Archive for February, 2010

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.

(more…)

The hologenome theory of evolution

February 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.

Purging the backlog of thoughts

February 12th, 2010

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

February 4th, 2010

At Cambia, to create the Patent Lens (www.patentlens.net) 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.  http://www.google.com/googlebooks/uspto-patents.html

(more…)