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A fruitful collaboration
"If I have seen farther, it is by standing on the shoulders of giants." Issac Newton
  
By Gerald M. Rubin


Commentary

Today is a day for celebration in biology. The Drosophila genome has been sequenced and published and an important new chapter in fly biology can be written—one with major implications for future study of human disease because the majority of genes whose alteration is known to cause disease in humans have counterparts in the fly. Even more remarkable is the fact that the complete sequence of the gene-rich regions of the fruit fly has been obtained 18 months ahead of schedule, while saving millions of research dollars in the process. Why? Because a remarkable collaboration between Celera Genomics and the Berkeley Drosophila Genome Project* was successful beyond all expectation.


By combining our efforts, it seemed likely that we could get the science done better and faster ...

In the spring of 1998, Celera's president, J. Craig Venter, approached me with an offer I could not refuse. He suggested that the Berkeley Project, which I head, work with Celera to apply to the Drosophila genome project the sequencing capacity, supercomputing power and mathematical algorithms that are the basis of Celera's whole-genome shotgun sequencing strategy. At this time we had only completed about a fifth of the genome and were eager to speed up our project. In addition to this finished genomic sequence, our contribution would be accurate clone-based genome maps and low-coverage sequence of the clones comprising the map. The collaboration would cost us nothing, we agreed that in the end all the data would be made public**, and we would share credit of the scientific papers that resulted from our work. Celera, in turn, would get to test shotgun sequencing on Drosophila in a trial run leading up to sequencing the much larger human genome. What a deal.

Many colleagues advised me to say no. As I said publicly last month at the annual meeting of the American Association for the Advancement of Science (AAAS), they were not enthusiastic about a collaboration with a for-profit company on the genome project, despite the fact that academic researchers develop partnerships with the pharmaceutical and biotechnology industry all the time. A lot of my friends were particularly leery of a collaboration with Celera. They warned me that I was going to get into real trouble and would feel badly treated at the end of the day. And as if to make this gloomy prophesy come true, the naysayers were widely quoted in the press.

But my interest in this collaboration was pretty simple. By combining our efforts, it seemed likely that we could get the science done better and faster than either group working alone. And that, after all, is what science is supposed to be about.

Isaac Newton epitomized one central tenant of good science with his much quoted tribute to those whose work he built on: "If I have seen farther, it is by standing on the shoulders of giants." Drosophila research is where it is today because of the work of giants who, in the early 20th century, understood the power of the fruit fly to reveal fundamental principles of genetics and established a ethic of collaboration: working together, sharing data, solving problems. The Drosophila community is just that—a community of researchers who have carefully built on the research of those who went before them and whose collective desire is to advance the field. And that is what's happened.

When I agreed to collaborate with Celera scientists, I must admit I considered the collaboration itself a form of experiment. When people asked me how I felt about it, I'd say "Ask me when it's done."

Well, it's done now and this is my answer. As I said at the AAAS, "Working with Celera has been one of the most pleasurable scientific experiences I have had in my 30-year career. It's been a ball. It's been great. Seldom have I encountered a group of individuals who were so dedicated and so hard working...They have exceeded all the commitments they made to me in this collaboration. They have behaved with the highest standards of personal integrity and scientific rigor."


Drosophila worldwide collaborators


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After all, because of the collaboration, we have the Drosophila genome sequence a year and a half ahead of our most optimistic estimates. The federal government should be delighted that the sequence is freely available to all their funded researchers. Instead of spending millions of tax dollars on sequencing, NIH money can now be spent on further improving the genomic infrastructure for fly research by sequencing cDNA clones and on doing important fly biology. We have all said getting a genome sequence is just the beginning, not the end, of a long research process.

Why, you might ask, am I so willing to go out on a limb in defense of a company that is sometimes portrayed as the Darth Vader of genomics? Precisely because I believe that image is wrong and because I believe our collaboration—contrary to all negative expectations—could serve as a model for future collaborations between the public and private sector. It worked.


Gerald M. Rubin is a Professor of Genetics at the University of California, Berkeley, a Howard Hughes Medical Institute investigator and head of the Berkeley Drosophila Genome Project. Since January 2000, he is also Vice President for Biomedical Research at the Howard Hughes Medical Institute in Chevy Chase, Maryland.

The Berkeley Drosophila Genome Project, based at the University of California, Berkeley, is a consortium of research groups including the Lawrence Berkeley National Laboratory, Baylor College of Medicine, and the Carnegie Institution of Washington. It is funded by the National Institutes of Health, the U.S. Department of Energy, and the Howard Hughes Medical Institute.

** Drosophila sequence data are freely available at Celera.com. the BDGP's web site (www.fruitfly.org) and in GenBank. Three manuscripts describing the research are published in the March 24 issue of Science.


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