NASA Press Conference Thursday 2nd December 2010

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Re: NASA Press Conference Thursday 2nd December 2010

Postby Access Denied » Sat Dec 11, 2010 7:18 pm

m0r1arty wrote:Could you elaborate upon what it is you see please?

I see someone who appears unqualified taking a cheap shot that has little or nothing to do with the actual paper and is promoting ignorance of the way scientific research is conducted and the results of experiments are reported.

A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus*
http://www.sciencemag.org/content/early ... 8.full.pdf

The beginning…

"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."

The middle....

"Our data show arsenic-dependent growth by GFAJ-1 (Fig. 1). Growth was accompanied by arsenate uptake and assimilation into biomolecules including nucleic acids, proteins and metabolites (Table 1 and 2, Figs. 2 and 3). In some organisms, arsenic induces specific resistance genes to cope with its toxicity (7); while some dissimilatory arsenicutilizing microbes can conserve energy for growth from the oxidation of reduced arsenic species, or ”breathe" AsO4 3-, as a terminal electron acceptor (18). Our study differs because we used arsenic as a selective agent and excluded phosphorus, a major requirement in all hitherto known organisms. However, GFAJ-1 is not an obligate arsenophile and it grew considerably better when provided with P (Fig. 1A, B)."

And the end...

"We report the discovery of an unusual microbe, strain GFAJ-1, that exceptionally can vary the elemental composition of its basic biomolecules by substituting As for P. How arsenic insinuates itself into the structure of biomolecules is unclear, and the mechanisms by which such molecules operate are unknown."

I don’t see a problem here. Let us know when you figure out how this microbe was able to reproduce under these conditions without incorporating As into it’s DNA as the evidence they obtained suggests. Perhaps something else is going on but that's beside the point. These are the results of the study they conducted. Until then, here’s a proper critical analysis…

http://www.physicsforums.com/showpost.p ... stcount=21

Here is my rather long analysis of the article. I've tried to write it so that non-chemists and non-biologists can understand it. If you're intimidated, you can skip to the last two paragraphs for a summary of my thoughts on the paper.

[…]

…the researchers obtained a bacterial strain, dubbed GFAJ-1, which seemed to incorporate arsenic in the place of phosphorus. This conclusion is based on five lines of evidence:

[…]

In summary, Wolfe-Simon and colleagues have identified a strain of bacteria that can survive in high arsenic, low phosphorus environments. Surprisingly, this bacteria can use arsenic to replace some of the roles of phosphorus. More work needs to be done to elucidate exactly in which roles arsenic can replace phosphate and in which roles arsenic does not replace phosphate. While the evidence may be consistent with these bacteria containing arsenic-based DNA, the data do not offer irrefutable proof of this hypothesis. A lack of arsenic-based DNA would be expected because previous work by chemists suggests that arsenic-based DNA would be too unstable to exist inside a living cell (Westheimer (1987) Why Nature Chose Phosphates. Science 235: 1173. link).

Nevertheless, Wolfe-Simon have made an important discovery identifying a bacterium where arsenic can replace some of the roles of phosphorus. The organism clearly has novel arsenic-based biochemistries that will be interesting to learn more about in the coming years. While it might be exciting to speculate that these bacteria represent a new form of life with a different type of genetic material than any other terrestrial organisms, we do not yet have enough evidence to say whether this is true or not.

The only problem I see here is how this was reported by some in the media.


*This research was conducted by Felisa Wolfe-Simon (NASA Astrobiology Institute, U.S. Geological Survey), Jodi Switzer Blum (U.S. Geological Survey), Thomas R. Kulp (U.S. Geological Survey), Gwyneth W. Gordon (Arizona State University), Shelley E. Hoeft (U.S. Geological Survey), Jennifer Pett-Ridge (Lawrence Livermore National Laboratory), John F. Stolz (Duquesne University), Samuel M. Webb (SSRL and SLAC), Peter K. Weber (Lawrence Livermore National Laboratory), Paul C.W. Davies (NASA Astrobiology Institute, Arizona State University), Ariel D. Anbar (NASA Astrobiology Institute, Arizona State University), and Ronald S. Oremland (U.S. Geological Survey).
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Re: NASA Press Conference Thursday 2nd December 2010

Postby m0r1arty » Sun Dec 12, 2010 10:39 am

Access Denied wrote:I see someone who appears unqualified taking a cheap shot that has little or nothing to do with the actual paper and is promoting ignorance of the way scientific research is conducted and the results of experiments are reported.


I grant that Thunderf00t's civility can be questioned however the motive which powers that is a steely resolve which explains, I think in a fairly simple way, the processes being discussed within the paper to the every man - not an easy task to do. I've not seen any mainstream media outlets explain it in such a fashion.

Having a paper written and published is no easy thing to achieve. Knowing that paper will be reviewed by anyone with access to academic journals is a factor in making every word count. Having a press release about a paper which is 2 years old is taking the biscuit.

If the paper states that a fundamental principle to life on Earth is different (which, granted the paper didn't say - but it was mentioned at the press conference) then you can expect everyone in science to sit up and take note. I don't have a molecular biology qualification, but as a chemist I can say that substituting one atom for another always has drastic effects and stating that it is the case with DNA itself asks for a huge suspension of belief just to digest and begs to be scrutinised if for nothing else to have the idea still standing afterwards.

The paper falls short of what was discussed at the press conference and the fact that a press conference was called for in either case smacks of an agenda which is currently unclear to me.

You might want to take a look at a few of Thunderf00t's videos - he heralds the scientific process above all else. And yes, his attitude is just a lively in those videos as it was in this one. He's not on my recommended reading list, but he's certainly an activist who I'd promote for those who wish to look at modern age community development to look at.

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Re: NASA Press Conference Thursday 2nd December 2010

Postby Access Denied » Thu Dec 16, 2010 6:50 am

m0r1arty wrote:I've not seen any mainstream media outlets explain it in such a fashion.

That’s probably a good thing… :)

m0r1arty wrote:Having a press release about a paper which is 2 years old is taking the biscuit.

Huh?

Received for publication 1 September 2010.
Accepted for publication 8 November 2010.
Published Online 2 December 2010.


m0r1arty wrote:If the paper states that a fundamental principle to life on Earth is different (which, granted the paper didn't say - but it was mentioned at the press conference) then you can expect everyone in science to sit up and take note.

Who mentioned that, Davies?

The 'Give Me a Job' Microbe
A young researcher risked it all to chase an arsenic-guzzling bug
http://online.wsj.com/article/SB1000142 ... 21092.html

The announcement by NASA this past Thursday of the discovery of an amazing arsenic-guzzling bacterium has made the bug's discoverer, Felisa Wolfe-Simon, into an overnight celebrity. What few people know, however, is the story behind the initials for her GFAJ-1 microbe, the first known organism to depart from the usual chemical formula for life. GFAJ stands for "Give Felisa a Job."

If so, Davies is a little out there I’m afraid…

Felisa was still in her 20s and had a career to build. Her temporary position was coming to an end, and competition for jobs in cutting-edge scientific research is intense. Most young scientists play it safe and focus on a mainstream topic. But Felisa is a free spirit with a healthy contempt for scientific and professional hierarchies, and she had faith in her hunch. She dyed her long hair a defiant bright pink and refused to be browbeaten. It was a career gamble that very few young scientists would have the courage to make.

I fell into a role as Felisa's unofficial mentor and encouraged her to stick to her guns. In this, I had the advantage of being unencumbered by knowledge. I dropped chemistry at the age of 16, and all I knew about arsenic came from Agatha Christie novels. But who was going to fund the search for arsenic life?

That’s the real story here I think, many in the scientific establishment don’t think Astrobiology/Exobiology is a legitimate pursuit and for obvious reasons, even more in the religious establishment don't. Others still are content to sacrifice NASA's science budget to spend billions more on another paper rocket to nowhere...

m0r1arty wrote:I don't have a molecular biology qualification, but as a chemist I can say that substituting one atom for another always has drastic effects and stating that it is the case with DNA itself asks for a huge suspension of belief just to digest and begs to be scrutinised if for nothing else to have the idea still standing afterwards.

Really, can you elaborate on that for us? As I understand it, As sits right below P on the periodic table which is what makes it so toxic and normally destroy DNA.

m0r1arty wrote:The paper falls short of what was discussed at the press conference and the fact that a press conference was called for in either case smacks of an agenda which is currently unclear to me.

Hmm, I wonder why NASA’s PR department would hold a press conference to promote an Astrobiology paper that was accepted for publication?

[scratches head]

I’m drawing a blank.

Anyway…

http://twitter.com/ironlisa/status/11468256942489600

“For all you grrls out there: stick to your guns. Even if you nail it, you will still be judged. (To guys out there, stay cool support women).”

And if you don’t? :)

http://twitter.com/ironlisa/status/14051784414724096

“Back in lab. Time blocking. Making forward progress :-)

Good for her, she certainly has her work cut out for herself now… :lol:
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Re: NASA Press Conference Thursday 2nd December 2010

Postby m0r1arty » Thu Dec 16, 2010 9:20 am

Access Denied wrote:Really, can you elaborate on that for us? As I understand it, As sits right below P on the periodic table which is what makes it so toxic and normally destroy DNA.


You are correct, heavier atomic mass + larger nucleus + wider atomic radius (and resulting polarization) means that, according to current thinking, arsenic could not replace phosphorous in the structure of DNA - as stated at the press conference.

As for the rest of it, publication date withstanding, I have no idea.

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Re: NASA Press Conference Thursday 2nd December 2010

Postby Access Denied » Thu Dec 16, 2010 9:51 am

From the PF post I linked to earlier...

"Arsenic sits below phosphorus in the periodic table and therefore shares many properties with phosphorus. Because of these similarities, arsenate (AsO43-) could possibly substitute for phosphate in organisms that live in environments rich in arsenate."

And...

"...it is well known that arsenate can substitute for phosphate; this substitution is the mechanism for arsenate toxicity. In human cells, our phosphate transporters cannot distinguish between arsenate and phosphate and therefore let arsenate into cells. Inside of the cell, some enzymes will substitute arsenate for phosphate, which gums up the cellular machinery eventually killing the cell. Obviously, the arsenate incorporation is not killing these bacteria and some of the arsenate-containing biomolecules are functional, but it is unclear which arsenate-containing molecules are functional and which ones are not, a distinction that cannot be made from the data presented in this paper."
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Re: NASA Press Conference Thursday 2nd December 2010

Postby m0r1arty » Thu Dec 16, 2010 10:05 am

Access Denied wrote:Obviously, the arsenate incorporation is not killing these bacteria and some of the arsenate-containing biomolecules are functional, but it is unclear which arsenate-containing molecules are functional and which ones are not, a distinction that cannot be made from the data presented in this paper."[/i]


Big jump from the press conference artists rendition of arsenic replacing phosphorous as the 'backbone' of a DNA molecules though eh?

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Re: NASA Press Conference Thursday 2nd December 2010

Postby Access Denied » Sat Dec 18, 2010 11:17 pm

Nope, I don’t see anyone besides “Thunderf00t” claiming it’s impossible to replace phosphorous in the structure of DNA with arsenic, just unprecedented which is why, as it should be, the detection methods used are being subjected to some intense scrutiny. In that respect the system appears to be working. Many have found the data to be inconclusive and Wolfe-Simon et. al. are getting the feedback they need in order to refine or reject their hypothesis.

“Thunderf00t” isn’t doing anyone any favors (especially the cause of science) by trying to make a mockery out of the press conference and claiming their hypothesis is ruled out a priori. This comment by Jim Handman, a CBC journalist, pretty much says it all I think…

Arsenic bacteria – a post-mortem, a review, and some navel-gazing
http://blogs.discovermagazine.com/notro ... ment-31737

I must say I have been extremely puzzled and bothered by 2 tendencies that I’ve observed during this chaotic week of blogging and Tweeting about the arsenic controversy:

a – the apparent malicious glee that many bloggers seem to take in pointing to the criticisms of the paper (and that includes some of Ed’s own Tweets). With few exceptions, everyone seemed to assume the authors were deliberately misleading, or had falsified results, or had intentionally disregarded certain observations, or were just plain sloppy scientists. Plus, there were some very nasty, inappropriate and personal attacks – including an incredibly sexist comment about Wolfe-Simon’s hair colour.

b – the rush by virtually everyone on the web to side with Rosie Redfield over Wolfe-Simon and Ron Oremland (whom we interviewed on our program). Both Redfield and Oremland are highly respected senior scientists, and I have no reason to believe one over the other. I don’t understand why the vast majority of bloggers (most of whom are not microbiologists or organic chemists) instantly assumed Redfield was right. I’m just a simple journalist, compeltely unquliafied to judge the claims of either. So like Ed, I await scientific attempts to replicate the results, before I “rush to judgement”.

Or put another way by "Dr. Isis" on her blog On Becoming a Domestic and Laboratory Goddess

Don't Like Arsenic Bacteria? Put Your Experiment Where Your Mouth Is!
http://scienceblogs.com/isisthescientis ... ia_put.php

Wolfe-Simon's response may not have been popular, but she is right. The real discussions about this work belong in the scientific literature. The language of those discussions needs to be data - either the citation of data that already exist or the creation of new data to reject or support a hypothesis.

And…

NASA's arsenic-eating life form gets a second look
http://www.asdnews.com/news/32462/NASA_ ... d_look.htm

"The controversy surrounding this organism is quite fascinating," Peter Gilligan, a professor of Microbiology-Immunology at the University of North Carolina told AFP in an email.

"First, the work was published in one of the most prestigious peer reviewed journals, Science. A sharp rebuttal that was peer reviewed by no one appears in a blog written Rosie Redfield," he wrote.

"What I find fascinating as a journal editor and senior scientist is how information can be disseminated so quickly globally and how at least in some quarters it seems, that peer reviewed information and blogging can be given equal weight," he added.

"It remains to be seen who will be proven to be correct."

Gilligan said that in his view, Wolfe-Simon "maintained the high ground in this controversy by offering the organisms she has studied to other investigators via the typical channels."

In fact as it turns out, Redfield’s criticism has now been subjected to some peer review (see the comments on her blog) and she has also apologized to Wolfe-Simon for her comments to the press…

An apologetic email
http://rrresearch.blogspot.com/2010/12/ ... email.html

Dear Dr. Wolfe-Simon,

I'm emailing you to apologize for quotes from me that have just appeared on the ABC News website. I wasn't misquoted, but some of the things I said in a phone interview yesterday morning came across more harshly than I had intended.

I told the interviewer that, even though I think your conclusions were wrong, I sympathize with the difficult position you're in (I've spent about 20 years championing a hypothesis that almost everyone thinks is wrong). I also said that what matters in science isn't whether we make mistakes (we all do) but how we deal with them, and that I think you're handling the situation well.

I feel particularly bad about the 'not calm and confident' quote, because in fact your press conference was very well done. I meant this statement to only emphasize that women in science know that they're being judged harshly, but instead I came across as someone doing precisely that.

Sorry,

Rosie Redfield

Iron Lisa responds…

Response to Questions Concerning the Science Article
http://ironlisa.com/gfaj/GFAJquestions_ ... ec2010.pdf
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Re: NASA Press Conference Thursday 2nd December 2010

Postby m0r1arty » Sun Dec 19, 2010 9:03 am

Access Denied wrote:Nope, I don’t see anyone besides “Thunderf00t” claiming it’s impossible to replace phosphorous in the structure of DNA with arsenic, just unprecedented which is why, as it should be, the detection methods used are being subjected to some intense scrutiny


At no point did Thunderf00t claim that it's impossible to replace phosphorous with arsenic in the structure of DNA (I've said it though).

We'll see how further study allows us to get more details on how this works.

Then I'll either be right or wrong in my thoughts regarding how this press conference was overstated to the extreme.

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