Thursday, December 9, 2010

Steph’s Science Corner: The Rise and Fall of Scientific Discovery in Arsenic-Based Life

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Arsenic microbesIt’s been all the rage lately.

On December 2nd, researchers at NASA held a press conference to unveil the latest news in the effort to discover extra-terrestrial life. The anticipation was thick after the classic stunt of pre-announcing their intentions to make an announcement. When finally it was bestowed upon us, a new phrase suddenly ignited our dormant, innate scientific curiosity:

“Arsenic-based life-forms”

At first, we reeled with the thrill of discovery, amplified by an untraceable, bloated rhetoric. We called down images of arsenic-eating aliens sipping tea with us as we speculated on how such a groundbreaking addition to biology text books could “change life as we know it.” But then, slowly at first, the skeptics began to leak in doubt like industrial waste seeping into a river. Over the last few days, the media has completely reversed its focus, invoking the wrath of scrutinizing experts in the field of microbiology and biochemistry who rejected the claim as “almost certainly wrong,” or at the very least, misleading.

Finding myself always the contrarian, I started on board with the first wave of NASA-denouncement, and had every intention of using this week’s segment to cast down the innocently hopeful eyes of my space-camp readers. Then I realized that I was too late. Everyone else was already doing it. That meant I had to change sides.

I have a confession to make before I begin this week’s discussion: I didn’t really pay attention in my college biochemistry class. I took it because it made my degree ACS-accredited, which I was pretty sure meant “more awesome.” I apologize in advance for any details that I stumble over or wave away in my ignorance.

Organic chemistry and the chemistry of life

There are many different ways to classify the elements that make up our universe. Sometimes we divide them up into metals and nonmetals. Sometimes we distinguish them by their state at room temperature (solid, gas, liquid). A common classification is “organic” versus “inorganic,” but what does that mean, exactly? The boundaries are somewhat debatable. Carbon is found in some form or another in all known life-forms, granting it an illustrious reputation as the building-block of life. In the human body, it is the second Why yes, that IS me doing organic chemistry. Shameless self promotion? No way.most abundant element after oxygen. For that reason, classroom organic chemistry is focused around carbon-based compounds that can contain any number of other elements, including hydrogen, nitrogen, oxygen, any of the halogens (The column in the periodic table that begins with F), as well as phosphorus, silicon, and sulfur. But organic compounds can be found in petrochemicals, plastics, paints, drugs, explosives, and plenty of other objects that are not, and were never, alive.

Life, however, is built on six elements: carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus. That’s not to say that you can’t find other elements in living organisms (we have calcium in our bones, iron in our blood), it merely means that these six elements are found in everything. They are nutrient elements; they make up the building blocks of DNA, proteins, and fats. They cannot be substituted for anything else...most of the time.

Remember the period table? It’s shaped like that for a reason

We have observed that some of the trace elements that compliment our biochemistry can be substituted for others that are chemically similar. For example, most life uses Iron (Fe) as an oxygen carrier in the blood, but some mollusks use copper (Cu) instead.

You can understand this by recalling that the periodic table is not just an arbitrary arrangement of the known elements, it is arranged in a specific pattern for specific reasons. Certain columns and sections are grouped together, and even named, as we see below: It took me about 40 minutes to pick out a period table that I liked, and I'm still not 100% happy with this one.

One key feature to this table is that elements in the same column all have the same number of outer-shell electrons, and it is these electrons that participate in the making and breaking of chemical bonds. For a visual example of this trend, watch this fantastic video showing how all the alkali metals (column 1) interact rather explosively with water.

Notice that arsenic (As) falls just below phosphorus (P) in the periodic table. Phosphorous is essential in biochemistry, notably present in ADP/ATP (the fuel that drives our metabolism) and in the backbone of DNA. Arsenic is similar to it, but not identical. It is this chemical similarity that makes arsenic toxic to living beings. It can make the same types of chemical bonds as phosphorus, but they are much less stable. The metabolic pathways in our body can’t really distinguish the two types of bonded compounds well enough to kick the wrong one out before it causes problems.

What we already know about alternative biochemistry

It’s fun to envision other planets on which these elemental substitutions are the preferred chemistry of life. What would a world where carbon is replaced with silicon look like? Back here on earth, there are cases of very tough organisms that have evolved to process unusual analogs of typical chemicals. Some bacteria can process both regular proteins and selenoproteins, in which selenium (Se) takes sulfur’s (S) place. And while most life on earth uses phosphorylated sugars, some microbes have been observed to be capable of using sugars with arsenate. In other words, they can “eat” and “breath” arsenic.

Coupling this observation with our beliefs about our primordial atmosphere, it has been speculated that the earliest forms of life on earth may have used arsenic rather than phosphorus not just as an energy form, but as the backbone of DNA and RNA -- our basic genetic material. The objection to this theory calls attention to how much less stable arsenic esters are than their phosphorus cousins. However, if it could be proven that life could exist at a genetic level with this arsenic-structure, a major piece of evidence would be collected that might support this thesis.

What NASA claimed: Felisa Wolfe-Simon’s research paper

Mono LakeNASA’s monumental project took place in California, originating from a striking body of water called Mono lake. It is a harsh ecological system that formed 760,000 years ago in a basin with no ocean outlet. Because of this cutoff, dissolved salts exist in high concentrations, making the lake very salty and giving it a high pH. Consequently, the ecosystem that evolved around the lake is as resilient as the environment is harsh. Most important for this research, however, is Mono Lake’s high levels of naturally occurring arsenic, which means that the bacteria growing within must tolerate it.

Wolfe-Simon and her team collected normal, phosphorus-eating bacteria from the lake and brought them back to the lab. From these samples, they grew cultures, and observed how the populations grew in different types of environments. In cultures completely bereft of all phosphates and arsenates, nearly no population growth was observed. When phosphates were added, the populations grew quickly, in exactly the same way they are known to do so. But when all the phosphates were diluted away, artificially replaced with high concentrations of arsenates, the microbes still showed population growth, albeit at a slower rate.

These new arsenic-nourished microbes looked different than they’re phosphorous cousins, and they contained such high levels of arsenic in the absence of phosphorus that the team suspected it was being incorporated into the backbones of DNA and RNA, which would be the first example of this behavior ever observed. The research group used a number of techniques to attempt to pinpoint the arsenic after figuring out its percentage by mass, including imaging, DNA extraction techniques, and radioactive labeling. After compiling all of their results, they asserted that their speculations had been proven and published them in Science.

Note that these microbes were not discovered, per se, in that they were found in nature. They were artificially created. Nevertheless, if NASA’s conclusions are indeed merited by their results – results that will soon be subject to rigorous scrutiny – it is the first observed instance that this kind of biology is indeed possible.

Criticism. Naturally.

After the initial thrill came the rolling waves of doubt. Biochemists, geochemists, and other high-end PhDs are arguing that the original work failed to convincingly show that arsenic was actually incorporated into the DNA rather than just hanging around it, sticking to things and fooling everyone with its presence. Many of these arguments center around the idea that arsenate easily hydrolyzes, meaning it should fall apart quickly when exposed to water, and yet these strands of DNA failed to disintegrate after an hour or more of submersion.

In some cases, the dissenters find the methodology flawed and unreliable. Mostly, however, people just don’t feel convinced. There isn’t enough evidence, some say, to make such bold claims. There are even angry whispers that NASA is simply pushing an agenda in order to attract funding in an economy that has been extremely harsh on the former representation of every young boy’s dream to be an astronaut.

My own analysis

I read NASA’s paper, and their website’s news release, and a whole host of other announcements and subsequent criticisms. I think that reactions on both sides have been a little overzealous. NASA and its team are perhaps too confident, advertising their results in language that I would call too certain. But I also don’t see that as abnormal. That behavior is common in the world of modern science. Publishing is about staking a claim – you observe something, and you let everyone know that you saw it first. You draw conclusions from your observations, tossing out ideas and either proposing new theories or addressing existing ones. Criticism always follows every major breakthrough, as it must. Methods are carefully investigated, results are replicated. Sometimes they don’t hold up. Sometimes a guess is wrong.

Not everything should be published. That’s why we have peer-reviewed journals, staffed by trained researchers. Results have to stand up to the rigors of the scientific method before they can be shared. But that doesn’t mean they have to be right. The work done by NASA’s team was most assuredly reviewed, and the work was deemed worthy enough by the team at Science to be released to the world for discussion. Because this journal is so popular, it has been criticized as favoring publicity-value over scientific merit. Some people boldly suggest that Science’s editors were blinded by their greed for high-impact publications, and might have pressured their reviewers to let a few things slide. That’s certainly possible to some degree, but does it matter?

The magnitude of the impact of this announcement is very real, but just like with any new piece of scientific understanding that we pull into our puzzle, everyone needs to calm the hell down about where it will eventually belong. And just like any opinionated citizen, I naturally blame the media for these reactive spikes in our attitudes. The value of each side has been magnified beyond its actual impact. Yes, this news was interesting, and it provides another potentially valuable stepping stone. It could help us discover the secrets of our primordial origins or the existence of extraterrestrial life, but it is not the answer, right now. It is also not infallible. It is not certain. Yet neither is this work trivial, or even, I believe, “seriously flawed.” Some news outlets have drawn attention to NASA’s lack of response to prompts by disagreeing experts, but I see it differently. Their response is exactly what any research group’s response should be: “If you have any better ideas, prove it.” Publish your own research and disagree that way.

So my message to my readers is this: step down a peg or two before you let your fire sweep you away. We didn’t discover aliens in California, nor did we find a new species. And in a few weeks, everyone will forget about this just like they forgot about cold fusion...oops.

See you back again next Thursday. Email suggestions or requests to!