The only purpose that legitimizes the granting of patents is that they encourage innovation. Patents on existing genetic sequences do no such thing. Indeed it prevents research on potentially life saving treatments. Consider the swine flu. If some enterprising managed to identify and patent the genetic sequence for the swine flu, it may well have prevented anyone from working on a vaccine or other treatment. Please tell me how that justifies the government intervention in the marketplace to grant a monopoly to the company that does this ? There is no social benefit that justifies any such government interference. If such a patent is allowed, what prevents a company from clandestinely inventing a particularly virulent disease, only to charge egregious fees on the only (allowed) treatment, which they then profit from ? Yes, that would be evil, and yes, there are people who would do that for the money involved.

There's a fascinating take on this at the Skeptic's Health Journal, sort of provides some of the background to the debate, if interested you can read on it here, http://healthjournalclub.blogspot.com/

The reason patent lawyers would have said this is a no-hope challenge is because it would take a serious deviation from the last 30 years of practice and precedent to accomplish.  This district judge did so by ignoring everything in those 30 years and casting Chakrabarty in a much narrower light than it has been understood.  The line is not nearly as clear as this analysis suggests, as most patented DNA compounds are every bit as altered from nature and engineered as the bacterium at issue in Chakrabarty.  The compounds can't be delivered for therapeutic or resarch use, for example, without splicing into a host vector, which results in a compound appearing nowhere in nature and with significant differences from nature.  Even if upheld on appeal (which seems doubtful) this ruling would likely only impact claims directed at "pure" sequences and not ones that specifically discussed combining the compounds with vectors overtly or other genetic manipulation - unless we start declaring that you can't derive anything from nature, which would destroy modern chemical patents.

As a ruling, I'm disturbed by the choice of precedents.  The cases relied on other than Chakrabarty predate any understanding of the use of DNA or its distinct usefulness in treating various illnesses by isolation and reproduction - a quality not shared by purified elements.   Whether the parties didn't brief it or the judge ignored it, there's also a body of law specifically on chemical challenges in the last 30 years at the Federal Circuit - including 101 challenges to gene sequences based on a lack of utiltity.  These are the sorts of cases that make litigators nuts - someone comes in with a theory with almost no law behind it, but it is so out there no one has ever had to rule on it directly at the appellate level so a district court judge can choose to run with it.

Still, I can't say I'm all that surprised at the result.  As DNA technology has evolved, the law and science have been on a collision course.  Unlike 20 years ago, gene sorting and typing today is pretty mundane stuff, so the science looks more and more like a way to rip something off from nature.  There's little to no risk anymore, as there was in the 1980s and 90s, of patenting a sequence that is off in a way that destroys the usefulness of the resulting compound.  However, the fact that there may be no protection for "pure" sequence claims won't stop companies from patenting DNA - it will just change the nature of the claims to focus more on applications, where this nature argument can't apply.