Gizmodo: NASA to announce possible 'alien' life form?

[Reic]

As far as it using As instead of P to connect to carbon, I don't see that as too major a difference. As Peter said, As and P are so close to one another on the periodic table they would bond with carbon almost essentially the same. The ATP-ADP cycle would be nonexistant, though, and we would have the opportunity to find out how the life form actually stores and uses energy to live using an entirely different process than every living thing on Earth.

[PeterMP]

As far as it using As instead of P to connect to carbon, I don't see that as too major a difference. As Peter said, As and P are so close to one another on the periodic table they would bond with carbon almost essentially the same. The ATP-ADP cycle would be nonexistant, though, and we would have the opportunity to find out how the life form actually stores and uses energy to live using an entirely different process than every living thing on Earth.

It is almost certainly using As in ATP instead of P and even ADP.

I would expect that you might get some mixed compounds too.

My GUESS is that it survives high As concentrations by converting it to arsenate, which is then chemically similar to phosphate and then the arsenate gets incoroparted into things like ATP (but P because it is As), and then form there to DNA (realistically you aren't getting As into DNA unless you have As based ATP).

---------- Post added December-2nd-2010 at 05:23 PM ----------

Thanks for the explanation Peter.

I'm with Vilandil in that I would be very interested to know how old this type of bacteria is. But as you pointed out on the other thread, there's no reason to think it is that old or has developed for very long on a separate evolutiounary path.

It has been classed into a subset of proteobacteria. Proteobacteria include your good old E. coli and Salmonella.

[Reic]

It is almost certainly using As in ATP instead of P and even ADP.

I would expect that you might get some mixed compounds too.

My GUESS is that it survives high As concentrations by converting it to arsenate, which is then chemically similar to phosphate and then the arsenate gets incoroparted into things like ATP (but P because it is As), and then form there to DNA (realistically you aren't getting As into DNA unless you have As based ATP).

---------- Post added December-2nd-2010 at 05:23 PM ----------

It has been classed into a subset of proteobacteria. Proteobacteria include your good old E. coli and Salmonella.

So would it be ATAs and ADAs?

[PeterMP]

So would it be ATAs and ADAs?

Yup.

[JMS]

Thanks for the explanation Peter.

I'm with Vilandil in that I would be very interested to know how old this type of bacteria is. But as you pointed out on the other thread, there's no reason to think it is that old or has developed for very long on a separate evolutiounary path.

Bacteria live a long time... some can live for hundreds of years. So this Bacteria could be as old or older than the scientists examining it.

[Baculus]

You've explained the chemistry. (In, frankly, more detail than I can follow.)

That's why I was asking "But what does it mean?"

(And yes, I wholeheartedly agree with requesting a merge.)

To quote from the NASA announcement:

"Carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur are the six basic building blocks of all known forms of life on Earth. Phosphorus is part of the chemical backbone of DNA and RNA, the structures that carry genetic instructions for life, and is considered an essential element for all living cells."

"We know that some microbes can breathe arsenic, but what we've found is a microbe doing something new -- building parts of itself out of arsenic," said Felisa Wolfe-Simon, a NASA astrobiology research fellow in residence at the U.S. Geological Survey in Menlo Park, Calif., and the research team's lead scientist. "If something here on Earth can do something so unexpected, what else can life do that we haven't seen yet?"

[PeterMP]

Unskilled labor?

Well, I wouldn't use the word unskilled. They are a lot more "skilled" than the ones we make.

Let me try an analogy. Let's say we have a bunch of machines that do different tasks, including finding the things they need to do them.

Now, the machines were designed based on metric things (e.g. bolts and the like).

Now, some don't use bolts, and if they run into a bolt, they just put it aside and keep looking for the right parts to do their tasks.

Others use a particular metric bolt, but they aren't used to distinguishing between the metric and similar sized English so they will use the English and maybe it even works less well, but in most cases it works at least well enough.

Then there are a few cases where the English bolt really messes things up. Sometimes the robot doesn't even need a bolt, but the size of the bolt is just the perfect size to fit in some space and so if they run into the bolt just right and it gets jammed in the space that causes the robot to break (and you die).

Now, what these organisms have done:

1. They removed the robots that had the issue with the English bolt.

2. They've modified those robots so that the English bolt is no longer a problem.

3. They've created another robot that changes the English bolt so that it is no longer a problem.

(Probably not a single one, but some combination of all 3.)

(Remember, we have multiple of each robot so some of them can be disabled without death.)

Now given that when you give these organisms lot's of the English bolts and not much of the metric bolts. The robots that can use the English bolts do so (and to make things a bit more complicated, they aren't even using the English bolt (As) directly. They are using something the English bolt has been inserted into (As containing ATP, which was made from arsenate likely) so if they've created a robot that makes something else from the English bolt (arsenate is made from As), then the robot that uses the metric related-form (phosphate) will plug in the English form (Arsenate), and then the other robots that use what the other machine made (ATP (As or P form) will keep going.)

(P occurs naturally in nature as phosphate. Not many organisms make phosphate. As is lethal. If you detoxify As by making arsenate, then your enzymes that use phosphate will likely just plug in the arsenate in many cases.)

The end result is that you get your English bolt in different places, even if metric bolt would be better.

---------- Post added December-2nd-2010 at 09:50 PM ----------

To quote from the NASA announcement:

"Carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur are the six basic building blocks of all known forms of life on Earth. Phosphorus is part of the chemical backbone of DNA and RNA, the structures that carry genetic instructions for life, and is considered an essential element for all living cells."

"We know that some microbes can breathe arsenic, but what we've found is a microbe doing something new -- building parts of itself out of arsenic," said Felisa Wolfe-Simon, a NASA astrobiology research fellow in residence at the U.S. Geological Survey in Menlo Park, Calif., and the research team's lead scientist. "If something here on Earth can do something so unexpected, what else can life do that we haven't seen yet?"

Which is really only a big deal if you ignore that several of the pretty major hypothesis related to the origin of life on Earth don't include the use of P:

http://en.wikipedia.org/wiki/Peptide_nucleic_acid

http://en.wikipedia.org/wiki/Iron-sulfur_world_theory

http://en.wikipedia.org/wiki/PAH_world_hypothesis

And you ignore all sorts of demonstrated cases where organisms manage to substitute things of similar chemical identity.

Including the substitution of arsenate in the production of ATP to produce asenylated derivatives (which this paper in fact makes the As more toxic (because then something else happens to it which requires another biological molecule), but if you have that handled somehow, which these organisms must, then it isn't such a big deal).

http://toxsci.oxfordjournals.org/content/early/2010/05/09/toxsci.kfq141

"Polynucleotide Phosphorylase and Mitochondrial ATP Synthase Mediate Reduction of Arsenate to the More Toxic Arsenite by Forming Arsenylated Analogues of ADP and ATP"

[twa]

Uh oh

added prose

You want thorough skepticism, read Rosie Redfield's drawing and quartering of the paper, which rips into the hasty methodology of the work. Man, after that, the body ain't even twitching any more, and they're going to have to clean up the pieces with a wet-vac. It's beautiful.

http://scienceblogs.com/pharyngula/

"This Paper Should Not Have Been Published"

Scientists see fatal flaws in the NASA study of arsenic-based life.

http://www.slate.com/id/2276919/

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.

[Corcaigh]

http://scienceblogs.com/pharyngula/

I bet that's your favorite site on a whole range of topics.

[twa]

I bet that's your favorite site on a whole range of topics.

I find his reasoning interesting,even when I disagree

and that was a great line

[Vilandil Tasardur]

I get that the substitution of As for P is only when starved for P. That still seems like a huge deal to me. I don't see this as a case of bacteria finding a way to survive arsenic. That's been known for a few years now. I still think the important here is the survivng without phosphorus.

How many other organisms do you know that can readily survive without one of the other 6 essential elements? Sure, on the surface it sounds like they just "switched parts" or "used a substitute." In fact, I encourage the use of said analogies because they are pretty good for understanding what's happening But that shouldn't diminish what's happening here.

If we were building a house, it would be one thing to substitute nails when we run out of screws. It's quite another to substitute steel when we run out of wood for the frame. Phosphorus is the back bone of DNA. When you see that classic double helix wound up with all the ATCG pairs, they are linked by phosphorus. Scientists didn't think life could exist using a substitute; they thought that if you starved for P your DNA would unravel. ATP is the source of our energy; it's your gasoline. Scientists didn't know if there was a diesel, or an ethanol, or an electric that could help power your engine as a source of alternative energy. They thought that if you didn't have gasoline you might not run.

I realize that these bacteria live in extreme conditions and that, given the choice, they still prefer the P. They haven't devolved the ability to metabolize P, which makes them neat hybrids. They are well adapted to either environment.

[No_Pressure]

I read something about photosynthesis on Arsenic found in Titan (Saturns moon).

So thats where you're from.

[HighOnHendrix]

To add to twa's post:

http://news.yahoo.com/s/yblog_thelookout/20101208/sc_yblog_thelookout/scientists-poking-holes-in-nasas-arsenic-eating-microbe-discovery

So why would NASA scientists make such a big deal out of a discovery that, according to critics, they must have suspected was questionable?

"I suspect that NASA may be so desperate for a positive story that they didn't look for any serious advice from DNA or even microbiology people," UC-Davis biology professor John Roth told Zimmer.

A NASA spokesperson brushed off the criticism. The paper's authors have not responded to the firestorm. Needless to say, that posture, too, has drawn the ire of critics. "That's kind of sleazy given how they cooperated with all the media hype before the paper was published," Redfield said.

[jnhay]

I was just about to make that distinction..... NOT..

Good job, you explained that very well. Even I understod it.

I think I need a dumbed down version of the dumbed down version, but oh well.

[PeterMP]

I get that the substitution of As for P is only when starved for P. That still seems like a huge deal to me. I don't see this as a case of bacteria finding a way to survive arsenic. That's been known for a few years now. I still think the important here is the survivng without phosphorus.

How many other organisms do you know that can readily survive without one of the other 6 essential elements? Sure, on the surface it sounds like they just "switched parts" or "used a substitute." In fact, I encourage the use of said analogies because they are pretty good for understanding what's happening But that shouldn't diminish what's happening here.

If we were building a house, it would be one thing to substitute nails when we run out of screws. It's quite another to substitute steel when we run out of wood for the frame. Phosphorus is the back bone of DNA. When you see that classic double helix wound up with all the ATCG pairs, they are linked by phosphorus. Scientists didn't think life could exist using a substitute; they thought that if you starved for P your DNA would unravel. ATP is the source of our energy; it's your gasoline. Scientists didn't know if there was a diesel, or an ethanol, or an electric that could help power your engine as a source of alternative energy. They thought that if you didn't have gasoline you might not run.

I realize that these bacteria live in extreme conditions and that, given the choice, they still prefer the P. They haven't devolved the ability to metabolize P, which makes them neat hybrids. They are well adapted to either environment.

1. They aren't living with no P. That would actually be impressive.

2. From twa's link it isn't even clear that they are living with less P than other organisms live with.

3. If you couldn't subsitute anything for P for DNA and you didn't have P your DNA wouldn't unravel. You wouldn't be able to make DNA.

4. There are lot's of buildings that don't have wood frames.

5. It isn't clear how many other organisms could do this IF the arsenic didn't kill them. It is possible that all of the "machines'" in other organisms can do this if given a chance, but they essentially never get the chance because the As kills the organism.

Generally, I don't think you understand the chemical similarity between As and P.

[Vilandil Tasardur]

1. They aren't living with no P. That would actually be impressive.

2. From twa's link it isn't even clear that they are living with less P than other organisms live with.

3. If you couldn't subsitute anything for P for DNA and you didn't have P your DNA wouldn't unravel. You wouldn't be able to make DNA.

4. There are lot's of buildings that don't have wood frames.

5. It isn't clear how many other organisms could do this IF the arsenic didn't kill them. It is possible that all of the "machines'" in other organisms can do this if given a chance, but they essentially never get the chance because the As kills the organism.

Generally, I don't think you understand the chemical similarity between As and P.

Well then the criticism makes much more sense. I just got a copy of the actual publication yesterday and haven't read it yet. To this point all I had read were the damned media publications. Scientific American and what have you.

Thanks for clearing that up for me. I'm pretty disappointed at how it was announced in the first place. There seems to be a trend right now with the scientists/media going for the shock value instead of the accuracy. The triceratops "not existing" deal comes to mind. I wonder how much of it is the media pouncing on a story and how much of it is scientists out to put their name in the papers.

[Vilandil Tasardur]

So the issue with the research here is that they didn't wash off the compounds that they fed to the bacteria? Meaning that some of the molecules might not have been eaten but merely stuck to them?

How could they have just "forgotten" that step? Is it just carelessness?

Like I said, I have the Science publication but still haven't gotten around to reading it. Sorry Pete, if I have no idea what I'm talking about. I'm just trying to understand this, cause I was really excited last week and now all signs point to this team just being lame:(.

[PeterMP]

So the issue with the research here is that they didn't wash off the compounds that they fed to the bacteria? Meaning that some of the molecules might not have been eaten but merely stuck to them?

How could they have just "forgotten" that step? Is it just carelessness?

Like I said, I have the Science publication but still haven't gotten around to reading it. Sorry Pete, if I have no idea what I'm talking about. I'm just trying to understand this, cause I was really excited last week and now all signs point to this team just being lame:(.

It isn't so much them "eating" it or it being outside of them. Even if the arsenic gets inside of them that doesn't mean it will be put in their DNA.

Things can get into your house without becoming part of your house.

They purified the DNA from other biomolecules using pretty standard procedures.. These people are saying they should have taken other steps though it isn't clear to me why they think that arsenate would easily stick to DNA. Sure in some simply separations where molecules have a choice between two "phases" to go into, you can imagine the arsenate would move with the DNA, but they also applied an electric field to the DNA, and the DNA moves based on its size. Here I don't think it is at all likely that the arsenate would have moved with the DNA.

I will say, I actually seem to be in a minority from what I've read, but I wouldn't be at all shocked if the DNA contained a combination of arsenates and phosphates (DNA normally contains thousands and even millions of phosphates. If some of them were replaced with arsenate, you'd get results consistent to everything we see here.)

I just don't think even that is such a big deal.