Scientist - test tubes

(I'm not) working for the clampdown

Researchers are trying to make biotechnology open source amid concerns that corporate interests will block their work with patents.

In 2003, Democrat congressman Dennis Kucinich proposed, in political magazine The Nation, the idea of 'public patents'. He was writing after the US Centers of Disease Control and Prevention said that it wanted an exclusive patent on the SARS virus in order to guarantee that the "discovery remains in the public domain".

Several laboratories filed for US patent applications for SARS virus genes, presenting the prospect of a situation where drugs to treat the disease might incur licence fees. "Faced with global public-health threats like SARS we must stop foolishly pandering to the pharmaceutical industry," Kucinich wrote.

"If smart people across the world can do this for computers, can we not do it for the sake of public health?" Kucinich concluded, with a nod to IT's open-source revolution.

The issue of patent-based monopolies in the drugs business became one of the campaigning issues for the Swedish Pirate Party, which won a seat in the European Parliament, ostensibly on the back of revulsion at anti-filesharing legislation introduced by the Swedish government.

Dean Baker co-director of the Center for Economic and Policy Research, argued last year that the situation with intellectual property in healthcare resulted in American citizens paying through the nose for medication. "The most remarkable part of this story is that we do not even have a public debate on how we finance drug research," he wrote.

People such as Baker have outlined alternatives to the current situation, in which, having paid for the research, pharmaceutical companies get to enjoy a monopoly supply situation for 20-odd years, assuming that the resulting treatment actually works. This is the pact that governments of industrialised nations made with inventors more than a century ago: in exchange for revealing trade secrets, inventors are protected from competition for a finite period of time.

Patent thickets

The problem that faces researchers is that a patent filed for one purpose can be used to block those working on a different project. Build up a collection of those and you have a 'patent thicket' - a body of IP that blocks competitors from working in spaces where one or more of those patents could be applied.

Biotechnology patents are not just a problem in healthcare, claim activists such as Pat Mooney of the Canada-based ETC Group, which campaigns against technologies such as genetic modification.

At a public meeting on IP in biotechnology at the Woodrow Wilson Center in Washington DC earlier this year, Mooney pointed to the example of the seeds industry. The development of hybrid corn after the dustbowl of the 1930s showed how genetic alterations, albeit made before recombinant-DNA techniques appeared, could be harnessed to improve crop yields. The promise of more efficient food production, Mooney claimed, encouraged governments to hand over development to private enterprise.

"The tool they use is to say 'we are going to take care of world hunger'," Mooney explained. "At the same time, they said, because biotechnology is so expensive, that is why public organisations can't develop new strains. And because it is so expensive to develop, that is why we need IP protection.

"Now, in 2009, they have that control. And one billion people are still hungry."

Patents helped fund the race to identify genetic diseases and shine light on the structure of the genomes of various species. Mark Bünger, director of research at emerging-technologies analyst firm Lux Research, claims governments made a quid pro quo trade with private companies to speed up genetic research, and encouraged the filing of patents not just on inventions but discoveries of individual genetic sequences. Simply identifying a sequence of DNA and linking it to a gene or function would qualify for a patent. Without that ability, companies would not have been so ready to reveal their expensively obtained DNA sequences.

But in the past 20 years, the cost of sequencing DNA has plummeted. We are still some years away from the $1,000 genome, but sequencing companies have made the process so straightforward that metagenomics has emerged as a useful technology. It has allowed geneticists such as J Craig Venter to sail their yacht into the Sargasso Sea, drag a bucket behind it, and collect the DNA from countless micro-organisms. Computers at the home lab chomp through the data produced from billions of DNA fragments that let the scientists identify and catalogue a huge number of genes.

"We have looked through our fingers at these patents that are really discoveries rather than inventions," says Bünger. "But as sequencing gets cheap, do we really want to continue this?"

Because a number of proponents of synthetic biology - or extreme genetic engineering as ETC has tagged it - believe it will be possible to produce new, useful species by adding and deleting genetic sequences, they are concerned that DNA patent thickets corporations have amassed could prevent them from commercialising their efforts or even working on them.

The BioBricks Registry of Parts, maintained by the BioBricks Foundation headquartered at the Massachusetts Institute of Technology (MIT), sits in a precarious position. The idea behind the registry is to provide researchers with easy access to segments of DNA that can be stitched together to build genetic circuits. The people who set up the registry admit the database includes segments of DNA that are almost certainly covered by existing patents.

For example, one gene that is used routinely in labs around the world - particularly as students put together experiments over the summer that will give them something to present at the International Genetically Engineered Machine (iGEM) competition - is the one used to make animals and cells glow green under fluorescent light. The green fluorescent protein (EGP) gene, which won its discoverers the Nobel Prize in 2008, and its many relatives and applications are covered by a forest of patents.

Students and academics work under what they believe is a research exemption. However, iGEM director Randy Rettberg pointed out to delegates at a July conference organised by the Organisation for Economic Cooperation and Development: "There is no actual research exemption. The courts struck that one down. There is a de facto exemption. Will this work for iGEM in the future? I worry that some patent troll will send a letter to MIT and I will be shut down."

Even venture capitalists have expressed concern over the IP situation: foreseeing the possibility that companies they want to invest in - and sell off at a profit - will be rendered unable to trade by patent thickets.

Jack Wadsworth of Morgan Stanley said in his keynote at the SB 4.0 conference on synthetic biology last October: "This field really is the next big thing. There is no doubt that the commercial opportunities are huge. With biotechnology, when the final outcome is to create medical products, it still takes a long time and a lot of money.

"Synthetic biology feels different. To take an idea to a commercial product may be a lot faster. If you are creating an alternative fuel, you probably won't have to deal with organisations such as the FDA to bring a product to market."

But Wadsworth acknowledged the tension between the hopes among the synthetic community that the knowledge will remain open versus the demand among commercial organisation for patent protection, which might slow down experimentation because some genes and sequences are rendered off-limits.

"I got very enthusiastic about the idea that open-source biobricks would accelerate the development of this field in a way that is unique," Wadsworth said, hoping that patent issues will not derail these efforts. "Isn't it important to step back and accelerate the development of this field to benefit humanity and all the businesses we are interested in?"

Richard Johnson, CEO of Global Helix and co-chair of the OECD working party on nanotechnology, says: "Concerns that have been expressed which are real are the patent thickets that are going to retard upstream and downstream the ability to do research, to commercialise and to have the beneficial global impact that we want."

Open-source biotechnology

In 2008, Janet Hope published the optimistic book 'Biobazaar', in which she argues optimistically for an open-source revolution that might unlock the hold that major corporations have on key components of biotechnology. For a number of those working in synthetic biology and biotechnology, a shift towards open source would do much to keep 'EvilCo' - a favourite epithet of prominent synthetic-biology promoter Drew Endy - under control.

Seizing on some of the ideas in 'Biobazaar', the BioBricks Foundation set about exploring whether synthetic biology researchers could set up a system analogous to that created by Richard Stallman, another MIT-based scientist, in the 1980s for open-source IT.

At the BioSysBio conference in April, Endy produced an early draft of an open-source licence for parts contributed to the registry. The licence called on researchers to promise not to assert patent rights over parts they donated to the library, an approach that could put researchers in conflict with their technology-licensing offices.

There is one further problem with open source in biology: it will almost certainly depend on different legal framework to the Gnu General Public Licence (GPL) devised by Stallman with legal experts such as Professor Eben Moglen of Columbia University.

"Over time, we're increasingly going to see a decoupling of design from manufacture and process. And that, I would argue, is going to increase the likelihood that there may be copyright issues," says Johnson. But copyright does not, for the most part, come into play when dealing with genetic information. Other than the trademarks used to protect branded products, biotechnology relies almost exclusively on the patent system. This provides organisations such as the BioBricks Foundation with a problem of funding. Endy estimated that attempting to patent the contents of the registry would currently cost $40m.

"We're not going to pay the lawyers that much money even if we had it. We'd probably make more parts," says Endy.

People such as Johnson are looking at IP law alternatives that might be cheaper. Design rights or utility patents are possibilities, but this is an area where the US system is very weak compared with Europe or the Far East. So, the synthetic biology community is still looking for a way in which it can guarantee freedom to operate and, possibly, provide an open-source framework analogous to that employed in software.

The changing attitudes of big biotechnology and pharmaceutical companies is likely to play a role in determining which types of blocking patent will cause the most aggravation for researchers, and which could possibly trigger government action of the kind recommended by Kucinich more than six years ago.

In his 'Biocapital', published in 2006, an attempt to describe biotechnology in the same way that Karl Marx drew Victorian capitalism, Kaushik Sunder Rajan of the University of California at Irvine, argued that large corporations have apparently embraced openness not through altruism but self-interest. The information they deposit in these databases is not seen as differentiating for them - they are more interested in discoveries that result from being able to access more comprehensive public databases (see 'Protective patents', below).

Rajan points out: "The downstream companies do not want information to be owned because their locus of surplus value generation is in selling the drug, and the less they have to dish out to upstream companies, the better for them."

Systems-biology diseases

Pharmaceutical companies have found over the past few years that their traditional practice of targeting specific genes and proteins with specific drugs is running out of steam. The most problematic diseases in the West, such as cancer, have picked up the tag "systems-biology diseases". They are the result of large-scale shifts in the balance of a genetic network, and do not respond well to a treatment that focuses on the action of a single gene. The solution may be to look at compound treatments, using extensive simulation to evaluate possible side-effects. But there is a problem for the existing drug-industry IP framework if some parts of the treatment are supplied by a competitor.

As with the semiconductor industry, which found progress stymied by mutually exclusive patent collections in the 1970s, the way forward was extensive cross-licensing with a shift to protect assiduously only those patents which supported a particular product. For example, Intel has cross-licences on chip manufacture with practically all other companies with fabs. But it has maintained a lock on key patents for the x86 architecture, such as the memory-management architecture, using them to prevent clone makers from gaining a foothold.

If individual genetic sequences and the chemical structures of drugs become less important for maintaining a monopoly, those companies are likely to look at other areas that they can protect. They may choose to patent their analyses of the networks rather than the genes, potentially leading to a new type of patent thicket. The question is whether governments can or will choose to buy up certain patents to guarantee freedom to operate.

Johnson says: "When SARS was an issue, most of the national health services and the NIH that were involved with doing some of the cutting edge research basically made a decision by saying that we want to be the ones who can control what happens with respect to this. They said: 'If we patent it, we don't have to go get royalties. We can make it royalty free. We get complete control over how this develops in terms of what the licensing terms are'."

"I think there is a growing number of people who think that it is better to have either public or other types of institutions controlling their own destiny," Johnson concludes, rather than taking the risk of seeing what happens with an entirely commercial infrastructure.

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