Slide 1

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.

They should have noticed all the discrepancies in their data and done experiments to find the causes.

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

it is NOT junk bloga blog about genomes, DNA, evolution, open science, baseball and other important thingsFelisa Wolfe-Simon (of arsenic infamy) is no more convincing in person than in printByMICHAEL EISEN|Published:MARCH 18, 2011And 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 alternatives means means she is not serious about answering the question.

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 publicTED 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, Wolfe-Simons response to the technical comments contained no new experiments. Jeez, Louise!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.http://www.nature.com/news/2011/110601/full/474019a.htmlSome:

This month, Redfield posted online mass spectrometry data: the conclusion she and her colleagues reachedthat the DNA from GFAJ-1 contains no arsenic.January 2012

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.