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Author Topic:   Nasa news conference (re: Arsenic-based life form?)
Taq
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Posts: 7673
Joined: 03-06-2009
Member Rating: 2.6


Message 61 of 78 (594513)
12-03-2010 5:43 PM
Reply to: Message 59 by Percy
12-03-2010 5:01 PM


Re: Disappointing Announcement
But it isn't a case of, "Omigod, who would ever have imagined that life could ever use any chemicals but those we already know it uses! I'm stunned. Amazed! Flummoxed! Flabbergasted!"

I guess I view it through a different lens. Biologists have many speculations about many things. It is going from speculation to verification that is the exciting part. Speculating that bacteria could replace phosphate with arsenate in something as fundamental as ATP is one thing. Showing it is another. To use an analogy, people had long speculated that humans could build a self powered flying machine. This didn't take away from the achievements of the Wright Bros.

As for the astrobiology aspect of the study, it is one thing to say that life could replace phosphates with arsenates, and it is an entirely different thing to show that it can indeed do it.


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 Message 59 by Percy, posted 12-03-2010 5:01 PM Percy has acknowledged this reply

  
CosmicChimp
Member
Posts: 306
From: Muenchen Bayern Deutschland
Joined: 06-15-2007


Message 62 of 78 (594520)
12-03-2010 6:41 PM
Reply to: Message 47 by Percy
12-03-2010 8:57 AM


Re: Disappointing Announcement
They let me down in 1996 with the Martian microbes-on-meteors thingy, so I was ready for 'em this time.
This message is a reply to:
 Message 47 by Percy, posted 12-03-2010 8:57 AM Percy has acknowledged this reply

  
Rrhain
Member
Posts: 6349
From: San Diego, CA, USA
Joined: 05-03-2003


Message 63 of 78 (594623)
12-04-2010 3:05 AM
Reply to: Message 42 by Bolder-dash
12-03-2010 6:28 AM


Bolder-dash writes:

quote:
the whole aliens and outer space thing gives NASA a more receptive audience

(*chuckle*)

And who said "aliens"? It wasn't NASA. They didn't claim to have found alien life, not even in their teasers. The finding does help us understand how to go about investigating xenobiology, but don't confuse popular press hyperventilation with statements from NASA.

The press couldn't even get the actual story right. The press is claiming that the experiment showed that arsenates were incorporated into the phosphate backbone of the DNA strands, but that's not what the paper stated. Instead, it showed that the presence of arsenic was increased and the presence of phosphorus was decreased. One reason for that is the substitution of arsenates for phosphates, but it is by no means shown. The bacteria are bloated and filled with vacuoles compared to the native population. Something unusual is going on in those bacteria, but we don't know exactly what.

So you (and your quote) seem to be sad that the popular press once again fucked up a science story and rather than blaming the press for being a bunch of hacks, you're blaming the scientists who were simply doing their job.

Does the word "projection" mean something to you?


Rrhain

Thank you for your submission to Science. Your paper was reviewed by a jury of seventh graders so that they could look for balance and to allow them to make up their own minds. We are sorry to say that they found your paper "bogus," specifically describing the section on the laboratory work "boring." We regret that we will be unable to publish your work at this time.

Minds are like parachutes. Just because you've lost yours doesn't mean you can use mine.
This message is a reply to:
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Replies to this message:
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Dr Jack
Member (Idle past 184 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 64 of 78 (594635)
12-04-2010 7:12 AM
Reply to: Message 60 by Percy
12-03-2010 5:14 PM


Re: PZ Myers Pipes Up
Yeah, I still think PZ Myers is hugely underplaying this.

It's true, Arsenic is only just below Phosphorous in the periodic table, but then it's also true that Phosphorous is just below Nitrogen and Silicon is just below Carbon - neither can be substituted by the element below.

Arsenic and Phosphorous are similar, but this doesn't mean their differences are unimportant. Arsenic-containing analogues of biological phosphorous-containing compounds are radically less stable, which has two consequences: firstly, molecules that should be stable (such as the DNA) will simply hydrolyse and, secondly, whereas the energy release involved in the detachment of phosphate groups is retained, the spontaneous detachment of arsenate would not allow this energy to be retained for useful work. Since this management of energy is the central plank of metabolism this is a massive issue and even if the stability issues of the arsenate can be controlled, the release of arsenate from ATA to form ADA is going to release a slightly different amount of energy to that released by the conversion of ATP to ADP.

As well as the stability problem there's also the issue of molecular size; now, Arsenic and Phosphate are similar in size to each other, but they are not identical. A DNA strand made with arsenate, rather than phosphate, linkage will have a slightly different length, with each base pair a slightly different distance apart which means the helix will be a different shape which means that the normal highly sensitive DNA-binding enzymes won't quite match up.

If this bacteria is really substituting arsenic for phosphate, the biochemical implications are huge.


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 Message 60 by Percy, posted 12-03-2010 5:14 PM Percy has responded

Replies to this message:
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Dr Jack
Member (Idle past 184 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 65 of 78 (594636)
12-04-2010 7:15 AM
Reply to: Message 63 by Rrhain
12-04-2010 3:05 AM


The press is claiming that the experiment showed that arsenates were incorporated into the phosphate backbone of the DNA strands, but that's not what the paper stated.

The paper does say that their data suggests that arsenate is being incorporated into the DNA backbone. The couch it in cautious terms but they do say it:

quote:
Therefore, our X-ray data support the position of arsenate in a similar configuration to phosphate in a DNA backbone...

This message is a reply to:
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Replies to this message:
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Percy
Member
Posts: 18309
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.7


Message 66 of 78 (594641)
12-04-2010 8:11 AM


NYT Article
Today's New York Times posted an article about the discovery:

Microbe Finds Arsenic Tasty; Redefines Life

This quote focuses on what is probably the core of our difference of opinion:

Felisa Wolfe-Simon, a NASA astrobiology fellow at the United States Geological Survey in Menlo Park, Calif., who led the experiment, said, This is a microbe that has solved the problem of how to live in a different way.

This story is not about Mono Lake or arsenic, she said, but about cracking open the door and finding that what we think are fixed constants of life are not.

The "fixed constants of life"? Did microbiologists as a group really believe that carbon, oxygen, phosphorus, and so forth, were "fixed constants of life"? If they did then I guess this discovery ranks way up there in significance. But I think it's much more like what Taq described in Message 61, that the significance is not that it changes our thinking, but rather that it verifies a broadly held expectation.

For me this is a case of, "Yep, just the kind of thing we would expect. Isn't adaptation amazing!" Evolutionary adaptation is always exploring and pushing up against the boundaries of what is possible. If something is possible then evolution will find it. Just look at the way genetic algorithms find solutions undreamt of by human designers. Where is the amazement of evolution finding solutions in nature that we didn't know were possible?

I just feel that all the attention and speculation leading up to the news conference was not justified by the substance that NASA eventually presented.

--Percy


    
Percy
Member
Posts: 18309
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.7


Message 67 of 78 (594645)
12-04-2010 9:16 AM
Reply to: Message 64 by Dr Jack
12-04-2010 7:12 AM


Re: PZ Myers Pipes Up
Mr Jack writes:

It's true, Arsenic is only just below Phosphorous in the periodic table, but then it's also true that Phosphorous is just below Nitrogen and Silicon is just below Carbon - neither can be substituted by the element below.

Can I assume that we know that nitrogen can't substitute for phosphorus and silicon can't substitute for carbon in the same way we knew that arsenic can't substitute for phosphorus?

At the NASA news conference one of the scientists explained why it was thought that arsenic could not replace phosphorus in the DNA backbone. Using a steel chain he explained how strong phosphorus bonds are, then he replaced one of the steel links with one crafted from crinkled up aluminum foil to illustrate how weak arsenic bonds are. A DNA backbone with some phosphorus replaced by arsenic would not be able to stay together for long and would soon split into fragments.

This argues against arsenic replacing phosphorus in the DNA backbone, but if it turns out it did (something they don't yet know) then what does that say about how sure we are about the impossibility of nitrogen and silicon as substitutes?

And of course the same arguments apply for cell chemistry outside DNA.

--Percy


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Rrhain
Member
Posts: 6349
From: San Diego, CA, USA
Joined: 05-03-2003


Message 68 of 78 (594680)
12-04-2010 2:32 PM
Reply to: Message 65 by Dr Jack
12-04-2010 7:15 AM


Mr Jack responds to me:

quote:
The paper does say that their data suggests that arsenate is being incorporated into the DNA backbone. The couch it in cautious terms but they do say it

But they're couching it because they didn't actually show it. Their experiments are highly suggestive, but they didn't actually look at the DNA strands directly. Instead, they examined the amount of phosphates compared to arsenates, saw that the phosphates went down while the arsenates went up, and made a very logical conclusion.

A lot more work needs to be done and it is very promising. But again, the press has this amazing habit of reporting things above and beyond what was actually said when it comes to science. You gotta sell papers and "alien life" sells better than "lab-cultured bacteria."


Rrhain

Thank you for your submission to Science. Your paper was reviewed by a jury of seventh graders so that they could look for balance and to allow them to make up their own minds. We are sorry to say that they found your paper "bogus," specifically describing the section on the laboratory work "boring." We regret that we will be unable to publish your work at this time.

Minds are like parachutes. Just because you've lost yours doesn't mean you can use mine.
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 Message 65 by Dr Jack, posted 12-04-2010 7:15 AM Dr Jack has responded

Replies to this message:
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Dr Jack
Member (Idle past 184 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 69 of 78 (594989)
12-06-2010 3:58 AM
Reply to: Message 68 by Rrhain
12-04-2010 2:32 PM


But they're couching it because they didn't actually show it. Their experiments are highly suggestive, but they didn't actually look at the DNA strands directly. Instead, they examined the amount of phosphates compared to arsenates, saw that the phosphates went down while the arsenates went up, and made a very logical conclusion.

Sure. But you seemed to be saying this was something the press was saying rather than something the researchers were saying. The researchers are saying its in the DNA backbone, they just don't have very strong evidence of this.

A lot more work needs to be done and it is very promising. But again, the press has this amazing habit of reporting things above and beyond what was actually said when it comes to science.

If you're simply saying that the press is reporting it as more certain than it deserves - then, yes, I agree.


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Minnemooseus
Member
Posts: 3708
From: Duluth, Minnesota, U.S. (West end of Lake Superior)
Joined: 11-11-2001
Member Rating: 3.9


Message 70 of 78 (594990)
12-06-2010 4:34 AM
Reply to: Message 29 by Minnemooseus
12-02-2010 8:28 PM


A couple of more links of skepticism
Larrry Moran says:

quote:
For a start, even the title of the paper is misleading. The title says "A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus" but all of the data show that there was phosphorus in the media and that the bacteria used it for growth and reproduction. This selected strain of bacteria incorporated more arsenic than non-selected species but it by no means did it replace all phosphate with arsenic. Only a few percent (at most) of the phosphorus atoms in DNA, for example, were replaced by arsenic.

He goes on to link to this more detailed review. I'll pull the following out of the cite, although I think PZ Myers more or less made the same observation in the link I previously cited:

quote:
Under the microscope the bacteria grown with arsenate and no added phosphate (Fig. 1 C) look like plump little corn kernels, about 1 m across and 2 m long. They contain many structures (Fig. 1 E) which the authors think may be granules of the wax-like carbon/energy storage material polyhydroxybutyrate (PHB). Bacterial cells produce this when their carbon/energy supply is good but other nutrients needed for growth are in short supply. Cells grown with phospate and no added arsenate are thinner and lack the granules (Fig. 1 D)

Much more gory detail at the source, but it sure seems to me that the bacteria were not "thriving" but rather were struggling to survive.

Moose


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Dr Jack
Member (Idle past 184 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 71 of 78 (594994)
12-06-2010 5:34 AM
Reply to: Message 70 by Minnemooseus
12-06-2010 4:34 AM


Re: A couple of more links of skepticism
Much more gory detail at the source, but it sure seems to me that the bacteria were not "thriving" but rather were struggling to survive.

If they had been surviving and reproducing using arsenate in key biological molecules that would still be a finding of staggering biological importance. And as the paper itself says (emphasis mine):

quote:
...GFAJ-1 is not an obligate arsenophile and it grew considerably better when provided with P

That said, having spent some time looking at the paper and reading what other, more qualified to comment, folks have said about the actual science in the paper it seems to me that it profoundly fails the "extraordinary claims require extraordinary evidence" test. There doesn't seem to have been the testing required to rule out the notion that this bacterium is merely using mechanisms to survive high arsenic and low phosphorous conditions rather than actually substituting arsenic for phosphorous.


This message is a reply to:
 Message 70 by Minnemooseus, posted 12-06-2010 4:34 AM Minnemooseus has responded

Replies to this message:
 Message 72 by Minnemooseus, posted 12-06-2010 6:04 AM Dr Jack has responded

  
Minnemooseus
Member
Posts: 3708
From: Duluth, Minnesota, U.S. (West end of Lake Superior)
Joined: 11-11-2001
Member Rating: 3.9


Message 72 of 78 (594999)
12-06-2010 6:04 AM
Reply to: Message 71 by Dr Jack
12-06-2010 5:34 AM


Re: A couple of more links of skepticism
Hey, I'm not even remotely a biologist (the closest I've ever come to a biology class was invertebrate paleontology) but I thought it a good thing to point out the opinions linked to in my previous message. But I had to throw something else in or be in violation of rule 5 (No bare links etc.).

There doesn't seem to have been the testing required to rule out the notion that this bacterium is merely using mechanisms to survive high arsenic and low phosphorous conditions rather than actually substituting arsenic for phosphorous.

The "bolded" is my "not based of any personal expertise" impression. I must leave it to those who can handle the "gory details" of that second cite to pass a much more qualified judgment.

Now, if you want to get into oddities in preCambrian geology, that's where I have a bit of personal expertise (but just a bit).

Moose


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Dr Jack
Member (Idle past 184 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 73 of 78 (595011)
12-06-2010 7:36 AM
Reply to: Message 72 by Minnemooseus
12-06-2010 6:04 AM


Re: A couple of more links of skepticism
this would seem to be pretty much a slam-dunk on the idea that the bacteria is actually using arsenate in its DNA backbone.

The skinny: an arsenate backbone should be unstable in water. The researchers theorise that the bacteria uses some unknown means to stabilise it. However, the extraction process they used effectively suspends the DNA in water if it truly had a Arsenate backbone then this should have resulted in it breaking up but their results show it didn't.

Disappointing.

Edited by Mr Jack, : No reason given.


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Dr Jack
Member (Idle past 184 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 74 of 78 (595022)
12-06-2010 9:49 AM


Confirmation bias?
If you want my idle speculation, I think this is a case of confirmation bias writ large. I've just been reading an earlier paper from Felisa Wolfe-Simon (et al), published last year* - it's basically a paper arguing for the plausibility and existence of life doing pretty much exactly what her group claim to have found. I suspect that because she was already strongly of the position it was possible and would be found, they looked and saw what they wanted to see.

* - F. Wolfe-Simon, P.C.W. Davies and A.D. Anbar (2009). Did nature also choose Arsenic? International Journal of Astrobiology. 8: 69-74.


  
crashfrog
Inactive Member


Message 75 of 78 (595028)
12-06-2010 10:29 AM
Reply to: Message 68 by Rrhain
12-04-2010 2:32 PM


Their experiments are highly suggestive, but they didn't actually look at the DNA strands directly.

I'm not sure that's correct. They did tests where they cultured on radiolabeled arsenate media and then fractioned the cells by organic extraction and centrifugation, and they found their radiolabeled arsenate in the fractions corresponding to proteins, nucelic acids, and lipids.

That's pretty suggestive, I would say.


This message is a reply to:
 Message 68 by Rrhain, posted 12-04-2010 2:32 PM Rrhain has not yet responded

  
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