BioImplement

Recent news of the 2009 Canadian Budget and the "missing" Genome Canada funding has created a minor media frenzy. Several Ontario scientists, my colleagues, friends and mentors, are being paraded by the news organizations as examples of how Genome Canada has created international leadership in cancer genomics and biodiversity research. Good for them, but I also I feel badly for them, for I know exactly what kind of career hit follows this kind of funding crisis.

While it is certain that many Genome Canada funded scientists have become international leaders in their fields, one problem is that Genome Canada has no long-term strategy to fund these projects. Industry partnered three-year projects with no provision for renewal are the staple of Genome Canada's co-funding strategy.

Expectations of commercial spin-offs and a market-driven afterlife is the fairy-tale ending for Genome Canada's approach to science. Yet the horizon for success in life sciences research can be longer than a decade. So, sadly, when a researcher becomes an international leader, Genome Canada has no strategy to keep them in that position, economic downturn or not.

Genome Canada is a market-driven organization. Perhaps it is reasonable to expect that co-funding - the money contributed by industry to the Genome Canada funding scheme - will simply dry up during this recession. By its own design, Genome Canada cannot hand out its money without co-funders. If Genome Canada has no hope of attracting co-funding this year, then this budget may in fact (gasp) be a reasonable one.

In my opinion, it is better to have the money spent updating college and university laboratories than sitting in Genome Canada's account waiting for co-funders to emerge from recession.

So how will the hit to Genome Canada affect the Brain Drain? In my own experience, Canadian universities and federal research agencies have not kept up with the international salaries paid to top-notch researchers. When research funding and infrastructure is plenty, scientists trade-off the benefits against the lower salary. Scientists tend to stay put if they have Genome Canada funding, OR new lab and infrastructure paid for by the Canada Foundation for Innovation.

CFI did get funding this year, and this will benefit far more scientists than the same funds in Genome Canada. In the past decade, the Brain Drain of top-paid researchers has been a slow drip. No doubt a few more scientists will retreat overseas and across borders, as I have, on the double justification of better salary and better research funds. But I predict these will be few, as CFI and many good new graduate students selecting academia over the workforce, will keep these researchers content.

I caution that it is up to the employers, universities, colleges and federal agencies to keep up with the price of leading scientific talent. Brain Drain in the coming years will be more squarely blamed on the scientists salary gap, rather than on large-scale funding opportunities enjoyed by the select few.

Another upside for Canadian scientists is that the paperwork for science funding can stand to be diminished, giving time back to the researchers. Canadian scientists will benefit from long needed consolidations in funding applications, programs and delivery that are being driven by the economics of the 2009 Budget. The time has come for a corrective contraction to Canadian science funding bloat, after which the nation will be much better positioned for a return to growth and merit-driven, rather than market-driven research.

And, after a big outburst of disbelief in their own misfortune from the 2009 Budget, Genome Canada has settled down. Now they are saying this budget is good for Canadian Science. They may just be right - better spent by CFI than sit in their bank account for the duration of the recession.

After a year of being in Singapore, I finally posted a new website for my current research lab activities. http://www.blueprint.org. Take a look, you may be pleasantly surprised by the content.

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The following disclaimer is posted for the benefit of my employer The National University of Singapore and to any other interested parties who are worried about liability. These parties should also note the extensive BLOGGER.COM terms of service.


The BioImplement Disclaimer V2.0

Like many other bloggers with good intentions, my blog has faded into oblivion. It seems "blogging" is a fad reserved for the interested few.

As an update, I am currently an Associate Professor in the Department of Biological Science at the National University of Singapore. I am working on research projects involving both Bioinformatics and wet-laboratory protein and nucleic acid biochemistry focusing on quantitative in-vitro approaches.

BIND and SeqHound/DogBox are now the products of Thomson-Reuters (BINDPlus and BONDPlus, respectively).

Thomson-Reuters provides the public BIND and sequence content - with a free login - at http://bind.ca

The book-writing mentioned in the previous email was put aside for a while, as I learned a lot about how not to write a book. It has transformed from 24 incomprehensible chapters into something much more focused, thanks to a number of readers who gave their feedback to my earlier drafts. For wading through the outline with 24 chapters, and getting back to me with their criticisms, I thank them.

It has been a long while since I posted last, and without summarizing events, I am no longer employed by Mount Sinai Hospital and the Blueprint Initiative is now, obsolete. My status-only position at the University of Toronto's Dept. of Biochemistry is dependent on my, now terminated, employment at MSH. So it appears like I am no longer a faculty member at Canada's largest University, and they don't seem to notice me as having gone missing...

For now I am self-employed as a writer and working part-time at Unleashed Informatics.

So what have I learned from this experience?
Enough to fill a few books.

First up:

The Convergence of Machines - Christopher Hogue Ph.D.
26 Chapters, 130 Figures. Illustrated by Jeff Dixon.

A scientist uses the industrialization of the glass industry to explain to laypersons the natural nanomachines found in all cells.

Manuscript to the publisher by Jun 30th 2007. Ready by Fall 2007.

Today, November 16 2005, it was announced that BIND curation activities have ceased, due to lack of public funding for the ongoing effort for the Blueprint Initiative in both Canada and Singapore. While it is difficult to provide public databases of the caliber of BIND without continued funding, I remain committed to public good research, open source software development and free data deposition, as do many others.

The problem now is, can it be resurrected? I will consider options made available, but no options are available on the public funding front at the moment. By the time funding becomes available, the software development team responsible for managing 3.5 million lines of source code will be all off to other jobs, and it may be impossible to return the operation to service if that happens. Several decades of person-years of experience that was accumulated in running this project will have toppled like a house of cards.

It seems like policy exists for providing open access to research data, and that policy should cover operations like Blueprint and BIND. On 30 January 2004 the Government of Canada, by Ministerial consent, adopted the OECD Declaration on Access to Research Data from Public Funding as policy. It is my hope that a long-term funding vehicle for sustainable database operations will result from the eventual deployment of this policy, and that Blueprint may apply for further funding through such a new funding vehicle.

I am not eager to re-apply for unsustainable funding, or further short-term financing for this resource. Its value, audience, and success have already been demonstrated and peer-reviewed. We are well-past proof of concept, having been peer-review funded to scale up from the original draft database architecture in 1999. None of our copycat competitors have come close to achieving what we have, in either the public or commercial sector, in providing first-rate data and database services of use to life-scientists.

To rebuild and then sustain Blueprint's database maintenance and curation operations, Blueprint will require a mix of co-funding and non-co-funding.

Co-funding schemes for funding scientific research have been criticized by a large number of Canadian scientists. I have not been among those making this criticism, for without co-funding schemes such as those of the Canadian Foundation for Innovation and later Genome Canada, it would have been impossible to bring you the accumulated infrastructure and knowledge behind Blueprint's databases and web services. Yet those same schemes have imperiled our service by not contemplating a measure of sustainability.

Co-funding schemes will remain important for federal and provincial investments in science, but the right balance is required for the benefit of all Canadian scientists. In addition, co-funding schemes must be able to break through the economic barriers between nations and be counted for international scientific projects, just as films and television productions are already co-funded jointly by partner nations.

It is up to funding agencies and governments to find the formula to fund this project. Fiscal surpluses in Canada are evident and we are not victim to austerity measures. I have done all that I can to fulfill my side of the commitment to providing open access to BIND.

I have already started up a spin-off company - Unleashed Informatics that has been making a highly affordable, auto-updated, commercial version of the SeqHound server. I am considering moving BIND into a commercial vehicle to preserve it, just as SwissProt did in 1996, but with the hope that a public-funded operation for Blueprint may return.

Keep watching this space.

Thanks for your ongoing support,
Christopher Hogue - chogue@blueprint.org

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The BioImplement Disclaimer V1.0