A scientist uses ‘open science' to find an answer
It was research that appeared set to turn the biological world on its head. A paper published online by the journal Science in December 2010 described a strain of bacteria that not only thrived in high levels of arsenic but appeared to incorporate it in its biomolecules, including DNA, displacing phosphorus that all other known forms of life utilise.
The U.S. space agency, the National Aeronautics and Space Administration (NASA), which had funded the research, loudly trumpeted the discovery. "The definition of life has just expanded," exulted a senior agency official in a press release.
But the paper by Felisa Wolfe-Simon and others failed to convince their peers in the scientific community. Instead, what followed was an outcry from scientists about flaws in the research. There was good reason, they said, to doubt that the bacterium was using arsenic in its DNA.
Science, according to its Editor-in-Chief, Bruce Alberts, received “a wide range of correspondence that raised specific concerns” about the paper's research methods and interpretation of results. In May 2011, the journal took the unusual step of publishing online eight technical comments that raised a number of issues.
But the question remained – shouldn't someone else try to replicate the experiment using methods that avoided the pitfalls of the earlier work? It was not an alluring prospect, considering that the most likely outcome would be to merely corroborate the flaws that had already been pointed out.
Rosemary Redfield, a microbiologist at University of British Columbia in Canada, decided to take on the task. In a post on her blog ‘RRResearch', which received a good deal of attention, she had criticised the Science paper as “lots of flim-flam, but very little reliable information.”
“I've been saying that researchers shouldn't invest the time and resources needed to test Wolfe-Simon et al's claims because of the vanishingly small probability that they are correct,” she remarked in a blog post in May last year. “But I'm having second thoughts because the most important claims can, I think, be very easily tested.”
Having got the bacterial strain from the original group of researchers, Dr. Redfield set about planning and carrying out experiments in a remarkably different fashion. The experiments she wanted to do, the problems that cropped up and the results she got were all written up on her blog. “One of the thing that had always been unusual about my blog was that I was writing openly about the experiments that I was doing before they were published,” she said on a recent episode of the podcast ‘This Week in Microbiology'. It was important that the process of science be made much more open. It was also a useful way to clarify her thinking.
By January this year, Dr. Redfield and her collaborators at Princeton University in the U.S. had finished the lab work and prepared a paper. The paper was submitted to Science. But she also did something that is common enough in physics but rare in biology. The full manuscript was posted on arXiv.org, the preprint server that is freely accessible.
“The advantage of arXiv is that the physicists all use it,” she remarked on the podcast. So Science would have had to deal with physicists posting papers there before or after they submitted them for publication. Indeed, the editor at Science handling their paper said that the journal had no problem with the manuscript being put on arXiv.
Science later responded with a provisional acceptance and comments from three reviewers. The manuscript was revised in the light of those comments and sent back to the journal.
But Dr. Redfield has also posted the full reviewers' comments on a web site and the revised manuscript was made available on arXiv.
Asked on the podcast whether the reviewers' comments could be released publicly, she responded, “I don't see why not.” There was nothing to indicate that those comments were to be kept in confidence. As for their finding, the manuscript declares that there was no sign that the bacterium was able to grow by using arsenic or that the element had been incorporated in its DNA. “On April 13, we submitted the revised version [of the manuscript to Science], and we're waiting with fingers crossed for final acceptance,” said Dr. Redfield on her blog.