torsdag 24 februari 2011

Carbon complexity and origin of life.

Carbon is primordial!
We don’t know how diamonds grow. There are diamonds the size of potatoes, but where did they come from?” Hazen said. Diamonds shoot up through the crust from a depth of 100 kilometers “without getting degraded into graphite. It must happen in an hour,” mineralogists believe. “How do fluids move that fast?”

The Hunt For Earth's Missing Carbon the 'most important element' on Earth.

The Deep Carbon Observatory aims to reshape our fundamental understanding of carbon's role in the biology, chemistry, and physics of Earth's interior. Carbon is among the most important chemical elements to humans. It forms the basis of life as we know it, is the central ingredient in many energy sources and plays a key part in our climate. In a planetary-scale machine called the carbon cycle, the element circulates among the oceans and atmosphere, into and out of the Earth's crust, and through living creatures. But even this immense cycle is thought to contain only a small part of total amount of carbon in our planet, with the rest locked deep beneath the surface. The goal of the project is to answer basic science questions, but industry already has its eyes on the research.

Eric Betz, 20.2.11. Inside Science News Service writes:
Deep beneath the surface of the Earth, a vast and unseen community of strange, microscopic lifeforms quietly subsists on the heat rising from our planet's interior.
In its total mass, this life might rival all that walks, crawls, stands, swims and soars above it, but scientists don't know for sure. Life has already been found in the deepest layer of Earth's crust, nearly one mile down, but scientists expect to find life thriving even deeper. Studying mysteries like this one is a task for the Deep Carbon Observatory, a new project that will search out not just life but everything carbon-related that lies beneath our feet.
“Twenty years ago, the idea that there was a deep underground biosphere would have been laughed at, now know there is, because anywhere you drill you find life. We're learning fascinating things about a biosphere that lives in very different conditions than we're familiar with.”

Scientists believe that the subterranean microbes, some of them isolated from Earth's surface since before the dawn of humanity, crucially influence the engines that drive our planet's interior. The microbes process carbon relatively quickly, making them an important step in the carbon cycle.

“Science is not cataloging all the things we know, it's exploring the things we don't know.”
  • Carbon Cycle at Depth, by Katrina Edwards, USC, explains how isotopic evidence indicates that a deep biosphere of microbes both scrubs ocean fluids of organic matter and produces new, yet old, organic carbon in situ.
  • Carbon Below the Sea Floor, by Dave Goldberg, LDEO, explores how basalt sills at young seafloor spreading centers may heat overlying sediments inducing natural carbon release while basalt flows elsewhere may serve to sequester anthropogenic carbon.
  • Bassez, M., Is high-pressure water the cradle of life, J. Phys.: Condens. Mat. 15, L353-L361, 2003.
  • More publications here.
Did deep biochemistry play a central role in life’s origins?
White paper.
Surprising discoveries of deep microbial life in terrestrial and oceanic environments point to a rich subsurface biota that, by some estimates, may rival all surface life in total biomass. Though many key discoveries have been made, we don’t know how life adapts to deep environments, what novel biochemical pathways sustain life at high P-T, or the extreme limits of life. Life holds only a small fraction of Earth’s carbon, yet biological cycling of carbon is relatively rapid.

Microbes are the principal innovators of Earth’s biogeochemical cycles. Their cell numbers in terrestrial and aquatic environments exceed 5 X 10^30 organisms with cellular carbon in excess of 10^17 grams. Yet we know very little about the abundance, distribution, diversity and activity of deep subsurface microbial life. One recent study indicates that deep subsurface life can persist in complete isolation: fixing its own carbon and nitrogen and living in complete indifference to photosynthesis-derived organics and O2. Such discoveries demand a profound recalibration of long-held principles of biology and ecology.
Carbon dynamics.
The dynamics in planet scale is poorly understood. The situation suggests that some very important piece might be missing from the existing models.

Pitkänen, Quantum Astrophysics: The vision about dark matter as a quantum phase with a gigantic Planck constant is an excellent candidate for this missing piece.
The hierarchy of Planck constants is realized by generalizing the notion of imbedding
space such that one has a book like structure with various almost-copies of imbedding space glued together like pages of book. Each page of book correspond to a particular level of dark matter hierarchy and darkness means that there are no Feynman diagrams in which particles with different value of Planck constant would appear. The interactions between di erent levels of hierarchy involve the transfer of the particles mediating the interaction between di erent pages of the book. Physically this means a phase transition changing the value of Planck constant assignable to the particle so that particle's quantum size is scaled. At classical level the interactions correspond to the leakage of magnetic and electric fluxes and radiation fields between di fferent pages of the book.

Quantum cosmology predicts that astrophysical objects do not follow cosmic expansion except in jerk-wise quantum leaps increasing the value of the gravitational Planck constant. This assumption provides explanation for the apparent cosmological constant. Also planets are predicted to expand in this manner. This provides a new version of Expanding Earth theory (R/2) originally postulated to explain the intriguing findings suggesting that continents have once formed a connected continent covering the entire surface of Earth but with radius which was one half of the recent one.
The most modern version of Expanding Earth theory is by Australian geologist Samuel W. Carey. He calculated that in Cambrian period (about 500 million years ago) all continents were stuck together and covered the entire Earth. Deep seas began to evolve then.
Physics and Chemistry of Carbon.
At their September 2010 meeting, the DCO Founders Committee voted to create this fourth directorate to focus on the physics and chemistry of deep carbon and carbon under extreme conditions.

White paper.
One of the main goals of DCO is to understand the present distribution of carbon throughout Earth (core, mantle, and surface) as a result of processes active during planetary accretion and the subsequent thermal and chemical evolution of Earth. During Earth’s formation, volatiles were incorporated by accreting planetesimals. Initially, the growth of small planetesimals did not involve significant heating; toward the end stages of the generation of (possibly mutltiple) magma oceans. The solubility of carbon and other volatiles in the magma ocean and the depth of the magma ocean determine how much carbon remains within the mantle and how much is outgassed to the atmosphere as the magma ocean cools.

It is generally accepted that the origin of methane and related light hydrocarbons found in surface and near-surface reservoirs is due to one of two mechanistic pathways: microbial-based digestion of organic matter or by thermal degradation of organic compounds. This long-held view has been challenged by reports of high-temperature methane-rich fluids venting from sediment-poor mid-ocean ridges, hydrocarbon seepages from terrestrial regions dominated by ultramafic rocks, methane-bearing fluids from Precambrian shields, and fluid inclusions in mantle and igneous rocks. Geochemical indicators, such as CH4/C2H6 + C3H8) ratios, and carbon and hydrogen isotope compositions of methane, heretofore thought to be adequate for distinguishing methane of different origins, have been brought into question for certain hydrocarbon occurrences.

In the context of the carbon cycle the origin and behavior of both oxidized and reduced carbon species are certainly better understood for near-surface reservoirs compared to the deep Earth where the distribution and behavior are poorly constrained. It is clear, however, that a fundamental knowledge of deep Earth carbon is necessary because of its potential impact on geodynamic processes and because of the influence of the deep carbon cycle on surface processes such as secular variations in atmospheric composition and the rate of production of hydrocarbon deposits.

Thermodynamics of Carbon-bearing systems.
A large integrated experimental-theoretical effort is needed to compile reliable thermodynamic data for the (C, H, O, salt) system and the solubility of carbon dissolved as a trace constituent in other phases under the conditions of the deep earth.

To explore the relationship between deep biosphere life and climate.
An improved understanding of the origin and reaction history of methane.
The magnitude of kinetic vs. equilibrium fractionations and effect of T on isotopologues

How does life interact with its environment, by changing the chemistry of fluids, by catalyzing reactions and mineral growth, and by generating or destroying porosity. Production and processing of nanoparticles produced via biochemical pathways. To find a global minimum structure (as might be present in the natural system) requires a search over configuration space. As the number of degrees of freedom grows the problem becomes intractable. The electrons in these materials are often highly correlated and their correct description might require higher level electronic structure calculations and in some cases new theory.

An area important to the understanding of life processes that has not received much attention is the simulation of bioenzyme reaction mechanisms and their effect on the carbon cycle (e.g., RNA self replication in prebiotic systems effects of mineral surfaces, the exoenzymes involved respiration based on iron minerals, etc). There has been impressive progress at the microbiological level (discovering what is happening) but much less progress on the chemical mechanism (why and how these reaction work, e.g., the atomic level biochemical mechanisms). First principles methods have been used in such applications in pharmaceutical drug design research. Similar concepts and calculations can be applied to the analysis of complex biogeochemical processes in extreme environments. The deeper understanding of the enzyme mechanisms obtained should improve the understanding of the chemistry utilized by living systems in extreme conditions of temperature, pressure and under anaerobic conditions. The better understanding of key enzyme reaction would support the development of biomimetric pathways in enhanced energy recovery strategies (e.g., the better understanding of the mechanism of carbonic anhydrase should lead to more efficient CO2 sequestration strategies).

Remarkably little is known about the physical chemistry of carbon in salt water in equilibrium with minerals at pressures of the deep crust and mantle. This is a major knowledge gap closely related also to thermodynamics and kinetics.

Starting with water itself, we need experimental measurements and theoretical calculations of the fundamental properties of water, water-CO2, and water-CH4 mixtures, including in the presence of salt. Specifically the dielectric constant and the dissociation constant of water at pressures greater than 5.0 kbars and at elevated temperatures are needed.

Theoretical and experimental studies of the potential role of metastability in mineral-water-hydrocarbon systems at elevated temperatures and pressures must be undertaken. Methane (like other hydrocarbons) is not thermodynamically stable but merely metastable over a large range of P, T conditions where it is observed or inferred to exist. It is unknown how high in temperature and pressure this metastability and/or kinetically inhibited stability persists. Incorporation of the results obtained above for water into the databases of chemical mass transfer codes would enable quantitative modelling of mineral-water interactions at high T and P. Specifically, the role of the oxygen fugacity fO2 (or hydrogen fugacity fH2) in such systems in influencing the relative metastabilities of different C-bearing species could be addressed.

Similar knowledge deficiencies plague our understanding of carbonate mineral formation and destruction. Carbonate mineral formation is critical to removing and storing carbon in both the shallow Earth (soils, sediment), and the deep Earth. Whether and how carbonates form, and their rates and mechanisms of precipitation and dissolution, all affect how the climate system works over geologic timescales.

There is good evidence that indicates that over geologic time the rates of sediment delivery have changed, controlled by changing tectonic and climatic triggers. What is unknown is whether modern sediments now entering the ocean are typical of the flux over longer periods of time and how much organic carbon has been locked up in these. Transformative understanding of the carbon cycle and the role of deep carbon will depend on our ability to characterize and describe it in terms of complex structures and their reorganization — i.e. interrogation of “dissipative structures.” In particular we need to quantify the consequences of both positive and negative feedback processes on carbon distributions among key reservoirs such as the atmosphere, oceans, continental waters (e.g. rivers, lakes) and the crust.

About carbon/carbomers.

Carbomers have the ability to absorb, retain water and swell to many times their original volume, used as thickening, dispersing (a dispersing agent or a plasticizer is either a non-surface active polymer or a surface-active substance added to a suspension, usually a colloid, to improve the separation of particles and to prevent settling or clumping), suspending and emulsifying agents.
Two representations exist for carbo-benzene. one has the aromatic core of benzene expanded, and one has the hydrogen substituents expanded. The substituted benzene derivative hexaethynylbenzene is a known compound, and the core-expanded molecule also exists, although with the hydrogen atoms replaced by phenyl groups. The final step in its organic synthesis is reaction of the triol with stannous chloride and hydrochloric acid in diethyl ether.

Did intra-terrestrial life burst to the surface of Earth during Cambrian expansion?
Intra-terrestrial hypothesis about the evolution of life is a prediction inTGD. Could the harsh pre-Cambrian conditions have allowed only intra-terrestrial multicellular life? Could the Cambrian explosion correspond to the moment of birth for this life in the very concrete
sense that the magma flow brought it into the day-light? Very many life forms of Cambrian explosion looked like final products of a long evolutionary process. It is quite possible that Earth's mantle contained low temperature water pockets, where the complex life forms might have evolved in an environment shielded from meteoric bombardment and UV radiation.

The vision known as RNA world.
It is assumed that RNA polymers serve all the basic functions associated with DNA, RNA and amino-acids. These functions are based on genetic and catalytic capacity of RNA. Later a genetic takeover occurred involving the emergence of DNA and genetic code in which amino-acids replaced RNA somehow. RNA seems able to serve synthetizing, transfer, messenger and ribosomal functions so that it can guide both its own replication and ordered polymerization of proteins.

King, view of complex systems, the basic mechanisms developed without genetic control and were nally taken under control as the genetic takeover occurred. These kind of generic
structures include proteins and nuclei acids, nucleotide coenzymes, bilayered membrane structures, ion transport and membrane excitability, membrane bound electron transport, glycolysis and the citric acide cycle. In TGD framework one can add to this list topologically quantized classical fields as universal structures. Atoms like C, N, and O and smaller amounts of P and S giving rise to bio-monomers, and metals like Al, Fe, and Zn are the basic building blocks. The formation of various chemical bonds like hydrogen bonds, covalent bonds, and peptide bonds is necessary.
Dr. Cairns-Smith has proposed that so called clay genes appeared as predecessors of genes.

6 kommentarer:

  1. Excellent Post, Ulla

    I recall reading somewhere that the biomass beneath the surface of the earth was much greater than that on the surface.

    Lately we find a bucky ball can behave as methane. And that we can make a gel of them that as a solid acts as a liquid. Surely the chemistry of carbon still holds surprising secrets.

    I like Pitkanen's notions of hierarchy of Planck constants- not sure if that is enough for dark matter candidates resolved. We can ask what the world would be like if the h changed. But what if in such a hierarchy anywhere in it things change? The vision certainly relates to the idea of dark matter as dynamical in the cosmos as part of a unified picture.

    I find it interesting too that the axons can communicate with each other contrary to the usual idea of direction of nerve transfer of information. But surely consciousness, that will arise from such considerations- is deeper and so the storage of unique memory. In many ways the behavior of dimers can indeed originate from clay for clay has such structural events- maybe even the important step of making membranes. This new finding may also shed some light on variations of our mental functioning.

    The structure of a diamond lattice can be inferred on the familiar scale even if we had never seen carbon atoms.

    I was not familiar with the carbomers, thanks.

    I mentioned you today on my post in relation to you insightful questions of the number 8 and the octal bases.


  2. Thanks,
    I was surprised that so much still is unknown about carbon.

    These carbomer-structures show in a beautiful way on the way carbon can act. Hydrogen makes the difference, as methyl-molecules for instance. They regulate the 'swelling' capacities, the growing and expanding. But in an model of the expanding earth (and every other model) nothing is said from where the water has come. The popular notion of watery comets is not sufficient, nor the freeing of 'bound water' in the rocks.

    Has our solar system moved through a water belt on its eternal journey through the space? Can that belt be dark?

    One way to look at it is to compare to the rains (mythical?) during the days of Noi. What happened then? A plausible answer is a disturbance in our atmosphere where was a water belt. Maybe enormous volcanos? But why would water be hanging in our atmosphere and no water be on Earth? Compare to the rings of Saturn. Are those rings an 'circular event' in time, prior to an expansive phase?

  3. The changing Planck constant or an changing alpha is almost the same. If a fundamental constant is changed then everything is changed. It goes invisible and cannot be measured anymore (compare dark matter). If an alpha is changed we hardly notice anything, because we are also changed.

    This question is also closely linked to the asymmetry of matter:antimatter.

    Also closely related to the question of time. And learning, memory. When we look back time is short, when we look forward into future it is an eternity.

  4. If you look at the carbon ring you can see the trigons.


    This transformation has been known about for many years, and occurs because the water wets the particles – in other words, it tends to adhere to the surface of the hydrophilic particles more readily than does the organic liquid and so forms a thin film around them. When two particles get close enough, the water's surface tension then dictates that it becomes energetically favourable for the coatings of water to join up and form a bridge, so binding the particles together and creating a network that makes the suspension more rigid.

    About 600 million years ago,the village of Lantian in central China was covered by an oxygenless ocean. The anoxic Lantian Basin would have been especially lonely, mostly unable to support large, complex, multicellular organisms that require oxygen for respiration.

    But for brief periods, the water in the basin did hold oxygen, a team of U.S. and Chinese scientists now proposes in a paper published on February 16 in Nature. (Scientific American is part of Nature Publishing Group.) In those oxygenated flashes of time seaweeds and what may be algae or worms took hold. They died again when the oxygen dissipated, leaving behind more than 3,000 well-preserved fossils, such as this one preserving a three-centimeter-long seaweed.

    Oxygen gives oxidation and symmetry breaking = decoherence. Cambrian explosion.
    All the basic body plans found in nature today are here: bodies with heads, tails, and appendages, all specialized segments performing specialized functions. All animal evolution for the last half billion years has come from tinkering with these Cambrian body plans.

    For most of the nearly 4 billion years that life has existed on Earth, evolution produced little beyond bacteria, plankton, and multi-celled algae. But beginning about 600 million years ago in the Precambrian, the fossil record speaks of more rapid change. First, there was the rise and fall of mysterious creatures of the Ediacaran fauna, named for the fossil site in Australia where they were first discovered. Some of these animals may have belonged to groups that survive today, but others don't seem at all related to animals we know.

    Then, between about 570 and 530 million years ago, another burst of diversification occurred, with the eventual appearance of the lineages of almost all animals living today. This stunning and unique evolutionary flowering is termed the "Cambrian explosion," taking the name of the geological age in whose early part it occurred. But it was not as rapid as an explosion: the changes seems to have happened in a range of about 30 million years, and some stages took 5 to 10 million years.

    Interpretations of this critical period are subject of lively debate among scientists like Stephen Jay Gould of Harvard University and Simon Conway Morris of Cambridge University. Gould emphasizes the role of chance. He argues that if one could "rerun the tape" of that evolutionary event, a completely different path might have developed and would likely not have included a humanlike creature. Morris, on the other hand, contends that the environment of our planet would have created selection pressures that would likely have produced similar forms of life to those around us -- including humans.