RAZD
Member (Idle past 1593 days) Posts: 20714 From: the other end of the sidewalk Joined: 03-14-2004
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Panspermic Pre-Biotic Molecules - Life's Building Blocks (Part I)
Thanks, I'll have to think about a title a bit I think ... Is anyone else seeing a lot of s (that's a black diamond with a questionmark in it on my machine) in the text? or is it just my browser\font setup?
The original essay seems to have gotten lost in the last forum update, so this is a copy from my files:
Building Blocks of Life A lot of creationist propaganda involves probabilities, with seemingly huge improbabilities calculated for such things as assembling complex organic molecules (usually calculated with them assembling completely from pure raw materials in one single random action). Such calculations are flawed on many levels, and one of them is addressed in this essay. This is the flaw of failing to properly account for the actual beginning basis: failing to take into account the organic molecules that were readily formed on the surface of the earth. This essay is a look at some of those molecules and the likely pre-existing conditions for the formation of life on earth. I call these {molecules \ conditions} "building blocks" to denote that the search for how life actually came to be was built on these foundations. If you are looking for discussions on the {actual \ initial} formation of RNA or DNA you will need to look elsewhere, as this is looking at a much more rudimentary level of the question. What is the status of what we know? First off we have some peptides built out of existing amino acids (reference 1), activated by geochemical conditions similar to possible early earth conditions. That these basic building blocks of life were formed by this process is not disputed by such creationist organisations as AnswerInGenesis (AIG) (reference 2). Then there is the question of hydrocarbons in outer space. The implications here are that a ready source of such organic compounds could seed a young planet with a bias for carbon based life centered on these molecules, and that this could in effect jump-start the development of life systems out of a chemical soup. From meteors we have mono- and dicarboxylic acids, dicarboximides, pyridine carboxylic acids, a sulfonic acid, and both aliphatic and aromatic hydrocarbons (reference 3) as well as hollow, bubble-like hydrocarbon globules similar to early membraneous formations (reference 4), and "polyols," components of the nucleic acids RNA and DNA, constituents of cell membranes and cellular energy sources (reference 5). In deeper space we find the signatures of other organics compounds: polycyclic aromatic hydrocarbon (PAH) molecules are the most abundant family of molecules in the interstellar medium after molecular hydrogen and carbon monoxide, and contain about 10% of all the interstellar carbon (reference 6) and not just in near space but light-years away at protostellar source S140 (ibid). This source is about 3,000 light-years away, more importantly it is a forming star, so this material is either older than the star or already made at the point of this stars stage of formation. Other deep space organic compounds that have been found are vinyl alcohol (reference 7) and the 8-atom molecule propenal and the 10-atom molecule propanal (reference 8), all in interstellar clouds of dust and gas near the center of the Milky Way Galaxy, which is ~26,000 light-years away. The significance of the distance is that these compounds existed that many years ago in those locations, they did not come from earth, and it is highly likely that they are much older. Note that so far over 130 different molecules have been discovered in interstellar clouds (ibid). Most contain a small number of atoms, and only a few molecules with eight or more atoms have been found so far. Panspermia is a theory that life was seeded on earth from other systems, perhaps older planetary systems or perhaps interstellar bacteria. This idea has been ridiculed, but the evidence is a strong correlation between patterns of light absorption by dust clouds and that made by small hollow spheres the size of common bacteria (reference 9). While there may be other possibilities for such conveniently sized hollow spheres, this basic concept has yet to be invalidated. It is also possible that this is the dust of life that evolved on other planets from similar chemical backgrounds and where the systems have met some catastrophic end (star system goes nova, collisions, etc) -- given that the universe is ~3 times older than the earth. Next we jump from looking at what is out there, to experiments on what might have been happening out there. Scientists made glycine, alanine and serine, three of the basic parts of proteins from which all life is made,by simulating conditions that are commonplace in interstellar space and shining ultraviolet light on deep-space-like "ices" (reference 10) - again pointing to a ready source of already formed amino acids from space rather than having them form on the surface. Formation of amino acids by bacteria is also well documented, but researchers have caused a "new" amino acid to be formed by one, p-aminophenylalanine, or pAF (reference 11), demonstrating that the 20 that are commonly used are not necessarily special to the formation of life, just that they were likely available at the time. The next question then is what earth was like in those early days and what kind of existence was possible. This was before oxygen was released into the atmosphere, so all early life had to be anaerobic. One possibility is the deep ocean floor around the thermal vents, where life today is still a bizarre chemistry for organisms compared to what we know. Recently, simulating such conditions amino acids were combined into peptides (reference 12), and the oldest evidence for life may be thermophile remnants in greenland rocks that are 3.7 to 3.9 billion years old, where some researchers have concluded that the grains contained carbon of biological origin (reference 13). Adding to this is further research synthesizing the critical compound pyruvic acid (CH3-CO-COOH) from CO in the presence of iron-sulphide at 250 C and pressures equivalent to a depth of 7 km within the rock (reference 14). There are many anaerobic bacteria, but the real insight is from the Archaea, similar to bacteria but from a seperate and earlier domain of life, and found in many extreme environments (remnants from an earlier time?). Some archaea found in the sediments of the Hydrate Ridge belong to the methanogens (microorganisms known for producing methane), were completely surrounded by sulfate reducing bacteria (reference 15). These organisms live buried in sediment at the bottom of the ocean, close to the conditions noted above. Bringing it all home, we return to peptides, this time self replicating, a 32-amino-acid peptide, can autocatalyse its own synthesis by accelerating the amino-bond condensation of 15- and 17-amino-acid fragments in solution (reference 16). Viruses may be older than other life forms (or have preceeded life depending on your definition of life), as coat proteins in all viral types that inhabit the three domains of lifeEukarya, Bacteria, and Archaeahave conformational similarities even though the genetics underlying them is quite different (reference 17). Another experiment shows how membranes can be formed from common chemicals like calcium chloride, sodium carbonate, copper chloride, sodium iodide, hydrogen peroxide and starch and that they contain chemical reactions (reference 18), and another shows that these compounds are common in meteor "ices" and that the meteor compounds would form vesicles with the addition of water (reference 19). My Conclusions From these information sections it seems to me that the building blocks needed for beginning the creation of life were plentiful, not just on Earth but in space in general and from the earliest of times. Probably they have been around since long before even the Earth formed from the cosmic debris left behind by the life and death cycle of previous stars and planets, back to the beginning of time. These "seeds of life" no doubt extend through the far reaches of the universe as well as the depths of time (cue Crosby, Stills, Nash and Young ... "We are star dust ..."). It also seems to me that the natural processes for forming more complex structures from those basic building blocks were likely prevalent on the earth 4.5 billion years ago in a variety of forms, levels of completion and locations. We end with a scenario that has a random combination of plentiful and multitudinous organic molecules forming amino acids all over the earth, with a membranous system to contain and concentrate those molecules and their interactions within a protocell type capsule. We also see that random combination of plentiful and multitudinous amino acids into peptides and proteins is feasible, and that concentration and recombination within the membranous protocells enhances the probability that random combinations of them into the first "replicators" (the predecessors to RNA and DNA) is not as far fetched as it seemed at first. A simple building block process where the probability of a successful combination is almost inevitable: it is no longer a matter of "if" but of "when" it will occur under these conditions ... and once self replication occurs the frequency of replication will necessarily outpace the random action, and replicators that are faster and stronger will outpace their competition ... life seems inevitable when given the conditions for life. That is my take on the probability of life on earth. Enjoy
Reference #1
C. Huber and G. Wchterhuser, "Peptides by activation of amino acids with CO on (Ni,Fe)S surfaces: implications for the origin of life," Science 281(5377):670?672, July 31, 1998
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 H2 S (or CH3 SH) as a catalyst and condensation agent at 100C 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. The activation of amino acids and the formation of peptides under primordial conditions is one of the great riddles of the origin of life. We have now found that under the hot, anaerobic, aqueous conditions of a setting with magmatic exhalations, amino acids are converted into peptides. Under these conditions we previously demonstrated the conversion of carbon monoxide into activated acetic acid in an aqueous slurry of coprecipitated (Ni,Fe)S at 100C (1). Peptides were formed from phenylalanine (F), tyrosine (Y), and glycine (G). In each run 500 mmol of the amino acid were reacted in a slurry of 1 mmol of FeS and 1 mmol of NiS in 10 ml of water with 4 mmol of CO gas (1 bar) in the presence of 500 mmol of hydrogen sulfide (H 2 S) or methanethiol (CH 3 SH) at 100C and pH 7 to 10. In some of the runs 500 mmol of Na 2 HPO 4 were added. After 1, 2, or 4 days, we determined the yield of the peptides and the pH in the water phase (2) (Table 1). No peptides were detectable, if under otherwise identical conditions CO was replaced by Ar, or if neither H 2 S nor CH 3 SH was added, or if both NiS and FeS were absent. In runs 13 and 14 and 19 to 22, about 3 nmol of tripeptides (Y-Y-Y) were detected after 1 and 4 days. Reference #2 AIG - Did scientists create life ... or did the media create hype?
As usual, the media pro-evolutionary hype is deceptive. Upon reading the original scientific paper by the chemists involved, Claudia Huber and Gnter Wchterhuser,(3) we find that all that was produced were a few building blocks joined in pairs (dipeptides) and a minuscule amount joined in threes (tripeptides). A few paired building blocks are a far cry from even one enzyme, let alone a living cell. Note that they concede the building blocks were created. {Please note the blatant strawmen and the arguments by incredulity in the article - quite funny.} Reference #3 Organic Content of the Tagish Lake Meteorite
September 21, 2001
The Tagish Lake meteorite fell last year on a frozen lake in Canada and may provide the most pristine material of its kind. Analyses have now shown this carbonaceous chondrite to contain a suite of soluble organic compounds (~100 parts per million) that includes mono- and dicarboxylic acids, dicarboximides, pyridine carboxylic acids, a sulfonic acid, and both aliphatic and aromatic hydrocarbons. The insoluble carbon exhibits exclusive aromatic character, deuterium enrichment, and fullerenes containing "planetary" helium and argon. The findings provide insight into an outcome of early solar chemical evolution that differs from any seen so far in meteorites. Reference #4 Researchers Find Possible Precursors to Early Life on Earth in Meteorite
December 11, 2002 {abe}
This is a new link, the original article is no longer available on-line, although it is still listed on
Center for NEO Studies
{/abe}
The Tagish Lake meteorite fell to Earth over the Yukon Territory of Canada on Jan. 18, 2000. Parts of the meteorite were collected and kept frozen in an unprecedented level of cleanliness to ensure that it was not contaminated by any terrestrial sources. Through extensive testing using, in part, electron microscopes, the researchers found numerous hollow, bubble-like hydrocarbon globules in the meteorite. They believe these organic globules, the first found in any natural sample, are very similar to those produced in laboratory simulations designed to recreate the initial conditions present when life first formed in the universe. "While not of biological origin themselves, these globules would have served very well to protect and nurture primitive organisms on Earth," said Dr. Michael Zolensky, an author of the paper and a researcher in the Office of Astromaterials Research and Exploration Science at NASA's Johnson Space Center in Houston. "They would have been ready-made homes for early life forms." Last year, researchers at NASA's Ames Research Center in Moffett Field, Calif., announced that they had made basically identical hydrocarbon globules in the laboratory from materials present in the early solar system and interstellar space. "What we have now shown is that that these globules were in fact made naturally in the early solar system, and have been falling to Earth throughout time," Zolensky said. Reference #5 Sweet Meteorites
September 20, 2001
A NASA scientist has discovered sugar and several related organic compounds in two meteorites -- providing the first evidence that another fundamental building block of life on Earth might have come from outer space. Dr. George Cooper and co-workers from the NASA Ames Research Center found the sugary compounds in two carbon-rich (or "carbonaceous") meteorites. Previously, researchers had found inside meteorites other organic, carbon-based compounds that play major roles in life on Earth, such as amino acids and carboxylic acids, but no sugars. "Finding these compounds greatly adds to our understanding of what organic materials could have been present on Earth before life began," Cooper said. "Sugar chemistry appears to be involved in life as far back as our records go." Recent research using ratios of carbon isotopes have pushed the origin of life on Earth to as far back as 3.8 billion years, he said. (An isotope is one of two or more atoms whose nuclei have the same number of protons but different numbers of neutrons.) Scientists have long believed meteorites and comets played a role in the origin of life. Raining down on Earth during the heavy bombardment period some 3.8 billion to 4.5 billion years ago, they brought with them the materials that may have been critical for life, such as oxygen, sulfur, hydrogen and nitrogen. Sugars and the closely related compounds discovered by Cooper, collectively called "polyols," are critical to all known life forms. They act as components of the nucleic acids RNA and DNA, constituents of cell membranes and cellular energy sources. Reference #6 Identifying Polycyclic aromatic hydrocarbon (PAH) molecules in Space
August 13, 2001
Polycyclic aromatic hydrocarbon (PAH) molecules are the most abundant family of molecules in the interstellar medium after molecular hydrogen and carbon monoxide, and contain about 10% of all the interstellar carbon. Recently, a spectral database has become available from the Infrared Space Observatory that contains objects in which we have found the C-H PAH stretch feature (near 3.26 m) in absorption. Using the database of isolated neutral PAHs generated by the Ames Astrochemistry Laboratory, we can match the interstellar feature fairly well with a mixture of PAH molecules. However, the mixture is not unique and does not tell us which particular PAHs are present in space. This is demonstrated in the Figure which shows two fits to the absorption observed towards the protostellar source S140. The laboratory database contains only a few PAHs as large as those expected to survive the rigors of the interstellar medium, so it is perhaps not surprising that a precise match is still not possible. Techniques for obtaining lab spectra of larger PAHs exist, but making large PAHs for lab studies is very difficult. Once such lab data exist, being able to directly compare lab and interstellar spectra without using uncertain models could provide the first identification of individual PAHs in space. Reference #7 Scientists Toast the Discovery of Vinyl Alcohol in Interstellar Space
October 1, 2001
Astronomers using the National Science Foundation's 12 Meter Telescope at Kitt Peak, AZ, have discovered the complex organic molecule vinyl alcohol in an interstellar cloud of dust and gas near the center of the Milky Way Galaxy. The discovery of this long-sought compound could reveal tantalizing clues to the mysterious origin of complex organic molecules in space. "The discovery of vinyl alcohol is significant," said Barry Turner, a scientist at the National Radio Astronomy Observatory (NRAO) in Charlottesville, Va., "because it gives us an important tool for understanding the formation of complex organic compounds in interstellar space. The astronomers were able to detect the specific radio signature of vinyl alcohol during the observational period of May and June of 2001. Their results have been accepted for publication in the Astrophysical Journal Letters. Reference #8 Two new interstellar molecules
June 22, 2004
A team of scientists using the National Science Foundation's Robert C. Byrd Green Bank Telescope (GBT) has discovered two new molecules in an interstellar cloud near the center of the Milky Way Galaxy. This discovery is the GBT's first detection of new molecules, and is already helping astronomers better understand the complex processes by which large molecules form in space. The 8-atom molecule propenal and the 10-atom molecule propanal were detected in a large cloud of gas and dust some 26,000 light-years away in an area known as Sagittarius B2. Such clouds, often many light-years across, are the raw material from which new stars are formed. So far, about 130 different molecules have been discovered in interstellar clouds. Most of these molecules contain a small number of atoms, and only a few molecules with eight or more atoms have been found in interstellar clouds. Each time a new molecule is discovered, it helps to constrain the formation chemistry and the nature of interstellar dust grains, which are believed to be the formation sites of most complex interstellar molecules. Starting with previously reported propynal (HC2CHO), propenal (CH2CHCHO) is formed by adding two hydrogen atoms. By the same process propanal (CH3CH2CHO) is formed from propenal. After these molecules are formed on interstellar dust grains, they may be ejected as a diffuse gas. If enough molecules accumulate in the gas, they can be detected with a radio telescope. As the molecules rotate end-for-end, they change from one rotational energy state to another, emitting radio waves at precise frequencies. The "family" of radio frequencies emitted by a particular molecule forms a unique "fingerprint" that scientists can use to identify that molecule. The scientists identified the two new aldehydes by detecting a number of frequencies of radio emission in what is termed the K-band region (18 to 26 GHz) of the electromagnetic spectrum. Complex molecules in space are of interest for many reasons, including their possible connection to the formation of biologically significant molecules on the early Earth. Complex molecules might have formed on the early Earth, or they might have first formed in interstellar clouds and been transported to the surface of the Earth. A lot of interstellar dust seems to be molecules of interest to the formation of organic life on earth. Perhaps "dust" is the wrong word. Reference #9 Bacteria Shells in Space?
... Now, however, that organic polymers in space are abundant and may be necessary for life is well accepted. Today we often see stories about things like vinegar among the stars, or "buckyballs" from space as "the seeds of life". To that extent the scientific paradigm for the origin of life on Earth has already shifted. But Hoyle and Wickramasinghe were not satisfied. In the middle 1970s, they turned their attention to an apparent anomaly in the spectrum. It had a low, broad "knee" centered at about 2.3 wavelengths per micrometer (the slight convexity on the slope at the left side of the graph). This spectral feature could be explained if the grains of dust were of a certain size, and hollow. After trying almost everything else first, in 1979, they looked at the spectrum for bacteria. Dried bacteria refract light as irregular hollow spheres, and their size range is appropriate. The match between the spectrum for dried bacteria (solid line) and the ones from the interstellar grains (dots, triangles and squares) was nearly perfect. Thinking without prejudice, Hoyle and Wickramasinghe concluded the grains probably were dried, frozen bacteria. This finding was ridiculed at the time, is still ridiculed today, and is definitely not accepted by mainstream science. ... Certain other scientists have roundly criticised them for such "inconststencies" and for sometimes having less than complete corroboration for their findings. Criticism so bitter discourages all pioneering scientific enquiry. Perhaps their work will be honored eventually. The evidence is for hollow shells that happen to match the size of bacteria. There may be other possibilities that have not been ruled out. Certainly this is not hard evidence that bacteria exist in space (and back in time due to speed of light), but it opens it up as a possibility that is not ruled out. Reference #10 NASA - Amino Acids Created and
NASA - Scientists Create Amino Acids
March 27, 2002
In a laboratory at NASA Ames Research Center in California's Silicon Valley, the team of astrobiologists shone ultraviolet light on deep-space-like "ices," simulating conditions that are commonplace in interstellar space. Deep-space ice is common water ice laced with simple molecules. The team subsequently discovered amino acids, molecules present in, and essential for, life on Earth. The amino acids they detected (glycine, alanine and serine) are the basic parts of proteins from which all life is made. Proteins provide the structure for, and do all the work in, living things. "This finding suggests that Earth may have been seeded with amino acids from space in its earliest days," said Jason Dworkin of Ames and the SETI Institute. "And, since new stars and planets are formed within the same clouds in which new amino acids are being created, this increases the odds that life also evolved in places other than Earth." More information is at Ames Research Center Astrochemical Laboratory Reference #11 Researchers create novel life form
January 13, 2003
Researchers said Monday they have manipulated an organism successfully to make it produce an unnatural amino acid in addition to its natural counterparts. "It's a bona fide unnatural organism now," said lead researcher Ryan Mehl, previously at Scripps Research Institute where the study was conducted and currently an assistant professor of chemistry at Franklin and Marshall College in Lancaster, Pa. The Scripps researchers used a strain of the common bacterium Escherichia coli and replaced a chunk of its genetic code called a stop codon -- whose function is to halt protein-making machinery -- with a code for the unnatural amino acid, p-aminophenylalanine, or pAF. As is common practice with scientists manipulating bacteria, the study's authors also altered the E. coli so it would not survive outside of the laboratory. Reference #12 Life's First Scalding Steps
January 9, 1999
The most detailed step-by-step blueprint for how Earth's oldest raw materials could have given rise to the stuff of life came out of the imagination of Gnter Wchtershuser, an organic chemist at the University of Regensberg in Germany. Ten years ago, Wchtershuser conceived of an assembly-line process at the ocean floor that transforms basic inorganic chemicals into organic chains, the biological molecules that are the building blocks of life. Wchtershuser's factory enlists the elements of modern industry - all readily available at vents. The conveyor belt is the flat surface of metal sulfide minerals, such as iron pyrite, abundant in seafloor rocks. The raw materials are carbon- and hydrogen-rich gases from volcanic belches dissolved in the seawater. The workers that drive the assembly line - the keys to the whole process - are metallic ions in the sulfides. In living cells, complex proteins called enzymes play the role of factory laborers, bringing certain molecules together and splitting others apart. Before enzymes appeared on the planet, Wchtershuser says that metallic ions filled that catalytic role. Without these mediators, reactions might take months or years, or never happen at all, he adds. New components would never get added to the molecules passing by on the conveyor. In Wchtershuser's theory, the first organic molecule put together on the conveyor belt was acetic acid, a simple combination of carbon, hydrogen, and oxygen that is best known for giving vinegar its pungent odor. Formation of acetic acid is a primary step in metabolism, the series of chemical reactions that provides the energy that cells use to manufacture all the biological ingredients an organism needs. Amino acids from a variety of sources almost certainly seasoned a broth on the planet's surface 4 billion years ago, Chyba says, but he points out that no one has ever satisfactorily explained how the widely distributed ingredients linked up into proteins. Presumed conditions of primordial Earth would have driven the amino acids toward lonely isolation. That's one of the strongest reasons that Wchtershuser, Morowitz, and other hydrothermal vent theorists want to move the kitchen to the ocean floor. If the process starts down deep at discrete vents, they say, it can build amino acids - and link them up - right there. Last year, Wchtershuser and Huber did just that. They reported in the July 31, 1998 Science that at 100C, they got amino acids to connect into short proteinlike chains called peptides. Reference #13 Hydrothermal Vents - Life's First Home?
... hydrothermal systems as the location for the emergence of life require no "special case" arguments. "They are probably one of the most common features throughout the entire history of the Earth," Shock says. A few years ago Shock turned from theoretical work to field work at the hydrothermal systems in Yellowstone National Park. He hopes that by studying present-day hydrothermal life, he can determine what geochemical signatures to look for in the most ancient rocks. Isua, on the on the edge of Greenland's ice cap, holds an outcrop of rock that appears to be 3.7 to 3.9 billion years old, only about half a billion years younger than the Earth itself. After slicing the rocks with a diamond saw, Touret studied the slices using a specially fitted microscope. He saw tiny "bubbles" in the quartz crystals, and the bubbles, like minute glass globes, contained a fluid, Rollinson says. "You see this half-filled inclusion, half water vapor, half liquid water, sort of wobbling under the effect of heating it up with the microscope lamp," Rollinson says. Other researchers have studied tiny carbon grains embedded in different rocks found in the Isua formations. By measuring the ratio of carbon isotopes, these researchers determined that the grains contained carbon of biological origin. Two common and stable isotopes of carbon, carbon 12 and carbon 13, occur in a mixture in the Earth's atmosphere. Biological processes build organic molecules with a higher carbon 12:13 ratio than abiotic processes. And because both isotopes are stable, the ratio remains in all of life's products, even after billions of years. Shock thinks these organisms may have left a detectable fossil record. But in this case, the fossils are chemical traces. "What are you going to look for? This is the question right now. By studying the active systems that are supporting hyperthermophiles [heat-loving organisms] you might have a better idea of what to go after in a fossil record that's hydrothermal. Reference #14 Origin of life in a hot iron-sulphur environment
German chemist Gunter Wachtershauser is a leader in the research on the hydrothermal origin of life, and has conducted numerous experiments which demonstrate how complex organic molecules can be formed from simple starting compounds - such as carbon monoxide (CO) - when metal sulphides are present as catalysts (Huber and Wachtershauser, 1997, Huber and Wachtershauser, 1998). It appears that the surfaces of metal sulphides can catalyze the binding of simple carbon molecules into new and more complex carbon molecules. Researchers from the Carnegie Institution in Washington have recently taken this idea a step further by synthesizing the critical compound pyruvic acid (CH3-CO-COOH) from CO in the presence of iron-sulphide at 250 C and pressures equivalent to a depth of 7 km within the rock (Cody et al., 2000). They suggest that this process may have taken place at depth in the oceanic crust, and that the compounds formed could have been moved by groundwater to the upper crust, where the critical life-forming processes might have taken place at lower temperatures (100 to 150 C) and pressures. The important components of this process are CO, Fe and/or Ni sulphides at high temperatures and pressures. All of these could have existed in proximity to volcanism in an early oceanic crust (Wachtershauser, 2000) Reference #15 The Methane Mystery and a symbiotic association
October 2000 {abe}
broken link no new one found yet
one listing the bacteria (with picture) is at
Page not found
{/abe}
Methane ( CH4) is a powerful greenhouse gas which is produced by microorganisms in terrestrial soils (especially rice paddies and rumen of cows) as well as in aquatic sediments. In the terrestrial environment a large fraction of the microbially produced methane is also consumed by microorganisms - by aerobic bacteria (methanotrophs) which depend on oxygen to gain energy from the oxidation of methane to carbon dioxide (CO2). In the marine environment, oxygen is quickly depleted below the seafloor. Still, most of the methane rising from deep below is consumed before it reaches the water column. Geochemical evidence shows that - in the absence of oxygen - methane is oxidized with sulfate (SO4) which is abundant in the sediment porewater. Hence, methane can be oxidized to CO2 in anoxic sediments. This process is of great importance to the global methane cycle. Gas hydrates contain enormous amounts of frozen methane exceeding all known fossil fuel stores. At our sampling station at the Hydrate Ridge such methane hydrates occur directly below the seafloor. At 800 m water depth and 5C the methane hydrates are at their stability limit and partly dissociate, releasing methane to the seafloor. Our working hypothesis was that sulfide could be the product of anaerobic oxidation of methane with sulfate. This was supported by the first analysis of sulfide concentrations in the sediments of the Hydrate Ridge which proved that the occurence of sulfide was restricted to the vicinity of hydrates. One way of detecting whole cells in their natural environment is the use of fluorescence in situ hybridization (FISH), a new method in the molecular ecology of aquatic environments. For FISH, a small sequence of the 16S ribosomal nucleic acid of a certain phylogenetic group of microorganisms can be linked to a fluorochrome, to obtain a probe which stains the respective bacteria in the sediment sample. With this method, specific groups of microorganisms can be identified and counted under the microscope. Using FISH, we discovered enormous amounts of archaea in the sediments above gas hydrate. These archaea were aggregated to clumps of ca. 100 cells. Archaea look like bacteria but they belong to a seperate and early domain of life. They are found in many extreme environments like hot springs and hypersaline ponds, but they can also be abundant in temperate seawater and sediments. The archaea which we found in the sediments of the Hydrate Ridge belong to the methanogens (microorganisms known for producing methane). However, the isotope signature of the archaeal biomarker lipids (e.g. archaeol) showed that these archaea must have consumed the methane from the gas hydrates. Most strikingly, the densly packed archaea were completely surrounded by sulfate reducing bacteria. These aggregates of archaea and sulfate reducing bacteria were very abundant above the methane hydrate. We counted up to 100 million aggregates per milliliter of mud - an enormous biomass for deep-sea sediments. These microorganisms were responsible for the rapid depletion of sulfate in the sediments above gas hydrate and apparently consumed a large fraction of the methane seeping from the hydrates. These observations are the first direct evidence for the existence of a methane-based symbiosis of archaea and bacteria. Together in close association, archaea and bacteria are able to make a living from the consumption of methane without oxygen. These findings have been published on 5 October 2000 in the journal NATURE (Boetius, A., Ravenschlag, K., Schubert, C., Rickert, D., Widdel, F., Gieseke, A., Amann, R., Jrgensen, B.B., Witte, U., Pfannkuche, O., 2000. A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature, Vol. 407, p. 623-626). Archaea feeding on Methane and sulfate reducing bacteria feeding on the byproduct of the archaea in an oxygen poor environment ... similar to early earth? Reference #16 Self-Replication: Even peptides do it By Stuart A. Kauffman
August 8, 1996
The authors show that a 32-amino-acid peptide, folded into an alpha-helix and having a structure based on a region of the yeast transcription factor GCN4, can autocatalyse its own synthesis by accelerating the amino-bond condensation of 15- and 17-amino-acid fragments in solution The design of this replicator was based on a protein found in nature, an alpha-helical coiled coil. Reasoning that a given alpha-helical subunit of the entire structure could be seen as a complementary binding surface, acting cooperatively to organize other participating peptide subunits in the coiling, the authors hoped that a similar 'template' function could be found in smaller fragments. The ligation, or joining, site was constructed so as to lie on the solvent-exposed surface of the alpha-helical structure of their 32-amino-acid sequence. Do these results reflect a rare chemical quirk in the repertoire of peptides and polypeptides, or might they hint at a route to self-reproducing molecular systems on a basis for wider than Watson-Crick base-pairing in polynucleotides? At this stage, we cannot know, but the way is now open to investigate. The new autocatalytic ligation-reaction system is merely exergonic: left to its own devices, the system will simply run to equilibrium. Can an autocatalytic system be created that carries out thermodynamic work cycles whereby the system sustains displacement from equilibrium, performs coordinated work and achieves such coordination by controlling, constraining and 'correcting' unwanted side reactions to enhance its own rate of reproduction? The dominant view of life assumes that self-replication must be based on something akin to Watson-Crick base pairing. The 'RNA world' model of the origins of life conforms to this view. But years of careful effort to find an enzyme-free polynucleotide system able to undergo replication cycles by sequentially and correctly adding the proper nucleotide to the newly synthesized strand have not yet succeeded. While this does not show actual spontaneous self-replication in a natural environment, it does show that such systems can occur given the right conditions. Reference #17 Did viruses precede other life?
May 6, 2004
Viruses share a common ancestor that existed over 3 billion years ago and may even have preceded cellular forms of life, according to a report in the May 3 PNAS by George Rice and colleagues at Montana State University. Based on a comparison of known virus types and an icosahedral virus isolated from a hot spring in Yellowstone National Park, the team found that coat proteins in all viral types that inhabit the three domains of lifeEukarya, Bacteria, and Archaeahave conformational similarities even though the genetics underlying them is quite different. Nearly all of the Yellowstone virus' 36 predicted open reading frame products showed no significant similarity to proteins in public databases, and so basic structural and assembly principles in this virus were compared instead, revealing an astounding similarity with all virus types, according to the authors. This suggests that this type of coat protein arrangement preceded the split of the three domains of life over 3 billion years ago, Mark A. Young, the team's leader and coauthor of the paper, told The Scientist. Young said that this kind of evidence supports the notion that viruses are indeed very old and likely were present at the time of first life, if not before. He said that he believed that virusesor progenitors of virusespreceded the formation of cellular life on this planet. Astrobiology often takes researchers into extreme environments so that they can understand how life may have begun. We use Yellowstone as a laboratory to develop techniques and to find interesting novel viruses that essentially replicate in boiling acid, said Young. There is some question about whether viruses qualify as forms of life, and this usually hinges on whether viruses can replicate themselves on their own in a natural environment. The environment in question would not be like the one we live in to day, as there is very strong evidence that the oxygen in the atmosphere is a result of life after it evolved. The logical conclusion is that the first forms of life would be different from later forms of life, and very possibly quite different. This is not to claim that the first life form was a virus so much as a question, whether viruses are remnants of that first form of life, a shell of their former existence, a clue. Reference #18 Mineral brew grows 'cells'
April 28, 2004 {abe}
Nature Journal on line sign-in required
{/abe}
It is an experiment you could do in a school chemistry lab. But it produces weird growths that, although made purely from inorganic materials, share some of the characteristics of living organisms. Maselko and Strizhak mixed calcium chloride, sodium carbonate, copper chloride, sodium iodide, hydrogen peroxide and starch. They found a fungus-like, soft membrane grows out of the mixture, enclosing a hollow cavity up to 1 cm across. Chemicals diffuse through this membrane, react inside the cavity, and then diffuse out, creating swirling clouds of violet liquid in the green base solution. Rather than reaching equilibrium, this process persists. The reactions, say the researchers, are reminiscent of the way living cells sustain themselves, driven from equilibrium by the flow of chemicals and energy across their membranes. Maselko and Strizhak even saw a kind of replication in their chemical brew. Sometimes the cell structures grew into forms with several lobes, or sprouted buds that split off from the parent membrane. But although they look impressive, can these structures tell us anything about the origin of true life-forms? It seems the answer might be yes, because the differences between the two processes are not as fundamental as one might assume. Maselko is keen to follow up his discovery to see just how far the parallels with life run. "This is only the beginning," he says. "We will see many other systems like this. The next step will be to get these systems to evolve."
but where does the mix to make the vesicles happen? Reference #19 Vesicles come from Outer Space?
January 30, 2001
... this new work shows that the early chemical steps believed to be important for the origin of life do not necessarily require an already formed planet to occur. Instead, they can readily be taken in the depths of space long before planet formation occurs. This implies that the vastness of space is filled with compounds which, if landing in a hospitable environment, can help jump-start the origin of life.
"Instead of finding a handful of molecules only slightly more complicated than the starting compounds, hundreds of new compounds are produced in every mixed ice we have studied," space scientist Scott Sandford said. He continued, "We are finding that the types of compounds produced in these ices are strikingly similar to many of those brought to Earth today by infalling meteorites and their smaller cousins, the interplanetary dust particles. ... Thus, much of the organic material found on the Earth in its earliest years probably had an interstellar heritage." "A number of years ago I found that some of the extraterrestrial organic compounds brought to Earth in the Murchison meteorite could form membranous vesicles when they interacted with water," said team member Dave Deamer, Professor of Chemistry at the University of California at Santa Cruz.
... "When I learned of the ice experiments at NASA Ames, I went to the Astrochemistry Lab intending to find out what would happen when their complex organic mixtures were allowed to interact with water. To our surprise and delight we found that vesicular structures formed that looked very much like those we saw in the Murchison material." "We now know that of the hundreds of new compounds we make in these interstellar ice simulation experiments, many have properties relevant to the origin of life," said biochemist Jason Dworkin. "Upon the addition of liquid water to the organics produced during ice irradiation, some of these new compounds, with no outside help, organize themselves into tiny vesicles with complicated structures. Other new compounds formed are so much more complex than what we started with that they glow when exposed to UV light. Not only that, but these molecules, which can convert energy from the ultraviolet light to the visible range, become part of the self-formed vesicles," continued Dworkin. Chemicals from space interacting with water on the surface of the early planet: the soup of life raining down from space and leaving a strange brew bubbling on the surface.
ps - I am adding this to be perfectly clear on my intentions. For me the search for the elusive transition from non-life to life has to be two pronged: (1) From the bottom up -- looking for what happens naturally in a variety of environments to build more and more complex molecules from the materials available. This search also includes simulating a variety of early earth environments and possible environments on other planets (mars) or moons (europa). These molecules are the building blocks for the foundation, making towers by building onto them until the clouds are reached is the quest. (2) From the top down -- reducing life to a bare minimum, also in a variety of environments to find what can be done away with from the evolved systems and still have a (possibly crude and likely inefficient) forms of life. The variables will likely change with different environments and sources of energy that go with them. This is also where LUCA comes into the picture ("it is widely accepted that ... there was a period where RNA carried out the roles now performed by proteins and DNA"). Taking the skyscraping towers of today and deciphering the support structure, going back through time, paring it down to the bare minimums to find what the first original huts may have looked like. This specific {topic thread} deals with (1), the bottom up approach, and involves known processes with known, verified results. A future essay may deal with (2), the top down approach, and how we got to RNA and DNA and other advanced molecules from previous stages. There is still a substantial gap between them, but as such research is done from both sides an awareness will build about how near one is to the other, very much like the way the (Golden Gate bridge was built from each side of the bay in closing increments (and even though most engineers of the day said it could not be done). It is also possible that future experiments based on the bottom up approach could result in a self-replicating proto-molecular system that fills some definitions of life without developing either RNA or DNA -- presupposing either is similar to presupposing the hand of a designer. Anyone with information on more "building blocks" is welcome to add them here, as is any information of further developments or refutations of points made above (please list block number for clarity). I apologize for the length, but this is a compilation I have made over the last two years of points that to me constitute an overview of the state of current knowledge. Thank you. Edited by RAZD, : added copy of essay Edited by RAZD, : subtitle update Edited by RAZD, : spl;ng
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