Tag: arsenic

New research points toward "no" on arsenic life

By Phil Plait | July 9, 2012 11:56 am

In December 2010 a team of researchers, with NASA’s blessing, announced a truly remarkable result: bacteria that lived in California’s Mono Lake not only thrive in the arsenic laced water, but have incorporated arsenic into their biophysical processes. This was a big deal, since it wasn’t thought that this was possible (while arsenic has similar properties to the biologically-necessary element phosphorous, replacing one for the other had never been seen before in nature).

However, the team found their findings immediately under fire by other biologists. Here is my initial report on the press conference announcement, and here’s my followup after severe doubt had been cast on the findings, and a third article from a few months later. Basically, the team’s methods, analysis, and results were found to be lacking, and two other groups of biologists started up their own investigation to replicate the research.

Today, Science magazine published the results. Arsenic? Nope. One team found that while the bacteria thrive in arsenic-rich water, there must be some phosphorus present for it to live (indicating the cells had not replaced As with P). The second team found no evidence that arsenic had been incorporated into the cells’ biochemistry.

This is disappointing but not unexpected news.

When NASA held the press conference, a lot of media – including me – were very excited. We trusted NASA that the work had been vetted by other scientists and was legit. While I think the work was done honestly – that is, the research team didn’t cheat or anything like that – it’s looking like they jumped to their conclusion, and the initial peer review process didn’t work as it should have.

But there’s more to it than this. The members of the original team are sticking by their results, saying that not finding something may not indicate it’s not there – in other words, the followup research may have missed the arsenic. While that’s possible, it comes across as stubbornness in the face of contradictory results. That is simply an interpretive opinion by me, but it does seem odd that they claim the new results actually don’t refute their original findings. It looks to me (though I’m no biologist) that they certainly do.

[UPDATE: Here's a good article by my pal Dan Vergano at USA Today about this, and he also got great quotes from both the original researchers and the other teams.]

Discover Magazine’s The Loom blogger Carl Zimmer – who has always been very skeptical of the results – live-blogged this new announcement, which makes for fascinating reading. There are some great quotes in there, and it’s worth your time to read through. DM’s 80 Beats blog also has relevant links about all this.

There are several lessons I think we can pull from all this:

1) The scientific process works, but there’s friction with the journalistic process. Of course, we’ve known that for a while!

2) Just because there’s a press conference, and just because it’s backed by NASA, doesn’t mean the results are true. That’s a hard-won thought for me, but one I take seriously.

3) The thing we shouldn’t forget: all the biological research teams do agree that the bacteria in Mono Lake actually do thrive in those arsenic-heavy waters!That itself is an important scientific result. While those bacteria may not incorporate the poison into their own biochemistry, it shows again that life can adapt to extremely difficult and even previously-thought toxic circumstances. The ramifications for astrobiology (finding life on other planets) are still important, and this gives us strong and critical insight into the very chemistry of nature itself.


Related Posts:

- NASA’s real news: Bacterium on Earth that lives off arsenic!
- Independent researchers find no evidence for arsenic life in Mono Lake
- Arsenic and old posts
- Arsenic and old Universe

Independent researchers find no evidence for arsenic life in Mono Lake

By Phil Plait | January 23, 2012 2:04 pm

Late in 2010, scientists participating in a NASA news conference dropped a bombshell: they had found evidence that bacteria in California’s Mono Lake were metabolizing arsenic and using it in their life processes.

This was huge news, since arsenic is toxic for carbon based life. If some forms of life evolved a way to process it, this would open up a whole new field of biochemistry!

However, almost immediately, the work came under attack. Biochemists accused the original team of not performing the research carefully (to put it delicately). Rosie Redfield, a microbiologist at the University of British Columbia in Vancouver, was particularly critical. She decided, in fact, to try to verify the original work, and set out to do so openly, writing up her progress on her blog.

And now, according to an article on Scientific American, she can confidently provide a "clear refutation" of the arsenic uptake in the organisms:

Their most striking claim was that arsenic had been incorporated into the backbone of DNA, and what we can say is that there is no arsenic in the DNA at all.

That’s a pretty clear statement! The original team, lead by Felisa Wolfe-Simon, has responded, saying they need to see a fully peer-reviewed paper before making up their minds.

I’ll note that emotions have run fairly high throughout this saga. Dr. Wolfe-Simon got a lot of attention, positive and negative, and the negative was pretty charged. I’m not surprised by the reactions of either side of this issue.

In the interest of full disclosure, when the press conference was aired, I wrote a pretty straight interpretation of it. As I wrote in a followup post, I am not a microbiologist, and I trust NASA at some level. This event shook that trust quite a bit, and I am now far less likely to take a claim at face value, even when it comes from a source like NASA.

Science is a balance of trust versus skepticism, even at the best of times. An extra layer is added when the media become involved; that impartiality which is always precarious can be sorely tested by the chance at media exposure.

That includes my desire to write about something particularly cool, of course, as well as the more fundamental results obtained from the scientific research itself.

I’m glad this news has come out, and I’ll be curious to see what happens next. Dr. Redfield will need to submit her team’s work to the peer review process. Assuming it survives, I have little doubt we’ll be hearing from Wolfe-Simon again as well. In the Scientific American article, Dr. Redfield is quoted as saying, "We’ve done our part. This is a clean demonstration [that the original positive findings were incorrect], and I see no point in spending any more time on this."

That may be true for her and her team’s work, though I have a suspicion more work will have to be done either by her or other teams to categorically rule out the arsenic. But either way, what I can be certain of is that we are not done hearing about this story just yet.

Tip o’ the phosphorus backbone to Jeffrey Sullivan on Google+.


Related posts:

- NASA’s real news: bacterium on Earth that lives off arsenic!
- Arsenic and old posts
- Arsenic and old Universe

Arsenic and old posts

By Phil Plait | September 30, 2011 10:26 am

Last year, with much ballyhoo, NASA held a press conference about a team of biologists claiming that they had found microorganisms that could use arsenic instead of phosphorous as a basis for biological processes.

However, it didn’t take too long before the work was under serious attack by other biologists. Some were snarky, others more reserved, but the message was clear: not too many professional biologists felt the arsenic claim held up to scrutiny. In fact, some said the research paper was so shoddy it should never have been published.

This whole event comes to my mind from time to time, and I’ve been meaning to revisit it. I’ll admit I’m a little embarrassed by how I participated in it — I reported it straight, writing up a blog post relaying what I had learned from the press conference and from reading the paper itself. I am not a biologist, so the details of the paper were beyond me. But being a scientist myself I could glean what I needed for a blog post, especially coupled with the comments from the press conference.

Or so I thought. As the criticism came in, and I looked into it more, I found myself agreeing with those who disagreed with the original findings. I’ll note that I can’t say for sure if the research was done poorly or not, but it has become more clear that the work itself needed more outside commentary before being released in a press conference at the level it was. My own mistake was trusting NASA PR to have vetted this thoroughly before holding the press conference, and not getting an outside opinion myself. I wrote a followup a few days later with my doubts.

The reason I bring all this up now is that PopSci recently posted an article about the lead scientist in the arsenic story, Felisa Wolfe-Simon. I read it yesterday, and felt that it was coming from an odd angle — as a personality profile on Dr. Wolfe-Simon it’s interesting, but as a background piece on the arsenic story itself it read to me as if it were slanted to support her.

Both my Discover Magazine colleagues Ed Yong and Carl Zimmer have a similar opinion — Carl is actually pretty blunt in his opinion on the article, giving details (and a timeline!) on where it goes astray. Wired Magazine blogger David Dobbs also write an interesting piece where at first he says he likes the article, then updates his post later saying that after more thought a lot of doubts arose. Given the size and impact this story had last year, I suggest you read those links. They’ll give you something to think about.

There are many lessons to be learned here, but the one I’ve walked away with is that since this story came out, I’ve been more careful to check with sources if I’m not familiar with the science myself (and even if I am familiar with it). It’s impossible to prevent all mistakes in writing science articles — in writing anything — but a healthy dose of skepticism is required to minimize them.

In fact, I’d say a healthy dose of skepticism is always required, in every situation. It’s a highly useful tool.

CATEGORIZED UNDER: NASA, Piece of mind, Skepticism

Arsenic and old Universe

By Phil Plait | December 7, 2010 1:58 pm

Two news updates, both of which are pretty interesting.

1) The arsenic-utilizing bacterium is still in the news… because a lot of scientists are casting serious doubt on the results. Carl Zimmer, biology journalist (and Discover blogger) wrote a very interesting article about it for Slate (and has followups on his Discover blog). The criticism is not mild, either, with words like "flim-flam" being used. Carl approached the investigators who wrote the paper for Science, and they declined to comment — that’s usually an excuse, but in this case I think they’re right; they don’t want to engage in a scientific debate through the media. But I certainly hope the investigations continue.

I’ll note I reported the press conference results straight — at some level, I have to trust the scientists know what they’re doing, that the peer-review process is working, and the results reliable. In this case, with a result depending on some relatively complex biological and chemical arguments, I was acting out of trust. This trust may yet be proven to be borne out, or it may not. It’s possible the original researchers are correct, and it’s possible their critics are. The best way to find out is more science.

But when it comes to astronomy news…
Read More

Brief arsenic followup

By Phil Plait | December 4, 2010 12:25 pm

Just to let y’all know, I did a short interview with the Canadian CBCRadio about the rumors and speculation on the ‘net leading up to the NASA announcement about the Mono Lake arsenic bacteria (here’s a direct link to the audio player). I also provided a very short quote about this to Radio Free Europe as well.

I know, this news is falling off everyone’s radar pretty quickly, which is to be expected. I may yet write my thoughts up about news embargoes and how media who use them shoot themselves in the foot. Sigh.

CATEGORIZED UNDER: NASA

NASA's real news: bacterium on Earth that lives off arsenic!

By Phil Plait | December 2, 2010 11:12 am

[UPDATE (Dec. 7): The research outlined below is under very heavy fire from other biologists. I've written a follow-up post about it.]

[Update (13:30 MT Dec. 2): I misunderstood a part of this research dealing with arsenic when I read the journal paper, which was made more clear during the press conference. I have corrected the relevant text below, and struck through the old text. Hope this doesn't confuse anyone, and sorry about that!]

NASA scientists announced today an incredible find: a form of microbe that apparently evolved the ability to use otherwise toxic arsenic in their biochemistry!

First off, just to be straight and to dispel the rumors: this is not aliens on Titan, or Mars, or anywhere else. This bizarre life form was found right here on good ol’ Earth. And don’t be disappointed: this is still pretty cool news.

Here are the critters in question:

bacteria_arsenic

Note the scale; a typical human hair is 100 times thicker than these beasties.

DM blogger Ed Yong of Not Exactly Rocket Science has written an in-depth and detailed account of all this as well. Highly recommended!

The bacteria (technically, the strain GFAJ-1 of Halomonadaceae) was found in Mono Lake, an extremely alkaline and salty lake in California near the Nevada border. And I do mean salty and alkaline: it has about twice the salt of ocean water, and has the incredible pH of 10 (neutral water has a pH of 7, and the pH scale is logarithmic; this means the lake water has the same alkaline strength as commercial antacids). Worse yet, the lake has a high concentration of arsenic, a deadly poison to many forms of life (including us). This makes the water toxic for most living creatures as we know them; for example there are no fish in the lake. However, there are algae, shrimp, and other such flora and fauna.

… including these new microbes. Dr. Felise Wolfe-Simon found them in the mud around the lake, and discovered that not only do they happily live with the arsenic that when subjected to high levels of arsenic in their environment, they actually incorporated it into their biochemistry!

Read More

CATEGORIZED UNDER: Cool stuff, NASA, Science, Top Post
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