Monday, August 8, 2011

The Abiogenesis of Petrol and Life

updated July 29, 2015

Iceworms (Hesiocaeca methanicola) infest a solid piece of orange methane ice at 540m depth in the Gulf of Mexico.
Photo by Ian MacDonald.

Ice shrimp congregate beneath the overhang that caps the methane hydrate.
Photo courtesy of WHOI.

The cartoon version of petroleum origin on Earth:
"In the geologic past, conditions have periodically recurred
in which vast amounts of organic matter
were preserved within the sediment of shallow, inland seas."
U.S. Dept. of Energy

The realistic version of petroleum
origin on Titan:

"The methane giving an orange hue to Saturn's giant moon Titan likely comes from geologic processes in its interior according to measurements from the Gas Chromatograph Mass Spectrometer (GCMS), a Goddard Space Flight Center instrument aboard the European Space Agency's Huygens Probe."
-Titan's Mysterious Methane Comes From Inside, Not The Surface
Goddard Space Flight Center, 2005

1. The enthalpy problem with fossil origin

Proceedings of the National Academy of Sciences of the United States of America
"The spontaneous genesis of hydrocarbons that comprise natural petroleum have been analyzed by chemical thermodynamic-stability theory. The constraints imposed on chemical evolution by the second law of thermodynamics are briefly reviewed, and the effective prohibition of transformation, in the regime of temperatures and pressures characteristic of the near-surface crust of the Earth, of biological molecules into hydrocarbon molecules heavier than methane is recognized.
For the theoretical analysis of this phenomenon, a general, first-principles equation of state has been developed by extending scaled particle theory and by using the technique of the factored partition function of the simplified perturbed hard-chain theory. The chemical potentials and the respective thermodynamic Affinity have been calculated for typical components of the H–C system over a range of pressures between 1 and 100 kbar (1 kbar = 100 MPa) and at temperatures consistent with those of the depths of the Earth at such pressures.
The theoretical analyses establish that the normal alkanes, the homologous hydrocarbon group of lowest chemical potential, evolve only at pressures greater than ≈30 kbar, excepting only the lightest, methane.
The pressure of 30 kbar corresponds to depths of ≈100 km. For experimental verification of the predictions of the theoretical analysis, a special high-pressure apparatus has been designed that permits investigations
at pressures to 50 kbar and temperatures to 1,500°C and also allows rapid cooling while maintaining high pressures.
The high-pressure genesis of petroleum hydrocarbons has been demonstrated using only the reagents solid iron oxide, FeO, and marble, CaCO3, 99.9% pure and wet with triple-distilled water. "
The evolution of multicomponent systems at high pressures: VI. The thermodynamic stability of the hydrogen–carbon system: The genesis of hydrocarbons and the origin of petroleum
--J. F. Kenney , Vladimir A. Kutcherov, Nikolai A. Bendeliani, and Vladimir A. Alekseev

"The capital fact to note is that petroleum was born in the depths of the earth, and it is only there that we must seek its origin."
--Dmitri Ivanovitch Mendeléev, 1877

2. The biological problem with fossil origin

E V O L U T I O N. In the beginning:
Simple cells emerge from prebiotic organic chemistry around 4 billion years ago. Photosynthesis evolves around a billion years later, with chemosynthesis supporting the first billion years of carbon-based life.

Petroleum Chemosynthesis--ubiquity and antiquity:

First reports on methane-oxidizing bacteria (methanotrophs), Kaserer (1905) and Söhngen (1906):
"Evidently, the discoverers of methanotrophic bacteria , Kaserer and Söhngen, could scarcely have imagined the importance of these bacteria or their ubiquity in nature. Furthermore, few microbiologists followed up the discovery of methanotrophs over the next 50 years and the cultures of methanotrophs were apparently lost."
--Advances in Applied Microbiology, Allen I. Laskin, Geoffrey M. Gadd, Sima Sariaslani - 2008

Science,  20 July 2001:
Vol. 293 no. 5529 pp. 418-419
DOI: 10.1126/science.293.5529.418
'Inconceivable' Bugs Eat Methane on the Ocean Floor
Most of the methane that rises toward the surface of the ocean floor vanishes before it even reaches the water. On page 484 of this issue, a team of researchers provides the clinching evidence for where all that methane goes: It is devoured by vast hordes of mud-dwelling microbes that belong to a previously unknown species of archaea. These methane-eating microbes--once thought to be impossible--now look to be profoundly important to the planet's carbon cycle.

Discovery of Viable Methanotrophic Bacteria in Permafrost Sediments of Northeast Siberia
V. N. Khmelenina, V. A. Makutina, M. G. Kalyuzhnaya, E. M. Rivkina, D. A. Gilichinsky and Yu. A. Trotsenko, 2008

Methane oxidation in Lake Tanganyika
"Methane is oxidized in lakes by a group of bacteria that convert methane and oxygen to cellular material and carbon dioxide" -John W.M. Rudd, 1980

Methane Devourer Discovered In The Arctic
ScienceDaily (Oct. 20, 2006) — Not lava, but muds and methane are emitted from the Arctic deep-water mud volcano Haakon Mosby. When it reaches the atmosphere, methane is an aggressive greenhouse gas, 25-times more potent than carbon dioxide. Fortunately, some specialised microorganisms feed on methane and thereby reduce emissions of this greenhouse gas. For the first time, a German-French research team showed which methane consuming microorganisms thrive in the ice-cold Arctic deep-sea.
[...]The mud volcano covers an area of a about 1 square km and is located at a water depth of 1250 m. The centre emits muds, water and methane that rise from a depth of about 2 km below the mud volcano. Helge Niemann and Tina Lösekann from the Max Planck Institute for Marine Microbiology in Bremen, Germany investigated in their PhD thesis which methanotrophic microorganisms could thrive in the -1°C cold Arctic deep-sea.
Haakon Mosby is a rather flat mud volcano rising only 10 m above the ocean floor. Visual inspection by the German and French researchers distinguished three distinct concentric ring-shaped zones: the centre, surrounded by a zone covered with sulphur bacteria and then the outer rim inhabited by tubeworms.
Although these habitats differ, methane is the primary food source for most microorganisms thriving in the ocean floor. At the surface of the centre, the scientists discovered formerly unknown bacteria that use oxygen to feed on methane. In sediment layers below the sulphur bacteria, Helge Niemann and Tina Lösekann found a new group of methane-consuming Archaea that live in symbiosis with bacteria. This community does not use oxygen but sulphate to oxidize methane. This process is called the anaerobic oxidation of methane (AOM) and is investigated in the research project MUMM. To their surprise, the scientists discovered that the majority of methane is consumed in the tubeworm habitat and not in the centre.

A chemotrophic ecosystem found beneath Antarctic Ice Shelf
Eugene Domack, Department of Geosciences, Hamilton College, Clinton, N.Y.
Scott Ishman, Department of Geology, Southern Illinois University, Carbondale
Amy Leventer, Department of Geology Colgate University, Hamilton, N.Y.
Sean Sylva, Woods Hole Oceanographic Institution, Mass.
Veronica Willmott, Department of Stratigraphy Paleontology and Marine Geosciences, University of Barcelona, Spain
Bruce Huber, Lamont-Doherty Earth Observatory, Palisades, N.Y.

A new habitat for chemotrophic ecosystems has been found beneath the former extent of the Larsen Ice Shelf in Antarctica. This is the first report of such ecosystems in the Antarctic. (Chemotrophic ecosystems derive their primary metabolic energy from chemical reactions other than those of photosynthetic origin.)

An association of microbial mats and cold seep clam communities, is described, that thrived within an 850-m-deep glacial trough some 100 km, or more, from the ice shelf front. However, the continued existence of this unique ecosystem is uncertain, given the increased loading of sediment to the seafloor as a result of the ice shelf's collapse in early 2002. The vent-related ecology could have a methane source, based upon the vent's similarity with other cold seeps located along continental margins.

When Seafloor Meets Ocean, the Chemistry Is Amazing
In more and more places, scientists are finding large amounts of natural gas on the ocean bottom
Jean K. Whelan, Senior Research Specialist
Marine Chemistry and Geochemistry Dept.
Woods Hole Oceanographic Institution
February 13, 2004
Source: Oceanus Magazine

Far more natural gas is sequestered on the seafloor—or leaking from it—than can be drilled from all the existing wells on Earth. The ocean floor is teeming with methane, the same gas that fuels our homes and our economy.
In some places, seeping methane sustains thriving communities of exotic organisms that harness the gas as an energy source in their sunless environment. Below the seafloor, an unknown but potentially vast biosphere of microbes may be making the methane that percolates upward.
Woods Hole Oceanic Institution

Methane seeping from the seafloor sustains microbes that serve as the base of the food chain for communities of animals, like these tubeworms, which thrive in the sunless depths. (High-definition images copyright Woods Hole Oceanographic Institution and the BBC Natural History Unit, courtesy of the WHOI Advanced Imaging and Visualization Laboratory and Johnson-Sea-Link submersible, Harbor Branch Oceanographic Institution.)

Life discovered in deepest layer of Earth’s crust
November 19, 2010

"… One key difference was that archaea were absent in the gabbroic layer. Also, genetic analysis revealed that unlike their upstairs neighbours, many of the gabbroic bugs had evolved to feed off hydrocarbons like methane and benzene. This could mean that the bacteria migrated down from shallower regions rather than evolving inside the crust.
"This deep biosphere is a very important discovery," said Rolf Pedersen of the University of Bergen, Norway. He added that the reactions that produce oil and gas abiotically inside the crust could occur in the mantle, meaning life may be thriving deeper yet.

Microorganisms living in anoxic marine sediments consume more than 80% of the methane produced in the world's oceans. In addition to single-species aggregates, consortia of metabolically interdependent bacteria and archaea are found in methane-rich sediments. A combination of fluorescence in situ hybridization and secondary ion mass spectrometry shows that cells belonging to one specific archaeal group associated with the Methanosarcinales were all highly depleted in 13C (to values of –96‰). This depletion indicates assimilation of isotopically light methane into specific archaeal cells. Additional microbial species apparently use other carbon sources, as indicated by significantly higher 13C/12C ratios in their cell carbon. Our results demonstrate the feasibility of simultaneous determination of the identity and the metabolic activity of naturally occurring microorganisms.

Deep Sea Methane Scavengers Captured
ScienceDaily (May 16, 2008)
Scientists of the Helmholtz Centre for Environmental Research (UFZ) in Leipzig and the California Institute of Technology (Caltech) in Pasadena succeeded in capturing syntrophic (means "feeding together") microorganisms that are known to dramatically reduce the oceanic emission of methane into the atmosphere. These microorganisms that oxidize methane anaerobically are an important component of the global carbon cycle and a major sink for methane on Earth. Methane - a more than 20 times stronger greenhouse gas than carbon dioxide - constantly seeps out large methane hydrate reservoirs in the ocean floors, but 80 percent of it are immediately consumed by these microorganisms.
The importance of the anaerobic oxidation of methane for the Earth’s climate is known since 1999 and various international research groups work on isolating the responsible microorganisms, so far with little success. [...]
Microorganisms are the unseen majority on our planet: There are more than 100 Million times more microbial cells than stars in the visible universe, accounting for more than 90 percent of the Earth's biomass.

Anaerobic oxidation of methane (AOM) is a microbial process occurring mainly in anoxic marine sediments. During AOM methane is oxidized with sulfate as the terminal electron acceptor:
CH4 + SO42- → HCO3- + HS- + H2O

Marine microorganisms make a meal of oil.
Head IM, Jones DM, Röling WF.
School of Civil Engineering and Geosciences, University of Newcastle upon Tyne, Newcastle upon Tyne NE1 7RU, UK.

Hundreds of millions of litres of petroleum enter the environment from both natural and anthropogenic sources every year. The input from natural marine oil seeps alone would be enough to cover all of the world's oceans in a layer of oil 20 molecules thick. That the globe is not swamped with oil is testament to the efficiency and versatility of the networks of microorganisms that degrade hydrocarbons, some of which have recently begun to reveal the secrets of when and how they exploit hydrocarbons as a source of carbon and energy.
PMID: 16489346 [PubMed - indexed for MEDLINE]

3. Serpentinisation

...hydrothermal activity at Lost City is driven by chemical reactions between seawater and mantle rocks that make up the underlying basement. [...]
The formation of magnetite during the serpentinization process involves the oxidation of ferrous iron (Fe2+) in olivine to form ferric iron (Fe3+) in magnetite and leads to what is called reducing conditions. As a consequence, reduced gas species, such as hydrogen gas (H2), methane (CH4) and hydrogen sulfide (H2S), can be produced during serpentinization. These dissolved gas species provide important energy sources for microbial activity at Lost City. Thus, the basement rocks and the porous Lost City structures that are bathed volatile-rich, highly alkaline fluids create vital niches for life.
The gases produced at Lost City, the organisms that thrive in them and the long-lived nature of this serpentinite-driven system are very distinct from black-smoker hydrothermal vents and may represent a modern analog for some of the oldest hydrothermal systems on Earth. Thus, understanding this system may provide important new insights for studying early life on Earth as well as for looking for signs of life on other planets.

4. Comet Halley

Some comets contain "massive amounts of an organic material almost identical to high grade oil shale (kerogen)," the equivalent of cubic kilometers of such* mixed with other material; for instance, corresponding hydrocarbons were detected during a probe fly-by through the tail of Comet Halley in 1986.
--Dr. A. Zuppero, U.S. Department of Energy, Idaho National Engineering Laboratory. Discovery Of Water Ice Nearly Everywhere In The Solar System
--Huebner, Walter F.(Ed) (1990). Physics and Chemistry of Comets. Springer-Verlag.
* "its hydrocarbon content may exceed 500 years of OPEC output" - Zuppero.

5. Titan

According to Cassini data, scientists announced on February 13, 2008, that Titan hosts within its polar lakes "hundreds of times more natural gas and other liquid hydrocarbons than all the known oil and natural gas reserves on Earth." The desert sand dunes along the equator, while devoid of open liquid, nonetheless hold more organics than all of Earth's coal reserves.
On May 12, 2007, Cassini completed its 31st flyby of Saturn's moon Titan, which the team calls T30. The radar instrument obtained this image showing the coastline and numerous island groups of a portion of a large sea, consistent with the larger sea seen by the Cassini imaging instrument (see Like other bodies of liquid seen on Titan, this feature reveals channels, islands, bays, and other features typical of terrestrial coastlines, and the liquid, most likely a combination of methane and ethane, appears very dark to the radar instrument.

Solving the puzzles of Saturn and Titan
Titan was also observed by the two Voyagers, as well as other telescopes. Both spacecraft could observe its mysterious orange atmosphere, rich in nitrogen, methane and other organic compounds. ESA’s Infrared Space Observatory found out in 1998 the presence of water vapour in Titan’s atmosphere. Basically Titan exhibits many similarities to conditions that may well once have prevailed on Earth.

Titan, Saturn's largest moon, is a mysterious place. Its thick atmosphere is rich in organic compounds. Some of them would be signs of life if they were on our planet.

Explanation: This color view from Titan gazes across a suddenly familiar but distant landscape on Saturn's largest moon. The scene was recorded by ESA's Huygens probe after a 2 1/2 hour descent through a thick atmosphere of nitrogen laced with methane. Bathed in an eerie orange light at ground level, rocks strewn about the scene could well be composed of water and hydrocarbons frozen solid at an inhospitable temperature of - 179 degrees C. The light-toned rock below and left of center is only about 15 centimeters across and lies 85 centimeters away. Touching down at 4.5 meters per second (16 kilometers per hour), the saucer-shaped probe is believed to have penetrated 15 centimeters or so into a surface with the consistency of wet sand or clay. Huygen's batteries are now exhausted but the probe transmitted data for more than 90 minutes after landing. Titan's bizarre chemical environment may bear similarities to planet Earth's before life evolved.
NASA - Astronomy Picture of the Day, 2005 January 17

Titan's Methane Not Produced by Life, Scientists Say
Melissa Eddy, Associated Press Writer, January 2005

FRANKFURT, Germany (AP) -- Saturn's largest moon contains all the ingredients for life, but senior scientists studying data from a European probe ruled out the possibility Titan's abundant methane stems from living organisms.
More than a week after the Huygens probe plunged through Titan's atmosphere, researchers continue to pore over data collected for clues to how the only celestial body known to have a significant atmosphere other than Earth came to be and whether it can provide clues to how life arose here. [...]
"This methane cannot be coming from living organisms," Jean-Pierre Lebreton, mission manager for the Huygens probe that landed on the surface of Titan Jan. 14, told The Associated Press on Wednesday.
[...] unlike water in the Earth's atmosphere that continually renews itself, methane is destroyed by ultraviolet light, so Titan must have a source deep inside, scientists said.
Based on data collected by Huygens' instruments, Sushil Atreya, a professor of planetary science at the University of Michigan in the United States, believes a hydro-geological process between water and rocks deep inside the moon could be producing the methane."I think the process is quite likely in the interior of Titan," Atreya said in a telephone interview.
The process is called serpentinisation and is basically the reaction between water and rocks at 100 to 400 degrees Celsius (212 to 752 degrees Fahrenheit), he said.

"Titan is a planet-sized hydrocarbon factory. Instead of water, vast quantities of organic chemicals rain down on the moon‘s surface, pooling in huge reservoirs of liquid methane and ethane. Solid carbon-based molecules are also present in the dune region around the equator, dwarfing Earth’s total coal supplies."
universe today

Gulf of Mexico's Methane Not Produced by Life, David Attenborough Says:


Earth is also a planet-sized hydrocarbon factory, producing underground oceans of the stuff, seemingly inexhaustible oil wells in Saudi Arabia, hydrocarbon rain under the Gulf of Mexico, ocean floors littered with vast tracts of methane hydrates, vast oil-shale deposits, oils sands, tar sands, coal seams, oil wells that spontaneously refill after being squeezed “dry,” and natural gas that percolates up from below the dune regions surrounding the Caspian:

(a 35 year old methane fire, Turkmenistan)

The principle of parsimony cautions against introducing unnecessary explanatory entities: Titan proves that fossils are an unnecessary entity in the explanation for Earth's hydrocarbons. Fossils are the cart before the horse; the saber-tooth preserved in the tar-pit; the bryzoan preserved in oil shale; the post hoc fallacy in fossil fuel "reasoning."
Abiotic petroleum is supported by mountains of geological evidence, by proof of principle in the laboratory, and by compliance with thermodynamic constraints (fossil theory violates the 2nd law of thermodynamics). Abiotic petroleum theory accounts not only for the extraordinary abundance of hydrocarbons here, but also on Titan.
Abiotic theory is fitting, predictive, universal, parsimonious, and requires no special pleadings (e.g., "some of them would be signs of life if they were on our planet")
  1. The fossil theory for Earth's hydrocarbon species is a western cartoon, the geological theory for Titan's hydrocarbon species--the reaction between water and rocks at high pressure-temperature-- is in contrast reasonable and reproducible.
  2. Accumulation of methane in the sediments is rendered improbable by the ubiquity of aerobic and anaerobic chemosynthetic archaea and bacteria that thrive on a variety of hydrocarbons, not limited to methane.
  3. Petroleum is feedstock for primary producers in a variety of marine ecosystems.
  4. Petroleum abundance more than likely preceded evolution and fossils
  5. Life on Earth likely emerged from prebiotic molecules mostly derived from petroleum.

Fossils preserved in oil shale, not converted to oil:


Fossils preserved in a tar pit, not converted to tar:

(La Brea tar pits)

Life produced from hydrocarbons, not converted to hydrocarbons:

This group of very old tubeworms (Lamellibrachia luymesi and Seepiophila jonesi) live on the same piece of carbonate rock as large colonies of the gorgonian Callogorgia Americana americana. Note the brittle stars and a galatheid crab crawling on the gorgonians.
Photo by Derk Bergquist.

Seafloor blanket of chemosynthetic communities on a methane hydrate-associated mound on the seafloor in the Santa Monica Basin. The white and orange microbial mats contain aerobic methanotrophs along with other chemosynthetic bacteria. The space between the mats is crowded with clams. Photo courtesy of Monica Heintz.

This ROV image shows a typical methane seep with white mats of bacteria ringed by
seep clams. In this case, several sea stars and fish seem to have claimed the high
ground at the top of the mound. Exactly how such mounds form is one of the main questions we are trying to answer on this cruise.

A close up of a group of Bathymodiolin mussels from a methane seep. These mussels
have the ability to harbor both sulfide-oxidizing as well as methanotrophic bacterial
symbionts within their gills. Photo courtesy of CRROCKS/NSF.

These methane mussels (Bathymodiolus childressi) live at the edge of Brine Pool NR1
at 650 m depth in the Gulf of Mexico. The pool of brine in the foreground is nearly
four times as salty as seawater and is so dense that the submarine can float on the
pool to take pictures such as this. Photo by Stephane Hourdez.

Addendum - Phylogeny

Beating the acetyl coenzyme A-pathway to the origin of life
(Published 10 June 2013)
Wolfgang Nitschke and Michael J. Russell


Attempts to draft plausible scenarios for the origin of life have in the past mainly built upon palaeogeochemical boundary conditions while, as detailed in a companion article in this issue, frequently neglecting to comply with fundamental thermodynamic laws. Even if demands from both palaeogeochemistry and thermodynamics are respected, then a plethora of strongly differing models are still conceivable. Although we have no guarantee that life at its origin necessarily resembled biology in extant organisms, we consider that the only empirical way to deduce how life may have emerged is by taking the stance of assuming continuity of biology from its inception to the present day. Building upon this conviction, we have assessed extant types of energy and carbon metabolism for their appropriateness to conditions probably pertaining in those settings of the Hadean planet that fulfil the thermodynamic requirements for life to come into being. Wood–Ljungdahl (WL) pathways leading to acetyl CoA formation are excellent candidates for such primordial metabolism. Based on a review of our present understanding of the biochemistry and biophysics of acetogenic, methanogenic and methanotrophic pathways and on a phylogenetic analysis of involved enzymes, we propose that a variant of modern methanotrophy is more likely than traditional WL systems to date back to the origin of life. The proposed model furthermore better fits basic thermodynamic demands and palaeogeochemical conditions suggested by recent results from extant alkaline hydrothermal seeps.


Abiotic condensation synthesis of glyceride lipids and wax esters under simulated hydrothermal conditions.
(Orig Life Evol Biosph. 2006 Apr;36(2):93-108. Epub 2006 Apr 27.)

"The results indicate that condensation reactions and abiotic synthesis of organic lipid compounds under hydrothermal conditions occur easily, provided precursor concentrations are sufficiently high."

primary resources for research, images and video (credits):
Leon Carter 2015