Corante

About this Author
DBL%20Hendrix%20small.png College chemistry, 1983

Derek Lowe The 2002 Model

Dbl%20new%20portrait%20B%26W.png After 10 years of blogging. . .

Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases. To contact Derek email him directly: derekb.lowe@gmail.com Twitter: Dereklowe

Chemistry and Drug Data: Drugbank
Emolecules
ChemSpider
Chempedia Lab
Synthetic Pages
Organic Chemistry Portal
PubChem
Not Voodoo
DailyMed
Druglib
Clinicaltrials.gov

Chemistry and Pharma Blogs:
Org Prep Daily
The Haystack
Kilomentor
A New Merck, Reviewed
Liberal Arts Chemistry
Electron Pusher
All Things Metathesis
C&E News Blogs
Chemiotics II
Chemical Space
Noel O'Blog
In Vivo Blog
Terra Sigilatta
BBSRC/Douglas Kell
ChemBark
Realizations in Biostatistics
Chemjobber
Pharmalot
ChemSpider Blog
Pharmagossip
Med-Chemist
Organic Chem - Education & Industry
Pharma Strategy Blog
No Name No Slogan
Practical Fragments
SimBioSys
The Curious Wavefunction
Natural Product Man
Fragment Literature
Chemistry World Blog
Synthetic Nature
Chemistry Blog
Synthesizing Ideas
Business|Bytes|Genes|Molecules
Eye on FDA
Chemical Forums
Depth-First
Symyx Blog
Sceptical Chymist
Lamentations on Chemistry
Computational Organic Chemistry
Mining Drugs
Henry Rzepa


Science Blogs and News:
Bad Science
The Loom
Uncertain Principles
Fierce Biotech
Blogs for Industry
Omics! Omics!
Young Female Scientist
Notional Slurry
Nobel Intent
SciTech Daily
Science Blog
FuturePundit
Aetiology
Gene Expression (I)
Gene Expression (II)
Sciencebase
Pharyngula
Adventures in Ethics and Science
Transterrestrial Musings
Slashdot Science
Cosmic Variance
Biology News Net


Medical Blogs
DB's Medical Rants
Science-Based Medicine
GruntDoc
Respectful Insolence
Diabetes Mine


Economics and Business
Marginal Revolution
The Volokh Conspiracy
Knowledge Problem


Politics / Current Events
Virginia Postrel
Instapundit
Belmont Club
Mickey Kaus


Belles Lettres
Uncouth Reflections
Arts and Letters Daily
In the Pipeline: Don't miss Derek Lowe's excellent commentary on drug discovery and the pharma industry in general at In the Pipeline

In the Pipeline

« Science, A Zero-Sum World, and the State of the Union | Main | Roche Goes Hostile for Illumina »

January 27, 2012

Arsenic Bacteria Ride Again. (Or Don't).

Email This Entry

Posted by Derek

You may not have heard much about the arsenic-bacteria controversy recently, but you're about to hear quite a bit more. Rosie Redfield of UBC, one of the fastest and most vocal critics of the original paper, has been trying to reproduce it in her own group. There's a manuscript in preparation, but since she's been blogging on some of the progress, the import is clear: it hasn't been going well for the "bacteria can take up arsenic in their biomolecules" hypothesis. Scrolling back at that link will give you the story.

Here's a summary at Nature News (with a clarification from Redfield on one point). I look forward to seeing how this plays out - but remember, the startling results always have to prove themselves by happening again. Einmal ist keinmal.

Update: there's another story here, too. Redfield has been posting results as they come along, in a very prominent example of "open science". The first question is: will this affect journal publication? That is, will some editors look askance? The second point is to be found in that Nature News article, where Felisa Wolfe-Simon refers to those "website experiments", and how she basically can't discuss them until she sees them in a journal. Note that it's not "the UBC experiments" or "Redfield's experiments" - they're "website experiments", and thus (apparently) have more to prove.

Comments (19) + TrackBacks (0) | Category: Life As We (Don't) Know It


COMMENTS

1. RB Woodweird on January 27, 2012 8:21 AM writes...

“We are thrilled that our results are stimulating more experiments from the community as well as ourselves,” first author Felisa Wolfe-Simon, now at the Lawrence Berkeley National Laboratory in California, wrote in an e-mail to Nature. “We do not fully understand the key details of the website experiments and conditions. So we hope to see this work published in a peer-reviewed journal, as this is how science best proceeds.”

Interesting that Felisa pulls out the peer-reviewed or bust card, seeing as how her results were communicated via press conference.

Permalink to Comment

2. Curious Wavefunction on January 27, 2012 8:25 AM writes...

Carmen Drahl also had a great piece about this over at C&E. The sad thing as someone noted there was that the arsenic proponents will fight a rearguard battle and gradually retreat into the shadows rather than capitulate outright and admit their fault; the whole thing is in danger of being slowly forgotten rather than going down in the history books as a glaring cautionary tale (which is should).

Permalink to Comment

3. Derek Lowe on January 27, 2012 8:57 AM writes...

RB, that's interesting. In between posting this on the train ride in to work and getting here to my office, I had exactly the same sort of thought, and thus the updated post. Then I read your comment!

Permalink to Comment

4. SP on January 27, 2012 9:32 AM writes...

There are some large subsets of journals (maybe the ACS family?) that require you to certify that the results have not been previously published in a public forum.

Permalink to Comment

5. chirality on January 27, 2012 10:19 AM writes...

The problem with this whole arsenic DNA debacle is that Felisa Wolfe-Simon's claims are not falsifiable. Therefore, this is not science. Initially, FWS led everybody to believe that arsenic was replacing phosphorous in DNA based on very flimsy evidence and wishful thinking. Faced with the well-deserved skepticism, FWS has changed her tune. Now the claim is that some biomolecules produced by her namesake bacteria incorporate As instead of P to SOME DEGREE. Therefore, to disprove this claim, one would have to show that no biomolecule incorporates any (we are talking single atoms here) As instead of P. Good luck with it! This is very much like the hexacyclinol parody. Everybody knows it is rubbish, but it is immensely difficult to prove it.
Personally, I would like to see this arsenic thing retracted just to deflate FWS's ego - who on Earth names an organism after oneself?

Permalink to Comment

6. GC on January 27, 2012 10:51 AM writes...

Speaking of web vs. journals, there's an Elsevier boycott now: http://science.slashdot.org/story/12/01/27/1322234/scientists-organize-elsevier-boycott

Permalink to Comment

7. David Sanders on January 27, 2012 11:30 AM writes...

The text of the original Science article misrepresents the data (Supplementary Table 1, for example) as does the authors' Response to the Technical Comments. The authors have committed misconduct both in the original publication and in their persistence in their pseudoscience after it has been demonstrated incontrovertibly that they provide no evidence for their claims.

Permalink to Comment

8. cirby on January 27, 2012 11:55 AM writes...

I figured it out.

They're not arsenic-based organisms.

One of the bacteria just took out an insurance policy on the rest, and is trying to collect on it by poisoning them.

Permalink to Comment

9. anchor on January 27, 2012 2:46 PM writes...

#5, well said! How can one prove the negative?

Permalink to Comment

10. paperclip on January 27, 2012 3:01 PM writes...

As to the the first question in Update, Dr. Redfield says that she has been blogging about her work for about 6 years, and it hasn't affected her ability to publish. (But her arsenic work has surely received much more attention than her other projects, so I'm not sure if past experience will be a reliable predictor.)

There's been a lot of talk about "open science" lately. The New York times covered it recently, and I noticed that most of the commenters were critical, many of them envisioning the process as a Facebook-style popularity contest. Whatever the case, for most of us article-writers, and I mean 99+%, things will remain the same. There are far too many articles for each of them to get attention from blogs and the like.

Permalink to Comment

11. spoons on January 27, 2012 7:09 PM writes...

@10 They say Facebook style popularity contest as a bad thing? I could easily imagine having a organized social network of the scientific community with their real names attached to all their work and comments, with information coming out in a relative real time.

Sure that is a bit of a pie-in-the-sky scenario I cooked up but some peoples apocalyptic visions of Facebook are a bit overblown in my opinion.

Permalink to Comment

12. WesvewatwolWeceptow on January 27, 2012 10:31 PM writes...

@Derek: u take the train? now that pfizer's in town why not hop on the chopper?

Permalink to Comment

13. Hap on January 27, 2012 10:34 PM writes...

I hope Dr. Wolfe-Simon doesn't become a prosecutor.

"Your Honor, the defendant haven't proven that he didn't do it, so he should be found guilty. In addition, the defense insists on bringing up inconsistencies in our case in public and not behind closed doors as they should."

(mumbled conversation with the judge)

"What? You mean we have to, like, prove our case, or at least not posit a story with more holes in it than a pound of Swiss cheese? That's preposterous."

Permalink to Comment

14. Anonymous on January 30, 2012 3:03 AM writes...

@5 chirality: I think the same type of person who names an institute after oneself.

In the same vein, @13 Hap: I agree, but can we leave out the sexist undertones? (If FWS had been male, would you have written the "like"? I hate when people conflate her femaleness with her ignorance.)

Permalink to Comment

15. Vader on January 30, 2012 12:21 PM writes...

@14: There are perils with that kind of self-promotion:

Patrick J. Sullivan Jr. booked into Patrick J. Sullivan Jr. Detention Center.

Permalink to Comment

16. Falanx on January 31, 2012 8:38 AM writes...

To #14:

Really? I saw no conflation. I saw the stylised representation of the words of a moron. I'd have phrased it equally so if 'Felix Wolfe-Simon'were our subject.

What I did see was an unfounded assumption, though...

Permalink to Comment

17. Dave on January 31, 2012 4:36 PM writes...

@1

The Wolfe-Simon results were communicated by press conference, but only after they had been peer reviewed and published. Redfield's have not been. What is so hard to understand about that?

Permalink to Comment

18. Hap on February 1, 2012 10:07 PM writes...

Sorry - the "like" was too feminine-implying. I would have had the same contempt for whoever made the argument (and since it's been a staple of ID, I would have had opportunity to use it against those of the other gender), but I didn't intend the sexual slight.

I used to use "like" too often, though that was in sixth grade and twenty-five years ago.

Permalink to Comment

19. Hap on February 2, 2012 11:49 PM writes...

17: Yeah, but so were cold fusion, NaH oxidation, and the JJLC hexacyclinol "synthesis" (and at least the last two had more than enough problems that their publication should have been aborted well before we ever saw them). The "reactome" paper was also published in the same journal, with chemistry in the schemes that would get you failed in a first-semester orgo or biochem course and a theory of biological action that seemed...sketchy. (See this comment and this comment for reasons why.)

Peer review is supposed to keep out crap, but it doesn't always do even that, even at the upper echelons of journaldom. It shouldn't be seen as a talisman to reject arguments of incorrectness. It lowers the likelihood of a paper being complete crap, but doesn't eliminate it, let alone validate the content (since you may not find fraud by peer review). There is also the step of having others reproduce your work. (You could argue that with other authors, the reproducibility of work is taken more for granted than in this case, and that that indicates a bias of some sort. People could be biased, either by sex or by youth, although the facility of exchanging ideas and results in some form would seem to be a greater factor in the assumption of fallibility.)

Even if a paper is peer-reviewed, and reasonably so, it's still possible to claim lots of things in a press conference that the data in the paper can't support. There are good reasons that publication by press release is so poorly regarded - you're not supposed to make claims that your data can't cash.

Permalink to Comment

POST A COMMENT




Remember Me?



EMAIL THIS ENTRY TO A FRIEND

Email this entry to:

Your email address:

Message (optional):




RELATED ENTRIES
XKCD on Protein Folding
The 2014 Chemistry Nobel: Beating the Diffraction Limit
German Pharma, Or What's Left of It
Sunesis Fails with Vosaroxin
A New Way to Estimate a Compound's Chances?
Meinwald Honored
Molecular Biology Turns Into Chemistry
Speaking at Northeastern