October 2010 Archives

Surprise Outbreak of Common Sense in Washington DC

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News today that the Justice Department has filed an amicus brief outlining a new position that naturally occurring genes should not be patentable.  The New York Times is reporting that "while the government took the plaintiffs' side on the issue of isolated DNA, it sided with Myriad on patentability of manipulated DNA."  The change in position was evidently prompted by the decision of a federal judge this past spring that certain claims in what are known as the BRCA 1/2 patents should be overturned because those genes are preexisting in nature.  Perhaps Jon Stewart has more influence in DC than we all thought.

I am largely on board with the line taken by the Justice Department.  It is pretty close to my own analysis, as described in my post from last spring: "Big Gene Patent (Busting) News???"  There are, however, a few bits that I am still chewing on, which I will get to later.

First, in broad strokes, the government's brief supports the decision of District Judge Robert Sweet that naturally occurring gene sequences are not patentable, but weighed in against Judge Sweet's analysis that DNA coding for natural genes is not patentable if it has been restructured in an artificial construct but is still the same sequence as occurs in nature.  The most obvious example of the latter is a coding sequence with all introns removed and packed in a plasmid as a cDNA.

Here is the Justice Department's language (the text of the brief is available via the NYT page):

The district court erroneously cast doubt on the patent-eligibility of a broad range of man-made compositions of matter whose value derives from the information-encoding capacity of DNA. Such compositions -- e.g., cDNAs, vectors, recombinant plasmids, and chimeric proteins, as well as countless industrial products, such as vaccines and genetically modified crops, created with the aid of such molecules -- are in every meaningful sense the fruits of human ingenuity and thus qualify as "'human-made inventions'" eligible for patent protection under section 101. (p.9)

...The district court correctly held, however, that genomic DNA that has merely been isolated from the human body, without further alteration or manipulation, is not patent-eligible. (p.10)

...Indeed, the relationship between a naturally occurring nucleotide sequence and the molecule it expresses in a human cell -- that is, the relationship between genotype and phenotype -- is simply a law of nature. (p.10
Here is the meat:

The chemical structure of native human genes is a product of nature, and it is no less a product of nature when that structure is "isolated" from its natural environment than are cotton fibers that have been separated from cotton seeds or coal that has been extracted from the earth.

The scope of Section 101 is purposefully wide and its threshold is not difficult to cross.  See Bilski, 130 S.Ct. at 3225.  New and useful methods of identifying, isolating, extracting, or using genes and genetic information may be patented (subject to the prohibition against patenting abstract ideas), as may nearly any man-made transformation or manipulation of the raw materials of the genome, such as cDNAs. Thus, the patent laws embrace gene replacement therapies, engineered biologic drugs, methods of modifying the properties of plants or generating biofuels, and similar advanced applications of biotechnology. Crossing the threshold of section 101, however, requires something more than identifying and isolating what has always existed in nature, no matter how difficult or useful that discovery may be. (p.11)

It might seem that the Justice Department gives back a lot of power to those who hold patents on natural genes by including cDNAs (with introns removed) as patentable material.  This would seem to give patent holders a lock on the human proteins those genes encode, because the most common way to make a protein is to use a cDNA (or similar) to express a protein in a host like E. coli or yeast.  So unless people come up with a good way to cause overexpression of human proteins from native genes via mechanisms that chop out the introns -- and some methods like that do exist -- the patent seems to block use of the protein.

But I am not sure that this brief gives any succor to those hoping for patent protection of a genetic diagnostic.  Those diagnostics generally work by using a short sequence of the gene in question as a PCR primer to find (or exclude) particular sequences of clinical interest in a patient's genome.  Those primers generally can be found in regions of DNA not interrupted by an intron, or can include the intron in the primer sequence, which means that the primer can consist of sequences that were preexisting in nature.  Only if the primer has to be composed of a sequence that -- in nature -- is interrupted by an intron but is only found in somebody's edited cDNA library without that intron would a patent protect the diagnostic assay.

A penultimate thought on the brief: I am still pondering whether the Justice Department lawyers, in their extended discussion of DNA as information carrying medium, got their analysis right.  I will have to read the brief again.  And perhaps again after that.

Finally, the brief leaves most of my previous conclusions intact, namely that the biggest impact of Judge Sweet's ruling that natural sequences cannot be patented may be for work in organisms other than humans.  From my post last May:

...the rest of the biotech industry shouldn't be concerned about this ruling, frankly.  They might even celebrate the fact that they now have access, potentially, to a whole bunch more genes that are naturally occurring.  Not just in humans, mind you, but any organism.  This opens up a rather substantial toolbox for anybody interested in using biological technologies derived from viruses, bacteria, plants, etc.  If it holds up over the long run, Judge Sweet's decision should accelerate innovation.  That is definitely a good thing.
Now we wait for what the appellate court has to say.

The Economist has just posted my invited comments on their current debate: "This house believes the development of computing was the most significant technological advance of the 20th century."

As with the last time I was invited to be a "guest speaker" (just one of the oddities of horning an Oxford-style debate into an online shoe), I have difficulty coloring between the lines.  Here are the first couple of graphs of today's contribution:

The development of computing--broadly construed--was indeed the most significant technological advance of the 20th century. New technologies, however, never crop up by themselves, but are instead part of the woven web of human endeavour. There is always more to a given technology than meets the eye.

We often oversimplify "computing" and think only of software or algorithms used to manipulate information. That information comes in units of bits, and our ability to store and crunch those bits has certainly changed our economies and societies over the past century. But those bits reside on a disk, or in a memory circuit, and the crunching of bits is done by silicon chips. Those disks, circuits and chips had to improve so that computing could advance.

Progress in building computers during the mid-20th century required first an understanding of materials and how they interact; from this knowledge, which initially lived on paper and in the minds of scientists and engineers, were built the first computer chips. As those chips increased in complexity, so did the computational power they conferred on computer designers. That computational power was used to design more powerful chips, creating a feedback loop. By the end of the century, new chips and software packages could only be designed using computers, and their complex behaviour could only be understood with the aid of computers.

The development of computing, therefore, required not just development of software but also of the ability to build the physical infrastructure that runs software and stores information. In other words, our improving ability to control atoms in the service of building computers was crucial to advancing the technology we call "computing". Advances in controlling atoms have naturally been extended to other areas of human enterprise. Computer-aided design and manufacturing have radically changed our ability to transform ideas into objects. Our manufactured world--which includes cars, aircraft, medicines, food, music, phones and even shoes--now arrives at our doorsteps as a consequence of this increase in computational power.

I go on to observe that computation is already having an effect on food through increased corn yields courtesy of gene sequencing and expression analysis.

Like so:

Biodesic_US_corn_yield.pngClick through to read the rest.

The Sims: Garage Biohacking

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This week's Nature is carrying a Feature by Heidi Ledford on garage biotech, "Life Hackers" (the PDF has additional photos). I make a little appearance.  So do Biodesic and the Lava Amp.  Then I get turned into a Sims character.  Here are a few posts about "Carlson Curves".

I guess I will have to pull that cap out of the drawer and start wearing it again.


Hey look -- I have an Idea!

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On my head, that is.  Not in, alas, but on.  That's the way it goes, some days.  But at least I am pressing forward.  Or the idea on my head is.  That is what the sign says, anyway. 

carlson.jpgWeek before last, I spent an enjoyable couple of days at The Economist's Ideas Economy: Human Potential 2010.  I'll post the video when it is available.

Among the most interesting things I heard: Richard Florida says that the "creative sector" has never been above 5% unemployment, and that sector now constitutes 30% of the US workforce.  Here is his presentation:

I also had the chance to meet Vivek Wadhwa (very smart fellow), whose recent fascinating blog post on whether job creation comes from big companies or startups I have been pondering for weeks.  Here is a snippet from the post: "Startups aren't just an important contributor to job growth: they're the only thing. Without startups, there would be no net job growth in the U.S. economy. From 1977 to 2005, existing companies were net job destroyers, losing 1 million net jobs per year. In contrast, new businesses in their first year added an average of 3 million jobs annually."

The differing impacts of startups and established companies on the economy and on innovation are much on my mind these last few months.  Unconventional innovation tends to come from startups, and often from garages, and as I examine in my book that is precisely where we should be looking for new biological technologies.  I've been pondering what it takes for a small company developing a biological technology to succeed in industries dominated by Goliaths.  Microbrewing provides a great existence proof of the potential.  Garage biology is here.  Hang on to your hats.