By Joannie Fischer
before has a new academic discipline burst so explosively into higher
education's hallways. Ten years ago, hardly anyone had even heard
of the newly coined term bioinformatics, but today, it dominates
the agenda of dozens of top universities across the country. They are
all racing to play a role in the hottest research arena on earth, one
that will redefine medicine forever, rewrite the story of how human
beings came to exist, and reveal the inner workings of the body and
the mid-1990s, advances in DNA sequencing have promised to change our
understanding of humanity and all other living creatures. But suddenly,
the completion of the human genome sequence and that of several other
animals over the past year has transformed the young bioinformatics
industry into the fastest growing field ever, with an almost insatiable
appetite for new researchers and new labs to analyze the mind-boggling
amounts of computer-generated data. In tremendously short order, bioinformatics
has traded the problem of a paucity of information for an embarrassment
of riches, and researchers are literally lost inside all of the information.
Once, you could print out most of the existing sequence databases
onto paper and cram them into a single binder, recalls Damian
Counsell, head of the bioinformatics department at the Institute for
Cancer Research in London. Now a search for actin
(one of the body's 200,000 proteins) will pull out hundreds and
hundreds of lengthy sequences.
States' publicly accessible genome database, GenBank, maintained
by the National Institutes of Health, already includes close to 13 billion
pairs of DNA letters, and is on pace to double in size every
year for the foreseeable future. A similar database called BLAST gets
more than 50,000 hits per day from scientists comparing the properties
of new genes they've found to ones that are already documented
in the database. Genome giant Celera's Craig Ventor predicts it
will take a century of constant research to understand the data that
has been produced so far. The promises of such a tireless endeavor are
especially great for human health. Bioinformatics could usher in a whole
new era of completely individually-tailored medicine.
a baby's genotype will be recorded, and a program of personalized
immunization, lifestyle management, and refined treatments will be developed
to target disease, says Phyllis Gardner, a Stanford dean who
is helping to launch the school's bioinformatics program.
that promise, she says, requires an army of scientists with abilities
that cross traditional disciplinary boundaries, [but] the dearth of
faculty trained across these disciplines is a global phenomenon.
Much Too Soon
Peltonen, chairwoman of the Department of Human Genetics at UCLA, says
that industry and academia alike were poorly prepared to handle this
avalanche of information, partly because no one realized the data would
start pouring in so soon. The need has grown drastically for trained
specialists and won't dry up anytime soon, she says. The National
Science Foundation estimates that 20,000 new bioinformatics jobs will
be created by 2005, and market estimates show the field is growing at
a phenomenal 50 percent annual rate and will remain at 25 percent or
above far into the future. And the growth is likely to accelerate as
the computerized study of genetics spreads from human medicine to animal
and plant research to agriculture. Twenty-five percent of all venture
capital money now goes into new life-sciences start-ups, which in turn
are hiring academics away from campuses at a dizzying speed, leaving
schools crippled in their ability to offer high-quality training for
this new research frontier.
interest in the new field is keen. Peltonen notes a huge leap in the
number of graduate students interested in bioinformatics, up 10
times from interest levels a year or two ago. One lure is the
lofty salaries: Unlike other fields where Ph.D.s face uncertain employment,
those talented in both biology and computer science enter into the field
at over $90,000 a year, almost double the entry-level computer scientist
salary and almost triple that of an average beginning biologist. Colleges
and universities are scrambling to meet student interest and industry
demand by coming up with the right combination of curricula, facilities,
and brainpower to train tomorrow's bioinformaticians.
no easy matter, says the first faculty to try to tailor the new programs.
Because bioinformatics is highly interdisciplinary, it requires
a significant course exposure to chemistry, biology, and math/statistics
courses, says Kenneth Marx, chemistry professor at the University
of Massachusetts, Lowell, who helped design a new bioinformatics/chemoinformatics
curriculum implemented last year. This high demand for different
courses makes it difficult to fit within the traditional four-year academic
structure for an undergraduate degree, as well as the course requirements
for M.S. and Ph.D. degrees. Furthermore, he adds, traditional
academic departments are hesitant to train Renaissance individuals
in all these academic disciplines. However, the marketplace will
drive academic departments to accommodate the necessary training.
has indeed become the ultimate interdisciplinary study area and will
forever blur the lines between engineering and biology, bringing together
researchers who previously spent their entire careers not interacting
with one another. But the new field is too complicated to be prepared
for simply by doubling up on traditional biology and computer courses.
Counsell calls bioinformatics a special kind of engineering discipline,
and attributes the burgeoning field's success to the fact that
it is driven by the characteristically practical and rigorous
approach of engineering. At first, bioinformatics was seen as
dealing specifically with sequence analysisfiguring out the genetic
lettering of everything from frogs to ferns. But as one genome after
another becomes completed, bioinformatics is moving into the post-genomic
age, and the field focuses on a whole array of additional endeavors.
Some research is aimed at comparative genomics: looking for key commonalities
or differences between the DNA of various species to learn more about
each type of creature and about evolution in general. One of the largest
areas of focus is now shifting from the genes themselves to the structure
and function of their productsnamely the proteins that carry out
the work of a body's daily life.
new area of research informatics is arising, in which all
data collected on any particular molecule are kept together and compared
in order to give a fuller picture of that entity, be it a new drug candidate
or one of the body's own proteins associated with battling cancer.
The computer software programs now being designed to advance the research
fall into four broad categories: those that search through sequences
of genes, those that analyze the sequences, those that predict the structure
of particular proteins, and those that provide imaging of molecules.
The computer power needed to drive the research is unprecedented. Until
now, the most complicated data handled by governments, industry, and
research was measured in terabytes (a trillion bytes). But bioinformatics
will soon become the first industry in which researchers measure their
data in pedabytes (a quadrillion bytes).
bioinformatics is the most challenging and promising area of research
to face both the life sciences and the computing worlds in recent memory,
most educators now agree that no biology degree or computer science
degree is complete without bioinformatics training. And because of the
new understanding it offers of the human body, some educators are pushing
to make bioinformatics courses a requirement in all medical schools.
Many note enthusiastically that the new field rejuvenates the older
disciplines, allowing biologists to escape the lab and computer scientists
to escape dull database work. But it also requires typically different
personality types to change their attitudes and aptitudes. Biology has
long been considered the least mathematical of the sciences, focusing
on wet, living things and their relationships to one another.
The dry, numbers-oriented, non-messy computer
science area has allowed people to work for years in virtual isolation.
But London's Counsell likes to joke to computer programmers that
you are as likely to be useful to biologists working in isolation
at the keyboard as you are to conceive a child with your clothes on.
president of the International Society for Computational Biology, adds
that these gaps are not bridged simply by taking a computer scientist
and then training him or her in biology. Not only is that process too
slow, expensive, and cumbersome, he says, but it does not reliably instill
some of the key traits necessary to perform bioinformatics successfully.
Altman has published a proposed curriculum for bioinformatics that serves
as a model for several universities now establishing major new centers,
including Stanford, Princeton, and the University of Chicago.The University
of California, Berkeley, is launching a half-billion dollar research
initiative that links a range of scientific disciplines to create a
facility to prepare the best minds in genomics. The initiative will
require a rethinking of the entire science education curriculum,
say leaders, and both undergraduate and graduate education at the school
will be permanently altered as a result.
are certainly not alone in their conviction that bioinformatics is the
key to their future. States such as Michigan, Georgia, and North Carolina
all see bioinformatics initiatives at state colleges as a way to spur
state economies and prestige, and state legislators are looking for
ways to give even more incentives to universities and businesses to
cooperate toward the goal. The National Institutes of Health has
persuaded the U.S. government to spend $10 million to fund 20 new biomedical
computing programs of excellence. And private foundations
are getting in on the act, too. For example, Johns Hopkins University
is launching a new computational biology program with the help of a
$2.5 million grant from the Burroughs Wellcome Fund. The Alfred P. Sloan
Foundation will fund new bioinformatics master's degree programs
starting this fall at several universities, among them the University
of California's Los Angeles and Santa Cruz campuses, the University
of Texas at El Paso, the New Jersey Institute of Technology, Boston
University, and Northeastern University. And in March, Renssalaer Polytechnic
Institute received an anonymous $360 million donation, the largest gift
ever to a U.S. college, and will direct a significant portion of the
money toward state-of-the-art biomedical computing facilities.
the most progress is being made by schools that forge aggressive and
substantial partnerships with industry and government. By forming the
Corporate Associates Program, Harvard has managed to avoid brain
drain by drawing on top minds in area biotechnology companies
to mentor its students. Even larger-scale partnerships are in the works,
such as in Virginia, where Virginia Polytechnic Institute is now spearheading
the launch of the Virginia Bioinformatics Institute, which will eventually
total a $100 million effort. The state government kicked in $12 million
to help get the Institute off the ground. So far, the project employs
25 researchers who share their expertise in physics, mathematics, biology,
and engineering to solve cutting-edge problems in bioinformatics. Next
year, the institute wants to double in size again, and one day, officials
hope to house 300 researchers there.
effort pales in comparison with a project afoot in North Carolina, where
more than 40 nonprofits, corporations, and public and private universities
have pooled their resources to become world leaders in the bioinformatics
field. For its part, Duke University may spend $200 million to create
an Institute for Genomic Sciences and Policy. Duke will cross-train
students and faculty together with North Carolina State University,
which recently opened the North Carolina Bioinformatics Research Center,
home to about 30 faculty and 40 graduate students. Wake Forest will
spend nearly $20 million for a new center, and UNC-Chapel Hill will
put $100 million toward advancing genomics research capabilities. The
massive campus spending is underwritten in part by grants from institutions
such as the National Science Foundation and the National Institutes
of Health. Some biotech corporations in the consortium are funding graduate
students' education in order to get the highly-skilled new employees
they so desperately need.
than looking for a corporate partner, faculty members at the University
of Massachusetts, Lowell, decided to create their own spin-off company,
AnVil Informatics, that helps the university by funding graduate students,
and in turn benefits by having the first crack at hiring the optimally
trained graduates to help develop the company's suite of data mining
and high dimensional visualization tools.
have decided to tackle the informatics revolution by carving out a particular
niche in the market. The University of Pennsylvania, with sponsorship
from a company called Pangea Systems, will use its new Center for Bioinformatics
to specialize in developing new software that can help researchers visualize
the biological data they study. The University of Massachusetts wants
to hire about 15 new faculty devoted to the study of exactly how genes
cause both healthy functioning and the onset of certain diseases. Harvard's
Institute for Proteomics (the area of bioinformatics that studies the
form and function of proteins) is creating a collection of cloned copies
of all known human genes in a massive storage system, or warehouse,
that could be conveniently used by researchers everywhere who want to
order a certain gene for a particular experiment. And MIT's Center
for Genome Research is using DNA chips to measure the actions of thousands
of genes all at the same time in an attempt to find the key differences
between various types of cancer. Led by top researcher Eric Lander,
the group has already identified the important distinctions between
two types of leukemia. Only by studying multiple genes at once can researchers
hope to get a true sense of how different diseases start.
one school, the new Keck Graduate Institute in California, has decided
to create a professionally oriented master of bioscience program that
combines bioinformatics training with more traditional business leadership
education so that students will emerge from the two-year program with
not only the skills that a master's in science affords but also
the talents conferred by an M.B.A. Already, science education consultant
Sheila Tobias has dubbed the bioinformatics degree the M.B.A.
of the new century. Adding business management skills to the mix
will only enhance the cachet of the new trainees, she says.
Hughes Medical Institute in Chevy Chase, Md., promises to steadily increase
the quality of bioinformatics scholars throughout higher education with
the $500 million it will use to build the Bell Labs of biology
near Ashton, Va. One of the world's top research institutions,
Howard Hughes already boasts more than 350 leading scientists who work
out of host universities across the nation. This time, the
institute will create its own campus with a staff of about 25 permanent
chief scientists, all with their own research staffs, plus
a revolving crop of visiting scientists from campuses and corporations
around the country.
genome chief, Francis Collins, has often said that the human brain is
far too puny to comprehend the full range of benefits that will emerge
from bioinformatics endeavors. Among the fruits of current efforts is
likely to be the know-how to fix faulty genes, discover new drugs, and
test their safety without using human guinea pigs: cure diseases; and
create disease-resistant plants and animals. For Jeff Bizarro, executive
director of the nonprofit Bioinformatics.org, and many fellow pioneers
in the new field, some of the sweetest rewards will be the intellectual
satisfaction of the knowledge itself. I think nearly all bioinformaticists
would agree that the most exciting promise of bioinformatics is...that
we can fully understand the nature' of life. Bizarro
is keen to discover, for example, where life originated, what makes
one organism different from another, what makes one being different
from another, where life is headed, and if and how humans can alter
their paths by extending and improving life. Part of me hopes
that the most interesting questions are yet to come, that there will
always be plenty of science to be done, Bizarro says. But
another part hopes that I will live to know all the answers. For
the first time in history, such a hope actually seems plausible.
Fischer is a freelance writer based in Palo Alto, Calif.
She can be reached at firstname.lastname@example.org.