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#arseniclife, social media and open science Redfield, Rosie Nov 1, 2012

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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:  What were the researchers looking for? A form of life that uses arsenic in place of phosphorus.  Why was NASA funding them? Their Astrobiology Program wants to understand how life can originate and what forms it can take.  All known life requires phosphorus  Arsenic is chemically similar.  We hypothesize that ancient biochemical systems... could have used arsenate in the equivalent biochemical role.  Such organisms may even persist on Earth today, undetected, in unusual niches.  The Shadow Biosphere  ?  ?  NASA gave Wolfe-Simon a fellowship to search for arsenic-using members of the Shadow Biosphere  Mono Lake mud (200 µM AsO4)  She added Mono Lake sediment to a culture medium containing AsO4 rather than PO4. Cells eventually grew, even in 40 mM AsO4. ‘GFAJ-1’  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).  F Wolfe-Simon et al. Science 2011 ;332:11631166  Fig. 2 NanoSIMS analyses of GFAJ1: extracted DNA and whole-cells elemental ratio maps.  Chemical clarification:  As  P  The -P growth medium had contaminating PO4, but nobody knew how much PO4 (µM)  Should be  0 0 0 0 1500  0  Most –P +As preps had enough PO4 for the observed growth  The amount of phosphate in the ‘no-phosphate’ culture medium  The number of cells that could be made using this phosphate  Maybe the arsenate was just carried along with the dirty DNA sample “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.”  Problem 2: The DNA was not purified from the gel before analysis.  70% EtOH  Aqueous (DNA, As) Phenol  DNA+? pellet  Problem 1: The DNA was not well purified before being loaded in the gel.  Gel  The As in the gel slices may not have been part of the DNA.  Chemical consideration: As-DNA bonds are unstable  Some people changed their minds about social media... Press Release by NASA (Nov. 29): 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.  NASA spokesman Dwayne Brown (Dec. 6, quoted by CBC News): 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.  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 Flaws in the the ‘prior-knowledge’ research obstacles.  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:  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)  Blog about every step...  1. Get GFAJ-1 cells from authors; check identity by 16S sequencing  Collaborators (at Princeton):  Precipice of irreproducible results  GFAJ-1 DNA  -As -P  liquid chromatographymass spectrometry  -As +P  +As +P  +As -P  The manuscript is available on the arXiv server.  The paper is ‘in press’ at Science .  Science had embargoed it until July 26...  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 Lead author  FAIL  Senior author (her supervisor)  FAIL Other authors  FAIL Reviewers Editors FAIL of Science  NASA FAIL  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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