Please note that this blog no longer accepts comments (there was
too much spam coming in!). If you're reading this blog and want to
respond then please use the contact form on the site.
You can also follow me on twitter.
My latest Mind and Matter column in the Wall Street Journal is
on citizen science:
The more specialized and sophisticated scientific research
becomes, the farther it recedes from everyday experience. The
clergymen-amateurs who made 19th-century scientific breakthroughs
are a distant memory. Or are they? Paradoxically, in an increasing
variety of fields, computers are coming to the rescue of the
amateur, through crowd-sourced science.
Last month, computer gamers working from home redesigned an
enzyme. Last year, a gene-testing company used its customers to
find mutations that increase or decrease the risk of Parkinson's
disease. Astronomers are drawing amateurs into searching for
galaxies and signs of extraterrestrial intelligence. The modern
equivalent of the Victorian scientific vicar is an ordinary person
who volunteers his or her time to solving a small piece of a big
Crowd-sourced science is not a recent invention. In the U.S.,
tens of thousands of people record the number and species of birds
that they see during the Christmas season, a practice that dates
back more than a century. What's new is having amateurs contribute
in highly technical areas.
Protein folding is certainly highly technical. The amino-acid
sequence of a protein, determined by a gene, in turn determines the
shape of the protein. Though our cells have no trouble following
instructions for building the protein, predicting that shape from
the amino-acid sequence is fiendishly hard for our minds, even
assisted by computers.
The correct result is usually the structure with the least
contorted shape, but there are so many ways you can go at each step
that you're soon lost in a 3-D jigsaw of astronomically large
This matters to drug designers and organic chemists, because
when they want to come up with a protein that will fit some target,
they have to predict what sequence of amino acids will give the
best shape. David Baker and Zoran Popović of the University of
Washington in Seattle had the idea of farming the problem out to
people who play computer games. Just like any other game, "Foldit" rewards
gamers who collaborate and compete to come up with ingenious
solutions to protein-folding problems.
Already Foldit players, who generally have no background in
biochemistry, have designed proteins with a good fit to the
antigens on the 1918 influenza virus and have helped to figure out
the structure of a retroviral protein.
Now they've come up with over 100,000 designs for an
improved version of an enzyme for catalyzing the Diels-Alder
reaction, which is useful in organic chemistry, but for which no
naturally occurring enzyme seems to exist. A protein that Dr. Baker
had designed didn't work well. The best of the Foldit players'
designs proved to be more than 18 times more efficient.
A similarly exciting result came last year from the firm
23andme, which markets direct-to-consumer genetic testing and now
does research (which it calls "23andwe") by, in effect, comparing
customers with each other. Their first target was Parkinson's
disease, not least because 23andme founder Anne Wojcicki's husband,
Google co-founder Sergey Brin, carries a rare mutation, called LRRK2, that
increases his risk of Parkinson's disease to roughly 50%.
By sequencing many parts of the genomes of 6,000 Parkinson's
patients (and counting) and comparing the data of many of their
120,000 other customers (90% of whom opt in to be part of such
studies), 23andme has found two genetic mutations that seem to raise
the risk of developing the syndrome. The firm also found that genes
at least partly determine when Parkinson's disease develops.
Recently 23andme said it had found a genetic variant, SGK1, that
seems to protect those with Mr. Brin's mutation against the
disease. Assembling and sharing so much data would be a tall order
for the conventional pharmaceutical industry. Crowd-sourced science
seems to be the future.