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NASA-Funded Research Discovers Life Built With Toxic Chemical

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glen ep ropella

NASA-Funded Research Discovers Life Built With Toxic Chemical

I presume most of you've seen this already, but just in case:

http://www.nasa.gov/topics/universe/features/astrobiology_toxic_chemical.html

"Researchers conducting tests in the harsh environment of Mono Lake in
California have discovered the first known microorganism on Earth able
to thrive and reproduce using the toxic chemical arsenic. The
microorganism substitutes arsenic for phosphorus in its cell components."

--
glen e. p. ropella, 971-222-9095, http://tempusdictum.com

============================================================
FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
lectures, archives, unsubscribe, maps at http://www.friam.org

Russ Abbott

Re: NASA-Funded Research Discovers Life Built With Toxic Chemical

Other than the fact that this is the first time we have seen a life form that uses arsenic as a chemical building block, why is this important? Is there something about arsenic that is so incompatible with other forms of life that it would seem to be impossible to do this?

-- Russ Abbott
_____________________________________________

Professor, Computer Science
California State University, Los Angeles

Google voice: 424-235-5752 (424-cell-rja)
blog: http://russabbott.blogspot.com/
vita: http://sites.google.com/site/russabbott/
_____________________________________________

On Thu, Dec 2, 2010 at 11:25 AM, glen e. p. ropella <[hidden email]> wrote:

I presume most of you've seen this already, but just in case:

http://www.nasa.gov/topics/universe/features/astrobiology_toxic_chemical.html

"Researchers conducting tests in the harsh environment of Mono Lake in
California have discovered the first known microorganism on Earth able
to thrive and reproduce using the toxic chemical arsenic. The
microorganism substitutes arsenic for phosphorus in its cell components."

--
glen e. p. ropella, 971-222-9095, http://tempusdictum.com

============================================================
FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
lectures, archives, unsubscribe, maps at http://www.friam.org

============================================================
FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
lectures, archives, unsubscribe, maps at http://www.friam.org

Russ Abbott

Re: NASA-Funded Research Discovers Life Built With Toxic Chemical

This (from another article) looks like a significant part of the answer.

Arsenic falls directly below phosphorus on the period table, and thus has many similar chemical properties. In contrast to relatively stable phosphorus-based molecules, however, arsenic compounds are extremely unstable. While phosphorus compounds take years, decades, or even millennia to break down, the rate of hydrolysis of arsenic compounds is usually measured in seconds or minutes.

In fact, its similarity to phosphorus and its instability partly explains why arsenic is so toxic. The body may not be able to distinguish between phosphate -- the most common form of phosphorus in organisms -- and its arsenic equivalent, arsenate. As a result, scientists suspect that arsenate can be incorporated into molecules and pathways that normally use phosphate, causing downstream processes to fail if the arsenate molecules are quick to break down or otherwise don't work properly.

-- Russ Abbott

_____________________________________________

On Thu, Dec 2, 2010 at 2:56 PM, Russ Abbott <[hidden email]> wrote:

Other than the fact that this is the first time we have seen a life form that uses arsenic as a chemical building block, why is this important? Is there something about arsenic that is so incompatible with other forms of life that it would seem to be impossible to do this?

-- Russ Abbott
_____________________________________________
Professor, Computer Science
California State University, Los Angeles

Google voice: 424-235-5752 (424-cell-rja)
blog: http://russabbott.blogspot.com/
vita: http://sites.google.com/site/russabbott/
_____________________________________________

On Thu, Dec 2, 2010 at 11:25 AM, glen e. p. ropella <[hidden email]> wrote:

I presume most of you've seen this already, but just in case:

http://www.nasa.gov/topics/universe/features/astrobiology_toxic_chemical.html

"Researchers conducting tests in the harsh environment of Mono Lake in
California have discovered the first known microorganism on Earth able
to thrive and reproduce using the toxic chemical arsenic. The
microorganism substitutes arsenic for phosphorus in its cell components."

--
glen e. p. ropella, 971-222-9095, http://tempusdictum.com

============================================================
FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
lectures, archives, unsubscribe, maps at http://www.friam.org

glen ep ropella

Re: NASA-Funded Research Discovers Life Built With Toxic Chemical

Russ Abbott wrote circa 10-12-02 03:04 PM:

> This (from another
> article<http://www.the-scientist.com/news/display/57851/#ixzz16zxXUGXe>)
> looks like a significant part of the answer.
> [...]
> In fact, its similarity to phosphorus and its instability partly explains
> why arsenic is so toxic. The body may not be able to distinguish between
> phosphate -- the most common form of phosphorus in organisms -- and its
> arsenic equivalent, arsenate. As a result, scientists suspect that arsenate
> can be incorporated into molecules and pathways that normally use phosphate,
> causing downstream processes to fail if the arsenate molecules are quick to
> break down or otherwise don't work properly.

I think this block of text from the original article is more indicative
of the importance[*] of the find:

"Although AsO_4^3- esters are predicted to be orders of
magnitude less stable than PO_4^3- esters, at least for simple
molecules (8), GFAJ-1 can cope with this instability. The
vacuole-like regions observed in GFAJ-1 cells when growing
under +As/-P conditions are potentially poly-β-
hydroxybutyrate rich [as shown in other Halomonas species
(19)] which may stabilize As(V)-O-C type structures because
non-aqueous environments appear to promote slower
hydrolysis rates for related compounds (8). We propose that
intracellular regions or mechanisms that exclude water may
also promote this stability."

The keyword being "non-aqueous".

[*] FWIW, I find it odd for you to ask, of this particular article, "why
is this important?" Of all the obscure, mumbo-jumbo journal articles
out there (our discussion of PoMo aside ;-), it seems blatantly obvious
to me that the substitution of As for P in DNA is important, even if we
don't know what the implications are. I am woefully ignorant of the
literature, though. Is it fairly common to find and report substitutes
for DNA components?

--
glen e. p. ropella, 971-222-9095, http://tempusdictum.com

============================================================
FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
lectures, archives, unsubscribe, maps at http://www.friam.org

Roger Critchlow-2

Re: NASA-Funded Research Discovers Life Built With Toxic Chemical

On Thu, Dec 2, 2010 at 4:39 PM, glen e. p. ropella <[hidden email]> wrote:

[*] FWIW, I find it odd for you to ask, of this particular article, "why
is this important?" Of all the obscure, mumbo-jumbo journal articles
out there (our discussion of PoMo aside ;-), it seems blatantly obvious
to me that the substitution of As for P in DNA is important, even if we
don't know what the implications are. I am woefully ignorant of the
literature, though. Is it fairly common to find and report substitutes
for DNA components?

No, it's not common, it's never been reported before, all DNA and RNA in life as we have known it up until today has been based on phospho-esters.

-- rec --

Nick Thompson

Re: NASA-Funded Research Discovers Life Built With Toxic Chemical

In reply to this post by Russ Abbott

Russ,

As Steve G. would say, Any Gradient in a Storm!

Nick

From: [hidden email] [mailto:[hidden email]] On Behalf Of Russ Abbott
Sent: Thursday, December 02, 2010 3:57 PM
To: The Friday Morning Applied Complexity Coffee Group
Subject: Re: [FRIAM] NASA-Funded Research Discovers Life Built With Toxic Chemical

-- Russ Abbott
_____________________________________________

On Thu, Dec 2, 2010 at 11:25 AM, glen e. p. ropella <[hidden email]> wrote:

Nick Thompson

Re: NASA-Funded Research Discovers Life Built With Toxic Chemical

In reply to this post by Roger Critchlow-2

I would say it’s about as important biololgically as the first rock that falls up would be important physically!

From: [hidden email] [mailto:[hidden email]] On Behalf Of Roger Critchlow
Sent: Thursday, December 02, 2010 6:03 PM
To: The Friday Morning Applied Complexity Coffee Group
Subject: Re: [FRIAM] NASA-Funded Research Discovers Life Built With Toxic Chemical

On Thu, Dec 2, 2010 at 4:39 PM, glen e. p. ropella <[hidden email]> wrote:

[*] FWIW, I find it odd for you to ask, of this particular article, "why
is this important?" Of all the obscure, mumbo-jumbo journal articles
out there (our discussion of PoMo aside ;-), it seems blatantly obvious
to me that the substitution of As for P in DNA is important, even if we
don't know what the implications are. I am woefully ignorant of the
literature, though. Is it fairly common to find and report substitutes
for DNA components?

No, it's not common, it's never been reported before, all DNA and RNA in life as we have known it up until today has been based on phospho-esters.

-- rec --

Russ Abbott

Re: NASA-Funded Research Discovers Life Built With Toxic Chemical

Strange set of comments. Why so much defensiveness? I asked why the discovery was important. It was only a question. It wasn't an implied assertion that it wasn't important. All I wanted was an intuitive explanation for why it was important. And in fact the paragraph that I quoted in my second post was the sort of answer I was looking for.

It may seem "blatantly obvious to [Glen] that the substitution of As for P in DNA is important," It wasn't to me, which is why I asked. Also the article Glen pointed to didn't say that As was substituted for P in DNA in particular. Nor was the paragraph Glen quotes in that article--not that I would have understood it anyway. I would still have asked what that means to a layman and why it matters.

Nor does saying that it's as important as the first rock that fall upward would be important physically answer the question of why it's important. It's just an assertion that it is important.

So my question now is why did such a simple and straightforward question elicited such defensive responses.

-- Russ

P.S. I don't get the any gradient in a storm joke. Yes, I know that life has to do with gradients, but how is that related to this issue?

On Thu, Dec 2, 2010 at 7:35 PM, Nicholas Thompson <[hidden email]> wrote:

I would say it’s about as important biololgically as the first rock that falls up would be important physically!

n

From: [hidden email] [mailto:[hidden email]] On Behalf Of Roger Critchlow
Sent: Thursday, December 02, 2010 6:03 PM

To: The Friday Morning Applied Complexity Coffee Group
Subject: Re: [FRIAM] NASA-Funded Research Discovers Life Built With Toxic Chemical

On Thu, Dec 2, 2010 at 4:39 PM, glen e. p. ropella <[hidden email]> wrote:

[*] FWIW, I find it odd for you to ask, of this particular article, "why
is this important?" Of all the obscure, mumbo-jumbo journal articles
out there (our discussion of PoMo aside ;-), it seems blatantly obvious
to me that the substitution of As for P in DNA is important, even if we
don't know what the implications are. I am woefully ignorant of the
literature, though. Is it fairly common to find and report substitutes
for DNA components?

No, it's not common, it's never been reported before, all DNA and RNA in life as we have known it up until today has been based on phospho-esters.

-- rec --

============================================================
FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
lectures, archives, unsubscribe, maps at http://www.friam.org

James Steiner

Re: NASA-Funded Research Discovers Life Built With Toxic Chemical

Hi, Russ!

One reason it is important is that it demonstrates that "life as we
know it" has a broader definition that previously thought.

It means that if we find an earth-like planet out there, except with
more arsenic than phosphorus -- in other words, a poisonous-to-us
planet -- we might still find life on that planet. The number of
planets that might support life-as-we-think-we-know-it just increased
significantly.

~~James

On Thu, Dec 2, 2010 at 11:14 PM, Russ Abbott <[hidden email]> wrote:

> Strange set of comments. Why so much defensiveness? I asked why the
> discovery was important. It was only a question. It wasn't an implied
> assertion that it wasn't important. All I wanted was an intuitive
> explanation for why it was important. And in fact the paragraph that I
> quoted in my second post was the sort of answer I was looking for.
> It may seem "blatantly obvious to [Glen] that the substitution of As for P
> in DNA is important," It wasn't to me, which is why I asked. Also the
> article Glen pointed to didn't say that As was substituted for P in DNA in
> particular. Nor was the paragraph Glen quotes in that article--not that I
> would have understood it anyway. I would still have asked what that means
> to a layman and why it matters.

Carl Tollander

Re: NASA-Funded Research Discovers Life Built With Toxic Chemical

In reply to this post by Russ Abbott

Well, hmm, ok, I'll take a stab at it. The reason it's important is that it may be the tip of the iceberg of a category of alternative biologies, ie 'if this can happen what else can' - is this kind of thing prevalent? If there are alternative biologies (or 'shadow ecologies') beyond what we have considered, then the question arises: where are they? There will be new ways for astrobiologists to look for signatures for life on other planets. Remember that not too long ago we didn't know about extremophiles or the archaea.

One other possible big thing would be, if there is a whole new category of alternative biologies (a ways to go before we can consider that seriously), and some of those are present here on earth, maybe even within us, then it's analogous to dark matter; we quite possibly don't know as much about our own biological or evolutionary dynamics as we currently think we know and a lot of current models will end up being bantha pudu. And just as extremophiles have opened up new frontiers in biotech, so will these if they turn out to be prevalent, in ways we can't conceive of yet. For example, there's coal, the burning of which yields a bunch of arsenic - if we have a bunch of life forms that like arsenic, then we have been thrown an interesting curve and our world, at least from today's perspective, may get very weird indeed. Maybe that's not saying much.

So this is one of those science surprises, that may be game-changing.

Carl

On 12/2/10 9:14 PM, Russ Abbott wrote:

Strange set of comments. Why so much defensiveness? I asked why the discovery was important. It was only a question. It wasn't an implied assertion that it wasn't important. All I wanted was an intuitive explanation for why it was important. And in fact the paragraph that I quoted in my second post was the sort of answer I was looking for.

It may seem "blatantly obvious to [Glen] that the substitution of As for P in DNA is important," It wasn't to me, which is why I asked. Also the article Glen pointed to didn't say that As was substituted for P in DNA in particular. Nor was the paragraph Glen quotes in that article--not that I would have understood it anyway. I would still have asked what that means to a layman and why it matters.

Nor does saying that it's as important as the first rock that fall upward would be important physically answer the question of why it's important. It's just an assertion that it is important.

So my question now is why did such a simple and straightforward question elicited such defensive responses.

-- Russ

P.S. I don't get the any gradient in a storm joke. Yes, I know that life has to do with gradients, but how is that related to this issue?

On Thu, Dec 2, 2010 at 7:35 PM, Nicholas Thompson <[hidden email]> wrote:

I would say it’s about as important biololgically as the first rock that falls up would be important physically!

n

From: [hidden email] [mailto:[hidden email]] On Behalf Of Roger Critchlow
Sent: Thursday, December 02, 2010 6:03 PM

To: The Friday Morning Applied Complexity Coffee Group
Subject: Re: [FRIAM] NASA-Funded Research Discovers Life Built With Toxic Chemical

On Thu, Dec 2, 2010 at 4:39 PM, glen e. p. ropella <[hidden email]> wrote:

[*] FWIW, I find it odd for you to ask, of this particular article, "why
is this important?" Of all the obscure, mumbo-jumbo journal articles
out there (our discussion of PoMo aside ;-), it seems blatantly obvious
to me that the substitution of As for P in DNA is important, even if we
don't know what the implications are. I am woefully ignorant of the
literature, though. Is it fairly common to find and report substitutes
for DNA components?

No, it's not common, it's never been reported before, all DNA and RNA in life as we have known it up until today has been based on phospho-esters.

-- rec --

============================================================
FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
lectures, archives, unsubscribe, maps at http://www.friam.org
============================================================
FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
lectures, archives, unsubscribe, maps at http://www.friam.org

Eric Charles

Re: NASA-Funded Research Discovers Life Built With Toxic Chemical

In reply to this post by glen ep ropella

Following Glen, Roger, and James, and also wondering why Nick is being a pill....

I believe the report is of interest for showing an organism that uses arsenic in interesting ways, but it gets its magical-shininess (i.e. Science worthiness) for showing an organism that does not use phosphorous. We have never found a life form that could do the "life" thing without phosphorous. It is almost (almost) like finding an organism that uses silicon instead of carbon.

Oh, and then there is the potential for practical application... like cleaning up arsenic, which is a common pollutant coming out of mines. But anything like that is a long way off.

Eric

On Thu, Dec 2, 2010 08:03 PM, Roger Critchlow <[hidden email]> wrote:

On Thu, Dec 2, 2010 at 4:39 PM, glen e. p. ropella <gepr@...> wrote:

[*] FWIW, I find it odd for you to ask, of this particular article, "why
is this important?" Of all the obscure, mumbo-jumbo journal articles
out there (our discussion of PoMo aside ;-), it seems blatantly obvious
to me that the substitution of As for P in DNA is important, even if we
don't know what the implications are. I am woefully ignorant of the
literature, though. Is it fairly common to find and report substitutes
for DNA components?

No, it's not common, it's never been reported before, all DNA and RNA in life as we have known it up until today has been based on phospho-esters.

-- rec --
============================================================
FRIAM Applied
Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's
College
lectures, archives, unsubscribe, maps at
http://www.friam.org

Eric Charles

Professional Student and
Assistant Professor of Psychology
Penn State University
Altoona, PA 16601

Nick Thompson

Re: NASA-Funded Research Discovers Life Built With Toxic Chemical

In reply to this post by Russ Abbott

Sorry, Russ. Certainly didn’t mean to be defensive. It’s just that many of us have been reading in EvoDevo this semester and, if there is one idea that we seem to have learned, it is that the basic chemistry of life is universal and of more than a billion years standing. A billion years. Or perhaps two. The discovery described either suggests that these arsenic creatures are of enormous antiquity or an extraordinary innovation or that the basic tenets of evo devo are wrong. Hence my comment about a rock falling up.

Does that help?

Nick

From: [hidden email] [mailto:[hidden email]] On Behalf Of Russ Abbott
Sent: Thursday, December 02, 2010 9:15 PM
To: The Friday Morning Applied Complexity Coffee Group
Subject: Re: [FRIAM] NASA-Funded Research Discovers Life Built With Toxic Chemical

Nor does saying that it's as important as the first rock that fall upward would be important physically answer the question of why it's important. It's just an assertion that it is important.

So my question now is why did such a simple and straightforward question elicited such defensive responses.

-- Russ

P.S. I don't get the any gradient in a storm joke. Yes, I know that life has to do with gradients, but how is that related to this issue?

On Thu, Dec 2, 2010 at 7:35 PM, Nicholas Thompson <[hidden email]> wrote:

I would say it’s about as important biololgically as the first rock that falls up would be important physically!

From: [hidden email] [mailto:[hidden email]] On Behalf Of Roger Critchlow
Sent: Thursday, December 02, 2010 6:03 PM

To: The Friday Morning Applied Complexity Coffee Group
Subject: Re: [FRIAM] NASA-Funded Research Discovers Life Built With Toxic Chemical

On Thu, Dec 2, 2010 at 4:39 PM, glen e. p. ropella <[hidden email]> wrote:

No, it's not common, it's never been reported before, all DNA and RNA in life as we have known it up until today has been based on phospho-esters.

-- rec --

Russ Abbott

Re: NASA-Funded Research Discovers Life Built With Toxic Chemical

In reply to this post by Eric Charles

OK. Thanks. I actually did get that from the article but didn't think of it as that far out. It probably reflects my biologically naivety rather than scientific imagination, but it hadn't occurred to me that we wouldn't find life with different chemistries than our own.

I think that extremophiles are wonderful. Although not extreme in the standard sense but related, two years ago there was a report of a bacterium discovered in a mine shaft in South Africa two miles beneath the earth's surface. It lives on the chemical energy stored by the effects of background nuclear reactions. Not only that, it is the only known life form that is completely independent of other forms of life. That is, its genome is sufficient to encode processes that sustain life. See, for example Discover. (I imagine its DNA, however, was of standard construction.)

-- Russ

On Thu, Dec 2, 2010 at 9:21 PM, ERIC P. CHARLES <[hidden email]> wrote:

Following Glen, Roger, and James, and also wondering why Nick is being a pill....

I believe the report is of interest for showing an organism that uses arsenic in interesting ways, but it gets its magical-shininess (i.e. Science worthiness) for showing an organism that does not use phosphorous. We have never found a life form that could do the "life" thing without phosphorous. It is almost (almost) like finding an organism that uses silicon instead of carbon.

Oh, and then there is the potential for practical application... like cleaning up arsenic, which is a common pollutant coming out of mines. But anything like that is a long way off.

Eric

On Thu, Dec 2, 2010 08:03 PM, Roger Critchlow <[hidden email]> wrote:

On Thu, Dec 2, 2010 at 4:39 PM, glen e. p. ropella <gepr@...> wrote:

[*] FWIW, I find it odd for you to ask, of this particular article, "why
is this important?" Of all the obscure, mumbo-jumbo journal articles
out there (our discussion of PoMo aside ;-), it seems blatantly obvious
to me that the substitution of As for P in DNA is important, even if we
don't know what the implications are. I am woefully ignorant of the
literature, though. Is it fairly common to find and report substitutes
for DNA components?

No, it's not common, it's never been reported before, all DNA and RNA in life as we have known it up until today has been based on phospho-esters.

-- rec --

============================================================

FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
lectures, archives, unsubscribe, maps at http://www.friam.org

Eric Charles

Professional Student and
Assistant Professor of Psychology
Penn State University
Altoona, PA 16601
============================================================
FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
lectures, archives, unsubscribe, maps at http://www.friam.org

Nick Thompson

Re: NASA-Funded Research Discovers Life Built With Toxic Chemical

In reply to this post by Eric Charles

Not quite sure where I earned the honor being called a “pill” on this one.

Having been often accused of being long winded, I was trying to be brief, and so, seem to have managed to insult both sides of the “yes-its-surprising”-“no, it’s not surprising” discussion, when I meant no insult to anybody.

I think the discovery is surprising, and I think it raises some pretty interesting issues of molecular taxonomy. Is the substitution of As for P the only difference in the chemistry of these critters? I don’t imagine it will be very long before somebody sequences them. I can’t wait!

Nick

From: [hidden email] [mailto:[hidden email]] On Behalf Of ERIC P. CHARLES
Sent: Thursday, December 02, 2010 10:22 PM
To: Roger Critchlow
Cc: The Friday Morning Applied Complexity Coffee Group
Subject: Re: [FRIAM] NASA-Funded Research Discovers Life Built With Toxic Chemical

On Thu, Dec 2, 2010 at 4:39 PM, glen e. p. ropella <[hidden email]> wrote:

No, it's not common, it's never been reported before, all DNA and RNA in life as we have known it up until today has been based on phospho-esters.

-- rec --

============================================================
FRIAM Applied

Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's

College
lectures, archives, unsubscribe, maps at

http://www.friam.org

Eric Charles

Professional Student and
Assistant Professor of Psychology
Penn State University
Altoona, PA 16601

Miles Parker

Re: NASA-Funded Research Discovers Life Built With Toxic Chemical

In reply to this post by Eric Charles

Yeah -- staying out of the name the pill controversy ;) -- one neat little tidbit in the "I'm always amazed by how little I know and how little I've thought about what I do know" category. We think of Arsenic as a poison, but the only reason we think of it as a "poison" is (duh) that it is bad for *us*, i.e. humans + every other critter that we've run into before now. But the reason that it is bad is not that it is different from our chemistry, like an acid, but that it is so close to our chemistry, being next to phosphorous on the old periodic table, thus disrupting cellular mechanisms. So while typically we think of things that are close in structure or design to be friendly in fact here a movement to our nearest neighbor represents a major boundary shift, while one to a distant neighbor would of course be quite unlikely as the chances of slotting into the same role would be very slim. That idea could certainly argue for the idea that the current six element setup is arbitrary against some set of possible configurations. Once a choice is made in that configuration space it would be very unlikely (and only under these kind of extreme conditions) that we would move off it. The fact that we can (hmm, I mean I actually probably can't so please don't subject me to any experiments) anyway makes the argument that "because that's the only way it works here" even more tenuous.

On Dec 2, 2010, at 9:21 PM, ERIC P. CHARLES wrote:

Following Glen, Roger, and James, and also wondering why Nick is being a pill....

I believe the report is of interest for showing an organism that uses arsenic in interesting ways, but it gets its magical-shininess (i.e. Science worthiness) for showing an organism that does not use phosphorous. We have never found a life form that could do the "life" thing without phosphorous. It is almost (almost) like finding an organism that uses silicon instead of carbon.

Oh, and then there is the potential for practical application... like cleaning up arsenic, which is a common pollutant coming out of mines. But anything like that is a long way off.

Eric

On Thu, Dec 2, 2010 08:03 PM, Roger Critchlow <[hidden email]> wrote:

On Thu, Dec 2, 2010 at 4:39 PM, glen e. p. ropella <<a href="x-msg://18/#">gepr@...> wrote:

[*] FWIW, I find it odd for you to ask, of this particular article, "why
is this important?" Of all the obscure, mumbo-jumbo journal articles
out there (our discussion of PoMo aside ;-), it seems blatantly obvious
to me that the substitution of As for P in DNA is important, even if we
don't know what the implications are. I am woefully ignorant of the
literature, though. Is it fairly common to find and report substitutes
for DNA components?

No, it's not common, it's never been reported before, all DNA and RNA in life as we have known it up until today has been based on phospho-esters.

-- rec --

============================================================
FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
lectures, archives, unsubscribe, maps at http://www.friam.org

Eric Charles

Professional Student and
Assistant Professor of Psychology
Penn State University
Altoona, PA 16601
============================================================
FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
lectures, archives, unsubscribe, maps at http://www.friam.org

Robert Holmes

Re: NASA-Funded Research Discovers Life Built With Toxic Chemical

http://xkcd.org/829/

On Thu, Dec 2, 2010 at 11:59 PM, Miles Parker <[hidden email]> wrote:

Yeah -- staying out of the name the pill controversy ;) -- one neat little tidbit in the "I'm always amazed by how little I know and how little I've thought about what I do know" category. We think of Arsenic as a poison, but the only reason we think of it as a "poison" is (duh) that it is bad for *us*, i.e. humans + every other critter that we've run into before now. But the reason that it is bad is not that it is different from our chemistry, like an acid, but that it is so close to our chemistry, being next to phosphorous on the old periodic table, thus disrupting cellular mechanisms. So while typically we think of things that are close in structure or design to be friendly in fact here a movement to our nearest neighbor represents a major boundary shift, while one to a distant neighbor would of course be quite unlikely as the chances of slotting into the same role would be very slim. That idea could certainly argue for the idea that the current six element setup is arbitrary against some set of possible configurations. Once a choice is made in that configuration space it would be very unlikely (and only under these kind of extreme conditions) that we would move off it. The fact that we can (hmm, I mean I actually probably can't so please don't subject me to any experiments) anyway makes the argument that "because that's the only way it works here" even more tenuous.
On Dec 2, 2010, at 9:21 PM, ERIC P. CHARLES wrote:
Following Glen, Roger, and James, and also wondering why Nick is being a pill....

I believe the report is of interest for showing an organism that uses arsenic in interesting ways, but it gets its magical-shininess (i.e. Science worthiness) for showing an organism that does not use phosphorous. We have never found a life form that could do the "life" thing without phosphorous. It is almost (almost) like finding an organism that uses silicon instead of carbon.

Oh, and then there is the potential for practical application... like cleaning up arsenic, which is a common pollutant coming out of mines. But anything like that is a long way off.

Eric

On Thu, Dec 2, 2010 08:03 PM, Roger Critchlow <[hidden email]> wrote:

On Thu, Dec 2, 2010 at 4:39 PM, glen e. p. ropella <[hidden email]> wrote:

[*] FWIW, I find it odd for you to ask, of this particular article, "why
is this important?" Of all the obscure, mumbo-jumbo journal articles
out there (our discussion of PoMo aside ;-), it seems blatantly obvious
to me that the substitution of As for P in DNA is important, even if we
don't know what the implications are. I am woefully ignorant of the
literature, though. Is it fairly common to find and report substitutes
for DNA components?

No, it's not common, it's never been reported before, all DNA and RNA in life as we have known it up until today has been based on phospho-esters.

-- rec --

============================================================
FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
lectures, archives, unsubscribe, maps at http://www.friam.org

Eric Charles

Professional Student and
Assistant Professor of Psychology
Penn State University
Altoona, PA 16601
============================================================
FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
lectures, archives, unsubscribe, maps at http://www.friam.org
============================================================
FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
lectures, archives, unsubscribe, maps at http://www.friam.org

Douglas Roberts-2

Re: NASA-Funded Research Discovers Life Built With Toxic Chemical

I would have thought that FRIAM had already suffiently proven that life can exist in a toxic environment...

--Doug

On Fri, Dec 3, 2010 at 7:32 AM, Robert Holmes <[hidden email]> wrote:

http://xkcd.org/829/
On Thu, Dec 2, 2010 at 11:59 PM, Miles Parker <[hidden email]> wrote:
Yeah -- staying out of the name the pill controversy ;) -- one neat little tidbit in the "I'm always amazed by how little I know and how little I've thought about what I do know" category. We think of Arsenic as a poison, but the only reason we think of it as a "poison" is (duh) that it is bad for *us*, i.e. humans + every other critter that we've run into before now. But the reason that it is bad is not that it is different from our chemistry, like an acid, but that it is so close to our chemistry, being next to phosphorous on the old periodic table, thus disrupting cellular mechanisms. So while typically we think of things that are close in structure or design to be friendly in fact here a movement to our nearest neighbor represents a major boundary shift, while one to a distant neighbor would of course be quite unlikely as the chances of slotting into the same role would be very slim. That idea could certainly argue for the idea that the current six element setup is arbitrary against some set of possible configurations. Once a choice is made in that configuration space it would be very unlikely (and only under these kind of extreme conditions) that we would move off it. The fact that we can (hmm, I mean I actually probably can't so please don't subject me to any experiments) anyway makes the argument that "because that's the only way it works here" even more tenuous.
On Dec 2, 2010, at 9:21 PM, ERIC P. CHARLES wrote:
Following Glen, Roger, and James, and also wondering why Nick is being a pill....

I believe the report is of interest for showing an organism that uses arsenic in interesting ways, but it gets its magical-shininess (i.e. Science worthiness) for showing an organism that does not use phosphorous. We have never found a life form that could do the "life" thing without phosphorous. It is almost (almost) like finding an organism that uses silicon instead of carbon.

Oh, and then there is the potential for practical application... like cleaning up arsenic, which is a common pollutant coming out of mines. But anything like that is a long way off.

Eric

On Thu, Dec 2, 2010 08:03 PM, Roger Critchlow <[hidden email]> wrote:

On Thu, Dec 2, 2010 at 4:39 PM, glen e. p. ropella <[hidden email]> wrote:

[*] FWIW, I find it odd for you to ask, of this particular article, "why
is this important?" Of all the obscure, mumbo-jumbo journal articles
out there (our discussion of PoMo aside ;-), it seems blatantly obvious
to me that the substitution of As for P in DNA is important, even if we
don't know what the implications are. I am woefully ignorant of the
literature, though. Is it fairly common to find and report substitutes
for DNA components?

No, it's not common, it's never been reported before, all DNA and RNA in life as we have known it up until today has been based on phospho-esters.

-- rec --

============================================================
FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
lectures, archives, unsubscribe, maps at http://www.friam.org

Eric Charles

Professional Student and
Assistant Professor of Psychology
Penn State University
Altoona, PA 16601
============================================================
FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
lectures, archives, unsubscribe, maps at http://www.friam.org
============================================================
FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
lectures, archives, unsubscribe, maps at http://www.friam.org
============================================================
FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
lectures, archives, unsubscribe, maps at http://www.friam.org

--
Doug Roberts
[hidden email]
[hidden email]
505-455-7333 - Office
505-670-8195 - Cell

Russ Abbott

Re: NASA-Funded Research Discovers Life Built With Toxic Chemical

!!!

-- Russ

On Fri, Dec 3, 2010 at 8:09 AM, Douglas Roberts <[hidden email]> wrote:

I would have thought that FRIAM had already suffiently proven that life can exist in a toxic environment...
--Doug
On Fri, Dec 3, 2010 at 7:32 AM, Robert Holmes <[hidden email]> wrote:
http://xkcd.org/829/
On Thu, Dec 2, 2010 at 11:59 PM, Miles Parker <[hidden email]> wrote:
Yeah -- staying out of the name the pill controversy ;) -- one neat little tidbit in the "I'm always amazed by how little I know and how little I've thought about what I do know" category. We think of Arsenic as a poison, but the only reason we think of it as a "poison" is (duh) that it is bad for *us*, i.e. humans + every other critter that we've run into before now. But the reason that it is bad is not that it is different from our chemistry, like an acid, but that it is so close to our chemistry, being next to phosphorous on the old periodic table, thus disrupting cellular mechanisms. So while typically we think of things that are close in structure or design to be friendly in fact here a movement to our nearest neighbor represents a major boundary shift, while one to a distant neighbor would of course be quite unlikely as the chances of slotting into the same role would be very slim. That idea could certainly argue for the idea that the current six element setup is arbitrary against some set of possible configurations. Once a choice is made in that configuration space it would be very unlikely (and only under these kind of extreme conditions) that we would move off it. The fact that we can (hmm, I mean I actually probably can't so please don't subject me to any experiments) anyway makes the argument that "because that's the only way it works here" even more tenuous.
On Dec 2, 2010, at 9:21 PM, ERIC P. CHARLES wrote:
Following Glen, Roger, and James, and also wondering why Nick is being a pill....

I believe the report is of interest for showing an organism that uses arsenic in interesting ways, but it gets its magical-shininess (i.e. Science worthiness) for showing an organism that does not use phosphorous. We have never found a life form that could do the "life" thing without phosphorous. It is almost (almost) like finding an organism that uses silicon instead of carbon.

Oh, and then there is the potential for practical application... like cleaning up arsenic, which is a common pollutant coming out of mines. But anything like that is a long way off.

Eric

On Thu, Dec 2, 2010 08:03 PM, Roger Critchlow <[hidden email]> wrote:

On Thu, Dec 2, 2010 at 4:39 PM, glen e. p. ropella <[hidden email]> wrote:

[*] FWIW, I find it odd for you to ask, of this particular article, "why
is this important?" Of all the obscure, mumbo-jumbo journal articles
out there (our discussion of PoMo aside ;-), it seems blatantly obvious
to me that the substitution of As for P in DNA is important, even if we
don't know what the implications are. I am woefully ignorant of the
literature, though. Is it fairly common to find and report substitutes
for DNA components?

No, it's not common, it's never been reported before, all DNA and RNA in life as we have known it up until today has been based on phospho-esters.

-- rec --

============================================================
FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
lectures, archives, unsubscribe, maps at http://www.friam.org

Eric Charles

Professional Student and
Assistant Professor of Psychology
Penn State University
Altoona, PA 16601
============================================================
FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
lectures, archives, unsubscribe, maps at http://www.friam.org
============================================================
FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
lectures, archives, unsubscribe, maps at http://www.friam.org
============================================================
FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
lectures, archives, unsubscribe, maps at http://www.friam.org
--
Doug Roberts
[hidden email]
[hidden email]
505-455-7333 - Office
505-670-8195 - Cell
============================================================
FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
lectures, archives, unsubscribe, maps at http://www.friam.org

glen ep ropella

Re: NASA-Funded Research Discovers Life Built With Toxic Chemical

In reply to this post by Russ Abbott

Russ Abbott wrote circa 10-12-02 08:14 PM:
> Why so much defensiveness?

I don't think anyone was being defensive. Personally, I was just very
surprised by the question. Sorry if my answer was inadequate.

On a tangent, however, I found this article interesting:

Citizens Against Peer Review
http://blogs.discovermagazine.com/intersection/2010/12/03/citizens-against-peer-review/

It's fun because when I first started reading it, I was thinking "OK.
So many Republicans can be wankers; but what's fundamentally wrong with
asking lay people to [pre]judge the merit of NSF applications?"

Then after the article author's rhetoric, I was persuaded! Ha! I'm too
dense and ignorant to be easily persuaded of anything. And I certainly
do _not_ buy Mooney's implicit assumption that peer review is somehow
automatically "merit-based", given that the "peers" doing the reviewing
are all biased in some way.

But it does bring up the point that we humans do as little work as we
can get away with. We're lazy. We won't dig into any subject unless we
must, for whatever reason. The reviewers will dig in deeper than the
lay person (mostly) because it's their job/profession to do so. Oh
sure, they may have chosen that job/profession based on some inherent
energy or curiosity about the domain; but in the end, they have
groceries to buy on the way home, yards to rake, burnt out light bulbs
to change, etc. So, they really do have to commit to work like this.

The lay person doesn't. When convenient or bored, she can make snap
[pre]judgments all she wants and if/when some particular phrase or
keyword pushes her buttons, she'll go to the minimal effort to pull up
Thunderbird and e-mail her congress person ranting and raving about
wasteful spending.

Then again, I really do think that finding ways to expose lay people to
science is a good thing. So, just like with the TSA backscatter
machines and pat downs, Rep. Smith's intentions don't matter one whit.
And Mooney's intentions in criticizing it also don't matter. What might
actually matter is getting more _eyeballs_ on the science!

I.e. although I am persuaded by Mooney's rhetoric, I would support
Smith's effort.

--
glen e. p. ropella, 971-222-9095, http://tempusdictum.com

============================================================
FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
lectures, archives, unsubscribe, maps at http://www.friam.org

Russ Abbott

Re: NASA-Funded Research Discovers Life Built With Toxic Chemical

In reply to this post by Robert Holmes

I his 1944 "What is Life," Schrödinger identifies a fundamental characteristic of living beings as being able to retain a relatively lower level of entropy by extracting energy from the environment. Since As compounds are so much less stable than P compounds the strategy that the As bacterium uses to maintain its low entropy level will probably constitute the most important aspect of this recent discovery. I wonder if these bacteria use relatively more energy to survive than comparable P bacteria or if they discovered a technique to maintain their structure that is not as dependent on stable As/P compounds.

-- Russ

On Fri, Dec 3, 2010 at 6:32 AM, Robert Holmes <[hidden email]> wrote:

http://xkcd.org/829/
On Thu, Dec 2, 2010 at 11:59 PM, Miles Parker <[hidden email]> wrote:
Yeah -- staying out of the name the pill controversy ;) -- one neat little tidbit in the "I'm always amazed by how little I know and how little I've thought about what I do know" category. We think of Arsenic as a poison, but the only reason we think of it as a "poison" is (duh) that it is bad for *us*, i.e. humans + every other critter that we've run into before now. But the reason that it is bad is not that it is different from our chemistry, like an acid, but that it is so close to our chemistry, being next to phosphorous on the old periodic table, thus disrupting cellular mechanisms. So while typically we think of things that are close in structure or design to be friendly in fact here a movement to our nearest neighbor represents a major boundary shift, while one to a distant neighbor would of course be quite unlikely as the chances of slotting into the same role would be very slim. That idea could certainly argue for the idea that the current six element setup is arbitrary against some set of possible configurations. Once a choice is made in that configuration space it would be very unlikely (and only under these kind of extreme conditions) that we would move off it. The fact that we can (hmm, I mean I actually probably can't so please don't subject me to any experiments) anyway makes the argument that "because that's the only way it works here" even more tenuous.
On Dec 2, 2010, at 9:21 PM, ERIC P. CHARLES wrote:
Following Glen, Roger, and James, and also wondering why Nick is being a pill....

I believe the report is of interest for showing an organism that uses arsenic in interesting ways, but it gets its magical-shininess (i.e. Science worthiness) for showing an organism that does not use phosphorous. We have never found a life form that could do the "life" thing without phosphorous. It is almost (almost) like finding an organism that uses silicon instead of carbon.

Oh, and then there is the potential for practical application... like cleaning up arsenic, which is a common pollutant coming out of mines. But anything like that is a long way off.

Eric

On Thu, Dec 2, 2010 08:03 PM, Roger Critchlow <[hidden email]> wrote:

On Thu, Dec 2, 2010 at 4:39 PM, glen e. p. ropella <[hidden email]> wrote:

[*] FWIW, I find it odd for you to ask, of this particular article, "why
is this important?" Of all the obscure, mumbo-jumbo journal articles
out there (our discussion of PoMo aside ;-), it seems blatantly obvious
to me that the substitution of As for P in DNA is important, even if we
don't know what the implications are. I am woefully ignorant of the
literature, though. Is it fairly common to find and report substitutes
for DNA components?

No, it's not common, it's never been reported before, all DNA and RNA in life as we have known it up until today has been based on phospho-esters.

-- rec --

============================================================
FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
lectures, archives, unsubscribe, maps at http://www.friam.org

Eric Charles

Professional Student and
Assistant Professor of Psychology
Penn State University
Altoona, PA 16601
============================================================
FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
lectures, archives, unsubscribe, maps at http://www.friam.org
============================================================
FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
lectures, archives, unsubscribe, maps at http://www.friam.org
============================================================
FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
lectures, archives, unsubscribe, maps at http://www.friam.org