The US Supreme Court recently sided with patient advocacy groups that a company cannot patent your genes.  Sounds like a pretty clear case, but the decision also creates some exceedingly odd loopholes, and even loopholes within loopholes, to say nothing of the fact that Justice Scalia dissented with the uncontroversial, basic science introduction to the case.

Get ready to go down the rabbit hole...
Our story begins with Myriad Genetics, which discovered and sequenced the BRCA1 and BRCA2 genes, certain variants of which drastically increase your risk for BReast CAncer.  Seeking to protect its investment, Myriad obtained a basketful of patents on those genes.  Some of those patents still stand; the controversial ones claimed exclusive right to "the isolated DNA" of the BRCA genes.  Which is to say, even though every cell in your body had a copy of BRCA1 and BRCA2 before Myriad came along, you were not allowed to isolate and sequence those genes to test for your risk of BReast CAncer through any company but Myriad. Outraged patient advocates, rabble-rousers that they are, sued against the idea that a company could patent an aspect of their bodies.

The Supreme Court agreed, saying patents are for creating something new – you cannot patent something simply for discovering it, even if that discovery is "groundbreaking, innovative, or even brilliant".  However, if you create something that "is not naturally occurring", only then can you get a patent.  The patent law SCOTUS must interpret allows patents on "any new and useful... composition of matter, or... improvement thereof", which the Court has held "contains an important implicit exception: Laws of nature, natural phenomena, and abstract ideas are not patentable."  So the real question, says SCOTUS, is whether Myriad created something new or not.  And here is where things get interesting.

A Federal Circuit court had earlier ruled in favor of Myriad, saying that by breaking the chemical bonds connecting a gene to the rest of your DNA, Myriad had created a new molecule, so patent granted.  Not so! said SCOTUS, for Myriad's claims "focus on the genetic information" in a gene, not "the specific chemical composition of a particular molecule."  In other words, Hamlet is Hamlet, whether it's on parchment, paper, a stage, or your video player of choice.  It's the content that matters, not its physical form.

Ah, said Myriad, but the original Hamlet had a bunch of commercial breaks interspersed in it, and we cut those out to create commercial-free Hamlet (c-Hamlet).  So can we patent that?  Hmm, well ok, said SCOTUS.  Back to genes: the genetic information in many genes has extra "junk" sequences called introns, which the body naturally cuts out when using the gene.  Since that splicing step happens with RNA, not DNA, the commercial-free version of the gene never exists as DNA.  If one was to make such an intron-free DNA (cDNA), that, apparently, is "not a product of nature and is patent eligible".
Can you patent this?  Depends on whether it has commercial breaks, and how smart its infesting bookworms are.
But wait!  SCOTUS just said the information is what matters, and the cDNA contains the same genetic information as the original DNA, just with the "junk" introns removed!  And what's more, the cDNA contains exactly the same genetic information as the inron-free RNA that your cells make naturally!  Doesn't matter, says SCOTUS, intron-free cDNA "is not naturally occurring", since DNA is a different molecule than RNA.  Which doesn't quite make sense considering the court's earlier statement that we are "concerned primarily with the information contained in the specific genetic sequence [not my italics], not with the specific chemical composition of a particular molecule."

Hold on though, if you don't like this cDNA loophole don't worry, there's a loophole in the loophole.  Buried in a footnote (number 8) is reference to the fact that we learned how to make cDNA from a class of viruses, and occasionally a virus will accidentally make a cDNA of the host's genes and insert it into the host genome.  That virally-inserted cDNA is almost never functional, so it's called a pseudogene.  If we can find a BRCA pseudogene in anyone anywhere, then Myriad would lose its cDNA patent.  But since the petitioners couldn't find a naturally occurring BRCA pseudogene, the cDNA patent stands.  Another semi-loophole in the cDNA loophole is that some short genes don't have exons, so for them there would be no way to get a patent.

To torture the Shakespearean analogy a bit longer, Hamlet is in the public domain (because it's old, but let's just call it "naturally occurring" and ignore the difference between patent and copyright), so you can't patent it.  But if the printed version has always had commercial breaks, you could remove them and patent a commercial-free printed version, even if it has already been produced commercial-free on stage.  Despite having the same informational content, the printed and stage versions are apparently different beasts, even though we've already said the content is what matters.  Oh, and if a bookworm has sometime, somewhere happened to accidentally chew out all the commercial breaks in any printed version, then your commercial-free patent is gone.

It would be easy to fling rocks at SCOTUS for the rather crazy loopholes in this decision.  Indeed, it's quite concerning that the court seemingly contradicted itself in the same opinion: first saying that informational content is what matters, so isolating a gene is not creating something new, but then saying that cDNA is different from naturally occurring RNA, even though both hold exactly the same genetic information.  But let's remember that SCOTUS doesn't write the law, it only interprets it.  And in deciding whether genes can be patented, SCOTUS had to interpret a law written in 1793.  I hate to suggest bringing Congress into this, but perhaps it's time for an update?