of Life explored with ITR awards
collaborate with a number of institutions on two separate Information
Technology Research (ITR) large (more than $5 million)
awards announced by the National Science Foundation recently.
The grants total more than $24 million and are two of only eight
awarded from an initial field of 70 proposals.
the second consecutive year UNM is the lead institution on a
large ITR grant. Last year it was the SEEK project led by Biology
Professor William Michener. UNM joins Carnegie Mellon University,
MIT, Cal-Berkeley, Cal-San Diego and the University of Florida
as one of the six institutions ever to be the lead institution
on more than one large ITR grant in the four-year history of
on the $11.6 million, 13-institution effort to develop computational
tools to explore evolutionary relationships among all species
of living organisms forming the Tree of Life. Spearheaded
by Project Director Bernard Moret, professor of computer science
in the School of Engineering (SOE), the main collaborative institutions
also include Florida State University, UC Berkeley, UC San Diego
and the University of Texas-Austin.
is an ambitious project to assemble an evolutionary Tree of
Life that includes all known plants and animals, said
Terry Yates, UNM Vice Provost for Research. It will provide
a predictive and comparative framework for all fundamental and
applied biology. This will basically provide the infrastructure
to allow us to pursue a variety of projects that benefit society
such as new drug discoveries, identify merging diseases and
predict outbreaks, to discover new life forms, to improve global
agriculture and many other things we couldnt do previously
because we didnt know how these organisms were related.
Developing a comprehensive understanding of lifes history
will advance all biology and provide enormous benefits to society.
of a comprehensive Tree of Life is like putting a man on the
moon in terms of the scope of the project...theres a lot
of computational challenges to handle in the assembly of roughly
1.7 million organisms.
the Tree of Life poses one of the most complex biological problems
and represents challenges much greater than sequencing the human
two million species of organisms have been discovered and described,
yet it is estimated that tens of millions remain to be discovered.
Some 60 to 70 thousand species have been studied in some detail,
but the resulting data are far from complete, so relatively
little is known about phylogenetic relationships of Earths
species or among the major branches of the Tree.
the Tree of Life is extremely important we will get a
better picture of how life has evolved on earth, a better understanding
of where we come from as humans, and a sense of where life may
be headed, on a very long time scale, said Moret. Among
the many consequences of obtaining an accurate reconstruction
of the Tree, our understanding of the relationships between
the genetic code and cell functions will expand enormously,
thus accelerating the pace of biomedical discoveries.
in the Tree of Life can be determined by comparing DNA sequences,
the encoded blueprint determining the characteristics of each
organism. The relative similarities between DNA sequences among
different organisms allow scientists to predict the relationships
of these organisms to their common ancestors.
Assembly of a comprehensive Tree
of Life is like putting a man on the moon in terms of the
scope of the project...theres a lot of computational
challenges to handle in the assembly of roughly 1.7 million
Terry Yates, UNM Vice Provost for Research
result is a map that describes species by their relationships
to their close common ancestors and to their more distant relations,
much like a family tree. The map will depict the evolutionary
relationships of Earths taxonomic diversity including
living and extinct forms over the past 3.5 billion years
of its existence. Developing this map has long been a high priority
for biologists, but doing so requires an extraordinary computational
computational problem is extremely difficult, said David
A. Bader, co-investigator on the project and UNM professor of
computer science. Even with entirely novel solutions methods,
an enormous amount of computational power will be required to
construct the first version of such a tree.
of the initiative is to establish a national resource to move
the research community closer to realization of the Tree of
Life. This resource will serve as an incubator to promote the
development of new ideas for this enormously challenging computational
task and to create a forum where experimentalists, computational
biologists and computer scientists share data, compare methods
and analyze results, thereby speeding up tool development while
also sustaining current biological research projects.
order to assemble a Tree of Life we are going to need two different
things. One is a lot of data on existing species, said
dont have nearly enough yet. Then, were going to
need computational methods and computational power to take the
data and make sense out of it.
the goal of our ITR project is to provide the computational
infrastructure including algorithms, software, machines
and databases to support the analysis once more data
have been collected, added Moret.
will do analyses all along the way, of course, but a full-scale
attempt at reconstructing the Tree of Life will not take place
for many years yet: just coming up with methods and platforms
to operate at that scale will take us at least five years, not
to mention that collecting enough
data to support the reconstruction will require the efforts
of teams of biologists all over the world for many years.