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What I learned from #arseniclife:Communication and quality control
in science
Rosie RedfieldUniversity of British Columbia
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What’s changing in science communication?
The arsenic-DNAdebacle
How can we make the most of it?
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Nov. 29 Press release from NASA
Nov. 29: NASA Sets News Conference on Astrobiology DiscoveryNASA 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.
Dec. 2 Press conference
NASA-funded astrobiology research has changed the fundamental knowledge about what comprises all known life on Earth
This finding of an alternative biochemistry makeup will alter biology textbooks and expand the scope of the search for life beyond Earth.
As we pursue our efforts to seek signs of life in the solar system, we have to think more broadly, more diversely and consider life as we do not know it.
The arsenic-DNA debacle
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A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus
Felisa Wolfe-Simon,1,2* Jodi Switzer Blum,2 Thomas R. Kulp,2 Gwyneth W. Gordon,3 Shelley E. Hoeft,2 Jennifer Pett-
Ridge,4 John F. Stolz,5 Samuel M. Webb,6 Peter K. Weber,4 Paul C. Davies,1,7 Ariel D. Anbar,1,3,8 Ronald S. Oremland2
1NASA Astrobiology Institute, USA. 2U.S. Geological Survey, Menlo Park, CA, USA. 3School of Earth and Space Exploration, Arizona
State University, Tempe, AZ, USA. 4Lawrence Livermore National Laboratory, Livermore, CA, USA. 5Department of Biological Sciences,
Duquesne University, Pittsburgh, PA, USA. 6Stanford Synchrotron Radiation Lightsource, Menlo Park, CA, USA. 7BEYOND: Center for
Fundamental Concepts in Science, Arizona State University, Tempe, AZ, USA. 8Department of Chemistry and Biochemistry, Arizona State
University, Tempe, AZ, USA.
*To whom correspondence should be addressed. E-mail: [email protected]
Life is mostly composed of the elements carbon, hydrogen,
nitrogen, oxygen, sulfur and phosphorus. Although these
six elements make up nucleic acids, proteins and lipids
and thus the bulk of living matter, it is theoretically
possible that some other elements in the periodic table
could serve the same functions. Here we describe a
bacterium, strain GFAJ-1 of the Halomonadaceae,
isolated from Mono Lake, CA, which substitutes arsenic
for phosphorus to sustain its growth. Our data show
evidence for arsenate in macromolecules that normally
contain phosphate, most notably nucleic acids and
proteins. Exchange of one of the major bio-elements may
have profound evolutionary and geochemical significance.
biology is phosphate (PO43-), which behaves similarly to
arsenate (AsO43-) over the range of biologically relevant pH
and redox gradients (6). The physico-chemical similarity
between AsO43- and PO43- contributes to the biological
toxicity of AsO43- because metabolic pathways intended for
PO43- cannot distinguish between the two molecules (7) and
arsenate may be incorporated into some early steps in the
pathways [(6) and refs therein]. However, it is thought that
downstream metabolic processes are generally not compatible
with As-incorporating molecules because of differences in the
reactivities of P- and As-compounds (8). These downstream
biochemical pathways may require the more chemically stable
P-based metabolites; the lifetimes of more easily hydrolyzed
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The arsenic-DNA debacle
Media blitz (credulous)
Peer criticism on blogs
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Media coverage of criticismSpread by Twitter
The arsenic-DNA debacle
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What were the problems?
1. The prior probability was VERY low.
2. The data was VERY unconvincing.
The arsenic-DNA debacle
Scientific consensus reached: Conclusions are not credible
100,000 people came to my blog!
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The prior probability that DNA could contain arsenic was VERY low.
The arsenic-DNA debacle
The half-life of arsenic diester bonds in DNA is predicted to be < 0.1 second.
If a DNA backbone contained a mixture of phosphorus and arsenic links, it would have an irregular structure (large and small atoms, long and short bonds). It could not be accurately replicated by DNA polymerase.
O
O As
P
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added PO4
added AsO4
plain
Growth in As stopped when phosphorus became depleted.
Did the cells really grow without phosphorus?
The arsenic-DNA debacle
Carbon storage was mistaken for growth.
plain medium
added AsO4
added PO4
plain
The ‘arsenic’ medium wascontaminated with phosphorus.
[P] (µM)3.7
<0.32.92.7
7.4
‘No added P’batch 1batch 2batch 3batch 4
wash sol’n
OD600 increased in As medium because cells filled with granules of poly-hydroxybutyrate.
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The DNAs were not purified away from the gel before analysis, so 99.9% of the mass analyzed was agarose and contaminants, not DNA.
The DNA from arsenic-grown cells contained only twice as much As:C as the controls.
This DNA was also used as a template for PCR; it worked fine!
The arsenic-DNA debacle Did the DNA really contain arsenic?
Analysis of ‘gel-purified’ DNA
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The ‘prior’ probability that bacteria could have replaced some P atoms in their DNA with As atoms was very very very very small.
The evidence for this is very weak.
The probability that the evidence is correct is very very very small.
and
so
The arsenic-DNA debacle
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Positive outcomes:
Efficient communication between scientists.
Clear scientific consensus that the conclusion was wrong.
Excellent media coverage.
Public demonstration of how science is self-correcting.
Negative outcomes:
Public demonstration of how science gets things wrong.
The creationists loved it.
Most people saw only the original (wrong) story.
The arsenic-DNA debacle
Four months later, the paper has not been formally published.
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What’s changing in scientific communication?
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NASA spokesman Dwayne Brown said that 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 said “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.”
Dec. 7:
“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.”
Nov. 29:
Compare and contrast...
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Publication:
What’s changing?
Communication only face-to-face and by personal letter
Paper publication in journals
Online-only publication
In-press papers available online
Paper+online publication
Published proceedings of scientific society meetings
Document-server ‘publication’
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What’s changing?
Searching (where):
Journal Table of Contents, annual subject index
Index Medicus, Chemical Abstracts etc.
Science Citation Index (paper)
Medline
PubMed
Web of Science
Google Scholar
NIH reporter, NSF FastLane
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What’s changing?
Paying the costs:
Institutional subscriptions
Individual subscriptions
Pay-per-view
Authors pay ‘open-access’ cost
Page charges, figure charges
Institutional subsidies for author costs
Billing Summary for JB 0476-09
Payment Information:Page Charge: $1520 Supplemental Data Charge: $ 190
Open Access Charge: $2000
Total Charges: $3710
Authors pay all costs
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$ELLWhat’s changing?
PDFs
Paper reprints and mailed reprint requests.
Photocopying
Sharing:
Who profits:
Societies use subscription fees for other goals
For-profit paper journals (Science, Nature)
Non-profit publications
For-profit online journals (BioMedCentral, Bentham, Hindawi, Frontiers in...)
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What’s changing?
How access is controlled:
Subscription/library only
PubMed Central
Open access only for original research papers
Full open access
NIH mandates open access 1 year after publication
The arXiv server
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What’s changing?
Semi-formal communications:
Journal club
Invited seminar
Poster at a conference
Podcast
SlideShare
Publish poster at Faculty of 1000
Talk at a conference
Post talk on YouTube
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What’s changing?
The Bermuda Accords(International Strategy Meeting onHuman Genome Sequencing, Bermuda 1996)
Automatic release of sequence assemblies larger than 1 kb (preferably within 24 hours).
Immediate publication of finished annotated sequences.
Aim to make the entire sequence freely available in the public domain for both research and development in order to maximise benefits to society.
Data sharing:
Genbank, SwissProt, etc.
Sequence submission required for publication
The human genome project (Bermuda Accords)
Open Science
The Open Science Project
The Chemistry Development Kit
Community standards for data submission
Ontologies
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What’s changing?
Collaboration:
Visits
Telephone
Polymath project
Community annotation projects
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What’s changing?
Quality control before publication (peer review)
Anonymous peer review
Personal reputation
Open peer review
Weird peer review
Double-blind peer review
No peer review (arXiv)
Frontiers full reviews are made up of two consecutive steps, an independent and an interactive review. In the independent review phase, review editors evaluate independently from each other whether the research is academically sound following a standardized review questionnaire. Then, Frontiers implemented for the first time the real-time Frontiers Interactive Review Forum, in which authors and review editors collaborate online via a discussion forum until convergence of the review is reached.
Peer review for quality but not impact
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What’s changing?
Quality control after publication:
Formal comments published in journal (±peer review)
No mechanism for comments
Independent reviews on blogs
Comments linked to article on journal web page
RetractionWatch
Twitter comments
Independent reviews aggregated (ResearchBlogging, The Third Reviewer)
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Whew!
How can we make the most of it?
No wonder we can’t keep up.
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How did #arseniclife fit into all this?
collaborative researchmanuscript
anonymous peer reviewacceptance
press release, embargopress conference
pre-publication (in-press) paywall access
media coveragecritical peer review on blogs
spread by Twittercritical articles in the media
open accessjournal articles
formal publication stalledformal comments in limbo
slow
slow
FAST
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Cooperation Competition
Scientificprogress
How can we make the most of it?
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Do your science openly: blog about your research
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Do your science openly: post your grant proposals
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Do your science openly: support open access
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• Include funds for open access publication costs in your grant proposal budgets.
• When choosing a journal, consider whether access is open, or whether you can pay to make it open.
• Review for non-profit open-access journals.
• Use Creative Commons copyright whenever possible.
• Ignore the evil rules imposed by other journals (sign the form and act as if you didn’t).
• Post your formatted pdfs.
• Contribute to #Icanhazpdf, ScienceLeaks, and other paper-sharing sites.
Do your science openly: support open access
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Inspirations and Credits:
Pedro Beltrao: His post about open science started me blogging.
Matt Meselson: Posted his grant proposals online circa 1995
Jon and Michael Eisen: PLoSpioneers, open access advocates
Canadian Institutes for Health Research