Origin of Life

In the Beginning was Abiogenesis

2008-12-31T23:59:00.000-11:00

In current biological terminology "abiogenesis" refers to the emergence of life as self-replicating assemblages of organic chemicals able to control chemical energy from non-life assemblages of chemicals. This is the hypothesis that primordial life originated within the first billion years of Earth's history as a result of chemical reactions that generated larger and larger organic polymers, which ultimately attained control of bioenergetics and the property of chemical self-replication. This modern conceptualization is reasonable in view of what is now known of the biochemical basis of all life.

The modern conceptualization replaces earlier notions of "spontaneous generation" that viewed life as arising fully formed from non-living matter, or de novo. Such Aristotelian notions of archebiosis probably arose because much of life exists at the microscopic level of prokaryotes and unicellular eukaryotes, and because some organisms living on detritus reach visible proportions after having been of microscopic size.

The term 'life' in relation to abiogenesis embraces the notion of utilization of energy sources and biochemical self-replication. This requires that an assembly of molecules and macromolecules acquired the ability to convert energy into growth and that informational macromolecules directed self-replication.

The processes that led from inorganic chemicals to the panoply of organic, carbon-based chemicals in primordial cells would have been governed by the non-random physical laws of chemistry, specifically those physical properties related to organic molecules. Since the processes involved would be widespread across the primordial planet, enormous numbers of molecules and macromolecules would have been generated in the first 10 billion years of Earth history. Because modern cells contain only L-amino acids, it is believed that a single primitive cell line, the universal cenancestor is the ancestor of all living cells. According to most theorists, conditions on Earth are no longer suitable for abiogenesis to occur. Unfavorable conditions apply because oxygen is 'toxic' to molecules.

The elucidation of abiogenetic mechanisms would be of enormous interest, yet this has not been a particularly active area of research because it has limited applications. The advent of space exploration has infused life into Astrobiology and the search for the Origin of Life.

The lack of a full scientific explication for abiogenesis does not mean that chemical evolution was not the origin of life. Rather, the difficulty in deciding between theoretical scenarios reflects difficulties in recreating conditions and the impossibility of recreating the time frame for biopoiesis. Certainly, biopoiesis is a much better explanation than the God of the Gaps, which is merely simplistic magic-thinking.

From NASA's Astrobiology Institute
Spitzer Telecope Data Suggest that Life's Building Blocks are Abundant
Finding Life in Mars Analog Sites on Earth
More on Astrobiology:
Evolution and Ecology Beyond the Planet of Origin
Evolution and Development Workshop
Evolution and Ecology Beyond the Planet of Origin
Evolution and Development Workshop
New York Center for Studies on the Origins of Life Ad Astra Magazine: Astrobiology Issue (January/February 1999)
The Astrobiology Web
Free audio on WAMC's Origins of Life Segments
Origins on Abiogenesis
Recommended on the Talk Origins Archive:
Lies, Damned Lies, Statistics, and Probability of Abiogenesis Calculations
Borel's Law and the Origin of Many Creationist Probability Assertions
Spontaneous Generation and the Origin of Life

What Is Life?

2008-12-31T23:58:00.000-11:00

What are the minimal descriptors of life – when do we decide that a collection of chemicals has crossed the line to that of inhering life processes?

The minimal essential features are compartmentalization, self-reproducibility, incorporation of energy controls, and adaptability to the environment. The essential features of biochemical systems include compartmentalization, genetic programming, and enzyme systems that both adapt to the environment (including feedback controls) and utilize or defy energy (generation of products in excess of non-enzymatic equilibria). In other words, if we put the most basic chemical constituents into a flask, we would not have life processes unless we also had the essential features listed above.

Compartmentalization within lipid-bilayer membranes permits seclusional selectivity and chemical control of reactants and products. Compartmentalization also permits the localization of energy storage/utilization, and the control of translation of genetic instruction. Further, membrane-bound systems control internal responses to the external environment. Self-reproducibility – regeneration – utilizes genetic programming. Molecular programming likely first utilized RNA, and later evolved DNA as a more stable system for storage of instructions.

PLoS Biology: What Is Life--and How Do We Search for It in Other Worlds?: " Koshland (2002) lists seven features of life: (1) program (DNA), (2) improvisation (response to environment), (3) compartmentalization, (4) energy, (5) regeneration, (6) adaptability, and (7) seclusion (chemical control and selectivity). A simpler definition is that life is a material system that undergoes reproduction, mutation, and natural selection. Cleland and Chyba (2002) have suggested that life might be like water, hard to define phenomenologically, but easy to define at the fundamental level. But life is like fire, not water--it is a process, not a pure substance. Such definitions are grist for philosophical discussion, but they neither inform biological research nor provide a basis for the search for life on other worlds."

Universal cenancestor

2008-12-31T23:57:00.000-11:00

The universal cenancestor is hypothesized as being at the ancestral root of all living organisms. Not the earliest or simplest living organism, and not necessarily the sole example of its type, this organism possessed the genetic material that diverged (about 3.5 Ga) into all current living organisms.

A number of terms are employed to refer to the universal cenancestor – last universal ancestor (LUA), last common ancestor (LCA), or last universal common ancestor (LUCA).

Origin of Life and Early Life on Earth

2008-12-31T23:50:00.000-11:00

Thematic Issue: Origin of Life and Early Life on Earth
1. Origin of Life on Earth: Prebiotic Synthesis
2. Continental Crust and Oceans on Ancient Earth.
3. On Carbon Monoxide in Comet Hale-Bopp.
4. On the Earliest Traces of Life on Earth.
5. On Earth's Earliest Fossils.
6. On the Evidence for Earth's Oldest Fossils.
7. On the Akilia Rocks and Earth's Earliest Life.
8. Early Earth: Carbonaceous Meteorites as a Source of Sugars
9. On the Origin of the Earth.
10. Life and the Evolution of Earth's Atmosphere.
11. On the RNA-World Hypothesis
12. Origin of Life: The Present Status of Chemical Theory

Evolutionary oscillation in prebiology: igneous activity and the origins of life. Entrez PubMed: "The processes of chemical evolution are responsible for the origin of life. Three such processes have special importance: oscillation, creation, and competition. An oscillation from one kind of environment to another provides a mechanism for instituting processes that can only take place under conditions far removed from equilibrium. Oscillating evolutionary processes are likely to have played an important part in the origin of life. It is a mistake to assume that life originated in any one environment. It did not arrive in a moment of time. It was the result of a long period of chemical evolution during which it passed through a variety of environments. Biopoesis took place in an environment in which a variety of different kinds of protolife were assembled and concentrated. One essential form of protolife involved in these processes is the protocell. The experiments of Fox suggest that the creation of protocells involves violent oscillations of temperature and hydration. Igneous activity is especially characterised by oscillating conditions. Volcanic eruptions consist of violent changes from one extreme condition to another. Temperatures, pressure, phase, concentration and hydration all oscillate violently, and are subject to shock pulses of many kinds. Protolife may well have passed through extremes of environment for wider that those that life itself can sustain. The most probable environment for the assembly of the various forms of protolife would be on mudbanks forming either at the mouth of streams draining regions of active vulcanicity, or round the edge of hot volclanic pools. In this situation one could fins concentrated not only the various stands of protolife necessary for the final act of biopoesis, but also perbiologically formed nutrients necessary as for the first eobionts. As soon as the first protocells start to grow, they start to compete with each other, and so initiate a new additional evolutionary process, that of natural selection. Only after such competition has been initiated is life itself likely to be established."
Sylvester-Bradley PC. Evolutionary oscillation in prebiology: igneous activity and the origins of life. Orig Life. 1976 Jan;7(1):9-18.

Impact frustration of the origin of life. : "One possible definition for the origin of life on Earth is the time at which the interval between devastating environmental insults by impact exceeded the timescale for establishing self-replicating proto-organisms. A quantitative relationship for the Hadean (pre-3,800 Myr ago) and Early Archean (3,800 to 3,400 Myr) impact flux can be derived from the lunar and terrestrial impact records. Also, the effects of impact-related processes on the various environments proposed for abiogenesis (the development of life through chemical evolution from inorganic materials) can be estimated. Using a range of plausible values for the timescale for abiogenesis, the interval in time when life might first have bootstrapped itself into existence can be found for each environment. We find that if the deep marine hydrothermal setting provided a suitable site, abiogenesis could have happened as early as 4,000 to 4,200 Myr ago, whereas at the surface of the Earth abiogenesis could have occurred between 3,700 and 4,000 Myr."
Maher KA, Stevenson DJ.Impact frustration of the origin of life.Nature. 1988 Feb 18;331(6157):612-4.

Before the Beginning

2008-12-31T17:58:00.000-11:00

Based on radio-dating of meteorites, the solar system is about 4600 Ma – 4600 million years, or 4.6 billion years old (Ga). This occurred 10 Ga after the Big Bang. The sun and planets condensed from a large, hot accretion disk.

When early Earth was cooling from its molten state, conditions would have been like hell on Earth – hence the term "hadean" for this earliest segment of the precambrian. Meteors rained down on the hot Earth, ultraviolet radiation was unchecked by an ozone belt, and volcanos belched fumes into a reducing atmosphere, which sparked with lightning.

Life, of course, had not yet evolved, but it may have had an earlier start than thought previously (see below).

The term "hadean" was coined to designate the time before the earliest known rocks. However, rocks have been found that are older than the 4550-3800 Ma time-frame of the Hadean.

The oldest rocks so far discovered on Earth are:
1) Jack Hills, Western Australia, a 4.4 Ga detrital zircon (sample W74) in the Jack Hills metaconglomerate, Eranondoo Hill. More at Earliest Piece of Earth
2) The Acasta Gneisses near Canada’s Great Slave Lake (4.03 Ga)
3) The Isua Supracrustal rocks of West Greenland (3.7 to 3.8 Ga)
4) Northern Michigan (3.5-3.7 Ga)
5) Swaziland (3.4-3.5 Ga)

“No known rocks have survived from the first 500 million years of Earth history, but studies of single zircons suggest that some continental crust formed as early as 4.4 Ga, 160 m.y. after accretion of the Earth, and that surface temperatures were low enough for liquid water. Surface temperatures are inferred from high d18O values of zircons. The range of d18O values is constant throughout the Archean (4.4-2.6 Ga) suggesting uniformity of processes and conditions. The hypothesis of a Cool Early Earth suggests long intervals of relatively temperate surface conditions from 4.4 to 4.0 Ga that were conducive to liquid-water oceans and possibly life. Meteorite impacts during this period may have been less frequent than previously thought.”A Cool Early Earth

More: Introduction to the Hadean / Palaeos Hadean: The Hadean Eon / Geol 2C Hadean lecture / Evolution: Change: Deep Time / Geologic Time: Age of the Earth /

Image "Evolutionist"

The RNA world on ice: a new scenario for the emergence of RNA information.

2008-12-31T17:44:00.000-11:00

Entrez PubMed: "The RNA world hypothesis refers to a hypothetical era prior to coded peptide synthesis, where RNA was the major structural, genetic, and catalytic agent. Though it is a widely accepted scenario, a number of vexing difficulties remain. In this review we focus on a missing link of the RNA world hypothesis-primitive miniribozymes, in particular ligases, and discuss the role of these molecules in the evolution of RNA size and complexity. We argue that prebiotic conditions associated with freezing, rather than 'warm and wet' conditions, could have been of key importance in the early RNA world."
Vlassov AV, Kazakov SA, Johnston BH, Landweber LF. The RNA world on ice: a new scenario for the emergence of RNA information. J Mol Evol. 2005 Aug;61(2):264-73. Epub 2005 Jul 13.

co-original

2007-12-01T01:00:00.000-11:00

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Primordial Atmosphere.

2006-11-30T17:58:00.000-11:00

A hydrogen-rich early Earth atmosphere. : "We show that the escape of hydrogen from early Earth's atmosphere likely occurred at rates slower by two orders of magnitude than previously thought. The balance between slow hydrogen escape and volcanic outgassing could have maintained a hydrogen mixing ratio of more than 30%. The production of prebiotic organic compounds in such an atmosphere would have been more efficient than either exogenous delivery or synthesis in hydrothermal systems. The organic soup in the oceans and ponds on early Earth would have been a more favorable place for the origin of life than previously thought."

Tian F, Toon OB, Pavlov AA, De Sterck H. A hydrogen-rich early Earth atmosphere. Science. 2005 May 13;308(5724):1014-7. Epub 2005 Apr 7. Comment in: Science. 2005 May 13;308(5724):962-3.

The evolution of the prebiotic atmosphere : "High CO2 levels are required to warm the primitive earth in the face of decreased solar luminosity. The atmosphere should have had an effective stratospheric cold trap, which would have limited the abiotic production rate of oxygen to relatively low values. Photostimulated oxidation of ferrous iron in the oceans should have been the dominant source of atmospheric H2. Rainout of H2O2 would have kept the atmospheric H2 content high and the O2 content low, even if other sources of H2 were small."
Article / PubMed / ChemPort
Kasting, J.E. The evolution of the prebiotic atmosphere. Origins of Life 14, 75−82 (1984).

Nitrogen fixation by corona discharge on the early precambrian Earth. : Entrez PubMed: "We report the first experimental study of nitrogen fixation by corona discharge on the anoxic primitive Earth. The energy yields of nitric oxide (NO) and nitrous oxide (N(2)O) were experimentally determined over a wide range of CO(2)-N(2) mixtures simulating the evolution of the Earth's atmosphere during the Hadean and Archean eras (from 4.5 ba to 2.5 ba). NO, the principal form of fixed nitrogen in lightning and coronal discharge in early Earth, is produced ten times less efficiently in the latter type of electrical discharge with an estimated maximum annual production rate of the order of 10(10) g yr(-1). For N(2)O the maximum production rate was estimated to be approximately 10(9) g yr(-1). These low rates of syntheses indicate that corona discharges as point discharges on the clouds and ground did not play a significant role in the overall pool of reactive nitrogen needed for the emergence and sustainability of life."

Nna-Mvondo D, Navarro-Gonzalez R, Raulin F, Coll P. Nitrogen fixation by corona discharge on the early precambrian Earth. Orig Life Evol Biosph. 2005 Oct;35(5):401-9.

Neon isotopes constrain convection and volatile origin in the Earth's mantle.: "Identifying the origin of primordial volatiles in the Earth's mantle provides a critical test between models that advocate magma-ocean equilibration with an early massive solar-nebula atmosphere and those that require subduction of volatiles implanted in late accreting material. Here we show that neon isotopes in the convecting mantle, resolved in magmatic CO2 well gases, are consistent with a volatile source related to solar corpuscular irradiation of accreting material. This contrasts with recent results that indicated a solar-nebula origin for neon in mantle plume material, which is thought to be sampling the deep mantle. Neon isotope heterogeneity in different mantle sources suggests that models in which the plume source supplies the convecting mantle with its volatile inventory require revision. Although higher than accepted noble gas concentrations in the convecting mantle may reduce the need for a deep mantle volatile flux, any such flux must be dominated by the neon (and helium) isotopic signature of late accreting material."Ballentine CJ, Marty B, Sherwood Lollar B, Cassidy M. Neon isotopes constrain convection and volatile origin in the Earth's mantle. Nature. 2005 Jan 6;433(7021):33-8. Comment in: Nature. 2005 Jan 6;433(7021):25-6.

Efficient near ultraviolet light induced formation of hydrogen by ferrous hydroxide.

2006-11-30T17:20:00.000-11:00

Entrez PubMed: "The formation of hydrogen on irradiating ferrous ion in aqueous solution or suspension was studied over a wide range of pH. In addition to the known reaction in acid solution which decreases in yield with increasing pH and required far UV light, there is an efficient reaction occurring between pH 6 and 9 which utilizes near UV light. The latter reaction is an approximately linear function of both the concentration of ferrous ion and the light intensity. The quantum yield of hydrogen from the suspension of Fe(OH)2 at pH 7.2 is very high: > or = 0.3. The quantum yield decreases by a factor of five at 1 mole percent of ferric ions. To explain these observations it is proposed that an intermediate formed on excitation of the Fe(OH)2 polymer is further reduced by a neighboring Fe(+2) to form H2. These results support the work of Braterman et al. (1983) which claimed that the near UV driven photooxidation of ferrous ions could be responsible for formation of the Banded Iron Formations on the early earth. The efficient photoreaction observed in the present work could also serve as a source of active reducing equivalents to reduce CO2 and thus provide a solution to a dilemma in the arguments on the role of reduced carbon in the origin of life."
Borowska ZK, Mauzerall DC. Efficient near ultraviolet light induced formation of hydrogen by ferrous hydroxide. Orig Life Evol Biosph. 1987;17:251-9.

Early Earth Atmosphere Hydrogen-rich, Favorable To Life

2006-11-15T16:41:00.000-11:00

U. Of Colorado Study Shows Early Earth Atmosphere Hydrogen-rich, Favorable To Life: "Published in the April 7 issue of Science Express, the online edition of Science Magazine, the study concludes traditional models estimating hydrogen escape from Earth's atmosphere several billions of years ago are flawed. The new study indicates up to 40 percent of the early atmosphere was hydrogen, implying a more favorable climate for the production of pre-biotic organic compounds like amino acids, and ultimately, life.

Toon said the premise that early Earth had a CO2-dominated atmosphere long after its formation has caused many scientists to look for clues to the origin of life in hydrothermal vents in the sea, fresh-water hot springs or those delivered to Earth from space via meteorites or dust.

The new study indicates the escape of hydrogen from Earth's early atmosphere was probably two orders of magnitude slower than scientists previously believed, said Tian. The lower escape rate is based in part on the new estimates for past temperatures in the highest reaches of Earth's atmosphere some 5,000 miles in altitude where it meets the space environment.

While previous calculations assumed Earth's temperature at the top of the atmosphere to be well over 1,500 degrees F several billion years ago, the new mathematical models show temperatures would have been twice as cool back then. The new calculations involve supersonic flows of gas escaping from Earth's upper atmosphere as a planetary wind, according to the study.

Despite somewhat higher ultraviolet radiation levels from the sun in Earth's infancy, the escape rate of hydrogen would have remained low, Tian said. The escaping hydrogen would have been balanced by hydrogen being vented by Earth's volcanoes several billion years ago, making it a major component of the atmosphere."

The sugar model: catalysis by amines and amino acid products.

2006-10-31T17:58:00.000-11:00

Entrez PubMed: "Ammonia and amines (including amino acids) were shown to catalyze the formation of sugars from formaldehyde and glycolaldehyde, and the subsequent conversion of sugars to carbonylcontaining products under the conditions studied (pH 5.5 and 50 degrees C). Sterically unhindered primary amines were better catalysts than ammonia, secondary amines, and sterically hindered primary amines (i.e. alpha-aminoisobutyric acid). Reactions catalyzed by primary amines initially consumed formaldehyde and glycolaldehyde about 15-20 times faster than an uncatalyzed control reaction. The amine-catalyzed reactions yielded aldotriose (glyceraldehyde), ketotriose (dihydroxyacetone), aldotetroses (erythrose and threose), ketotetrose (erythrulose), pyruvaldehyde, acetaldehyde, glyoxal, pyruvate, glyoxylate, and several unindentified carbonyl products. The concentrations of the carbonyl products, except pyruvate and ketotetrose, initially increased and then declined during the reaction, indicating their ultimate conversion to other products (like larger sugars or pyruvate). The uncatalyzed control reaction yielded no pyruvate or glyoxylate, and only trace amounts of pyruvaldehyde, acetaldehyde and glyoxal. In the presence of 15 mM catalytic primary amine, such as alanine, the rates of triose and pyruvaldehyde of synthesis were about 15-times and 1200-times faster, respectively, than the uncatalyzed reaction. Since previous studies established that alanine is synthesized from glycolaldehyde and formaldehyde via pyruvaldehyde as its direct precursor, the demonstration that the alanine catalyzes the conversion of glycolaldehyde and formaldehyde to pyruvaldehyde indicates that this synthetic pathway is capable of autocatalysis. The relevance of this synthetic process, named the Sugar Model, to the origin of life is discussed."

Weber AL. The sugar model: catalysis by amines and amino acid products. Orig Life Evol Biosph. 2001 Feb-Apr;31(1-2):71-86.

Chemical constraints governing the origin of metabolism: the thermodynamic landscape of carbon group transformations under mild aqueous conditions.

2006-10-31T17:56:00.000-11:00

Entrez PubMed: "The thermodynamics of organic chemistry under mild aqueous conditions was examined in order to begin to understand its influence on the structure and operation of metabolism and its antecedents. Free energies (deltaG) were estimated for four types of reactions of biochemical importance carbon-carbon bond cleavage and synthesis, hydrogen transfer between carbon groups, dehydration of alcohol groups, and aldo-keto isomerization. The energies were calculated for mainly aliphatic groups composed of carbon, hydrogen, and oxygen. The energy values showed (1) that generally when carbon-carbon bond cleavage involves groups from different functional group classes (i.e., carboxylic acids, carbonyl groups, alcohols, and hydrocarbons), the transfer of the shared electron-pair to the more reduced carbon group is energetically favored over transfer to the more oxidized carbon group, and (2) that the energy of carbon-carbon bond transformation is primarily determined by the functional group class of the group that changes oxidation state in the reaction (i.e., the functional group class of the group that donates the shared electron-pair during cleavage, or that accepts the incipient shared electron-pair during synthesis). In contrast, the energy of hydrogen transfer between carbon groups is determined by the functional group class of both the hydrogen-donor group and the hydrogen-acceptor group. From these and other observations we concluded that the chemistry involved in the origin of metabolism (and to a lesser degree modern metabolism) was strongly constrained by (1) the limited redox-based transformation energy of organic substrates that is readily dissipated in a few energetically favorable irreversible reactions; (2) the energy dominance of a few transformation half-reactions that determines whether carbon-carbon bond transformation (cleavage or synthesis) is energetically favorable (deltaG < -3.5 kcal/mol), reversible (deltaG between +/-3.5 kcal/mol), or unfavorable (deltaG > +3.5 kcal/mol); and (3) the dependence of carbon group transformation energy on the functional group class (i.e., oxidation state) of participating groups that in turn is contingent on prior reactions and precursors in the synthetic pathway."

Weber AL. Chemical constraints governing the origin of metabolism: the thermodynamic landscape of carbon group transformations under mild aqueous conditions. Orig Life Evol Biosph. 2002 Aug;32(4):333-57.

On the emergence of biological complexity: life as a kinetic state of matter.

2006-10-31T17:54:00.000-11:00

Entrez PubMed: "A kinetic model that attempts to further clarify the nature of biological complexification is presented. Its essence: reactions of replicating systems and those of regular chemical systems follow different selection rules leading to different patterns of chemical behavior. For regular chemical systems selection is fundamentally thermodynamic, whereas for replicating chemical systems selection is effectively kinetic. Building on an extension of the kinetic stability, concept it is shown that complex replicators tend to be kinetically more stable than simple ones, leading to an on-going process of kinetically-directed complexification. The high kinetic stability of simple replicating assemblies such as phages, compared to the low kinetic stability of the assembly components, illustrates the complexification principle. The analysis suggests that living systems constitute a kinetic state of matter, as opposed to the traditional thermodynamic states that dominate the inanimate world, and reaffirms our view that life is a particular manifestation of replicative chemistry."

Pross A. On the emergence of biological complexity: life as a kinetic state of matter. Orig Life Evol Biosph. 2005 Apr;35(2):151-66.

Kinetics of organic transformations under mild aqueous conditions: implications for the origin of life and its metabolism.

2006-10-31T17:52:00.000-11:00

Entrez PubMed: "The rates of thermal transformation of organic molecules containing carbon, hydrogen, and oxygen were systematically examined in order to identify the kinetic constraints that governed origin-of-life organic chemistry under mild aqueous conditions. Arrhenius plots of the kinetic data were used to estimate the reaction of half-lifes at 50 degrees C. This survey showed that hydrocarbons and organic substances containing a single oxygenated group were kinetically the most stable; whereas organic substances containing two oxygenated groups in which one group was an alpha- or beta-positioned carbonyl group were the most reactive. Compounds with an alpha- or beta-positioned carbonyl group (aldehyde or ketone) had rates of reaction that were up to 10(24)-times faster than rates of similar molecules lacking the carbonyl group. This survey of organic reactivity, together with estimates of the molecular containment properties of lipid vesicles and liquid spherules, indicates that an origins process in a small domain that used C,H,O-intermediates had to be catalytic and use the most reactive organic molecules to prevent escape of its reaction intermediates."

Weber AL. Orig Life Evol Biosph. 2004 Oct;34(5):473-95. Kinetics of organic transformations under mild aqueous conditions: implications for the origin of life and its metabolism. Orig Life Evol Biosph. 2004 Oct;34(5):473-95.

Primordial carbonylated iron-sulfur compounds and the synthesis of pyruvate.

2006-10-31T17:41:00.000-11:00

Entrez PubMed: "Experiments exploring the potential catalytic role of iron sulfide at 250 degrees C and elevated pressures (50, 100, and 200 megapascals) revealed a facile, pressure-enhanced synthesis of organometallic phases formed through the reaction of alkyl thiols and carbon monoxide with iron sulfide. A suite of organometallic compounds were characterized with ultraviolet-visible and Raman spectroscopy. The natural synthesis of such compounds is anticipated in present-day and ancient environments wherever reduced hydrothermal fluids pass through iron sulfide-containing crust. Here, pyruvic acid was synthesized in the presence of such organometallic phases. These compounds could have provided the prebiotic Earth with critical biochemical functionality."
Cody GD, Boctor NZ, Filley TR, Hazen RM, Scott JH, Sharma A, Yoder HS Jr. Primordial carbonylated iron-sulfur compounds and the synthesis of pyruvate. Science. 2000 Aug 25;289(5483):1337-40.
Comment in: Science. 2000 Aug 25;289(5483):1307-8.

Iron-sulfur world

2006-10-31T17:35:00.002-11:00

Wächtershäuser, in the iron-sulfur world theory, postulates that an early form of metabolism predated genetics. By metabolism, Wächtershäuser refered to a cycle of chemical reactions that produce energy in a form that can be harnessed by other processes. Wächtershäuser's idea was that a primitive metabolic cycle could produce increasingly complex compounds.

A key concept within the iron-sulfur theory was that this early chemistry of life occurred on mineral surfaces, such as iron pyrites, near deep submarine hydrothermal vents. This was an anerobic, hyperthermic (near 100^oC), high pressure environment. Acetic acid plays a special role in Wächtershäuser's theory because acetic acid is part of the citric acid cycle that is fundamental to cellular metabolism.

Discussing the origin of life. [Science. 2002] PMID: 12400544
Origin of life. Some like it hot, but not the first biomolecules. [Science. 2002] PMID: 12065824
Origin of life. II. From prebiotic replicators to protocells. [Arch Sci Compte Rendu Seances Soc. 1999] PMID: 14677551
The role of accuracy for early stages of the origin of life. [Orig Life Evol Biosph. 1995] PMID: 11536674
Electroweak enantioselection and the origin of life. [Orig Life Evol Biosph. 1995] PMID: 11536670

Critique of the hypothesis: Two-dimensional life? [Proc Natl Acad Sci U S A. 1991]
A model [Wachtershauser, G. (1988) Microbiol. Rev. 52, 452-484], according to which life started in the form of a monomolecular layer of interacting anionic metabolites electrostatically bound to a positively charged surface, is examined critically. The model raises a number of thermodynamic and kinetic difficulties.
de Duve C, Miller SL. Two-Dimensional Life? (Free Full Text pdf) Proc Natl Acad Sci U S A. 1991 Nov;88:10014-7.

Polymerization on the rocks: theoretical introduction. [Orig Life Evol Biosph. 1998] PMID: 9611763
The reactions of methanimine and cyanogen with carbon monoxide in prebiotic molecular evolution on earth. [Orig Life Evol Biosph. 2001] PMID: 11770257
Gunter Wachtershauser profile. Between a rock and a hard place. [Science. 2002] PMID: 11896256
The REH theory of protein and nucleic acid divergence: a retrospective update. [J Mol Evol. 1978] PMID: 722809
Reaction sequence of iron sulfide minerals in bacteria and their use as biomarkers
Primordial carbonylated iron-sulfur compounds and the synthesis of pyruvate. [Science. 2000] PMID: 10958777
A sulfurous start for protein synthesis? [Science. 1998] PMID: 9714669
Prebiotic chemistry. Where smokers rule. [Science. 1997] PMID: 9132945

Structure of subtilosin A, a cyclic antimicrobial peptide from Bacillus subtilis with unusual sulfur to alpha-carbon cross-links: formation and reduction of alpha-thio-alpha-amino acid derivatives. [Biochemistry. 2004] PMID: 15035610
The emergence of life from iron monosulphide bubbles at a submarine hydrothermal redox and pH front. [J Geol Soc London. 1997] PMID: 11541234
Ammonia formation by the reduction of nitrite/nitrate by FeS: ammonia formation under acidic conditions. [Orig Life Evol Biosph. 2005] PMID: 16228644

Peptides by activation of amino acids with CO on (Ni,Fe)S surfaces: implications for the origin of life. [Science. 1998] PMID: 9685253
Activated acetic acid by carbon fixation on (Fe,Ni)S under primordial conditions. [Science. 1997] : modified: "In experiments modeling the reactions of the reductive acetyl-coenzyme A pathway at hydrothermal temperatures, it was found that an aqueous slurry of coprecipitated NiS and FeS converted CO and CH3SH into the activated thioester CH3-CO-SCH3, which hydrolyzed to acetic acid. In the presence of aniline, acetanilide was formed. When NiS-FeS was modified with catalytic amounts of selenium, acetic acid and CH3SH were formed from CO and H2S alone. The reaction can be considered as the primordial initiation reaction for a chemoautotrophic origin of life."
Huber C, Wachtershauser G. Activated acetic acid by carbon fixation on (Fe,Ni)S under primordial conditions. Science. 1997 Apr 11;276(5310):245-7. Comment in: Science. 1997 Apr 11;276(5310):222..

More from Wächtershäuser:
Review : Before enzymes and templates: theory of surface metabolism. Microbiol Rev. 1988 Dec;52(4):452-84.

A possible primordial peptide cycle. [Science. 2003] PMID: 12920291
A sulfurous start for protein synthesis? [Science. 1998] PMID: 9714669
Origin of life. Life as we don't know it. [Science. 2000] PMID: 10979855
Organic sulfur compounds resulting from the interaction of iron sulfide, hydrogen sulfide and carbon dioxide in an anaerobic aqueous environment. [Orig Life Evol Biosph. 1996] PMID: 11536750

Historical perspective: the problem of the origin of life in the context of developments in biology. [Orig Life Evol Biosph. 1988] PMID: 3285284
Evolution of the first metabolic cycles. [Proc Natl Acad Sci U S A. 1990] PMID: 2296579
Life in a ligand sphere. [Proc Natl Acad Sci U S A. 1994] PMID: 8183902
Between history and physics. [J Mol Evol. 1982] PMID: 6178836
Obcells as proto-organisms: membrane heredity, lithophosphorylation, and the origins of the genetic code, the first cells, and photosynthesis. [J Mol Evol. 2001] PMID: 11675615

Investigation of the prebiotic synthesis of amino acids and RNA bases from CO2 using FeS/H2S as a reducing agent. [Proc Natl Acad Sci U S A. 1995] PMID: 8524872
[FeS/FeS2], a redox system for the origin of life (some experiments on the pyrite-hypothesis). [Orig Life Evol Biosph. 1994] PMID: 11536658
Energetics and kinetics of the prebiotic synthesis of simple organic acids and amino acids with the FeS-H2S/FeS2 redox couple as reductant. [Orig Life Evol Biosph. 1999] PMID: 10077866
Activated acetic acid by carbon fixation on (Fe,Ni)S under primordial conditions. [Science. 1997] PMID: 9092471

The origin of life and its methodological challenge. [J Theor Biol. 1997] PMID: 9299293
Evolution of the first metabolic cycles. [Proc Natl Acad Sci U S A. 1990] PMID: 2296579
A model for the origin of life. [J Mol Evol. 1982] PMID: 7120429
On the origin of metabolic pathways. [J Mol Evol. 1999] PMID: 10486000
Noisy clues to the origin of life. [Proc Biol Sci. 2002] PMID: 12495484

The iron-sulphur proteins: evolution of a ubiquitous protein from model systems to higher organisms. [Orig Life. 1974] PMID: 4416334
Chemical evolution. [Nature. 1971] PMID: 4923113
Chemical evolution. [Am Sci. 1975] PMID: 1115436
Ambiguity in the interpretation of abiotic syntheses. [Orig Life. 1975] PMID: 1153186
Life's beginnings--origin

Photoelectrochemical power, chemical energy and catalytic activity for organic evolution on natural pyrite interfaces. [Orig Life Evol Biosph. 2003] PMID: 12967264
Reaction sequence of iron sulfide minerals in bacteria and their use as biomarkers. [Science. 1998] PMID: 9572727
Asymmetric adsorption by quartz: a model for the prebiotic origin of optical activity. [Orig Life. 1975] PMID: 171608
No soup for starters? Autotrophy and the origins of metabolism. [Trends Biochem Sci. 1995] PMID: 7482696

A theoretical approach to the link between oxidoreductions and pyrite formation in the early stage of evolution. [Biochim Biophys Acta. 2002] PMID: 11997130
The origin of intermediary metabolism. [Proc Natl Acad Sci U S A. 2000] PMID: 10859347
The origin of life and its methodological challenge. [J Theor Biol. 1997] PMID: 9299293
Formation of amide bonds without a condensation agent and implications for origin of life. [Nature. 1994] PMID: 8159243

The chemical basis of membrane bioenergetics.
All organisms rely on chemiosmotic membrane systems for energy transduction; the great variety of participating proteins and pathways can be reduced to a few universal principles of operation. This chemical basis of bioenergetics is reviewed with respect to the origin and early evolution of life. For several of the cofactors which play important roles in bioenergetic reactions, plausible prebiotic sources have been proposed, and it seems likely that these cofactors were present before elaborate protein structures. In particular, the hydrophobic quinones require only a membrane-enclosed compartment to yield a minimum chemiosmotic system, since they can couple electron transport and proton translocation in a simple way. It is argued that the central features of modern bioenergetics, such as the coupling of redox reactions and ion translocation at the cytoplasmic membrane, probably are ancient features which arose early during the process of biogenesis. The notion of a thermophile root of the universal phylogenetic tree has been discussed controversially, nevertheless, thermophiles are interesting model organisms for reconstructing the origin of chemiosmotic systems, since they are often acidophiles and anaerobic respirers exploiting iron-sulfur chemistry. This perspective can help to explain the prominent role of iron-sulfur proteins in extant biochemistry as well as the origin of both respiration and proton extrusion within the context of a possible origin of life in the vicinity of hot vents.
Berry S. The chemical basis of membrane bioenergetics. J Mol Evol. 2002 May;54(5):595-613.

More abstracts on membrane bioenergetics on PubMed:
Evolution of membrane bioenergetics. [J Supramol Struct. 1980] PMID: 6453255
Chemiosmotic systems in bioenergetics: H(+)-cycles and Na(+)-cycles. [Biosci Rep. 1991] PMID: 1668527
Bioenergetics of the Archaea. [Microbiol Mol Biol Rev. 1999] PMID: 10477309
Obcells as proto-organisms: membrane heredity, lithophosphorylation, and the origins of the genetic code, the first cells, and photosynthesis. [J Mol Evol. 2001] PMID: 11675615
The first cellular bioenergetic process: primitive generation of a proton-motive force. [J Mol Evol. 1991] PMID: 1663558

Entropy and charge in molecular evolution--the case of phosphate.

2006-10-31T17:35:00.000-11:00

Entropy and charge in molecular evolution--the case of phosphate. : "Biopoesis, the creation of life, implies molecular evolution from simple components, randomly distributed and in a dilute state, to form highly organized, concentrated systems capable of metabolism, replication and mutation. This chain of events must involve environmental processes that can locally lower entropy in several steps; by specific selection from an indiscriminate mixture, by concentration from dilute solution, and in the case of the mineral-induced processes, by particular effectiveness in ordering and selective reaction, directed toward formation of functional biomolecules. Numerous circumstances provide support for the notion that negatively charged molecules were functionally required and geochemically available for biopoesis. Sulfite ion may have been important in bisulfite complex formation with simple aldehydes, facilitating the initial concentration by sorption of aldehydes in positively charged surface active minerals. Borate ion may have played a similar, albeit less investigated role in forming charged sugar complexes. Among anionic species, oligophosphate ions and charged phosphate esters are likely to have been of even more wide ranging importance, reflected in the continued need for phosphate in a proposed RNA world, and extending its central role to evolved biochemistry. Phosphorylation is shown to result in selective concentration by surface sorption of compounds, otherwise too dilute to support condensation reactions. It provides protection against rapid hydrolysis of sugars and, by selective concentration, induces the oligomerization of aldehydes. As a manifestation of life arisen, phosphate already appears in an organic context in the oldest preserved sedimentary record."

Arrhenius G, Sales B, Mojzsis S, Lee T. Entropy and charge in molecular evolution--the case of phosphate. J Theor Biol. 1997 Aug 21;187(4):503-22.

Ammonia formation by the reduction of nitrite/nitrate by fes: ammonia formation under acidic conditions.

2006-10-31T13:00:00.000-11:00

Entrez PubMed: "One issue for the origin of life under a non-reducing atmosphere is the availability of the reduced nitrogen necessary for amino acids, nucleic acids, etc. One possible source of this nitrogen is the formation of ammonia from the reduction of nitrates and nitrites produced by the shock heating of the atmosphere and subsequent chemistry. Ferrous ions will reduce these species to ammonium, but not under acidic conditions. We wish to report results on the reduction of nitrite and nitrate by another source of iron (II), ferrous sulfide, FeS. FeS reduces nitrite to ammonia at lower pHs than the corresponding reduction by aqueous Fe(+ 2). The reduction follows a first order decay, in nitrite concentration, with a half-life of about 150 min (room temperature, CO(2), pH 6.25). The highest product yield of ammonia measured was 53%. Under CO(2), the product yield decreases from pH 5.0 to pH 6.9. The increasing concentration of bicarbonate, at higher pH, interferes with the reaction. Comparing experiments under N(2) CO(2) shows the interference of bicarbonate. The reaction proceeds well in the presence of such species as chloride, sulfate, and phosphate, though the yield drops significantly with phosphate. FeS also reduces nitrate and, unlike with Fe(+ 2), the reduction shows more reproducibility. Again, the product yield decreases with increasing pH, from 7% at pH 4.7 to 0% at pH 6.9. It appears that nitrate is much more sensitive to the presence of added species, perhaps not competing as well for binding sites on the FeS surface. This may be the cause of the lack of reproducibility of nitrate reduction by Fe(+ 2) (which also can be sensitive to binding by certain species)."

Summers DP. Orig Life Evol Biosph. 2005 Aug;35(4):299-312. Ammonia formation by the reduction of nitrite/nitrate by fes: ammonia formation under acidic conditions.

What Is Life and How Do We Search for It in Other Worlds?

2006-10-31T11:59:00.000-11:00

PLoS Biology: What Is Life and How Do We Search for It in Other Worlds?: "The obvious diversity of life on Earth overlies a fundamental biochemical and genetic similarity. The three main polymers of biology-the nucleic acids, the proteins, and the polysaccarides�are built from 20 amino acids, five nucleotide bases, and a few sugars, respectively. Together with lipids and fatty acids, these are the main constituents of biomass: the hardware of life (Lehninger 1975, p 21). The DNA and RNA software of life is also common, indicating shared descent (Woese 1987). But with only one example of life�life on Earth�it is not all that surprising that we do not have a fundamental understanding of what life is. We don't know which features of Earth life are essential and which are just accidents of history."

Top Down & Bottom Up

2006-09-30T17:59:00.000-11:00

ORIGIN OF LIFE: IN SEARCH OF THE SIMPLEST CELL: Modified: "There are two approaches to the 'minimal cell': the top-down and the bottom-up.
The top-down approach aims at simplifying existing small organisms, possibly arriving at a minimal genome.
The bottom-up approach aims at constructing artificial chemical supersystems that could be considered alive. No such experimental system exists yet; at least one component is always missing.

Metabolism seems to be the stepchild in the family. Basically, what most researchers in the field used to call 'metabolism' is typically the trivial outcome of need for material input of both template replication and membrane growth. This input is usually simplified to a conversion reaction from precursors to products."

Primordial Soup : Theories

2006-09-30T16:59:00.000-11:00

The Woodstock of Evolution -- The World Summit on Evolution (ScientificAmerican.com): Antonio Lazcano, President of the International Society for the Study of the Origins of Life and a scientist at the Universidad Autónoma de México, theorized that there were three sources for the primordial soup:

1) A reducing atmosphere from volcanic outgassing,
2) High-temperature submarine vents and fumaroles -- black smokers, and
3) Space--for example, the 4.6 billion-year-old Murchison meteorite, discovered in Australia in 1969 was loaded with amino acids, aliphatic and aromatic hydrocarbons, hydroxy acids, purines, pyrimidines, and other chemical building blocks of life.

'The evidence strongly suggests that prior to the origin of life the primitive Earth already had many different catalytic agents, polymers with sequences of nucleotides, and membrane-forming compounds,' Lazcano concluded. This prebiotic soup led to a catalytic and replicative RNA world, which led to the DNA world of today."

The Miller-Urey experiments and beyond

2006-09-30T16:58:00.000-11:00

In 1953, graduate student Miller set up an experiment in which he passed an electrical current (to simulate lightning discharges in the primordial atmosphere) through the gases then believed to constitute the primordial atmosphere – methane (CH4), ammonia (NH3), hydrogen (H2), and water (H2O). After a WEEK, Miller assayed the resulting chemicals and found that up to 15% of the carbon had been converted to organic compounds. Two percent of the carbon had formed amino acids, including 13 of the 21 that comprise the proteins of living cells. The smallest amino acid, glycine, was the most abundant.

It turns out that Miller’s and Urey’s guess about the composition of the primordial atmosphere was wrong, yet the Miller-Urey products and many more products (including nucleotides) have repeatedly been generated in similar experiments that more accurately replicate the early atmosphere.

The salient point is that in a very short time, a variety of life-related chemicals will generate themselves from simple molecules provided that some energy is supplied to the system. Considering the billions of years before recognizable life appeared on the entire planet, it is clear that chemical evolution could yield cellular life. In fact, the earliest discovered microfossils date from about 3 ½ billion years ago, and this is a minimum 1 billion years since the origin of the planet.

Similar processes to those above must be occurring in the energy-riddled immensity of space, because many organic compounds have been identified spectroscopically in space and have been found in meteorites.

RNA world hypothesis

2006-08-31T17:59:00.000-11:00

ScienceWeek: Modified: "The 'RNA world hypothesis' is the concept that RNA nucleotide sequences with catalytic and self-replicating capabilities predated catalytic protein systems in prebiological epochs. It is believed, however, that the nucleotides constituting RNA were scarce on early Earth. This requires that RNA-based life must have acquired the ability to synthesize RNA nucleotides from simpler and more readily available precursors -- such as sugars and nucleic acid bases. Apparently plausible prebiotic synthesis routes have been proposed for sugars, sugar phosphates, and the four RNA bases. However, the coupling of these molecules into nucleotides, specifically pyrimidine nucleotides, poses a challenge to the RNA world hypothesis."

Some consequences of the RNA world hypothesis. : "It is now generally accepted that our familiar biological world was preceded by an RNA world in which ribosome-catalyzed, nucleic-acid coded protein synthesis played no part. If the RNA world was the first biological world there is little that one can learn from biochemistry about prebiotic chemistry, except that the formation and polymerization of nucleotides were once prebiotic processes. If the RNA world was not the first biological world, the above conclusion may not be justified, and one can speculate that the monomers of earlier genetic polymers might be recognizable as important biochemicals. This suggests that the construction of replicating polymers from simple, not necessarily standard, aminoacids should be explored."
Orgel LE. Some consequences of the RNA world hypothesis. Orig Life Evol Biosph. 2003 Apr;33(2):211-8.

The Woodstock of Evolution -- The World Summit on Evolution (ScientificAmerican.com): Asked about primordial conditions, participant UCLA paleobiologist William Schopf answered: 'We know the overall sequence of life's origin, from CHONSP (carbon, hydrogen, oxygen, nitrogen, sulfur, phosphorus), to monomers, to polymers, to cells; we know that the origin of life was early, microbial, and unicellular; and we know that an RNA world preceded today's DNA-protein world. "

[RNA world and its evolution] : "The early idea of A. N. Belozersky on the precedence of RNA in the origin of life on Earth is developed. Basing on the present knowledge of functional omnipotence of RNA, the author considers three novel mechanisms that could play a critical role in the origin and evolution of the ancient RNA world: (1) the reaction of spontaneous transesterification of polyribonucleotides in aqueous media, discovered by A.B. Chetverin, which could result in elongation of primary short oligoribonucleotides and generation of sequence variants for subsequent selection; (2) compartmentation of functional RNA ensembles in the form of mixed molecular colonies on moist solid surfaces, in the absence of membranes and any other coats; (3) systematic exponential enrichment of RNA population in functionally 'the best' molecules by means of alternately dissolving the colonies upon flooding and forming new ones upon drying a pool ('primordial natural SELEX')."
Sinrin AS. [RNA world and its evolution] Mol Biol (Mosk). 2005 Jul-Aug;39(4):550-6.

Hyperthermophily and the origin and earliest evolution of life.: "The possibility of a high-temperature origin of life has gained support based on indirect evidence of a hot, early Earth and on the basal position of hyperthermophilic organisms in rRNA-based phylogenies. However, although the availability of more than 80 completely sequenced cellular genomes has led to the identification of hyperthermophilic-specific traits, such as a trend towards smaller genomes, reduced protein-encoding gene sizes, and glutamic-acid-rich simple sequences, none of these characteristics are in themselves an indication of primitiveness. There is no geological evidence for the physical setting in which life arose, but current models suggest that the Earth's surface cooled down rapidly. Moreover, at 100 degrees C the half-lives of several organic compounds, including ribose, nucleobases, and amino acids, which are generally thought to have been essential for the emergence of the first living systems, are too short to allow for their accumulation in the prebiotic environment. Accordingly, if hyperthermophily is not truly primordial, then heat-loving lifestyles may be relics of a secondary adaptation that evolved after the origin of life, and before or soon after separation of the major lineages."
Islas S, Velasco AM, Becerra A, Delaye L, Lazcano A. Hyperthermophily and the origin and earliest evolution of life. Int Microbiol. 2003 Jun;6(2):87-94. Epub 2003 Jun 28.

Thermosynthesis as energy source for the RNA World: a new model for the origin of life: modified: The thermosynthesis concept, biological free energy gain from thermal cycling, is combined with the concept of the RNA World. The resulting overall origin of life model gives new explanations for the emergence of the genetic code and the ribosome. The first protein named pF1 obtains the energy to support the RNA world by a thermal variation of F1 ATP synthase's binding change mechanism. This pF1 is the single translation product during the emergence of the genetic machinery. During thermal cycling pF1 condenses many substrates with broad specificity, yielding NTPs and randomly constituted protein and RNA libraries that contain (self)-replicating RNA. The smallness of pF1 permits the emergence of the genetic machinery by selection of RNA that increases the fraction of pF1s in the protein library: (1) a progenitor of rRNA that concatenates amino acids bound to (2) a chain of 'positional tRNAs' linked by mutual recognition, yielding a pF1 (or its main motif); this positional tRNA set gradually evolves to a set of regular tRNAs functioning according to the genetic code, with concomitant emergence of (3) an mRNA coding for pF1.
Anthonie W. J. Muller Thermosynthesis as energy source for the RNA World: a new model for the origin of life. Full-text: PDF only

Effect of temperature on the adsorption of adenine. : "Equilibrium adsorption isotherms for the purine base adenine on the surface of graphite crystals have been obtained at 30, 40, 50, and 60 degrees C by frontal analysis using water as a mobile phase. These data were fitted to the Langmuir isotherm model and interpreted in terms of the well-characterized adsorbate monolayer structure. A van't Hoff plot was used to estimate the adsorption enthalpy, -delta H degree which we determined to be 20 kJ mol-1. The susceptibility of nucleic acid bases to aqueous-phase hydrolysis may have been a limiting feature for their inclusion in the primordial genetic architecture; our results suggest that the effects of temperature and the presence of inorganic solids must also be included when assessing the prebiotic availability of adenine."
Sowerby SJ, Morth CM, Holm NG. Effect of temperature on the adsorption of adenine. Astrobiology. 2001 Winter;1(4):481-7.

Survival of the fittest before the beginning of life: selection of the first oligonucleotide-like polymers by UV light. :"BACKGROUND: A key event in the origin of life on this planet has been formation of self-replicating RNA-type molecules, which were complex enough to undergo a Darwinian-type evolution (origin of the "RNA world"). However, so far there has been no explanation of how the first RNA-like biopolymers could originate and survive on the primordial Earth. RESULTS: As condensation of sugar phosphates and nitrogenous bases is thermodynamically unfavorable, these compounds, if ever formed, should have undergone rapid hydrolysis. Thus, formation of oligonucleotide-like structures could have happened only if and when these structures had some selective advantage over simpler compounds. It is well known that nitrogenous bases are powerful quenchers of UV quanta and effectively protect the pentose-phosphate backbones of RNA and DNA from UV cleavage. To check if such a protection could play a role in abiogenic evolution on the primordial Earth (in the absence of the UV-protecting ozone layer), we simulated, by using Monte Carlo approach, the formation of the first oligonucleotides under continuous UV illumination. The simulations confirmed that UV irradiation could have worked as a selective factor leading to a relative enrichment of the system in longer sugar-phosphate polymers carrying nitrogenous bases as UV-protectors. Partial funneling of the UV energy into the condensation reactions could provide a further boost for the oligomerization. CONCLUSION: These results suggest that accumulation of the first polynucleotides could be explained by their abiogenic selection as the most UV-resistant biopolymers."
Mulkidjanian AY, Cherepanov DA, Galperin MY. Survival of the fittest before the beginning of life: selection of the first oligonucleotide-like polymers by UV light. BMC Evol Biol. 2003 May 28;3:12. Epub 2003 May 28. Free Full Text article

Thermosynthesis as energy source for the RNA World: a model for the bioenergetics of the origin of life. : "The thermosynthesis concept, biological free energy gain from thermal cycling, is combined with the concept of the RNA World. The resulting overall origin of life model suggests new explanations for the emergence of the genetic code and the ribosome. It is proposed that the first protein named pF(1) obtained the energy to support the RNA World by a thermal variation of F(1) ATP synthase's binding change mechanism. It is further proposed that this pF(1) was the single translation product during the emergence of the genetic machinery. During thermal cycling pF(1) condensed many substrates with broad specificity, yielding NTPs and randomly constituted protein and RNA libraries that contained self-replicating RNA. The smallness of pF(1) permitted the emergence of the genetic machinery by selection of RNA that increased the fraction of pF(1)s in the protein library: (1) an amino acids concatenating progenitor of rRNA bound to (2) a chain of 'positional tRNAs' linked by mutual recognition, and yielded a pF(1) (or its main motif); this positional tRNA set gradually evolved to a set of regular tRNAs functioning according to the genetic code, with concomitant emergence of (3) an mRNA coding for pF(1)."
Muller AW. Thermosynthesis as energy source for the RNA World: a model for the bioenergetics of the origin of life. Biosystems. 2005 Oct;82(1):93-102.

A deoxyribozyme that harnesses light to repair thymine dimers in DNA -- Chinnapen and Sen 101 (1): 65 -- Proceedings of the National Academy of Sciences: "The RNA world hypothesis (1) postulates that RNA or RNA-like polymers, capable of genetic as well as catalytic function, may have constituted primitive "life" in the course of evolution. Currently, in vitro selection (2, 3) experiments from random sequence DNA and RNA libraries permit the identification of novel catalytic activities for nucleic acids, in support of the RNA world hypothesis. To date, such selections have indicated a substantially broader catalytic repertoire for RNA and DNA than found in naturally occurring ribozymes (4). We were interested in investigating whether reactions that use light energy could be catalyzed by nucleic acid enzymes.Thymine (or pyrimidine) dimers are the major lesions formed in DNA as a result of exposure to UV light. Two major kinds of dimer are known, the cyclobutane and the (6—4) photoproduct (5). Different organisms use a variety of strategies to repair these lesions, among the more interesting of which is the use of light of substantially lower energy (longer wavelength) than the natural absorption of thymine dimers (>250 nm wavelength) to reactivate the dimers back to monomers. Such "photolyase" enzymes for the repair of both cyclobutane and (6—4) dimers have been studied extensively (6). The cyclobutane (CPD) photolyases harness a broad spectrum of light by using a number of chromophores such as methenyltetrahydrofolate (MTHF), flavin nucleotides, and tryptophan side chains (7). Photoexcitation culminates in electron donation from the excited-state flavin directly to the thymine dimer, leading to destabilization of the 5—5 and 6—6 bonds of the dimer, and thus, reversion to base monomers. Interestingly, studies have shown that a single strategically positioned tryptophan residue in the Escherichia coli enzyme's active site is able to provide a significant photoreactivation, even in the absence of the FADH and MTHF cofactors (8). "
Chinnapen DJ, Sen D. A deoxyribozyme that harnesses light to repair thymine dimers in DNA. Proc Natl Acad Sci U S A. 2004 Jan 6;101(1):65-9. Epub 2003 Dec 22.

Concentration of simple aldehydes by sulfite-containing double-layer hydroxide minerals: implications for biopoesis.: "Environmental conditions play an important role in conceptual studies of prebiotically relevant chemical reactions that could have led to functional biomolecules. The necessary source compounds are likely to have been present in dilute solution, raising the question of how to achieve selective concentration and to reach activation. With the assumption of an initial 'RNA World', the questions of production, concentration, and interaction of aldehydes and aldehyde phosphates, potential precursors of sugar phosphates, come into the foreground. As a possible concentration process for simple, uncharged aldehydes, we investigated their adduct formation with sulfite ion bound in the interlayer of positively charged expanding-sheet-structure double-layer hydroxide minerals. Minerals of this type, initially with chloride as interlayer counter anion, have previously been shown to induce concentration and subsequent aldolization of aldehyde phosphates to form tetrose, pentose, and hexose phosphates. The reversible uptake of the simple aldehydes formaldehyde, glycolaldehyde, and glyceraldehyde by adduct formation with the immobilized sulfite ions is characterized by equilibrium constants of K=1.5, 9, and 11, respectively. This translates into an observable uptake at concentrations exceeding 50 mM."
Pitsch S, Krishnamurthy R, Arrhenius G. Concentration of simple aldehydes by sulfite-containing double-layer hydroxide minerals: implications for biopoesis.Helv Chim Acta. 2000 Sep-Oct;83(9):2398-411.

A primordial RNA modification enzyme: the case of tRNA (m1A) methyltransferase.: "The modified nucleoside 1-methyladenosine (m(1)A) is found in the T-loop of many tRNAs from organisms belonging to the three domains of life (Eukaryota, Bacteria, Archaea). In the T-loop of eukaryotic and bacterial tRNAs, m(1)A is present at position 58, whereas in archaeal tRNAs it is present at position(s) 58 and/or 57, m(1)A57 being the obligatory intermediate in the biosynthesis of 1-methylinosine (m(1)I57). In yeast, the formation of m(1)A58 is catalysed by the essential tRNA (m(1)A58) methyltransferase (MTase), a tetrameric enzyme that is composed of two types of subunits (Gcd14p and Gcd10p), whereas in the bacterium Thermus thermophilus the enzyme is a homotetramer of the TrmI polypeptide. Here, we report that the TrmI enzyme from the archaeon Pyrococcus abyssi is also a homotetramer. However, unlike the bacterial site-specific TrmI MTase, the P.abyssi enzyme is region-specific and catalyses the formation of m(1)A at two adjacent positions (57 and 58) in the T-loop of certain tRNAs. The stabilisation of P.abyssi TrmI at extreme temperatures involves intersubunit disulphide bridges that reinforce the tetrameric oligomerisation, as revealed by biochemical and crystallographic evidences. The origin and evolution of m(1)A MTases is discussed in the context of different hypotheses of the tree of life."Roovers M, Wouters J, Bujnicki JM, Tricot C, Stalon V, Grosjean H, Droogmans L. A primordial RNA modification enzyme: the case of tRNA (m1A) methyltransferase. Nucleic Acids Res. 2004 Jan 22;32(2):465-76. Print 2004. Free Full Text article

Concentration of simple aldehydes by sulfite-containing double-layer hydroxide minerals: implications for biopoesis.

2006-08-31T13:00:00.000-11:00

Entrez PubMed: "Environmental conditions play an important role in conceptual studies of prebiotically relevant chemical reactions that could have led to functional biomolecules. The necessary source compounds are likely to have been present in dilute solution, raising the question of how to achieve selective concentration and to reach activation. With the assumption of an initial 'RNA World', the questions of production, concentration, and interaction of aldehydes and aldehyde phosphates, potential precursors of sugar phosphates, come into the foreground. As a possible concentration process for simple, uncharged aldehydes, we investigated their adduct formation with sulfite ion bound in the interlayer of positively charged expanding-sheet-structure double-layer hydroxide minerals. Minerals of this type, initially with chloride as interlayer counter anion, have previously been shown to induce concentration and subsequent aldolization of aldehyde phosphates to form tetrose, pentose, and hexose phosphates. The reversible uptake of the simple aldehydes formaldehyde, glycolaldehyde, and glyceraldehyde by adduct formation with the immobilized sulfite ions is characterized by equilibrium constants of K=1.5, 9, and 11, respectively. This translates into an observable uptake at concentrations exceeding 50 mM."

Pitsch S, Krishnamurthy R, Arrhenius G.
Concentration of simple aldehydes by sulfite-containing double-layer hydroxide minerals: implications for biopoesis.
Helv Chim Acta. 2000 Sep-Oct;83(9):2398-411.

Origin of Life: In the Beginning was Abiogenesis

2006-07-31T08:41:00.000-11:00

Origin of Life: In the Beginning was Abiogenesis

Abiogenesis & Evolution: In the Beginning was Abiogenesis

2006-07-31T08:38:00.001-11:00

Abiogenesis & Evolution: In the Beginning was Abiogenesis

2006-07-31T08:38:00.000-11:00

Abiogenesis & Evolution: In the Beginning was Abiogenesis

Abiogenesis & Evolution: Prokaryote Systematics: The Evolution of a Science

2006-07-31T08:37:00.000-11:00

Abiogenesis & Evolution: Prokaryote Systematics: The Evolution of a Science

2006-07-31T08:36:00.003-11:00

Abiogenesis & Evolution: Prokaryote Systematics: The Evolution of a Science

Abiogenesis & Evolution: Proterozoic and Archaean

2006-07-31T08:36:00.002-11:00

Abiogenesis & Evolution: Proterozoic and Archaean

Abiogenesis & Evolution: Protists in Evolution, and Symbiogenesis

2006-07-31T08:36:00.001-11:00

Abiogenesis & Evolution: Protists in Evolution, and Symbiogenesis

2006-07-31T08:36:00.000-11:00

Abiogenesis & Evolution: Protists in Evolution, and Symbiogenesis

Abiogenesis & Evolution: Horizontal Gene Transfer in Prokayotes

2006-07-31T08:35:00.000-11:00

Abiogenesis & Evolution: Horizontal Gene Transfer in Prokayotes

Abiogenesis & Evolution: Genomes and the Tree of Life

2006-07-31T08:34:00.002-11:00

Abiogenesis & Evolution: Genomes and the Tree of Life

Abiogenesis & Evolution: Comparing Gene Trees and Genome Trees: A Cobweb of Life?

2006-07-31T08:34:00.001-11:00

Abiogenesis & Evolution: Comparing Gene Trees and Genome Trees: A Cobweb of Life?

Abiogenesis & Evolution: Tree of Life or Fuzzy Bush of Life

2006-07-31T08:34:00.000-11:00

Abiogenesis & Evolution: Tree of Life or Fuzzy Bush of Life

Abiogenesis & Evolution: Tree of Life

2006-07-31T08:33:00.002-11:00

Abiogenesis & Evolution: Tree of Life

Abiogenesis & Evolution: Evolutionary Distance Analysis & Maximum Parsimony Analysis

2006-07-31T08:33:00.001-11:00

Abiogenesis & Evolution: Evolutionary Distance Analysis & Maximum Parsimony Analysis

Abiogenesis & Evolution: PLoS Genetics: The Evolutionary Value of Recombination Is Constrained by Genome Modularity

2006-07-31T08:33:00.000-11:00

Abiogenesis & Evolution: PLoS Genetics: The Evolutionary Value of Recombination Is Constrained by Genome Modularity

Abiogenesis & Evolution: Logic & Science

2006-07-31T08:32:00.002-11:00

Abiogenesis & Evolution: Logic & Science

Abiogenesis & Evolution: optimization

2006-07-31T08:32:00.001-11:00

Abiogenesis & Evolution: optimization

Abiogenesis & Evolution: Multi-Level Selection

2006-07-31T08:32:00.000-11:00

Abiogenesis & Evolution: Multi-Level Selection

Abiogenesis & Evolution: Analyses of physiological evolutionary response.

2006-07-31T08:31:00.001-11:00

Abiogenesis & Evolution: Analyses of physiological evolutionary response.

Abiogenesis & Evolution: MicroRNAs Have Shaped The Evolution Of The Majority Of Mammalian Genes

2006-07-31T08:31:00.000-11:00

Abiogenesis & Evolution: MicroRNAs Have Shaped The Evolution Of The Majority Of Mammalian Genes

Abiogenesis & Evolution: Darwin in the Galapagos

2006-07-31T08:30:00.002-11:00

Abiogenesis & Evolution: Darwin in the Galapagos

Abiogenesis & Evolution: evolution and organogenesis

2006-07-31T08:30:00.001-11:00

Abiogenesis & Evolution: evolution and organogenesis

2006-07-31T08:30:00.000-11:00

Abiogenesis & Evolution: evolution and organogenesis

Abiogenesis & Evolution: DNA evolutionary connections

2006-07-31T08:29:00.003-11:00

Abiogenesis & Evolution: DNA evolutionary connections

Abiogenesis & Evolution: Ancient DNA

2006-07-31T08:29:00.002-11:00

Abiogenesis & Evolution: Ancient DNA

Abiogenesis & Evolution: mtDNA

2006-07-31T08:29:00.001-11:00

Abiogenesis & Evolution: mtDNA

Abiogenesis & Evolution: Evidence Found for Origin of Genes

2006-07-31T08:29:00.000-11:00

Abiogenesis & Evolution: Evidence Found for Origin of Genes

Abiogenesis & Evolution: genome and proteome

2006-07-31T08:28:00.002-11:00

Abiogenesis & Evolution: genome and proteome

Abiogenesis & Evolution: protein catalysts and ribozymes

2006-07-31T08:28:00.001-11:00

Abiogenesis & Evolution: protein catalysts and ribozymes

Abiogenesis & Evolution: RNA world

2006-07-31T08:28:00.000-11:00

Abiogenesis & Evolution: RNA world

Abiogenesis & Evolution: Illogical Deceit theory

2006-07-31T08:27:00.001-11:00

Abiogenesis & Evolution: Illogical Deceit theory

Abiogenesis & Evolution: Archaea

2006-07-31T08:27:00.000-11:00

Abiogenesis & Evolution: Archaea

Abiogenesis & Evolution: Minimal Genome

2006-07-31T08:26:00.000-11:00

Abiogenesis & Evolution: Minimal Genome

Abiogenesis & Evolution: Primordial Soup : Theories

2006-07-31T08:25:00.000-11:00

Abiogenesis & Evolution: Primordial Soup : Theories

Origin of Life: Primordial Atmosphere.

2006-07-31T08:24:00.000-11:00

Origin of Life: Primordial Atmosphere.

Abiogenesis & Evolution: CHONSP and RNA world

2006-07-31T08:23:00.002-11:00

Abiogenesis & Evolution: CHONSP and RNA world

Origin of Life: The RNA world on ice: a new scenario for the emergence of RNA information.

2006-07-31T08:23:00.001-11:00

Origin of Life: The RNA world on ice: a new scenario for the emergence of RNA information.

Abiogenesis & Evolution: Miller-Urey & Beyond

2006-07-31T08:23:00.000-11:00

Abiogenesis & Evolution: Miller-Urey & Beyond

Origin of Life: Before the Beginning

2006-07-31T08:22:00.002-11:00

Origin of Life: Before the Beginning

Abiogenesis & Evolution: Timeline of Life

2006-07-31T08:22:00.001-11:00

Abiogenesis & Evolution: Timeline of Life

Origin of Life: Origin of Life and Early Life on Earth

2006-07-31T08:22:00.000-11:00

Origin of Life: Origin of Life and Early Life on Earth

Abiogenesis & Evolution: Before the Beginning

2006-07-31T08:21:00.002-11:00

Abiogenesis & Evolution: Before the Beginning

Origin of Life: Universal cenancestor

2006-07-31T08:21:00.001-11:00

Origin of Life: Universal cenancestor

Abiogenesis & Evolution: LUCA

2006-07-31T08:21:00.000-11:00

Abiogenesis & Evolution: LUCA

Origin of Life: In the Beginning was Abiogenesis

2006-07-31T08:20:00.001-11:00

Origin of Life: In the Beginning was Abiogenesis

2006-07-31T08:20:00.000-11:00

Origin of Life: In the Beginning was Abiogenesis

Origin of Life: What Is Life?

2006-07-31T08:19:00.000-11:00

Origin of Life: What Is Life?

Abiogenesis & Evolution: LUCA

2006-07-31T08:16:00.000-11:00

Abiogenesis & Evolution: LUCA

Primordial Peptides and Proteins

2006-07-30T17:59:00.000-11:00

GADV-protein world hypothesis.: "Based on the fact that RNA has not only a genetic function but also a catalytic function, the RNA world theory on the origin of life was first proposed about 20 years ago. The theory assumes that RNA was amplified by self-replication to increase RNA diversity on the primitive earth. Since then, the theory has been widely accepted as the most likely explanation for the emergence of life. In contrast, we reached another hypothesis, the [GADV]-protein world hypothesis, which is based on pseudo-replication of [GADV]-proteins. We reached this hypothesis during studies on the origins of genes and the genetic code, where [G], [A], [D], and [V] refer to Gly, Ala, Asp, and Val, respectively. In this review, possible steps to the emergence of life are discussed from the standpoint of the [GADV]-protein world hypothesis, comparing it in parallel with the RNA world theory. It is also shown that [GADV]-peptides, which were produced by repeated dry-heating cycles and by solid phase peptide synthesis, have catalytic activities, hydrolyzing peptide bonds in a natural protein, bovine serum albumin. These experimental results support the [GADV]-protein world hypothesis for the origin of life."
Ikehara K. Possible steps to the emergence of life: the [GADV]-protein world hypothesis. Chem Rec. 2005;5(2):107-18.

Catalytic Activities Of [GADV]-Peptides Formation and Establishment of [GADV]-Protein World for the Emergence of Life. : "We have previously postulated a novel hypothesis for the origin of life, assuming that life on the earth originated from '[GADV]-protein world', not from the 'RNA world' (see Ikehara's review, 2002). The [GADV]-protein world is constituted from peptides and proteins with random sequences of four amino acids (glycine [G], alanine [A], aspartic acid [D] and valine [V]), which accumulated by pseudo-replication of the [GADV]-proteins. To obtain evidence for the hypothesis, we produced [GADV]-peptides by repeated heat-drying of the amino acids for 30 cycles ([GADV]-P(30)) and examined whether the peptides have some catalytic activities or not. From the results, it was found that the [GADV]-P(30) can hydrolyze several kinds of chemical bonds in molecules, such as umbelliferyl-beta-D-galactoside, glycine-p-nitroanilide and bovine serum albumin. This suggests that [GADV]-P(30) could play an important role in the accumulation of [GADV]-proteins through pseudo-replication, leading to the emergence of life. We further show that [GADV]-octapaptides with random sequences, but containing no cyclic compounds as diketepiperazines, have catalytic activity, hydrolyzing peptide bonds in a natural protein, bovine serum albumin. The catalytic activity of the octapeptides was much higher than the [GADV]-P(30) produced through repeated heat-drying treatments. These results also support the [GADV]-protein-world hypothesis of the origin of life (see Ikehara's review, 2002). Possible steps for the emergence of life on the primitive earth are presented."
Oba T, Fukushima J, Maruyama M, Iwamoto R, Ikehara K. Catalytic Activities Of [GADV]-Peptides Formation and Establishment of [GADV]-Protein World for the Emergence of Life. Orig Life Evol Biosph. 2005 Oct;35(5):447-60.

Dynamic co-evolution of peptides and chemical energetics, a gateway to the emergence of homochirality and the catalytic activity of peptides. : "We propose a scenario for the dynamic co-evolution of peptides and energy on the primitive Earth. From a multi component system consisting of hydrogen cyanide, several carbonyl compounds, ammonia, alkyl amine, carbonic anhydride, borate and isocyanic acid, we show that the reversibility of this system leads to several intermediate nitriles, that irreversibly evolve to alpha-amino acids and N-carbamoyl amino acids via selective catalytic processes. On the primitive Earth these N-carbamoyl amino acids combined with energetic molecules (NOx) may have been the core of a molecular engine producing peptides permanently and assuring their recycling and evolution. We present this molecular engine, a production example, and its various selectivities. The perspectives for such a dynamic approach to the emergence of peptides are evoked in the conclusion."Commeyras A, Taillades J, Collet H, Boiteau L, Vandenabeele-Trambouze O, Pascal R, Rousset A, Garrel L, Rossi JC, Biron JP, Lagrille O, Plasson R, Souaid E, Danger G, Selsis F, Dobrijevic M, Martin H.Dynamic co-evolution of peptides and chemical energetics, a gateway to the emergence of homochirality and the catalytic activity of peptides. Orig Life Evol Biosph. 2004 Feb;34(1-2):35-55.

Peptides by activation of amino acids with CO on (Ni,Fe)S surfaces: implications for the origin of life. : "In experiments modeling volcanic or hydrothermal settings amino acids were converted into their peptides by use of coprecipitated (Ni,Fe)S and CO in conjunction with H2S (or CH3SH) as a catalyst and condensation agent at 100 degreesC and pH 7 to 10 under anaerobic, aqueous conditions. These results demonstrate that amino acids can be activated under geochemically relevant conditions. They support a thermophilic origin of life and an early appearance of peptides in the evolution of a primordial metabolism."
Huber C, Wachtershauser G. Peptides by activation of amino acids with CO on (Ni,Fe)S surfaces: implications for the origin of life. Science. 1998 Jul 31;281(5377):670-2.
Comment in: Science. 1998 Jul 31;281(5377):627, 629.

A possible primordial peptide cycle. : "alpha-Amino acids can undergo peptide formation by activation with carbon monoxide (CO) under hot aqueous conditions in the presence of freshly coprecipitated colloidal (Fe,Ni)S. We now show that CO-driven peptide formation proceeds concomitantly with CO-driven, N-terminal peptide degradation by racemizing N-terminal hydantoin and urea derivatives to alpha-amino acids. This establishes a peptide cycle with closely related anabolic and catabolic segments. The hydantoin derivative is a purin-related heterocycle. The (Fe,Ni)S-dependent urea hydrolysis could have been the evolutionary precursor of the nickelenzyme urease. The results support the theory of a chemoautotrophic origin of life with a CO-driven, (Fe,Ni)S-dependent primordial metabolism."
Huber C, Eisenreich W, Hecht S, Wachtershauser G. A possible primordial peptide cycle. Science. 2003 Aug 15;301(5635):938-40.

[The simultaneous synthesis of peptides and oligonucleotides on kaolinite with the participation of aminoacyladenylates] "A simultaneous synthesis of peptides (2-5 residues) and oligonucleotides (3-9 residues) has been carried out on caolinite matrix using amino acids and aminoacyladenylates as substrates. The rate of oligomer synthesis on mineral surface is higher than that in solution. The mechanism of synthesis has been described. The data has been discussed in connection with abiogenesis of two major types of biopolymers, proteins and nucleic acids."
[The simultaneous synthesis of peptides and oligonucleotides on kaolinite with the participation of aminoacyladenylates]Egofarova RKh, Vasil'eva NV, Moiseeva LN, Otroshchenko VA, Pavlovskaia TE.Izv Akad Nauk SSSR Biol. 1990 Jan-Feb;(1):136-40.

Comparative study of abiogenesis of cysteine and other amino acids catalyzed by various metal ions. : "The present work pertains to the study of the influence of nickel, cobalt, thorium, vanadium, molybdate, ferrous ions on the formation of cysteine which is synthesized abiogenically together with other amino acids in sterilized aqueous mixtures of ammonium thiocyanate, formaldehyde, potassium dihydrogen phosphate, calcium acetate, and biological minerals after irradiating by artificial light. The effect of these catalysts on cysteine formation was of the order: Fe++ greater than Mo++ greater than Th++++ greater than V++ greater than Co++ greater than Ni."Bahadur K, Sen P.Comparative study of abiogenesis of cysteine and other amino acids catalyzed by various metal ions.Z Allg Mikrobiol. 1975;15(3):143-7.

Aqueous synthesis of Peptide thioesters from amino acids and a thiol using 1,1'-carbonyldiimidazole. : "A new method was developed for the synthesis of peptide thioesters from free amino acids and thiols in water. This one-pot simple method involves two steps: (1) activation in water of an amino acid presumably as its N-carboxyanhydride (NCA) using 1,1'-carbonyldiimidazole (CDI), and (2) subsequent condensation of the activated amino acid-NCA in the presence of a thiol. With this method citrulline peptide thioesters containing up to 10 amino acid residues were prepared in a single reaction. This aqueous synthetic method provides a simple way to prepare peptide thioesters for studies of peptide replication involving ligation of peptide thioesters on peptide templates. The relevance of peptide replication to the origin-of-life process is supported by previous studies showing that amino acid thioesters (peptide thioester precursors) can be synthesized under prebiotic conditions by reaction of small sugars with ammonia and a thiol."
Weber AL. Aqueous synthesis of Peptide thioesters from amino acids and a thiol using 1,1'-carbonyldiimidazole. Orig Life Evol Biosph. 2005 Oct;35(5):421-7.

A model for the role of short self-assembled peptides in the very early stages of the origin of life : "The molecular basis of the origin of life is one of the most fundamental questions in modern biology. While the 'RNA world' hypothesis offers a very sensible model for the evolvement of the current biochemical networks, there is a lack of knowledge about the early steps that led to the formation of the first RNA molecules. This issue is essential as it is practically impossible that complex molecules as functional RNA oligonucleotides had evolved spontaneously. It was recently demonstrated that peptide molecules as simple as dipeptides can self-assemble into well-ordered tubular, fibrilar, and closed-cage structures. Other studies have confirmed the ability of dipeptides to act as catalysts and the capability of other peptides, as short as tripeptides, to serve as a template for nucleotide binding and orientation. Unlike complex RNA molecules, the spontaneous formation of functional short peptides in the primordial earth conditions is very likely. We suggest a novel mechanism for the origin of life that is based on the ability of short peptides to form encapsulated structures, catalyst chemical reaction, and serve as highly ordered template for the assembly of nucleotides. This model may explain the early events that led to the formation of the current biochemical machinery that combines the elaborated and coordinated interaction between nucleic acids and proteins to allow the function of living systems."
Carny O, Gazit E. A model for the role of short self-assembled peptides in the very early stages of the origin of life. FASEB J. 2005 Jul;19(9):1051-5.

N-carbamoyl-alpha-amino acids rather than free alpha-amino acids formation in the primitive hydrosphere: a novel proposal for the emergence of prebiot : "Our previous kinetic and thermodynamic studies upon the reactional system HCHO/HCN/NH3 in aqueous solutions are completed. In the assumed prebiotic conditions of the primitive earth ([HCHO] and [HCN] near 1 g L-1, T = 25 degrees C, pH = 8, [NH3] very low), this system leads to 99.9% of alpha-hydroxyacetonitrile and 0.1% of alpha-aminoacetonitrile (precursor of the alpha-amino acid). The classical base-catalyzed hydration of nitriles, slow and not selective, can not modify significantly this proportion. On the contrary, we found two specific and efficient reactions of alpha-aminonitriles which shift the initial equilibrium in favor of the alpha-aminonitrile pathway. The first reaction catalyzed by formaldehyde generates alpha-aminoamides, precursors of alpha-aminoacids. The second reaction catalyzed by carbon dioxide affords hydantoins, precursors of N-carbamoyl-alpha-aminoacids. In the primitive hydrosphere, where the concentration in carbon dioxide was estimated to be higher than that of formaldehyde, the formation of hydantoins was consequently more efficient. The rates of hydrolysis of the alpha-aminoacetamide and of the hydantoin at pH 8 being very similar, the synthesis of the N-carbamoyl-alpha-amino acid seems then to be the fatal issue of the HCHO/HCN/NH3 system that nature used to perform its evolution. These N-protected alpha-amino acids offer new perspectives in prebiotic chemistry, in particular for the emergence of peptides on the prebiotic earth."
Taillades J, Beuzelin I, Garrel L, Tabacik V, Bied C, Commeyras A.
N-carbamoyl-alpha-amino acids rather than free alpha-amino acids formation in the primitive hydrosphere: a novel proposal for the emergence of prebiotic peptides. Orig Life Evol Biosph. 1998 Feb;28(1):61-77.

Prebiotic transamination : "Biological amino acids and alpha keto acids directly condense with decarboxylation and transamination to yield product amino acids. This process is closely related to unusual amino acid decarboxylase enzymes in certain microorganisms and may represent a primordial mode of amino acid metabolism."
Bishop JC, Cross SD, Waddell TG. Prebiotic transamination. Orig Life Evol Biosph. 1997 Aug;27(4):319-24.

Evolution of selenocysteine-containing proteins: significance of identification and functional characterization of selenoproteins. : "In the genetic code, UGA serves as either a signal for termination or a codon for selenocysteine (Sec). Sec rarely occurs in protein and is different from other amino acids in that much of the biosynthetic machinery governing its incorporation into protein is unique to this amino acid. Sec-containing proteins have diverse functions and lack a common amino acid motif or consensus sequence. Sec has previously been considered to be a relic of the primordial genetic code that was counter-selected by the presence of oxygen in the atmosphere. In the present report, it is proposed that Sec was added to the already existing genetic code and its use has accumulated during evolution of eukaryotes culminating in vertebrates. The more recently evolved selenoproteins appear to take advantage of unique redox properties of Sec that are superior to those of Cys for specific biological functions. Further understanding of the evolution of selenoproteins as well as biological properties and biomedical applications of the trace element selenium requires identification and functional characterization of all mammalian selenoproteins."
Gladyshev VN, Kryukov GV. Evolution of selenocysteine-containing proteins: significance of identification and functional characterization of selenoproteins. Biofactors. 2001;14(1-4):87-92.

Theoretical Biology and Medical Modelling Full text Three subsets of sequence complexity and their relevance to biopolymeric information: "In life-origin science, attention usually focuses on a theorized pre-RNA World [52-55]. RNA chemistry is extremely challenging in a prebiotic context. Ribonucleotides are difficult to activate (charge). And even oligoribonucleotides are extremely hard to form, especially without templating. The maximum length of such single strands in solution is usually only eight to ten monomers (mers). As a result, many investigators suspect that some chemical RNA analog must have existed [56,57]. "
Abel DL, Trevors JT. Three subsets of sequence complexity and their relevance to biopolymeric information. Theor Biol Med Model. 2005 Aug 11;2:29. Free Full Text article

Modeling the emergence of multi-protein dynamic structures by principles of self-organization through the use of 3DSpi, a multi-agent-based software. : "BACKGROUND: There is an increasing need for computer-generated models that can be used for explaining the emergence and predicting the behavior of multi-protein dynamic structures in cells. Multi-agent systems (MAS) have been proposed as good candidates to achieve this goal. RESULTS: We have created 3DSpi, a multi-agent based software that we used to explore the generation of multi-protein dynamic structures. Being based on a very restricted set of parameters, it is perfectly suited for exploring the minimal set of rules needed to generate large multi-protein structures. It can therefore be used to test the hypothesis that such structures are formed and maintained by principles of self-organization. We observed that multi-protein structures emerge and that the system behavior is very robust, in terms of the number and size of the structures generated. Furthermore, the generated structures very closely mimic spatial organization of real life multi-protein structures. CONCLUSION: The behavior of 3DSpi confirms the considerable potential of MAS for modeling subcellular structures. It demonstrates that robust multi-protein structures can emerge using a restricted set of parameters and allows the exploration of the dynamics of such structures. A number of easy-to-implement modifications should make 3DSpi the virtual simulator of choice for scientists wishing to explore how topology interacts with time, to regulate the function of interacting proteins in living cells."Soula H, Robardet C, Perrin F, Gripon S, Beslon G, Gandrillon O. Modeling the emergence of multi-protein dynamic structures by principles of self-organization through the use of 3DSpi, a multi-agent-based software. BMC Bioinformatics. 2005 Sep 19;6:228. Free Full Text article

Investigation of the prebiotic synthesis of amino acids and RNA bases from CO2 using FeS/H2S as a reducing agent. : "An autotrophic theory of the origin of metabolism and life has been proposed in which carbon dioxide is reduced by ferrous sulfide and hydrogen sulfide by means of a reversed citric acid cycle, leading to the production of amino acids. Similar processes have been proposed for purine synthesis. Ferrous sulfide is a strong reducing agent in the presence of hydrogen sulfide and can produce hydrogen as well as reduce alkenes, alkynes, and thiols to saturated hydrocarbons and reduce ketones to thiols. However, the reduction of carbon dioxide has not been demonstrated. We show here that no amino acids, purines, or pyrimidines are produced from carbon dioxide with the ferrous sulfide and hydrogen sulfide system. Furthermore, this system does not produce amino acids from carboxylic acids by reductive amination and carboxylation. Thus, the proposed autotrophic theory, using carbon dioxide, ferrous sulfide, and hydrogen sulfide, lacks the robustness needed to be a geological process and is, therefore, unlikely to have played a role in the origin of metabolism or the origin of life."Keefe AD, Miller SL, McDonald G, Bada J. Investigation of the prebiotic synthesis of amino acids and RNA bases from CO2 using FeS/H2S as a reducing agent. Proc Natl Acad Sci U S A. 1995 Dec 5;92(25):11904-6. Free Full Text article

Hydrothermal vents

2006-06-30T17:59:00.000-11:00

ScienceDirect - Trends in Biochemical Sciences : The rocky roots of the acetyl-CoA pathway: "Geologists have suggested that life might have emerged at hydrothermal vents, chemists have shown that metal sulphides such as FeS and NiS can catalyse biochemical reactions in the absence of proteins, and biologists have suggested that the acetyl-coenzyme-A (CoA) pathway of CO2 fixation might be very ancient. New findings from the enzymes at the heart of the acetyl-CoA pathway, carbon monoxide dehydrogenase (CODH) and acetyl-CoA synthase (ACS), indicate that metals and metal sulphides do the biochemical work of CO2 fixation. Here we propose that biochemistry got started when the two volatiles that were thermodynamically furthest from equilibrium on the early Earth -- namely, marine CO2 from volcanoes and hydrothermal H2 -- met at a hydrothermal vent rich in metal sulphides. In this 'hydrothermal reactor' hypothesis, a primitive, inorganically catalysed analogue of the exergonic acetyl-CoA pathway, using H2 as the initial electron donor and CO2 as the initial acceptor, was instrumental in the synthesis of organic precursors to fuel primordial biochemical reactions. We suggest that primordial biochemistry was housed in an acetate-producing hydrothermal reactor that retained reduced carbon compounds produced within its naturally forming inorganic confines."Michael J. Russell and William Martin, The rocky roots of the acetyl-CoA pathway Trends in Biochemical Sciences Volume 29, Issue 7 , July 2004, Pages 358-363

Hydrothermal simulation experiments as a tool for studies of the origin of life on Earth and other terrestrial planets: a review. : "The potential of life's origin in submarine hydrothermal systems has been evaluated by a number of investigators by conducting high temperature-high pressure experiments involving organic compounds. In the majority of these experiments little attention has been paid to the importance of constraining important parameters, such as the pH and the redox state of the system. This is particularly revealed in the apparent difficulties in interpreting experimental data from hydrothermal organic synthesis and stability studies. However, in those cases where common mineral assemblages have been used in an attempt to buffer the pH and redox conditions to geologically and geochemically realistic values, theoretical and experimental data seem to converge. The use of mineral buffer assemblages provides a convenient way by which to constrain the experimental conditions. Studies at high temperatures and pressure in the laboratory have revealed a number of reactions that proceed rapidly in hydrothermal fluids, including the Strecker synthesis of amino acids. In other cases, the verification of postulated abiotic reaction mechanisms has not been possible, at least for large molecules such as large fatty acids and hydrocarbons. This includes the Fischer-Tropsch synthesis reaction. High temperature-high pressure experimental methods have been developed and used successfully for a long time in, for example, mineral solubility studies under hydrothermal conditions. By taking advantage of this experimental experience new and, at times, unexpected directions can be taken in bioorganic geochemistry, one being, for instance, primitive two-dimensional information coding. This article critically reviews some of the organic synthesis and stability experiments that have been conducted under simulated submarine hydrothermal conditions. We also discuss some of the theoretical and practical considerations that apply to hydrothermal laboratory studies of organic molecules related to the origin of life on Earth and probably also to the other terrestrial planets."
Holm NG, Andersson E. Hydrothermal simulation experiments as a tool for studies of the origin of life on Earth and other terrestrial planets: a review. Astrobiology. 2005 Aug;5(4):444-60.

Nitrogen reduction under hydrothermal vent conditions: implications for the prebiotic synthesis of C-H-O-N compounds. : "Dinitrogen is reduced in dilute hydrogen sulfide (H2S) solutions to ammonium at 120 degrees C. Experiments with dissolved dinitrogen (partial pressure 50 bar) in a 12 x 10(-3) mol/L H2S(aq) solution yield approximately 10(-5) mol/L NH4+ within 2-7 days. These yields are consistent with the equilibrium NH4+ concentration for the N-S-H system under these conditions. The formation of ammonium is catalyzed by the presence of freshly precipitated iron monosulfide. These results indicate that dinitrogen can be reduced at moderate temperatures in hydrothermal vent systems. Abiotic nitrogen reduction could have taken place within primordial hydrothermal vents, supplying some ammonia for the synthesis of C-H-O-N compounds via abiotic processes. The yield of ammonia via dinitrogen reduction by hydrogen sulfide, however, is so low that it is doubtful this process could have produced enough ammonia to sustain prebiotic hydrothermal synthesis of C-H-O-N compounds in or around vent systems."
Schoonen MA, Xu Y. Nitrogen reduction under hydrothermal vent conditions: implications for the prebiotic synthesis of C-H-O-N compounds. Astrobiology. 2001 Summer;1(2):133-42.

Sulphate metabolism among thermophiles and hyperthermophiles in natural aquatic systems.

2006-06-30T17:40:00.000-11:00

Entrez PubMed: "Although controversial, the idea that hydrothermal systems may have been the site for prebiotic synthesis of organic molecules and origin of life is widely supported. For the nascent life to survive, it must have had some sort of metabolic mechanism for generating energy. However, little is known of the specific metabolic pathways utilized by the early life forms or the effect of high temperatures on their activity. Recent research on natural high temperature aquatic environments, though limited because of difficult field logistics and experimental problems, is revolutionizing our understanding of possible energy-generating redox pathways, such as sulphate reduction. An abridged review of research on thermophilic sulphate reduction is presented here. Because of a complex interplay between microbiological and geochemical entities involved, and the uncertainties that modern hydrothermal systems are proxy for biogeochemical conditions on early Earth, great caution is required for interpretation and extrapolation of data from these studies to primordial times. Furthermore, a general lack of integrated geological and microbiological studies towards a common understanding of origin and sustenance of life on Earth is starkly evident from this review."

Roychoudhury AN. Sulphate metabolism among thermophiles and hyperthermophiles in natural aquatic systems. Biochem Soc Trans. 2004 Apr;32(Pt 2):172-4.

The emergence of life from iron monosulphide bubbles at a submarine hydrothermal redox and pH front.

2006-06-30T17:33:00.000-11:00

Entrez PubMed: "Here we argue that life emerged on Earth from a redox and pH front at c. 4.2 Ga. This front occurred where hot (c. 150 degrees C), extremely reduced, alkaline, bisulphide-bearing, submarine seepage waters interfaced with the acid, warm (c. 90 degrees C), iron-hearing Hadean ocean. The low pH of the ocean was imparted by the ten bars of CO2 considered to dominate the Hadean atmosphere/hydrosphere. Disequilibrium between the two solutions was maintained by the spontaneous precipitation of a colloidal FeS membrane. Iron monosulphide bubbles comprising this membrane were inflated by the hydrothermal solution upon sulphide mounds at the seepage sites. Our hypothesis is that the FeS membrane, laced with nickel, acted as a semipermeable catalytic boundary between the two fluids, encouraging synthesis of organic anions by hydrogenation and carboxylation of hydrothermal organic primers. The ocean provided carbonate, phosphate, iron, nickel and protons; the hydrothermal solution was the source of ammonia, acetate, HS-, H2 and tungsten, as well as minor concentrations of organic sulphides and perhaps cyanide and acetaldehyde. The mean redox potential (delta Eh) across the membrane, with the energy to drive synthesis, would have approximated to 300 millivolts. The generation of organic anions would have led to an increase in osmotic pressure within the FeS bubbles. Thus osmotic pressure could take over from hydraulic pressure as the driving force for distension, budding and reproduction of the bubbles. Condensation of the organic molecules to polymers, particularly organic sulphides, was driven by pyrophosphate hydrolysis. Regeneration of pyrophosphate from the monophosphate in the membrane was facilitated by protons contributed from the Hadean ocean. This was the first use by a metabolizing system of protonmotive force (driven by natural delta pH) which also would have amounted to c. 300 millivolts. Protonmotive force is the universal energy transduction mechanism of life. Taken together with the redox potential across the membrane, the total electrochemical and chemical energy available for protometabolism amounted to a continuous supply at more than half a volt. The role of the iron sulphide membrane in keeping the two solutions separated was appropriated by the newly synthesized organic sulphide polymers. This organic take-over of the membrane material led to the miniaturization of the metabolizing system. Information systems to govern replication could have developed penecontemporaneously in this same milieu. But iron, sulphur and phosphate, inorganic components of earliest life, continued to be involved in metabolism."
Russell MJ, Hall AJ. The emergence of life from iron monosulphide bubbles at a submarine hydrothermal redox and pH front. J Geol Soc London. 1997 May;154(3):377-402.

On the origin of genomes and cells within inorganic compartments.

2006-06-30T16:58:00.000-11:00

Entrez PubMed: "Building on the model of Russell and Hall for the emergence of life at a warm submarine hydrothermal vent, we suggest that, within a hydrothermally formed system of contiguous iron-sulfide (FeS) compartments, populations of virus-like RNA molecules, which eventually encoded one or a few proteins each, became the agents of both variation and selection. The initial darwinian selection was for molecular self-replication. Combinatorial sorting of genetic elements among compartments would have resulted in preferred proliferation and selection of increasingly complex molecular ensembles - those compartment contents that achieved replication advantages. The last universal common ancestor (LUCA) we propose was not free-living but an inorganically housed assemblage of expressed and replicable genetic elements. The evolution of the enzymatic systems for (i) DNA replication; and (ii) membrane and cell wall biosynthesis, enabled independent escape of the first archaebacterial and eubacterial cells from their hydrothermal hatchery, within which the LUCA itself remained confined."

Koonin EV, Martin W. On the origin of genomes and cells within inorganic compartments. Trends Genet. 2005 Oct 10; [Epub ahead of print]

Thermal force approach to molecular evolution.

2006-06-30T16:50:00.000-11:00

Entrez PubMed: "Recent experiments are discussed where temperature gradients across mesoscopic pores are shown to provide essential mechanisms for autonomous molecular evolution. On the one hand, laminar thermal convection can drive DNA replication as the molecules are continuously cycled between hot and cold regions of a chamber. On the other hand, thermophoresis can accumulate charged biopolymers in similar convection settings. The experiments show that temperature differences analogous to those across porous rocks present a robust nonequilibrium boundary condition to feed the replication and accumulation of evolving molecules. It is speculated that similar nonequilibrium conditions near porous submarine hydrothermal mounds could have triggered the origin of life. In such a scenario, the encapsulation of cells with membranes would be a later development. It is expected that detailed studies of mesoscopic boundary conditions under nonequilibrium conditions will reveal new connecting pieces in the fascinating puzzle of the origins of life."

Braun D, Libchaber A. Thermal force approach to molecular evolution. Phys Biol. 2004 Jun;1(1-2):P1-8.

Review: Controversies on the origin of life

2006-06-22T10:26:00.000-11:00

International Microbiology - Controversies on the origin of life: "Different viewpoints, many with deep philosophical and historical roots, have shaped the scientific study of the origin of life. Some of these argue that primeval life was based on simple anaerobic microorganisms able to use a wide inventory of abiotic organic materials (i.e. a heterotrophic origin), whereas others invoke a more sophisticated organization, one that thrived on simple inorganic molecules (i.e. an autotrophic origin). While many scientists assume that life started as a self-replicative molecule, the first gene, a primitive self-catalytic metabolic network has also been proposed as a starting point. Even the emergence of the cell itself is a contentious issue: did boundaries and compartments appear early or late during life's origin? Starting with a recent definition of life, based on concepts of autonomy and open-ended evolution, it is proposed here that, firstly, organic molecules self-organized in a primordial metabolism located inside protocells. The flow of matter and energy across those early molecular systems allowed the generation of more ordered states, forming the cradle of the first genetic records. Thus, the origin of life was a process initiated within ecologically interconnected autonomous compartments that evolved into cells with hereditary and true Darwinian evolutionary capabilities. In other words, the individual existence of life preceded its historical-collective dimension."

Juli Peretó Controversies on the origin of life INT. MICROBIOL. vol.8 no.1 Madrid Mar. 2005

Astrobiology

2006-05-31T17:59:00.000-11:00

Chemical evolution and the origin of life. : "During the last three decades major advances have been made in our understanding of the formation of carbon compounds in the universe and of the occurence of processes of chemical evolution. 1) Carbon and other biogenic elements (C,H,N,O,S and P) are some of the most abundant in the universe. 2) The interstellar medium has been found to contain a diversity of molecules of these elements. 3) Some of these molecules have also been found in comets which are considered the most primordial bodies of the solar system. 4) The atmospheres of the outer planets and their satellites, for example, Titan, are actively involved in the formation of organic compounds which are the precursors of biochemical molecules. 5) Some of these biochemical molecules, such as amino acids, purines and pyrimidines, have been found in carbonaceous chondrites. 6) Laboratory experiments have shown that most of the monomers and oligomers necessary for life can be synthesized under hypothesized but plausible primitive Earth conditions from compounds found in the above cosmic bodies. 7) It appears that the primitive Earth had the necessary and sufficient conditions to allow the chemical synthesis of biomacromolecules and to permit the processes required for the emergence of life on our planet. 8) It is unlikely that the emergence of life occurred in any other body of the solar system, although the examination of the Jovian satellite Europa may provide important clues about the constraints of this evolutionary process. Some of the fundamental principles of chemical evolution are briefly discussed."
Oro J. Chemical evolution and the origin of life. Adv Space Res. 1983;3(9):77-94.

The universe: a cryogenic habitat for microbial life.

2006-05-31T17:42:00.000-11:00

Entrez PubMed: "Panspermia, an ancient idea, posits that microbial life is ubiquitous in the Universe. After several decades of almost irrational rejection, panspermia is at last coming to be regarded as a serious contender for the beginnings of life on our planet. Astronomical data is shown to be consistent with the widespread distribution of complex organic molecules and dust particles that may have a biological provenance. A minuscule (10(-21)) survival rate of freeze-dried bacteria in space is all that is needed to ensure the continual re-cycling of cosmic microbial life in the galaxy. Evidence that terrestrial life may have come from elsewhere in the solar system has accumulated over the past decade. Mars is seen by some as a possible source of terrestrial life, but some hundreds of billions of comets that enveloped the entire solar system, are a far more likely primordial reservoir of life. Comets would then have seeded Earth, Mars, and indeed all other habitable planetary bodies in the inner regions of the solar system. The implications of this point of view, which was developed in conjunction with the late Sir Fred Hoyle since the 1970s, are now becoming amenable to direct empirical test by studies of pristine organic material in the stratosphere. The ancient theory of panspermia may be on the verge of vindication, in which case the entire universe would be a grand crucible of cryomicrobiology."

Wickramasinghe C. The universe: a cryogenic habitat for microbial life. Cryobiology. 2004 Apr;48(2):113-25.

Possible steps to the emergence of life: the [GADV]-protein world hypothesis.

2006-05-13T09:24:00.000-11:00

Possible steps to the emergence of life: the [GADV]-protein world hypothesis.: "Possible steps to the emergence of life: the [GADV]-protein world hypothesis.
Chem Rec. 2005; 5(2):107-18 (ISSN: 1527-8999)
Ikehara K
Department of Chemistry, Faculty of Science, Nara Women's University, Kita-uoya-nishi-machi, Nara, Nara 630-8506, Japan. ikehara@cc.nara-wu.ac.jp

Based on the fact that RNA has not only a genetic function but also a catalytic function, the RNA world theory on the origin of life was first proposed about 20 years ago. The theory assumes that RNA was amplified by self-replication to increase RNA diversity on the primitive earth. Since then, the theory has been widely accepted as the most likely explanation for the emergence of life. In contrast, we reached another hypothesis, the [GADV]-protein world hypothesis, which is based on pseudo-replication of [GADV]-proteins. We reached this hypothesis during studies on the origins of genes and the genetic code, where [G], [A], [D], and [V] refer to Gly, Ala, Asp, and Val, respectively. In this review, possible steps to the emergence of life are discussed from the standpoint of the [GADV]-protein world hypothesis, comparing it in parallel with the RNA world theory. It is also shown that [GADV]-peptides, which were produced by repeated dry-heating cycles and by solid phase peptide synthesis, have catalytic activities, hydrolyzing peptide bonds in a natural protein, bovine serum albumin. These experimental results support the [GADV]-protein world hypothesis for the origin of life."

Metabolic Life Theory

2006-05-12T11:40:00.000-11:00

Extremophiles 2002 -- Rossi et al. 185 (13): 3683 -- The Journal of Bacteriology: "most molecules with essential biological functions, such as nucleotides, some amino acids, and nucleic acids, are thermolabile. Miller's 'primitive soup' hypothesis, implying that the first living organisms used RNA as the information molecule, has been challenged by the 'metabolic life ' theory. This hypothesis suggests that primordial 'life' was nothing other than a series of self-catalyzed reactions based on simple compounds such as CO2 and CO. Since many reactions are thermodynamically more favorable at high temperatures, it has been suggested that hydrothermal environments were the cradle of this 'metabolic life.' "

Minimal Genome

2006-04-30T05:59:00.000-11:00

2001: Mycoplasma genitalium with 517 genes has the smallest gene complement of any independently replicating cell so far identified. Analysis suggests that 265 to 350 of the 480 protein-coding genes of M. genitalium are essential under laboratory growth conditions, including about 100 genes of unknown function. Science -- Abstracts: Hutchison et al. 286 (5447): 2165

2002: Here we show evidence of six species with a genome size smaller than Mycoplasma genitalium, the smallest bacterial genome reported thus far (580 kb). Our findings strongly suggest that the Buchnera genome is still experiencing a reductive process toward a minimum set of genes necessary for its symbiotic lifestyle. Extreme genome reduction in Buchnera spp.: Toward the minimal ...

2001: 2001: Genome Biology Full text The complexity of simplicity

Another Minimal Genome: Microbe Needs Just 271 Genes : Free Full Text : Modified: "A minimal genome is the smallest set of genes that an organism needs to live in a particular environment. While most microbes have hundreds or thousands of genes, some use only a fraction of these at any one time, depending on their surroundings."

The bacterium Bacillus subtilis needs just 271 genes to live in an experimental environment that is rich in nutrients, a new study has found. The calculated minimum of 271 genes is a small fraction of the organism's roughly 4,100 genes. To arrive at the number 271, the researchers grew thousands of B. subtilis cells and systematically inactivated one gene per cell.

The ideal test of a minimal genome would be to inactivate every non-essential gene in a single cell, but the technology to accomplish this does not yet exist. The vast majority of essential genes in B. subtilis belong to one of five categories, such as “information processing” and “protein synthesis.” Only a few essential genes could not be categorized because so little was known about them.

“One of the interesting aspects of the study was that we found so few essential genes of unknown function,“ says Dusko. “This shows that there are fewer holes in our understanding of the living cell than early studies led us to believe.”

Researchers hope ultimately to construct a minimal genome, using information about different microbes. Hundreds of "essential" genes in bacteria have been identified in recent years, providing a rough idea of what minimal genomes might look like.

The minimal genomes published to date range in number from about 260 genes to 670 genes, depending upon the organism, the environment in which it grows, and the strategy used to calculate which genes are essential."

Kobayashi, K. et al. Essential Bacillus subtilis genes. Proc Natl Acad Sci USA 100, 4678-4683 (April 15, 2003).

2005 : PEC (Profiling of E.coli Chromosome) : 250 genes minimal : 3,262,049 bp - genome map
: 3,262,049 bp - genome map

GENETICS:Ethical Considerations in Synthesizing a Minimal Genome -- Cho et al. 286 (5447): 2087 -- Science: "Researchers are attempting to model and eventually to create 'minimal organisms,' organisms with the smallest set of genes that allow for survival and reproduction. Although the ability to create such an organism is beyond current technology, the work of Hutchison et al., reported in this issue, represents an important step in the path toward the creation of such an organism. Here we identify ethical, social, and religious issues raised by this research. Issues discussed include the potential abuse of the technology (biological weapons, environmental problems), as well as the challenge it poses to our conception of the meaning of life."

Cairns-Smith model

2006-03-31T17:59:00.000-11:00

ScienceWeek: Modified: "in 1982, the chemist A.G. Cairns-Smith suggested that life developed from crystals, with organic evolution coupled to the replication of clay crystals. In the Cairns-Smith model, life is envisaged as beginning through the influence of natural selection on the growth of inorganic crystals. Clay structures are conceived of as the first carriers of genetic information. Replication is viewed as occurring by the accidental detachment of layers in the clay
lattice, these layers serving as nuclei for the growth of new daughter molecules. Later, organic chemicals were incorporated into the structure of the replicating crystallites. Competition favored those systems that were more adaptable by virute of employing used organic molecules to carry out their functions. Nucleic acids (RNA and DNA) evolved next, and replaced clay crystals as the basic information repository making up the genes of the organism. Under the pressure of natural selection, the original clay-mineral component was dispensed with entirely."

Clay Material May Have Acted As 'Primordial Womb' For First Organic Molecules: "Williams' research suggests how some of the fundamental materials necessary for life might have come into existence deep in the sea. The results of Williams' experiments were published in the article, "Organic Molecules Formed in a Primordial Womb," in the November issue of Geology.Williams and her team mimicked the conditions found in hydrothermal vents along the lines where tectonic plates converge on the ocean floor. The vents are fissures in the seafloor that spew out super-hot water much like an underwater volcano.From earlier work, the researchers knew that with high enough temperatures and pressure, volcanic emanations could produce the chemical compound methanol. What scientists did not know was how the methanol could survive intense temperatures of 300 to 400 C.Williams and her team simulated the intense heat and pressure of the ocean floor within a pressurized vessel. The reaction of the clay and methanol was monitored over six weeks. The team found that the expandable clay not only protected the methanol, but also promoted reactions that formed even more complex organic compounds. The mineralogical reaction between the clay and methanol was facilitating the production of new organic material.Scientists theorize that the diverse organic molecules protected within the clay might eventually be expelled into an environment more hospitable to life, leading to an 'organic soup.' What makes the finding so exciting is that the experimental conditions reflect scientists' best estimations of the simplest conditions that likely existed when life began, Williams said."

Adsorption On Clay Accounts For Organic-Rich Rocks: "Kennedy explained that smectite crystals bear a large charged surface area that is attractive to organic molecules. As smectite sinks through sea water it adsorbs carbon-rich molecules into its intercrystalline surfaces.The existence of organic matter on smectite surfaces also helps understand an important process -- natural clay catalysis -- in the formation of petroleum."

Differential Adsorption of Nucleic Acid Bases: ScienceWeek: Modified: "Researchers nowreport they have determined the equilibrium adsorption isotherms for the nucleic acid purine and pyrimidine bases dissolved in surface water on crystalline graphite. The bases exhibited different adsorption behavior, generating an elution series: guanine > adenine > hypoxanthine > thymine > cytosine > uracil. Such differential adsorption properties may have been relevant to the prebiotic chemistry of the bases, and may have influenced the composition of the primordial genetic architecture."S.J. Sowerby et al: Proc. Natl. Acad. Sci. US 30 Jan 01 98:820

Intercalation of amino acids and peptides into Mg-Al layered double hydroxide by reconstruction method.

2006-03-31T17:32:00.000-11:00

Entrez PubMed: "The intercalation of amino acids and some peptides into Mg-Al layered double hydroxide known as hydrotalcite was examined. Although the intercalation by ion-exchange method was unsuccessful, all the amino acids except for Lys and Arg, and peptides examined could be intercalated into the layered double hydroxide by reconstruction method using Mg-Al oxide precursor. The uptake amounts of amino acids and peptides were 0.9-2.7 mmol per 1 g of LDH. Intercalation compounds were examined by using XRD and solid-state NMR. For Gly, Ala, Ser, Thr, Pro, Asn, Gln, Asp, Glu, and aspartame the intercalation accompanied the expansion of interlayer distance of the solid products, whereas the other amino acids and oligoglycine showed no expansion. The intercalation mechanism and release profile in K(2)CO(3) aqueous solution were also investigated. And the cointercalation of amino acids and peptides into Mg-Al LDH and easy release of amino acids from the LDH layer were found."
Nakayama H, Wada N, Tsuhako M. Intercalation of amino acids and peptides into Mg-Al layered double hydroxide by reconstruction method. Int J Pharm. 2004 Jan 28;269(2):469-78.

In Search of the Simplest Cell

2006-02-28T17:59:00.000-11:00

ORIGIN OF LIFE: IN SEARCH OF THE SIMPLEST CELL: "In investigating the origin of life and the simplest possible life forms, one needs to enquire about the composition and working of a minimal cell that has some form of metabolism, genetic replication from a template, and boundary (membrane) production."

Hypothesis: the origin of life in a hydrogel environment. : "A hypothesis is proposed that the first cell(s) on the Earth assembled in a hydrogel environment. Gel environments are capable of retaining water, oily hydrocarbons, solutes, and gas bubbles, and are capable of carrying out many functions, even in the absence of a membrane. Thus, the gel-like environment may have conferred distinct advantages for the assembly of the first cell(s)."
Trevors JT, Pollack GH. Prog Biophys Mol Biol. 2005 Sep;89(1):1-8. Hypothesis: the origin of life in a hydrogel environment.

Possible impact of a primordial oil slick on atmospheric and chemical evolution.: "Low molecular weight liquid hydrocarbons from various sources, could have formed an oil layer covering the primeval ocean (present already 4.0-4.4 x 10(9) yr ago), preventing water from evaporating into the atmosphere. Water from other sources, precipitated by cold traps at higher altitude in the atmosphere, becomes trapped in the ocean. In a thereby more dry and presumably reducing atmosphere (before 3.9 x 10(9) yr ago) even more hydrocarbons, as well as reactive molecules will form. An oil layer can possibly act as a dry solvent for reactions, where the reactive molecules can produce monomers and condensing agents. Monomers and eventual polymers formed could become strongly concentrated at the oil-water interface, favouring molecular interactions at high mobility and low dilution, without exposure to the destructive action of UV-light. Increased water leakiness of the oil layer due to accumulation of polar molecules within, would lead to photooxidation of liquid hydrocarbons, and subsequent emulsification at the oil-water interface, forming cellular structures. The atmosphere would then have lost its reducing character."
Nilson FP. Possible impact of a primordial oil slick on atmospheric and chemical evolution. Orig Life Evol Biosph. 2002 Jun;32(3):247-53.

Growth of organic microspherules in sugar-ammonia reactions : "Reaction of small sugars of less than four carbons with ammonia in water yielded organic microspherules generally less than ten microns in size. The time course of microspherule growth was examined for the D-erythrose-ammonia reaction that yielded microspherules attached to the glass walls of containers. Measurements were made of the elemental composition and infrared spectrum of the microspherule material. These viscose semi-solid microspherules are viewed as possible containers for prebiotic catalytic processes relevant to the origin of life."
Weber AL. Growth of organic microspherules in sugar-ammonia reactions. Orig Life Evol Biosph. 2005 Dec;35(6):523-36.

The possible origin of the first cell biosystem in the thermal subsurface environment of the earth. : "Bacteria are the simplest living biosystems or organisms that exhibit all the characteristics of life. As such, they are excellent models to examine the cell as the basic unit of life and the cell theory which states that all organisms are composed of one or more similar cells. In this article I examine the hypothesis that the primordial soup so often referred to in science was possibly an oil/water interface and/or emulsion in the Earth's, warm, anaerobic subsurface. This warm subsurface location, protected from surface radiation, could have been a favourable location for the assembly of the first bacterial cells on the Earth capable of growth and controlled division or the first biosystem."
Trevors JT. The possible origin of the first cell biosystem in the thermal subsurface environment of the earth. Riv Biol. 2004 Jan-Apr;97(1):79-90.

An archaeal antioxidant: characterization of a Dps-like protein from Sulfolobus solfataricus. : "Evolution of an oxygenic atmosphere required primordial life to accommodate the toxicity associated with reactive oxygen species. We have characterized an archaeal antioxidant from the hyperthermophilic acidophile Sulfolobus solfataricus. The amino acid sequence of this approximately 22-kDa protein shares little sequence similarity with proteins with known function. However, the protein shares high sequence similarity with hypothetical proteins in other archaeal and bacterial genomes. Nine of these hypothetical proteins form a monophyletic cluster within the broad superfamily of ferritin-like diiron-carboxylate proteins. Higher order structural predictions and image reconstructions indicate that the S. solfataricus protein is structurally related to a class of DNA-binding protein from starved cells (Dps). The recombinant protein self assembles into a hollow dodecameric protein cage having tetrahedral symmetry (SsDps). The outer shell diameter is approximately 10 nm, and the interior diameter is approximately 5 nm. Dps proteins have been shown to protect nucleic acids by physically shielding DNA against oxidative damage and by consuming constituents involved in Fenton chemistry. In vitro, the assembled archaeal protein efficiently uses H2O2 to oxidize Fe(II) to Fe(III) and stores the oxide as a mineral core on the interior surface of the protein cage. The ssdps gene is up-regulated in S. solfataricus cultures grown in iron-depleted media and upon H2O2 stress, but is not induced by other stresses. SsDps-mediated reduction of hydrogen peroxide and possible DNA-binding capabilities of this archaeal Dps protein are mechanisms by which S. solfataricus mitigates oxidative damage."
Wiedenheft B, Mosolf J, Willits D, Yeager M, Dryden KA, Young M, Douglas T. An archaeal antioxidant: characterization of a Dps-like protein from Sulfolobus solfataricus. Proc Natl Acad Sci U S A. 2005 Jul 26;102(30):10551-6. Epub 2005 Jul 15.Free Full Text article

Cyanophyta

2006-02-28T17:31:00.000-11:00

Two alternative views on the relationship of the major lineages (omitting viruses) based on phylogenies of Life on Earth (right - click to enlarge image).

The Cyanobacterial radiation within the Eubacteria consists of several lineages of phyletically (morphologically and genetically) related organisms. Several of these organisms show a striking resemblance to fossil counterparts (images). [R]

Cyanobacteria abstracts

2006-02-28T17:30:00.000-11:00

The bioenergetic role of dioxygen and the terminal oxidase(s) in cyanobacteria. : "Owing to the release of 13 largely or totally sequenced cyanobacterial genomes, it is now possible to critically assess and compare the most neglected aspect of cyanobacterial physiology, i.e., cyanobacterial respiration, also on the grounds of pure molecular biology (gene sequences). While there is little doubt that cyanobacteria (blue-green algae) do form the largest, most diversified and in both evolutionary and ecological respects most significant group of (micro)organisms on our earth, and that what renders our blue planet earth to what it is, viz. the O(2)-containing atmosphere, dates back to the oxygenic photosynthetic activity of primordial cyanobacteria about 3.2x10(9) years ago, there is still an amazing lack of knowledge on the second half of bioenergetic oxygen metabolism in cyanobacteria, on (aerobic) respiration. Thus, the purpose of this review is threefold: (1) to point out the unprecedented role of the cyanobacteria for maintaining the delicate steady state of our terrestrial biosphere and atmosphere through a major contribution to the poising of oxygenic photosynthesis against aerobic respiration ("the global biological oxygen cycle"); (2) to briefly highlight the membrane-bound electron-transport assemblies of respiration and photosynthesis in the unique two-membrane system of cyanobacteria (comprising cytoplasmic membrane and intracytoplasmic or thylakoid membranes, without obvious anastomoses between them); and (3) to critically compare the (deduced) amino acid sequences of the multitude of hypothetical terminal oxidases in the nine fully sequenced cyanobacterial species plus four additional species where at least the terminal oxidases were sequenced. These will then be compared with sequences of other proton-pumping haem-copper oxidases, with special emphasis on possible mechanisms of electron and proton transfer."

Paumann M, Regelsberger G, Obinger C, Peschek GA. The bioenergetic role of dioxygen and the terminal oxidase(s) in cyanobacteria. Biochim Biophys Acta. 2005 Apr-May;1707(2-3):231-53. Epub 2005 Jan 26.

Common freshwater cyanobacteria grow in 100% CO2. : "Cyanobacteria and similar organisms produced most of the oxygen found in Earth's atmosphere, which implies that early photosynthetic organisms would have lived in an atmosphere that was rich in CO2 and poor in O2. We investigated the tolerance of several cyanobacteria to very high (>20 kPa) concentrations of atmospheric CO2. Cultures of Synechococcus PCC7942, Synechocystis PCC7942, Plectonema boryanum, and Anabaena sp. were grown in liquid culture sparged with CO2-enriched air. All four strains grew when transferred from ambient CO2 to 20 kPa partial pressure of CO2 (pCO2), but none of them tolerated direct transfer to 40 kPa pCO2. Synechococcus and Anabaena survived 101 kPa (100%) pCO2 when pressure was gradually increased by 15 kPa per day, and Plectonema actively grew under these conditions. All four strains grew in an anoxic atmosphere of 5 kPa pCO2 in N2. Strains that were sensitive to high CO2 were also sensitive to low initial pH (pH 5-6). However, low pH in itself was not sufficient to prevent growth. Although mechanisms of damage and survival are still under investigation, we have shown that modern cyanobacteria can survive under Earth's primordial conditions and that cyanobacteria-like organisms could have flourished under conditions on early Mars, which probably had an atmosphere similar to early Earth's."
Thomas DJ, Sullivan SL, Price AL, Zimmerman SM. Common freshwater cyanobacteria grow in 100% CO2. Astrobiology. 2005 Feb;5(1):66-74.

Modern stromatolites -- living fossils

2006-02-28T17:25:00.000-11:00

Stromatolites in Shark Bay, Western Australia -- exposed (left) and submerged (right).

This extensive field of relict organisms was discovered in 1956. More examples occur in other locations on the ancient shield of western Australia. Map. Western Australia boasts some of the oldest known examples of stromatolites (3.45 billion years old), occurring as fossils in the Pilbara region between Marble Bar and Port Hedland. More recently, stromatolite colonies have been discovered in locations such as the Bahamas, the Indian Ocean, Yellowstone National Park, and Poza Azul lake at Cuatro Cienegas, Mexico.
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At low (left) and higher tides (right).

The water of Hamelin Pool within Shark Bay is twice as saline as typical sea-water because of rapid evaporation from the shallow water, and because a bar across the bay's entrance reduces mixing with normal brine. This hypersaline water is inhospitable to marine animals, which which otherwise would feed on the bacteria that construct stromatolites. As a result stromatolites can grow undisturbed in Shark Bay. Most stromatolites are extremely slow growing. Those in Hamelin Pool grow at a maximum of .3mm a year. This means that those that are up to a metre high are several thousands of years old. More images of stromatolites of Hamelin Pool (Shark Bay) / stromatolites displaying weathering / partly submerged / partly exposed

Structure of stromatolites

2006-02-28T17:20:00.000-11:00

Stromatolites grow slowly – layer upon layer – as mats of cyanobacteria grow atop older layers. Because this process still occurs today, paleontologists were able to determine the origin of carbonaceous material in fossilized laminated domes found widely around the globe.

Bacterial photosynthesis depletes carbon dioxide in the surrounding water, initiating precipitation of calcium carbonate. Layers of CaCO3 precipitate over the growing mat of bacterial filaments. This mineral, together with grains of sediment precipitating from the water, is trapped within a sticky layer of mucilage that surrounds the bacterial colonies. The cyanobacteria continued to grow upwards through this sediment to form a new layer. As this process occurs over and over again, layers of sediment are created.

Hamelin Pool in Shark Bay in western Australia is well known for the stromatolite "turfs" rising along its beaches. Meter-high stromatolites in the northern Bahamas are alternately buried and exhumed by carbonate sand bodies in an area of active bedform migration. Marooned Mexican stromatolites in Poza Azul lake at Cuatro Cienegas, Mexico, are of interest to NASA scientists who believe that these calcified clumps of primitive bacteria lurking in cactus-ringed lagoons could provide important clues in their search for extraterrestrial life. Images: diagram of stromatolites in dolomite block / fossil showing columnar structure / cylindrical structure / fossil showing striations / diagram of stromatolite morphology / stromatolite types /

Fossilized stromatolites

2006-02-28T17:15:00.000-11:00

Ancient fossilized strata of stomatolites at Steep Rock Iron Mine Steep Rock Stromatolites, Canada (right)

Originating over 3 billion years ago, stromatolites are the oldest known fossils. Fossilized stromatolites were laid down by colonial structures built by photosynthesizing cyanobacteria and other microbes. The cyanobacteria, also called blue-green algae, were likely responsible for the creation of earth's oxygen atmosphere. These organisms are prokaryotic – cells lacking a cellular nucleus – and thrived in warm aquatic environments, building reefs much as coral does today. Domed columns are typical, and the fossilized structures were quite extensive. Cyanobacteria were the dominant lifeform on Earth for over 2 billion years.

Today they are nearly extinct, living a precarious existence in only a few localities worldwide – the most famous location is Shark Bay in Western Australia. Domed columns are typical, and the fossilized structures were quite extensive.
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Close-up of Precambrian stromatolites of the 1.3 Ga Siyeh Formation in Glacier National Park (left).

NW Ontario, Canada contains the Archean Steep Rock carbonate platform, noted as one of the best-exposed and preserved platforms of this age on the planet. Stromatolite in ferruginous chert-carbonate unit, Kakabeka Falls Carbonate Chert Picture

More images of fossilized stromatolite reefs: Gunflint formation stromatolites on shore of Lake Superior / exhumed stromatolites 1.8 Ga near Great Slave Lake, Canada / close-up of Great Slave Lake stromatolites / Siyeh Formation stucture / bioherm of intertidal columnar stromatolites / domal stromatolites / Petrified Springs Reef near Saratoga Springs / Petrified Springs "Lion" / Lykins Formation / Table Head Group, Nfld / Ordovician St. George Group, Nfld / patch reef Middle Cambrian, Nfld / Durness Group, Scotland / stromatolite reef bed in Glacier National Park / Johnnie formation, California, 65 Ma / stromatolite reef Auvergne, France and close up of fossilized stromatolite / fossilized stromatolite reef in Mungok Ri, Korea / close-up of reef

"The centres of many stromatolites in the Siyeh Formation are concave downward rather than domed upward, as if they have collapsed. This may, indeed, have happened. The region lay close to the edge of the continent, where frequent earthquakes would have shaken the stromatolites, perhaps damaging them in this way." Source

Stromatolite fossils

2006-02-28T17:10:00.000-11:00

The fine details of fossilized stromatolites, together with chemical profiles and observation of modern stromatolites, reveal their origin in the slow accretion of minerals associated with cyanobacteria.

Three subsets of sequence complexity and their relevance to biopolymeric information.

2006-01-31T17:59:00.000-11:00

Entrez PubMed: "Genetic algorithms instruct sophisticated biological organization. Three qualitative kinds of sequence complexity exist: random (RSC), ordered (OSC), and functional (FSC). FSC alone provides algorithmic instruction. Random and Ordered Sequence Complexities lie at opposite ends of the same bi-directional sequence complexity vector. Randomness in sequence space is defined by a lack of Kolmogorov algorithmic compressibility. A sequence is compressible because it contains redundant order and patterns. Law-like cause-and-effect determinism produces highly compressible order. Such forced ordering precludes both information retention and freedom of selection so critical to algorithmic programming and control. Functional Sequence Complexity requires this added programming dimension of uncoerced selection at successive decision nodes in the string. Shannon information theory measures the relative degrees of RSC and OSC. Shannon information theory cannot measure FSC. FSC is invariably associated with all forms of complex biofunction, including biochemical pathways, cycles, positive and negative feedback regulation, and homeostatic metabolism. The algorithmic programming of FSC, not merely its aperiodicity, accounts for biological organization. No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization. Organization invariably manifests FSC rather than successive random events (RSC) or low-informational self-ordering phenomena (OSC)."

Abel DL, Trevors JT. Three subsets of sequence complexity and their relevance to biopolymeric information. Theor Biol Med Model. 2005 Aug 11;2:29.
Free Full Text article

Photosynthesis and the origin of life.

2006-01-31T17:58:00.000-11:00

Entrez PubMed: "The origin and evolution of photosynthesis is considered to be the key to the origin of life. This eliminates the need for a soup as the synthesis of the bioorganics are to come from the fixation of carbon dioxide and nitrogen. No soup then no RNA world or Protein world. Cyanobacteria have been formed by the horizontal transfer of green sulfur bacterial photoreaction center genes by means of a plasmid into a purple photosynthetic bacterium. The fixation of carbon dioxide is considered to have evolved from a reductive dicarboxylic acid cycle (Chloroflexus) which was then followed by a reductive tricarboxylic acid cycle (Chlorobium) and finally by the reductive pentose phosphate cycle (Calvin cycle). The origin of life is considered to have occurred in a hot spring on the outgassing early earth. The first organisms were self-replicating iron-rich clays which fixed carbon dioxide into oxalic and other dicarboxylic acids. This system of replicating clays and their metabolic phenotype then evolved into the sulfide rich region of the hotspring acquiring the ability to fix nitrogen. Finally phosphate was incorporated into the evolving system which allowed the synthesis of nucleotides and phospholipids. If biosynthesis recapitulates biopoesis, then the synthesis of amino acids preceded the synthesis of the purine and pyrimidine bases. Furthermore the polymerization of the amino acid thioesters into polypeptides preceded the directed polymerization of amino acid esters by polynucleotides. Thus the origin and evolution of the genetic code is a late development and records the takeover of the clay by RNA."
Hartman H. Photosynthesis and the origin of life. Orig Life Evol Biosph. 1998 Oct;28(4-6):515-21.

A model for the origin of photosynthesis--III. The ultraviolet photochemistry of uroporphyrinogen. : "The photochemical ramifications of the high ultraviolet flux on the primordial earth prior to the formation of the ozone layer have been considered in a study of the ultraviolet photochemistry of uroporphyrinogen (urohexahydroporphyrin), a colorless compound which absorbs strongly at wavelengths less than 220 nanometers. Urohexahydroporphyrin was investigated since it is the first macrocycle formed on the biosynthetic pathway of chlorophyll and can be used to test the hypothesis that the biosynthetic pathway to chlorophyll recapitulates the evolutionary history of photosynthesis. When urohexahydroporphyrin is illuminated in aqueous anaerobic solution, hydrogen gas is produced. More hydrogen gas is produced in the presence of a colloidal platinum catalyst. The products of the photooxidation of urohexahydroporphyrin are urotetrahydroporphyrin (uroporphomethene) and uroporphyrin. This research shows how the oxidation of uroporphyrinogen to uroporphyrin, the first biogenetic porphyrin, could have occurred anaerobically and abiotically on the primordial earth."
Mercer-Smith JA, Raudino A, Mauzerall DC. A model for the origin of photosynthesis--III. The ultraviolet photochemistry of uroporphyrinogen. Photochem Photobiol. 1985;42(3):239-44.

Evolution of Photosynthesis' (1970), re-examined thirty years later. : "I have re-examined my 1970 article 'Evolution of Photosynthesis' (Olson JM, Science 168: 438-446) to see whether any of my original proposals still survive. My original conviction that the evolution of photosynthesis was intimately connected with the origin of life has been replaced with the realization that photosynthesis may have been invented by the Bacteria after their divergence from the Archea. The common ancestor of all extant photosynthetic bacteria and cyanobacteria probably contained bacteriochlorophyll a, rather than chlorophyll a as originally proposed, and may have carried out CO(2) fixation instead of photoassimilation. The first electron donors were probably reduced sulfur compounds and later ferrous iron. The common ancestor of all extant reaction centers was probably similar to the homodimeric RC1 of present-day green sulfur bacteria (Chlorobiaceae) and heliobacteria. In the common ancestor of proteobacteria and cyanobacteria, the gene for the primordial RC1 was apparently duplicated and one copy split into two genes, one for RC2 and the other for a chlorophyll protein similar to CP43 and CP47 in extant cyanobacteria and chloroplasts. Homodimeric RC1 and homodimeric RC2 functioned in series as in the Z-scheme to deliver electrons from Fe(OH)(+) to NADP(+), while RC1 and/or RC2 separately drove cyclic electron flow for the production of ATP. In the line of evolution leading to proteobacteria, RC1 and the chlorophyll protein were lost, but RC2 was retained and became heterodimeric. In the line leading to cyanobacteria, both RC1 and RC2 replaced bacteriochlorophyll a with chlorophyll a and became heterodimeric. Heterodimeric RC2 further coevolved with a Mn-containing complex to utilize water as the electron donor for CO(2) fixation. The chlorophyll-protein was also retained and evolved into CP43 and CP47. Heliobacteria are the nearest photosynthetic relatives of cyanobacteria. The branching order of photosynthetic genes appears to be (1) proteobacteria, (2) green bacteria (Chlorobiaceae plus Chloroflexaceae), and (3) heliobacteria plus cyanobacteria."Olson JM. Evolution of Photosynthesis' (1970), re-examined thirty years later. Photosynth Res. 2001;68(2):95-112.

Chance and necessity do not explain the origin of life.

2006-01-31T03:44:00.000-11:00

Entrez PubMed: "Where and how did the complex genetic instruction set programmed into DNA come into existence? The genetic set may have arisen elsewhere and was transported to the Earth. If not, it arose on the Earth, and became the genetic code in a previous lifeless, physical-chemical world. Even if RNA or DNA were inserted into a lifeless world, they would not contain any genetic instructions unless each nucleotide selection in the sequence was programmed for function. Even then, a predetermined communication system would have had to be in place for any message to be understood at the destination. Transcription and translation would not necessarily have been needed in an RNA world. Ribozymes could have accomplished some of the simpler functions of current protein enzymes. Templating of single RNA strands followed by retemplating back to a sense strand could have occurred. But this process does not explain the derivation of 'sense' in any strand. 'Sense' means algorithmic function achieved through sequences of certain decision-node switch-settings. These particular primary structures determine secondary and tertiary structures. Each sequence determines minimum-free-energy folding propensities, binding site specificity, and function. Minimal metabolism would be needed for cells to be capable of growth and division. All known metabolism is cybernetic--that is, it is programmatically and algorithmically organized and controlled."

Trevors JT, Abel DL. Chance and necessity do not explain the origin of life. Cell Biol Int. 2004;28(11):729-39.

Of Ice and Then

2005-12-31T17:59:00.000-11:00

Entrez PubMed: "Sea ice occurs abundantly at the polar caps of the Earth and, probably, of many other planets. Its static and dynamic properties that may be important for prebiotic and early biotic reactions are described. It concentrates substrates and has many features that are important for catalytical actions. We propose that it provided optimal conditions for the early replication of nucleic acids and the RNA world. We repeated a famous prebiotic experiment, the poly-uridylic acid-instructed synthesis of polyadenylic acid from adenylic acid imidazolides in artificial sea ice, simulating the dynamic variability of real sea ice by cyclic temperature variation. Poly(A) was obtained in high yield and reached nucleotide chain lengths up to 400 containing predominantly 3'--> 5' linkages."
Trinks H, Schroder W, Biebricher CK. Ice and the origin of life. Orig Life Evol Biosph. 2005 Oct;35(5):429-45.

Ligation activity of fragmented ribozymes in frozen solution: implications for the RNA world -- Vlassov et al. 32 (9): 2966 -- Nucleic Acids Research

2005-12-31T17:25:00.000-11:00

Ligation activity of fragmented ribozymes in frozen solution: implications for the RNA world -- Vlassov et al. 32 (9): 2966 -- Nucleic Acids Research: "The RNA World (1-3) refers to an evolutionary period prior to coded peptide synthesis in which RNA may have been the major genetic and catalytic agent. If the prebiotic conditions were 'warm and wet' as is usually assumed, the RNA world hypothesis has a major difficulty. Under those conditions the RNA backbone undergoes rapid cleavage through transesterification. This reaction is accelerated by divalent metal ions, which would have been abundant in aqueous solutions (4,5). Thus, the evolution of RNA sequence complexity must have occurred under conditions in which RNA synthesis was more efficient than random degradation. Since the first ribozymes are likely to have been inefficient, the most straightforward way for RNA synthesis to outpace random degradation would be if conditions were such that degradation was slow. Degradation could have been reduced at low concentrations of divalent metal ions, low temperature, reduced water activity and upon adsorption to surfaces so as to stabilize phosphodiester bonds (4-9). Most of these conditions, and particularly low temperature, may have been available on the early Earth. Indeed, some investigators have argued that at the time of prebiotic evolution much of the water in the oceans was frozen but underwent periodic melting due to large meteor impacts or volcanic activity (8-10). "
Vlassov AV, Johnston BH, Landweber LF, Kazakov SA. Ligation activity of fragmented ribozymes in frozen solution: implications for the RNA world. Nucleic Acids Res. 2004 May 25;32(9):2966-74. Print 2004.

Acetogenic bacteria: what are the in situ consequences of their diverse metabolic versatilities?

2005-11-30T17:59:00.000-11:00

Entrez PubMed: "The four decades of the now classic studies by Harland G. Wood and Lars G. Ljungdahl lead to the resolution of the autotrophic acetyl-CoA 'Wood/Ljungdahl' pathway of acetogenesis. This pathway is the hallmark of acetogens, but is also used by other bacteria, including methanogens and sulfate-reducing bacteria, for both catabolic and anabolic purposes. Thus, the pathway is wide spread in nature and plays an important role in the global turnover of carbon. Because most historical studies with acetogens focused on the biochemistry of the acetyl-CoA pathway, the metabolic diversity and ecology of acetogens remained largely unexplored for many years. Although acetogens were initially conceived to be a somewhat obscure bacteriological group with limited metabolic capabilities, it is now clear that acctogens are arguably the most metabolically diverse group of obligate anaerobes characterized to date. Their anaerobic metabolic arsenal includes the capacity to oxidize diverse substrates, including aromatic, C1, C2, and halogenated compounds, and engage a large number of alternative energy-conserving, terminal electron-accepting processes, including classic fermentations and the dissimilation of inorganic nitrogen. In this regard, one might consider acetogens on a collective basis as the pseudomonads of obligate anaerobes. By virtue of their diverse metabolic talents, acetogens can be found in essentially all habitats. This review evaluates the metabolic versatilities of acetogens relative to both the engagement (regulation) of the acetyl-CoA pathway and the ecological roles likely played by this bacteriogical group."
Drake HL, Daniel SL, Kusel K, Matthies C, Kuhner C, Braus-Stromeyer S. Acetogenic bacteria: what are the in situ consequences of their diverse metabolic versatilities? Biofactors. 1997;6(1):13-24.

Liquid Water At Earth's Surface 4.3 Billion Years Ago, Scientists Discover

2005-11-18T12:01:00.000-11:00

Liquid Water At Earth's Surface 4.3 Billion Years Ago, Scientists Discover: "'We don't know when life began on Earth yet, but it potentially could have emerged as early as 4.3 billion years ago because we infer that all three required conditions for life existed then,' said T. Mark Harrison, professor of geochemistry at UCLA, who directs UCLA's W.M. Keck Foundation Center for Isotope Geochemistry, and is a co-author of the Nature paper. 'There was a source of energy: the sun; a source of raw minerals: complex organic compounds from meteorites or comets; and our inference that liquid water existed at or near the Earth's surface. Within 200 million years of the Earth's formation, all of the conditions for life on Earth appear to have been met.'

The scientists analyzed a rock from Western Australia that was more than three billion years old with UCLA's high-resolution ion microprobe — an instrument that enables scientists to date and learn the exact composition of samples — which Mojzsis described as the "world's best instrument" for this research. The microprobe shoots a beam of ions — charged atoms — at a sample, releasing from the sample its own ions that are analyzed in a mass spectrometer. Scientists can aim the beam of ions at specific microscopic areas of a sample and analyze them without destroying the object.

The scientists learned that while the rock was deposited about three billion years ago, it contains ancient mineral grains — zircons — that were much older; two of the zircons were 4.3 billion years old, and nearly a dozen others were older than four billion years. The Earth is 4.5 billion years old. In addition, the researchers learned that the zircons contained a unique and revealing ratio of oxygen isotopes.

"We were stunned to discover a very distinctive oxygen isotopic signature in this rock — a rock that significantly predates the Earth's oxygen atmosphere — which tells us that it interacted with cold water at temperatures appropriate to the Earth's surface," Harrison said. "Many scientists did not think rocks older than two billion years could provide this information. Was there liquid water at the Earth's surface 4.3 billion years ago? We have not had any way to answer that question before until these measurements, which suggest that the answer is yes."

The telltale sign is the ratio of the very common 16O to the much rarer and heavier 18O.

"The ratio of these isotopes reveals whether water has interacted with a rock," Harrison explained. "If a rock has been to the Earth's surface and interacted with water, it will be significantly ‘heavier' and more enriched in 18O, which is precisely what we have found in these ancient zircons."

Zircons are heavy, durable minerals related to the synthetic cubic zirconium used for imitation diamonds and costume jewelry. The zircons studied in the rock are about twice the thickness of a human hair.

"These zircons tell us that they melted from an earlier rock that had been to the Earth's surface and interacted with cold water," Harrison said. "There is no other known way to account for that heavy oxygen."

The ion microprobe is the first instrument that allows high-resolution isotope analysis of inorganic and biological material only a few millionths of a meter in diameter, Harrison said.

"The microprobe is a fantastic instrument in its sensitivity, its accuracy and its versatility," Mojzsis said. "With the microprobe, we can determine the oxygen isotopic composition of individual spots within the tiny zircons, and measure with enormous precision the ages of these spots. We can determine when the zircons formed and how they formed."

Without the ion microprobe, the scientists would have been able to learn only the average age of the zircons in the rock, not the ages of the various zircons, which varied substantially, the scientists said.

Harrison and Mojzsis' colleague on the research is Robert Pidgeon, a professor of applied geology at Curtin University of Technology in Perth, Australia, who first discovered the very ancient zircons in the rock.

The research was funded by the National Science Foundation and NASA's Center for Astrobiology.

The oldest known rocks are about four billion years old, but Harrison suspects that older rocks could be found that would reveal significant information about the Earth's evolution — including perhaps the source rocks that first contained the 4.3 billion-year-old zircons — if a coordinated effort to search for ancient rocks were undertaken.

"Zircons are forever," Harrison noted."