The Nature of Science

There's a difference between

controls done to genuinely
test your hypothesis and
those done when you just
want to show that your
hypothesis is true.

December 2010

Alex Bradley: One thing that everyone agrees on is that all

things being equal, DNA with an arsenate backbone will
hydrolyze quickly in water, while DNA with a phosphate
backbone will not. The half-life of the hydrolysis reaction is
about 10 minutes.
Wolfe-Simon et al. recognize this, but claim that the bacterium
must have some unknown biological mechanism to
compensate, and this prevents the DNA from falling apart in the
cells. Lets assume for now that they are correct: biology has all
kinds of strange tricks and this idea cant be quickly dismissed,
even if it seems radical.
But chemistry is much more predictable. Once DNA is out of the
cell, pure chemical processes take over, and experimentshave
demonstrated that hydrolysis of arsenate links is fast. So you
could do a simple experiment to test whether DNA had a
phosphate or arsenate backbone: just remove DNA from the cell
and put it in water for a few minutes. Then examine whether it
hydrolyzes or not.

Rosie Redfied: There's a difference between controls done

to genuinely test your hypothesis and those done when you
just want to show that your hypothesis is true. The authors
have done some of the latter, but not the former.
They should have mixed pregrownE. colior other cells with
the arsenate supplemented medium and then done the
same purifications.
They should have thoroughly washed their DNA preps (a
column cleanup is ridiculously easy), and maybe incubated
it with phosphate buffer to displace any associated
arsenate before doing the elemental analysis.
They should have mixed E. coli DNA with arsenate and then
gel-purified it.
They should have tested whether their arsenic-containing
DNA could be used as a template by normal DNA
polymerases.

http://blog.chembark.com/2011/06/16/felisa-wolfe-simon-does-not-getit/

What is also absurd is that in the face of a hurricane of criticism

from nearly all of the heavy-hitters in the origin-of-life
community,Wolfe-Simon seems to be taking credit for catalyzing
how the system is supposed to work and pushing science forward
at a faster rate. Listen to what shetoldC&EN:
Wolfe-Simon, who works at NASAs Astrobiology
Institute and the U.S. Geological Survey in Menlo Park,
Calif., tells C&EN she thinks the controversy has primed
the scientific process. Weve been able to gain so much
because of discussion and collaboration, she says.
This is moving science forward faster.
What planet does this woman live on?This islike a serial killer
taking credit for increasing vigilance in a victimized
neighborhood. Yes,all of the uproar has moved Wolfe-Simons
study forward faster than she was capable, but only becauseshe
shamelessly trumped it upto the point that others felt compelled
to deal with it. All of the attention paid toher study has robbed
scientists time and attention from more interesting areas. The
uproar has also jerked around the public and the press.

it is NOT junk blog

a blog about genomes, DNA, evolution,
open science, baseball and other
important things

Felisa Wolfe-Simon (of arsenic infamy) is no

more convincing in person than in print
ByMICHAEL EISEN|Published:MARCH18,2011

And the key test of arsenic incorporation was

done on a highly impure sample. Iasked her
about this later point during the Q&A.And
she gave the astonishing answerthat they
lacked the equipment needed to purify DNA.
I find it hard to believe Wolfe-Simon thinks
you need an HPLC to separate agarose from
DNA a google search for DNA purification
reveals many simple alternatives. But even if
she does think this, her failure to investigate

http://www.nature.com/news/2011/110601/full/474019a.html

Some are also frustrated that the authors did

not release any new data in their response,
despite having had ample time to conduct
follow-up experiments of their own to bolster
their case.
Some:
First, she participated in adreadfulpress conference to promote
the work, and the media blitz quickly backfired when it brought
with it the magnified scrutiny of the scientific community. Then
Wolfe-Simon decided to lie low and not answer questions from
the press, saying that she wanted to be able to have that
discourse in the scientific community, as a record. But look at
what has transpired in the interim: She gave a public
TED lecturein March andprovided extensive commentaryfor a
rising-star advice piecein the June edition
ofGlamourmagazine. She also appearedin aprofile
inTimemagazine as one of the 100 most influential people in the
world.As an excuse to avoid the (unwanted negative) press, she
saidin December that she really wanted to get back home and
back into the lab. But as Rosie Redfield and otherspoint out,

January 2012

This month, Redfield posted online mass

spectrometry data: the conclusion she and her
colleagues reachedthat the DNA from GFAJ-1
contains no arsenic.

There's a difference between

controls done to genuinely
test your hypothesis and
those done when you just
want to show that your
hypothesis is true.