virus: Fwd: Life: What Exactly Is It?

Wade T. Smith (morbius@channel1.com)
Sat, 26 Jun 1999 20:06:06 -0400

This is the first article from
http://www.biomednet.com/hmsbeagle/57/viewpts/synopsis -a site requiring free membership, but it's a goodie, IMHO.


Life: What Exactly Is It?

Synopsis

In science, the basic questions are often the most difficult to answer. Philosophers and biologists alike have been struggling for centuries over the basic question, What is life and how is it defined?

Although there have been tremendous advances in both technological possibilities and knowledge concerning our understanding of the components of life, the actual working definition has not changed substantially for many years. What has changed is where the boundaries lie and how far each advance in the quest to unravel the ultimate question pushes those boundaries.

This debate approaches the question from a variety of different fields, including biochemistry, evolutionary microbiology, philosophy, zoology, computer science, and top-level gene research. Collectively, the opinions form a fascinating vista of current thought on the evolution of life and its origins, as well as the basic components all agree must be present.

Taken from Elsevier Science's ScienceChannel, the current debate has a different form than most others published in HMS Beagle. The participants do not exchange views; they contribute only once, and briefly. We welcome your comments as well.

The debate begins with biochemist Stanley L. Miller, whose early experiments (1953) with amino acids gave rise to the term "prebiotic soup." By showing that amino acids, the building blocks of proteins, could be synthesized by naturally occurring spark discharges in the atmosphere, his research supports the idea that life occurred naturally on Earth early in its history. These conditions exist on other planets as well. "If you have the same conditions you had on primitive Earth on another planet, then you make the same compounds, and presumably you would get life. It's simple chemistry," Miller states.

It is not the amino acids themselves that make them "living," Miller points out, but their ability to self-replicate. This key point is echoed throughout the debate, from a variety of different views. But Miller goes further in stating that "the origin of life is the origin of evolution," which requires three things: replication, selection, and mutation. "We can define what it would take to replicate and become life, but to actually show what happened 3.5 billion years ago, we don't know."

Miller is skeptical about discussions on the definitions of life, but biologist Antonio Lazcano disagrees: "I think the question is a fascinating, philosophical quest, but biologists are frequently accused of not being able to provide a basic definition of life. Try asking a physicist what space is, or energy, and you will see they have the same problem."

Lazcano is skeptical of the theory of the prebiotic synthesis of RNA in the primitive waters of Earth. He raises the question, What happened in the intermediate stages that gave rise to catalytic RNA? His research focuses on understanding the origin and early evolution of life by making comparisons between gene sequences.

Lazcano points out the historical changes in our definition and understanding of life. At the turn of the century, life was minimally defined as photosynthetic unicellular organisms. "Some people would say that as long as you have a single molecule that is able to replicate and evolve, that is enough. My own tendency is to define life as a system that is able to undergo Darwinian evolution," he states. He further defines this as "a chemical system that can actually undergo a process of mutations and rearrangement of the genetic material, and can adapt to the environment." Two classic exceptions to the rule that life must be both carbon-based and self-replicating are nuns and mules. Lazcano is ready for that argument: "Keep in mind that mules, nuns, or my grandmother, for that matter, may not reproduce but are the outcome of biological evolution, and that every single cell in their bodies does reproduce."

Lazcano sadly refers to Western science as "this enormous building that has clay foundations, grounded on the absence of deep philosophical inquiry of the essential points." Philosopher and systems scientist Mark Bedau agrees that the basic definition of life falls between the cracks of several disciplines; philosophers say it is a biological question, whereas biologists refer back to philosophy.

In Bedau's opinion, the whole question is much more complex than most people realize and is often confused with other questions: What is the nature of life, and how do people conceive of it? "The true 'nature' of life may be quite different from the way we think about it. . . . people always assume that examples of things that are alive are like us: a tree, maybe a single cell; they typically think of whole organisms," he says. Bedau believes it is an essential question to address - not only for philosophers, but for those studying origins of life and exobiologists -
"because you have to ask 'the origins of what?'"

He refers to his own research as "the philosophy of biology and the mind," which strives to look at questions such as, What does it mean for a system to be evolving, and what is it that enables a system to show a boundless growth in evolutionary creativity? "This might be happening in real-world evolutionary systems such as the biosphere, the global economy, technology, and a variety of other systems that show exponential growth in evolutionary creativity," he notes.

According to Bedau, "Primarily, we should call life a system that is undergoing supple adaptation, or open evolution. It means adapting and continuing to adapt as circumstances change in an open-ended way; being able to respond appropriately in a variety of ways as circumstance requires." For him, the key issue is whether it allows a system to survive and flourish at its most basic level. "The things that we now call alive are unified by this process of a supplely adapting system like a complex and adaptive organization. . . . What I claim is that the thing that is primarily alive is the whole biosphere and not things like us. In that way, it makes sense that all of those hallmarks of living things are present. . . . If you find a process of supple adaptation, then you find life."

Zoologist Thomas Ray, who created the artificial life system Tierra, agrees that the definition of life goes far beyond being carbon-based but must include evolution and self-replication. "Tierra is an instance of evolution independent from the evolution of life on Earth. It's the process of evolution embedded in the medium of digital computation, rather than the medium of carbon chemistry."

Ray points out that our only example of evolution is Earth itself, and although science is trying to broaden the concept of life and evolution, even examples found on other planets would probably also be carbon-based.
"Tierra is an independent example of evolution that is not carbon-based,
built from self-replicating, evolving machine codes," he adds.

Tierra works by using a computer as the environment that houses the
"organism," or computer program. As Ray describes it, "The Tierra server
creates a space where digital organisms can come in off the network and live off the energy provided by your CPU cycle and occupy the space provided by your RAM memory. Think of it as a wildlife preserve, or a piece of rain forest that we have set aside to protect."

For Ray, defining life would require making a list of qualifying characteristics. "For example, it has to reproduce, evolve, have self-repair, development, metabolism, etc. The problem is that we can't agree on what to put on the list. Some of those items may be peculiar to our one example of life and not general properties of life. There is no agreed-upon list."

Ray sees himself as a sort of "refugee" from the question of defining life. "Developments like Tierra have forced us to deal with the issue. It's no longer just science fiction. Now they are in our world. I have started to avoid the question of defining life because the word 'life' is emotionally charged. . . . That's why I refer to Tierra as an evolving system; it doesn't have the same definitional problem as 'life' does."

The last participant in the debate has also come face-to-face with the emotionality of the question. Claire Fraser is president and director of The Institute of Genomic Research (TIGR), an organization recently accused of trying to "create life in a test tube." The institute is responsible for pioneering research on the first complete genetic sequence for a free-living organism. "This was a milestone in genomics and microbiology. It provided us with a complete view, for the very first time, of all of the genes that are required of this particular organism to divide, to cause disease in humans, and do all of the things it does."

The initial elation of such a feat quickly led to the stark realization that knowing the entire gene sequence of an organism would not automatically provide all the information required to understand all the biological workings of the organism. According to Fraser, "40% of the genes in this organism were new genes that had never been described before. There were genes for which we could assign no biological function. Four years later, we still know almost nothing about them."

Fraser notes that "there is a lot of very basic biology that we simply don't understand." The first experiments were followed by others on an even simpler organism: a human parasite called Mycoplasma genitalium, which exists in several places in the human body. This organism has only 470 genes. "To our amazement, this simplest of all free-living organisms still contains about 30% of genes that were new and of unknown biological origin."

In the process of trying to define which of these genes were more important, less important, or vitally important to the survival of the organism, TIGR was accused of trying to create life. "We used a microbiological technique called transposon mutagenesis that allows you to disrupt the coding sequence in the gene, one at a time, and essentially eliminate its functioning in the cell," Fraser explains. Through this process, TIGR is attempting to define what genes are required for life in the laboratory setting. "The genes we identify under these conditions may not be, and are very likely not, the same set of genes required for growth in a human host," she emphasizes. "The idea of creating life in a test tube, or creating an artificial chromosome, came from our realization that to rigorously test our hypotheses of essential versus nonessential genes, we would have to be able to come up with a new chromosome that contains a reduced set of genes. That gets into some very complicated technical and ethical challenges."

Like the other participants, the key for Fraser is self-replication. "Our definition of life requires that it is able to replicate DNA. The problem is that there are so many technical hurdles to overcome. And we did not set out to answer the question, Can we create life in a test tube? . . . Recent advances in our knowledge have helped to clarify for me how little we understand about life, or what is required for an organism to live. But it has not redefined life. . . . We still have a tremendous way to go before we can really answer the question, What is life?"

A fascinating puzzle and perhaps one of the oldest questions in science: What exactly is life?

Andrzej Krauze is an illustrator, poster maker, cartoonist, and painter who illustrates regularly for HMS Beagle, The Guardian, The Sunday Telegraph, Bookseller, and New Statesman.

1999 BioMedNet Ltd. All rights reserved.