From the archive, originally posted by: [ spectre ]

EXTREMOPHILES
http://www.resa.net/nasa/extreme_chart.htm
http://www7.nationalacademies.org/ssb/

http://oregonstate.edu/dept/ncs/newsarch/2003/Dec03/bacteria.htm

BACTERIA DISCOVERED IN 4,000 FEET OF ROCK FUELS MARS COMPARISON

12-29-03 By Mark Floyd, 541-737-0788
SOURCE: Martin Fisk, 541-737-5208

CORVALLIS, Ore. – A team of scientists has discovered bacteria in a
hole drilled more than 4,000 feet deep in volcanic rock on the island
of Hawaii near Hilo, in an environment they say could be analogous to
conditions on Mars and other planets.

Bacteria are being discovered in some of Earth’s most inhospitable
places, from miles below the ocean’s surface to deep within Arctic
glaciers. The latest discovery is one of the deepest drill holes in
which scientists have discovered living organisms encased within
volcanic rock, said Martin R. Fisk, a professor in the College of
Oceanic and Atmospheric Sciences at Oregon State University.

Results of the study were published in the December issue of
Geochemistry, Geophysics and Geosystems, a journal published by
the American Geophysical Union and the Geochemical Society.

“We identified the bacteria in a core sample taken at 1,350 meters,”
said Fisk, who is lead author on the article. “We think there could be
bacteria living at the bottom of the hole, some 3,000 meters below the
surface. If microorganisms can live in these kinds of conditions on
Earth, it is conceivable they could exist below the surface on Mars as
well.”

The study was funded by NASA, the Jet Propulsion Laboratory, California
Institute of Technology and Oregon State University, and included
researchers from OSU, JPL, the Kinohi Institute in Pasadena, Calif.,
and the University of Southern California in Los Angeles.

The scientists found the bacteria in core samples retrieved during a
study done through the Hawaii Scientific Drilling Program, a major
scientific undertaking run by the Cal Tech, the University of
California-Berkeley and the University of Hawaii, and funded by the
National Science Foundation.

The 3,000-meter hole began in igneous rock from the Mauna Loa volcano,
and eventually encountered lavas from Mauna Kea at 257 meters below the
surface.

At one thousand meters, the scientists discovered most of the deposits
were fractured basalt glass – or hyaloclastites – which are formed when
lava flowed down the volcano and spilled into the ocean.

“When we looked at some of these hyaloclastite units, we could see they
had been altered and the changes were consistent with rock that has
been ‘eaten’ by microorganisms,” Fisk said.

Proving it was more difficult. Using ultraviolet fluorescence and
resonance Raman spectroscopy, the scientists found the building blocks
for proteins and DNA present within the basalt. They conducted chemical
mapping exercises that showed phosphorus and carbon were enriched at
the boundary zones between clay and basaltic glass – another sign of
bacterial activity.

They then used electron microscopy that revealed tiny (two- to
three-micrometer) spheres that looked like microbes in those same parts
of the rock that contained the DNA and protein building blocks. There
also was a significant difference in the levels of carbon, phosphorous,
chloride and magnesium compared to unoccupied neighboring regions of
basalt.

Finally, they removed DNA from a crushed sample of the rock and found
that it had come from novel types of microorganisms. These unusual
organisms are similar to ones collected from below the sea floor, from
deep-sea hydrothermal vents, and from the deepest part of the ocean –
the Mariana Trench.

“When you put all of those things together,” Fisk said, “it is a very
strong indication of the presence of microorganisms. The evidence also
points to microbes that were living deep in the Earth, and not just
dead microbes that have found their way into the rocks.”

The study is important, researchers say, because it provides scientists
with another theory about where life may be found on other planets.
Microorganisms in subsurface environments on our own planet comprise a
significant fraction of the Earth’s biomass, with estimates ranging
from 5 percent to 50 percent, the researchers point out.

Bacteria also grow in some rather inhospitable places.

Five years ago, in a study published in Science, Fisk and OSU
microbiologist Steve Giovannoni described evidence they uncovered of
rock-eating microbes living nearly a mile beneath the ocean floor. The
microbial fossils they found in miles of core samples came from the
Pacific, Atlantic and Indian oceans. Fisk said he became curious about
the possibility of life after looking at swirling tracks and trails
etched into the basalt.

Basalt rocks have all of the elements for life including carbon,
phosphorous and nitrogen, and need only water to complete the formula.

“Under these conditions, microbes could live beneath any rocky planet,”
Fisk said. “It would be conceivable to find life inside of Mars, within
a moon of Jupiter or Saturn, or even on a comet containing ice crystals
that gets warmed up when the comet passes by the sun.”

Water is a key ingredient, so one key to finding life on other planets
is determining how deep the ground is frozen. Dig down deep enough, the
scientists say, and that’s where you may find life.

Such studies are not simple, said Michael Storrie-Lombardi, executive
director of the Kinohi Institute. They require expertise in
oceanography, astrobiology, geochemistry, microbiology, biochemistry
and spectroscopy.

“The interplay between life and its surrounding environment is
amazingly complex,” Storrie-Lombardi said, “and detecting the
signatures of living systems in Dr. Fisk’s study demanded close
cooperation among scientists in multiple disciplines – and resources
from multiple institutions.

“That same cooperation and communication will be vital as we begin to
search for signs of life below the surface of Mars, or on the
satellites of Jupiter and Saturn.”

CONTACT
Martin Fisk
http://www.coas.oregonstate.edu/faculty/fisk.html
email: mfisk [at] coas [dot] oregonstate [dot] edu

Evidence of biological activity in Hawaiian subsurface basalts
http://www.agu.org/pubs/crossref/2003/2002GC000387.shtml

Abstract

The Hawaii Scientific Drilling Program (HSDP) cored and recovered
igneous rock from the surface to a depth of 3109 m near Hilo, Hawaii.
Much of the deeper parts of the hole is composed of hyaloclastite
(fractured basalt glass that has been cemented in situ with secondary
minerals). Some hyaloclastite units have been altered in a manner
attributed to microorganisms in volcanic rocks. Samples from one such
unit (1336 m to 1404 m below sea level) were examined to test the
hypothesis that the alteration was associated with microorganisms. Deep
ultraviolet native fluorescence and resonance Raman spectroscopy
indicate that nucleic acids and aromatic amino acids are present in
clay inside spherical cavities (vesicles) within basalt glass. Chemical
mapping shows that phosphorus and carbon were enriched at the
boundary between the clay and volcanic glass of the vesicles.
Environmental scanning electron microscopy (ESEM) reveals two to
three micrometer coccoid structures in these same boundaries. ESEM
-linked energy dispersive spectroscopy demonstrated carbon,
phosphorous, chloride, and magnesium in these bodies significantly
differing from unoccupied neighboring regions of basalt. These
observations taken together indicate the presence of microorganisms
at the boundary between primary volcanic glass and secondary clays.
Amino acids and nucleic acids were extracted from bulk samples of
the hyaloclastite unit. Amino acid abundance was low, and if the
amino acids are derived from microorganisms in the rock, then there
are less than 100,000 cells per gram of rock. Most nucleic acid
sequences extracted from the unit were closely related to sequences
of Crenarchaeota collected from the subsurface of the ocean floor.

Received 3 June 2002; accepted 16 October 2003; published 11 December
2003

http://www.pmel.noaa.gov/vents/geology/video_other.html
http://news.nationalgeographic.com/news/2004/04/0422_040422_lavamicrobes.html
http://newsfromrussia.com/science/2004/04/23/53601.html

http://www.astrobio.net/news/modules.php?op=modload&name=News&file=article&sid=2034&mode=thread&order=0&thold=0
http://www.astrobio.net/news/modules.php?op=modload&name=News&file=article&sid=344

Astrobiology Magazine (AM): You’ve said that, in our investigations
of the solar system, you hope we find a completely alien life form.
Could you explain what you mean by that?

Chris McKay (CM): I think one of the key goals for astrobiology should
be the search for life on other planets, and in particular the search
for a second genesis. And by that, I mean life that represents an
independent origin from life on Earth. All life on Earth is related;
all can be mapped onto a single web of life.

If there is a form of life that started separately, it might have some
important differences from Earth life. It might still be DNA-based, but
with a different genome than life on Earth. Or it might not be
DNA-based at all.

Think of Earth life as a book written in English. There’s an
alphabet, there’s words, and there’s a language structure. A book
in Spanish has the same alphabet, but it’s clear that it’s a
different language — there are different words with different
constructions. A book in Hebrew, meanwhile, has a different alphabet. A
book in Chinese doesn’t even have an alphabet. It has a completely
different logic, using symbols to represent ideas or words directly.
All four of those books — English, Spanish, Hebrew and Chinese —
could be about the same topic, and therefore contain the same
information. So at an ecological level they would all be the same, but
they have fundamentally different ways of representing that
information.

In our biology, the alphabet is A, T, C, and G — the letters in the
genetic code. The words are the codons that code for that. It could be
that alien life will have the same alphabet but different words, the
way Spanish is different from English. But it could be something
completely different that doesn’t use DNA, like the Chinese book.

AM: So if we did find a completely different basis for life, what would
we learn from the comparison studies? For instance, could it help us
develop a standard definition for life?

CM: It certainly will contribute to understanding life in a more
general sense. But it may not contribute to a definition. In the end,
we may have a complete understanding of life and still no definition.
There are some things that are like that — for example, fire. We have
a complete understanding of fire, and yet it’s very hard to define it
in such a way that distinguishes between a hot charcoal and a raging
flame and something like the sun. Fire is a process, so it has
different aspects.

Carol Cleland and Chris Chyba have said that defining life is like
trying to define water before the development of modern chemistry.
Once we know what it is — H2O — we’ll have a definition for it. But
there are a lot of things that we understand and can duplicate and
simulate, but we still don’t have a definition for. That’s a
limitation of what a definition is — it tries to categorize things in
a simple way. Some things, like a molecule of water, are ultimately
simple. But a process like fire is not a simple thing, and it resists
being categorized in a simple way.

Life may be that way. Even after we’ve discovered many examples of
it, even after we can reproduce it in the lab and can tie it to
fundamental physical and chemical principles, we may not have a simple
definition.

AM: If there is alien life out there, how could we hope to detect it
with current exploration methods?

CM: We know how to detect Earth-based life, but to detect alien life we
need a more general test. We could use a property of life that I call
the LEGO Principle. Life is made up of certain blocks that are used
over and over again. Life is not just a random collection of molecules.
For example, life on Earth is made up of 20 L-amino acids which form
the proteins, the five nucleotide bases which form RNA and DNA, some
D-sugars which form the polysaccharides, and some lipids which form the
lipid membranes and fatty molecules. So that kit of molecules — the
LEGO kit of Earth — is used to build biomass.

Life has to pick a set of molecules that it likes to use. A random
distribution of organic molecules is going to have a smooth
distribution, statistically-speaking. For instance, for the amino acids
found in meteorites, there are no systematic differences in the
concentrations of L versus D. Certainly in a Miller-Urey experiment, L-
and D-amino acids are produced equally.

But for organic molecules associated with life on Earth, the
distribution is not smooth. Life uses molecules it likes in very high
concentrations, and it doesn’t use the molecules it doesn’t like.
So you’re much more likely to find the L-amino acids on Earth than
their D counterparts. You’re much less likely to find amino acids
that aren’t in that set of 20 that life uses.

I think that test can be generalized if we find organic material on
Mars or on Jupiter’s moon Europa. We can analyze the distribution of
organic molecules, and if they represent a very unusual distribution,
with concentrations of certain molecules, that would be an indication
of biological origin. If the molecules are different than the molecules
of Earth life, then that would be an indication of an alternative
biological system.

AM: Since all the planets in the solar system formed from the same
basic materials, do you think life elsewhere could have the same
preferences and biases as life on Earth?

CM: Certainly the places we’re looking for life — Mars and Europa
— are going to have carbon-based, water-based life, for the reasons
you just said. That’s what those planets are made out of; that’s
what is in those environments. But whether they’re going to be
exactly the same as Earth life at the next level of complexity is, I
think, debatable. By the next level of complexity, I mean how those
carbon atoms arrange to form the basic building blocks.

Some people have argued that there is only one way to do it — that the
fitness landscape of life has a single peak, and no matter where you
start, life is going to climb that peak to the summit. And life
anywhere is going to end up using the same molecules because they’re
the best, most efficient molecules. There’s one best biochemistry,
and we’re it.

Does life always evolve to reach the same fitness peak, or can there be
multiple peaks that different life forms could strive to reach?

That assumes the fitness landscape is just a single peak, like Mount
Fuji. But maybe the landscape is a mountain range with a bunch of
peaks, and the range is not continuous. If you start in one place,
there are only certain fitness peaks that you could reach, and if you
start somewhere else, there’s no way to get over to those peaks
because there’s a zone in-between that’s not a viable biological
system.

We don’t know what the fitness landscape for life looks like. All we
know is that there’s one peak at least that we’re sitting on, but
we don’t see the topography of the whole system. I would argue that
organic chemistry is sufficiently complicated and diverse to have more
than one single, global maximum.

AM: Do you think it might be related to a planet’s environment? That
there might be a peak for Earth, a peak for Mars, a peak for Europa?
That chemical systems will develop and adapt in an optimum way to their
particular environment?

CM: It could be, but I would guess not. I think that as long as the
environment is defined by liquid water, the differences will be just
chance. The molecules that life happened to put together are what
evolutionists call “frozen accidents.”

Life uses L-amino acids, but why not D-amino acids? We don’t think
there’s any selective pressure of L versus D. It’s a trivial
difference. Perhaps life just had to choose one or the other.

It’s like driving, where everybody has to drive on one side of the
road. It really doesn’t matter if everybody drives on the left, like
England, or on the right, like most of the rest of the world. The fact
that England drives on the left and others drive on the right is just a
frozen accident. It would be very hard to change now, but there’s no
fundamental physical reason why they drive on the left and we drive on
the right. It’s a historical artifact.

My guess is that a lot of biochemistry is just a historical artifact.
Where you start off in this biochemical landscape determines where you
end up, and you end up at the optimum near you. Whereas if you start
off, for some reason, someplace differently, you might end up in a
completely different optimum, with a completely different set of
molecules — all operating in water because that’s the medium that
all these environments that we’re looking at have in common. Because
they have water in common, the range of possible environmental
influences, I think, is small.

AM: But if that were true, then why aren’t there multiple unrelated
forms of life on Earth?

CM: I think the answer is because life is a winner-take-all game.
There’s no mercy. If at one time there were many competing forms of
life on Earth, the others were driven to extinction because life is
competing at a system level for resources — physical space,
sunlight, nutrients, and so on.

As long as different species have different ecological space, they
don’t compete directly. But species that directly compete face an
unstable situation. If there’s a complete overlap on their needs and
requirements, then one will win and one will lose. For an entire system
of life, the requirements are energy, nutrients, and space. Since those
are exactly the same requirements of an alternative system, there’s a
hundred percent competition.

Now, that doesn’t prove that alternate life forms couldn’t be here.
There’s been some speculation that there might be a shadow biosphere
on Earth, and some people are trying to find traces of that. But so
far, they’ve found nothing.