by David Toomey
Finally, there is the possibility—this perhaps the strangest of all—of weird microbes and familiar microbes in symbiotic relations that benefit both, trading chemical compounds, enzymes, or even genes. Symbiotic relations in the microbial realm have a long history—a history demonstrating that, contra ideas of nature as “red of tooth and claw,” there is as much cooperation as competition, and perhaps a good deal more.* Consider the strange case of mitochondria, the organelles that perform respiration and generate chemical energy. It is thought that some 3 billion years ago they were oxygen-respiring purple bacteria and microbial nomads, finding comfort and sustenance where they could, and otherwise making do in a harsh world. Then, one or several of them found refuge in the warm, wet, pH-balanced interior of a cell, and took up permanent residence. Others followed, and achieving survival more by snuggle than struggle, host and guest eventually negotiated terms. The cell provided the bacteria protection, and the bacteria supplied the cell with oxygen-derived energy and disposed of its waste. In the fullness of time, the arrangement developed into a codependency so complete that today, the cells in your body would die without the mitochondria inside them.
If weird microbes exist, it is possible they’ve established similar arrangements with familiar microbes. They would comprise a biosphere biochemically integrated with our own. If ecologically separate weird life is the person you’ll never meet, and ecologically integrated weird life is that utterly silent and all but invisible boarder, then biochemically integrated weird life is the roommate who shares your toothbrush, borrows a twenty from your wallet and forgets she did it, but at regular intervals thoughtfully leaves a bouquet of flowers and a bottle of wine on the kitchen table.
At least in theory, there is no good reason to suppose that weird life doesn’t exist on Earth. Suppose, then, that it does. The prospect is exciting for all the same reasons that the prospect of life on other worlds is exciting—perhaps more so, for the simple reason that weird life on Earth might be easier to find.
The search for life on other worlds—which began in earnest with recommendations from NASA subcommittees in the 1960s—has proved more challenging than many had anticipated, and it is unlikely to yield results anytime soon. The difficulty lies in the distance between researchers and their possible subject. Earthbound astronomers using long-range detection techniques like spectrometry can examine the atmospheres of planets and moons in our Solar System—and when conditions are right, some planets in other systems—for chemical compounds commonly called “biosignatures” that may have been produced by living organisms. But without on-site study by astronaut-scientists, sample-return missions, or at the very least, sophisticated unmanned probes, they can’t know whether such compounds are true biosignatures or merely the product of an exotic chemistry.* To date, the only in situ search for life elsewhere came in NASA’s Viking missions—with results that were inconclusive. The next-generation Mars Science Laboratory, which began its journey to the Red Planet in late 2011, is designed to answer questions about how well the Martian environment is suited to life, not to seek life directly. At the time of this writing, missions to Mars and elsewhere designed specifically to look for weird life are distant prospects at best.
By way of contrast—and this is a point Davies and Cleland make rather tirelessly—a systematic search for weird life on Earth could begin immediately and at a far lower cost. The only real question is how best to go about it.
SEEKING WEIRD LIFE ON EARTH
In a search for weird life on Earth, the standard tools and techniques for identifying microbes are unlikely to be of much help. The similar appearance of archaea and bacteria under a microscope suggests that their shapes—spheres and rods—have real evolutionary advantages, and we can expect that weird microbes will look much the same. Staining can highlight gross features of cells, but it can miss smaller ones, and these might be the very features that make the cells weird. Attempts to culture weird microbes would be especially challenging. Microbiologists trying to culture familiar microbes must make an educated guess as to the microbes’ needs in the way of temperature, humidity, and nutrients. As to the needs of weird life, they might have no idea. It is true that there is a relatively new tool used to identify microbes, called “DNA amplification.” But it works only if the DNA in question uses the sugars and bases of familiar life. It also works, of course, only with a microbe that has already been isolated. It would be of little use in distinguishing a weird-life microbe from the thousands of species of familiar life in that pinch of soil from the forest floor.
For that, Davies proposes a general rule of thumb: the more fundamental an organism’s differences from familiar life, the greater its chances of being weird. For instance, if an organism uses a different amino acid, it is probably an unusual form of familiar life. But if it uses ammonia (not water) as a solvent, or silicon (not carbon) as a binding molecule, it is almost certainly weird. The hard calls would be in the middle, and one reason to expect some in the middle is a phenomenon called convergent evolution. This is the process by which two species respond to the same environmental challenge and take advantage of the same environmental circumstance by developing features that are similar—and in some cases identical.
The eyes of humans and octopi are an oft-cited but nonetheless remarkable example. Even in their details the two eyes are astonishingly similar, yet the fact that one sort belongs to a cephalopod mollusk with eight sucker-bearing arms, a saclike body, and a beak and the other sort belongs to a species of primate means that they evolved along entirely different evolutionary lines. Those lines converged because the need to detect predators and prey at a distance is well met by a feature sensitive to electromagnetic radiation in the visible spectrum. In fact, the advantages of sight are so pronounced that eyes evolved independently in marine worms, mollusks, insects, and vertebrates—organisms whose common ancestor was sightless. Convergent evolution, then, is a powerful force, and it is known to operate at the cellular level. Some enzymes in familiar life are remarkably similar, yet have entirely different ancestries. If convergent evolution operates for weird life (and there is no obvious reason it should not), then forms of weird life and forms of familiar life, while radically different from each other when they first appeared, may have grown so alike over time as to be nearly indistinguishable.
A scientist verifying an organism as weird faces yet another challenge—this having to do with the nature of life’s beginnings. Some biologists suspect that the transition from nonliving to living (that is, from complex chemistry to simple biology) was abrupt, akin to the phase transition of water as its temperature is lowered through the freezing point and it crystallizes—the moment at which its molecules suddenly snap to attention in rigid lattices. If one could define life as, for instance, having the ability to store and process information, one could establish a similar boundary. On one side would be complex chemistry that could not store and process information; on the other would be simple biology that could. The transition from one to the other, had anyone been around to witness it, would have been unmistakable. And if it happened a second time, even with slightly different results, it would have been just as unmistakable.
A well-defined transition would mean that scientists who discovered a candidate for weird life might trace its lineage to the moment of transition with some hope of success. But if, as others suspect, the transition was gradual—a long series of steps, some quite small, and no particular step of which anyone could say with certainty, “This is where chemistry ends and biology begins”—then scientists tracing the lineage of weird life would have no hope of identifying a point and moment of origin. Of course, neither would they have any hope of identifying a point and moment of familiar life’s origin. To follow either line would be like following two rivers upstream and finding that both began in a single network of smaller streams and rivulets, and that these were fed in turn by moving groundwater. It would be impossible to identify precisely where either river began, and i
t would be impossible to say whether they arose from separate sources. In fact, it would be pointless even to try.
Again, we may be getting ahead of ourselves. Before we trace an organism’s provenance and make a case for classifying it as weird, we need to find it. How then to begin? Davies and his colleagues recommend designing searches targeted around a particular type of shadow biosphere. If, for instance, we’re looking for weird life in a shadow biosphere that is ecologically separate, we might look for that separation. Suppose we discover a community of extremophiles in 200°C water ringing a hydrothermal vent. If we found that the hotter water just inside the ring and nearer the vent was sterile, we might reason that the inside edge of the ring marks the upper temperature limit for these particular extremophiles. But suppose that even nearer the vent, where the water is hotter still, we found, after minding the gap, a second ring of living organisms, clearly separated from the first. We would have some distance to go to prove it, but we would have reason to suspect that life in the second ring was weird.
If on-site identification proves difficult—and in these locales it often is—then Davies and his colleagues suggest we retrieve a sample of water, soil, or ice from a place too harsh even for extremophiles and, difficult as the prospect might be, try to culture any microbes present and wait for signs of life. Exactly what signs of life?
Steven Benner, another coauthor of the NRC report, has some ideas. Benner is a fellow at the Foundation for Applied Molecular Evolution, an organization whose rather audacious name is likely to prompt a few late-night discussions: Can we really apply evolution? Should we? Whatever the answers, the startling fact is that in the last twenty-five years, Benner and his colleagues have engineered several artificial biological components and systems. They have, for instance, synthesized a gene for an enzyme and built proteins with amino acids not used by natural proteins. Their work has practical benefits, having led, for example, to improvements in medical care for HIV patients. It might also be used in somewhat more arcane pursuits, like guiding searches for weird life. This because not only can Benner and his colleagues identify the parts of an organism that might be vulnerable to extreme conditions; they can also imagine substitutions for those parts. And because nature has had at least a 3.5-billion-year head start, so the thinking goes, anything Benner and company can imagine might already be out there somewhere.
For instance, the upper temperature limit for some hyperthermophiles is set by some of their amino acids, which denature at higher temperatures. Benner knows of another amino acid—2-methylamine acid—that folds in such a way that it can withstand those temperatures. If you are seeking weird life, you might retrieve a water sample from a place too hot even for hyperthermophiles, take it into the lab, and test for 2-methylamine acid. If you find it, you may also find weird life.
Alternatively, you might look for substitutions in the parts of DNA. Recall that if the DNA molecule is a flexible ladder whose ends have been given a few twists, then its long backbone (the two legs of the ladder) is made of sugar and phosphate molecules, and its rungs—all 3 billion of them—are made of chemicals called bases. There are four, and when the DNA molecule is intact, each is paired to its complement: adenine always with thymine, and guanine always with cytosine. This much is taught in any introduction to biology. What is seldom taught—and what might be of interest to seekers of a certain sort of weird life—is that the bases are what limit the pH levels tolerable for many extremophiles. Acidophiles can stand only so much acidity because the bases adenine and cytosine are relatively alkaline, and alkaliphiles can tolerate only so much alkalinity because thymine and guanine are relatively acidic. If weird-life DNA used different bases, it could withstand pH levels more extreme than those tolerated by known extremophiles.
ARSENIC
The weird life of an ecologically separate shadow biosphere might differ from familiar life in another fundamental way: its chemical composition. The fact that our bodies and the bodies of all life we know are made of a few simple chemical elements has been much used as a hard lesson in humility, a “to dust ye shall return” for secular types. But perhaps the better lesson is that the whole can be greater, much greater, than the sum of the parts. The whole—here meaning incredibly complex structures like proteins and lipids—is ordered almost entirely from a spare menu of six chemical elements: carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus.*
“Phosphorus” means “light-bearing,” and although we in the macroscopic world know it to be capable of fireworks, in the living cell it stores and transfers energy slowly and (one might say) carefully, as part of the chemical compound adenosine triphosphate, or ATP. It has other roles too, most notably in the phosphate (a molecule of one phosphorus atom and four oxygen atoms) that, along with sugar molecules, goes to make the spiraling backbone of the DNA molecule. What is interesting to weird-life research is that the roles of phosphorus could be performed as well by an element with a rather more sinister reputation: arsenic.
Arsenic is notorious as a poison and, perhaps as befits its part in many a murder mystery, it works on a biochemical level by stealth, mimicking phosphorus so well that it can gain entrance to a cell and make its way into metabolic pathways. Once inside, it turns ATP’s careful distribution of energy into exchanges that are more explosive—and destructive. Nonetheless, like phosphorus, arsenic can bond molecules and store energy. If, some billion years ago, a set of complex, self-organizing prebiotic molecules was in need of an ingredient to do what phosphorus does for familiar life, and it happened to be in a place where phosphorus was rare but arsenic was plentiful, it might well have used arsenic for all its bonding and energy-storing needs—assuming, of course, that it could develop means to cope with arsenic’s instability.
It is worth noting that an organism using arsenic in the roles that familiar life gives to phosphorus would regard phosphorus as poisonous. If life had taken a different course, then we—or weird-life versions of us—might be suffering through summer stock productions of Phosphorus and Old Lace. But even given the course we know familiar life to have taken, it is possible that a second genesis of life chose arsenic, or that an early offshoot of familiar life substituted arsenic for phosphorus. It is also possible that in hydrothermal vents, hot springs, and closed-basin lakes—all places poor in phosphorus but rich in arsenic—it might still be hanging on.
In fact, this was the hypothesis that, in 2007, was put forth by a young postdoctoral researcher named Felisa Wolfe-Simon. She was already something of an iconoclast, having begun a career as a musician (trained as an oboist) but in time having earned a PhD from Rutgers in oceanography. In 2007 she was present in a workshop on weird life convened at Arizona State University by Davies, who was newly arrived there and laying groundwork for a research center that would address fundamental questions in science. Davies recalled, “We were kicking vague ideas around, but she had a very specific proposal and then went out and executed it.”15
Wolfe-Simon’s proposal had to do with Mono Lake, a closed basin in California’s high desert some 20 kilometers across. Waters from the Sierra Nevada flow into the lake, and because they escape only by evaporation, the lake water is saturated with salts and minerals. Some of these precipitate into formations called “tufa towers” that, when the water level is low, rise above the surface like open-air stalagmites. Seen against the stark beauty of the Sierra, the shoreline is decidedly unearthly. A good place, it would seem, to seek weird life, and—since the lake water has some of the highest concentrations of arsenic on Earth—especially weird life that likes arsenic.
In August 2009, Wolfe-Simon began working with Ron Oremland, a senior research scientist the US Geological Survey (USGS) and something of an expert in microbes that tolerate arsenic. They collected samples of water and sediment, and Wolfe-Simon carefully cultured bacteria from those samples, gradually and by stages diluting out the amount of phosphorus in their nutrients and increasing the amount of arsenic, with the intention of starving the
phosphate users and nourishing the arsenic users, if there were any. By late fall of 2010, she and her research team had concluded that there was at least one arsenic user.
In a paper published in the journal Science, and at a NASA-sponsored news conference before a wall-sized image of Mono Lake at its otherworldly best, Wolfe-Simon reported that a bacterium of the family Halomonadaceae used arsenic in many important molecules, including DNA.16 (She had named it GFAJ-1, an acronym for “Give Felisa a Job”—this an inside joke on anxieties concerning the temporary nature of her position with the USGS and hopes that the discovery might be a career maker.)
The claim was extraordinary, but the evidence for it—at least to many scientists—was less than compelling. They questioned whether the DNA had been sufficiently cleaned, suggested that water would have denatured any (alleged) arsenate-linked DNA, and claimed that remaining traces of phosphorus might have sustained the bacterium’s growth. Norman Pace, an internationally respected microbiologist who, with Carl Woese, had done pioneering work on phylogeny and who, as another coauthor of the 2007 NRC report harbored no particular ill will for weird-life research in general, dismissed the work as unworthy of consideration, parsing the blame more or less evenly among “low levels of phosphate in the growth media, naïve investigators and bad reviewers.”17 Shelley Copely gave her own rather devastating take, opining, “This paper should not have been published.”18 There followed a days-long debate among scientists worldwide, much of it carried out in tweets and blog entries, over flaws in the experiment, the problems inherent in scientific peer review, and the general unreliability of NASA’s public relations efforts, especially when they concerned microbiology. The paper’s authors answered questions in a subsequent issue of Science but did not offer to revisit the study, and their critics were unappeased.
