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

[Roger Critchlow]

The author of the original paper speaks to criticisms:

http://news.sciencemag.org/scienceinsider/2010/12/author-of-controversial-arsenic-.html?rss=1

Science
is making the paper freely available for the next two weeks so anyone who
wants to chime in doesn't need to buy a copy:

http://www.sciencemag.org/content/early/2010/12/01/science.1197258.abstract

-- rec --


On Tue, Dec 7, 2010 at 11:07 AM, Stephen Guerin
wrote:

> Russ, you had a small typo in your Shrödinger quote.
>
> Instead of extracting "energy", Schrödinger actually defined living systems
> as extracting "negative entropy" from the environment:
> "the only way a living system stays alive, away from maximum entropy or
> death is to be continually drawing from its environment negative entropy.
> ..Thus the devise by which an organism maintains itself stationary at a
> fairly high level of orderliness (= fairly low level of entropy) really
> consists in continually sucking orderliness from its environment."
>
> You can download the original at
> http://whatislife.stanford.edu/LoCo_files/What-is-Life.pdf. In the notes
> area he says negative entropy is equivalent to free energy but didn't want
> to confuse non physicists.
>
> You can see this quote and a nice discussion on by Eric Schneider and James
> Kay in "What Is Life: The Next 50 Years" http://bit.ly/dO7mCE
>
> Feeding on free energy is very similar to Kauffman defining living systems
> as autonomous agents that extract work from their environment.
>
> BTW, Boltzmann also said a related bit:
> "The general struggle for existence of animate beings is therefore not a
> struggle for raw materials - these, for organisms, are air, water and soil,
> all abundantly available - nor for energy which exists in plenty in any body
> in the form of heat (albeit unfortunately not transformable), but a struggle
> for entropy, which becomes available through the transition of energy from
> the hot sun to the cold earth."
> You can read this chapter at http://bit.ly/hYsuUd
>
>
>
>
>
>
> On Fri, Dec 3, 2010 at 2:27 PM, Russ Abbott  wrote:
> >
> > 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
>
>
>
> 
> 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

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

[Stephen Guerin]

Russ, you had a small typo in your Shrödinger quote.

Instead of extracting "energy", Schrödinger actually defined living systems
as extracting "negative entropy" from the environment:
"the only way a living system stays alive, away from maximum entropy or
death is to be continually drawing from its environment negative entropy.
..Thus the devise by which an organism maintains itself stationary at a
fairly high level of orderliness (= fairly low level of entropy) really
consists in continually sucking orderliness from its environment."

You can download the original at
http://whatislife.stanford.edu/LoCo_files/What-is-Life.pdf. In the notes
area he says negative entropy is equivalent to free energy but didn't want
to confuse non physicists.

You can see this quote and a nice discussion on by Eric Schneider and James
Kay in "What Is Life: The Next 50 Years" http://bit.ly/dO7mCE

Feeding on free energy is very similar to Kauffman defining living systems
as autonomous agents that extract work from their environment.

BTW, Boltzmann also said a related bit:
"The general struggle for existence of animate beings is therefore not a
struggle for raw materials - these, for organisms, are air, water and soil,
all abundantly available - nor for energy which exists in plenty in any body
in the form of heat (albeit unfortunately not transformable), but a struggle
for entropy, which becomes available through the transition of energy from
the hot sun to the cold earth."
You can read this chapter at http://bit.ly/hYsuUd





On Fri, Dec 3, 2010 at 2:27 PM, Russ Abbott  wrote:
>
> 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

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

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

[glen e. p. ropella]

Nicholas Thompson wrote  circa 12/07/2010 08:53 AM:
> You know, it wasn't SO long ago (i.e., I remember it) that SOME journals
> thought of themselves as "archival," and their reviewers* saw their role as
> defending the pages of those journals against error.  In that context,
> getting published was supposed to be the end of a conversation, not a
> beginning.   I don't know if, and where, that view survives.  

I hope it's completely dead.  It should be obvious that authoritarianism
is bad.

-- 
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

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

[Nicholas Thompson]

Glen, and All, 

You know, it wasn't SO long ago (i.e., I remember it) that SOME journals
thought of themselves as "archival," and their reviewers* saw their role as
defending the pages of those journals against error.  In that context,
getting published was supposed to be the end of a conversation, not a
beginning.   I don't know if, and where, that view survives.  

Nick 


*PS, Sort of like those people who defend the internet against people who
use UPPER CASE for emphasis.  (};-])

-Original Message-
From: friam-boun...@redfish.com [mailto:friam-boun...@redfish.com] On Behalf
Of glen e. p. ropella
Sent: Tuesday, December 07, 2010 9:21 AM
To: The Friday Morning Applied Complexity Coffee Group
Subject: Re: [FRIAM] NASA-Funded Research Discovers Life Built With Toxic
Chemical

Roger Critchlow wrote  circa 12/06/2010 09:39 PM:
> Ah, a microbiologist rips the NASA research: 
> 
>   
> http://rrresearch.blogspot.com/2010/12/arsenic-associated-bacteria-nas
> as.html

Very cool!  Thanks, Roger.

> <http://rrresearch.blogspot.com/2010/12/arsenic-associated-bacteria-na
> sas.html>Via
> Maggie Koerth-Baker at Boing Boing:
> 
>http://www.boingboing.net/2010/12/06/microbiologist-turns.html

Reading the comments to this one, I'm always amazed how people misunderstand
peer review.  Some people speak as if a panel of 3 ... or
12 ... reviewers (who do have _other_ things to do in their life) are
responsible for omnisciently accepting truth and rejecting falsity.
Publishing research that _later_ is criticized and turns out to be fatally
flawed is all part of the process.  Peer review is just 1 step in the
process.  Hopefully, Redfield's criticism will get published and we'll
quickly follow an asymptote to a definitive conclusion that can be used in
more research.

One thing that's sure, though, is brought out nicely by this comment:

"Maybe she's wrong. But it deserves a quick response, not a plodding
discussion in the editorial pages of a magazine that most everyone can't
afford."

--
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

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

[glen e. p. ropella]

Roger Critchlow wrote  circa 12/06/2010 09:39 PM:
> Ah, a microbiologist rips the NASA research: 
> 
>   
> http://rrresearch.blogspot.com/2010/12/arsenic-associated-bacteria-nasas.html

Very cool!  Thanks, Roger.

> Via
> Maggie Koerth-Baker at Boing Boing:
> 
>http://www.boingboing.net/2010/12/06/microbiologist-turns.html

Reading the comments to this one, I'm always amazed how people
misunderstand peer review.  Some people speak as if a panel of 3 ... or
12 ... reviewers (who do have _other_ things to do in their life) are
responsible for omnisciently accepting truth and rejecting falsity.
Publishing research that _later_ is criticized and turns out to be
fatally flawed is all part of the process.  Peer review is just 1 step
in the process.  Hopefully, Redfield's criticism will get published and
we'll quickly follow an asymptote to a definitive conclusion that can be
used in more research.

One thing that's sure, though, is brought out nicely by this comment:

"Maybe she's wrong. But it deserves a quick response, not a plodding
discussion in the editorial pages of a magazine that most everyone can't
afford."

-- 
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

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

[Douglas Roberts]

Sounds like an extremely toxic research environment.  Poisonous reviews...

On Mon, Dec 6, 2010 at 10:39 PM, Roger Critchlow  wrote:

> Ah, a microbiologist rips the NASA research:
>
>
> http://rrresearch.blogspot.com/2010/12/arsenic-associated-bacteria-nasas.html
>
> finding lots of places where they didn't do (or didn't report the results
> of) additional experimental work she would have sent any graduate student
> back to the lab to do.
>
> Via
> Maggie Koerth-Baker at Boing Boing:
>
>   http://www.boingboing.net/2010/12/06/microbiologist-turns.html
>
> -- rec --
>
>
> On Thu, Dec 2, 2010 at 12:25 PM, glen e. p. ropella  > 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

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

[Roger Critchlow]

Ah, a microbiologist rips the NASA research:


http://rrresearch.blogspot.com/2010/12/arsenic-associated-bacteria-nasas.html

finding lots of places where they didn't do (or didn't report the results
of) additional experimental work she would have sent any graduate student
back to the lab to do.

Via
Maggie Koerth-Baker at Boing Boing:

  http://www.boingboing.net/2010/12/06/microbiologist-turns.html

-- rec --

On Thu, Dec 2, 2010 at 12:25 PM, glen e. p. ropella
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

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

[Russ Abbott]

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 wrote:

> http://xkcd.org/829/
>
>
> On Thu, Dec 2, 2010 at 11:59 PM, Miles Parker 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 * wrote:
>>
>>
>>
>> On Thu, Dec 2, 2010 at 4:39 PM, glen e. p. ropella > > 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 athttp://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
>

FRIAM Applied Complexity Group listserv
Me

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

[glen e. p. ropella]

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

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

[Russ Abbott]

!!!
*
-- Russ *



On Fri, Dec 3, 2010 at 8:09 AM, Douglas Roberts 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 wrote:
>
>> http://xkcd.org/829/
>>
>>
>>
>> On Thu, Dec 2, 2010 at 11:59 PM, Miles Parker 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 * wrote:
>>>
>>>
>>>
>>> On Thu, Dec 2, 2010 at 4:39 PM, glen e. p. ropella <
>>> g...@tempusdictum.com> 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 athttp://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
> drobe...@rti.org
> d...@parrot-farm.net
> 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
>

FRIAM Applied Complexity Group listserv
Meet

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

[Douglas Roberts]

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 wrote:

> http://xkcd.org/829/
>
>
>
> On Thu, Dec 2, 2010 at 11:59 PM, Miles Parker 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 * wrote:
>>
>>
>>
>> On Thu, Dec 2, 2010 at 4:39 PM, glen e. p. ropella > > 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 athttp://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
drobe...@rti.org
d...@parrot-farm.net
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

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

[Robert Holmes]

http://xkcd.org/829/


On Thu, Dec 2, 2010 at 11:59 PM, Miles Parker  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 * wrote:
>
>
>
> On Thu, Dec 2, 2010 at 4:39 PM, glen e. p. ropella 
> 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 athttp://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

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

[Miles Parker]

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

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

[Nicholas Thompson]

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: friam-boun...@redfish.com [mailto:friam-boun...@redfish.com] 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

 

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  wrote:



 

On Thu, Dec 2, 2010 at 4:39 PM, glen e. p. ropella  
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

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

[Russ Abbott]

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  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 * wrote:
>
>
>
> On Thu, Dec 2, 2010 at 4:39 PM, glen e. p. ropella 
> 
> > 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 athttp://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

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

[Nicholas Thompson]

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: friam-boun...@redfish.com [mailto:friam-boun...@redfish.com] 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

 

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
 wrote:

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

 

n

 

From: friam-boun...@redfish.com [mailto:friam-boun...@redfish.com] 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 
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

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

[ERIC P. CHARLES]

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

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

[Carl Tollander]

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 
mailto:nickthomp...@earthlink.net>> wrote:


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

n

*From:*friam-boun...@redfish.com
<mailto:friam-boun...@redfish.com>
[mailto:friam-boun...@redfish.com
<mailto:friam-boun...@redfish.com>] *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
mailto:g...@tempusdictum.com>> 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

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

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

[James Steiner]

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  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.


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

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

[Russ Abbott]

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 <
nickthomp...@earthlink.net> wrote:

> I would say it’s about as important biololgically as the first rock that
> falls up would be important physically!
>
>
>
> n
>
>
>
> *From:* friam-boun...@redfish.com [mailto:friam-boun...@redfish.com] *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 
> 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

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

[Nicholas Thompson]

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

 

n

 

From: friam-boun...@redfish.com [mailto:friam-boun...@redfish.com] 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 
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

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

[Nicholas Thompson]

Russ, 

 

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

 

Nick 

 

From: friam-boun...@redfish.com [mailto:friam-boun...@redfish.com] 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

 

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 
wrote:


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

http://www.nasa.gov/topics/universe/features/astrobiology_toxic_chemical.htm
l

"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

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

[Roger Critchlow]

On Thu, Dec 2, 2010 at 4:39 PM, glen e. p. ropella 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

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

[glen e. p. ropella]

Russ Abbott wrote circa 10-12-02 03:04 PM:
> This (from another
> article)
> 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

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

[Russ Abbott]

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*
*_*
*  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 2:56 PM, Russ Abbott  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  > 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

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

[Russ Abbott]

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
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