Who Wrote The Book of Life?

Picking Up Where D'Arcy Thompson Left Off

Correction -- June 4, 1999: The speed of the Leibniz computer was originally quoted as 12 Gflops. In fact the speed is much closer to 1.2 Gflops. We regret the error.

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.

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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."

Left: Karner Blue butterfly. Photo credit: US Fish & Wildlife Service/John & Karen Hollingsworth.

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.

Right: Professor D'Arcy Thompson (1860-1948) of the University of St. Andrews in Scotland.

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.

Left: Three shapes of microbial life. Photo Credit: University of Miami Department of Biology.

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 computer. NASA developed the Beowulf Project to address scientific problems associated with large data sets.

Left: The logo for the Beowulf Project shows the Anglo-Saxon hero Beowulf encircled by LINUX penguins. A Beowulf-class computer is a cluster of personal computers running LINUX, connected by its own private LAN (Local Area Network).

Scientists at Marshall have named the new parallel computer "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 computer 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.

Left: How the computer neural network sees microbial life forms. From left to right: rods, cocci, filaments. An 8x8 pixel microbial image represents a 64-dimension classification problem, with a pixel array where each binary [0 or 1] value requires a connection in the neural network. Although the microbial images must be simplified in the same way that computer scanners reduce alphabetic letters to a skeleton representation, the basic templates for classifying microbial shapes can still discriminate enough to give identifications. These images were included in the paper, "Microbial Morphometry: Automated AI Approaches," presented at the 50th anniversary D'Arcy Thompson conference by Dr. David Noever of NASA/Marshall.

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."

Left: Thompson's sketches of human, chimpanzee and baboon skulls overlaid with mathematical grids.

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 computers 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.

Right: Mission Specialist Richard Linneham works out to combat the effects of microgravity onboard Space Shuttle Columbia.

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 Linux-based computer at Marshall speeds up this process dramatically, processing over a billion connections per second.

Web Links

The Beowulf Project - Developed by NASA to run complex scientific computer programs. NASA Institute for Advanced Concepts Origins Project -at NASA's Jet Propulsion Laboratory Search for Extraterrestrial Intelligence - SETI Institute homepage Astrobiology at NASA - Ames Research Center Meteorites from Mars - National Science Foundation with NASA's Johnson Space Center.

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.

Right: The Allan Hills meteorite (ALH 84001) discovered by ANSMET is believed to be of Martian origin. A possible microfossil found in a sample of the meteorite measures less than 1/100th the width of a human hair.

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.

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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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Author: Leslie Mullen Curator: Linda Porter NASA Official: Gregory S. Wilson