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.
Continued…
Posted in General.
Tagged with beyond model systems, hologenome, video.
By Richard Jefferson
– February 22, 2010
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. Continued…
Posted in BiOS Licensing, Patents, Science, Social Enterprise.
By Richard Jefferson
– February 28, 2008
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’.
Continued…
Posted in Evolution, Science.
By Richard Jefferson
– September 9, 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.
Continued…
Posted in Evolution, Science.
By Richard Jefferson
– September 6, 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.
Posted in General, Patents, Science, Social Enterprise.
By Richard Jefferson
– September 5, 2007
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.
Continued…
Posted in General.
By Richard Jefferson
– April 5, 2007
Almost all technologies in the life sciences are intertwined and interdependent. Few discoveries stand on their own, and fewer inventions. Not only do they each depend on the pre-existing knowledge base, they almost always incorporate components of many other technologies in their execution.
This is particularly true for tools and technologies that are what I call ‘meta-technologies’, whose effects are broad and that are useful for communities of innovators who are quite distant from the inventor of the tool.
Consider the wheel. It is clearly a tool, and clearly a meta- technology. In some ways, it is the most fundamental and important tool in society, as it has so many uses, unanticipated by its inventor(s). These uses are countless, and they are mostly made by people who are not wheel-builders.
Continued…
Posted in BiOS Licensing, General, Patents.
By Richard Jefferson
– April 4, 2007
With the welcome attention to ‘neglected diseases’ such as malaria and tuberculosis associated with poverty, there is a tendency to forget the many health challenges such as heart disease, diabetes and cancer which wreak havoc in both worlds. These ‘shared diseases’ have dramatically different markets in both first and third world, and some thoughts about the disparity in options exposes some structural failings and innovation opportunities.
Leaving the development of diagnostics and treatments of such diseases and conditions to market forces, especially when intellectual property can be used to control entry of new players, will continue to render these debilitating but familiar illnesses a sad litany of social inequities. Are there ways that research-intensive solutions can be cooperatively generated that can grapple with this challenge?
More of the world dies of cancer than almost any other single disease. According to the WHO, cancer kills almost
seven million people a year of whom about half are in the developing world. By comparison, AIDS-related conditions kill about three million people a year.
In the industrialized world, the availability of diagnostics and therapeutics for cancer, while often outrageously expensive, can lead to very favorable outcomes. In the poorer parts of the world, diagnostic technology, when available, is inadequate to the task, and few therapeutics are affordable. There are literally millions of people who die of cancer each year in the poorer parts of the world, many of whom could have had longer and more productive lives if the diagnostic and therapeutic options available to their rich neighbors were available to them.
With cancer, it is not the disease that is neglected, but the diseased.
Telomerase is an enzyme in human cells which repairs the ends of chromosomes, and is tightly regulated in normal and normally aging cells. However in tumor cells and tissues, telomerase is often wildly de-regulated, rendering such cells virtually immortal. As such, it has been viewed as the platform from which a key ‘silver bullet’ for cancer therapeutics, for diagnostics, for gerontology, even for production of stem cells, could evolve.
This was the focus of a fascinating press piece by Judy Foreman in 2003 called “Telomerase: a promising cancer drug stuck in patent hell?”
Continued…
Posted in General.
By Richard Jefferson
– April 4, 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.
Continued…
Posted in General, Patents, Science.
By Richard Jefferson
– April 4, 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 navigate
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’.
Continued…
Posted in Patents, Science, Social Enterprise.
By Richard Jefferson
– April 4, 2007
