In contrast to so many current political debates–climate change, abortion, health care–intellectual property law often appears to occupy a rarefied perch accessible only to patent experts, clerks and judges.  Patent policy is unnervingly complicated, with deceptively simple patent laws that are burdened with complicated webs of judicial interpretations.  It is little wonder, then, that most of us take for granted our government’s policy of granting and enforcing patents–if only as a cognitive coping strategy.  This complexity-induced apathy, by the way, suits patent lawyers just fine, and might be acceptable most of the time because, as in the case of an undersea oil-well blowout-preventer, patents may work pretty well, except when they don’t.

Patents on human DNA sequences (at least 20% of our genes are locked up) are increasingly viewed as deterrents to a new generation of genetic-diagnostic technologies, as well as to basic biomedical research itself.  That is the belief held growing number of physicians, researchers and legal experts, as well as this author.

Why do I use the word, “belief”?  Simply put, though the specifics of patent law are largely excluded from raucous public debate, the costs and benefits of patent reform are nevertheless as hypothetical, and worthy of argument, as in the cases of health-care reform, climate-change strategy or nuclear disarmament.  Proponents of the current system claim that the current patent regime is nothing less than vital to innovation.  As in any debate, those in favor of the status quo can point to experience, arguing that current technology would not have arisen without patent protection.  The apparent conservatism of this position belies the fact that our current patent regime–and any patent regime–is an artificial, legislated concept.  Defending it from alteration by claiming that it is an optimal policy is, thus, rationally unfeasible.

Some of the current momentum behind the reform of gene patent policy results from evidence that future genetic tests will be hamstrung by patents held by universities and companies–patents that give these organizations control over virtually any use of the human genes they claim.  That is the conclusion shared by a recent report from the HHS Secretary’s Advisory Committee on Genetics, Health, and Society (SACGHS).  The prediction that patents will impede progress may not, in itself, be sufficient reason to make changes to the policy.  However, the Committee points out the exceptionalism of patient care:

Indeed, in the realm of commodities or consumer electronics it may well be that dramatic harms and a profound lack of benefit should be required to compel any recommendation for change. But genetic tests affect patients’ lives and health.  Thus, the current system’s net negative effects on test development and patient access to these tests argue strongly for the narrowly tailored changes that are proposed.

These proposed changes are two-fold: (1) a diagnostic test exemption, allowing human genes to be analyzed even if they are protected from other uses (i.e. as therapeutics) by patents; and (2) a research exemption, allowing any use of patented genes in the pursuit of biomedical research.  This second exemption may come as a surprise to many, even to scientific researchers themselves.  Many scientists I’ve talked to either assume that common law (or common sense) already exempts their work from violating patents (mostly because it is unbelievable to many genetic researchers that DNA sequences could be patented in this way).  However, court decisions have decreased the research exemption to nil.  The SACGHS report argues for the clear enunciation of the legality of research on patented genes, if only to promote the rule of law.

Agree or disagree with these proposals–that is their major benefit!  They give something concrete to agree or disagree with to those citizens (especially relatively apolitical research scientists) who may have felt sidelined by the complexities of patent law debates.  Furthermore, gene patents are a natural starting point for a more general debate over patent policy because they affect anyone who intends to ever get medical care.

I’m back from defending my thesis (apparently successfully), just in time for  big news in the biomedical patent world.  The summary judgment ruling against Myriad Genetics and its BRCA gene patents, announced yesterday, brings up many questions about the future of patents covering genes and, potentially, other biological phenomena.   Obvious, however, is that the US patent office (USPTO) was shamefully uncritical of the claims from the original patent applications, a problem that extends to many, many similar patents.

Valid patent claims are meant to be narrow and novel but, by claiming invention of a short (15 nucleotide) DNA sequence, the BRCA1 patent clearly violates these criteria.  This is the conclusion that Duke researchers elaborate in a recent investigation, where they elegantly demonstrate what should be obvious to anyone with a minimal understanding of statistics (which was clearly not the case for the patent examiner).  The BRCA1 patent claims (in language similar to many gene patents): “An isolated DNA having at least 15 nucleotides of the DNA of claim 1″ (claim 1 being the protein sequence BRCA1).  Thomas B. Kepler, Colin Crossman, and Robert Cook-Deegan at Duke calculated that BRCA1 contains 5,575 individual 15-nucleotide sequences (15-mers).  Since the same protein sequences can be encoded in different DNA sequences, there are actually 1.6 × 10⁶ 15-mers that could encode the patented sequence of BRCA1.  As there are only 1.07 × 10⁹ possible 15-mers (DNA only has four letters), the patent could actually cover 1 in 600 of all possible 15-nucleotide DNA sequences (1.6 × 10e6/1.07 × 10e9).  The authors calculate that an average human gene would have 15 of the 15-mers covered by the patent! It should be noted (and this is a compliment, not a criticism) that this theoretical analysis requires nothing more than a calculator.  Searching for DNA or protein sequences can be done, for free, by anyone with a web browser; it was a bit more difficult, but not impossible, when the Myriad patents were filed in the late ’90s.  The merit of patenting such sequences may be debated as a point of policy; their novelty and uniqueness may not.

The court didn’t look into such specifics, but rather at the broader applicability of patent law to genetic information   Yesterday’s ruling focuses on whether the BRCA patents fall within the realm of “products of nature”, which have been held to be non-patentable.  The court found the genes to, indeed, be such a natural product.

Though there will certainly be much to debate in the ruling (which, no doubt, will be appealed), one of my favorite parts is a not-so-subtle rebuke of the USPTO, as well as Myriad’s argument that the government’s wisdom in granting patents should be respected:

The Federal Circuit has previously held that it owes no deference to USPTO legal determinations.  See, e.g., Arnold Pship v. Dudas, 362 F.3d 1338, 1340 (Fed. Cir. 2004) (“This court reviews statutory  interpretation, the central issue in this case, without deference.”).  While Congress has created a presumption of validity for issued patents, approximately 40% of patents challenged in the courts have been found invalid, demonstrating that this presumption is far from absolute.

yalepatents.org is on temporary hiatus while I finish my dissertation, but I thought I’d share some relevant sources of procrastination from the past few weeks.  First of all, On Point, the news program from WBUR-Boston, hosted a discussion on gene patenting and the Myriad/BRCA case.  Tom Ashbrook and his guests hold an accessible discussion, providing a nice starting point for those interested in gene patenting and biotech industry.  Notably, Chris Hansen of the ACLU defends his organization’s side in the case, arguing that a ruling in favor of the plaintiffs will not hinder biotech patents, but will promote competition and innovation in the industry.

Getting away from the economic immediacy of biotech intellectual property, some recent literature begs the question: what is professional bioethics good for?  Some of the recent discussion has been prompted by a new book, Observing Bioethics, by Renee C. Fox and Judith P. Swazey.  Though I look forward to reading it as soon as possible, Sally Satel provides a provocative review in The New Republic. Satel, a resident scholar at the conservative American Enterprise Institute, has written that the political and professional wing of the bioethics movement (in government and on hospital staffs) has distracted attention from its academic soul, transforming a philosophical field into an activist one.

Arriving as populist movements battle healthcare reform, this critique of bioethics is quite timely.  However, the anti-bioethics position conveniently, and attractively, avoids anti-elitism.  Satel argues in a recent essay from the Hoover Institution that bioethicists simply don’t have an expert advantage over average citizens the way geologists do in the climate change debate.  Rather, when they participate in the political discussion or on hospital review boards, “their value is mainly cosmetic or bureaucratic”.

Among other things, the healthcare debate has revealed to a large audience that our attempts at shaping the drug market are a cats-cradle of contradictory regulation.  A short history: Academic scientists who research future drugs are well aware of the Bayh-Dole Act which, in 1980, enabled researchers to patent and profit from taxpayer-funded innovation.  It was a bold attempt to encourage the movement of ideas from universities into the marketplace, where they can benefit society.   Meanwhile, the same federal government, cognizant that patents are actually monopolies designed to boost drug prices, realized that this effect must be mitigated to keep healthcare costs down.  In 1984, the Hatch-Waxman Act enacted regulations to encourage generic-drug manufacturers (representing the competitive threat that patents were meant to address in the first place) to contest the original patents in court.  How would the government get generic manufacturers to challenge the brand-name patents?  By promising the generic manufacturer a second round of protection from competition in the event it wins the dispute.  Today the Federal Trade Commission releases its new report, complaining that brand-name and generic drug manufacturers have found a profitable loophole by entering into agreements to avoid fighting over patents in the first place.  The proposed remedy?  The FTC wants to enact new legislation, making these anticompetitive agreements (over patent monopolies) illegal.

Michael Kinsley’s “Cut This Story!” is a must-read for anyone who writes (or reads) in 2010.  The article, in this month’s Atlantic, offers the latest diagnosis on the decline of print media: the excessive wordiness of traditional newspaper articles.  Long, comma-laden sentences, once useful for providing context in the slow, print-only world, now only distract from the the modern, networked reader’s main goal: extracting useful bits of newsworthy information.

Kinsley writes of the print-journalism trade, but in his description of the modern information-seeker, he identifies a general problem yet unsolved by internet technology.  People and software become better and faster at searching through data–articles, databases, images–but accessing that data is still like using a glorified card catalog: entering in a search term, finding a set of web pages that might be relevant, and then wading through content to find an answer.  The goal of computer scientists is to turn the internet into an intelligent research librarian, able itself to sift through information to answer questions directly.  The so-called “semantic web” promises to transform the way we interact with information, especially in fields like the life sciences, where the research community has been side-swiped by a flood of interdisciplinary data coming from new technologies.  However, for the semantic web to become a reality is going to require a revolution in the way scientists and others share data that is currently proprietary, and, even among government-funded academics, the incentives for opening up such data are still missing.

Many talk about the “disruptions” to media, commerce and communication caused by the online, computerized world.  Compared to the advanced information network represented by the semantic web ideal, however, our current internet seems fairly tame.  Today, new knowledge is still mainly transmitted in media forms that would have been largely familiar in 1990, except in quantity and access speed.  In science, freely available, web-only journals are a recent innovation, but the fundamental medium of the journal article has evolved little since the middle of the 20th century, if not before.

Simply put, the semantic web is (or will be) “semantic” because information content is tagged in such a way as to organize and connect it with other related information.  The intent is to embed these content descriptions in a standardized way that is both intelligible to humans and also efficiently interpreted by computers.  It is meant to be a broad movement and guiding philosophy for anyone who wants to put information online and make it useful for future “semantic” applications (such as intelligent, interpretive search engines of the future).

For science, the semantic web promises to solve the barriers in communicating the overwhelming abundance of data that is produced from modern technologies, such as ultra-high-throughput DNA sequencing.  Ideally, it will provide a way for scientists to knit together large amounts of data from different projects in a way that other researchers will be able to query through it, asking questions and receiving intelligent answers.  And, because well designed semantic tags should slice through jargon, the semantic web will be ideal for nonspecialists–for instance, non-scientists who wish to investigate pharmaceutical interactions or climate research.

Tim Berners-Lee, the internet pioneer and semantic web visionary, wrote in 2001 of the enormous change in the scientific publishing model represented by the semantic web.  An important consideration is that semantically-tagged content is only as useful as the careful knowledge curation that goes into building it:

The concept of machine-understandable documents does not imply some magical artificial intelligence allowing machines to comprehend human mumblings. It relies solely on the machine’s ability to solve well-defined problems by performing well-defined operations on well-defined data.

Thus, building this new information network requires experts to input their data into pre-established semantic frameworks, where new information about molecular interactions or genetic traits can be read by database software itself.  At the least, this process would add a new computer-readable component to traditional journal articles.  More likely, it would provide a way to share information that would eventually side-step journal publication completely.  Berners-Lee predicted that the semantic web could based, at first, on traditional articles but would evolve to a model that is decentralized and side-steps the current process of journal publications:

Papers that include this new mark-up language will be found by new and better search engines, so users will be able to issue significantly more precise queries. More importantly, experimental results can themselves be published on the web, outside the context of a research paper. So a scientist can design and run an experiment, and create an emerging web page containing the information that he or she wants to share with trusted colleagues.

As traditional publication loses importance, new questions about data integrity arise: how do you peer-review data incorporated into the semantic web, or otherwise ensure trust?  Just as significantly, it adds layers of complexity on assigning attribution to research data.  Academic scientists judge each other on the quality and quantity of the journal articles they produce.  In the scientific world, journal publication is the standard for scientific success.  If science is to benefit from the futuristic information environments promised by the semantic web, which relies on the prompt and full disclosure of data analysis, it is going to require sufficient incentives for individual investigators to contribute.

New incentives or mandates will be necessary to overcome the increasingly burdensome task of preparing highly complex research findings for machine-readable databases.  Formatting findings to be machine-readable might be feasible in the case of a small-scale study of the interactions or regulation of a single molecule or complex.  But what about experiments using new technologies that is based on tens of thousands (if not millions) of new pieces of information, such as the analysis of a whole transcriptome?  Who is going to curate this information for the semantic web?

There is an even more fundamental issue regarding the full release of raw data, and it must be resolved before data-intensive findings may be incorporated into the semantic web.   Currently, biomedical researchers often amass data from a number of sources–both small-scale and large-scale–before summarizing, analyzing and communicating it in the form of the journal article.  Currently, in many fields, it is common for a research paper might be based on gigabytes (if not terabytes) of data, but in a the journal article this data, after extensive computer processing, is condensed into several graphical figures and text.  Since they don’t fit into the traditional format of a journal article, the original raw data become de facto proprietary–in some cases merely because there is no established clearinghouse for it.  Such a situation is becoming increasingly common–just last week, I was attempting to compare new deep-sequencing data to similar, large datasets summarized in recent publication.  The recent (government-funded) publication, however, had no link to their original data.  Sure, I could email the lead author to get access to the data, but then they would know what I’m working on before I get a chance to publish.

Not providing a way to access the primary data behind a publication runs counter to the policies of most funding agencies (e.g. the UK’s Wellcome Trust), but in the situations I’ve encountered, it was not likely that the authors or journal were acting particularly malevolently.  Even in 2010, it is logistically difficult to post many gigabytes of data on public servers.  Moreover, most scientists are accustomed to submitting journal articles with 3-5 figures containing gels and microscopic images (and perhaps video) as the data supporting their claims, relying on their peers to trust their analysis.  Submitting raw digital data (whether from deep sequencing or high-resolution microscopy) is a new paradigm for accountability that diminishes, if only superficially, the author’s authority.

One way to ensure that new forms of data are available (and eventually incorporated into semantic-based information structures) may be with a centralized, government mandate.  The past few years have seen new rules requiring government-funded research to be freely available to the community within a certain time-frame after publication.  The Obama administration is currently drafting new requirements for the public release of government-funded research data, as part of its general initiative to open access to government data.  However, the current federal effort is still focused on ensuring public access to traditional publications, an effort that began a few years ago at the NIH’s PubMed Central.

As the U.S. Office of Science and Technology Policy puts it in a recent invitation to comment on publication access policies: “Access demands not only availability, but also meaningful usability.”  Organization of new research knowledge into semantic-web repositories represents the future of “meaningful usability”.  Will government be able to mandate that scientists contribute data to the semantic web, when that effort simultaneously disrupts the traditional publication process on which reputations are based?  To get the research community to take full advantage of the semantic web and related knowledge-organizing technologies will require a total rethinking of the incentives for knowledge sharing–one that replaces the rewards currently conferred when a peer-reviewed article is accepted for publication.

In a post last week, I was critical of the Connecticut Stem Cell Program, a 4-year-old fund for research grants that was cut out of the current budget proposal.  My main criticism was that $10 million/year and an ad-hoc oversight board are not sufficient to justify the praise and hopes directed towards the program by state politicians–such programs are a distraction from the task of rebuilding the Connecticut economy.  The larger issue, however, is whether states competing against each other to offer research incentives is really the best use of tax revenue in general.  A new essay in the Chronicle of Higher Education argues that investing in technology research is a risky game for states, and that the federal government should step in and increase research funding in their place.

The article, written by three professors from the University of Michigan, describes the declining state-funding of research universities, and the need to return to a more centralized model for expanding education and innovation.  States, originally the beneficiaries of the federal land used to build the great “land-grant” universities (including UConn and the Connecticut Agricultural Experiment Station), are currently slashing costs like student aid and capital investments.

Why is state funding for higher education disappearing?  The shocking budgetary situation in most states has resulted in cost-cutting throughout public programs.  The authors point out, however, that local investment in research is also inherently risky:

The model of state-based support of graduate training made sense when university expertise was closely tied to local natural-resource bases like agriculture, manufacturing, and mining. But today’s university expertise has implications far beyond state boundaries. Highly trained and skilled labor has become more mobile and innovation more globally distributed. Many of the benefits from graduate training—like the benefits of research—are public goods that provide only limited returns to the states in which they are located. The bulk of the benefits is realized beyond state boundaries.

Any state politician claiming that high-tech research incentives will resurrect our local economy is in denial about the risks of these investments.  It takes much more imagination to devise state programs to improve less tangible things like infrastructure and lifestyle–investments that will stick around and attract the high-earning employers and employees that the Nutmeg State so desperately wants.

Bono, the lead singer of U2 (and the leading anti-poverty sunglasses model), has little apparent connection with biomedical patents.  However, featured prominently on the Times Op-Ed page last week was his version of the 10 ideas most likely to “change our world” over the next decade.  Number 2?  Enforcing intellectual property rights. Many people probably wonder why that seemingly simple priority is the slightest bit controversial (I used to be one of them).  This confusion is rooted in the pervasive, often unconscious, and wholesale embrace of the role of the state in enforcing claims to ideas and knowledge.  Indifference toward our government-imposed model of intellectual property has enormous implications for the status of knowledge, the relations between government and industry, and the future of a technological society.

Photo: David Shankbone

Maybe I’m taking Bono a bit too seriously.  (In all honesty, I haven’t really thought of him much since my days as a 14-year-old Achtung Baby fan).  In spite of his many good intentions, his status as an official, though occasional, Times Op-ed writer has seemed like an embarrassing attempt at hipness by the paper.  At least the Times hasn’t run an entire issue dedicated to Bono’s causes, as the UK’s Independent did in 2006.  From any reasonable perspective, the argument he makes about enforcing intellectual property rights is cringe-worthy, and reveals a surprising lack of political sophistication from someone who regularly meets with world leaders.  Claiming, as he does, that we should model a music-sharing crackdown on China’s internet censorship techniques, by encouraging the government to “track content” as it attempts to do with child pornography, is downright scary.

Scholars of law and society have said it before, much more eloquently, but our collective attitude toward the way our government administers knowledge and ideas is simple: indifference.  This contrasts starkly with many other issues that get people riled up: healthcare legislation, global warming, red-light cameras, terrorist investigations, vaccinations.  Even (or especially) among the tea-party masses supposedly surging up in a populist roar, it is clear that a large portion of our society cares about way the state treats them, and has some notion of their ideal government.  If the issue is guns or estate taxes, different groups are readily massed to debate the benefits and evils of government regulation.

Except among an echo chamber of legal and tech nerds, however, intellectual property is one gigantic role that government has carved out for itself that no one else really seems to notice, or care about.  As Bono points out, technology has brought huge changes to the ways that knowledge and technology is created and disseminated.  He fails to point out the equally gigantic power the government has taken, with surprisingly little public outcry, to protect those who would be considered “special interests” in any other political battle: copyright and patent holders.

There are several factors that have led to this situation, but the blame lies with the public itself.  There has been excellent PR on the part of those that benefit from lengthy copyrights and patent tangles–content owners, attorneys and other powerful institutions.  And, as imperfect and irrational beings we, ourselves, are confounded by this thing called intellectual property.  In the context of copyrights, James Boyle terms it “cultural agoraphobia”: a natural human tendency “to undervalue the importance, viability, and productive power of open systems, open networks and nonproprietary production.”  (For more, read his excellent book, The Public Domain).  He and others have also pointed how difficult for us to determine ownership, if any, of knowledge and content that flow as easily as bits, since we still mostly among physical property.

This is not a diatribe against the government’s role in maintaining a system of intellectual property rights.   However, I’ll give my own prediction for the next decade’s “big idea”: unless the public asks much more serious questions about how intellectual property rights are created and enforced, those who profit from them will see to it that our government expands to their aid, at an incalculable cost to all of us.

I’ve previously raised the possibility that, in its quest for economic revitalization, state governments are not suited to pick and choose among emergent industries to invest in, much less make the risky decision to invest in unproven technologies. Now I wonder whether some taxpayer-funded initiatives to attract high-tech jobs to Connecticut amount to anything more than glossy-sounding buzz-words thrown out by policymakers who have very little idea how to get the lagging Nutmeg State back on track.

Exhibit A for exciting-to-talk-about but dubiously significant state job-growth efforts is the Connecticut Stem Cell Research Program. The state initiative came up on Tuesday, in a discussion of the state job situation on Where We Live, WNPR’s daily Connecticut news program (disclaimer: my wife, Libby, is a producer for the show). Stem-cell jobs were one of the few items that the state politicians and economist on the show were particularly upbeat about.   Is the stem-cell program really something worthy of so much hope and attention?

First of all, no one is jumping out of their seats to say anything bad about an emergent scientific field that has enormous potential to cure many diseases. (Though I must interject that biomedicine has a history of “magic bullets” that didn’t really pan out; real advance comes from broad efforts combining many independent–and often iconoclastic–researchers and disciplines.)

In the midst of a depressing discussion of Connecticut’s daunting problems (regulatory instability, high energy costs, poor infrastructure, a 20-year slide in employment), one of the show’s guests, UConn economist Fred Carstensen, brought up the stem-cell initiative, in part because its continued funding is in question in the new, downsized state budget.  He described it as “phenomenally successful…we’ve had some extraordinarily important breakthroughs.”  He cites the fact that “we literally have had world-class researchers moving to Connecticut and looking to move to Connecticut because of our stem-cell initiative”.

Stem-cells funding may have brought a few researchers and their labs to Connecticut, and encouraged good ones that are already here to apply for more funding and, perhaps, hire a few new postdocs or technicians to perform research.  But Yale already has over 270 different labs working on biomedical science.  In 2008, it received $300 million from the NIH alone, not counting that from other major funders like the Howard Hughes Medical Institute.  UConn took in over $70 million from the NIH last year.  The total outlay of the Connecticut Stem Cell Initiative?  Ten million dollars per year.  Denise Merrill, the majority leader of the state house of representatives said that with stem cells, the state brings benefits “for a relatively small amount of money”.  The characterization of price is true, but what benefits do $10 million bring when spent on stem-cells instead of, say, transportation or inner-city education?

Proponents argue that stem-cells will become a centerpiece of some future, high-tech Connecticut economy.  However, a brief history of turbulent stem-cell politics brings this aspiration into doubt.  Connecticut began the stem-cell initiative in 2005, hoping to get a corner on the research after the Bush Administration had announced tight restrictions.  However, the Nutmeg State was not alone.  Our neighbors in Massachusetts, which considerably outranks Connecticut in the biotech sector, got in on the act, pledging $100 million over 10 years.  California voters approved a $6 billion state stem-cell initiative; unsurprisingly, perhaps, this program has been criticized for its enormous cost and lax oversight.

The problem with these programs is that they represent frenzied competitive maneuvering between states, but with dubious outcomes, especially for those that, like Connecticut, didn’t put that much on the table in the first place.  In fact, our tax dollars are already hard at work on biomedical research in a very serious way, through the NIH and other, federal, entities.  Compared with our centralized national programs, state science initiatives, on the other hand, are heavy with ambition but starved for good organization and sufficient money to fund more than a few research goals.

In hindsight, the stem-cell money appears to have been thrown at a good, celebrity-supported cause, but with uncertain prospects for Connecticut.  We absolutely need research investment to create future jobs.  I say “future”, because the short-term expense of research is not only in personnel, but in equipment, expendables, and energy, which might provide jobs where they are manufactured or generated, but that is unlikely to be Connecticut.  Why should we bet that Connecticut research dollars will stay, as future employment, in Connecticut if the research might be spun-off more efficiently in one of the big biotech regions already humming with infrastructure?

At its best we can hope that a bit of good science was supported by the CT stem-cell initiative.    At worst, the state stem-cell program is a rather pathetic talking point for politicians without the nerve to tell their constituents how poorly their state competes for jobs compared to other regions.  If policymakers want to use the state budget resources to engineer our way into the future, they should focus on the tasks that state government does best.  Oh, hold on, perhaps the Connecticut should figure out how to do the things it should be doing best first, instead of waiting for a small investment in stem cells to grow into a fresh, economic heart-transplant for the state.

• Update: John Dankosky and the folks over at Where We Live put up this post on their blog that summarizes the main discussion points in Tuesday’s “jobs” show.   The show included an interview with an official from Virginia, which leads the 37 states doing a better job than Connecticut in growing their economies, according to one survey.

I entered my PhD program in cell biology with some knowledge about molecular biology, a dose of scientific ambition and a shiny new Powerbook G4.  For the first half of my PhD research, the laptop mostly idled on my desk, waiting patiently for me to take breaks from my bench-work to check email, search for technical literature or assemble figures for a presentation.

It was after a year or two of such “wet-lab” work–biochemistry and microscopy–that my colleagues and I encountered pressing biological questions that, we hoped, might be answered using a new technology: “deep” DNA sequencing.  This process, much-anticipated in the past few years, allows for the simultaneous, parallel sequencing of millions of short lengths of DNA.  A single run produces gigabytes of pure data; analyzing and displaying that data in useful ways required me to revisit my relationship with my computer.  Beyond being my robotic secretary, research assistant and conduit to YouTube-style procrastination, my computer suddenly became the fulcrum of my research.

In short, I was introduced to the world of bioinformatics–and by that I don’t simply mean the protocols and theory of digital data analysis applied to biology.  Computational biology is, significantly, a field composed of real computer geeks more aligned, culturally, with the modern silicon-based tech sector than with the traditions of biological science.  As a young biologist, communicating with bioinformaticians finally opened my eyes to technological and economic trends in software and networking.

Leaders in the field have long been dedicated devotees to the open-source model of software distribution, and have developed a software ecosystem based on collaborative communities of developers.  Accessing the collective knowledge of these communities is as easy as joining an email list or online forum.  For the purposes of even advanced data analysis, basic Perl scripting, command-line Linux administration and the willingness to find information online are the only costs of entry.  Some of the most useful and active open-source bioinformatics environments include BioPerl and Bioconductor (for the R statistical software).   There are many smaller, single-purpose tools (such as the fast alignment programs that have grown out of the sequencing revolution) that function on the same premise: an online community of users contributing advice and improvements based on access to source code.

Academic biomedical scientists, which I use as a catch-all term to encompass researchers in fields like molecular and cell biology, immunology and infectious disease research, do not usually consider themselves technologically conservative.  However, the reality is that many experiments rely on decades-old technology–gel electrophoresis, microscopy, automated cell-sorting.  After all, time-tested techniques have been carefully honed through generations of scientists, and their results are easily judged during peer-review.

My point is that inherent conservatism of scientists (no different from their peers elsewhere in academia) predisposes them to an ignorance toward the newer, technology-enabled forms of collaborative research represented by bioinformatics–and advanced information technology in general.  Obviously, developing code to analyze data is a much different process than experimenting on living systems in the lab–not to mention trying to convert biological knowledge to improvements in drugs and diagnostics.  However, as a younger generation of biologists responds to the computational demands of processing enormous piles of data, it will be interesting to see whether the FOSS ethos of academic bioinformatics pollinates the more traditional world of the wet-lab.

In their book, Patent Failure, James Bessen and Michael J. Meurer provide a sober critique of the U.S. patent system, focusing on doctrinal and technological shifts that have fundamentally disrupted the efficiency of the rights we bestow on technological inventions.  Their conclusion: during the last decade, our patent system has broken down because it failed to operate as a transparent system of property rights for inventions.  As a result of, among other factors, the huge cost of identifying relevant, competing patents–often claiming broad, early-stage innovations–the authors argue that patents cost industry more than they deliver, especially in high-tech sectors.

Bessen, a former software executive and currently lecturing at Boston University and Meurer, a law professor at BU, base their evaluation of the modern patent system on cost-benefit estimates for inventors of different scales in different industries.  Their conclusion, that patents do not provide the clear boundaries that are necessary in a workable system of property rights, is based heavily on a comparison of different industries.  Their research indicates that one modern industry where patents are particularly efficient–in that they impose very little cost on the profits they provide–is the chemical industry, where there is very little to argue about when it comes to a specific molecule that is patented.

Though they focus on software patents as an example the deleterious effects of overly vague patent claims, they highlight biotechnology as an industry similarly fraught with bad patent practices.  They blame the legacy of the Bayh-Dole act, encouraging universities to patent basic research, as well as a reduced requirement that patents be shown to have “utility”, a legacy of sometimes-conflicting rulings by the Federal Circuit during the ’90s.  The reduced burden of demonstrating that an invention is useful, or that it has been developed beyond the discovery stage has at least two negative implications: (1) that patents on basic scientific discoveries have become overly vague and discouraging to future inventors and (2) an oft-cited “flood” of patents has overwhelmed both the patent office and the ability of inventors and firms to search for patents that might compete with their ideas or research.

From the perspective of biomedical patenting, Bessen and Meurer’s contrasting characterization of chemical-pharmaceutical patents from those in the  biotech/biologic drug industry highlights one broad confusion over drug patents.  Contrary to many claims, the apparent success of traditional chemical patents does not portend the same happy fate for patents on complex biological drugs, much less patents on gene sequences or discoveries about basic biological systems.  When patent apologists claim that patents are essential for the drug industry, their enthusiasm may be outdated.

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Book – Patent Failure: How Judges, Bureaucrats, and Lawyers Put Innovators At Risk, by James Bessen and Michael J. Meurer (Princeton, 2008).