Science as Social Enterprise - Thoughts from Richard Jefferson and Cambia on democratizing science-enabled innovation

Innovation cartography: Mapping and navigating the IP landscape

The Unknown

“As we know,
There are known knowns.
There are things we know we know.
We also know
There are known unknowns.
That is to say
We know there are some things
We do not know.
But there are also unknown unknowns,
The ones we don’t know
We don’t know.”

—Feb. 12, 2002, Department of Defense news briefing, Donald Rumsfeld
These now immortal words of the neo-bard Donald Rumsfeld, though often lampooned, actually provide a helpful insight into the nature of innovation and landscapes on which it occurs.
Innovation, like navigating the high seas, is as much a matter of not steering a wrong course as it is steering the right one.   This is particularly so for those whose resources are limited, and where the risk of failure courts disaster.
In innovation thinking – itself almost an oxymoron – talking about how to make right choices and fostering sparks of creativity seems the dominant discourse.
But the realities of innovation are that most of the innovation process is grueling hard work, and the hard yakka is in avoiding stuff ups: endeavouring mightily not to ‘run aground, or crash into continents’.

So what are these continents, the reefs, the shoals and the currents that could take our ship of creative product and service delivery down to Davy Jones?

In those sectors driven by science-and technology-enabled innovation (SEI),  much of the uncertainty, the obscurity, the buried bommies are in the world of intellectual property, and most of this in the patent literature.

Curiously however – much of the excitement and opportunity of future and futuristic problem solving also lies in this same byzantine, obscure, clergy-ridden literature.

So what is it and how do we navigate it?


The Hologenome: the Cold Spring Harbor 1994 presentation

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.


The hologenome theory of evolution

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.

In 2009, I found some Rosenberg papers describing the hologenome theory from 2008 and 2009.  I was delighted at the clear and lucid writing and exposition, and that their observations leading to the hologenome concept came from such a different field to my own.

My  development of the hologenome theory in 1991-1994 came from two avenues of work I’d been pursuing for some years:

1)  vertebrate commensal microbes and their role in controlling critical hormones necessary for macro-organism fitness and

2) the role of endophytic and epiphytic microbes in plant performance in agriculture, including of course rhizobia and numerous other plant-associated bacteria.

Purging the backlog of thoughts

I’ve had an absurd number of people urge me to break my life-long writers’ block and start to put some of the lessons from the last couple of decades on (virtual) paper, so others can learn, criticize and comment, and so I can improve our strategies.

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.

USPTO Delivers big time: Free, fast, timely public access to the best patent data

At Cambia, to create the Patent Lens ( we’ve probably spent USD 300,000 or more over the years to acquire and serve to the public the full text and images of  US Patents and Applications.   This is a pretty heavy load for a small non-profit, but through commitment by our supporters, we’ve managed.

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.


Why should a multinational (e.g Monsanto) participate in an open source initiative?

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. (more…)

Hologenomics II: Type IV Secretion Systems and horizontal gene transfer

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’.


The Hologenome & Hologenomics: a different lens on evolution

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.


Initiative for Open Innovation

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.

Freedom to innovate as a human right: The Lost First Page

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.