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Master of Scaremonies
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A Shadow Biosphere

Could there be aliens here on Earth? While this question tends to bring out tales of UFOs and bug-eyed interstellar voyagers, it is not considered a bizarre urban legend by some astrobiologists. By "alien" they don't mean "coming from beyond Earth," they mean "other" -- other forms of DNA, other amino acids used to build proteins, any other means by which the chemistry of early Earth could have combined to form life we're not familiar with. If there are forms of life on Earth today with a biochemistry not like our own, how would we even know it?

Carol Cleland is a professor of philosophy at the University of Colorado, Boulder, and a member of the NASA Astrobiology Institute. In the third of our series of "gedanken" thought experiments, Cleland explores the possibility that Earth could be host to an undiscovered "shadow biosphere" of alternative forms of microbial life.

A Shadow Biosphere
By Carol Cleland

When scientists speculate about life as we don't know it, they typically have in mind extraterrestrial life. The possibility that the present day Earth might harbor an alternative form of life is rarely considered.

Given that biologists have yet to encounter an alternative form of Earth life, this may seem reasonable. Indeed, if there were alternative forms of life analogous to plants and animals on Earth, we undoubtedly would have stumbled upon them by now.

However, the situation is quite different for microbes, which are too small to be seen with the unaided eye. Could the contemporary Earth be host to "shadow microbes" -- undiscovered alternative forms of microbial life?

Philosophers and scientists traditionally focus upon two characteristics that distinguish a living system from a nonliving system. First, the capacity of a system to maintain itself as self-organized unit against both internal and external perturbations. And second, the ability to reproduce and transmit to its descendants adaptive heritable modifications.

Molecular biology provides an account of how our familiar Earth life realizes these abstract functional properties in a concrete physical system. Life as we know it on Earth today is based upon a complex cooperative arrangement between proteins and nucleic acids. Proteins supply the bulk of the structural material for building bodies, as well as the catalytic material for powering and maintaining them. Nucleic acids store the hereditary information required for reproduction and for synthesizing the enormous quantity and variety of proteins required by an organism during its life span.
The Earth is host to a large variety of species. But could life on Earth be even more diverse than we realize?
Image credit: University of Michigan

The crucial process of coordinating these functions-of translating the hereditary information stored in nucleic acids into proteins for use in growth, maintenance, and repair-is handled by ribosomes, minuscule but highly complex molecular devices composed of both protein and nucleic acid (RNA).

Admittedly, we don't know how different life could be from life as we know it, because we don't know all the ways in which a physical system could realize the functions attributed to life. Moreover, we can't rule out the possibility that the most important characteristics of life have yet to be discovered. The functions traditionally attributed to life may be little more than symptoms of more fundamental but as yet unknown properties.

Some of the molecular building blocks of proteins and nucleic acids could have been modestly different without affecting their biological functionality. Although abiotic processes produce over 100 amino acids of mixed chirality (molecular "handedness"), familiar Earth life constructs its proteins from the same 20 amino acids, and they all have the same "left-handed" chirality. From a molecular and biochemical perspective, this is mysterious. Proteins synthesized in the laboratory from combinations of alternative amino acids or amino acids of the opposite chirality fold into complex three-dimensional structures having structural and catalytic potential. They undoubtedly would be functional in appropriate environments.

Furthermore, with the exception of RNA viruses, all life on Earth utilizes DNA to store its hereditary information. Four bases -- adenine, thymine, guanine, and cytosine -- are arranged in two mutually exclusive pairs to encode the information. But the molecular building blocks of DNA could have been different. As Steve Benner and his co-workers have demonstrated, double-stranded DNA can accommodate at least 12 bases arranged in six mutually exclusive pairs.

Hereditary information is encoded on nucleic acids by means of a unique but somewhat redundant correspondence between amino acids and triplets of bases (codons). But there is little reason to suppose that some codons couldn't have been paired with different amino acids. It has been argued that a triplet coding scheme is the most efficient for 4 bases and 20 amino acids. It is unlikely, however, that the same would be true for a form of life using a different number of bases or amino acids.
DNA bases stacked together along the double helix. The atoms of the sugar-phosphate backbone are shown in gray, and the ultraviolet-absorbing portions of DNA -- the bases -- are shown in blue or magenta, depending on which side of the DNA strand they are located.
Credit: Bern Kohler, Ohio State University.

So why does life as we know it on Earth today use its particular combinations of molecular building blocks? The best explanation is that they are the result of conditions on the early Earth. This is true not only for proteins and nucleic acids, but also for ribosomes. Because they physically realize the translation of hereditary information into functioning, self-maintaining organisms, ribosomes lie at the very heart of the molecular architecture of familiar life. Their unique characteristics are almost certainly the product of historical contingencies. So it is unlikely that the ribosomes found in the cells of familiar life represent the only possibility for translating hereditary information stored on nucleic acids into proteins, let alone the original mechanism utilized by the first proto-cells. Had circumstances on the early Earth been different, familiar life would also have been different.

This opens up a provocative possibility. It is commonly assumed that life originated only once on Earth. But if the emergence of life is highly probable under certain physical and chemical circumstances that were present on the early Earth, then there could have been multiple cradles of life. There must have been natural variations in the collections of organic molecules available in different regions on the early Earth. Assuming that life did originate on Earth and was not transported here from elsewhere, then it is unlikely that the first forms of Earth life were all built from exactly the same molecular building blocks.

While many biologists and biochemists are willing to concede that the first proto-organisms may have used different molecules, few are willing to take the next step and seriously entertain the possibility that their microbial descendents may still be with us today. Three reasons are commonly cited. First, any variations in the earliest forms of life would have been combined by lateral gene transfer into a single form of life. Second, our ancestors would have eliminated other life forms long ago in the ruthless Darwinian competition for vital resources. And third, if alternative forms of life existed, we would have discovered them, or at the very least stumbled upon signs of them. But as my colleague Shelley Copley and I have argued, none of these reasons stand up under close scrutiny.

"Lateral" gene transfer is when genes are transferred from the genome of one microbe to that of another, rather than being transferred "horizontally," from parent to child. Lateral gene transfer is very common among microbes, occurring among widely different varieties, including those from the different domains of life (Archaea, (Eu)bacteria, and unicellular Eukaryia). Not unsurprisingly, lateral gene transfer is thought to have played a central role in microbial evolution. Carl Woese speculates that the earliest proto-cells engaged exclusively in lateral gene transfer. He contends this process would have combined any alternative forms of primitive life into a single homogenous pool of proto-cells, from which life as we know it today eventually emerged.

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