It came from Mono Lake
But is NASA’s finding truly a previously undiscovered form of ‘weird life’ on Earth? Many scientists, including some noted experts at CU, have doubts
By Clint Talbott
The New York Times, NASA and the prestigious journal Science announced startling news recently. “Microbe Finds Arsenic Tasty; Redefines Life,” a page-one Times headline proclaimed.
The Washington Post and others went further, stating, “Bacteria stir debate about ‘shadow biosphere,’” a previously undetected environment that harbors “weird life.”
But the University of Colorado professors who coined the term “shadow biosphere” contend that the study’s findings do not buttress the headlines. Other CU microbiologists make similar arguments.
The story started with a cryptic media advisory from NASA on Nov. 29. The advisory noted that NASA would hold a news conference on Dec. 2 “to discuss an astrobiology finding that will impact the search for evidence of extraterrestrial life.”
Astrobiology is the study of the origin, evolution, distribution and future of life in the universe.
NASA’s press conference was scheduled to coincide with the publication in the journal Science of a study led by Felisa Wolfe-Simon, a NASA astrobiology research fellow in residence at the U.S. Geological Survey in Menlo Park, Calif.
NASA’s news release stated that its researcher had discovered “life built with toxic chemical.” Wolfe-Simon stated, “What we’ve found is a microbe doing something new—building parts of itself out of arsenic.”
Wolfe-Simon and her colleagues had “trained a bacterium to eat and grow on a diet of arsenic, in place of phosphorous—one of the six elements considered essential for life,” the Times reported.
The finding raised the possibility that other forms of life could exist on earth or elsewhere in the universe.
“The definition of life has just expanded,” Ed Weiler, NASA’s associate administrator for the Science Mission Directorate at the agency’s headquarters, stated.
Arsenic sits just below phosphorous on the periodic table (which means that the two elements have similar patterns of chemical reactivity), and the implication of the research was that the bacterium’s DNA had substituted arsenic for phosphorous and kept growing.
Science itself published a news summary of the work, and while its headline stated that the bacterium “uses arsenic to build DNA and other molecules,” the story also quoted scientists who were skeptical. One scientist told Science that the proposition that the bacterium had replaced phosphorous with arsenic, “is, in my opinion, not established by this work.”
Within days, scores of scientists worldwide joined the debate, often expressing similar doubts.
Some of these experts are on the faculty at CU, are recognized experts in astrobiology and, in one case, have even collaborated with Wolfe-Simon and one of her colleagues, Paul. C.W. Davies.
Not a ‘shadow biosphere’
Carol Cleland, a philosophy professor and co-investigator at CU’s Center for Astrobiology, has written extensively on the search for alternative life. She and CU microbiologist Shelley Copley published a 2005 paper on the possibility of “alternative microbial life on Earth.” They coined the term “shadow biosphere.”
Last year, Cleland and Wolfe-Simon were among several co-authors on an article titled “Signatures of a Shadow Biosphere,” which was published in the journal Astrobiology.
Additionally, Cleland has co-authored a paper on the definition of “life” and is writing a book for Cambridge University Press titled “The Quest for a Universal Theory of Life: Searching for Life as We Don’t Know It.”
Cleland said Wolfe-Simon’s results are “intriguing,” especially if it were true that bacterial cells were using arsenic in place of phosphorous in their nucleic acids and proteins.
“Unfortunately, the evidence deployed in their paper does not support this claim,” Cleland said.
In the media and during the NASA press conference, experts also asserted that the results challenged our concept of what constitutes life and offered evidence of a possible shadow biosphere—previously undetected life on Earth.
“This is not anything close to a shadow biosphere,” Cleland said. “The most that their work shows, however, is that familiar life is chemically more flexible than previously thought.”
The bacterium from the bottom of arsenic-rich Mono Lake, in California, is from the same tree of life as all other known life on Earth, Cleland noted.
“When subjected to an arsenate-enriched, phosphate-depleted medium these bacteria grew, but it would be a mistake to characterize them as “thriving” (in the ordinary, everyday sense of the word),” Cleland wrote. “Growth was faster and more extensive when phosphate was added to the culture medium.”
Further, Cleland notes, the bacteria in the arsenate-rich environments looked malformed compared to those in phosphate-rich media. “This suggests that the bacteria were stressed and trying to cope with the high levels of arsenic in their environment.”
Instead of being “weird life,” the bacterium is an “extremophile,” an organism that has adapted to a harsh environment, Cleland said.
“The metabolic pathways used by highly evolved, familiar, contemporary life cannot distinguish between phosphate and arsenate, which is why arsenic is poisonous to it. A truly novel form of life, descended from a separate origin, is unlikely to share the same high-level metabolic pathways as our form of life,” she said.
“As a consequence, even if they established the substitution of arsenate for phosphate at significant levels in (the Mono Lake bacterium), their work does not challenge our current concept of life,” Cleland said. “And for the same reason, it does not provide support for the possibility of a shadow biosphere.”
“At best, the work of Wolfe-Simon and colleagues adds another page to our growing knowledge of the astonishing environmental toughness and perhaps metabolic diversity of familiar Earth microbes.”
‘Premature and misleading’
Copley, a CU professor of molecular, cellular and developmental biology, is co-investigator at CU’s Center for Astrobiology. As Copley notes, the Wolfe-Simon paper describes the isolation of a bacterium from sediments in Mono Lake that grow only when either arsenate or phosphate is added to the medium.
“This finding gave rise to the idea that the cells might be using As (arsenic) in place of P (phosphorous). The authors focused on whether P in DNA was replaced by As, since that would indeed be a stunning finding,” Copley wrote.
“However, the data do not show that all of the P in DNA has been replaced by As, which seems to be the interpretation that is playing out in the media.
“To be fair, nowhere in the paper do the authors make a quantitative statement. They say that the bacterium ‘can vary the elemental composition of its basic biomolecules by substituting As for P,’” Copley continued.
“It is unclear whether they mean complete substitution or partial substitution, and whether substitution at a level of, say, 1 percent, would actually be very exciting.” Based on the data in the paper, “it appears that there may be some low level incorporation of As into DNA, but the data are not completely convincing.”
Experiments that would have been conclusive were not performed, and some of the data are of dubious quality and were not interpreted critically, Copley said. The paper raises many questions that should have been addressed by the authors before this work was published, she added.
“Unfortunately, publication of work that makes premature and misleading claims in a high-profile venue like Science, followed by the excitement fomented by NASA’s promotion of the work, is likely to damage the credibility of origin-of-life-researchers and scientists in general in the eyes of the public.”
Norman Pace, a distinguished professor of molecular, cellular and developmental biology at CU and a co-investigator at CU’s Center for Astrobiology, said the conclusion of arsenate in the DNA is “probably bogus.”
“No evidence at all was presented that showed the specific incorporation of arsenic into any biomolecule,” Pace said. “All of the data were inferential and easily explainable by contamination of analyzed samples with arsenate, on one hand, and phosphate on the other. The study was amateurish.”
Like Cleland, Pace said there is nothing particularly novel about the Mono Lake bacterium. “It is a so-called gamma-group proteobacterium, a close relative of many well-known organisms, e.g. Escherichia coli. There are a lot of organisms known that metabolize arsenate and arsenite,” Pace said.
“Based on what I know, the story is largely hype; NASA needed some news, so they jumped on this.”
Michael Yarus, a professor of molecular, cellular and developmental biology, co-investigator at the Center for Astrobiology and author of the book “Life from an RNA World,” characterizes Wolfe-Simon’s article as making an “extraordinary claim,” which requires excellent evidence.
“Strikingly, strong evidence should be easily found—if any mainline biochemical has a high frequency of arsenic instead of phosphorus (for example: DNA, RNA or AMP), that would be convincing, a ‘smoking gun,’” Yarus said.
“However, the published evidence does not approach this level. In fact, the attempt to demonstrate arsenic in DNA is very unconvincing and suggests instead that As may be present as a prevalent cellular contaminant, say as some small-molecule form made in high concentrations to detoxify an otherwise poisonous environmental hazard,” he added.
“I therefore remain to be convinced.”
As it is elsewhere, opinion about the NASA study is mixed at CU. Rob Knight, CU associate professor of chemistry and biochemistry, leads one of 13 interdisciplinary research projects on synthetic biology that were awarded by the National Academies Keck Futures Initiative. Knight’s research combines computational and experimental techniques to ask questions about the evolution of the composition of biomolecules, genomes and communities.
Knight said Wolfe-Simon’s findings “provide a fascinating insight into the limits of metabolic adaptation: although more work remains to be done in order to confirm that As can substitute for P in a range of biological RNAs and DNAs, the results presented here are amazing in that they are the first direct evidence that life can substitute one of its key elements for another.”
On Dec. 16, Felisa Wolfe-Simon published her first detailed responses to questions about her research. Those may be viewed here. On Dec. 17, The Washington Post published a story about the authors’ response to the criticism. It may be seen here. A similar piece in the Philadelphia Inquirer can be seen here. The journal Nature published an editorial about the need for researchers to respond to criticism from scientific bloggers. That editorial can be read here. On Dec. 20, Science published an exclusive interview with Felisa Wolfe-Simon. That can be seen here.
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