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"[M]arkedly different characteristics from a product of nature"

So I've finally had the time to read through last week's 156-page ruling in "Association for Molecular Pathology v. US PTO", the case which challenged the patents held my Myriad Genetics on the BRCA1 and BRCA2 breast cancer genes. It's a delight to read, in that Judge Sweet clearly took great pains to understand the molecular biology involved.

There are two basic types of claims in the patents under discussion: some on the "composition of matter" that is the actual, physical molecules encoding the BRCA genes, in purified form, and some "method" claims on the way to use the BRCA sequences to diagnose cancer questions. The method claims were ruled invalid mostly under the precedent from in re Bilski, a Federal Circuit decision which is in the middle of being appealed to the Supreme Court, which pretty much sets the standard for what method claims can cover.

But the really interesting part is the invalidation of the "composition" claims, in which Judge Sweet lays out a clear case for the idea that, as a matter of law, human genes are inherently not patentable.

Everyone agrees that you can't patent a "product of nature" — if there is some naturally-occurring bacterium that has useful properties, for example, you can't discover that this is the case and patent it. Things are a little trickier when you purify some substance found in nature; in that case, it may be possible to patent the resulting purified substance if it has "markedly different characteristics" from the naturally-occurring material. Myriad wants to prevent any other company from diagnosing breast cancer tendencies based on mutations of the BRCA genes, so it needed to argue that its molecules of pure BRCA-sequence DNA has markedly different characteristics from DNA found in your body.

And Judge Sweet found that it did not. His argument (pp. 121–135) comes in three parts, and I like every one of them:
  1. The primary characteristic of DNA — as distinct from just about every other molecule that occurs in nature! — is the information carried in the sequence of Cs, Gs, As, and Ts that make it up. The isolated DNA has just the same information content as the naturally-occurring molecules inside your cells, so this can't possibly be the marked difference. (The ruling nicely addresses splicing and intron issues here too.)

  2. Aside from information content, purified DNA can also be used chemically — as a probe, or as a primer for PCR, for example. This works because of single-stranded DNA's vital chemical property of binding with another strand that is a perfect base-for-base complement. But in that case, Judge Sweet keenly observed, the purified DNA that Myriad uses must be acting identically to DNA already inside your body: the DNA in your cells does the base-pairing trick, and Myriad's purified DNA would be useless if it weren't acting identically to the naturally-occurring stuff.

  3. Finally, there's a very on-point precedent: Funk Brothers v. Kalo, in which the Supreme Court invalidated a patent on a certain combination of strains of bacteria that fixed nitrogen without inhibiting each other. In Funk Brothers, the patent attempted to cover (a) the discovery that these particular strains didn't inhibit each other, and (b) the innovation of aggregating these specific strains together. Part (a) was rejected on the grounds that you can't patent the discovery of some fact of nature; part (b) created a new composition of matter by applying that discovery, but only using "techniques well-known to those skilled in the art" once you know (a). The parallel is that Myriad's case included (a) figuring out which segments of DNA were the genes now called BRCA1 and BRCA2, and (b) isolating those sequence fragments outside the cell. Yep.
I'm in no position to judge the appeals to come, of course. But this opinion looks deeply right to me.
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Whose DNA anyway?

Yesterday, a US District Court judge issued a ruling which invalidated the patents on the BRCA1 and BRCA2 genes. The patent-holder, Myriad Genetics, sells genetic testing services that predict likelihoods of getting breast cancer: women with certain mutations in these genes have an 85% lifetime chance of getting breast cancer, unless they get prophylactic mastectomies, which can bring the risk down to 1%.

That genetic test could only be done by one company, because they were granted the patent on the BRCA1/2 genes. Well, no, technically you can't do that — but you could get a patent on "isolated DNA", once it's extracted from the body and purified, on the theory that at that point it's just a chemical like any other, and you can definitely patent a chemical. In the 156-page opinion (which I haven't read!), Judge Robert Sweet rejects that reasoning and invalidates the patents.

Needless to say, this will be appealed. But wow, if upheld, it's a game-changer.

http://www.nytimes.com/2010/03/30/business/30gene.html
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Hue Knew?

A (age 3½): Daddy, do you know that chameleons can change their color?
me: You're right, they can!
A: Is that because they have rainbows inside them?
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Overachiever

Surely a new entry in the annals of bedtime procrastination should be made for "Daddy, I can't go to sleep, there's dirt behind my ears!"
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Oops Tenenbaum?

So Joel Tenenbaum admitted he'd done all the file sharing the RIAA accused him of, and all the judge asked the jury to decide was the size of the monetary damage. They found him liable for a total of $675,000 for the 30 songs — kind of an arbitrary number, don't you think? Check out this observation passed on by David Post at the Volohk Conspiracy:
One interesting little aspect of the judgment: The jury awarded the record companies $675,000 in damages — $22,500 for each of the 30 songs on which the suit was based. As my colleague James Grimmelmann of NY Law School has pointed out, that's a curious number for the jury to have chosen. The statutory damage provisions of the Copyright Act (17 USC sec. 504) allow a jury to award damages of $750 (minimum)to $30,000 (maximum) for each work infringed (which can be raised, or lowered, by the judge in certain circumstances). The minimum amount that the RIAA could have been awarded, then, would have been a total of $22,500 ($750 x 30 songs). Could it be they got mixed up, and instead awarded plaintiffs $22,500 for each song? Why else would they have chosen that amount? Strange ...
Man, that would make for great numerology, wouldn't it? And yet, it sounds like there's good evidence against this, from a comment on the blog by Ben Sheffner:
I was in the courtroom for the trial, including the reading of the verdict. When the number was announced, I, too, initially thought there might be a mistake, that the jury meant to award the minimum of $750 per work, and that the $22,500 was supposed to be the total award.

However, Judge Gertner said very clearly that the $22,500 was per work, and she asked the jury whether that was accurate. They collectively said "yes." Also, I spoke with one of the jurors shortly after the verdict. From that conversation, I am very confident that the $22,500 per work figure was not an accident or mistake.
So much for that...
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Fortune Favors the... Huh?

We had a pleasant dim sum lunch at Green Tea today — ordering off a menu, not hunter-gatherer style, but tasty nonetheless. And then came the fortune cookies for dessert, in which, I kid you not, A. received:


"The rubber bands are heading in the right direction." What?!

Of course, in this day and age, we're not the only one: Google currently reports about 116 hits for that exact phrase, and it's the second auto-complete suggestion when you type "the rubber b" into the Google search box.

None of the links I followed up made it any less baffling, though...
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The Naming of Things

I love watching language acquisition in kids. A, now two and a half, still provides occasional gems.

So he's been reading D's old copy of A Pocket for Corduroy, with D's name (written in 4-year-old block caps) inside the front cover. We read the name to him the first time, and now that he knows what it says, every time he opens the book he points out to us "That spells Daniel!"

And then the other day D. was in the room — and A. opened the book, and said "Look, Daniel, that spells you!"
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Sixth Sheik's Sixth Sheep's Sick

"List ten things you like beginning with a letter" meme, caught from ruthling. She gave me S.
  1. Sour pie cherries — this year, all of a sudden, available fresh in stores near you! Yum!
  2. Socializing. Thursday night dinner is a high point of my week.
  3. Shakespeare. I'm sad that we missed "As You Like It" on the commons this year.
  4. 1729
  5. Storms, with thunder and lightening. I think "lack of thunderstorms" was my only complaint about the weather in Berkeley. Adam howls in terror of thunder, unfortunately, which has made them less fun this summer.
  6. Sierpinski Gasket, my favorite fractal.
  7. Sleep. Good stuff. I should do it more.
  8. Semi-colons! I love 'em, even if they do get beat up on these days.
  9. (Jonathan) Strange and Mr. Norrell. Wasn't that a great book?
  10. Sex. Heh.

Want a letter?