
Microbes use arsenic in their DNA:  Proves phosphorus is not required for life - roadnottaken
http://www.scribd.com/doc/44550217/Science-2010-Wolfe-Simon-Science-1197258
======
cstross
As Mono Lake is of volcanic origin and formed around 760,000 years ago (per
Wikipedia) I'd be astonished if the arsenophile(?) evolved there in that short
a time span. Which leaves open the question of where it came from, and whether
arsenic tolerance is present but dormant in other extremophiles.

Other points of note: never mind the cellular DNA integrating arsenate, the
whole respiration cycle seems to be affected, presumably running on ATA rather
than ATP. Which implies huge amounts of molecular booty in the shape of
enzymes that are powered by a different reduction gradient (ATA-AMA rather
than ATP-AMP).

Possible down to earth applications? Lest we forget, Pakistan has a
_monstrous_ problem with arsenic-contaminated wells (
<http://www.irc.nl/page/16331> ) and a bacterial culture that thrives on
arsenic could offer new approaches to arsenic sequestration. And that's just
off the top of my head. (My biochemistry is, alas, too rusty to go much
further without a refresher course. Hmm ...)

~~~
jacquesm
If a bacterium consumes the arsenic from a contaminated well the well is now
contaminated with the corpses of bacteria that are rich in arsenic.

You'd have to add another pass to get rid of the bacterial residue (possibly
easier, but still).

~~~
InclinedPlane
Arsenic is this big: (makes gesture with thumb and forefinger a few angstroms
apart), bacteria are this big: (makes gesture with thumb and forefinger a few
microns apart).

OK, that's not overly helpful, the point being, you can filter bacteria out of
water a whole hell of a lot easier than you can filter out dissolved arsenic.

~~~
niels_olson
Couple of thoughts:

1) precipitating arsenic salts directly might be easier and a whole hell of a
lot easier to provably run to completion.

2) to filter out bacteria, you'd have to grow bacteria. In addition to
arsenic, you'd also have to add sugar and protein. Last I checked, Islam take
a pretty hard line on beer.

~~~
freiheit
However, beer is made with _yeast_ , not bacteria. And from what I can tell,
most reasonable forms of Islam interpret the beer thing as forbidding
intoxication. I don't think any forbid bread (solid beer), for instance.
Yogurt and pickles are also made with bacterial processes and I don't think
they're forbidden in Islam.

------
drcode
OK, this news is very interesting, but it does not prove much about
extraterrestrial life.

We know that organisms can adapt to their environment. Incorporating some
fraction of arsenic into a cell's dna is an example of such adaptation.

The question that really matters is "has life originated more than once in the
universe?" This experiment has no bearing on that: They took a standard
terrestrial cell, with a carbon-based history, and simply subjected it to some
new conditions. This is NOT a new life form that originated from a novel
environment and using a different chemistry. However, NASA is getting awfully
close to selling it as such in their press conference, which is misleading.

~~~
noodle
if you're watching the press conference, they're very adamant that it doesn't
prove anything about extraterrestrial life and they aren't able to yet say if
life evolved with the arsenic or if it adapted.

but they're pointing out that it does show that forms of life different from
our current definitions can exist and therefore the possibility of
extraterrestrial life in non-earthlike environments exist.

~~~
jerf
"but they're pointing out that it does show that forms of life different from
our current definitions can exist"

Yes, but not _meaningfully_ different from previous definitions. If this is
simply an evolution of existing earth life, then it's just another in a long
list of things that we were surprised evolved from conventional Earth life,
but is, nevertheless, conventional Earth life. It's more indicative of a
_slight flaw_ in our definitions, not time for a radical reexamination of our
assessment of the universe.

As I commented in a previous message, people have a history of getting far
more excited about this sort of thing than they have scientific justification
for. This sure looks like another one of those.

Now, if they could establish that this has to be the actual entirely new
branch of life that can be provably not traced back to the same Earth ancestor
as everything else, _that_ would be a groundshaking discovery.

Those of us pondering the Great Questions were already not assuming that
everything has to look exactly like known Earth life to work. There are
numerous obvious different, incompatible mechanism that could exist (different
RNA transcription tables, the other chirality for proteins) and an unknown and
presumably vastly larger number of unobvious different mechanisms even just
for basically Earth life before we really go out into new territory. We've
already speculated endlessly about silicon life, ammonia life, mechanisms
other than photosynthesis, etc. Don't get me wrong, this is legitimately
_interesting_ , and would on its own be worthy of HN, but I have to say the
implications for the Great Questions are basically zip. Announcing proof that
life can _only_ exist in precisely Earthlike conditions with incredibly tight
tolerances would be the surprise.

~~~
noodle
i think that it _is_ meaningfully different from previous definitions.

perhaps all sparks of life would require the same stuff that it did on earth,
that is unclear. but it shows that the continuation of life doesn't
necessarily require that same stuff. it means that in searching for life, you
don't necessarily have to limit it to the proverbial class M planets.

~~~
jerf
But how is that a change? We _already_ knew that to the point that we're
looking at non-Earthlike planets. We're _already_ looking for life on Titan
and Europa, already looking on Mars to see if it had life. We're already
talking about life on that tidally-locked mega-Earth that came up a couple of
months ago, with otherwise-respectable scientists saying it's 100% likely [1].
We're already not convinced that life has to start exactly as Earth does.

If it's "different", what's the actual _difference_? What actually changed?

[1]: [http://www.space.com/scienceastronomy/earth-like-
exoplanet-p...](http://www.space.com/scienceastronomy/earth-like-exoplanet-
possibly-habitable-100929.html)

~~~
noodle
no. we already _theorized_ that, we didn't _know_. we didn't have proof. now
we do; now we know. the actual tangible differences are likely going to be in
funding, research direction, and scope of effort on the topic. who knows what
future research will generate off of this?

no, the world hasn't changed. sorry. not yet, at least. but its kind of like
watching the moon landing in '69 and scoffing at it because you knew it was
coming, you've been reading about NASA working on it for years in the paper.

~~~
jerf
You're badly misunderstanding my point. I'm not saying this isn't interesting.
I'm saying this isn't actually all that interesting when it comes to the Great
Questions. It doesn't significantly expand where we already thought life could
be. It has not yet established that it is anything other than another
evolution of Earth life, which would be a big deal, and from the sounds of it
that's still what it is, an adaptation.

This isn't some amazing announcement with profoundly unsettling implications
for life in the Universe. It's another in a long series of announcements about
how our understanding was limited about how far Earth life could travel. It's
roughly similar to how we found non-photosynthetic life around the ocean vents
[1], or the recent discoveries of strange life several miles underground [2],
or the sky bacteria [3]. I think quite a few people here are not understanding
just how _many_ similar discoveries have _already_ been made, we moved on from
"all life in the universe will look just like the standard sun-powered
ecosystem we live in" quite a while ago.

I guess you could say to the extent this is amazing, we've _already_ been
amazed this way. It's cool, but it's a discovery that fits quite comfortably
with a number of other interesting discoveries. We're not going to be talking
about this in another year. (Except possibly because once people start looking
for more examples of this sort of thing I'd lay money they find them.)

[1]:
[http://en.wikipedia.org/wiki/Hydrothermal_vent#Biological_co...](http://en.wikipedia.org/wiki/Hydrothermal_vent#Biological_communities)

[2]:
[http://www.livescience.com/animals/061019_otherworldly_bacte...](http://www.livescience.com/animals/061019_otherworldly_bacteria.html)

[3]:
[http://www.wired.com/science/planetearth/news/2008/02/bacter...](http://www.wired.com/science/planetearth/news/2008/02/bacteria_clouds)

------
civilian
Huh! Biochemistry major here... So I guess that the bacteria just rarely uses
Sulphur-Sulphur (thiol) bonds in it's proteins, since Arsenic has a high
affinity for it (and that's what causes arsenic toxicity in everything else).
[http://en.wikipedia.org/wiki/Arsenic#Biochemical_basis_of_ar...](http://en.wikipedia.org/wiki/Arsenic#Biochemical_basis_of_arsenic_toxicity)

"suggesting the possibility of a biochemistry very different from the one we
know" Seems like a bit of an exaggeration, but news will be news. Thiols are
important for the structure & enzymatic activity, but this bacteria is proof
that there are ways around it. Besides that difference, I'm guessing they're
the same.

~~~
jaysonelliot
You don't think that the discovery of the first organism to use a different
element than phosphorous is a big deal?

Cynicism is cool and all that, but this sure sounds like big news to me.

~~~
sandipc
it's a really big deal... provided the arsenic is actually incorporated into
nucleic acids, and the bacteria aren't just surviving on background levels of
phosphate.

it will be interesting to read the original paper when it comes out in Science
later today, and not just accounts of the paper from other sources

------
dnautics
high resolution Mass spec is such a shitty technique and is completely non-
quantitative. How do you know that arsenic isn't associated with, say, a
protein that makes the DNA resistant to being taken apart chemically. I will
believe this result when they stain the DNA and run samples of the DNA down a
density gradient ultracentrifugation and show that arsenic content in the
media correlates with increased density of DNA, as you would expect if the
arsenic is replacing phosphorus. If you don't know what i'm talking about,
it's this classical experiment:

[http://en.wikipedia.org/wiki/Semiconservative_replication#Bi...](http://en.wikipedia.org/wiki/Semiconservative_replication#Biophysical_evidence)

Here is my personal scientific experience speaking: If you see it everywhere,
then it's likely to be an artefact. Clean up your technique, clean your
instruments, and go back to an old school technique. Remember how the
physicists who discovered CMB cleaned out the pigeon scat from their microwave
horn telescope before they started to believe what they saw.

------
sorbus
"The researchers isolated the organism and found that when cultured in
arsenate solution it grew 60% as fast as it did in phosphate solution — not as
well, but still robustly. The culture did not grow at all when deprived of
both arsenate and phosphate."

------
jaysonelliot
Felisa Wolfe-Simon's name is going to end up in the history books along with
Leeuwenhoek and Darwin.

Talk about a life-changing discovery!

~~~
spot
Maybe but not for this work. This wasn't the 2nd origin of life story that was
predicted.

~~~
mechanical_fish
Yes, the touchstone of everyone's work should be how well it compares to the
figments of one's imagination.

Poor Einstein! If only he'd discovered warp drive, he'd be as famous as
Zephraim Cochrane!

~~~
badkungfu
Wow, snarky.

I had the same impression. This sounds really, really cool but it's still an
organism that uses DNA, and we're still related to it. As a layperson, I don't
see why this says a lot more about the potential for life elsewhere. If it's
not a wholly new occurrence of life, then it's something that "did life" the
same way we do until it happened to need this really cool adaptation.

I understand that my lack of biology training probably contributes to my not
getting it, but that's where most people are coming from. A lot of time has
been spent explaining the significance of Einstein's work and most people
still don't "get it", we may need the same here.

So, instead of snarking...explain again/better/differently than others have.

~~~
cryptoz
> This sounds really, really cool but it's still an organism that uses DNA

Are we 100% certain of that? I'm not a biologist, however it seems to me that
DNA is in part defined by the usage of Phosphorus. Maybe we need to redefine
DNA? Or does this organism not use DNA at all?

<http://en.wikipedia.org/wiki/DNA#Properties>

Please correct me if I'm not understanding correctly!

~~~
badkungfu
Yeah, I don't know either. Sounds like DNA is the strand/mechanism and using
phosphates is all we know of so far. IANAS

But if it's not-technically-DNA-anymore because it can use an arsenate instead
of a phosphate, it's still part of our tree of life. That's the part that
seems to have dampened enthusiasm somewhat.

------
stavrianos
bicycle discovered constructed entirely from wood: proves metal not required
for transportation

[http://www.leevalley.com/newsletters/woodworking/2/3/article...](http://www.leevalley.com/newsletters/woodworking/2/3/article1-1.jpg)

~~~
anigbrowl
We already knew that because we have had wooden boats, carts, and planes
(gliders).

~~~
jjs
You're missing the point—this is the single greatest discovery in
exobicyclology since _E.T._!

~~~
anigbrowl
Tee-hee - it's true that these NASA announcements are often a bit of an
anticlimax, but I suppose that's the price of having so much science-fiction
to enjoy.

Oddly enough,the first bicycles were actually made out of wood - they were
called velocipedes and today we call them balance bikes. Like scooters, they
were powered by pushing feet along the ground. I was going to link to an
amusing site about these, but while looking it up I was surprised to discover
that there are in fact modern bicycles mostly made from wood, although they're
quite expensive: <http://www.renovobikes.com/>

...so I wasn't as well well-informed as I thought I was.

------
dnautics
I don't know. You would think, but you can autoclave a solution of "deionized
ultrafiltered water" which should have "no" carbon in it at all, and bacteria
will find a way to grow in it if you get it contaminated, they will
concentrate the trace trace trace amounts of carbon.

How carefully did they prep their DNA? These days nobody is careful and they
use these crap kits which are good enough, convenient enough to get molecular
biology done. The other day in lab I suggested someone isolate DNA using
caesium chloride gradient ultracentifugation and the only people who knew what
I was talking about were the two old (70+) year old senior scientists but they
agreed that it was the way to go.

------
bld
Here's the press conference in three ~10 minute parts: Part 1:
<http://www.youtube.com/watch?v=hu5dXnCUs7I> Part 2:
<http://www.youtube.com/watch?v=0LsihAsX4z8> Part 3:
<http://www.youtube.com/watch?v=Nu0VvxuicLw>

The lead author gives a talk at 2:26 in Part 1 that I thought was an excellent
example of how to communicate science (or other technical subject) and
implications to a general audience.

------
roadnottaken
Here's the article from Science:
[http://www.scribd.com/doc/44550217/Science-2010-Wolfe-
Simon-...](http://www.scribd.com/doc/44550217/Science-2010-Wolfe-Simon-
Science-1197258)

------
joelburget
Perhaps NASA should be more cautious about holding a press on astrobiology,
and with a Science embargo. Clearly everyone will immediately think of aliens,
and for good reason. It's NASA, it's about astrobiology, and it's something
big enough to embargo Science. They're just asking for all the alien stories.
And let's be clear, these are not aliens.

~~~
ugh
Holding a press conference for this pretty sweet discovery was completely
justified. The language in the press release made it clear ahead of time that
Nasa didn’t make any discovery related to life on other worlds, only a few
overly eager bloggers spun crazy theories like that.

Whoever is disappointed by this and claims that Nasa hyped too much doesn’t
have her or his head screwed on right.

~~~
joelburget
I agree that it's an amazing discovery. Admittedly I didn't read the actual
press release so you're probably right that they acted correctly. I only read
second hand accounts of what they were going to announce.

------
olalonde
Most theories[1] agree to say that replicating life predates DNA. Wouldn't
that mean that we could still have a common ancestor with this life form?

[1] <http://en.wikipedia.org/wiki/Abiogenesis#Other_models>

~~~
joelburget
We not only could have a common ancestor, it seems to me to be almost certain.
What are the chances that some other life has evolved with DNA completely
independently

~~~
yread
Why do you consider it certain? It could have just died off being much less
efficient than us.

~~~
joelburget
Well, DNA is fairly complex. Of all the elements and compounds life could
involve it seems rather unlikely that DNA evolved in two places completely
separately. Not impossible, but very unlikely.

~~~
dnautics
actually, no. DNA/RNA are in fact, just about the simplest chemical choices
that can perform replication. Ribose, for example is the lowest energy
pentafuranose, which means in a random mix of sugars you'll find ribose in the
highest concentration. The funny thing is that the KSS principle seems to hold
in nature, we've tried in the lab to design alternatives to DNA/RNA, and none
of them seem to work quite so well.

<http://www.sciencemag.org/content/284/5423/2118.short>

~~~
joelburget
Very good point.

------
frisco
This seems silly. Phosphorous not being required for life seems obvious to me:
ok, maybe it's believed to be used in all Earth-originated, carbon-based life,
but why would we believe a priori that it's an absolutely necessary component
of any biological life anywhere (which seems to be what's implied by NASA and
the relation of this to exobiology)? If we develop silicon-based artificial
intelligence (how do you define life, anyway? That matters when you're talking
about astrobiology), would we run a headline, "Researchers prove carbon not
required for life"?

I've always thought the scientific community stated that alien life may use a
totally different biochemistry from us?

Edit: so, in some senses this is like P!=NP being proven, except less
important, since it's only one component (phosphorus). It's scientifically a
big deal but doesn't change the world because it's largely what we've always
expected (the metaphor breaks down that this doesn't have the major secondary
consequences like N=NP would).

~~~
davidsiems
<http://lesswrong.com/lw/im/hindsight_devalues_science/>

~~~
frisco
I don't think this is hindsight bias though. As a scientist (not in
biochemistry or astrobiology, though) I understand this had to be specifically
shown, but this is one of those things that most people I talk to and I have
always just casually treated as obvious. The confirmation is important
scientifically, but shouldn't change our viewpoint, since it's what we've
always expected. Am I wrong here? Any computational biologists or biochemists
want to tell me this wasn't expected at all?

~~~
varjag
You can argue that possibility of alien life is also quite a common idea. Yet
a confirmation of that would be considered a major scientific breakthrough.

~~~
frisco
Yes, I agree here. Slightly stronger because though the possibility of alien
life is entertained, it's not necessarily the common viewpoint that its
widespread and will eventually be found in droves (like I see non-carbon based
life). On the other hand, I expect fully us to be looking back several hundred
years from now wondering how we could have ever thought we were the along
lifeform in the universe. But a major scientific accomplishment it will be
when it's first discovered, for sure.

------
akharris
Two weeks ago: antimatter contained long enough to be studied.

This week: life without phosphorous.

Next week: flying skateboards?

~~~
cryptoz
I think the first artificial, human directed production of antimatter was by
CERN in 1995. I'm not sure what you mean by "two weeks ago", but antimatter
has been around a lot longer than that.

~~~
akharris
Two weeks ago, CERN made the announcement that they had contained antimatter
long enough (at LHC) to study it properly. First time it's ever been done that
well. Pretty stunning accomplishment.

~~~
cryptoz
Ah, right! Thanks

------
gort
If you have access (i.e. from university or whatnot) the actual paper is now
online at:

[http://www.sciencemag.org/content/early/2010/12/01/science.1...](http://www.sciencemag.org/content/early/2010/12/01/science.1197258.full.pdf)

------
vibragiel
"It's not arsenic-based life"

[http://scienceblogs.com/pharyngula/2010/12/its_not_an_arseni...](http://scienceblogs.com/pharyngula/2010/12/its_not_an_arsenic-
based_life.php)

------
bradfordw
It has its own twitter account! <https://twitter.com/#!/ArsenicBacteria>

~~~
cryptoz
s/it's/its

------
TheSOB88
Why people constantly stick to the idea that all possible organisms must have
similar biochemistry to us is beyond me.

Think about it: Out of the humongous search space of chemicals, the ones we
use happened to work for us. A combination of randomness and building on what
worked before got us to where we are. Why should life not be able to use
chemistry in completely different ways in order to replicate itself? Why are
we so arrogant as to think that our design is the only design?

Edit: My point is that our ratio of "shit we know" to "shit we don't know we
don't know" is infinitesimally small in the field of possible lifeforms'
biochemistry. That is, we only know stuff _very_ close to us on a cosmic
scale; we effectively have blinders to all other _possibilities_. And there's
already a lot of biochemical variation on Earth: To give some small examples,
viruses don't even have DNA, and plants use less amino acids than animals.

The self-similarity of what we have so far can be explained, I think, by
evolution. We all started out from the same point, so there's very little
incentive to "reinvent the wheel" as it were. Only under extreme conditions
like we have here, or the geothermal vents underwater, do we observe marked
differences.

~~~
cryptoz
> Why are we so arrogant as to think that our design is the only design?

We're not. Nobody is. The reason scientists don't look for life on other
planets that is made of other chemicals is that _we may not be able to
recognize that as life_. It's much better - read, scientific - to look for
something we can recognize.

Also, there are chemical properties of the elements that make up life on Earth
that allow for fast reactions, bonding, etc. Most of the rest of the elements
in the periodic table react more slowly in normal conditions, making the
process for life less likely. _Not impossible_. Just less likely. We think.

So we focus on looking for what we know about. That's the best way to do it.
Nobody worth their degree will ever claim that our "design" (bad word choice,
by the way) is the only one.

~~~
TheSOB88
I wasn't trying to address any bearing this has on _finding_ alien life, just
speaking theoretically - we shouldn't assume that everything should be like
us. If it hasn't been your experience that most people think that way, then I
must have misjudged.

I agree on the second paragraph, but especially the last sentence.

I know "design" is used by IDers, but what other word can adequately reference
the incredibly complicated way our cells and bodies work?

Thanks for the response.

~~~
foobarbazoo
Use "structure", not "design". As in: "The human body's structure is...", not
"The human body's design is...".

There is no need to use the word "design" to refer to the complexity of the
human body. "Design" implies a creator; "structure" simply describes those
aspects of the human body (or life in general) that makes it "work" and does
not imply a creator.

~~~
ced
So when Google uses A/B testing to improve their design, we should call it
"web structure", not "web design"?

Human minds and evolution are both algorithms.

------
EGreg
Don't mean to get all religious on ya, but I wanted to ask here...

Is there any evidence of macro-evolution having ever taken place in recorded
history? I'm asking this with no agenda, but curious. As far as I know, no new
species have ever been produced, despite natural or unnatural selection.

So what makes us say that there is no other force or process that causes
speciation? How are scientists so convinced that mutation and natural
selection is all that is required, despite never having observed a single
instance of speciation?

To be scientific, a theory has to make some potentially falsifiable, non-
obvious predictions. Then we can test those predictions, and if our
experiments confirm them then the theory survives. I totally agree that the
hypothesis "natural selection occurs" has been proven in ample ways (ok, maybe
the white->dark->white butterflies was a bad one, but bacteria and their
resistance to antibiotics is proof enough). But to form a completely new
species...

Species is defined as "as a group of organisms capable of interbreeding and
producing fertile offspring" according to Wikipedia. Two animals are of
different species if none of their offspring have ever been observed to be
fertile. At least, that's a good working definition.

It bothers me that scientists have been interbreeding literally thousands of
generations of fruit flies and despite all selection pressures, artificial or
not, were never able to produce a single new species. Sure, it's hard to try
and mate every fruit fly with every other fruit fly, so maybe there were
divergent species, but after a few generations, this should have revealed
itself. If this is really the case, then how come we take it for granted that
humans, homo erectus, neanderthals etc. were all divergent species that had a
common ancestor something like 50,000 years ago? Am I way off? If you take the
fruit fly lifetimes and human lifetimes, in those 50,000 years we had about as
many generations as the fruit fly generations. And we got all this speciation
supposedly, using nothing more than mutation and natural selection. But where
is the proof?

I'm not necessary arguing that one of the religions is right and there is
another force. But are scientists being biased here when they simply assume
there isn't any other force? It's as if I was looking at cars from the 1920s
all the way up until now, and I saw gradual change, and based on this I
decided that there was no designer of these cars. I don't think that follows
at all.

Just curious if someone knows links that can resolve this for me :)

~~~
jerf
<http://www.talkorigins.org/faqs/comdesc/>

~~~
EGreg
Yes, I have seen talkorigins before and I use this all the time when people
ask "how do you prove macroevolution"?

Certainly I can prove that macroevolution has taken place, if by that you mean
that natural selection and mutation take place, and that the change is
gradual, and topologically continuous.

"A unique, historical phylogenic tree" -- this pretty much expresses that
idea.

But where in that paper does it talk about actual testable predictions of the
hypothesis: "all speciation came about as a result of mutation and natural
selection with no other factors or forces"?

Each section has a "predictions" section. But notice that even if all these
predictions come true 100% of the time, this does not rule out the possibility
that new species of sexually reproducing organisms are created specially by
God, much like new cars are created by humans, despite there being an
observably continuous change through time.

[http://www.talkorigins.org/faqs/comdesc/section5.html#specia...](http://www.talkorigins.org/faqs/comdesc/section5.html#speciations)

Look at this. We are almost there, to what I am looking for. Are these
"speciation events" fitting the "mating preference" criteria or "cannot
produce fertile offspring" criteria? If the latter, I am satisfied!

~~~
scott_s
_But notice that even if all these predictions come true 100% of the time,
this does not rule out the possibility that new species of sexually
reproducing organisms are created specially by God, much like new cars are
created by humans, despite there being an observably continuous change through
time._

That's just how the scientific method works. If you're looking for certainty,
this isn't where you'll find it. Science can only tell us what we think is
most likely to be true based on what we can observe.

