Science as Social Enterprise Thoughts from Cambia about the Biological Open Source movement 2010-03-04T22:54:22Z WordPress http://blogs.cambia.org/raj/index.php/feed/atom/ Richard Jefferson http://www.cambia.org <![CDATA[Hologenome: the video. Not Avatar, but I did have hair at the time.]]> http://blogs.cambia.org/raj/?p=55 2010-02-23T03:14:37Z 2010-02-22T00:29:42Z I finally unearthed the old videos of my Cold Spring Harbor talk in 1994 in which I outlined the ideas and context of the ‘Hologenome’ as a new lens on evolution.  Cold Spring Harbor actually packaged and (briefly and presumably unsuccessfully) marketed these videos of the meeting.  Now out of print.

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.

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Richard Jefferson http://www.cambia.org <![CDATA[Why should a multinational (e.g Monsanto) participate in an open source initiative?]]> http://blogs.cambia.org/raj/index.php/2008/02/28/why-should-a-multinational-eg-monsanto-participate-in-an-open-source-initiative/ 2008-02-28T05:57:44Z 2008-02-27T23:54:07Z A couple of years ago, a contributor to the BioForge forum, ‘Meredith’, asked me why Monsanto would ever participate in the BiOS Initiative or any other open source idea. I decided to repost an edited form of my reply here, since many others ask the same question. Well, Monsanto STILL hasn’t signed up. It has however published patent applications showing that our Transbacter technology – which is a core CAMBIA BiOS work product – works well in their key crops (soybean, corn, canola, cotton). It validates both our technology and more importantly, the premise that a dominant patent could be used to leverage community access to improvements.

“……..
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.

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Richard Jefferson http://www.cambia.org <![CDATA[Hologenomics II: Type IV Secretion Systems and horizontal gene transfer]]> http://blogs.cambia.org/raj/index.php/2007/09/09/hologenomics-ii-type-iv-secretion-systems-and-horizontal-gene-transfer/ 2007-09-18T09:18:44Z 2007-09-09T11:27:01Z This topic is such fun, I could log in each day and all the ideas I’ve had for thirty years would start lining up on the framework of hologenomics.

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.

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Richard Jefferson http://www.cambia.org <![CDATA[The Hologenome & Hologenomics: a different lens on evolution]]> http://blogs.cambia.org/raj/index.php/2007/09/06/the-hologenome-hologenomics/ 2010-02-24T08:00:51Z 2007-09-06T00:45:37Z This one is a treat. An opportunity to blog about my ideas on science! It seems that most of my efforts these days are focused on BiOS, patent transparency and innovation strategies. Science is still an important part of my life, but my dismay at the way it has been co-opted and made less relevant to society has left a bitter taste.

Still, there are new fields that are breathtaking in their implications (to me at least) and which do not lend themselves to being ‘owned’, but – at least at this stage in their development – rather shared.

The single most exciting development in the biological sciences to occur in my lifetime is the idea that microbes are not only ubiquitous but that they may be the most important component that drives the evolution of macro-organisms.

In fact, I’d venture to say that multicellular eukaryotes only exist in nature as complexes of organisms in which microbial genomes are critical, essential contributors to the fitness of the overall ‘individual’ (which itself needs redefining).

Back in September of 1994 I gave an invited presentation at a Symposium at Cold Spring Harbor sponsored by Perkin Elmer Corporation: “A Decade of PCR“.   The symposium was only a couple of days, was a celebration of the impact and future of PCR on life sciences, and featured Jim Watson, Kary Mullis, and a number of other prominent speakers. I was given the task of talking about Agriculture, Environment and the Third World. Rather dauntingly broad marching orders. But I decided that I’d try something fun out on the audience, which was a pretty substantial group of scientists.

While setting the scene with our observations about the complexity of agricultural systems, I wanted mostly to talk about ‘Hologenomics’, a term I coined and defined for that seminar.   As with most of my ideas, I’ve never written it down, but I have spoken about it alot, and thought about it even more. (This comment is a response to a quote from my PhD thesis advisor, who wrote in my letters of recommendation that “Jefferson thinks incredibly quickly, but speaks even faster”….sigh).

For years I’ve been studying the metabolism of glucuronide conjugates by Escherichia coli, and many other microbes associated with vertebrates. Vertebrates, including many humans (!) have a remarkable mode of turning over small molecules from their systems. Most small molecules, including steroid hormones, vitamins, xenobiotics (including most pharmaceuticals and dietary secondary metabolites) are excreted from the body as conjugates of glucuronic acid known as ‘glucuronides’ .

Glucuronic acid is simply glucose in which the 6-carbon is in the form of a carboxylic acid or carboxylate. The conjugates are typically (but not always) beta-1-O-linked glycosides of the aglycone. This conjugation is done in many tissues of the body, including of course the liver, but also epidermis and almost everywhere we look. The conjugates so generated tend to be much more water soluble than the aglycone (for instance, testosterone), and thus can more readily be transported in the aqueous circulatory system, where they can be transfered (recognizing the highly stereospecific glucuronic acid moiety) to an excretion pathway. The conjugates find their way to the kidneys for excretion in urine; the pancreas/bile ducts where they are dumped into the upper intestine; and the axils where they are excreted in apocrine and merocrine excretions (eg. sweat).

Turns out that the majority of steroid hormones are excreted this way, into the bile, where they end up feeding the enormous diversity of bugs in the upper and lower intestine. E. coli is just one of the myriad microbes there, and not even the most prominent one.

But it seems that the excretion of the hormone conjugates (and you can substitute almost any word for ‘hormone’ there, including ‘drug’, ‘toxin’, ‘metabolite’ etc) does not see the story end. Rather, the microbial populations have evolved the ability to transport these compounds selectively (in our own work, through a glucuronide transporter we call glucuronide permease, encoded by gusB locus of E. coli), where the aglycone (the steroid for instance) is cleaved off (by glucuronidase, encoded by gusA) and the sugar (glucuronic acid) metabolized by the microbe. The freed aglyone is then available for re-absorption in the gut.

Thus, thousands of compounds actually cycle through the intestine of vertebrates. Conjugated in the body, transported by circulatory system to a distal site of excretion, imported into microbial systems, cleaved to free the aglycone, which is then reabsorbed into the body. This has been called enterohepatic circulation, back when it was thought that the liver was the only site of glucuronic acid conjugation. I’ve read that as much as 65% of the circulating testosterone, for instance, has already passed through an enterohepatic circulation route.

Glucuronidation, and sulfation to a lesser extent (though this depends on species of molecule and species of macrobiont), are used on most steroids and most drugs to excrete. Hence the cleavage and re-presentation of the aglycone by the microbial populations are critical to controlling the level of these compounds.

Well these compounds include the entire range of steroids that have seminal impacts (excuse the pun) on reproduction, and reproductive fitness, including fertility, fecundity and mate choice. Estrogens, progesterone, testosterone, estradiols, all of them are excreted as glucuronides, and reabsorbed after microbial cleavage. Even the pheromones excreted from the armpits (or legpits…axils…) are generally non-aromatic. Some would say VERY non-aromatic. Perhaps better to say, they are excreted as water soluble, non-volatile compounds. It is the skin microbes that cleave the compounds to release the volatile steroids, such as androstenols, which impact on mate selection and population behaviour of the macrobiont (the big animal we see, for instance the human, mouse, fish, etc)..

Ok, so what is it about hologenomics and evolution? Well any sensible student of evolution will note that the traits that I mentioned, which are hugely impacted by steroid balance, which itself is determined (!) by the turnover of the glucuronide conjugates, are the very core traits that are key to natural selection, namely fertility, fecundity and mate choice.

Holy Cow! The evolutionarily most important traits of a mouse (or human) are encoded by bacteria!

And more importantly, by the balance of extraordinarily complex populations of bacteria in diverse settings. As anyone who has read this far (ie no one) would know, as we get better at looking for microorganisms we get much better at finding them – and it seems that the vast majority of the genomes associated with a human are non-human. Or are they? They are microbial (including eubacteria, but also protists, fungi, archae perhaps) but why are they not ‘human’?

They are causally associated with the behaviour and performance characteristics that have allowed us (or indeed any macrobiont) to persist and flourish under natural selection. So really, that means they are integral to ‘human’. In fact, I would argue they’re as ‘human’ as ‘we’ are. You see, we’re used to seeing our big sloppy nucleus and chromosomes and thinking ‘Yup, that’s the human genome; the book of life’…well, it seems that that’s only the scaffold! The real genome is what I call a hologenome. The apobiont (that would be what looks like me, if I had NO microbes associated with me) is not a holobiont (a complete organism) until the population structure makes it so. So the human genome hasn’t been sequenced, just the parts in a bag that replicates slowly. The little bags that replicate, migrate and reassort rapidly, and which clearly have mission critical functions, are only now being discovered.

And their importance is not yet appreciated. And its not just animal! All macrobionts (big multicellular organisms), including plants, are also a pastiche, an amalgam of many genomes. And so a rice plant is not really a rice plant in the absence of the microbial populations that allow it to perform in the environment.

This concept has big implications for our world view. For science. For medicine and agriculture. It is the tip of a very big iceberg. Its has been said in the last ten years by many scientists that most of the microorganisms in the world are unculturable (some would say that about humans too). Its true that as we begin our exploration of the microbiome we find vast numbers and diversity of microbes that have never been cultivated on media in the laboratory. The likelihood is that they never will. I guess that’s part of why I think they are a part of a hologenome that contributes to the overall natural selective fitness of the holobiont (and perhaps a holosystem?), and can only be thought of in that light.

So if we drop a mouse in a blender, we get (besides a visit from the site bioethics committee) more ‘bacterial’ than ‘mouse’ genomes. By a factor of nearly a hundred! This is the new wisdom. But its wrong. We definitely get more ‘microbiont’ than ‘macrobiont’ genomes. But the mouse is not the macrobiome. The mouse is the sum of these genomes – the holobiont expressing the hologenome – and it is that sum that contributes to the success of the mouse (not of course the blender mouse itself, who would not look at its role as a big success) under evolutionary selection.

And what gets very exciting about this is the following: If I were a macro-genetic-engineer (eg. teleologically speaking) I’d design most of the dull, workaday, scaffold functions to be encoded by slowly evolving, slowly replicating packets – ie nuclear genes. But I’d put the really critical, environmentally responsive functions in packets that could amplify quickly and specifically, could be traded (or not) through well crafted horizontal transfer mechanisms, which could replicate, and hence evolve, very rapidly. In short, I’d put the really cool important stuff in the microbial genomes, and leave the big macrobiont nucleus as a pretty pedestrian framework.

So are we really doing a great job yet at studying human (or mouse, or rouse – isn’t that the singular of rice?) genomics? Nope. Not until we think of the suite of genomes – the apogenomes and their aggregation into a hologenome – as the performance unit of natural selection. A nd therefore of the repository of the logic of life.

It would mean that the logic of ‘eukaryotic’ genomes will be incomplete, maybe even dead wrong, in the absence of the full appreciation of the impact of populations of microbes, which are lynchpins.

So I’m wondering, how do we set up experimental systems to prove this beyond a shadow of a doubt? How do we show that evolution works at that hologenome? Or doesn’t.

I’m rather optimistic that the glucuronide system may afford a model. And the new tools of massive high-throughput environmental sequencing will be a platform. I will be musing on this rather alot.

So let’s keep talking about hologenomics, and even its practical implications.

In a talk in South Africa at the 14th Conference of the South African Society of Biochemistry and Molecular Biology in 1997, in Grahamstown South Africa,  I called this Ecotherapeutics.

The idea that adjusting the balance and constitution of the microbial populations would have huge repercussions on disease and health. Both plant and animal. And that this could constitute the next revolution in life sciences, in which the interventions could be intrinsically ‘un-ownable’, context dependent and robust.

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Richard Jefferson http://www.cambia.org <![CDATA[Initiative for Open Innovation]]> http://blogs.cambia.org/raj/index.php/2007/09/05/initiative-for-open-innovation/ 2007-09-05T00:41:04Z 2007-09-05T00:41:04Z Well, its been a busy few months since my last post. I’ve been constantly traveling to meetings and working with prospective partners to try to generalize our work.

It now seems that the fundamental power of a harmonized patent informatics platform and a facility for supporting open innovation work has become widely appreciated. We’ll be going to scale soon with a sector-agnostic activity we call the Initiative for Open Innovation (IOI) under which the Patent Lens will be a prominent platform.

I’ll write extensively over the next weeks about this, but briefly the idea is to form a worldwide open access capability to integrate, parse, visualize and analyze patent data over all nations and all innovation sectors. We will develop – collaboratively – open source, community participation web apps which will allow creation and curation of ‘landscapes’ of key IP areas, for instance, influenza vaccines, RNAi technologies, cancer diagnostics, agricultural genetic resources and so on.

However, its now becoming clear that this should extend well beyond the life sciences, as indeed virtually all innovation activity is facing the complexities of a patent system in meltdown. Transparency really is critical, but the transparency must provide for high level oversight, not just the piecemeal ability to search for patents. Rather it will be critical that all interested citizens, scientists, business people and policy makers should be able to visualize and appreciate the nature and extent of current and projected patent coverage over areas of particular interest. This will require highly professional curation, annotation and involvement, but it will be greatly facilitated by sophisticated informatics.

Our intention is to work with many nations to digitize and integrate their own patent information so it can be searched in their own languages, and with natural language translation where possible, to open it for inspection to all citizens, everywhere. Of course, APIs provision and mirroring in diverse locations is part of the plan; but the foundation of the platform – the Patent Lens – is anticipated to become an enabling facility for open innovation.

Much more to come in future posts.

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Richard Jefferson http://www.cambia.org <![CDATA[Freedom to innovate as a human right: The Lost First Page]]> http://blogs.cambia.org/raj/index.php/2007/04/04/freedom-to-innovate/ 2010-02-22T00:14:42Z 2007-04-04T21:11:05Z It seems there has been a great, but hitherto unmentioned bureaucratic stuff up. The first page of the Universal Declaration of Human Rights was lost at some point by a harried office worker, perhaps stuck in a printer, and so neglected; or missed in a mass photocopying and stapling exercise. But never included in the versions we see. So our Declarations of Human Rights and their pursuant discussions now seem to start breathlessly with the second page – hastily renumbered of course – but still talking about what we ought to do. Perhaps there was a cover-up, perhaps not

I sensed that there was something fundamental missing. What is it about ‘human rights’ that is uniquely ‘human’, which would constitute such a critical feature of being ‘human’ that it should be articulated as a right, and which informs and grounds all discourse?

Of course it must be right there on the Lost First Page.

Jane Goodall drew my attention to it, as did Charles Darwin, perhaps without meaning to, and posthumously of course.

When in October of 1960, Jane Goodall made the shattering observation in the dry streambeds of Gombe that David Greybeard had been seen tearing leaves off of a tree branch, and using the trimmed stick to fish out and eat termites, it neatly framed the core issue of human existence. Her keen eyes and iconic method created a furor precisely because her description of David – a chimpanzee – designing, making and using tools to solve his problem – was precisely the capability that had been jealously but inchoately guarded as that one, uniquely human characteristic.

And indeed if exceptions can prove a rule, it still is that most telling capacity. Homo sapiens is blithely and banally called ‘the tool user’ in so many text books that we have forgotten how critically important this is. Not to be a tool user only, but to be a designer, builder and user of tools.  Recent DNA evidence may even indicate that this is not an exception but a species descriptor after all!

It’s right there on the Lost First Page.

The fundamental human right from which all others flow, is the right to be human – To Innovate. For indeed the designing, building and using of tools really is the very heart of innovation.

We really must look with great care and scrutiny at any societal interventions that curtail or constrain this right – indeed this human imperative. And while we often focus on the social aspects of this innovation capacity, this human right – for instance in rights to the ‘tools’ of governance, speech, assembly – we curiously have left the technological and material innovation to the vicissitudes of markets and forces with no oversight.

Of course this doesn’t mean every chimpanzee and every human is equally good at innovation or that they all even chose to innovate. But as social beings, they do chose who or what entity will innovate on their behalf. And the emotional resonance of this granting of proxy is almost as fundamental as the actual innovation itself. In many ways this may well be the biological logic that is the core of social grouping – the proxy innovators, or what I later call a ‘representational technocracy’.

Biological Innovation

What I term ‘Biological Innovation’ is the oldest and most fundamental form of human innovation – involving as it does the getting of food, the striving for health, the making of homes and the building of communities.

Biological innovation has been informed and guided for thousands of years by keen observation and the accumulation and sharing of generations of empirical knowledge.

But the explosion of possibility that began when, post-Enlightenment, the unprecedented power of science became focused on food, agriculture, health, medicine and environment seemed to dwarf all previous attainments. And indeed in the last hundred years, with the advent of genetics, the pace has been gathering.

But thirty years ago, it became breathtaking; we found the gear-shift. We may just have lost our grip on the steering wheel.

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