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Comment Re:Guy deserves getting beaten (Score 0) 188

The state doesn't post videos of peoples on the Internet for shits and giggles and companies like Google take quite some effort to blur everybody faces before publishing anything. Furthermore the problem with this guy isn't even the camera, if he would just walk around and stare at people he would get pretty much the same reaction. So all he is showing is essentially that people get aggressive when you violate social norms. Surveillance on the other side doesn't really do that, England is full of cameras, yet reports on people going crazy because of it are extremely rare, a surveillance camera in the background will simply get ignored by people assuming that they even notice it in the first place.

Comment Re:With all due respect... (Score 2) 22

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.

Comment Re:It is a hopeful, small step in the right direct (Score 1) 22

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.)

Comment Re:It is a hopeful, small step in the right direct (Score 1) 22

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).

Comment Re:It is a hopeful, small step in the right direct (Score 1) 22

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.

Comment Re:It is a hopeful, small step in the right direct (Score 4, Informative) 22

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.)

Comment Some details missing... (Score 4, Informative) 89

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.)

Comment Re:The system worked (Score 1) 470

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".

Comment Re:It runs benchmarks real fast (Score 1) 125

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.)

Comment Re:Supercomputers are pretty useless (Score 1, Insightful) 125

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.)

Comment Re:In Japan?! (Score 4, Informative) 71

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.

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