The talk was introduced by Illahee’s Director, Peter Schoonmaker.   In his  blog post, Peter described his summary of my presentation.

I used the occasion to wax lyrical about the congruence of the hologenome theory of evolution with our work on creating an open and transparent innovation cartography tool.

I tried to find a common thread of ‘biological innovation’ that can guide not only the practical realities of improving health, agriculture, environment and energy, but also the formation of productive and equitable economic and social structures and tools.

The full video of this presentation is available on Vimeo:   Enabling Innovation

Jan Huygens van Linschoten

The world’s greatest disruptive act of  Open Access Publishing.

The Dutch are pragmatists.   If there’s a more practical, hard-nosed, outcome-oriented culture that is steeped in business and trade, it might be the Chinese.  But the Dutch are (in so many ways) giants in the history of trade and commerce.

So it may be surprising that what is arguably history’s most disruptive act of creating a ‘commons of knowledge’ that opened up global trade to competition and fair-play came from a Dutchman,   Jan Huygens van Linschoten.

van Linschoten managed in a single act of sharing – in his case the pilfered Portuguese portolans and charts – to open the world of maritime commerce up to free and open competition, stimulating an era of growth and innovation in technology – shipbuilding, sailing, logistics, cartography and navigation – and in business – insurance, investment tools, financial instruments – that changed civilization for ever.

In 1596 or thereabouts, van Linschoten published what had for over a century and a half, the state secrets of Portugal – the maritime cartography of the Indies – West and East.

After over twenty years of laboratory work in CambiaLabs, creating, distributing and supporting openly available biological enabling technologies to the global research community –  some of which are amongst the most widely used in the field – we hung up our lab coats and put away our pipettes a few years back.

After over ten years of developing, improving and hosting the Patent Lens,  a hugely popular open web resource, we’re soon to be retiring the site per se.

After almost ten years designing, launching and supporting the BIOS Initiative (Biological Innovation for Open Society, aka Biological Open Source), its new ‘open source’ licensing strategies and its online collaboration platform Bioforge, we pretty much stopped about three years ago.  We turned off bioforge.net.

So we’re quitting?  We’ve run out of steam?    Is this the inevitable demise of the simplistic, science as social enterprise, sharing paradigm?

No bloody way, mate.

We have worked hard, contributed some and learnt much in these decades.   But progress through scientific method is based on having hypotheses *disproved*, not proved.     In the course of this – with careful design and with some grudging willingness be wrong – one gets closer to a truth.

So, doing all this stuff, we identified a common global, structural and systemic opportunity to change the system.

Biological Open Source won’t work without it.   Bioforge didn’t work without it. The Public Sector works very poorly without it.   Small enterprise desperately needs it.  Big business wastes billions to get it.

The biggest inefficiency in the history of post-enlightenment civilization is now entrenched, ubiquitous and feels inevitable.

And its pretty similar to the development of clergy, with their ecclesiastical literature, liturgy and their choke hold on society for the previous millenium.

Put simply,  we have to completely shift the demographics of problem solving by creating a global, open and dynamic resource for ‘innovation cartography’.

We must make it possible for virtually anyone to understand the landscapes of science, intellectual property, business, regulation and other innovation ‘intelligence’ that is necessary to make creative enterprise a possibility at all levels of society.

Creating and using credible dynamic landscapes showing the What, Who, Which, When, Where and Why of science-enabled innovation,  individuals and institutions in public and private sector can envision trajectories, partnerships, strategies, risks and opportunities.   We can engage untapped social, financial and intellectual capital to solve real and compelling problems.

These may be food, health, environment, energy or virtually any other productive economic activity.

The Lens

It would have been unthinkably hard ten years ago.  Five years ago, untenable and outrageously expensive.

Now, its manageable, affordable.  And essential.

The next posts will be about the ‘how’.

But it will *start* with  the world’s patents as the entry point to innovation intelligence.

// //

I’d like to share an email exchange I had some months ago with Eugene Rosenberg, one of the authors of some extremely interesting papers outlining the hologenome theory of evolution.   He and his wife, Ilana Zilber-Rosenberg apparently completely independently from me articulated the hologenome theory from their experiences in microbiology and nutrition, and coral microbiology in particular.

Rosenberg E, Koren O, Reshef L, Efrony R, Zilber-Rosenberg I.

Nat Rev Microbiol. 2007 May;5(5):355-62. Epub 2007 Mar 26. Review.PMID: 17384666 [PubMed - indexed for MEDLINE]

http://www.ncbi.nlm.nih.gov/pubmed

Email thread:

from: Eugene Rosenberg <eros@post.tau.ac.il>

to: Richard Jefferson <raj@cambia.org>

date: Wed, Mar 10, 2010 at 7:25 PM

subject: Re: Hologenome theory, microbiome / holobiont

Dear Richard,

Wow. What a joy to read your e-mail and blog. Before commenting, let me inform you that I am a young 75 year old general microbiologist that has published 250 scientific articles, almost exclusively on experimental studies on myxobacteria, hydrocarbon degradation by bacteria and more recently bacterial diseases of corals. My wife, Ilana, is the best nutritionist in Israel, with a strong background in biochemistry and microbiology. We came to the concept of the hologenome (I now include you in the “we”) from am attempt to explain how a particular coral became resistant to bacterial bleaching. Clearly, we share your view of the holobiont as a unit of selection in evolution of animals and plants.

Where do we go from here? Your clear discription of the glucuronide conjugate system is a fine example of how the microbes are an integral part of host metabolism. Furthermore you speculate that these reactions can lead to mating selection. Now to blow your mind- We have been working on the role of bacteria in mating selection for the last two years. It started when my wife found a paper in Evolution, published 20 years ago by Diane Dodd. She took a population of Drosophila from Bruce Canyon and raised half of them on a starch diet and the other half on maltose. After a year, she mixed them, and found the “starch flies” perfered to mate with ”starch flies” and “maltose flies” perfered to mate with “maltose flies.” Although they offered no explaination for this mating selection, my wife and I immediately thought bacteria. So, I put a graduate student, Gil Sharon, on the problem. He first repeated Dodd’s experiment using the standard laboratory strain of D. malanogaster and sucrose instead of maltose. Mating selection occurred after two generations and was maintained for 30 generations. When we added antibiotics, mating selection was abolished, indicating bacteria were responsible. Furthermore, we infected the antibiotic-treated flies with their homologous bacteria (isolated prior to antibiotic treatment) and mating selection was reestablished. We sent a manuscript to Nature and they rejected it, saying they would reconsider if we identified the specific bacterium responsible for the mating selection. This has not been an easy task, but we are still working on it.

Regardless of the particular bacterium, what is the mechanism? We have been extracting flies with pentane and doing GC-MS. There are differences between the “starch flies” and the “sucrose flies”.

Maybe the glucuronide system is involved.

It was a pleasure to hear from you. Let’s keep in contact.

Shalom

Eugene

Eugene Rosenberg, Professor Emeritus
Dept. of Molecular Microbiology and Biotechnology
Tel Aviv University
eros@post.tau.ac.il
+972-3-6409838

—– Original Message —–

From: Richard Jefferson

To: eros@post.tau.ac.il

Sent: Wednesday, March 10, 2010 8:27 AM

Subject: Hologenome theory, microbiome / holobiont relationships etc

Dear Professor Rosenberg,

I am writing firstly to compliment you and Professor Zilber-Rosenberg on your clear, lucid and compelling writing in the last years on the hologenome theory.

I have read these with great interest and pleasure.  I particularly commend you for the fine exposition in the FEMS and the Environmental Microbiology review and opinion piece, respectively.

I am a molecular biologist, and now as well innovation system strategist, currently with funding from the Gates Foundation.    I started work in molecular biology in 1974, and in the late 70′s and subsequently I began working with the glucuronide metabolism pathways of commensal vertebrate microbes, including E. coli.   It became very clear to me fairly early that the suite of capabilities to import, metabolize and ‘share’ the products of xenobiotic and endobiotic metabolism by gut microbes was central to the selective performance of the host and microbiome – the holobiont.

As I became involved in the earliest days of agricultural biotechnology, my focus on systems-level understanding and intervention continued to be informed by this awareness.   I was convinced that the model system approaches which were and are so joyously productive, may not have been as joyously instructive as to the workings and logic of natural systems as embedded through natural (or in agriculture, human) selection.

I’ve written about this approach a little, but I’m not very prolific as a writer (I would make a terrible academic, alas).  I have however been speaking and promoting this work for many years as part of my work as founder of Cambia – an international non-profit institution.

I attach to this a link to my blog (rarely visited, rarely updated) in which I wrote down some of my thoughts.  ( http://blogs.cambia.org/raj/index.php/2007/09/06/the-hologenome-hologenomics/ ).  I also have in my blog (the top of the blog) links to videos of lectures I”ve given at Cold Spring Harbor in 1994 on the hologenome, and its implications; and presentations in South Africa in 1997 (I’d love to share with you my old powerpoint if you’re interested) in which I refer to our molecular work on glucuronide metabolism and the logic of applying eco-therapeutics and the understanding and adjustment of the hologenome to health challenges.     Term ‘hologenome’ and ‘holobiont’ and its critical role in evolution were proposed by me at that CSH lecture and since, and I was overjoyed to read your parallel and independent articulation of their importance, especially with regard to the critical horizontal inheritance opportunities for the fitness of the selected holobiont in a complex environment.

This has continued to be my intellectual focus for much of the last 30 years, but most of my work has been focused on democratizing science-enabled innovation through ‘open source’ type approaches, and through increasing the transparency and fairness of intellectual property systems.

I would be thrilled to be in correspondence with you about these ideas – they shape my thinking in many fields, and I’m musing very hard about setting up experimental systems to test the hologenome theory, which to me is compelling.  My laboratory has been in storage now for over a year since our institute moved from Canberra to Brisbane, but within a year I expect I may be back to full steam.  I’ll likely be doing a ‘sabbatic’ of sorts at Berkeley  from July – December and look forward to getting back into the game, as our Initiative for Open Innovation goes to scale and can be taken over by other champions.

Again, my warmest wishes and congratulations for some of the best science writing I’ve read in a long time.  That we have arrived at virtually identical conclusions from such different perspectives is itself most gratifying.

Best wishes

Richard

Richard A. Jefferson PhD
Chief Executive Officer, Cambia
Director, Initiative for Open Innovation (IOI)
Professor of Science, Technology & Law
Queensland University of Technology (QUT)
G301, 2 George St, Brisbane 4000, QLD Australia
+61 419 499 753 (mobile)  +61 7 3138 4419 (work) +61 7 3138 4405 (fax)
www.bios.net |  www.cambia.org |  www.patentlens.net  | www.openinnovation.org
e: r.jefferson@cambia.org

So I’ve undertaken that in the next year, I’ll write extensively on innovation systems, biological evolution, agriculture, patents, new technologies, social equity, biotechnology, environmental interventions, hologenomes, open stuff, and so on.

I haven’t decided if I’ll do it just on this blog, which seems one of the best-kept secrets on the internet, or publish in more conventional outlets, and mirror and discuss those pieces here.   Probably a bit of both.

When the Open Government Directive was announced in the current administration, I was hopeful that the US Patent and Trademark Office would begin to make its bulk patent data available at no cost, and as well, create a way for the public to access the important ancillary data relating to status and prosecution history, called ‘PAIR’.

When USPTO announced the unusual partnership with Google to do just that, I was both pleased and a bit nervous that this was creating a cozy relationship with one big player in the information space, reminiscent of the relationships that EPO has had with ‘added value’ information gatekeepers.   I was also a bit skeptical that it would work and would deliver.

What happened in the last months since Jon Orwant at Google began hosting the bulk data was remarkable.    But it was incomplete.   The most valuable information (financially and often technically) is the most recent set of documents – the applications and grants published this year – and ideally this minute.      And these were lacking.    Until a couple of weeks ago, there was essentially no 2010 data on the Google bulk site.

I was concerned by this, and spent some serious time and bandwidth in conversations and emails with people in the Government and at Google, and in the last couple of weeks, the responsiveness of the USPTO, Google, the Commerce Department and the Office of Science & Technology Policy  has been nothing short of spectacular.   In fact, the whole experience made me realize that ‘Open Government’ is a passion and a mission to many of its practitioners in Washington and Virginia, and that there are some real heroes in the system who should get recognition.

In short, they made very courageous decision to provide to the public the highest margin data that they currently sell, at no cost, and on time.  And then they actually did it.  http://www.google.com/googlebooks/uspto-patents.html

This is no small thing.

The USPTO is expected to raise the revenue from its services to pay for those services.   This should be the subject of further discussion, no doubt, as it is a pernicious way to trap an agency into the status quo.  And one way to raise that revenue is to charge for the most valuable and difficult-to-provide data – the comprehensive ‘Redbook’ data from 2010.     Redbook refers to a quality XML format that also includes the chemical structures, DNA sequences, drawings, mathematical equations and so on, that comprise a machine readable comprehensive disclosure or ‘teaching’.   Redbook is the Gold standard.  The TIFF images of the actual applications and grants are also critical files.     What many don’t know is that the USPTO charges quite a bit for these.   For the US Grants in Redbook format for 2010, they charge 39,000.  For the aggregate 2010 files, Patents, Applications and images, it sets you back USD 94,100.  And yes, each year its about this much.

So imagine the courage and leadership necessary for David Kappos and his team to look at the revenue from selling these products, and to say ‘No, that’s wrong.  The Presidents Open Government Directive makes it clear that these should be public goods, available without fee or favor; bundle them into the bulk downloads’.

Breaking free from institutional capture by revenue stream is amongst the most difficult and bold leadership decisions anyone responsible for an enterprise can make.

So hats off to the whole team at USPTO, to Joey Hutcherson at Commerce and to the Deputy  CTO in OSTP, Beth Noveck, and to Jon Orwant and his team at Google.    Real good citizens!

I attach the letter I sent to David Kappos to thank USPTO.  They are always getting beat up in the blogosphere, but there’s courage there and commitment.   If anyone out there reads this (and I am always feeling like I’m singing in the shower) send them a nice note.

…………….

Mr David Kappos

Under Secretary of Commerce for Intellectual Property and

Director of the United States Patent and Trademark Office (USPTO)

P.O. Box 1450

November 1, 2010

Dear David,

I am writing to commend and congratulate the USPTO for its exceptional and wholly successful initiative to make comprehensive, timely and highest-quality text and data from US Patent Applications and Grants available to the public, in bulk and at no charge.

We also applaud the remarkable progress towards providing other critical data, such as PAIR, Assignment data and Petitions.

The public spirit and professionalism exemplified by these efforts admirably reflect the aspirations and intentions of the Open Government Directive.

It also reflects very well on your partner in this effort, Google, and its willingness and capability to host this bulk data without favor or fee, and to work with USPTO to overcome technical challenges.

In times of economic and environmental crisis, creating a more efficient, productive, transparent and inclusive innovation system is of paramount importance.

The fundamental and legitimate driver of the patent system is to advance the public good.    This is served by balancing the responsibility to explicitly share the teachings of inventions with the public,  with the limited right to exclude others, determined by a judicious and careful examination by the USPTO.    Responsibility must always go hand-in-hand with rights.

While rights are overseen by administrative procedure, the courts, and by competition and antitrust law, the responsibility side of the equation has often languished.

We recognize the unprecedented pressures under which the USPTO operates caused by the number, the volume and the scientific, technical, informational, business and legal complexity of the patent applications and patents it must administer.   We understand how this overwhelming load has made it difficult to meet the full spectrum of responsibilities and expectations to your own or to the public’s desired standard.

Now to its great credit, the USPTO has made a great leap towards ensuring that the teachings of US Patent Applications and Grants are shared effectively and openly.

This in turn will yield great dividends in engaging the public to use these disclosures to enable social and economic progress, and in so doing, finding the value and honing the role of the USPTO in innovation.

If we are to be an engaged and democratic society, the ball is now in our court.     Together we need to make the innovation system more efficient, effective and fair.

Cambia is a globally operating non-profit that has worked for over two decades to change the demographics of innovation, to broaden the scope and diversity of problem solvers and the problems solved, and to enable informed decisions around science- and technology-enabled innovation.

We have done this through CambiaLabs, which has designed, developed and delivered biological enabling technologies with extensive use of the patent system;  Patent Lens, which for over a  decade has provided free, open full text search and analysis of patents worldwide, and shed light on their meaning in open patent landscapes; and through BIOS (Biological Innovation for Open Society, aka Biological Open Source), which explores new cooperative tools, norms and legal instruments for increasing efficiency in life sciences-enabled innovation through improved sharing and distribution of pre-competitive platforms.

In 2009, with funding from the Bill & Melinda Gates Foundation and The Lemelson Foundation, we and our colleagues at the Queensland University of Technology began work to integrate these lessons through creation of an open, global facility called the Initiative for Open Innovation (IOI), to promote and enable public ‘Innovation Cartography’.  The IOI benefits from contributions from an extraordinary International Advisory Council which we would be honored for you to join.

IOI strives to make the innovation system more efficient, transparent, inclusive and fair.    We want to enable more people to make better decisions, informed by evidence, but guided by imagination.

We want to enable ‘cartography’ of the innovation landscape, so navigation through from idea to product or service and back again can rapidly and affordably produce new value to society.

Like cartography of the physical world, which for millenia guided trade and commerce, these open and public tools will allow us to minimize avoidable risks and uncertainty, create new partnerships and explore and navigate new trajectories to use inventions and ideas for public benefit.

The core of this open global facility will hinge on the world’s patent information, and the gold standard for that inventive literature corpus is from the USPTO.    This data serves as an entry point for  innovation intelligence and cartography when integrated with global science and technology literature, business, regulatory and standards data.  This will in turn provide a growing public resource for visualization and navigation of the innovation space.

Your actions in going the full distance in providing such high quality and comprehensive data to the public in a form that lends itself to such a global vision, is extraordinarily laudable and shows the highest levels of governmental integrity.

I commend your team for its exemplary public service,

Sincerely,

Richard

Richard A. Jefferson PhD
Chief Executive Officer, Cambia
Director, Initiative for Open Innovation
Professor of Science, Technology & Law,

Queensland University of Technology (QUT)
G301, 2 George St, Brisbane 4000, QLD Australia
+61 419 499 753 (mobile)  +61 7 3138 4419 (work) +61 7 3138 4405 (fax)
www.bios.net |  www.cambia.org |  www.patentlens.net  | www.openinnovation.org
e: r.jefferson@cambia.org

Cambia\’s Youtube Channel, including Cold Spring Harbor presentation

At that time (September, 1994)  I was trying to set the scene for why studying, understanding and manipulating complex systems with tools and approaches of reductionism would not be enough.

I started in part one with the concept of getting ‘Beyond the Model System’, and used real-world agriculture and environment as the entry point for that discussion.

I then went on in parts II & III to discuss the complexities of crops that were really not ‘model systems’ by any measure, sugarcane and cassava being exemplars. For this I referred to the excellent work of my friend and colleague Bruno Sobral, then at the California Institute of Biological Research and affiliated with Cambia.

Next I outlined the Hologenome concept and the idea that the microbial constitution of the entire ‘selected unit’ was the Great Unknown but perhaps – I argued – the biggest opportunity to create sustainable and robust interventions that were congruent with the logic of natural selection and evolution.

Finally in part V I discussed our thoughts on forming an international activity to create the technologies and thought framework for understanding genetic and organismal diversity. I called this the GRIT initiative at the time, but alas, for all the promotion and exhortation we were unable to secure the momentum necessary to make it happen.

Perhaps we were way before our time? Shortly after this, huge sums of money were spent on DNA sequencing and genome analysis facilities. Probably money well spent in that now we have solid data that supports the contention that the majority of the biosphere is the microbiome, and that most of the ‘visible’ biosphere is itself comprehensively populated with such a microbiome.

Maybe now we can start asking how to go from this observation and from the ability to sequence and describe the numbers and diversity of these microbes to a new ability to grok their role in biological system performance and robustness.

“……..
Of course the only entity that can speak for Monsanto is Monsanto, so commentary by any of us about why or whether they’ll participate is only conjecture.

However, I would comment that ‘financial savvy’ is a great reason for them to participate on several fronts. By thinking of the different ‘levels’ at which technologies act, one can imagine different treatments of these technologies with regard to sharing or hoarding.

This is similar to considerations of the ‘stack’ in software, where such components as operating systems, programming languages, interoperability standards, middleware are generally shared tools required to move the sector forward. Then applications or suites of capabilities represent commercially viable products and services.

The same distinction works in biotechnology.

Core technologies we call ‘enabling technologies’ are required by all players in the game – whether ‘mom and pop’ plant biotech or Monsanto. And these tools require constant improvements, tunings, expansions and revisions. Such tools would be, for instance, the basic ability to transfer genes to plants, the ability to visualize or select these genes when they are transfered, the ability to modulate, enhance or repress endogenous genes, the ability to map and monitor the genetic segregation and location of genes and so on. These tools are not typically specific to any one crop, or even a particular commercial challenge, but are required for almost any plant biotechnology intervention.

Because these tools are complex and are constantly being revised and extended, there exists a very cumbersome thicket of rights and an unfortunate ‘silo-ing’ of activity on their enhancement and replacement.

This basically means that each improvement often yields yet more patents, or more closed and innefficient nnovation systems, and a fragile innovation ecology.   And research to invent truly creative solutions to such core enabling technology challenges is not sufficiently incented because it is virtually certain not to be able to provide a complete solution to the technical challenge – at least in its first iteration.

A typical technology may require dozens of ‘rights’ to be navigated to ensure commercial use without legal vulnerability. There are hundreds of patents associated with the first act of plant gene transfer – the ‘transformation of plants’ by Agrobacterium. And other steps in the complex pathways are similarly complex. One key right withheld is sufficient to stop a commercial project from proceeding, or at least exposing the commercial entity to serious vulnerability. This vulnerability is typically experienced by any entity – small or large – that is embarking on commercial activity (a single farmer is ‘commercial’, so don’t get tied up thinking it only means multinationals).

However, larger corporations have both more exposure (more assets to lose if litigated successfully or subject to brand-associated market losses) and more financial and business means to bring to a solution to this problem; albeit a short-sighted solution.

Academic use is irrelevant and almost always misleading. In the US and elsewhere academics routinely use countless patented inventions with no licenses, and thus their work is not ‘permissive’ in that it cannot routinely be converted to commercial products without much additional ‘freedom to operate’ analysis and R&D.

And yet here is a point at which the economics comes very much to the rescue.

If all entities need these core tecnologies to advance real applications in the sector (agriculture and food – although exactly the same arguments apply to public health and medicine), then there is massive waste of resources by duplication of efforts, and in cross-licensing, non-licensing, re-invention of the tools and work-arounds that effect no substantial commercial advantage.   They simply allow companies to get to the starting gate of product development.  There is also a huge opportunity to harness and galvanise new technology development by collaborative and shared approaches that has been untapped.

There are however Balrogs in the Woodpile (problems) with this vision that are being opportunistically leveraged by ‘middlemen’. Companies that are own rights to key tools – or companies that are spun off to develop these tools – are generally looking to maximize their financial returns, and this strategy, while of questionable value in wealth creation in a sector or society, is being actively pursued as a wealth accumulation tool by these companies (and indeed some universities who use this ‘ransom’ or ‘last brick’ tool in negotiations).

There are companies that build ‘portfolios’ of patents and rights that make use of particular tools either expensive or impossible (remember many of these companies are not obligated to grant licenses!).

I frankly don’t see much added value in these holders of rights to low-level enabling technology, especially for society or for the sectoral advancement. If Monsanto and others do their sums, they may come to the conclusion that the expense of protecting, licensing and acquisition of enabling technology has added almost nothing to their (black ink) bottom line, but rather has cost them very substantial sums of money – and perhaps as importantly – public respect and goodwill that could be associated with greater communication, and more attention to product and service provision.

If on the other hand, a substantial decentralized open source initiative on key enabling technologies is pursued, with a guarantee that all parties may use the technologies at no cost (other than the summed, sunk costs of their actual development), then the transactions would be almost eliminated (a huge cost in itself), the quality of the technology could rapidly be increased, tested, expanded and adapted, regulatory compliance and standards could be harmonized, and the burdens on acquisition of rights and stacking of royalties would be greatly reduced or eliminated.

Take an example that is very important in biotechnology whether agricultural or medical. Homologous recombination technologies. This suite of technologies – which is not yet practically available – will allow subtle, nuanced changes in genomes that are informed and inspired by the now-routine sequencing of genomes and their variants. Done correctly, there is no reason these should trigger expensive regulatory burdens, and so could be a three-fold boon to agriculture; making immediate value of the massive sequence data greatly increasing the robustness of gene expression by modulating it in situ (where it has evolved to be) and by (potentially) dropping regulatory burdens back to levels associated with any conventional agricultural innovation.

There are many extraordinary publicly funded laboratories who have developed – with taxpayer’s money – components of this suite of technologies which I call collectively ‘HARTs’. These university scientists have often filed patents, and these patents are in some cases then exclusively licensed to a very aggressive company that is in fact not a serious player in the actual ‘sectors’ that stand to benefit. Rather this company is a middleman, potentially extracting massive rents (fees) and otherwise slowing the adoption (and as importantly the critical improvements and evolutions) of the technologies.

This is shameful and a huge loss to the worldwide community, and is typical of why the whole open source biology movement is so important. Whle one can argue facilely (and they do) that these ‘tool companies’ make money for themselves – they do – one cannot so easily see that they participate in social wealth creation.

In the IT industry, these types of entities are called ‘trolls’ or ‘patent terrorists’ or worse. Frankly, they are an aberration in my view. With such fine science in the public interest, with proper coordination and a new, low-transaction cost mechanism (BiOS and BioForge), these investigators are at least and in my view more creative and innovative than the trolls. And should thus contribute to society through provision of their tools to the sectors at no additional cost, allowing private and public resources to be focused on development and performance of new products in real markets, or the accommodation of the needs of small or neglected markets – a critical role of public sector that has been apparently lost in the ozone.

But this cannot happen in a ‘back to the future’ mode of publish and make it in the public domain, much as I would love to see this happen. We need leverage tools to ensure that the information and capabilities are coordinated, pooled and their availability is ensured. This is the power of open source. Not the ‘free’ of cost. But the ability to leverage creative improvements of core technology, and to ensure availability for use by those seeking advancement of society through ethical but sound business practices.

So, in summary, I think Monsanto should participate; I think Dupont and Syngenta and Bayer and Dow and others should participate. But they must not drive the agenda by any means. BASF and many smaller companies are participating in fact. As of 2008, we have over 150 licensees of these technologies

However, these companies – and their counterparts in the pharmaceutical and other life-science fields – are like large political entities – countries – that have embarked in a Mutually Assured Destruction scenario. Who will have the courage to blink? And more importantly, how long will the short sightedness that makes cooperation and open collaboration untenable – persist? Think of the arms race.

Who will say – this is foolish, unimaginative and wasteful?

Its a very hard question. I’m in negotiations with many of these companies, and while privately their senior executives and scientists may agree (and their accountants certainly will), they are – like political entities- themselves subject to huge inertial forces.

Imagine their share values when their courageous CEO gets up and says that their business models based on mergers, acquisitions, agressive litigations etc regarding core technologys, are flawed. Imagine his (or rarely her) rapid departure for ‘more time with their family’. They are strangely boxed into a very difficult situation.

So I don’t see an immediate sea-change unless we are successful (which I think we will be) on going towards new ground and new technologies which they can agree to treat differently than the old ones. I doubt that many of the multinationals will suddenly begin freeing up their existing patent portfolios. But I imagine the smarter of them will see the opportunities to redraw the terms of engagement for future technologies and the powerful economics of shared innovation. In spite of their well deserved reputation for hard-nosed, hard-assed business practice, I find there are still some very thoughtful people in Monsanto who may not see the world in a completely oppressive way, and who may be able to engage in this open source revolution.

But frankly, if they don’t, I’m not losing any sleep. There are way too many smart, ethical and committed scientists and citizens to allow science to become a high-cost tool available only to high-capital enterprises. Too much of agriculture, nutrition, natural resource management, energy, public health, and medicine requires new low-margin, localized innovations. And the power of open innovation can help address this.

Some have asked me how we can fight the powerful, carnivorous Tyrannosaurus of the Multinationals. My answer is to look around.

Where are the Terrible Lizards now? Gone. They’ve been out-evolved by mammals.

We just need to out-evolve them. They can adapt or become extinct.

In the last few years our lab has been getting more deeply into Type IV Secretion Systems. We set out some years back to ‘re-invent’ the Agrobacterium tumefaciens plant gene transfer capability in other families and genera of bacteria.

The reasons were twofold. First to invent around a very egregious and complex patent ‘thicket’.

Agrobacterium had been discovered to be capable of transferring genes from itself into higher plants, using a mechanism that is very similar to that used by virtually all bacteria to transfer genes (and proteins) from one bacterial cell to another, and often from one bacterial species to another. This observation was the first prominent inter-kingdom gene transfer described, and was the foundation of plant genetic engineering. So of course, it was patented up and down, backwards and forwards; every improvement, every species of plants…obscene greedfests of patenting. Until no one could actually use Agrobacterium to create crops (not just plants) that were improved. Except of course for a very few multinationals that had acquired strong portfolios and were willing to cross license them narrowly.

Anyway, we found that all the patents referred to this biologically unique (now there’s an oxymoron) capability of Agrobacterium tumefaciens. We reasoned that nothing in biology is unique. (Or as Jeff Goldblum’s darkly prescient character in Jurassic Park opines “Nature finds a way”). So we looked at moving this capacity to diverse bacteria and thus rendering the patents interesting and informative, but not legally restrictive.

It was surprisingly easy! And every one of the bacteria we tried it in worked, and in every plant species combination. Hmmm… so interkingdom gene transfer wasn’t hard? Well….

The other reason we set out to do this work-beyond, which we called Transbacter, was to make the process better. To use bacteria that had evolved a benign and symbiotic relationship with plants (and hence did not induce a pathogenesis response) to do our gene transfer, nicely.

Well, all that is pretty well described. But as we get more into these natural gene transfer capabilities, which are loosely clustered as ‘Type IV secretion systems (T4SS)’ I start to realize that the movement of genes between bacteria and likely, between bacteria and fungi, protists, plants, animals, you name it, is probably hugely more common than previously supposed.

The antibiotic resistance factors that are so promiscuously shared on broad host range plasmids (like the ubiquitous RK2) are moved around with T4SS’s, and of course the first system I cut my teeth on – the E. coli ‘F’ factor (fertility factor) is yet another of these. No self-respecting bacteria seems to lack such a capability.

If our observations about how the Ti-encoded Agrobacterium system can be so effective inother bacteria can be generalized, I think it may mean that a very serious force in metazoan and plant apogenome evolution will be from horizontal gene transfer from microbes. Note I say ‘microbes’ not bacteria, because I bet these types of systems pop up in fungi, protists, archae…etc.

Ok…my fingers are sore from typing this little blog. But there’s the convergent evolution in my scientific thinking – from glucuronide metabolism (and GUS the Wonder Gene) to horizontal gene transfer…now coming full circle.

What fun this period of life sciences could be. I really find 99% of molecular biology boring as bat shit these days. I can’t bear reading journals. But these ideas are much more envigorating, as they seem to smell of a pervasive logic. And as usual, I adore going where the metrics are tough. If you can’t see it and measure it, its not there? No way.