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Who Wrote The Book Of Life?


Who Wrote The Book of Life?
Marshall Space Flight Center
http://science.nasa.gov/newhome/headlines/ast28may99_1.htm

Picking Up Where D'Arcy Thompson Left Off

May 28, 1999: During the May 18th press conference announcing Nobel Laureate
Dr. Baruch Blumberg as the new head of NASA's Astrobiology Institute,
Blumberg posed a challenge to the scientific community.

"The mission is to look for life without any specifications. Nothing in the
mission would preclude looking for rather strange and unusual life forms
that we can't even imagine right now," said Blumberg.

NASA Administrator Dan Goldin concurred, stating, "We're looking for any
form of biological life. Single-cell (organisms) would be a grand slam."

In order to effectively search for life on other planets, we first have to
come to an understanding about what life IS. One way to do this is to study
the forms that life can take.

In his 1917 work, "On Growth and Form," D'Arcy Thompson altered mathematical
functions in order to visualize how species changed shape over time.

NASA scientists are using Thompson's biomathematical studies of life forms
on Earth to postulate about life forms throughout the universe. There are
certain universal conditions that will always affect the shape of a life
form, wherever that life may be.

"Everywhere Nature works true to scale, and everything has a proper size
accordingly," wrote Thomspon. "Cell and tissue, shell and bone, leaf and
flower are so many portions of matter, and it is in obedience to the laws of
physics that their particles have been moved, moulded and conformed."

Gravity, for instance, acts on all particles and affects matter cohesion,
chemical affinity and body volume. Other influences that are consistent
throughout the universe are temperature, pressure, electrical charge and
chemistry.

But before we can conduct a comprehensive search for unknown
extraterrestrial forms of life, there needs to be an extensive
classification of known life forms on Earth. The history of life on Earth
provides us with a good model for how life can evolve in the universe.
Fossils, even microbial fossils, can tell us a great deal about all the
different life forms that have at one time or another shown their face on
our planet.

"Some fossils in the ancient Burgess shale are so alien we can't determine
which end of the creatures are up, and yet these monsters evolved right here
on Earth from the same origins that we did," wrote Johan Forsberg, a Swedish
psychologist.

By becoming forensic scientists, researchers at the Space Sciences
Laboratory at the Marshall Space Flight Center can develop an encyclopedia
of microbial life forms that have developed on Earth. Because so many life
forms need to be catalogued, the scientists are working to develop a "D'Arcy
Machine" to help them create a comprehensive "Book of Life."

This Book of Life project has three phases. Phase 1 - compiling a beginning
database of microbial life forms - has already been completed. This image
database is composed of 10,000 examples and distinguishes the basic
microbial shapes such as rods, spheres, filaments, clusters that look like
grapes (cocci), and spirochete (spirals). A computer neural network has been
trained to recognize and classify these microbial life forms with 90 percent
accuracy.

Phase 2 of the project will expand the basic database by using a more
powerful neural network. Funds from the NASA Advanced Concepts Office
provided Marshall scientists with a Beowulf-class parallel supercomputer.
NASA developed the Beowulf Project to address scientific problems associated
with large data sets.

Scientists at Marshall have named the new parallel supercomputer "Leibniz,"
after the German mathematician whose lifelong goal was to organize all human
knowledge. This computer system will expand the image database by acquiring
and classifying new and ambiguous images. To discriminate organic life forms
from inorganic shapes, microbiologists often use the vague criteria, "Does
it look alive to you?" A parallel supercomputer using pattern recognition
can make this task easier and more exact by breaking the starting image down
into identifiable parts.

"Human judgement is still very much depended upon for identifying microbial
life forms," says Dr. David Noever of NASA's Marshall Space Flight Center.
"Automated filters would be much like the filters commonly used to sort out
useful e-mails from useless ones. The user of the neural network would get a
morning menu of microbial candidates for further detective work."

Although the trained human eye is better at recognizing microbial life
forms, using a computer "filter" to check for life-like patterns could help
cut the immense scale of the Book of Life project down to a more manageable
size.

By Phase 3 of the project, the neural network will be so advanced in its
learning that it will be able to acquire and classify new images with
minimal human supervision. This network would then be equipped for future
search scenarios, including the examination of meteorites found on Earth and
samples retrieved from lunar or interplanetary space missions. This advanced
neural network will be a fast and efficient classifier of the vast amount of
microbial images that will need to catalogued.

A Big Problem

This speed and efficiency are extremely important due to the detail with
which the samples must be analyzed. Not only are there a lot of samples to
study, but there are multiple dimensions to consider. D'Arcy Thompson used
mostly linear and quadratic maps to compare different life forms. Linear
maps between two shapes require four coefficient variables, while quadratic
maps use 10 variables.

Thompson wrote in "On Growth and Form," "I know that in the study of
material things number, order, and position are the threefold clue to exact
knowledge: and that these three, in the mathematician's hands, furnish the
first outlines for a sketch of the Universe."

While Thompson and other biomathematicians used almost exclusively linear
and quadratic distortions to study how life forms change over time, it is
unlikely that complex life forms throughout the universe will be confined to
these narrow statistical relationships. In a paper presented last September
at the 50th anniversary D'Arcy Thompson conference in Dundee, Scotland,
Noever asked, "What if D'Arcy had had a computer?"

When D'Arcy Thompson introduced the idea of studying organisms by their
geometric shapes, he could only draw figures by hand. The supercomputers of
today can take Thompson's research much further. By repeatedly comparing and
contrasting learnable imagery, a D'Arcy machine would expand the chapters of
the Book of Life Project and give us an interplanetary version of D'Arcy
Thompson's classic "On Growth and Form."

Computers with artificial intelligence using neural networks provide more
opportunities to answer complex astrobiology imaging questions. The
non-linear evolution of artificial intelligence is customized to handle the
learning of multiple patterns or images. Computers with artificial
intelligence could accommodate various influencing variables (such as
gravity) that change over scales much larger than a linear variance can
include. Changes in the effects of gravity on a body can occur, for
instance, when humans go into outer space. Astronauts often experience fluid
retention, excessive bone loss and muscle wasting due to the effects of
microgravity.

The neural network at Marshall will be able to rapidly process the complex
computations necessary for mathematically analyzing the shapes of life
(morphometrics). If someone continuously used a hand calculator to tabulate
just linear connections, at a rate of one calculation per second it would
take forty years to finish a billion calculations. The 12 GigaFlop
supercomputer at Marshall speeds up this process dramatically, processing 12
billion connections per second.

Writing the Interplanetary Book of Life

The powerful capabilities of a D'Arcy classification machine could also be
used to study and catalogue images from the 14 known Martian meteorites. The
total mass to be scanned exceeds 20 kilograms (44 lbs.), so if micron scale
images are included in future projects (1 micron is 1-millionth of a meter,
or 1/25,000 of an inch) the combined image handling capabilities for
biogenic classification will exceed several trillion frames.

"Looking for life forms in Mars rocks means analyzing microfossils - like
potential nanometer-size - so small that 50,000 could fit across the width
of a single strand of human hair," says Noever.

Based on past performance, the Antarctic meteorite (ANSMET) field teams are
likely to recover at least 1,000 meteorites over the next three years.
Although it is likely that only a small fraction of these meteorites will be
of interest scientifically, already AMNSET has discovered 28 meteorites that
are often sampled for study. Since 1976, 301 individual investigators
representing 24 nations have received more than 10,800 meteorite samples.

To put this scale of computer acquisition and search in context, compare it
to the challenge of creating the 1996 animated feature "Toy Story." It took
nearly 3 hours for a supercomputer to process each one of that film's
140,000 frames. The challenge of classifying images of life forms
constitutes a task exceeding the creation of more than 10,000 high quality
computer-animated films.

Life is not an easy thing to define. Even now, we're finding life forms on
Earth that we never before thought possible. Extremeophiles (bacteria that
live in extreme environments) have recently been found living in
hydrothermal vents and in high salt environments - areas once thought to be
completely inhospitable to life. In 1997, Stephen Zinder of Cornell
University discovered the existence of bacteria that thrive in the harsh
solvents perchloroethylene and trichloroethylene that are used to clean
machine parts. An acid-loving bacteria, Sulfolobus acidocaldarius, can live
under conditions that would dissolve human skin in seconds.

By using a D'Arcy machine to begin a morphometric study of microbial life on
Earth, someday remote and automated instruments may be able to identify life
elsewhere in the universe - whatever form that life may take.

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