[extropy-chat] volcanic gas- origins of life?

Amara Graps amara at amara.com
Tue Oct 19 11:23:49 UTC 2004


 From hal at finney.org ("Hal Finney"), Mon, 11 Oct 2004:

>Amara Graps writes:
>>  Filling in some parts from what Jeff Davis pointed extropy-chat to:
>>
>>  http://www.eurekalert.org/pub_releases/2004-10/sri-cov100704.php
>>  ...
>  Looking up the paper, to see the abstract and some details:
>>
>>  Science, Vol 306, Issue 5694, 283-286 , 8 October 2004
>>
>  Carbonyl Sulfide-Mediated Prebiotic Formation of Peptides
>>  Luke Leman,1 Leslie Orgel,2 M. Reza Ghadiri1*
>>
>>  ... We show that carbonyl sulfide (COS), a simple
>>  volcanic gas, brings about the formation of peptides from amino acids
>>  under mild conditions in aqueous solution. Depending on the reaction
>>  conditions and additives used, exposure of -amino acids to COS
>>  temperature.

Dear Hal,

I think you might like the following article. It's current, and
it is readable:

--------------------------

J.L. Bada / Earth and Planetary Science Letters 226 (2004) 1-15

How life began on Earth: a status report by Jeffrey L. Bada

Scripps Institution of Oceanography, University of California at San
Diego, La Jolla, CA 92093-0212, United States
Received 7 January 2004; received in revised form 16 July 2004;
accepted 22 July 2004
Editor: A.N. Halliday

Abstract

There are two fundamental requirements for life as we know it, liquid
water and organic polymers, such as nucleic acids and proteins. Water
provides the medium for chemical reactions and the polymers carry out
the central biological functions of replication and catalysis. During
the accretionary phase of the Earth, high surface temperatures would
have made the presence of liquid water and an extensive organic carbon
reservoir unlikely. As the Earth's surface cooled, water and simple
organic compounds, derived from a variety of sources, would have begun
to accumulate. This set the stage for the process of chemical
evolution to begin in which one of the central facets was the
synthesis of biologically important polymers, some of which had a
variety of simple catalytic functions. Increasingly complex
macromolecules were produced and eventually molecules with the ability
to catalyze their own imperfect replication appeared. Thus began the
processes of multiplication, heredity and variation, and this marked
the point of both the origin of life and evolution. Once simple
self-replicating entities originated, they evolved first into the RNA
World and eventually to the DNA/Protein World, which had all the
attributes of modern biology. If the basic components water and
organic polymers were, or are, present on other bodies in our solar
system and beyond, it is reasonable to assume that a similar series of
steps that gave rise of life on Earth could occur elsewhere.

-------------------------------

>It seems strange that only now would people be doing testing to see
>how reactions would occur in the presence of what I gather is a
>relatively common gas in the atmosphere of the early earth. I watched
>the PBS show Origins a few weeks ago, and they were still talking
>about the 1953 Urey-Miller experiment in which an atmosphere thought
>to mimic that of the prebiotic Earth was exposed to a spark gap (meant
>to simulate lightning); after a few days testing showed the presence
>of amino acids.

This is what Bada's article says regarding Miller's experiments:

--------------------

In 1953, Stanley L. Miller demonstrated the ease by which important
biomolecules, such as amino and hydroxy acids, could be synthesized
under what were viewed at the time as plausible primitive Earth
conditions (see [31] for a summary of this classic experiment). A key
aspect of the experiment was the formation of hydrogen cyanide (HCN),
aldehydes and ketones produced during the sparking of the reduced
gases H2 ,CH4 and NH3 . The formation of these reagents suggested that
the compounds were produced by the Strecker-Cyanohydrin reaction,
first discovered in 1850 by the German chemist Adolph Strecker. The
actual synthesis takes place in aqueous solution, implying that on the
early Earth, amino acids could have been produced in bodies of water,
provided the necessary reagents were present. Only a-hydroxy acids are
formed in the absence of ammonia. Thus, the concentration of ammonia
in the primitive oceans would have been critical in determining
whether amino acids would be have been synthesized by this process.

[...] This result strongly suggests that in order for HCN to play a
significant role in prebiotic chemistry on the early Earth,
temperatures at the time must have been cool.
[...]
If the primitive oceans were cool and more acidic than today, the
ammonia would have been mainly dissolved in the ocean present as NH4+.
This implies that even if there was adequate NH4+ dissolved in the
oceans to support prebiotic reactions, the atmospheric ammonia levels
may have been too low to provide for sufficient greenhouse warming to
keep the early Earth's surface temperature above freezing.
[...]
One often-overlooked aspect of the Miller experiment is that the main
product was oily goo. With a methane-rich atmosphere, oily material
would have been produced in huge quantities on the early Earth,
forming an oil slick that would have unimaginable on the Earth today.
Oily material could have formed a protective layer on the primitive
ocean surface that allowed not only for molecules to be protected from
destruction by the sun's ultraviolet light [36], but also may have
helped promote the condensation of simple monomeric compounds into
polymers by acting as an anhydrous solvent [37]. In addition, the oily
layer could have decreased the vapor pressure of water and thus the OH
radical concentration in the atmosphere. As a consequence, the
atmospheric lifetimes of reducing gases, such as methane and ammonia,
could have been substantially increased [37].

Since the classic Miller experiment, numerous researchers have
demonstrated that a large assortment of organic molecules can be
synthesized using a variety of gaseous mixtures and energy sources
(for example, see [38,39]). Most of the molecules that play an
essential role in modern biochemistry, such as amino acids,
nucleobases, sugars, etc., have been synthesized under plausible
geochemical conditions. The conditions employed have ranged from the
highly reducing conditions first used by Miller to less reducing
mixtures containing CO and CO2 [40]. However, with neutral atmospheric
mixtures containing CO2 and N2, the yields of amino acids and other
essential organic compounds is vanishingly low.

Many geoscientists today doubt that the primitive atmosphere had the
highly reducing composition used by Miller in 1953. Although reducing
conditions may not have existed on a global scale, localized high
concentrations of reduced gases may have existed around volcanic
eruptions, especially in hot-spot island-arc systems that may have
been common on the early Earth. Whether reducing volcanic gases would
have been dominant in these systems on the early Earth would depend on
the oxidation state of the early mantle, which could have been more
reducing than today [41]. The localized release of reduced gases by
volcanic eruptions on the early Earth would likely have been
immediately exposed to intense lightning (see Fig. 2), which is
commonly associated with volcanic eruptions today [42,43]. With
present day volcanic gas mixtures, NO is the main product [44], but
with more reducing mixtures containing H2 ,CH4 and N2 , acetylene, HCN
and other prebiotic reagents would have been produced [45]. Thus, in
localized volcanic plumes, prebiotic reagents may have been produced,
which after washing out of the atmosphere could have become involved
in the synthesis of organic molecules. Island-arc systems may have
been particularly important in localized Strecker-type syntheses
because the reagents could have rained out into tidal areas where they
could be concentrated by evaporation or periodic freezing.

--------------------


>The problem is that the gases used in that experiment are no longer
>thought to represent a good model of Earth's atmosphere.

Yes. Bada's article supports this.

The expression: "reducing atmosphere" is one that contains molecules
saturated with hydrogen atoms, which are able to reduce other
molecules. Miller and Urey used in their experiments a mixture of CH4,
NH3, H2  to mimic the early Earth, but many scientists in this area
don't believe that the Earth's atmosphere contain those molecules.
They think instead it was full of oxidants (neutral, not permitting
organic chemistry): CO2 and N2. Bada's writes (above) that there are
some problems with amino acid yields with this kind of atmosphere too,
however.

If you Google-Search on 'reducing atmosphere', you will find more on
this topic.

>That makes the experiments somewhat meaningless as evidence of
>anything other than that amino acids can form in some hypothetical
>conditions that as far as we know never occured anywhere but in that
>experiment.  Yet people still point to this experiment as evidence of
>how life originated.

>Why don't we hear about people running revised versions of that experiment
>with a more accurate mixture of gases, including the one used in this
>experiment, carbonyl sulfide?

I don't know about 'hearing', but my guess is that many experiments
on variations of early atmosphere have been made. (But
this is out of my area a bit, so I don't know)

However, Bada says:
"Since the classic Miller experiment, numerous researchers have
demonstrated that a large assortment of organic molecules can be
synthesized using a variety of gaseous mixtures and energy sources
(for example, see [38,39]). [...] The conditions employed have ranged
from the highly reducing conditions first used by Miller to less
reducing mixtures containing CO and CO2 [40]."


>Is it that there is still too much uncertainty about what was present
>and their relative concentrations?

Perhaps yes, This statement by Bada struck me:

"Whether reducing volcanic gases would have been dominant in these
systems on the early Earth would depend on the oxidation state of the
early mantle, which could have been more reducing than today [41]."

I think that no one is sure what was the exact components of the
early atmosphere, because I don't think that enough is known about
the oxidation state of the early mantle. More on that in my long
addendum below.

>One page I found that sheds some light on this is by Leslie E. Orgel,
>http://www.geocities.com/CapeCanaveral/Lab/2948/orgel.html.  He describes
>Miller's work and then discusses some followups:

>"Since then, workers have subjected many different mixtures of simple
>gases to various energy sources. The results of these experiments can be
>summarized neatly. Under sufficiently reducing conditions, amino acids
>form easily. Conversely, under oxidizing conditions, they do not arise
>at all or do so only in small amounts."
>...
>"Doubt has arisen because recent investigations indicate the earth's
>atmosphere was never as reducing as Urey and Miller presumed. I suspect
>that many organic compounds generated in past studies would have been
>produced even in an atmosphere containing less hydrogen, methane and
>ammonia. Still, it seems prudent to consider other mechanisms for the
>accumulation of the constituents of proteins and nucleic acids in the
>prebiotic soup."

>It seems strange that the question of the effects of today's best
>models of the early atmosphere must be disclaimed with an "I suspect".
>Apparently the work has not been done.

It might have been done, but results were not conclusive, or else
the experiments are very hard to make.

>And now in this new research, someone throws in a new gas and gets a new
>result, the formation of peptides (chains of amino acids).  I can't help
>wondering, what might happen if you put in yet other gases that would
>have been present?  And how meaningful is it to leave out gases that
>might have significant effects?  I realize that it makes the experiment
>easier to have just a few gases, but who knows whether some gas you
>are leaving out of the experiment might totally change the results?

>In general, the quality of work in this area seems to leave much to be
>desired.  Granted, it is an extremely difficult and frustrating problem,
>the origin of life, and perhaps not one that gets much funding.  But it
>surely is of great philosophical interest.  And when you look at how
>much money NASA is spending on Mars probes whose purpose is largely to
>shed light on this area, it would seem easy to spare a few billion for
>Earthly lab experiments, which is probably about a thousand times more
>than is currently being spent.

I think that anyone working in this field would have to be a
multidisciplinary scientist and a specialist at the same time. I don't
see how one can address these questions without having a deep
understanding of geochemistry, microbiology, marine chemistry, and
geophysics.

Another reference that you might like:

book: _Life in the Universe_ by Dirk Schulze-Makuch and Louis Irwin,
Springer-Verlag, 2004. It is a thin book, but with many references so
that the reader can follow up in more detail on any of the topics.

Chapter Headings:

Definition of Life
Lessons from the History of Life
Energy Sources and Life
Building Blocks of Life
Life and the Need for a Solvent
Habitats of Life
Ideas of Exotic Forms of Life
Signatures of Life and the Question of Detection

-----------------------

If you don't mind my diverging on a related topic, this might address
why it looks like progress is slow. I would like to talk a bit on the
largest puzzle today in planetary science: "how did Earth get its
water?" It seems to me that the multidisciplinary aspects of this
question, and the rate of progress parallels that in the area of
emergent life on the prebiotic Earth.

Water is one of the key molecules of life, and a fundamental solvent
of our own human life form. Despite our living embedded in the Earth
environment, the origin of our atmosphere is one of the most puzzling
enigmas in the planetary sciences. The processes and sources that
contributed to its formation require knowledge of the formation of the
solar nebula, Earth and its planetary neighbors, and each of their
subsequent interactions, including the smaller members of the clan:
asteroids, meteorites and comets. Timing and location is everything in
this story and the main tool we have for trying to understand the
puzzle is geochemistry.

Earth has substantially more water than scientists would expect to
find at 1 A.U.  Other compounds and elements also readily vaporize at
Earth's distance. Typical protoplanetary disk models and meteorite
data suggest that the 1 A.U. zone where the Earth formed was too hot
for water to be directly incorporated in local planetesimals. Water
must have been acquired by the Earth from material that formed farther
from the Sun. This puzzle is not new, but it was addressed by A.
Delsemme, who proposed that Earth's water came from comets. Delsemme's
theory was not completely satisfactory, but it provided a working
hypothesis, until spectral measurements of comets Halley, Hyakutake,
and Hale-Bopp, during their near-Earth passes in 1986, 1996 and 1997.
The spectral analysis of the three comets showed that the abundance of
the deuterium isotope of water is twice that found in Earth's water.
Earth's water could not have come all from comets.

What we can consider as today's oceans is essentially liquified early
atmosphere. Planetary atmospheres are an expected consequence of
planetary formation and evolution because gases such as the noble
gases, and nitrogen, water, and carbon dioxide were present in the
solar nebula. When the Earth in its early formation held enough mass
to directly attract gases from the protoplanetary nebula, that initial
inventory of nebular gases eventually became Earth's "first
generation", or "primary", atmosphere. The first generation atmosphere
is a captured solar atmosphere.

But timing is everything. The Earth is melting and cooling as it is
accreting, gaining mass, differentiating, thereby providing favorable
or unfavorable conditions to capture nebular gases and for nebular
gases to dissolve into the rock.  After the core formed, and after
about a 100 million year melting process, the differentiated mantle
formed, which is the driver for the geothermal cycle. Gases that were
dissolved into the rock bubbled to the surface, where they escaped to
space or were held by the gravity to form our atmosphere. When the
Earth cooled enough, clouds formed and a steady rain gave rise to the
oceans. Other processes added to the water, such as the breaking apart
of chemical bonds by light (photolysis), volcanic eruptions, and the
release of gases via geothermal vents.

With a first generation atmosphere assumption, we would expect that
the elemental abundances to match the solar composition. Here begins
one of the puzzles. It doesn't. Measurements of the noble gases in our
present day atmosphere don't match the elemental signatures of the
solar nebula. In addition, the protoplanetary disk models suggest that
the 1 A.U. zone, where the Earth formed, was too hot for water to be
directly incorporated. Therefore, we must consider the possibility
that the Earth's present atmosphere might not be primary, and might be
(at least) Earth's second generation atmosphere, with the water added
after its initial formation. If so, then where could Earth have
acquired its water?

Some new-ish hypotheses for the origin of Earth's water

1)  "Late-veneer Theory Modified"
The starting point is Delsemme's ideas, but now assume that some of
Earth's water still comes from comets, but that water is supplemented
with that from the planetesimals from orbital reservoirs of objects of
the outer asteroid belt.
2)  "Wet-accretion Theory"
The Earth formed 'wet'. In this scenario, the Earth must have accreted
from, and then _entirely depleted_, an ancient supply of water-rich
material located at the same heliocentric distance as the silicate
material that formed the Earth.
3) "One Large Splash" (or the Stochastic Wet-accretion Theory)
The Earth formed not from materials within a narrow band located a
specific distance from the Sun, but from one or a few large (~1000 km
in size) bodies arriving from the outer asteroid belt. This chance
occurrence in the first 50 My of solar system evolution brought the
water and volatiles to the Earth in one large splash, sparing Mercury,
Venus, and Mars.

These theories, especially 3), could solve the puzzle if we are only
concerned with matching the deuterium (D/H) isotopic ratio between
Earth's ocean water and carbonaceous chondrite meteorites. However,
you cannot ignore the noble gases, and the above theories do poorly to
address the questions posed by measurements of the noble gases. By
noble gases, I mean the volatile, unreactive, silicate-incompatible
noble gases helium (He), neon (Ne), argon (Ar), krypton (Kr), and
xenon (Xe). Each of the noble gases give a different story.  Since a
noble gas doesn't react, it cannot be removed easily. The noble gases
trapped in the Earth's silicate mantle give us the best keys for
unlocking the water question because they give information for the
processes and conditions in early Earth history, they constrain how
much of the gases have escaped to the atmosphere over the Earth's
history, and they tell us what remains of the primitive volatile gas
reservoirs within the deep Earth. Obtaining useful isotopic data with
high precision is hard work, though, so progress in isotopic
geochemistry is slow.

In addition, one must have a working, accurate model of the interior
of the Earth in which the gases were stored. From my readings in the
geosciences during the last couple of years, it seems to me that
scientists don't have this working model, anymore, due to better data.
(Google on the words: "Mantle Plumes" to see the controversy) The old
"Standard Model" in geosciences assumes that plumes from the Earth's
core-mantle boundary are able to cross the upper and lower mantle
regions, providing glimpses into the Earth's transition region and
lower mantle, but noble gas isotopic measurements are no longer clear
whether there is an upper mantle and a lower mantle, so it is no
longer clear where exactly are the reservoirs in which the noble gases
are stored.

In addition to the theories being overturned and reworked, progress is
slow because the measurements are difficult. One must be very careful
and precise when collecting geochemical data. One progress I've
noticed in my readings is the most accurate measurements of noble gases
use a method called: "Stepwise heating". In the lab it might look
like this:

Procedure: crushed sample, baked in ultra-high vacuum gas extraction
system and backed at ~120C for ~day. the gases are extracted by a
"resistively-heated Ta furnace" at temps of 600, 800, 900, 1000,
1100, 1200, 1400, and 1600C. For the gas fraction of each temp step,
elemental and isotopic compositions of he, Ne, ar, Kr, and Xe are
analyze by a mass spectrometer.

You cannot contaminate your sample with atmospheric gas, either, or
the sample is meaningless. Of course, atmospheric measurements are
important for gaining the whole picture of noble gas evolution too,
because the atmospheric gases are derived, in part, from outgassing of
the Earth's interior, via volcanoes and other processes.

I separate the questions about the origin of the Earth's water, which
the noble gases can address, in this way:

1. Helium - the 'where'
2. Neon - the 'how'
3. Xenon - the 'when'
4. Argon and Krypton - mix of the 'how and 'when'

1. Helium was one of the first noble gases to be considered by
geochemists in their studies of the processes and conditions in the
formation in the early Earth.  Helium has two stable isotopes: 3He and
4He. The first is considered a primordial isotope, because it has not
been produced in any significant quantities since the Big Bang. The
second, 4He, is constantly being produced, mostly by the decay of
uranium and thorium. The ratio of the two: 3He/4He, in mid-ocean-ridge
basalts (MORBs: samples upper mantle) and ocean-island basalts (OIBs:
samples lower mantle ... maybe) is about eight times the ratio in the
Earth's atmosphere, suggesting that helium in the mantle originated
from an early time in the Earth's formation. Did the two different
basalts originate from different reservoirs in the Earth's interior?
Many geochemists say 'yes'. One idea to explain the helium data is
that a thorough mixing of a dense primary atmosphere with a magma
ocean created a high 3He concentration. Another idea to explain the
data is the accretion of planetesimals buried deep in the mantle that
survived the main degassing during Earth's accretion and are,
therefore, still releasing helium.

2. Neon. If one succeeds in explaining the neon data, then one can
answer, in some detail, how most of Earth's water arrived on Earth.
Isotopic abundances of neon can answer if the solar nebula gas,
including the water, was trapped directly via a magma ocean into the
Earth's mantle, before the solar nebula dispersed. If not this
scenario, then the neon isotopic abundances can demonstrate that a
(small/large) contribution of noble gases arrived later from impacts
of planetesimals.

Data from MORBs and OIBs measurements indicates that solar-like neon
was incorporated into the deep mantle directly from the solar nebula.
However, other neon isotopes are found as well, giving another story
of its history. Planetesimals acquired a "neon-B" isotope at a stage
when the solar nebula gas had dissipated, and the accreting
planetesimals were small (0.1-1 km). Furthermore, the Ne-B identified
implies that solar neon trapped within the Earth has remained
virtually unchanged over the past ~4.5 Ga. This is not the whole story
either, because neon in the atmosphere gives another clue. The
atmospheric neon isotopes show extreme 'fractionation', which is when
the heavier isotopes are enriched relative to the lighter isotopes.
The process that the neon fractionation requires is a gravitational
capture of a primary atmosphere from a dense solar nebula, which is
subsequently lost to space, as the light volatile gases streamed from
the early Earth's atmosphere.

3. Xenon. Xenon measurements can give the 'when' for which the Earth
accreted material, differentiated, and released gas from its interior.
As a dating tool, the nine terrestrial xenon isotopes include products
of 129I and 244Pu, which are called 'extinct radionuclides' because
they were formed by a process of stellar nucleosynthesis prior to the
formation of the solar system, radionuclides which have subsequently
decayed away to zero. The variety of xenon isotopes give investigators
a finer-scaled chronometer because the different radiogenic isotopes
have different half-lives, which can be ratioed in order to determine
specific ages.

Dating results using xenon show a total time scale of 150 million
years for accretion, MORB differentiation, and degassing of the Earth.
Some scientists' model calculations indicate that the mantle started
to partially retain radiogenic and fissiogenic xenon isotopes no later
than 50-70 million years after solar system formed, which is just
after the extraction of the Moon from the young Earth by a giant
impact 4.5 billion years ago. Other xenon measuremnets indicate that
solar nebular-like xenon was incorporated into the Earth's mantle
while it was still forming, and that a mass fractionation event, such
as what is seen in neon, occured later, after the Earth's formation
and its atmosphere. In addition, other xenon measurements suggest a
deeper reservoir of pristine solar nebular-like xenon enriched with
some lighter xenon isotopes feeding the upper mantle. In other words,
this deeper reservoir of primitive noble gases, which are caught in
certain areas of the mantle, are slowly making their way through the
mantle and ultimately into the atmosphere 4.6 billion years later.

I'll skip 4.) for now, because this message is already so long, and it
gives similar answers as 2) and 3).

I hope that I have convinced you of the complexities. It seems that in
answering this simple question: "How did Earth get its water?", more
data gives more questions, and it is clear to me that we don't have
all of the answer yet. At least,  if one were to look at all of the
pieces of the water puzzle, the solution is that we need _all_ of the
available solar system processes running at the time, in order to
bring the water to Earth.

So if the question on how life began is similar in complexity, and
involving many different fields, I am not surprised if progress looks
slow. I would bet that significant progress is made, even if there are
no earth-shattering press releases about it.

Amara

-- 

********************************************************************
Amara Graps, PhD          email: amara at amara.com
Computational Physics     vita:  ftp://ftp.amara.com/pub/resume.txt
Multiplex Answers         URL:   http://www.amara.com/
********************************************************************
"And chase down any of those noble gases or whatever that crud is."
    -- Apollo 12 Astronaut Alan Bean



More information about the extropy-chat mailing list