. No one is preventing their government (or anyone else) from researching a cure; it's simply another excuse to bash Western pharmaceutical companies, as if any more excuses were needed.
The Indonesians, and the Saudis, want to put the lives of their "throw-away" citizens (third-worlders, Muslims, riff-raff, you know) ahead of the profits curing only those who can afford the cure and sucking off funds of charities to pay the margins their patents etc. add on, may provide them.
I was going to respond to this, but another comment already made my point. The Indonesians and Saudis are grandstanding, because everyone hates Western pharmaceutical companies (I don't like them either) and they make easy targets. There is still nothing stopping them from making their own cures if they so desire. I think Erasmus University is being pretty stupid about this (and probably unethical as well), but most of the controversy is being manufactured by corrupt third-world governments. As usual.