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Author Topic:   Nasa news conference (re: Arsenic-based life form?)
cavediver
Member (Idle past 1594 days)
Posts: 4129
From: UK
Joined: 06-16-2005


Message 46 of 78 (594366)
12-03-2010 8:30 AM
Reply to: Message 45 by Dr Jack
12-03-2010 8:16 AM


Re: Disappointing Announcement
I profoundly disagree with PZ Myers on this. I think he is massively underplaying how big a bit of biological news this is. That a bacterium has successfully evolved a means to substitute one of the absolutely fundamental building blocks of every key cellular mechanism and structure is most certainly a "big whoop".

I agree - I think it is very exciting.

The problem was that there were two successive disappointments: some thought that they were being led to believe that this was going to be about exobiology, and then as a consolation, they thought that a new strain of terrestrial life had been found that used different chemistry to all other life, and so could be evidence of a second abiogenetic event.

Me, knowing all too well how these things pan out, had zero expectations despite the media back-out, and was and still am delighted with this discovery...


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Percy
Member
Posts: 17875
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.3


Message 47 of 78 (594371)
12-03-2010 8:57 AM
Reply to: Message 45 by Dr Jack
12-03-2010 8:16 AM


Re: Disappointing Announcement
I'm not pooh-poohing the discovery, I'm pooh-poohing the buildup and hype. This isn't a discovery that warrants this kind of showcasing. This recently discovered extremophile is a just another example of the evolution of terrestrial lifeforms in action. While one can't predict the specifics of what will be discovered in the future, this is exactly the kind of thing that one would expect. I'm sure there are many more similarly amazing things waiting to be discovered in extreme environments such as arsenic lakes and black smokers and dead seas and buried deep within the ground and so forth.

I think the next time NASA ballyhoos some announcement related to the search for extraterrestrial life that it should really be much more directly related.

--Percy


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crashfrog
Inactive Member


Message 48 of 78 (594458)
12-03-2010 1:21 PM
Reply to: Message 45 by Dr Jack
12-03-2010 8:16 AM


Re: Disappointing Announcement
That a bacterium has successfully evolved a means to substitute one of the absolutely fundamental building blocks of every key cellular mechanism and structure is most certainly a "big whoop".

I don't think it's "every", though. Actually I don't think they even checked "every", they cultured the bacterium on an arsenate media and then found arsenate in the bacterium's DNA. So, at best all they know is that this strain can substitute arsenate for phosphate in deoxynucleotides.

That's pretty cool, but is there evidence of arseneylation of proteins, for instance? (Activating enzymes by phosphorylation is another important biological function of phosphate.) Just based on the morphological differences that emerge in the cells on arsenate media seems to indicate that the changeover isn't a completely transparent process for the cell, so it wouldn't surprise me if these unique nucleotide-arsenates are being localized to very specific cell processes.

I'm not trying to be all up on PZ's dick about this (hometown shout-out, yo!) but I think he's mostly right - this is probably going to merit little more than a sidebar in most biochemistry texts. It's cool, but not really a game-changer. Most people studying biology or biochemistry already kind of assume that the only inviolable rule is that there are no inviolable rules.


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Replies to this message:
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Dr Jack
Member (Idle past 55 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 49 of 78 (594463)
12-03-2010 1:54 PM
Reply to: Message 48 by crashfrog
12-03-2010 1:21 PM


Re: Disappointing Announcement
Disclaimer: not read the paper yet hopefully have time tomorrow.

As I understand it: they found arsenate in place of phosphate everywhere. Although they were looking at it by fractionation rather than isolating the particular molecules involved which makes the result less certain than it could be.

That's pretty cool, but is there evidence of arseneylation of proteins, for instance?

If it's correct that the phosphate groups in ATP are being replaced by arsenate, at the researchers claim, then this would mean that proteins are being arseneylated.

I'm not trying to be all up on PZ's dick about this (hometown shout-out, yo!) but I think he's mostly right - this is probably going to merit little more than a sidebar in most biochemistry texts. It's cool, but not really a game-changer.

Yeah, it'll be a sidebar at most because, in the end, it's an extremophile living in a pond; it's just not that relevant to life as a whole.

Most people studying biology or biochemistry already kind of assume that the only inviolable rule is that there are no inviolable rules.

I'm astonished by this. And I would put good money that if you'd asked the world's molecular biologists last Tuesday whether this is something we'd find they'd have lumped down pretty heavily on the "not on this Earth" side of the fence.


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jar
Member
Posts: 30934
From: Texas!!
Joined: 04-20-2004
Member Rating: 1.3


Message 50 of 78 (594465)
12-03-2010 2:00 PM
Reply to: Message 49 by Dr Jack
12-03-2010 1:54 PM


Re: Disappointing Announcement
So should we look for forms that replace carbon with silicon, oxygen with sulfur or selenium, phosphorus with nitrogen...?


Anyone so limited that they can only spell a word one way is severely handicapped!
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crashfrog
Inactive Member


Message 51 of 78 (594466)
12-03-2010 2:04 PM
Reply to: Message 49 by Dr Jack
12-03-2010 1:54 PM


Re: Disappointing Announcement
If it's correct that the phosphate groups in ATP are being replaced by arsenate, at the researchers claim, then this would mean that proteins are being arseneylated.

Not necessarily. Maybe the arsenic-substituted ATP is specifically directed to nucleic acid synthesis.

I'd like to know if I'm wrong, though.

And I would put good money that if you'd asked the world's molecular biologists last Tuesday whether this is something we'd find they'd have lumped down pretty heavily on the "not on this Earth" side of the fence.

Well, I'd take that bet, I guess, but it depends what you're asking. Are you asking them if we would ever find "arsenic-based life", as this has been erroneously described; or are you asking them if we would ever find bacteria with mutations that have allowed them to be arsenic-tolerant? I don't think you'd have found many skeptics for the latter point.


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Percy
Member
Posts: 17875
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.3


Message 52 of 78 (594470)
12-03-2010 2:20 PM
Reply to: Message 49 by Dr Jack
12-03-2010 1:54 PM


Re: Disappointing Announcement
Mr Jack writes:

I'm astonished by this. And I would put good money that if you'd asked the world's molecular biologists last Tuesday whether this is something we'd find they'd have lumped down pretty heavily on the "not on this Earth" side of the fence.

Before the discovery of nylon metabolizing bacteria, if you had asked the world's molecular biologists if bacteria could evolve to take advantage of nylon I hope they would have come down clearly on the side of it being possible. Before the discovery of life around black smokers, if you had asked the world's molecular biologists if life could exist at such high temperatures I hope they would have believed it was possible. We now have plenty of examples of organisms evolving the ability to live in extreme environments, metabolize new chemicals, and evolve immunity or tolerance to poisons and such. If molecular biologists truly would have collectively objected "not on this Earth" to the possibility of microbes evolving the ability to incorporate arsenic or any poison then I would find that unexpected.

I assume, or at least hope, that those searching for signs of extraterrestrial life assume that the type of life found on Earth is not the only type of life possible. It would seem to make little sense to conclude, for example, that "The signatures we're observing for life-related elements and molecules on planet X is not what we see here on Earth, therefore this planet cannot harbor life."

The definitions of life I've liked most talk about metabolism and reproduction and so forth, not about requiring carbon and oxygen and phosphorus and such. I hope exobiologists feel the same way.

--Percy

Edited by Percy, : Grammar.


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Replies to this message:
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Taq
Member
Posts: 7594
Joined: 03-06-2009
Member Rating: 3.4


Message 53 of 78 (594473)
12-03-2010 2:34 PM
Reply to: Message 45 by Dr Jack
12-03-2010 8:16 AM


Re: Disappointing Announcement
I profoundly disagree with PZ Myers on this. I think he is massively underplaying how big a bit of biological news this is.

Agreed. This goes beyond mutations which confer protein stability in high salt or temperature. This is NEW biochemistry at a very fundamental level. Something as conserved and basic as ATP was replaced by new chemistry. It is a big find that tells us that even the foundations of long standing evolved pathways can still be changed to fit new conditions.

Edited by Taq, : No reason given.


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Replies to this message:
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Dr Jack
Member (Idle past 55 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 54 of 78 (594476)
12-03-2010 2:42 PM
Reply to: Message 52 by Percy
12-03-2010 2:20 PM


Re: Disappointing Announcement
We're not talking about merely tolerating or incorporating arsenic, we're talking about using it in place of one of the most fundamental building blocks of life and using it in key roles in absolutely central molecules.
This message is a reply to:
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crashfrog
Inactive Member


Message 55 of 78 (594480)
12-03-2010 2:47 PM
Reply to: Message 53 by Taq
12-03-2010 2:34 PM


Re: Disappointing Announcement
Something as conserved and basic as ATP was replaced by new chemistry.

New in what way? Arsenate is pretty similar, chemically, to phosphate. That is, after all, why it's a poison and why these bacteria can use it.

Genuine new chemistry would be something like the UWash group that designed a new enzyme that catalyzes a Diels-Alder reaction ("Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction", Science 329, 309) That's a form of chemistry that, to our knowledge, no living thing performs.

Again, I think this is neat - it's just not a game-changer. They only found it because they already speculated it was possible, and on that basis they went looking for it just precisely where you would expect to find it - a low-phosphorus, high arsenic environment. Didn't I speculate about this possibility a few months ago? I assure you, I'm not clairvoyant, I just made a guess based on phosphorus and arsenic being in the same period. I made a point about competition, too, and that holds up - when phosphorus is present, I doubt this strain uses any arsenic at all.


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Percy
Member
Posts: 17875
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.3


Message 56 of 78 (594490)
12-03-2010 3:16 PM
Reply to: Message 54 by Dr Jack
12-03-2010 2:42 PM


Re: Disappointing Announcement
Mr Jack writes:

We're not talking about merely tolerating or incorporating arsenic,...

Uh, yes we are talking about tolerating and incorporating arsenic.

...we're talking about using it in place of one of the most fundamental building blocks of life and using it in key roles in absolutely central molecules.

I guess to someone who assumed that evolutionary change was limited to nucleotides, genes and chromosomes it must seem an incredible thing, but the assumption doesn't seem warranted and it isn't one I've ever shared myself. Jurassic Park had it right: "Life will find a way."

--Percy


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Taq
Member
Posts: 7594
Joined: 03-06-2009
Member Rating: 3.4


Message 57 of 78 (594505)
12-03-2010 4:29 PM
Reply to: Message 55 by crashfrog
12-03-2010 2:47 PM


Re: Disappointing Announcement
New in what way? Arsenate is pretty similar, chemically, to phosphate.

"New" as in all other life we know of uses phosphate attached to an adenosine as a fundamental storehouse of energy while these bacteria use arsenate instead (and by extension the arsenate backbone of their DNA). If it so easy to switch between the two then why isn't it more common? It's not as if these bacteria have produced a protein that breaks down arsenic to reduce it's toxicity (which is what bacteria do for many antibiotics). Instead, this bacteria has turned a toxin into an integral part of it's metabolism.

I guess that the coolness of this is quite subjective, but from my own view as someone who has worked in the lab with metabolism and protein chemistry this is pretty cool stuff.


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crashfrog
Inactive Member


Message 58 of 78 (594507)
12-03-2010 4:50 PM
Reply to: Message 57 by Taq
12-03-2010 4:29 PM


Re: Disappointing Announcement
I guess that the coolness of this is quite subjective, but from my own view as someone who has worked in the lab with metabolism and protein chemistry this is pretty cool stuff.

I'm not saying it's not cool.


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Percy
Member
Posts: 17875
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.3


Message 59 of 78 (594508)
12-03-2010 5:01 PM
Reply to: Message 57 by Taq
12-03-2010 4:29 PM


Re: Disappointing Announcement
Taq writes:

I guess that the coolness of this is quite subjective, but from my own view as someone who has worked in the lab with metabolism and protein chemistry this is pretty cool stuff.

I don't think Crashfrog and myself are saying that it isn't cool stuff. It *is* very cool!

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!" And as an aside, I think the more we learn about what was actually discovered we'll find that they discovered less than was implied. I'll be pleasantly surprised to be proven wrong, but I think NASA exaggerated the significance, but they had committed themselves for who knows what reason and so were driven to make the discovery seem as amazing and unexpected as possible. Like the nightly news, they have to make every event seem as significant or dire or whatever as possible to maintain the public's attention.

Anyone remember the original Star Trek from the 1960's? There was one episode about the Horta, a lifeform based upon silicon instead of carbon, a common speculation in science fiction. Today's youngest exobiologists are the grandchildren of people who grew up with Star Trek. Now nearly a half century later I would have expected we're all familiar with the concept that the fundamental building blocks of life don't have to be just like our own, and that just like Burger King life in each environment can have things its own way.

--Percy


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Percy
Member
Posts: 17875
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.3


Message 60 of 78 (594509)
12-03-2010 5:14 PM


PZ Myers Pipes Up
Someone earlier mentioned that PZ Myers had blogged about this, and I just now got around to reading it:

http://scienceblogs.com/...its_not_an_arsenic-based_life.php

The whole thing is well worth reading, only takes a couple minutes, but here's a fuller excerpt of the key part, and he pretty much confirms what us skeptics have been saying:

PZ Myers writes:

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.

--Percy


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