[BLOG-LIKE POSTING] On the purported Mono Lake discovery of arsenic-using bacteria

[rfmcdonald]

The recent, highly-hyped announcement by a team of scientists that they found a species of bacteria, founded in California's Mono Lake, that used arsenic in place of phosphorous, is one result of the ongoing search for a shadow biosphere. Used by Paul Davies among others, the term "shadow biosphere" refers to life that evolved alongside our DNA-using form we all know, but which is based on different forms--RNA, perhaps, or something more exotic. If a shadow biosphere of non-DNA life was found, this would have profound implications, not least on the search for extraterrestrial life; if life evolved at least two separate times here on Earth, that would tend to suggest that there should be plenty of life out there. The scientists' paper is available in full here, at Science. Wired Science goes into more detail about the discovery here.

rsenic is toxic and is thought to be too chemically unstable to do the work of phosphorus, which includes tasks such as holding DNA in a tidy double helix, activating proteins and getting passed around to provide energy in cells. If the new results are validated, they have huge implications for basic biochemistry and the origin and evolution of life, both on Earth and elsewhere in the universe.

“This is an amazing result, a striking, very important and astonishing result — if true,” says molecular chemist Alan Schwartz of Radboud University Nijmegen in the Netherlands. “I’m even more skeptical than usual, because of the implications. But it is fascinating work. It is original, and it is possibly very important.”

The experiments began with sediment from eastern California’s Mono Lake, which teems with shrimp, flies and algae that can survive the lake’s strange chemistry. Mono Lake formed in a closed basin — any water that leaves does so by evaporation — making the lake almost three times as salty as the ocean. It is highly alkaline and rich in carbonates, phosphorus, arsenic and sulfur.

Led by Felisa Wolfe-Simon of NASA’s Astrobiology Institute and the U.S. Geological Survey in Menlo Park, California, the researchers cultured microbes from the Lake Mono sediment. The microbes got a typical diet of sugar, vitamins and some trace metals, but no phosphate, biology’s favorite form of phosphorus. Then the team started force-feeding the critters arsenate, an analogous form of arsenic, in greater and greater quantities.

One microbe in particular — now identified as strain GFAJ-1 of the salt-loving, mostly marine family Halomonadaceae — was plucked out and cultured in test tubes. Some were fed loads of arsenate; others got phosphate. While the microbes subsisting on arsenate didn’t grow as much as those getting phosphate, they still grew steadily, doubling their ranks every two days, says Wolfe-Simon. And while the research team couldn’t eliminate every trace of the phosphate from the original culture, detection and analytical techniques suggests that GFAJ-1 started using arsenate as a building block in phosphate’s place.

“These data show that we are getting substitution across the board,” Wolfe-Simon says. “This microbe, if we are correct, has solved the challenge of being alive in a different way.”

Arsenic sits right below phosphorus in the periodic table and so, chemically speaking, isn’t that different, Wolfe-Simon notes. And of the six essential elements of life — carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur (aka CHNOPS) — phosphorus has a relatively spotty distribution on the Earth’s surface. If a microbe in a test tube can be coerced to live on arsenic, perhaps life’s primordial home was also arsenic-rich and life that used phosphorus came later. A “shadow biosphere” of arsenic-based life may even exist unseen on Earth, or on some lonely rock in space.

The problems with this are also outlined by Wired Science.

[O]there biologists started raising red flags almost immediately, questioning the methods the team used to purify the DNA and asking why the researchers skipped certain tests.

“It seems much more likely that the arsenic they’re seeing is contaminating arsenic that’s going along for the ride,” biologist Rosie Redfield of the University of British Columbia told Wired.com.

Redfield posted a biting critique Dec. 4 on her research blog. As of today, the post has received more than 40,000 hits.

She points out that the team didn’t properly clean their DNA before or after running it through a standard device for separating DNA and RNA from other molecules, a technique called gel electrophoresis.

Cleaning the samples would require “a little kit that costs $2 and takes 10 minutes, and then you have pure DNA that you can analyze,” Redfield said. The researchers used this method elsewhere in the paper, but not in the critical experiment that was supposed to show arsenic was incorporated into the bacteria’s DNA.

“That’s just asking for contamination problems,” she said. The arsenic they found could have been hanging around in the gel, not in the cells, she added. “It’s as if they wanted to find arsenic, so they didn’t take a lot of trouble to make sure they didn’t find it by mistake.”

In a guest post on the blog “We, Beasties,” Harvard microbiologist and geochemist Alex Bradley raised another issue.

The NASA team immersed the DNA in water, where arsenic compounds quickly fall apart. If the DNA was really built from arsenate, it should have broken into pieces, Bradley wrote. But it didn’t. That suggests the molecules were still using stronger phosphate to hold themselves together.

The paper's authors have declined to respond to critiques from blogs, saying that this should be something for scientists to discuss not blogs, notwithstanding the huge publicity and hype that had been built up before and after the presentation. The general consensus among some experts seems quite negative, some going so far as to say that the paper should never have been published, others repeating the criticisms above or adding others (suggesting that the bacteria are actually bloating and sequestering the bacteria). I've seen some people suggest that an adaptation to arsenic-heavy environments is possible for a DNA-based life form without any shadow biosphere at all, especially over the seven or eight hundred thousand years that Mono Lake has existed. Compare the bacterial life in Spain's highly acidified Rio Tinto, which adapted over successive generations in a five thousand year time period to increasing amongs of mine waste.