Courtesy of Science
Nearly anyone who’s taken a high school chemistry class remembers that sodium can react violently with water. You may have seen a video—either in class, or online, showing how elements in the same column as sodium on the periodic table (potassium, rubidium, cesium, francium) also combine with water, with progressively more explosive results. The periodic table is designed so that elements in the same column share similar properties, which has led some science fiction writers to speculate that silicon might be the foundation of life on an alien world—after all, it’s right below carbon in the same column. Just like carbon, which forms the basis for all known organisms, a single silicon atom can bond with up to four other atoms, which would seem to open the way for a complex life form to develop.
So far, no silicon-based life has been discovered, whether in outer space or in a lab, but last week, bloggers and journalists went wild with speculation when NASA released a titillating announcement of a potentially dramatic discovery that was rumored to involve another key element of biochemistry: phosphorus. Phosphorus has long been considered to be essential to all life. It’s a part of the backbone of the DNA molecule, and also a component of ATP (adenosine triphosphate), which is the fuel for nearly all cellular processes. NASA’s announcement hinted that an “alien” life form had been discovered, and other tidbits leaking across the internet suggested that it shunned phosphorus in favor of its periodic column-mate, arsenic (yes, that arsenic, the one used as a poison in countless mystery novels). The details, however, would not be released until the journal article discussing the research was published, three days later.
Meanwhile, at least one (non-scientist) blogger, Jason Kottke, was speculating that arsenic-based life had been found on Saturn’s moon Titan. While that rumor was quickly batted down and even corrected on the blog post itself, Reuters Health editor Ivan Oransky wondered on his blog if it wouldn’t have been better for NASA (and Science) to release the full results early, in order to quell wrongheaded speculation.
When the results finally were released, about 90 minutes ahead of schedule, they were dramatic enough to merit significant attention, if not of the comic-book alien variety. As British science writer Ed Yong explained on his blog, the researchers, led by Felisa Wolfe-Simon, took mud from arsenic-laden Mono Lake in California, then put it in progressively stronger arsenic-rich growing environments in the lab, isolating the bacteria that were able to survive. Simultaneously, phosphorus was removed. One type of bacteria, called GFAJ-1, continued to thrive and even reproduce. Wolfe-Simon’s team then subjected GFAJ-1 cells to extensive chemical analysis, showing that lots of arsenic was present in the organisms. Next the bacteria were grown in radioactive arsenic, which enabled further testing. The researchers claimed these tests showed that the arsenic was present not only within the cells, but within the actual proteins that made up the bacteria themselves. They even made the astonishing claim that arsenic had replaced phosphorus in the backbone of the bacteria’s DNA. If this was true, it would mean that these bacteria were using a completely novel way of transmitting genetic information—something that presumably could no longer even be called DNA.
Unfortunately, as more scientists began to take a closer look at the paper, potential problems came to light. Last Saturday, microbiologist Rosie Redfield posted a scathing critique of the study, arguing that the researchers used poor lab techniques, and so were unsuccessful at removing phosphorus from the solution. Redfield says enough phosphorus remained in the solution to support the survival and growth of GFAJ-1 populations. According to Redfield, Wolfe-Simon’s team had not demonstrated that the bacteria incorporated arsenic into its very structure—the arsenic could have simply been present within the bacterium (much like water, salt, and many other substances are found inside our own cells). Redfield’s conclusion: “If this data was presented by a PhD student at their committee meeting, I’d send them back to the bench to do more cleanup and controls.”
Microbiologist Alex Bradley, in a guest post on the blog “We, Beasties,” offers an even stronger critique of the Science paper. Bradley notes that DNA containing arsenic, in which the ion arsenate replaces phosphate in the DNA backbone, is actually very unstable in water. While this might not be a problem within GFAJ-1 bacteria, where some other chemical process could potentially stabilize it, the researchers actually removed the DNA from the cells in order to analyze it. The process they used, Bradley says, requires that the DNA be in water for over an hour. DNA with an arsenate backbone has a half-life in water of just 10 minutes, meaning it would certainly have been destroyed by the time it had been successfully separated from the rest of the cell. The images of DNA from the experiment clearly show that it is intact.
This sounds quite damning, but one might reasonably ask, if the bacteria were deprived of phosphorus, how they could have reproduced at all. Bradley says there probably was enough phosphorus, even in the depleted laboratory conditions, to enable the DNA in the bacteria to replicate with a standard phosphate backbone. In the Sargasso Sea, in the middle of the Atlantic Ocean, there are areas with even lower phosphate levels than what Wolfe-Simon’s team achieved in the lab, and yet bacteria and other organisms survive there. What’s more, Bradley says, there are other techniques the researchers could have used to conclusively show whether arsenate is actually part of the bacteria’s DNA. Bradley would like to see a mass spectrum of the DNA molecules the researchers obtained, which would show clear differences between DNA bound together by arsenate rather than phosphate.
Despite all the misinformation and, perhaps, overhyping of the study, the findings are still very interesting. Arsenate is poisonous to nearly all organisms on Earth because it does an exceptional job of imitating phosphate—enough to make its way past a cell’s defenses, but not enough to assume phosphate’s role within a cell. The fact that this bacteria can survive in such an extreme environment, and the lingering questions about how it adapts and whether it puts the arsenic to use in any way, make this research important for understanding how life continues to evolve.
What went wrong, then? Astronomer Phil Plait says that PR representatives at NASA may have been too cavalier in what they hinted in advance of the release, thus setting off a wave of unfounded speculation by bloggers like Kottke, who didn’t have access to the research itself. Redfield suggests that the journal Science may have succumbed to the desire to publish high-profile research that might not be ready for prime time.
Perhaps the most important lesson is this: A single study rarely causes a revolution in science all on its own. Only through repeated confirmation and refinement of research can we come any where near something like “truth.” In the larger scheme of things, maybe nothing did go wrong. Findings like these were bound to attract a lot of attention—informed and uninformed—regardless of how they are released to the public. Now, in the aftermath, in just a few days’ time we’re starting to get a better picture of what it all means, and scientists can get to work on the next steps.
Dave Munger is editor of ResearchBlogging.org, where you can find thousands of blog posts on this and myriad other topics. Each week, he writes about recent posts on peer-reviewed research from across the blogosphere. See previous Research Blogging columns »
Originally published December 7, 2010