archive: SETI [ASTRO] Who Wrote The Book Of Life?

SETI [ASTRO] Who Wrote The Book Of Life?

Larry Klaes ( lklaes@bbn.com )
Fri, 28 May 1999 14:17:18 -0400

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>Date: Fri, 28 May 1999 17:33:25 GMT
>From: Ron Baalke <BAALKE@kelvin.jpl.nasa.gov>
>To: astro@lists.mindspring.com
>Subject: [ASTRO] Who Wrote The Book Of Life?
>Sender: owner-astro@brickbat12.mindspring.com
>Reply-To: Ron Baalke <BAALKE@kelvin.jpl.nasa.gov>
>
>
>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.
>