The computing revolution is not the only one driven by constant scaling of technologies: the field of genomics -- the study of DNA sequences -- has also enjoyed rapid falls in basic costs over the last decade and a half. This means that whereas the first human genome cost around $3 billion to sequence, we are fast approaching the point where it will cost first a few thousand, and then a few hundred dollars to sequence anyone's complete DNA. An interesting post on the Health Affairs Blog points out that neither the law nor society is ready for this.

Companies like 23andMe are already offering people the ability to find out about a range of important genes very simply, and for relatively low cost:

The concern is that someone might learn of that same risk [for breast cancer] for $499 by spitting in a tube and hitting the "breast cancer result" button at 23andMe, a company that will test saliva samples for diseases as well as for DNA ancestry. No one should take an action, such as prophylactic surgery without confirming results from 23andMe, which reports on only the three most common mutations.

Against that background of possibly life-changing or even life-threatening decisions being made on the basis of results obtained from a blob of saliva, the Food and Drug Administration (FDA) is now looking to regulate this market. But in the opinion of the article's authors, there's a danger here:

If regulators impose rules that allow us to obtain genomic data only as a medical service and through a health professional, however, access will never be cheap because it will always be bundled with expensive professional medical services. This is what Germany has done, and we should not follow their lead. By equating genome services to medical services, the German Government has reduced access, significantly limited the possible benefits to their citizens, and dramatically increased the costs.

The authors make a suggestive comparison:

It’s as if [governments] had decided to cut off access to the World Wide Web in response to fears of pornography and copyright infringement. Imagine what the world would be like today if we had passed the Draconian Internet regulation bills proposed a decade ago when the Internet was as young as the nascent genomics sector is now. We would have sucked the water out of the pond that gave birth to the marvels of Google, Wikipedia and Facebook.

There's another parallel, too. Just as with the Internet and its digital deluge, the imminent world of abundant, ultra-cheap genomic data could also could power the growth of a huge new economic sector:

Our curiosity -- and sometimes our health -- will require 'experts' to do the science and to explain its implications. Some of these "genomicists" will be health professionals no doubt: genetic counselors, nurses, social workers, or physicians who learn the intricate math and follow the exploding technical literature. Others will be experts in genealogy, history, ethnicity, engineering and anthropology. New businesses are emerging to create interpretive software and interactive websites that walk us through tours of our genomic data. If you’re young and computer savvy; if you study genetics and read anthropology and history, you may have a job in a field that is just coming to life. That is, if we don’t screw it up by strangling this nascent field in its cradle.

The trick will be to allow these new businesses to aggregate and analyze DNA information while preserving individual privacy and control over genomic data that is unequivocally yours. That's going to be hard, but the potential benefits in terms of improving people's health make it worth striving for. For more information, check out the original post which goes into greater detail.

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As we expected, following the Supreme Court's excellent rejection of medical diagnostic patents, it's now set aside the appeals court's ruling upholding gene patents, and asked the appeals court to review the case in light of its ruling last week. Again, this is not a surprise, but it's good that the court so quickly recognized that the two cases have similar issues, and that the appeals court ought to revisit the Myriad (gene patents) ruling so quickly. Hopefully, CAFC (the appeals court in question) will come to its senses and recognize that you can't patent genes. Either way, no matter what CAFC decides, expect that to also be appealed right back to the Supreme Court.

Brand name pharmaceutical drugs are ridiculously expensive, but how much does it really cost to manufacture a drug? A potentially low-cost method is to use microorganisms -- which are plentiful -- to synthesize chemical compounds. For example, synthetic insulin is now made using genetically modified bacteria. Here are a few other examples.

• Are you depressed? You can use open-source DNA code from the Registry of Standard Biological Parts to genetically engineer yogurt bacteria to make Prozac. The process takes 4-5 days, and anyone can purchase the DNA code online. [url]
• Researchers at the Salk Institute for Biological Studies have created a strain of bacteria that can incorporate artificial amino acids into proteins at multiple sites. This could be used to engineer bacteria to produce a variety of synthetic chemicals. [url]
• Green algae could be a cheaper alternative to bacteria in the manufacture of therapeutic drugs. While bacterial cultures require lots of energy and nutrients to maintain, the algae need only sunlight and carbon dioxide in the air. [url]
• To discover more interesting science-related stuff, check out what's currently floating around the StumbleUpon universe. [url]  

By the way, StumbleUpon can recommend some good Techdirt articles, too.

One new approach to teasing apart the complex relationships between genes and common diseases such as cancer, heart disease, asthma and diabetes is by creating huge biobanks of medical data and samples. The idea is that by tracking the health and habits of very large populations across many years, and then examining their DNA, it will be possible to spot factors in common. Here's a major biobank that is shortly opening up its holdings for research:

UK Biobank recruited 500,000 people aged between 40-69 years in 2006-2010 from across the country to take part in this project. They have undergone measures, provided blood, urine and saliva samples for future analysis, detailed information about themselves and agreed to have their health followed. Over many years this will build into a powerful resource to help scientists discover why some people develop particular diseases and others do not.

Anything that brings us closer to understanding and treating diseases that affect hundreds of millions of people is obviously to be welcomed. But DNA is special: for a start, it is unique for each of us (even "identical" twins seem to have different DNA.) This has made DNA of particular interest to the police, since it appears to offer a perfect way for identifying those at a crime scene (not necessarily the perpetrators, of course.) Which raises the question: what happens when the police realize that biobanks offer a great way to get DNA they can't obtain in the usual ways?

The UK Biobank addresses this issue in its FAQ:

Will access be allowed for purposes other than health-related research?

The UK Biobank Resource has been established for health-related research that is in the public interest. Any attempts to use it for other purposes will be resisted. So, for example, insurance companies and employers will not be allowed to access the Resource to look at information, samples or test results for any identifiable participants. Nor will UK Biobank allow access by the police, security services or other law enforcement agencies, unless it is forced to do so by the courts.

Clearly the UK Biobank wants to do the right thing here, but that last phrase "unless it is forced to do so by the courts" means that the police will probably get what they want once they start invoking "terrorism" or asking us to think of the children.

And once they have a sample, they might well decide to sequence its DNA to help identify the likely hair, eye and skin color of the person concerned – and perhaps much else besides, as gene analysis techniques advance, including highly-sensitive areas such as mental and reproductive health.

Investing your DNA in a biobank might seem like a noble act today, but who knows what the payback will be in years to come?

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A year ago, we wrote about a legal challenge concerning the constitutionality of a California law that requires police to collect and store DNA of anyone arrested (not convicted). A California state appeals court has now struck down the law, saying that it's a violation of the 4th Amendment. Considering all of the rulings lately that seem to have done away with the 4th Amendment, it's nice to see one going in the other direction, though I'm sure there's still going to be an appeal. And, unfortunately, the article linked above suggests that this ruling will likely get reversed on appeal, noting that a federal appeals court (third circuit) recently ruled on the same issue, and said it's fine to collect DNA from arrestees. Still, while this court ruling is still in effect in CA, we might as well quote the judge:

Even focusing on the DNA profile alone, the analogy to fingerprints is blind to the nature of DNA. Courts are well aware that—[r]ecent studies have begun to question the notion that junk DNA does not contain useful genetic programming material and that an intense debate on this subject is now taking place in scientific and legal communities. ... Like the DNA laws of almost every other state and federal law, the DNA Act is silent as to how long these specimens and samples may be kept, and it is reasonable to expect they will be preserved long into the future, when it may be possible to extract even more personal and private information than is now the case. ... [T]he Act places few restrictions on the law enforcement uses to which such information may be put. This raises questions both about the kind of personal and private information that may be derived from the DNA samples in the DOJ's possession, and the uses of that biometric data as scientific developments increase the type and amount of information that can be extracted from it. For example, commentators have discussed the potential for research to identify genetic causes of antisocial behavior that might be used to justify various crime control measures. Fingerprinting presents no comparable threat to privacy.

One hopes the CA Supreme Court or another federal court comes to its senses and agrees on this, but it seems unlikely.

Well, this is unfortunate. We were quite happy with US district court judge Robert Sweet last year for making it clear that isolated genes are not patentable material in the Myriad Genetics case. This was one of those annoying patent situations where so many people had just assumed that genes were patentable for decades, without a single court testing that theory out. So industries were built up around the idea that genes could be patented. Thankfully, Sweet didn't let that bother him in pointing out that gene patents "are directed to a law of nature and were therefore improperly granted."

Of course, as expected, Myriad appealed, and even the Justice Department weighed in, saying genes shouldn't be patentable. However, the results of the appeal are in... and the Federal Circuit appeals court (CAFC) has reversed the lower court and said that patenting genes is just fine. The reasoning is bordering on ridiculous. The court effectively states that because isolated genes are isolated rather than a part of the full DNA strand, they are not "found in nature."

It is undisputed that Myriad’s claimed isolated DNAs exist in a distinctive chemical form--as distinctive chemical molecules--from DNAs in the human body, i.e., native DNA. Native DNA exists in the body as one of forty-six large, contiguous DNA molecules. Each DNA molecule is itself an integral part of a larger structural complex, a chromosome. In each chromosome, the DNA molecule is packaged around histone proteins into a structure called chromatin, which in turn is packaged into the chromosomal structure....

Isolated DNA, in contrast, is a free-standing portion of a native DNA molecule, frequently a single gene. Isolated DNA has been cleaved (i.e., had covalent bonds in its backbone chemically severed) or synthesized to consist of just a fraction of a naturally occurring DNA molecule.

Later, it reiterates that separating out these genes make them somehow "different" and not a part of nature:

In this case, the claimed isolated DNA molecules do not exist as in nature within a physical mixture to be purified. They have to be chemically cleaved from their chemical combination with other genetic materials. In other words, in nature, isolated DNAs are covalently bonded to such other materials. Thus, when cleaved, an isolated DNA molecule is not a purified form of a natural material, but a distinct chemical entity. In fact, some forms of isolated DNA require no purification at all, because DNAs can be chemically synthesized directly as isolated molecules.

Basically, they seem to be arguing that because a severed finger is not attached to a hand, the finger is not naturally occurring, and, thus, is patentable. Think about that. The dissenting judge in this ruling used a slightly less gruesome analogy, saying that the majority was basically saying that while a tree occurs in nature, snapping a leaf off the tree makes that leaf patentable.

The one good thing about the ruling is that it still rejects parts of Myriad's patents, but for other reasons, not because they're unpatentable parts of nature. The dissenting opinion from Judge Bryson (starting on page 88 of the ruling) is well worth reading. It starts out by attacking the problem with common sense, saying that if you were to ask someone if genes should be patented, they would answer, "Of course not. Patents are for inventions. A human gene is not an invention." But then Bryson goes on to discuss the more specific points raised by Myriad. First, he points out that Myriad didn't even really "invent" the key parts here:

At the outset, it is important to identify the inventive contribution underlying Myriad’s patents. Myriad was not the first to map a BRCA gene to its chromosomal location. That discovery was made by a team of researchers led by Dr. Mary-Claire King.... And Myriad did not invent a new method of nucleotide sequencing. Instead, it applied known sequencing techniques to identify the nucleotide order of the BRCA genes. Myriad’s discovery of those sequences entailed difficult work, and the identified sequences have had important applications in the fight against breast cancer. But the discovery of the sequences is an unprotectable fact, just like Dr. King’s discovery of the chromosomal location of the BRCA1 gene.

From there, Judge Bryson points out that an isolated gene clearly is a part of nature, and thus unpatentable:

Myriad is claiming the genes themselves, which appear in nature on the chromosomes of living human beings. The only material change made to those genes from their natural state is the change that is necessarily incidental to the extraction of the genes from the environment in which they are found in nature. While the process of extraction is no doubt difficult, and may itself be patentable, the isolated genes are not materially different from the native genes. In this respect, the genes are analogous to the “new mineral discovered in the earth,” or the “new plant found in the wild” that the Supreme Court referred to in Chakrabarty. It may be very difficult to extract the newly found mineral or to find, extract, and propagate the newly discovered plant. But that does not make those naturally occurring items the products of invention.

The same is true for human genes.

This case is far from over. It seems likely that CAFC will quickly be asked to rehear the case en banc (with the full slate of judges in the court, rather than just a panel of three), and after that it will likely go to the Supreme Court. Still, it's unfortunate that CAFC went this way, and hopefully a later ruling rejects this momentary lapse of reason.

In the meantime, it'll be important to pay close attention to what happens in the "sister" case to this one, Prometheus Laboratories v. Mayo Collaborative Services, in which there's a question of whether or not diagnostic tests can be patentable. In that case, like this one, CAFC said diagnostic tests are patentable, and that case has now moved on to the Supreme Court, which will likely hear the case in the fall. That may be a precursor to the final result in this case.

Eriq Gardner has a great and very detailed article over at ABA Journal exploring questions about the legality of collecting someone's DNA and using it. Apparently, right now, there is a hodgepodge of state laws, with more on the way, and a lot of these issues are likely to end up in court. Realistically speaking, this is a privacy issue, but it's being framed by some as a "property rights" issue, specifically with some new legal proposals:

Perhaps it’s not surprising then to see some of the toughest proposed legislation coming from the New England hotbed of genetics research, specifically in Massachusetts and Vermont, where some bold politicians and health policy think tanks introduced in January a Genetic Bill of Rights for citizens, proposing that individuals should have property rights over their own DNA.

Their legislative proposals would go even further than Alaska’s statute. They would not only mandate consent for the collection and use of DNA but also spell out that individuals have a right to privacy with respect to their genetic information. They would also prohibit entities like auto insurers and money lenders from misusing DNA info. The statute recognizes that DNA has “a fair market value” and carves out only limited exceptions for violating someone else’s DNA property rights: those working under judicial order, such as police investigators. Intentional violations of the statute would carry both prison time and civil fines.

I'm actually a bit surprised that supporters of this type of law think that a property rights model makes sense, because it's then easy to counter with the point that DNA that you leave behind is effectively "discarded" property. That is, if you leave behind a cup you drank out of, does it make sense that you still retain a "property right" over the microscopic DNA you left on the cup?

The fears, of course, are not too difficult to imagine. There have been books and movies written about a world with genetic profiling. But does that really justify some of these laws? And, perhaps, the bigger fear might not be laws about what private parties can do, but what law enforcement is already doing -- such as using DNA analysis to implicate family members in certain crimes. And, as the article notes, even if such laws are put in place, does anyone really think it would stop surreptitious DNA collection and analysis?

To be honest, this is one story where I can definitely see and understand both sides, but I do worry when people seek to go too far with laws to protect what they think is really a privacy issue (especially by conveying property rights), where there may not be a real privacy issue at all.

Cross posted from Open....

The oceans belong to everyone - well, more or less. That is, they form a classic commons. But of course, that fact doesn't stop people from claiming that they own stuff even here:

Molecules derived from marine resources and used for medical applications were worth over $1 billion in 2005, and heat-stable enzymes obtained at undersea vents were worth $150 million. Not surprisingly, the business community has responded by patenting genes derived from marine organisms; the authors were able to identify over 8,500 sequences derived from a total of 520 species in a US gene patent database.

This is a double insult to humanity. Genes are part of the DNA commons and "belong" to everyone or to no one, but certainly not to any one entity. Those genes were extracted from marine animals, which form part of another commons, the oceans' ecosystems, that also belong to everyone or to no one.

But instead of simply recognising those commons, and letting everyone benefit from them directly, the best the patent maximalists can come up with is a cartel, a.k.a. patent pool:

they also suggest that, in the case of marine materials, a patent pool organized within this framework might improve access to genetic information and distribute the risk and profits broadly among far more nations, rather than limiting it to the few countries that can afford high-throughput DNA sequencing.

The logic here seems to be that, of course we need patents, otherwise nobody will go to the trouble of sequencing all of these interesting organisms. What this overlooks is that the cost of sequencing genomes has come down from a billion dollars (for the first human genome) to a few thousand. Next year it will probably be under $1000, and the year after that a few hundred. In a decade, sequencing will cost almost nothing.

What this means is that, once more, intellectual monopolies are being given away needlessly - no quid pro quo is in fact necessary because practically anyone will be able to do this for very low cost. And, once again, it's you and me who lose out, as knowledge is sent to the intellectual equivalent of Davey Jones' Locker....

Craig Venter, who is no stranger to advocating stronger and stronger IP laws -- especially in the area of "synthetic life" -- apparently learned recently how those laws can reach ridiculous levels. In a recent presentation, he noted that his team had encoded a James Joyce quote in the DNA of the "synthetic life" he's been trying to create. However, the James Joyce estate was not amused and sent him a cease-and-desist. Venter notes that he felt that it was fair use to include a quote. The quote was really short:

“To live, to err, to fall, to triumph, to recreate life out of life.”

To claim that this is infringement seems pretty ridiculous. What's unclear from the article, though, is whether or not Venter fought this or just accepted it and agreed to take the quote out. This isn't the first time that the Joyce estate has done stuff like this, including an attempt to stifle a biography by use of a copyright claim. In that case, the estate finally learned that they had no claim when they actually had to pay up to settle the case.

The chief of police of the greater Rotterdam area has called for the creation of a DNA-database for all 16.6 million Dutch citizens. There is already a DNA-database in existence, but it only contains the DNA of 11,000 people since the policy is to only take DNA from people sentenced to prison for at least four years.

According to the chief of police the privacy of civilians is not as important as tracking down criminals, stating that society is "too careful" and that "if you want to make the world safer, there's a price to pay." In a statement released later he added that safety is partly paid for by reducing privacy.

Of course, one could argue that it's not the privacy-concerned people being "too careful," but that there are some people that are so obsessed with security that they're willing to have others pay the price in giving up their privacy. Such a database will not prevent crime, since most crimes don't originate from rational risk-calculation. Any errors in the database could also have disastrous effects on people's lives in the case of a mistaken identity for instance, not to mention the implications of potential function creep. It really is a big price to pay for a small piece of security in one of the safest places in the world.

After a few hours of outrage from civilians and politicians, the Dutch Ministry of Justice and Security released a statement that they do not support the plan and stated that it was not the first time such ideas have been suggested. It is probably not the last time, either.