I think you mean "a study revealed that it produces false negatives".
posted by ssg at 10:33 AM on May 13, 2009

Aw hell. I sure did. :(

Thanks for pointing that out, ssg.
posted by zarq at 10:35 AM on May 13, 2009

All tests give false positives. Does Myriad's tight hold on its intellectual property prevent a better test from reaching the market? The patent and reliability issues probably wouldn't be as important if the test that Myriad licensed weren't so expensive.

Patenting genes does seem silly, but the ACLU seems to have an uphill fight here, given how much big pharma and biotech IP would potentially be nullified by a ruling in its favor. It would be easier to try to invalidate Myriad's patents on the basis that they are stifling research and innovation, than to invalidate gene patents altogether.
posted by Blazecock Pileon at 10:37 AM on May 13, 2009

GATTACA! GATTACA!
posted by Joe Beese at 10:39 AM on May 13, 2009

/Motions to patent the gene for brown eyes and charge royalties for use of said gene.
posted by jmd82 at 10:40 AM on May 13, 2009

Time for me to patent my own genome.
posted by kldickson at 10:43 AM on May 13, 2009

Or, on the other hand, we can look at the empirical data on whether gene patents are actually causing these problems, as published in Nature Biotechnology. Short answer: patents aren't the problem; researchers cite commercial concerns, scientific competition, and friction in sharing physical materials as the real problems. Among academic biotech researchers in the US, only 1% report having to delay a project and none had abandoned a project as a result of others' patents.

What this is all about is producing a so-called 'research exemption' to patent infringement that would allow the plaintiffs in the suit to engage in short-term freeriding while ultimately harming the biotechnology industry and future patients.

Full disclosure: I work with one of the co-authors of that paper at the Project for Commercializing Innovation.
posted by jedicus at 10:43 AM on May 13, 2009

Here's a direct link to the PDF of the complaint, linked from a couple of the ACLU pages above.

One of the BRCA1 patents in question includes the following claims, among others:

1. An isolated DNA coding for a BRCA1 polypeptide, said polypeptide having the amino acid sequence set forth in SEQ ID NO:2.

2. The isolated DNA of claim 1, wherein said DNA has the nucleotide sequence set forth in SEQ ID NO:1.

...

5. An isolated DNA having at least 15 nucleotides of the DNA of claim 1.

6. An isolated DNA having at least 15 nucleotides of the DNA of claim 2.

Wow, they are claiming not only a patent on the whole gene, but on any DNA sharing at least 15 nucleotides in common with the sequenced gene.

We need to restore the original purpose of patents and copyright as outlined in the Constitution: "To promote the progress of science and useful arts, by securing for limited times to authors and inventors the exclusive right to their respective writings and discoveries." The profiteering view of "intellectual property" has gone too far.
posted by grouse at 10:43 AM on May 13, 2009 [8 favorites]

Brown eyes? Fuck brown eyes, I want to patent homeobox genes.
posted by kldickson at 10:43 AM on May 13, 2009 [1 favorite]

I think my favorite was the guy they pulled a tumor out of, then the corporation merrily went on and based patents around it. He earned not a penny from it and the courts ruled that the ownership went entirely to the corporation. I am fuzzy on the details; I'll have to dig up my copy of Database Nation for an exact reference. This seems to be the general trend.

Frankly, I am against granting intellectual property rights for any genes or sequences which have been previously found in nature, just as we do not have a patent on lithium. Rewarding companies for their research — it costs a ridiculous amount to bring a drug to market — is difficult, but I'd rather not see humanity go down that route. I often struggle with developing an appropriate system for it that recoups losses and rewards innovation.

I bring up lithium with full knowledge that it was ignored as a treatment for various mood disorders for so long precisely because corporations could not patent it. Lithium carbonate is simple enough that one could probably make it in an undergraduate chemistry lab. It languished as a treatment, albeit imperfect, for quite some time because no profit margin was to be had.

I find the alternative, the strands of DNA in my body being the IP of faceless corporations, responsible only to the hypothetical ravenous stockholder, chilling at the least.
posted by adipocere at 10:44 AM on May 13, 2009 [6 favorites]

Cortex, you rock. Thank you!! :)
posted by zarq at 10:45 AM on May 13, 2009

which the ACLU says is unconstitutional and inhibits researchers from finding treatments and cures.

On the other hand, dangling the potential of a 20-year patent in front of biotech companies encourages researchers to find treatments and cures. Somewhere, there's a way to keep the baby and remove the bathwater.

But Myriad has refused to work with her insurance plan, Mass Health, and paying for the test herself is beyond her means.

That's not a problem with the patent law. That's a problem with a health insurance company refusing to live up to its policy.
posted by Cool Papa Bell at 10:45 AM on May 13, 2009

This is good. Genetic patents on natural genes are like an oil company who finds a new way to identify oil deposits claiming control over every new deposit their processes can identify. A paleontologist saying no one can dig up and study the species of dinosaur he already dug up. Or a ornithologist claiming world wide rights to breed and sell a new species of bird she discovered. They can patent the process used in the discovery, and even keep the genetic code, results, etc secret if they want, but they can't claim the fucking gene as theirs.

If a company designs an artificial gene that is judged to be novel enough to deserve a patent (by a competent patent office), let them charge out the ass for it, it's their creation, but this is fundamentally stupid.
posted by Science! at 10:47 AM on May 13, 2009 [6 favorites]

On a serious note, the idea of patenting genes makes me slightly angry.

A few years ago, I was working in an ovarian cancer research lab at a university. Our team was to study various cell lines, with varying maturities of cancer. The goal was to identify genetic markers (ie, entire dna sequences) that are more common in cancer lines than non-cancerous lines, or something along those lines.

I wonder what would have happened if one of those markers we found happened to be BRCA1/2? Would we retroactively owe money for studying? Would our research become the property of Myriad? I should also note that my portion of the genetic testing was blind in regards to the gene sequence itself- all I knew is the cell line was cancerous, had a dna sequence from other labs, and used pcr/gel electrophoresis and other techniques to find genetic commonalities within the cell lines.
posted by jmd82 at 10:48 AM on May 13, 2009

From the spur or stifle research link:

In May 2004, the European Patent Office revoked Myriad¡¯s patents. The removal of the patents, an almost unprecedented event in patent history, came because the Europeans decided that while Myriad had figured out the composition of key genetic sequences, it had not done enough to meet the "inventiveness" standard required of a patent.

In other words, even though the company had figured out hundreds of the key genes involved with a higher risk of breast and ovarian cancer, they had not invented anything. Rather they had simply found something already existing in nature.

Yes, just like Columbus invented the New World. He and his crew risked their lives or whatnot to cross The Great Unknown, and Queen Isabella forked out a lot of money, but nothing was invented there.

The one thing that somewhat pushes this towards "making something new" is the fourth element of a patentable gene: "enable one skilled in the field to use the sequence for its stated purpose." The article goes on to note: "As disease genes are found, complementary gene tests are developed to screen for the gene in humans who suspect they may be at risk for developing the disease. These tests are usually patented and licensed by the owners of the disease gene patent." Not being in this field in the slightest, I can't say how much of the total efforts are involved with making this test. It seems it's not all that hard, if Canadians were charged a third of the cost of Myriad's test and women got the results eight weeks sooner than Myriad provided them.
posted by filthy light thief at 10:50 AM on May 13, 2009

Time for me to patent my own genome.

The ultimate submarine patent - patent your own genome and then sue your descendants. If they have kids, you can even get their spouses!
posted by zippy at 10:52 AM on May 13, 2009

it costs a ridiculous amount to bring a drug to market

Not really. R&D expenses of Big Pharma are usually less than SG&A and net income to shareholders.
posted by toroi at 10:52 AM on May 13, 2009 [1 favorite]

Wow, they are claiming not only a patent on the whole gene, but on any DNA sharing at least 15 nucleotides in common with the sequenced gene.

Okay, did you look at the sequence listing? It's hundreds of pairs long. 15 nucleotides is a very small change. It's the biotech equivalent of saying "a mixture of 10-11% compound X and 89-90% compound Y."

Frankly, I am against granting intellectual property rights for any genes or sequences which have been previously found in nature, just as we do not have a patent on lithium.

That's not what the patent claims. The patent claims an isolated or purified version of the DNA, which most certainly does not occur in nature. You don't infringe gene patents by having the genes in your body; you infringe them by making, using, or selling an isolated or purified version, typically in research, diagnostics, or treatment. This is not a patent on lithium. It's more like a patent on a new process for purifying lithium or the purified version of a rare lithium compound found in nature discovered to have therapeutic properties.
posted by jedicus at 10:53 AM on May 13, 2009

You'd think at least Creationists would be against patenting existing genes found in nature, since you can show prior art.

The patent claims an isolated or purified version of the DNA, which most certainly does not occur in nature.

So I can patent a rock if I brush the dirt off it first?
posted by George_Spiggott at 10:58 AM on May 13, 2009 [1 favorite]

What this is all about is producing a so-called 'research exemption' to patent infringement that would allow the plaintiffs in the suit to engage in short-term freeriding while ultimately harming the biotechnology industry and future patients.

On the other hand, without the foundation of basic, publicly-funded research (such as the Human Genome Project), the biotech industry wouldn't exist to the same degree it does today, and patents exist to provide a public good. The level of exclusivity that gene patenting provides may be interfering with that public good (at least, it seems that there is evidence that this is the case for Myriad).
posted by Blazecock Pileon at 11:05 AM on May 13, 2009

Okay, did you look at the sequence listing?

Yes, I did, as a matter of fact. There are 5900 unique 15-mers in the sequence from the patent (yes, I even counted how many were unique). This means that if you just generated 15-mers at random, one out of every 181,990 would contain one of the 15-mers. The latest release of GenBank contains approximately 85 billion 15-mers, meaning more than 467,000 matches of one of these sequences just by chance. A claim so broad never should have been allowed.

It's the biotech equivalent of saying "a mixture of 10-11% compound X and 89-90% compound Y."

Sorry, as a professional human genomics researcher with a PhD based on nucleotide sequence analysis work, I have to say that this analogy makes zero sense given the claim.
posted by grouse at 11:13 AM on May 13, 2009 [21 favorites]

Patenting genes does seem silly, but the ACLU seems to have an uphill fight here, given how much big pharma and biotech IP would potentially be nullified by a ruling in its favor.

Oh no! If that happens, everyone knows that if you post-facto take away someone's motivation for having done something, their work will be undone. Why, decades of research into genetics and biology will be wiped away by a single court ruling!

We need to restore the original purpose of patents and copyright as outlined in the Constitution: "To promote the progress of science and useful arts, by securing for limited times to authors and inventors the exclusive right to their respective writings and discoveries." The profiteering view of "intellectual property" has gone too far.

One could argue that allowing companies to patent genes provides incentives for them to actually put in the time and investment in sequencing them. But, I think it's ridiculous to allow companies to patent things that exist in all (or many) humans already.

As far as funding goes, it could easily be done by, for example, a government bounty on useful discoveries, with a mandatory licensing scheme for commercialization - so that if researcher A discovers something, and researcher B figures out a profitable product based on A, there would be a standard fee that B pays to A. This would eliminate the need to negotiate a price or provide exclusivity, etc. The government could also simply pay for research directly.

Those things would have been difficult to accomplish in the 1800s, but with today's databases and large government budget it wouldn't be that hard.
posted by delmoi at 11:14 AM on May 13, 2009 [1 favorite]

This is not a patent on lithium. It's more like a patent on a new process for purifying lithium or the purified version of a rare lithium compound found in nature discovered to have therapeutic properties.

I disagree. The thing is, even if the DNA is isolated and purified, the information contained therein is still exactly the same as the original (minus Taq error rates and such). And the processes for isolating, amplifying, and sequencing DNA are nothing new; any schmuck can come up with a way to sequence BRCA1 and BRCA2. What else are they adding to the world besides the knowledge that breast cancer and BRCA mutations are related?
posted by greatgefilte at 11:16 AM on May 13, 2009

So I can patent a rock if I brush the dirt off it first?

I'm going to take your question seriously, rather than as argument-by-hyperbole. The answer is yes, so long as you meet the requirements for patentability.

Basically, your rock must be: new, non-obvious, and useful. To be new that particular substance must not have been described before. To be non-obvious it must be non-obvious to one having ordinary skill in the relevant art to use that particular substance, given the substances already known in the art. To be useful it must have some utility; merely describing a new compound is insufficient: it must have a use. There are other requirements, but those are the big three.

In this case, the isolated DNA sequence was new in that no one had described it before. It was non-obvious in that a person of ordinary skill in the biotechnology field would not have thought that particular sequence obvious. And it was useful because the isolated form can be used to perform diagnostics.

Note that the gene as it exists in the human body is not new nor is it useful (except to give someone cancer). These are just two of the reasons why one cannot patent the gene as it exists in nature.

without the foundation of basic, publicly-funded research (such as the Human Genome Project)

Except that the privately funded competing project was working just fine. As the above linked paper shows, patents aren't the problem. If Celera had been the sole provider of a sequenced genome, the likely outcome would've been similar to what we have today, except that researchers would pay Celera for data instead of taxpayers paying the HGP.

For an overview of this topic from a variety of points of view, I recommend Perspectives on Properties of the Human Genome Project. (Full disclosure: I work with the editor of that book and some of the contributors)
posted by jedicus at 11:17 AM on May 13, 2009

What else are they adding to the world besides the knowledge that breast cancer and BRCA mutations are related?

Fundamentally that's precisely what they're adding. And that's a pretty important piece of knowledge. If it weren't, there wouldn't be a line of aggrieved parties claiming that their work and lives are disrupted by Myriad's patent. The patent system doesn't allow claiming of a simple fact, though, so it's couched in terms of an isolated gene sequence.

grouse: My apologies, I misread the claim to be the inverse of what it is (i.e., to cover any sequence at most 15 nucleotides different than the listing). In any event, if those claims are too broad, then they should be attacked as too broad in reexamination. Saying the entire patent is per se unconstitutional is tremendously short-sighted.

Oh no! If that happens, everyone knows that if you post-facto take away someone's motivation for having done something, their work will be undone. Why, decades of research into genetics and biology will be wiped away by a single court ruling!

What has been done will not be wiped away, but it will wipe away the value of investing in future research. It will also greatly reduce the value of companies that depend on such patents, which will in turn lead to investors not recouping their investments. So there is both present and future harm, financial, scientific, and medical.
posted by jedicus at 11:22 AM on May 13, 2009

Yes, I did, as a matter of fact. There are 5900 unique 15-mers in the sequence from the patent (yes, I even counted how many were unique). This means that if you just generated 15-mers at random, one out of every 181,990 would contain one of the 15-mers. The latest release of GenBank contains approximately 85 billion 15-mers, meaning more than 467,000 matches of one of these sequences just by chance. A claim so broad never should have been allowed.

I cannot favorite this enough.
posted by Hutch at 11:24 AM on May 13, 2009 [1 favorite]

The patent system doesn't allow claiming of a simple fact, though, so it's couched in terms of an isolated gene sequence.

The patent system does allow for therapeutic tests to be protected. So it is possible for Myriad to profit from its research by patenting tests which look for haplotypes, SNPs, and other variants more subtly associated with the disease. This would constitute genuinely novel works, in my mind, as compared with a simple start/end pair of DNA coordinates that are (by definition of a reference sequence) shared by all.

I understand your side of it, even if I don't agree with it. However, it does seem that Myriad is not using its patent privilege well, and it seems a case can certainly be made against it for its privileges to be revoked.
posted by Blazecock Pileon at 11:38 AM on May 13, 2009 [1 favorite]

What else are they adding to the world besides the knowledge that breast cancer and BRCA mutations are related?

Fundamentally that's precisely what they're adding. And that's a pretty important piece of knowledge.

This was known for at least five years* before the filing of the patent, so that is not a bit of knowledge the "inventors" contributed. What they contributed was the sequence of the gene and mutations, and a system for testing those mutations. Few are saying that the system should not have patented, only the natural genes and mutations as found in the wild.

In any event, if those claims are too broad, then they should be attacked as too broad in reexamination. Saying the entire patent is per se unconstitutional is tremendously short-sighted.

That is exactly what is happening. If you read the complaint, you will find they are not asking for the entire patent to be thrown out, only specific claims, starting with the very same ones I find most egregious.

So there is both present and future harm, financial, scientific, and medical.

Present harm? I don't think so. Myriad isn't going to stop allowing any breast cancer susceptibility tests out of pique. Future harm in terms of decreased investment in biotechnology research? Maybe.
But for this particular kind of research I think that is far outweighed by the clear and present harms that this kind of patent claim causes, which are spelled out quite well in the complaint and supporting documents. In general, the contribution to the useful arts and sciences provided by the mere sequence of a natural gene, is so minimal that it should not be protected by a monopoly of such a lengthy duration.

* Full disclosure: the principal investigator of the original BRCA1 study is employed by my department.
posted by grouse at 11:41 AM on May 13, 2009 [12 favorites]

Why do we use the term intellectual property? I was under the impression that historically, at least, patents and copyright are temporary monopolies granted with the aim of fostering innovation. How is it accurate to describe a temporarily granted monopoly on the production of something as owning the idea. Wouldn't it be more accurate to describe this as a lease?
posted by [expletive deleted] at 11:51 AM on May 13, 2009 [2 favorites]

A claim so broad never should have been allowed.

For what it's worth, such claims haven't been allowed for years now.
posted by exogenous at 11:57 AM on May 13, 2009

What has been done [in regards to research behind patenting genes] will not be wiped away, but it will wipe away the value of investing in future research. It will also greatly reduce the value of companies that depend on such patents, which will in turn lead to investors not recouping their investments. So there is both present and future harm, financial, scientific, and medical.

I may be sniffing too much fairy dust, but doesn't that all boil down to financial harm? Privately funded future investments in gene patenting will decrease, which is bad because so much work is privately funded. And investors in this will be hit with a loss where they assumed gains, which is bad for investors who back privately funded research.

The current situation has more short-comings than simply defending gene patents. Because there were scientific, medical, and financial gains based on the actuality that money could be made from patenting genes, all will be harmed if/when gene patents are voided.
posted by filthy light thief at 12:09 PM on May 13, 2009

Is patenting a genome the same as trying to patent an element found in the periodic table? At one point, the atomic make up of an element wasn't known. Not all are found in nature, and rarely, if ever, are they found in a pure form. Yet I doubt too many people would be willing to grant a patent on Oxygen to any specific corporation. How is this different, except given the level of complexity?
posted by ShadowCrash at 12:53 PM on May 13, 2009 [1 favorite]

I fail to see how describing a pattern which already exists in nature somehow entitles someone to claim ownership of that pattern. Gene patents seem to be down there with software patents, in that they're innovation-stifling schemes propped up a bunch of rent-seekers.
posted by mullingitover at 1:13 PM on May 13, 2009

your [invention] must be: new, non-obvious, and useful.... There are other requirements, but those are the big three

Significant to this discussion, the invention must also be patentable subject matter under 35 USC 101. See Diamond v. Chakrabarty and other cases.
posted by exogenous at 1:26 PM on May 13, 2009 [1 favorite]

Subject matter is largely irrelevant here because the patent claims a composition of matter (a large, complicated composition, but a composition nonetheless)
posted by jedicus at 1:58 PM on May 13, 2009

There are 5900 unique 15-mers in the sequence from the patent (yes, I even counted how many were unique).

I'm curious as to how you arrived at that number considering that the sequence is only 5711 bases long? Did you include the primers?
posted by euphorb at 2:02 PM on May 13, 2009

Subject matter is largely irrelevant here because the patent claims a composition of matter

Although I don't think the ACLU has a great chance at the 101 argument, I respectfully disagree. Look at Diamond v. Chakrabarty, 447 U. S. 303 at page 309:

This is not to suggest that ¡ì 101 has no limits, or that it embraces every discovery. The laws of nature, physical phenomena, and abstract ideas have been held not patentable. See Parker v. Flook, 437 U. S. 584 (1978); Gottschalk v. Benson, 409 U. S. 63, 409 U. S. 67 (1972); Funk Brothers Seed Co. v. Kalo Inoculant Co., 333 U. S. 127, 333 U. S. 130 (1948); 56 U. S. 112-121 (1854); 55 U. S. 175 (1853). Thus, a new mineral discovered in the earth or a new plant found in the wild is not patentable subject matter. Likewise, Einstein could not patent his celebrated law that E=mc2; nor could Newton have patented the law of gravity. Such discoveries are "manifestations of . . . nature, free to all men and reserved exclusively to none." Funk, supra at 333 U. S. 130.

These are the very issues that trouble so many people about gene patents. See also MPEP 2105.
posted by exogenous at 2:17 PM on May 13, 2009 [1 favorite]

adipocere, you mean Moore v. Regents of the University of California. The wikipedia article has a link to a pdf of the decision.
posted by dilettante at 2:19 PM on May 13, 2009 [2 favorites]

I'm curious as to how you arrived at that number considering that the sequence is only 5711 bases long? Did you include the primers?

I don't know where you get 5711. SEQ ID NO:1 has 5914 base pairs, and it even says so on page 53 of the patent PDF. Whatever the sequence is that is before and after the coding sequence (which is 5588 bp long), it is still claimed.
posted by grouse at 3:00 PM on May 13, 2009

> Among academic biotech researchers in the US, only 1% report having to delay a project and none had abandoned a project as a result of others' patents.

Wouldn't the researcher would conduct an initial literature review that identifies roadblocks like this before investing effort and time? For that matter, the researcher may not bother trying a project at all because the patents and patent-holders are commonly known.
posted by ardgedee at 4:02 PM on May 13, 2009 [3 favorites]

Ah, I see the problem. OncorMed has the patent for the BRCA1 gene consensus sequence (5,654,155). Myriad has the patents for BRCA1 mutations (5,693,473 and others). The patents give different gene lengths. The two companies sued each other and eventually settled their dispute out of court with Myriad getting exclusive rights to BRCA1 testing.
posted by euphorb at 4:23 PM on May 13, 2009

If you read the complaint, you will find they are not asking for the entire patent to be thrown out, only specific claims, starting with the very same ones I find most egregious.

The complaint attacks the independent claims of the patent. If those fail, then the entire patent fails. In any event, that's only a procedural issue. The stated goal of the suit is to invalidate all human gene patents categorically, which is what the plaintiffs will argue for on the inevitable appeal.

From the ACLU's FAQ: "We believe the USPTO should never have granted these patents in the first place, because patenting human genes is unconstitutional and unlawful. In order to invalidate gene patents, we have to challenge at least one specific gene patent."
posted by jedicus at 6:48 PM on May 13, 2009

Excellent post. Thanks, zarq.

That reminds me, I need to make a donation to the ACLU.

Yeah, me too.
posted by homunculus at 6:57 PM on May 13, 2009

The complaint attacks the independent claims of the patent. If those fail, then the entire patent fails.

How are claims 16, 18, and 19 of patent 5,747,282 not independent claims?
posted by grouse at 6:59 PM on May 13, 2009

it costs a ridiculous amount to bring a drug to market

Not really. R&D expenses of Big Pharma are usually less than SG&A and net income to shareholders.

Not sure what you mean by the "net income to shareholders" reference. R&D as a percent of revenue is around 19% for pharmaceutical companies, according to the industry association, and around 10% according to the National Science Foundation. (The NSF includes revenue from non-prescription products like vitamins, while the industry association does not).

It takes almost 12 years to bring a new drug to market, and cost estimates range from $137 to $802 million (I also saw $1.3 trillion floated around but the congressional budget office (PDF) used the 137-802 range).

In any case it's a non-trivial amount.
posted by txvtchick at 7:07 PM on May 13, 2009

How are claims 16, 18, and 19 of patent 5,747,282 not independent claims?

They're independent claims, but they aren't about the gene sequence per se, so they aren't really relevant to the issue at suit.

In any case, I like Prof Crouch's take from Patently-O: "The gene patenting debate has been interesting - emphasis here on has been. The genome has been mapped and sequences published. Very few new patents claiming isolated human genes are being filed. The ones already patented will expire within the next decade -- most of them will expire before being put to any practical use."
posted by jedicus at 7:23 PM on May 13, 2009

The complaint attacks the independent claims of the patent. If those fail, then the entire patent fails.

What leads you to this conclusion? If it were true, why would anyone bother including dependent claims?
posted by exogenous at 7:40 PM on May 13, 2009

What leads you to this conclusion? If it were true, why would anyone bother including dependent claims?

It's true that normally dependent claims don't necessarily fall with the independent claim because they include additional limitations. In this case, however, the complaint alleges that the kind of claims at issue are per se invalid, so it's sufficient to attack the independent claims.
posted by jedicus at 7:49 PM on May 13, 2009

They're independent claims, but they aren't about the gene sequence per se, so they aren't really relevant to the issue at suit.

1. When I said that the claims on gene sequences were too broad, you said that these claims should be attacked rather than "the entire patent."
2. When I pointed out that it was these sequence claims that were being challenged, and not the whole patent, you falsely asserted that as these were the independent claims, if they failed "the entire patent" failed.
3. When I pointed out that they were not the only independent claims, you then changed the argument saying that "they aren't really relevant to the issue at suit."

I'll take this as, at long last, a tacit admission that it is not "the entire patent" that is being attacked after all, but forgive me if I'm not very impressed by this latest turn in your argument.
posted by grouse at 10:28 PM on May 13, 2009

mullingitover: I fail to see how describing a pattern which already exists in nature somehow entitles someone to claim ownership of that pattern.

This is exactly what I have never understood. It isn't as if they created the gene.

There was a case in the gardening world recently where a seed company was attempting to patent to gene that causes warts on pumpkins and other squash-like fruit. The Patent Office refused the patent, because warts on pumpkins and other squash-like fruit existed long before they filed for a patent on them. There have been a couple of other cases involving plant DNA with seed companies trying to patent a long-existing gene in some produce crop, and they have been turned down.

Seems to me that human genes were in existence (even these specific sequences) long before these people wanted to patent them. So, why aren't human genes as incapable of being patented as the warts on pumpkins?

I will admit it's possible I just don't understand some of the finer details, but if someone can patent a human gene (for whatever reason), shouldn't I be able to patent the red on tomatoes?
posted by Orb at 2:29 AM on May 14, 2009

I'm with Orb. If anyone "owns" the patent on a gene, wouldn't it be the person within whose genome it was originally identified? Granting a patent to the person/company who finds the gene seems like it would give me ownership rights over anything I harvested myself. This sounds like theft, but like orb said, it's not unlikely that I'm missing some legal subtlety here.
posted by nax at 5:08 AM on May 14, 2009

It isn't as if they created the gene.

The nuance is that there is the natural thing ¡ª a stretch of DNA in your cells ¡ª and then there's a map ¡ª a novel, human creation ¡ª that says you may find these natural things at so-and-so locations that are related to some function or malfunction of interest, with some technical complications about the makeup of those components (natural variations, some of which cause disease).

The matter at contention is to what extent this mapping should receive patent coverage, with both sides arguing for the extremes of both positions.

A literal analogy to Myriad's patent ownership would be Rand McNally being the first to make road maps of the United States, and having roughly twenty years in which they can prevent all other companies from publishing any road maps of the US whatsoever, without first obtaining Rand McNally's permission, paying a licensing fee, etc.

For the next twenty years, if you want to find your way around the US, you'd need to buy a Rand McNally or RM-licensed map. After the twenty years are up, you are then free to get your road maps from Google or MapQuest, etc.

Myriad would probably argue that, if you're the first to "draw" a map to point to a gene, you should be able to make a profit from your exploration for twenty years (minus a few, generally). The argument is that patent ownership encourages private investment and speeds advances in biotechnology.

The ACLU is arguing that that the benefits of that exploration should be immediately available to the public, because the map is a discovery, not an invention, and that patent ownership actually slows technological progress and causes damage to the public good, by limiting access. The public has a vested health interest in making genetic research freely available.

There seem several obvious ways in which the ACLU can demonstrate that Myriad is mishandling its patent rights (that's even assuming Myriad located BRCA in the first place, which is not clear) and deserves to have those patents revoked.

It will be interesting to see if the ACLU can demonstrate that gene mapping is a discovery, as opposed to an invention. That would be a very significant change.

if someone can patent a human gene (for whatever reason), shouldn't I be able to patent the red on tomatoes?

You can patent a strain of tomato which you invent through breeding efforts. To the extent that a tomato's appearance is genetically determined, you might be able to indirectly claim some ownership on the appearance of a tomato, if its genetic constitution is man-made and sufficiently novel. You can also give your breed a trademark, like UglyRed™, which distinguishes it further from other tomatoes.
posted by Blazecock Pileon at 5:28 AM on May 14, 2009

BP,
The map argument is interesting. I'd assume maps are covered under trademark and copyright laws, and I can't just photocopy a map and sell it as my own. But as long as the roads are open to the public, I see no reason others can't measure and map them on their own. So by the same logic, mapping DNA entitles you to sell your map, but shouldn't prevent others from carrying out their own research and discovering the same information.

I think a better analogy would be if a map maker declared that their map gave them royalty rights whenever someone uses any type of map to determine their location or route.

I think patenting a machine or process to map DNA is valid. But trying to patent the actual information about the DNA sounds worse than patenting a mathematical equation or programming method.
posted by ShadowCrash at 6:27 AM on May 14, 2009

homunculus, thanks. :)
posted by zarq at 6:44 AM on May 14, 2009

I think patenting a machine or process to map DNA is valid. But trying to patent the actual information about the DNA sounds worse than patenting a mathematical equation or programming method.

In theory, yes. However, DNA is a molecule, and there are already multiple precedents in US pharmaceutical law which allow companies to patent and license the products (not just the methods) of biomolecular screening assays. The US patent office's decision is based on the concept that gene fragments / nucleotide sequences are fundamentally no different than any other molecule -- and here's where it gets interesting: RNA sequences (gene fragments!) are used in the pharmaceutical industry as (among other things,) primers to help isolate a variety of DNA and cellular structures.

Delineating the difference between RNA tools/processes and human DNA that should, perhaps remain in the public domain is going to be quite a challenge.

I suspect lawyers repping pharmaceutical companies are sweating bullets over this suit.
posted by zarq at 7:05 AM on May 14, 2009

In any case, I like Prof Crouch's take from Patently-O: "The gene patenting debate has been interesting - emphasis here on has been. The genome has been mapped and sequences published. Very few new patents claiming isolated human genes are being filed. The ones already patented will expire within the next decade -- most of them will expire before being put to any practical use."

I'm not familiar enough with the industry to know whether or not the Nature Biotechnology article you linked to takes into account whether the patents might potentially inhibit a non-profit group's efforts to do *basic* research on the genes in question. Does it? I do know that such problems were a consequence of Diamond v. Chakrabarty in the biotech world. Upstream companies and organizations were forced to conform their methods / technologies to downstream pharmas, which constrained research and limited results.

So... I'll phrase this is a hypothetical: If gene patents do stifle basic research, then we'd be looking at ten years before a needless obstacle to potentially finding treatments or cures are eliminated.
posted by zarq at 7:32 AM on May 14, 2009

zarq,
Isn't the patents around molecules protecting the creation of the the molecule? Would they effect research into detecting, mutating, or altering the molecule? I thought the reason Lithium wasn't patentable was because there was no trick to creating it. So if the drug companies come up with a DNA sequence that needs to be created in the lab, they can receive a patent on it, but merely mapping existing DNA seems the equivalent of granting patents on nitrogen because someone determined it's atomic make-up.
posted by ShadowCrash at 9:00 AM on May 14, 2009

shadowcrash:

This is from the ACLU:

What are gene patents?

The U.S. Patent and Trademark Office (USPTO) grants patents on human genes, which means that the patent holders own the exclusive rights to those genetic sequences, their usage, and their chemical composition. Anyone who makes or uses a patented gene without permission of the patent holder ¨C whether it be for commercial or noncommercial purposes ¨C is committing patent infringement and can be sued by the patent holder for such infringement. Gene patents, like other patents, are granted for 20 years.

For example, Myriad Genetics, a private biotechnology company based in Utah, controls patents on the BRCA1 and BRCA2 genes. Because of its patents, Myriad has the right to prevent anyone else from testing, studying, or even looking at these genes. It also holds the exclusive rights to any mutations along those genes. No one is allowed to do anything with the BRCA genes without Myriad's permission.

(Emphasis mine.)

Since the ACLU could be considered a biased source, here's a portion of a statement released by Myriad in today's NYTimes:

"We have rights to 23 granted U.S. patents which cover a number of important aspects related to the detection of mutations in the BRCA1 and BRCA2 genes. These patents cover not only isolated gene sequences, but also methods of isolating, analyzing and detecting mutations."

So yes, according to both parties, the patents definitely affect research into the molecule, and their protections extend beyond mere creation.
posted by zarq at 9:52 AM on May 14, 2009

That's crazy. I realize it might be reality now, but I don't see why someone should be granted a patent that prevents anyone from analyzing or detecting changes to the object they patented. It would seem that could be used to prevent independent testing or even verification of the patent itself.

Thanks for the info zarq!
posted by ShadowCrash at 10:53 AM on May 14, 2009

OK, as a qualified European patent attorney, I feel compelled to note that this sentence from the spur or stifle research link (quoted above by filthy light thief) is utter and complete balderdash:

In May 2004, the European Patent Office revoked Myriad¡¯s patents. The removal of the patents, an almost unprecedented event in patent history, came because the Europeans decided that while Myriad had figured out the composition of key genetic sequences, it had not done enough to meet the "inventiveness" standard required of a patent.

In other words, even though the company had figured out hundreds of the key genes involved with a higher risk of breast and ovarian cancer, they had not invented anything. Rather they had simply found something already existing in nature.

First of all, revoking a patent in opposition proceedings is certainly not "almost unprecedented" at the European Patent Office. Opposition is a post-grant adversarial procedure for revocation which can be introduced up to nine months after grant. The main reason for it is that, afterwards, European patents become a bundle of national countries which would have to be revoked in court country by country. Thousands of oppositions are introduced yearly and, roughly, one-third fails, one-third succeeds partially (limiting the scope of the patent) and one-third succeeds completely (revoking the patent altogether).

Secondly, in European patent law "inventiveness" is what Americans call "non-obviousness". If the Opposition Division revokes a patent on lack of inventiveness it is because it considers that the subject-matter possibly passes the first hurdle of being new, but would nevertheless have been obvious for the skilled person.

While novelty is clear-cut (something is new or it isn't), obviousness is a much more fraught concept. While something may appear obvious to us after it is invented, it may not have been quite so obvious before. For this reason different jurisdictions have developed different tests for determining obviousness. The EPO swears for its "problem-solution-approach" or PSA: comparing the invention with the closest prior art, you determine which problem has been solved by the invention and by which new means. If those same means had been proposed to solve the same problem in a related area, then it is considered that it would have been obvious to combine them to the closest prior art. The USPTO, following US case law, used to apply the "teaching, suggestion, or motivation" or TSM test, requiring that there was a teaching, suggestion, or motivation for the skilled person to be obvious to combine two pieces of prior art. The TSM test, however, was criticised as leading far too easily to something being considered "non-obvious", and last year the Supreme Court scuttled it in KSR vs. Teleflex. Unfortunately, it didn't bother to propose a new test to take its place, asking instead for the application of "common sense" (which, as I like to say, is surprisingly uncommon). This IMHO has left US patent law in some state of disarray.

Finally, the decisions of Opposition Divisions of the EPO can be appealed, and the Myriad decisions were. As it happens, at least two of the Myriad patents have been reinstated in Europe as a result...

BTW, neither in the opposition nor in the appeal do the "ethical" objections appear to have been given much weight.

With respect to the ACLU lawsuit, I consider it a disastrous precedent to name the USPTO as a defendant. The USPTO has to process hundreds of thousands of patent applications yearly with limited means. It may do its job more or less well, but bad patents can alway be revoked in court. If the USPTO is held responsible for each and every patent it grants (or refuses to grant!), then it will never be able to do its job at all again.
posted by Skeptic at 2:44 PM on May 14, 2009

Shadowcrash, you're very welcome. :)

The rules are there to protect drug and technology companies, so they can protect the massive investments they put into bringing a drug or diagnostic technology to market. But when it comes to genes, it's not clear if those broad protections are necessary, or even wise.
posted by zarq at 3:01 PM on May 15, 2009