Tag Archives: Creative Commons

Competion in Science

A recent NYT article on competition and collaboration in science made me think about my own work.  What are my natural tendencies?   Is it better in one situation to collaborate instead of compete?

Some argue that competition is the best way to develop a diverse set of scientific theories.  Karl Popper discusses competition as means for generating competing conjectures or tentative theories (TT)  when studying a problem situation (PS).  Through a process of theory formulation and error checking  (EE), we can evolve towards newer and more interesting problems (Wikipedia).

PS_1 \rightarrow TT_1 \rightarrow EE_1 \rightarrow PS_2

What does this mean for science?  For me, it means I have the freedom to generate new theories, test them and not be afraid.   Whether I am right or wrong I’m stretching the field and challenging assumptions.

Competitions raise a complicated set of issues. When people compete, they may be more likely to cut corners and make unethical decisions.  Competitions encourage a redundancy of human thought, time, money, and effort.  The many teams competing to sequence 100 human genomes in 10 days can’t all win.

A look back to 2003 and the first human genome project is a successful/helpful competition between Craig Venter and Francis Collins of The Human Genome Project. Venter’s team finished first by using shotgun sequencing, though the slower team used a clone-by-clone method that in the end produced more accurate results. Picture 1

How would a collaborative process have changed the human genome project?  It would have produced a broad agreement over which method is best to sequence a genome, and likely would have considerably slowed the final outcome, a complete human genome.  In another example of consensus building, Jack Colford, a UC Berkeley professor, mentioned to me that he watched the distasteful congealing of settled science occur at an experts working group he attended.  So, when is collaboration beneficial for science?

As a dreamer,  I want to believe that sharing and generosity will prevail in some situations.  Take for example the sharing of scientific information pioneered by members of the Open Access publishing  movement, Science Commons (Creative Commons), PLOS, NCBI – GenBank, and others.  180px-Open_Access_logo_PLoS_white.svg-1Providing free peer-reviewed scientific findings in the original format will hopefully reduce the number of people tirelessly and accidentally duplicating existing work, and improve circulation of data to poorer countries. Can Popper imagine that this new group of Open Access collaborators evolved because they are more ‘fit’ for the current environment that those who compete for paying users (as in the standard model of science journals).  Have we evolved to become collaborators in this instance?

Along the path of scientific development, it appears that the use of collaboration and competition each generate thousands of side-paths that split from the main trail  and may provide short-cuts… or take us to new, more interesting paths.  In this metaphore, the width of the path is created by the number of users who walk it.  So paths generated by collaborations, or paths like NCBI-GenBank with huge repositories of free sequence information, are more like highways than unmarked trails.  The exciting thing is that, just like my weekend hikes in Marin Co,  I get to choose my own path.

Please chime in if you have any thoughts on this or want to correct me!

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Open access genomes! (but how is OA protected?)

[image from PGP website]

A new project by the Personal Genome Project (PGP) will create an open access (OA) human genomic database for scientists and others to study. Apparently, in the first Human Genome Project, linking biographical or phenotypic data from humans with their genomes was not kosher. The “genome” in the Human Genome Project was actually an amalgamation of male and female volunteers, with a big chunk of the genome from an anonymous donor from Buffalo, NY called RP11 (wiki), but with new technology scientists can speed up the sequencing process so many individuals can have their genome sequences.  PGP will match genomes with personal traits, characteristics, and histories to make better inferences about genetic diseases, for example.  They are taking applications now, and you can sign up to get on a waiting list as I have done.

We have come a long way in the last 15 years since Craig Venter and his company, Celera, refused to deposit their human genomic sequence in NCBI/GenBank and others who practice gene patenting deflated our collective tyres. I think that PGP understands the benefits of being OA, but I didn’t see anything on their website about a legal backbone to protect that access, such as a Creative Commons copyrights. I hope they will get some advice on this from librarians, lawyers, publishers, and others in the OA community!


The Personal Genome Project: “…an open-ended research study that aims to improve our understanding of genetic and environmental contributions to human traits. In the second half of 2008, we will begin to enroll members of the public who are willing to share their genome sequence and other personal information with the scientific community and the general public… so that together we will be better able to advance our understanding of genetic and environmental contributions to human traits and to improve our ability to diagnose, treat, and prevent illness.”

New York Times: “The project is as much a social experiment as a scientific one. ‘We don’t yet know the consequences of having one’s genome out in the open,’ said George M. Church, a human geneticist at Harvard who is the project’s leader and one of its subjects. ‘But it’s worth exploring.’ ”

Wired Magazine: George Church is dyslexic, a narcoleptic, and a vegan. He is married with one daughter, weighs about 210 pounds, and has worn a pioneer-style bushy beard for decades. He has elevated levels of creatine kinase in his blood, the consequence of a heart attack. He enjoys waterskiing, photography, rock climbing, and singing in his church choir. His mother’s maiden name is Strong. He was born on August 28, 1954. If this all seems like too much information, well, blame Church himself. As the director of the Lipper Center for Computational Genetics at Harvard Medical School, he has a thing about openness…”

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Open Access Day

I spent most of Open Access Day in the lab grinding out bench work and preparing our new (to us) CO2 incubator for HEK293 cells tomorrow. Filling the water jacket, adjusting the CO2 level, and sterilizing the innards amounted to little more than swabbing the deck instead of attending a ball. When I arrived at PLoS (Public Library of Science) at 5pm to celebrate the 5th anniversary of the internet, or something like that (jk), most of the events had mellowed out. I had some interesting conversations with Gavin, an editor at PLoS Medicine, and Shabnam, the publication manager for Neglected Tropical Diseases about OA and their place in the new world of publishing.

I am just learning about OA, and its various colors (green, gold, grey, white), but the more I learn the more excited I get. For next manuscript with my name on it, I’ll push for a PLoS journal– probably PLoS ONE. I guess that would be a study of sunlight and it’s effects on viruses at a polluted swimming beach in California. Besides the OA and Creative Commons copyright, which are important in their own regard, I also like that there is no print version, which allows for more focus on web-based tools like a comments and questions feature that allows readers and authors to discuss the manuscript online (as a short-circuit to writing damn-awful published responses that seem to just start feuds). I feel like many of my colleagues in Environmental Microbiology don’t know about OA gold journals or PLoS, so I’ll try to (re)educate them as to their amazing benefits over paid access journals.

Perhaps the best analogy I can come up with is this: Democrats are to OA journals as Republicans are to paid access journals. Does this make sense? A vote for Obama is a vote for change and open access! It doesn’t roll of the tongue, but I’m going with it for now.

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