louisville1

What I learned from #arseniclife:Communication and quality control

in science

Rosie RedfieldUniversity of British Columbia

What’s changing in science communication?

The arsenic-DNAdebacle

How can we make the most of it?

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

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: felisawolfesimon@gmail.com

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

The arsenic-DNA debacle

Media blitz (credulous)

Peer criticism on blogs

Media coverage of criticismSpread by Twitter

The arsenic-DNA debacle

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!

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

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.

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

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

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.

What’s changing in scientific communication?

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...

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’

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

Google Scholar

NIH reporter, NSF FastLane

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

$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...)

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

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

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

What’s changing?

Collaboration:

Visits

Telephone

Email

Polymath project

Community annotation projects

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

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)

Whew!

How can we make the most of it?

No wonder we can’t keep up.

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

Cooperation Competition

Scientificprogress

How can we make the most of it?

Do your science openly: blog about your research

Do your science openly: post your grant proposals

Do your science openly: support open access

• 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

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