Federal judges decide that private companies own your DNA

Many scientists cheered last year when a federal judge ruled that human genes couldn't be patented. The case involved Myriad Genetics, which holds the patent rights on two genes, BRCA1 and BRCA2, that are associated with increased risks for breast and ovarian cancer. Thanks to these patents, you can't look these genes in your own body without paying a fee to Myriad. Sounds ridiculous, right? Well, that was the state of gene patents until last May, when judge Robert Sweet ruled that the Myriad's patents were invalid.

But now the courts have reversed themselves again. In a 105-page decision, two federal judges decided that the whole matter comes down to the meaning of the word "isolated." I kid you not.

Judge Sweet's ruling last year was based on the obvious scientific fact that genes are a product of nature, not an invention, and therefore they could not be patented. Patent lawyers were very upset over Sweet's ruling. Why was this controversial? Well, because the U.S. Patent and Trade Office has been granting gene patents for decades. Basically, once the USPTO decided to allow one gene patent, they never looked back, and they've now given out patents for over 4,000 human genes.

But this past week, an appeals court reversed last year's ruling and said yes, Myriad Genetics does indeed own the rights to the BRCA genes. The decision by Judge Alan Lourie reveals an astounding lack of understanding of DNA, genes, and genomes. I guess I shouldn't be surprised, but I had been hopeful that after the earlier ruling throwing out these patents, science and logic would prevail. I guess I should never underestimate the scientific ignorance of judges, though I should add that one of the three judges voted against his colleagues.

What was their contorted reasoning? They decided that "isolated DNA" is not the same as the natural DNA in your body, and that this distinction allows companies to patent it. (The word "isolated" occurs 219 times in the decision.) The judges wrote:
"According to Myriad, isolated DNA does not exist in nature, and isolated DNAs, unlike native DNAs, can be used as primers and probes for diagnosing cancer."

The mind boggles. Following this nugget, Judges Lourie and Moore give us a little mini-lesson in molecular biology:
"Native DNA exists in the body as one of forty-six large, contiguous DNA molecules…. Isolated DNA, in contrast, is a free-standing portion of a native DNA molecule, frequently a single gene…. Accordingly, BRCA1 and BRCA2 in their isolated state are not the same molecules as DNA as it exists in the body."

This is scientific nonsense, but the court bought it. (Over at TechDirt.com, Mike Masnick made the colorful analogy that this is like "arguing that because a severed finger is not attached to a hand, the finger is not naturally occurring, and, thus, is patentable.") Wrote the judges:
"we conclude that the challenged claims are drawn to patentable subject matter because the claims cover molecules that are markedly different—have a distinctive chemical identity and nature—from molecules that exist in nature."

Among other problems, Judges Lourie and Moore don't understand a basic fact of genetics: that genes are "isolated" by our body's own genetic machinery when they are copied into RNA and then translated into proteins. Or perhaps they do understand, but they don't care because they just want an excuse to keep gene patents around. This is what can happen when lawyers (judges) make scientific decisions: they go on for pages and pages about the semantics of a word ("isolated"), and produce a result that is scientifically meaningless.

Judge Bryson makes much more sense in his dissent, writing:
"the question in this case is whether an individual can obtain patent rights to a human gene. From a common-sense point of view, most observers would answer, `Of course not. Patents are for inventions. A human gene is not an invention.' The essence of Myriad’s argument in this case is to say that it has not patented a human gene, but something quite different—an isolated human gene."

So that's two judges (Sweet and Bryson) against human gene patents, and two in favor. This case isn't over yet; last week's ruling by the 3-judge panel will likely be appealed to the full appeals court next. It's hard to predict what they will say. Meanwhile, Myriad charges $4000 to run tests on BRCA1 and BRCA2, as I wrote last year. This means that if a woman wants to test her own DNA for any mutations in the BRCA genes - including mutations that weren't even known when Myriad got the patent - she must pay Myriad merely to look at her own genes.

I'm not a lawyer, but I already see one way around Myriad's patents in this flawed decision. The judge's (and Myriad's) reliance on "isolated BRCA genes" refers to the process of isolating and copying the genes using a laboratory method called RT-PCR, and then sequencing just the isolated bits. Today, though, we can sequence a person's entire genome, without "isolating" any particular genes, for under $5000, and then we can test for mutations in the BRCA genes without ever "isolating" them. In fact, a colleague and I published a paper just last year describing how to do this, and we released a free software package that allows anyone to test their BRCA genes at home on a desktop computer. Genomics Law Report has a detailed legal analysis of what our software means for the Myriad case.

Scientifically, it shouldn't matter how the judges define "isolated" DNA. And as two federal judges have now ruled, genes are not inventions, full stop. What's more, gene patents slow down science by throwing legal barriers in the path of anyone who wants to work on those genes. Finally, I'm amazed at the hubris of companies like Myriad - or anyone else - who claim they "own" a gene. Let's hope the full appeals court will reverse the tortured reasoning of Judges Lourie and Moore, and get the patent lawyers out of the laboratory.

The Baltimore Sun dives into the anti-vaccination pool

In recent weeks, the Baltimore Sun, once an excellent newspaper, has dived headfirst into the pool of anti-vaccination pseudoscience. With two prominent opinion pieces, the Sun has given a platform to the anti-vaccine movement that they probably didn't expect, and that they certainly didn't deserve. The puzzle is, why? Who on the Sun's editorial board decided to offer their pages to the voices of fear and unreason?

First, on June 16, the Sun printed an Opinion article by Mark Geier, where he argued that his unfounded theories about the causes of autism make it okay for him to chemically castrate young boys. (I know this sounds shocking, but it's all too true.) I wrote about Geier two years ago: he and his son David administer what they called the "Lupron protocol" to autistic boys. They charge $5000-$6000 per month for their treatment, which is based on their belief that autism is caused by an excess of testosterone. Lupron, the drug they give to children, is a testosterone-suppressing drug that is the chemical equivalent of castration. It is a harsh treatment used to treat advanced prostate cancer. There is no evidence that it helps autistic boys. When the Chicago Tribune interviewed Simon Baron-Cohen, a professor and director of the Autism Research Center at Cambridge University, here was his reaction:
"The idea of using it [Lupron] with vulnerable children with autism, who do not have a life-threatening disease and pose no danger to anyone, without a careful trial to determine the unwanted side effects or indeed any benefits, fills me with horror."
Finally, after Geier had spent many years of selling his quack treatment to vulnerable families, the state of Maryland suspected his medical license suspected in April. Now, for reasons I cannot fathom, the Baltimore Sun has given him a huge billboard to ask for his license back so he can resume his discredited Lupron protocol.

(Geier also claims that mercury in vaccines causes the rise in testosterone levels that he claims to treat. He ignores the overwhelming evidence, re-affirmed again last year, that there is no link between mercury-containing vaccines and autism.)

This wasn't enough bad science for the Sun, which just a few weeks later published another Opinion piece, this one by anti-vaccine activist Margaret Dunkle. In her article, Dunkle claims that the vaccine schedule includes too many doses, and she further claims that these are harmful to children. This "too many, too soon" argumen is a constant refrain of the anti-vax movement (particularly Jenny McCarthy), despite the lack of science to support it. The evidence on her side: a new study published by Gayle Delong, claiming that autism rates and vaccination rates are linked. Who is Gayle Delong? It turns out she is an economist, not a scientist, and she's a board member of SafeMinds, a well-known anti-vaccination group. Delong's study has already been thoroughly debunked by Neuroskeptic, Sullivan, Liz Ditz, and others, who pointed out its deeply flawed statistics and other problems. Dunkle, though, was happy to jump on this junk science and ignore the real science.

The real science tells just the opposite tale. For example, a thorough review published in Pediatrics in 2002 showed that infants today are exposed to fewer antigens than they were 40 years ago, due to better vaccine formulations. It also found that vaccines "prevent the weakening of the immune system." Countless other articles have shown the efficacy of vaccines; the Immunize for Good site is a good source for a realistic picture of the risks versus the benefits.

Is the Baltimore Sun responsible for the anti-vaccination stories appearing on its Opinion pages? I can imagine their response: "we're just presenting both sides," they might argue. Debates are just fine when political opinions are concerned, but you don't get to argue about facts. Scientific facts are not debated from "both sides" - for example, we don't waste time arguing that diseases are caused by "miasmas" as was once believed. And when the subject is vaccines, presenting the anti-science, anti-vaccine argument has real, and harmful, consequences.

The science is clear: vaccines have been the single greatest boon to public health in the history of mankind. Vaccines have saved millions of lives, and allowed parents to live without the fear that their children will sicken and die. Here are some facts: pre-vaccination, whooping cough caused 9000 deaths per year in the U.S. Post-vaccine, this has dropped to 20 deaths per year. Pre-vaccination, there were 350,000 polio cases worldwide in 1988. In 2009, there were just 1,604, and there's a chance we can eliminate polio entirely. Back in 1921, diptheria caused 206,000 cases in the U.S. alone. In 2001, there were just 2 cases.

If we stop vaccinating, these diseases will return. And make no mistake about it: if measles, whooping cough, polio, and other vaccine-preventable diseases return, children will die. I'm sure that the editors of the Baltimore Sun don't want this to happen. But through their ignorance of the science around vaccines, they have allowed their newspaper to become a voice for a dangerously misinformed group of activists whose main goal is to stop vaccines.

How to correct the damage? Well, the Sun could publish multiple articles on their Opinion pages explaining how many lives vaccines have saved. They could help to re-educate parents about how valuable these medicines are, so they will demand them for their children, rather than refusing them as some parents now do. I have only a faint hope that the Sun's editors will take such action, but I'm calling for it anyway. They owe it to the public.

They engineered a better salmon, so why can't I eat it?

What happened to genetically modified salmon? A few months back I was looking forward to my first taste of the new AquaBounty salmon, which grows to maturity twice as fast as wild salmon. Will it taste just as good? Better? I thought I'd know soon. But then politics intervened.

It's almost always bad when politicians meddle in science. Usually they do so because they just don't like what they're hearing, as they have done time after time with global warming. Now it's genetically modified salmon. What happened? The FDA was ready to approve the new salmon until two weeks ago, when Congressman Don Young from Alaska, under heavy lobbying pressure from the Alaskan fisheries industry, simply stepped in to block it. The FDA had already found that the fish was safe to eat, but hadn't yet issued final approval. So Congressman Young and his pals decided to pass legislation to halt the process.

I wrote about AquaBounty's salmon last year, when the FDA was holding hearings to approve it for human consumption. Ironically, the FDA doesn't get to approve genetically modified crops, and our food supply is filled with GM corn, soy, and other plants. But thanks to the vagaries of U.S. law, the FDA gets to weigh in on salmon.

The science is pretty cool: AquaBounty took two genes from other fish and added them to Atlantic salmon. They added a growth gene from Pacific Chinook salmon, and another gene from a fish called ocean pout (Trisopterus luscus). Together, these genes allow AquaBounty's new salmon, called AquAdvantage ®, to grow to maturity in 18 months rather than 3 years. This promises to make salmon farming much more efficient, if we ever allow it.

Better fish farming is incredibly important for the future of wild fish on our planet. Wild fish populations have plunged 90-99% all over the planet, and many fish populations have been completely wiped out. Here on the east coast of North America, wild cod populations completely crashed in the 1990s, and by 2004 the World Wildlife Fund predicted that wild cod would disappear completely in 15 years. The situation isn't any better for Atlantic salmon, which are at "perilously low levels." The U.S. declared Atlantic salmon an endangered species in 2000, and added more salmon populations to the endangered list in 2009.

The solution, obviously, is to farm our fish, just like we do with every other food we eat. As I wrote last year:
"We farm all the other animals that we eat. Imagine that we only ate wild cows, or chicken, or pigs. The human race can't be fed by wild animals alone - we're too numerous and too hungry. Sooner or later, we will drive wild fish to extinction, unless we make the switch to farmed fish."
To make fish farming more efficient, we need to apply new genetic technologies to increase yields the way we have with our crops and with domesticated animals.

These new salmon are nothing to be afraid of, but anti-GMO activists have labelled them "Frankenfish" as a transparent scare tactic. I'm neither a fan nor an opponent GMO foods, but knee-jerk opposition to all GMOs doesn't make any sense. Modifying crops to make them more resistant to pesticides, as Big Agriculture firms (Monsanto in particular) have done, strikes me as a terrible use of the technology. "Roundup Ready" corn and soy allow Monsanto to sell more of their herbicide, and make farmers dependent on it. If anti-GMO forces want to boycott this type of genetically modified organism, I'm on their side.

But not with salmon. AquaBounty salmon doesn't promote the use of pesticides or other industrial chemicals. It just makes salmon farming more efficient. The genes added to the salmon are naturally-occurring ones from other fish, so they are still 100% fish. (In contrast, GM crops have genes injected into them from bacteria and other foreign species.) Furthermore, the farming operations by AquaBounty are all inland farms, so there's almost zero chance of the fish escaping into the wild. (I went to one of the FDA hearings last fall and heard a detailed description of the farms.) And even if they did escape, it wouldn't matter because the AquAdvantage salmon are sterile, and couldn't breed with wild fish.

Despite these facts, environmental organizations such as Food and Water Watch are waging a campaign to "Stop Frankenfish,", and spreading misinformation about the science. I was particularly disappointed by the comments from the Union of Concerned Scientists at last September's FDA hearing. Jane Rissler from the UCS compared GM salmon to the massive BP oil spill in the Gulf of Mexico, a ridiculous bit of overstatement. I thought the UCS were the good guys! I agree with their stances on many issues, but they do not speak for me on this one.

I can't resist pointing out that Republicans such as Alaska's Rep. Young claim to hate regulation, and favor the free market - except when they don't. Here we have Young stepping in and imposing regulation to halt the free market under pressure from lobbyists. Not surprisingly, Young is joined by Alaska Senator Lisa Murkowski, but his efforts are also supported by Democratic Senator Patty Murray from Washington, who also has a salmon industry to protect. As happens all too often, politicians are in favor of science only when they agree with it. They're all too happy to pass laws on behalf of special interests, even if it goes against with their supposed political positions on government regulation.

Sadly, environmentalists who oppose GM salmon don't seem to realize that they are acting against their own interests. The same is true of the fishing industry. If they win, the result will be the eventual extinction of many wild fish species, with unpredictable consequences for the ocean's ecosystem. The arguments about the threat posed by GM salmon haven't stood up to scientific scrutiny, so these groups have turned to politics instead. It looks like they might win, in the short term. But if we insist on taking so many of the ocean's fish for our dinner plates, the wild fish will soon be gone.