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#arseniclife, social media and open science [videorecording] Redfield, Rosie 2012-11-01

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#arseniclife, social media and open science #evol2012 #arseniclife Rosie Redfield Dept. of Zoology, UBC that will impact the search for evidence of extraterrestrial life. Twitter response: Their Astrobiology Program wants to understand how life can originate and what  forms it can take. Why was NASA funding them? A form of life that uses arsenic in place of phosphorus. What were the researchers looking for? All known life requires phosphorus may even persist on Earth today, undetected, in unusual niches. Such organisms could have used arsenate in the equivalent biochemical role. We hypothesize that ancient biochemical systems... Arsenic is chemically similar. ? ? The Shadow Biosphere Mono Lake mud NASA gave Wolfe-Simon a fellowship to search for arsenic-using members of the Shadow Biosphere (200 µM AsO4) Cells eventually grew, even in 40 mM AsO4. She added Mono Lake sediment to a culture medium containing AsO4 rather than PO4. ‘GFAJ-1’ Fig. 2 NanoSIMS analyses of GFAJ- 1: extracted DNA and whole-cells elemental ratio maps.  F Wolfe-Simon et al. Science 2011 ;332:1163- 1166 Fig. 3 X-ray analysis of GFAJ-1 +As/–P described similarity of As coordinated like P in DNA. (A) EXAFS comparisons of the Fourier transformed data for As in model environments and GFAJ-1 (washed and fixed, collected on whole cells).  As Chemical clarification:  P The -P growth medium had contaminating PO4, but nobody knew how much PO4 (µM) Should be 0 0 0 0 1500 0 The amount of phosphate in the ‘no-phosphate’ culture medium The number of cells that could be made using this phosphate Most –P +As preps had enough PO4 for the observed growth Problem 1:  The DNA was not well purified before being loaded in the gel. Problem 2:  The DNA was not purified from the gel before analysis. Phenol Aqueous (DNA, As) DNA+? pellet 70% EtOH The As in the gel slices may not have been part of the DNA. Gel “NanoSIMS analyses. Individual cells and DNA in high purity agarose gel sections were analyzed for As and P abundance by high-resolution secondary ion mass spectrometry.” Maybe the arsenate was just carried along with the dirty DNA sample Chemical consideration:  As-DNA bonds are unstable Dwayne Brown, NASA Headquarters, Washington                                WASHINGTON -- NASA will hold a news conference at 2 p.m. EST on Thursday, 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.  Press Release by NASA (Nov. 29):  Wolfe-Simon will not be responding to individual criticisms, as the agency doesn't feel it is appropriate to debate the science using the media and bloggers. Instead, it believes that should be done in scientific publications. NASA spokesman Dwayne Brown (Dec. 6, quoted by CBC News): Some people changed their minds about social media... Felisa Wolfe-Simon (Dec. 7, quoted by Carl Zimmer): Any discourse will have to be peer-reviewed in the same manner as our paper was, and go through a vetting process so that all discussion is properly moderated. The flawed evidence for arsenic in DNA is overwhelmed by  the ‘prior-knowledge’  obstacles. Flaws in the research Nevertheless,  the blogosphere,  the twitterverse, and  the mainstream media all agreed: ‘Someone should put the claims to an experimental test!’ Social media: Why I blog The minimal experiments needed to test the #arseniclife claims: 1. Get GFAJ-1 cells from authors; check identity by 16S sequencing 2. Measure growth (# of cells/ml) in AML-60 medium ±PO4 and ±AsO4  3. Thoroughly purify DNA from cells grown ±AsO4; check stability 4. Assay DNA for arsenic (send DNA to collaborators with expertise) Bl o g about  eve ry step ... Collaborators (at Princeton): results irreproducible Precipice of GFAJ-1 DNA -As -P -As +P +As +P +As -P liquid chromatography- mass spectrometry  The manuscript is available on the arXiv server.  Science had embargoed it until July 26...  The paper is ‘in press’ at Science . Some journals use ‘press embargos’ to control how research is publicized. Journalists get advance copies of papers, on condition that they don’t publish anything until the paper appears in the journal. Authors are instructed not to speak to the press except under this condition. Your cooperation protects you from problems that may jeopardize your paper’s publication. FAIL FAIL FAIL FAIL FAIL FAIL Reviewers Editors  of Science Senior author       (her supervisor) Other authors Lead author NASA But science (the process) worked well. Credits and Inspirations • Pedro Beltrao:  His blog post about open science started me blogging. • Sunita Sinha (my lab RA):  She did the 16S rDNA sequencing and helped write the paper. • Leonid Kruglyak, Josh Rabinowitz and especially Marshall Reaves:  They did the arsenate analysis and helped write the paper. • Canadian Institutes for Health Research:  They paid for the arsenate and Sunita’s time. • Science (the journal): They gave us an easy target, and then a hospitable environment for rebutting it.  


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