Friday, December 10, 2010

Desperate Living

Amidst this week’s buzz surrounding Wikileaks, the arsenic-eating bacteria of California’s Mono Lake is almost forgotten. But last week, it was front-page news and people who normally cared little for microbiology were updating their Facebook pages with exuberant quotes about a newly-discovered organism that “redefined life” and somehow related to NASA and the existence of space aliens. In actuality, the discovery was not quite as earth-shattering as your friends would have had you believe. Ever the voice of reason, I’d like to offer a bit of perspective, along with some other organisms to get excited about.

In case you somehow missed the headlines, here’s happened in California. NASA-funded scientists scooped some bacteria out of Mono Lake, a salt-water lake with a high arsenic concentration, brought it back to the lab and then tried to grow it in an arsenic-rich, phosphorus-deprived environment. The idea was to see if the bacteria could be persuaded to replace phosphorus, an element essential to all previously-discovered life, with arsenic, which is conveniently located one row directly below phosphorus on the periodic table and shares certain chemical properties with it. Phosphorus is incorporated into proteins and lipids, fuels metabolic reactions in the form of ATP and, perhaps most notably, helps form the backbone of DNA. It’s an important element.*

Well, the big news was that the bacteria, christened strain GFAJ-1, lived. This bacteria was selected specifically because it was already tolerant of arsenic, an element that is toxic to many living things.† The hopeothesis‡ was that this tolerance would enable it make do with arsenic in its daily maintenance if phosphorus was unavailable. And make do it did. However, that is all it did. GFAJ-1 didn’t exactly thrive on its new diet. While the bacteria still managed to grow in arsenic, it fared much better when provided with phosphorus.

More disappointingly, in recent days criticism from numerous biologists has threatened to turn an unexceptional experiment into an embarrassing one. The NASA team has been accused of science that is literally sloppy – poor washing of DNA and that sort of thing. Critics suggest that arsenic found in GFAJ-1 may be from contamination rather than actual incorporation into its DNA, and that the bacteria simply survived by grabbing every shred of phosphorus it could find (phosphorus couldn’t be completely removed from the growth medium, just significantly reduced). Luckily for the authors of the original paper, which appeared online in Science last week, these concerns have thus far appeared mostly on blogs, and everyone know you can’t trust those things. Nonetheless, doubts have been planted that GFAJ-1 is merely an arsenic-tolerant bacteria that builds its DNA using phosphorus just like the rest of us.

And why should you be impressed by an arsenic-tolerant bacteria? GFAJ-1 is just one of many extremophiles living in equally improbable environments on our planet. Extremophiles are organisms that live at temperatures, pH and salinity well outside the norm.§ They not only live in these environments, they grow best in them, having adapted to their unique challenges. You don’t read about these life forms very often because they are incompatible to your own external, and often even internal, environment. Their names don’t turn up food recalls. Such microorganisms would wither and die if exposed to a world as ordinary as an undercooked hamburger or a sun-soaked potato salad.

Take, for instance, psychrophiles, who have optimum growth temperatures below -20°C. They won’t even start growing until the thermometer gets down to 0°C (the freezing point of water). They live in climates where the snow never melts; permanent ice fields. If normal bacteria could do this, the freezer would be as bad a choice as a cupboard for storing your perishables. Thermophiles and hyperthermophiles live on the opposite end of the temperature spectrum, with optimum growth temps of above 45°C (113°F) and above 80°C (176°F) respectively.** These organisms can grow in places like hot springs, which are often at boiling point for their altitude, and have been known to find their way into artificial hot spots, such as water heaters. Changes in enzymes and cell membrane structure enable these organisms to flourish in environments that would quickly kill mesophiles like ourselves.

Thermophiles add brilliant colors to a hot spring at Yellowstone National Park, while psychrophiles can turn ice red. How cool is that?

Other organisms have adaptations that allow them to live in extremely salty environments (these are called halophiles) or strongly acidic or alkaline environments (acidophiles and alkaliphiles respectively). The acidophilic (and thermophilic) archaeon Thermoplasma acidiphilum was originally discovered in a self-heating coal refuse pile (pH of about 2), which sounds easily as uninviting as an arsenic-filled lake. And if there is no oxygen available, that’s not a problem. Thermoplasma acidiphilum can also use sulfur for respiration, which is unequivocally awesome. You are amazed.

So where does this leave poor GFAJ-1? Well, to survive in Mono Lake it already had to be a halophile and an alkaliphile, not to mention its striking ability to handle arsenic. It was an impressive bacteria in its own right before it got swept up in all this arsenic-eating hype and inevitable backlash. And there is no reason to think any less of it. It’s still a fine extremophile, it’s just not the organism that revolutionized biology.

But let’s pretend for a moment that the lab techniques of the NASA experiment were flawless and that the entire scientific community agreed on the results. How important is the creation of an organism that can build DNA from arsenic? How does this “redefine life”? The definition of life is already a complicated and changing one, which can’t be summarized in a single sentence. While living things tend to be made up of the same batch of elements (carbon, hydrogen, nitrogen, oxygen, sulfur and phosphorus), being assembled from these ingredients is not the criteria for being considered alive. Living things grow and reproduce. They have some sort of metabolism. They hold their cellular components together and resist entropy, at least while they are alive. In theory, anything that succeeds in these activities could be categorized as “life”, regardless of which elements it uses. The reason the word “life” is often paired with qualifiers like “as we know it” or “carbon-based” is that we acknowledge that the organisms we have found thus far may not represent the only possibly system of life. Had scientists made or discovered an organism that actually used arsenic in its DNA, this would not overturn previously held scientific beliefs, it just would confirm ideas that have yet to be matched to empirical evidence. We can’t say that arsenic-based or silicon-based organisms do not or cannot exist. But we might have to admit that nobody, including the folks at Mono Lake, has yet encountered such an organism.

* Phosphorus in living things exists mostly as phosphate (PO43-). The arsenic analog is arsenate (AsO43-). These molecules, rather than elemental P and As, were used in the NASA experiment.

† Arsenate can be harmful specifically because it is so similar to phosphate. It bonds to receptors intended for phosphate and gums up all sorts metabolic pathways.

‡ This is my attempt to create a new word. It means a hypothesis that is based more on wishful thinking than on likelihood of outcome. You can help me get it to catch on by using it in daily conversation.

§ Most known extremophiles are microorganisms in the domains Archaea and Bacteria. However they don’t have to be. Who knows, perhaps in the future some lucky explorer will find a species of squirrel or cat that lives in active volcanoes. It could happen.

** The recommended setting for a hot tub is no higher than 104°F, and even then you might pass out and drown if you stay in it for over 20 minutes. And you shouldn’t be in the thing at all if you’re pregnant or on blood thinners or have a heart condition….The list goes on. Humans are sissies.

Who told you this?

Wolfe-Simon, F. et al. “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus.” Science. Published Online December 2, 2010.

Feller, G. and Gerday, C. 2003. “Psychrophilic Enzymes: Hot Topics in Cold Adaption.” Nature Reviews Microbiology 1: 200-208.

Stetter, K.O. 2006. “Hyperthermophiles in the History of Life.” Philosophical Transactions of the Royal Society of Biological Sciences 361: 1837-1843.

Baker-Austin, C. and Dopson, M. 2007. “Life in acid: pH homeostasis in acidophiles.” Trends in Microbiology 15: 165-171.

Grossman, L. “Doubts Brew About NASA’s New Arsenic Life.” December 7, 2010.

Zimmer, C. “‘This Paper Should Not Have Been Published’.” December 7, 2010.

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