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Kil
Evil Skeptic

USA
13467 Posts

Posted - 12/02/2010 :  13:51:58  Show Profile  Visit Kil's Homepage  Send Kil an AOL message  Send Kil a Yahoo! Message Send Kil a Private Message  Reply with Quote
As you may or may not know, NASA had a news conference today to announce an astonishing discovery. Phil Plait has wasted no time in blogging about it:

NASAís real news: bacterium on Earth that lives off arsenic!

Iím going to cut to the chase and post the end of his blog, but do read the whole thing.

ÖBut these microbes in Mono Lake, at some point in their evolution, decided that if you canít lick Ďem, join Ďem. They have somehow been able to utilize the arsenic in the lake, using it instead of phosphorus in their biochemistry. To determine this, Dr. Wolfe-Simon took samples of the microbes, adding more and more arsenic while decreasing the amount of phosphorus in their environment to essentially zero. This would kill almost everything known to man, yet these little critters thrived. Even weirder, the bacteria were able to survive when either the phosphorus or the arsenic was reduced, but not both. So somehow, itís able to use both of these elements as needed to survive.

Amazingly, using radioisotope-tagged molecules containing arsenic, they were able to find that the microbes incorporated the arsenic into their very DNA! Itís hard to stress how shocking this is; as I understand it, saying something like that to a microbiologist without evidence wouldíve had them slowly backing away from you and looking for weapons or an escape route.

That is seriously freaky. So what does this mean in the scale of things?
For one thing, it means that life, as Jeff Goldblum so eloquently stated in "Jurassic Park", will find a way. Itís not clear at all how these bacteria were able to figure out how to utilize arsenic, but itís not hard to imagine that understanding this will have all sorts of implications for biology, and perhaps even medicine.

And for another, it means that we need to be a little more open-minded when it comes to looking for life on other worlds. If a strain of bacterium this truly and awesomely bizarre can be right here under our noses ó in California, for frakís sake! ó then what the heck will we find on other planets?


Also see:

NASA Finds New Arsenic-Based Life Form in California

When cooking up the stuff of life, you canít just substitute margarine for butter. Or so scientists thought.

But now researchers have coaxed a microbe to build itself with arsenic in the place of phosphorus, an unprecedented substitution of one of the six essential ingredients of life. The bacterium appears to have incorporated a form of arsenic into its cellular machinery, and even its DNA, scientists report online Dec. 2 in Science.


This will be headline news tomorrow.

Uncertainty may make you uncomfortable. Certainty makes you ridiculous.

Why not question something for a change?

Genetic Literacy Project

filthy
SFN Die Hard

USA
14408 Posts

Posted - 12/02/2010 :  14:12:00   [Permalink]  Show Profile Send filthy a Private Message  Reply with Quote
Dang! Ya scooped me again!

I have said before that it is very difficult to predict the sort of life might be found in the universe. We simply don't know what might comprise it and if this little bacterium is any example, it might be wilder than we ever imagined.

Phil Rocks!




"What luck for rulers that men do not think." -- Adolf Hitler (1889 - 1945)

"If only we could impeach on the basis of criminal stupidity, 90% of the Rethuglicans and half of the Democrats would be thrown out of office." ~~ P.Z. Myres


"The default position of human nature is to punch the other guy in the face and take his stuff." ~~ Dude

Brother Boot Knife of Warm Humanitarianism,

and Crypto-Communist!

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Kil
Evil Skeptic

USA
13467 Posts

Posted - 12/02/2010 :  14:57:01   [Permalink]  Show Profile  Visit Kil's Homepage  Send Kil an AOL message  Send Kil a Yahoo! Message Send Kil a Private Message  Reply with Quote
Originally posted by filthy

Dang! Ya scooped me again!

I have said before that it is very difficult to predict the sort of life might be found in the universe. We simply don't know what might comprise it and if this little bacterium is any example, it might be wilder than we ever imagined.

Phil Rocks!




Also, Greg Laden has weighed in with a very interesting question.

NASA's new organism, the meaning of life, and Darwin's Second Theory

In his highly readable book, One Long Argument, Ernst Mayr breaks down the body of thought often referred to as "Darwin's Theory" into five separate and distinct theories, the second of which being "common descent." Darwin's second evolutionary theory (second by Mayr's count, not Darwin's) is really a hypothesis that could be worded this way:

All life on earth descended from a single, original, primordial form that arose eons ago.

The evidence in favor of this hypothesis is strong, but the test of the hypothesis ... the means of disproving it, which is, after all, the point of stating it to begin with ... is difficult to define, but like pornography to a judge, one would know it when one sees it.

The question at hand is, does the current finding reported moments ago by NASA relate to this concept at all? The answer, as you'll see, is yes. And no...


Ya know, speaking of scooped, the NASA news conference was barely over before Phil and Greg had posted, which makes me wonder, because neither of them just presented the news. They both went much further than the dry facts. The basic news is all over the place and was being released before the press conference was over. But still... Either they are faster than a speeding bullet, or they knew what was going to be announced. I just can't see how they could have gotten so much down so fast without some inside knowledge. I suppose I could be wrong about that. Hmmmm...

Uncertainty may make you uncomfortable. Certainty makes you ridiculous.

Why not question something for a change?

Genetic Literacy Project
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Dr. Mabuse
Septic Fiend

Sweden
9677 Posts

Posted - 12/02/2010 :  15:18:58   [Permalink]  Show Profile  Send Dr. Mabuse an ICQ Message Send Dr. Mabuse a Private Message  Reply with Quote
Having arsenic replace phosphor makes sense, they are in the same period in the periodic system. Which means they are more or less chemically interchangeable. But only so much.

Just like silicon may sometimes replace carbon.

But those heavier atoms make more brittle molecules. That's why you don't find silicon-based versions of carbon-based amino-acids.

It's also why I don't think we'd find silicon-based life on other planets.
This arsenic news really was unexpected, because I didn't think it was possible to have viable DNA with arsenic atoms instead of phosphor in it. For all I know, the DNA should break in pieces.

I wonder what makes this possible.

Dr. Mabuse - "When the going gets tough, the tough get Duct-tape..."
Dr. Mabuse whisper.mp3

"Equivocation is not just a job, for a creationist it's a way of life..." Dr. Mabuse

Support American Troops in Iraq:
Send them unarmed civilians for target practice..
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Dude
SFN Die Hard

USA
6891 Posts

Posted - 12/02/2010 :  17:38:25   [Permalink]  Show Profile Send Dude a Private Message  Reply with Quote
They probably had a pre-release copy of the paper. This stuff isn't some giant secret until a paper is published, it's just unprofessional to talk about it publicly until the primary investigators officially publish.

Pretty interesting bacteria though.

Also, it's getting coverage (headline blurbs) on news channels right now. Just heard it.


Ignorance is preferable to error; and he is less remote from the truth who believes nothing, than he who believes what is wrong.
-- Thomas Jefferson

"god :: the last refuge of a man with no answers and no argument." - G. Carlin

Hope, n.
The handmaiden of desperation; the opiate of despair; the illegible signpost on the road to perdition. ~~ da filth
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Dude
SFN Die Hard

USA
6891 Posts

Posted - 12/02/2010 :  18:02:50   [Permalink]  Show Profile Send Dude a Private Message  Reply with Quote
I want to know how extensive the arsenic substitution is. Does it sub in other pathways? Instead of ATP do we get ATA? How does the arsenic alter DNA structure, the bond geometry is going to be a little different, and that will impact all DNA binding proteins (from histones to transcription factors).

Phosphorus is a major player in biochemistry, I can't think of a biological process that doesn't use it...

Going to have to dig up a copy of the paper and probably going to have to wait for future papers to get the answers.


Ignorance is preferable to error; and he is less remote from the truth who believes nothing, than he who believes what is wrong.
-- Thomas Jefferson

"god :: the last refuge of a man with no answers and no argument." - G. Carlin

Hope, n.
The handmaiden of desperation; the opiate of despair; the illegible signpost on the road to perdition. ~~ da filth
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filthy
SFN Die Hard

USA
14408 Posts

Posted - 12/02/2010 :  18:21:18   [Permalink]  Show Profile Send filthy a Private Message  Reply with Quote
Upon more sober reflection:

"It's not an arsenic-based life form
Category: Evolution ē Science
Posted on: December 2, 2010 5:28 PM, by PZ Myers

Oh, great. I get to be the wet blanket.

There's a lot of news going around right now about this NASA press release and paper in Science ó before anyone had read the paper, there was some real crazy-eyed speculation out there. I was even sent some rather loony odds from a bookmaker that looked like this:

WHAT WILL NASA ANNOUNCE?

NASA HAS DISCOVERED A LIFE FORM ON MARS +200 33%
DISCOVERED EVIDENCE OF LIFE ON ONE OF SATURNS MOON +110 47%
ANNOUNCES A NEW MODEL FOR THE EXISTENCE OF LIFE -5000 98%
UNVEILS IMAGES OF A RECOVERED ALIEN SPACECRAFT +300 25%
CONFESSES THAT AREA 51 WAS USED FOR THE ALIEN STUDIES +500 16%

[The +/- Indicates the Return on the Wager. The percentage is the likelihood that response will occur. For Example: Betting on the candidate least likely to win would earn the most amount of money, should that happen.]
I think the bookie cleaned up on anyone goofy enough to make a bet on that.

Then the stories calmed down, and instead it was that they had discovered an earthly life form that used a radically different chemistry. I was dubious, even at that. And then I finally got the paper from Science, and I'm sorry to let you all down, but it's none of the above. It's an extremophile bacterium that can be coaxed into substiting arsenic for phosphorus in some of its basic biochemistry. It's perfectly reasonable and interesting work in its own right, but it's not radical, it's not particularly surprising, and it's especially not extraterrestrial. It's the kind of thing that will get a sentence or three in biochemistry textbooks in the future.

Here's the story. Life on earth uses six elements heavily in its chemistry: carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur, also known as CHNOPS . There are other elements used in small amounts for specialized functions, too: zinc, for instance, is incorporated as a catalyst in certain enzymes. We also use significant quantities of some ions, specifically of sodium, potassium, calcium, and chloride, for osmotic balance and they also play a role in nervous system function and regulation; calcium, obviously, is heavily used in making the matrix of our skeletons. But for the most part, biochemistry is all about CHNOPS."


It continues explaining in detail, most of which, I confess, I didn't understand. I'll leave it to others to comment.




"What luck for rulers that men do not think." -- Adolf Hitler (1889 - 1945)

"If only we could impeach on the basis of criminal stupidity, 90% of the Rethuglicans and half of the Democrats would be thrown out of office." ~~ P.Z. Myres


"The default position of human nature is to punch the other guy in the face and take his stuff." ~~ Dude

Brother Boot Knife of Warm Humanitarianism,

and Crypto-Communist!

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Dude
SFN Die Hard

USA
6891 Posts

Posted - 12/03/2010 :  00:46:26   [Permalink]  Show Profile Send Dude a Private Message  Reply with Quote
The media hype is, as always, misleading. Especially Wired's "Arsenic Based Life" headline.... /facepalm

PZ's downplay is perhaps unwarranted as well.

I still need to get my hands on the actual paper, but I'll go this far- If the DNA of this bacteria is actually using arsenate instead of phosphate in it's physical structure, that is a pretty big deal. The fact that it still uses phosphate does suggest it is not the product of a second genesis event though, more likely (as PZ said) it just evolved to fit it's environment.


Ignorance is preferable to error; and he is less remote from the truth who believes nothing, than he who believes what is wrong.
-- Thomas Jefferson

"god :: the last refuge of a man with no answers and no argument." - G. Carlin

Hope, n.
The handmaiden of desperation; the opiate of despair; the illegible signpost on the road to perdition. ~~ da filth
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Kil
Evil Skeptic

USA
13467 Posts

Posted - 12/03/2010 :  14:10:33   [Permalink]  Show Profile  Visit Kil's Homepage  Send Kil an AOL message  Send Kil a Yahoo! Message Send Kil a Private Message  Reply with Quote
Originally posted by Dude

The media hype is, as always, misleading. Especially Wired's "Arsenic Based Life" headline.... /facepalm

PZ's downplay is perhaps unwarranted as well.

I still need to get my hands on the actual paper, but I'll go this far- If the DNA of this bacteria is actually using arsenate instead of phosphate in it's physical structure, that is a pretty big deal. The fact that it still uses phosphate does suggest it is not the product of a second genesis event though, more likely (as PZ said) it just evolved to fit it's environment.


What is significant is not that this microbe is an extremophile bacterium which is probably the case. What is significant is that it can live on a 7th element once thought to be too toxic for life. That widens the number of elements that we have allowed for life to exist from 6 to 7. The implication being that what we expect to see on another planet or here on Earth is life that can live in a range outside of the basic 6. When we look at a planet with what we once thought of as having too much arsenic on it for life to be present, that might not be the case.

I think Myers is downplaying the significance of that change of thinking too much. That's like downplaying the significance of thermal vents in the ocean that can sustain life suited to it without any help from the sun. These kinds of discoveries keeps widening the parameters of what we think of as necessary for life to exist. And that's no small thing.

Uncertainty may make you uncomfortable. Certainty makes you ridiculous.

Why not question something for a change?

Genetic Literacy Project
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Dude
SFN Die Hard

USA
6891 Posts

Posted - 12/03/2010 :  15:19:42   [Permalink]  Show Profile Send Dude a Private Message  Reply with Quote
Originally posted by Kil

Originally posted by Dude

The media hype is, as always, misleading. Especially Wired's "Arsenic Based Life" headline.... /facepalm

PZ's downplay is perhaps unwarranted as well.

I still need to get my hands on the actual paper, but I'll go this far- If the DNA of this bacteria is actually using arsenate instead of phosphate in it's physical structure, that is a pretty big deal. The fact that it still uses phosphate does suggest it is not the product of a second genesis event though, more likely (as PZ said) it just evolved to fit it's environment.


What is significant is not that this microbe is an extremophile bacterium which is probably the case. What is significant is that it can live on a 7th element once thought to be too toxic for life. That widens the number of elements that we have allowed for life to exist from 6 to 7. The implication being that what we expect to see on another planet or here on Earth is life that can live in a range outside of the basic 6. When we look at a planet with what we once thought of as having too much arsenic on it for life to be present, that might not be the case.

I think Myers is downplaying the significance of that change of thinking too much. That's like downplaying the significance of thermal vents in the ocean that can sustain life suited to it without any help from the sun. These kinds of discoveries keeps widening the parameters of what we think of as necessary for life to exist. And that's no small thing.

I agree. I think PZ is looking at it from a strictly evolution point of view, and his take is fair. If the thing still uses phosphorus then it probably evolved the ability to use arsenic. If this were an actual second genesis type of find, which I don't think it is (nor does PZ), that would be huge news.

It's use of arsenic is still a big deal though. If, as suggested, it has incoporated arsenate molecules into roles usually filled by phosphorus, and has compensated for the changes in molecular geometry (wich would be significant), then we now have positive evidence that life can use other elements in familiar roles. That is, without a doubt, a major find. It increases the chance of finding life outside our planet, it gives us new places to look for life on our planet, and once we start to peel back the biochemistry it will probably send us in directions we can't imagine now.

So yes, it's a big deal.


Ignorance is preferable to error; and he is less remote from the truth who believes nothing, than he who believes what is wrong.
-- Thomas Jefferson

"god :: the last refuge of a man with no answers and no argument." - G. Carlin

Hope, n.
The handmaiden of desperation; the opiate of despair; the illegible signpost on the road to perdition. ~~ da filth
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gregladen
New Member

USA
1 Post

Posted - 12/05/2010 :  09:13:25   [Permalink]  Show Profile Send gregladen a Private Message  Reply with Quote
Kil said: speaking of scooped, the NASA news conference was barely over before Phil and Greg had posted, which makes me wonder, because neither of them just presented the news.

Yeah, some people get pre-prints. For human evol and anthro, I may well get a pre-print from a colleague, as a blogger/science communicator who has insinuated himself into the science journalism world (thanks to people like Bora who have insisted that journalists are kind of faking it when they say journalists are the only journalists) I get a LOT of embargoed pre-prints, way more than I can deal with.

In this particular case, even before I got the pre-print, I knew roughly what it said from colleagues who had already seen it and read it. My post actually is about parallel topics: The details of how much A replaces P and which P's are replaced and all that don't matter much to the specific points I made, and my objective was to use this as an opportunity to bring together in one blog post ideas about astrobiology and evolution on Earth that I think are pretty interesting but rarely get to talk about.


Greg Laden
http://scienceblogs.com/gregladen/
and
http://scienceblogs.com/gregladen/
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Kil
Evil Skeptic

USA
13467 Posts

Posted - 12/05/2010 :  11:13:25   [Permalink]  Show Profile  Visit Kil's Homepage  Send Kil an AOL message  Send Kil a Yahoo! Message Send Kil a Private Message  Reply with Quote
Originally posted by gregladen

Kil said: speaking of scooped, the NASA news conference was barely over before Phil and Greg had posted, which makes me wonder, because neither of them just presented the news.

Yeah, some people get pre-prints. For human evol and anthro, I may well get a pre-print from a colleague, as a blogger/science communicator who has insinuated himself into the science journalism world (thanks to people like Bora who have insisted that journalists are kind of faking it when they say journalists are the only journalists) I get a LOT of embargoed pre-prints, way more than I can deal with.

In this particular case, even before I got the pre-print, I knew roughly what it said from colleagues who had already seen it and read it. My post actually is about parallel topics: The details of how much A replaces P and which P's are replaced and all that don't matter much to the specific points I made, and my objective was to use this as an opportunity to bring together in one blog post ideas about astrobiology and evolution on Earth that I think are pretty interesting but rarely get to talk about.


Welcome to sfn, gregladen! Thanks for responding to my how do you guys do that? question. So science bloggers like you don't actually have super human blogging abilities? What a let down...

Things have changed much over the last ten years or so. It's nice to not have to rely on a media headline analysis, which so often skips the meat and goes straight for the sensational, or having to wait for more sober articles published in some of the better popular science magazines to get the lowdown and possible implications of important scientific discoveries from people who are actually qualified to say something about them. For the laypersons like me, with a keen interest in science, science blogging by scientists has been one of the better developments that the web has brought to us. It has also helped to popularize science, which is a good thing.

That's not to say that all is smooth sailing for those of us who read the science blogs. For example, your faithing it blog post was heavily debated here at SFN (and no doubt on other skeptic sites). But then again, that's a good thing too.

Anyhow, thanks for the clarification. And thanks for being one of the voices out there in the science blogosphere.


Uncertainty may make you uncomfortable. Certainty makes you ridiculous.

Why not question something for a change?

Genetic Literacy Project
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Kil
Evil Skeptic

USA
13467 Posts

Posted - 12/07/2010 :  12:35:38   [Permalink]  Show Profile  Visit Kil's Homepage  Send Kil an AOL message  Send Kil a Yahoo! Message Send Kil a Private Message  Reply with Quote
Oopsy:

"This Paper Should Not Have Been Published"

...As soon Redfield started to read the paper, she was shocked. "I was outraged at how bad the science was," she told me.
Redfield blogged a scathing attack on Saturday. Over the weekend, a few other scientists took to the Internet as well. Was this merely a case of a few isolated cranks? To find out, I reached out to a dozen experts on Monday. Almost unanimously, they think the NASA scientists have failed to make their case. "It would be really cool if such a bug existed," said San Diego State University's Forest Rohwer, a microbiologist who looks for new species of bacteria and viruses in coral reefs. But, he added, "none of the arguments are very convincing on their own." That was about as positive as the critics could get. "This paper should not have been published," said Shelley Copley of the University of Colorado...


Of course, I'm completely unqualified to have an opinion on this, but hey, this is how science works. I'll be watching for further developments...

Uncertainty may make you uncomfortable. Certainty makes you ridiculous.

Why not question something for a change?

Genetic Literacy Project
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filthy
SFN Die Hard

USA
14408 Posts

Posted - 12/07/2010 :  13:22:48   [Permalink]  Show Profile Send filthy a Private Message  Reply with Quote
Damn, Kil scooped me again! And on the same topic, too! It was a different article, though, that pretty much said the same thing. Curse this short attention span that makes me put stuff off or even forget it.

Nevertheless, I find it fascinating that a bacterium can substitute arsenic, which is thought in some quarters to have murdered Napoleon, for potassium. It sort of raises the bar a bit for what is possible.

Welcome to SFN, greg!




"What luck for rulers that men do not think." -- Adolf Hitler (1889 - 1945)

"If only we could impeach on the basis of criminal stupidity, 90% of the Rethuglicans and half of the Democrats would be thrown out of office." ~~ P.Z. Myres


"The default position of human nature is to punch the other guy in the face and take his stuff." ~~ Dude

Brother Boot Knife of Warm Humanitarianism,

and Crypto-Communist!

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Kil
Evil Skeptic

USA
13467 Posts

Posted - 12/07/2010 :  14:53:39   [Permalink]  Show Profile  Visit Kil's Homepage  Send Kil an AOL message  Send Kil a Yahoo! Message Send Kil a Private Message  Reply with Quote
Originally posted by filthy

Damn, Kil scooped me again! And on the same topic, too! It was a different article, though, that pretty much said the same thing. Curse this short attention span that makes me put stuff off or even forget it.



It's facebook, filthy. I'm "friends" with lots of these bloggers. The info comes up fast. Almost before the ink is dry. It's an information paradise if you work it right.

Uncertainty may make you uncomfortable. Certainty makes you ridiculous.

Why not question something for a change?

Genetic Literacy Project
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On fire for Christ
SFN Regular

Saudi Arabia
1266 Posts

Posted - 12/07/2010 :  14:54:59   [Permalink]  Show Profile Send On fire for Christ a Private Message  Reply with Quote
NASA jump the gun again

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