Archive for the ‘Science’ Category

The Illahee Talk: opening the innovation ecology

August 31st, 2011

A few months ago, I had the opportunity to speak in Portland, Oregon on my thoughts of opening the innovation ecology.   The talk was sponsored by a non-profit, Illahee.org.

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

Innovation cartography: Mapping and navigating the IP landscape

January 10th, 2011


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?

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The hologenome theory of evolution

November 16th, 2010

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.

The Hologenome: the Cold Spring Harbor 1994 presentation

February 22nd, 2010

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.

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

February 28th, 2008

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

September 9th, 2007

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’.

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The Hologenome & Hologenomics: a different lens on evolution

September 6th, 2007

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.

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Initiative for Open Innovation

September 5th, 2007

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.

World Congress of Science Journalists

April 4th, 2007

In two weeks – April 19th – I’ll be at another conference in Melbourne, the World Congress of Science Journalists. At that congress, I’ll be producing a session about who benefits from science in a world where virtually every scientific discovery and platform is patented, and the elephant in the room: capability to use science. Phil Campbell, the editor of Nature (the magazine, not the phenomenon) will participate and we hope to expose the journalists to the realities of what’s happened as science becomes fragmented and owned. Few understand the world of patents, fewer still appreciate the profound impacts on our society.

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Mapmakers & mariners, shipwrights & sailors

April 4th, 2007

I made a presentation at the A2K meeting last year called Mapmakers and Mariners, Shipwrights and Sailors. I had prepared it while sitting on the stage listening to the other speakers (my preferred mode of preparation). it was inspired by a conversation I had with a fine journalist named Kenn Cukier.

In that discussion we were exploring the parallels between the intense competition to navigate the oceans during the creation of the European mercantile empires of the 1400-1800s, and the ability to navigatekenn-cukier.jpg the patent world now in the new millennium. In both cases, the proprietary knowledge of the routes, the shoals, the dangers, the currents and the ports was of enormous importance for achieving commercial advantage, and of course economic primacy.

Kenn later went on to write an exceptional piece for Nature Biotechnology about navigating patents in biotechnology, further exploring this metaphor.   In the late 1600’s, the Spanish could risk the Manila Galleon traveling from the far East to Spain via the Pacific Ocean – and many of the annual Galleons sunk – because the reward was so high. The profits on silk, silver and spices were astronomical. Navigation and seamanship would have to be exquisitely well developed to justify smaller profits; simply to drop the risk profile. And indeed over the years, as both cartography and maritime technology improved, so did the volume, quality and reciprocity of trade. And of course it was the tools development that drove the navigational capability: the marine sextant allowed latitude to be calculated, the marine chronometer, the longitude.

It is clear that the ability to see the dangers and opportunities, the detritus and the value within the patent system was going to be critical if science and technology is to achieve a greater social good, especially for small markets or weak market signals – one way to say ‘for the benefit of poor people’.

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