The Cross Of The Moment: philosophical issues of life on Earth

The Cross Of The Moment is a documentary feature film currently in production focusing on the greater philosophical issues of life on Earth.

The Film is devided into five chapters; Fermi's Paradox, Climate Change, Capitalism , Collapse, and Wisdom.

Below is a rough cut of the first chapter featuring Robin Hanson, Donald Brownlee, and Peter D.Ward.

http://www.crossofthemoment.com/

Nick Lane - Membrane bioenergetics as power for origin of life

Nick Lane http://www.nick-lane.net/Nick%20Lane%20Publications.htm who publishes CHASM: The Outlandish Origins of Complex Life. August 2014 http://amzn.to/14tt8nv

http://www.nick-lane.net/Nick%20Lane%20Talks.htm - his past talks

this will take you back to the 70s! December 2012 Cell article (free) on The Origin of Membrane Bioenergetics: http://www.nick-lane.net/Lane-Martin%20Cell%20origin%20membrane%20bioenergetics.pdf and 2010 Nature Education (free): http://www.nature.com/scitable/topicpage/why-are-cells-powered-by-proton-gradients-14373960 - easier read

Adam Rutherford - Origin of Life - The future of life

Origin of life came from a single cell. Cell theory was death nell of spontaneous generation which reined for 2000 years eg Adam - creation ex nihilo. Aristotle claimed to have seen spontaneous generation. Rotting logs could mutate into crocodiles. SG killed in 1850s. Louis Pasteur swan neck experiment. Cell theory + Evolution ---> one first single cell (Last Universal Common Ancestor). Panspermia - life abounds in universe and was delivered to Earth. Rule it out, no evidence for life outside earth, just science fiction, currently.

Haldane & Oparin - warm little pond - spontaneous life in a primordial soup. Stanley Miller mixed ammonia, methane, hydrogen, carbon dioxide + electrical spark gave 5 amino acids. But AA are not life.

RNA World - can act as catalyst. Ribozymes (RNA enzymes that can self catalyse their own replication) (Joyce et 2009). Life is the opposite of decay (23m). Times law through 2nd law of thermodynamics predicts chaos but life manages to battle against that chaos for almost 4bn year. Life is a tiny pocket of order in a universe of chaos. Life is process of energy capture, primary function is to reproduce. Life is a metabolic process fundamentally, capture of energy. In 1980s, origin of life - an alkaline vent, hydrogen & methane, membranes, maintained energetic disequilibrium. In lab Nick Lane in 2012 in UCL is experimenting with bioreactor. (27m) A porous ceramic material, he will look for basic biochemistry.

Part 2: The sequel. Synthetic Biology. Goats that express spider thread. Fluorescent jellyfish and mice. 35m: Craig Venter in 2011 creation of synthetic life 'Synthia'. Copied and rebooted life. Hela Cells. Cusp of drug and fuel production.

Q&A at Pod Delusion (50 mins)

The evolutionary burst that made Earth oxygen-rich

http://www.newscientist.com/article/mg20827922.400-the-evolutionary-burst-that-made-earth-oxygenrich.html?DCMP=OTC-rss&nsref=online-news

• 23 December 2010
• Magazine issue 2792. 

GENE families involved in respiration and photosynthesis arose in a short evolutionary burst that began nearly a billion years before Earth's atmosphere became rich in oxygen.

Lawrence David and Eric Alm from the Massachusetts Institute of Technology mapped the evolutionary history of 3983 gene families that occur in a wide range of modern species. They were able to show that 27 per cent of these gene families appeared in a short evolutionary burst which began about 3.3 billion years ago (Nature, DOI: 10.1038/nature09649).

Many of the genes from this time were involved in electron transport - a key step in respiration and photosynthesis, which ultimately led, say David and Alm, to oxygen-producing photosynthesis and the "great oxygenation event" 2.4 billion years ago, when the atmosphere became oxygen rich.

Meteor blasts led to explosion of life on Earth

Posted from Sunday Times, 24th October 2010

my highlights

Asteroids may have had a deeper impact on Earth than previously thought. Scientists have found evidence that the planet could owe its biological diversity to a 10m-year bombardment of giant rocks about 470m years ago.

They suggest that the break-up of a huge asteroid at that time meant Earth was repeatedly struck by its fragments at a key period in the evolution of life. Before the impacts, Earth’s animal life was dominated by a small number of species. After they began, however, the fossil record shows that the number of life forms soared.

The scientists involved in the research suggest that the ecological disruption caused by the impacts spurred existing life forms to evolve much faster — eventually giving rise to the ancestors of dinosaurs, mammals and fish.

The theory makes a stark contrast to the common view that meteorites are destructive. The best-known impact, which caused the giant Chicxulub crater on the coast of Mexico, happened 65m years ago and is thought to have wiped out the dinosaurs.

The theory that other meteorites helped evolution is set out in a new book, Incoming!, by Ted Nield, editor of Geoscientist, the journal of the Geological Society of London.

He said: “The picture emerging from new research is that around 470m years ago a stupendous collision in the asteroid belt bombarded the Earth with meteorites and this may have been responsible for the single greatest increase in biological diversity since the origin of complex life.”

Nield’s book is based partly on the work of Birger Schmitz, professor of bedrock geology at Lund University in Sweden. He analysed rock samples taken from five Swedish quarries, finding that the layers of rock from 470m years ago contained an amazingly high number of fossilised meteorites.

The number of meteorites that hit the earth at present is about one for every 7,700 square miles per year. In the Swedish quarries Schmitz found a 100-fold increase in meteorite strikes, starting 470m years ago and lasting around 10m years.

He said: “The original asteroid that broke up was perhaps a few hundred kilometres in diameter so there were a lot of fragments. The size would have been up to 10km — the same size as the one that wiped out the dinosaurs.

“We think that there were quite a few really big impactors and these would have had the power to change life on earth.”

Schmitz has travelled to China and other parts of the world where rocks of a similar age and type can be sampled — and found similar increases in the number of meteorites.

The evidence that Earth underwent an intense bombardment is increasingly accepted — but did this really cause the sudden increase in life forms also seen in the fossil record over the same period?

Here, Schmitz is more cautious. He said: “The theory is controversial because most scientists believe that meteorite impacts cause extinction.

“This is true, but 470m years ago diversity was pretty low — so there were far fewer species to wipe out. Our theory is that the impacts changed the climate and geology of the earth and species had to adapt rapidly to big changes or go extinct.”

The fossil record suggests that at the time the bombardment started Earth was going through an evolutionary lull. The first great expansion of animal life, the Cambrian explosion, had taken place about 80m years earlier. During the Cambrian period animals with hard parts to their bodies, such as shells, appeared, leaving a fossil record. After that, however, evolution appears to have paused. Most life was marine-based and there were relatively few species.

Nield points out that the Earth was a different place then, with most of the land concentrated in the southern hemisphere around a single giant supercontinent that researchers call Gondwanaland.

With relatively few complex species on land, the most advanced forms of life were primitive jawless fish and squid-like cephalopods, mostly living in shallow seas. Something influenced evolution — and meteorites could have been the cause.

Expanding the limits of life

by Scientific American - december 2009 - Dr Alexander S Bradley.

Few places on Earth’s continents remain to be explored, and it is unlikely that many new natural wonders await discovery in some forgotten corner. But below the ocean surface is a different story. We know more about the facade of Mars than about the 75 percent of our own planet’s surface that lies underwater. Untold surprises await us there.

One such revelation occurred in December 2000. An expedition mapping a submerged mountain known as the Atlantis Massif, midway between Bermuda and the Canary Islands and half a mile under the surface of the North Atlantic, came across a pillar of white rock as tall as a 20-story building rising from the seafloor. Using the remotely operated ArgoII vehicle and the manned submersible Alvin, scientists surveyed and sampled the mysterious formation. The researchers determined that the white pillar was just one of several such structures in the area that were emitting heated seawater. They had discovered a field of undersea hot springs they named the Lost City Hydrothermal Field. It was unlike anything seen before, including the now famous black smokers.

The initial report describing the discovery, published in the journal Nature in July 2001, sent waves of excitement throughout the scientific community. Lead author University of Washington geologist Deborah S. Kelley and her colleagues raised many fundamental questions. How did this hydrothermal field form? What kinds of organisms live there, and how do they survive? In 2003 Kelley led a full-scale, six-week expedition to Lost City to find out. After years of painstakingly analyzing the samples collected during that mission, specialists are now beginning to compose fascinating answers.

The findings from Lost City have prompted reconsideration of long-standing notions about the chemistry that may have set the stage for the emergence of life on Earth.

The results have expanded researchers’ ideas about where life beyond the Blue Planet might exist—and challenged established ideas about how to search for it. Chemistry Scientists have known about undersea hydrothermal vents since the 1970s. The black smoker systems are the most familiar; they occur at mid ocean ridges—those strings of volcanoes overlying spots where tectonic plates are pulling away from one another. The water at these vents can reach temperatures above 400 degrees Celsius because of their proximity to molten rock. With a pH similar to lemon juice, the scorching water leaches sulfide, iron, copper and zinc as it filters through the volcanic rocks below the sea floor. As this hot, acidic fluid then rises back to the surface of the sea floor, it is discharged through the vents into cold seawater, where the dissolved metal sulphide quickly cool and precipitate out of the fluid, producing a cloudy mix that looks like billowing black smoke. These metal sulphides accumulate into ever taller chimneys atop the vents. Despite their hostile chemistry, the areas surrounding these vents teem with exotic animals, such as giant, red-tipped Riftia tube worms, which lack both mouths and guts but thrive by a symbiotic association with internal bacteria that consume poisonous hydrogen sulphide gas emanating from the vents.

Compared with the savage black smoker environment, the Lost City vents are eerily tranquil. Located about 15 kilometers to the west of the tectonic plate boundary at the Mid-Atlantic Ridge, this vent field atop the Atlantis Massif is too distant for rising magma to heat the fluids to the blistering temperatures found at black smokers. Instead the water is heated by circulation through the merely warm rock below, and the highest measured temperature is only 90 degrees C. Neither are the Lost City fluids acidic. They are alkaline, with a pH between 9 and 11—similar to milk of magnesia or household ammonia solution. Because these waters cannot readily dissolve high concentrations of metals such as iron and zinc, Lost City does not produce the metal sulphide plumes that characterize black smokers. Rather Lost City vent waters are rich in calcium, which on mixing with seawater produces calcium carbonate (limestone). This limestone forms giant white chimneys, the largest of which towers nearly 60 meters above the seafl oor—significantly taller than the loftiest black smoker chimney. The strange chemistry at Lost City derives from its unique geologic setting, which is rooted in the structure of the planet itself.

Picture Earth as a peach. The skin represents the crust, the flesh is equivalent to the underlying solid mantle layer, and the pit stands in for the hot iron core. At the Mid-Atlantic Ridge, the crust is being slowly pulled apart as North America and Africa move away from each other at a sluggish 25 millimeters a year [250km over 100 million years]. The separation of the crust has exposed parts of Earth’s mantle at the seafloor, and uplift of this exposed mantle has formed the Atlantis Massif.

The mantle consists mainly of a rock called peridotite, which turns out to be the key to the Lost City’s distinctive chemistry.

When peridotite comes into contact with water, it undergoes a chemical reaction called serpentinization. As seawater seeps into the depths of the massif, the peridotite is altered to serpentinite, and the percolating waters become more alkaline as a result of that reaction. By the time fluids reemerge and mix with the ocean waters, they are loaded with calcium released during serpentinization.

Most significant of all, they are now highly reduced, meaning that all the oxygen has been stripped from the water and replaced with energy-rich gases such as hydrogen, methane and sulfide.

The concentrations of hydrogen, in particular, are among the highest ever encountered in a natural environment. And that is where things begin to get really interesting.

In the Beginning

Hydrogen is full of energy as a consequence of its ability to transfer electrons to other compounds, such as oxygen, releasing energy in the process. Compounds that can readily donate electrons to other compounds are described somewhat confusingly as “chemically reduced.” Scientists have long suspected that reduced gases played an important role in the origin of life on Earth. In the 1920s Russian biochemist Alexander Oparin and British evolutionary biologist J.B.S. Haldane each suggested that the primitive atmosphere of Earth might have been very rich in reduced gases such as methane, ammonia and hydrogen. If the atmosphere had high concentrations of these gases, they proposed, the chemical ingredients required for life might have formed spontaneously. The idea gained credibility several decades later with the famous 1953 experiment by chemists Stanley Miller and Harold Urey of the University of Chicago. By heating and discharging sparks through a mixture of reduced gases, Miller and Urey were able to create a range of organic compounds (most compounds containing carbon and hydrogen), including amino acids, the building blocks of proteins used by all life-forms on Earth. In the years after the Miller-Urey experiment, however, geologists concluded that the early atmosphere was not nearly as reduced as the duo had assumed. The conditions that formed amino acids and other organic compounds in their experiment, these scientists said, probably never existed in the atmosphere. But reduced gases abound in the Lost City hydrothermal vents.

Could it be that billions of years ago, vents similar to these had the right organic compounds required for life? Some geochemists investigating this question think so. A number of studies conducted over the past decade have suggested that the chemical reactions that occur during serpentinization are ideal for the production of organic compounds from carbon dioxide. Hydrothermal systems akin to Lost City might have been primitive factories that churned out methane, simple organic acids and perhaps even more complex fatty acids—essential components of the cellular membranes of all organisms. And the vents might have been able to generate these organic compounds without the assistance of living organisms. Lost City is a natural laboratory for testing these ideas. In 2008 chemist Giora Proskurowski of the Woods Hole Oceanographic Institution and his colleagues published a paper in the journal Science demonstrating that the hydrothermal fluids at Lost City do indeed contain small organic compounds such as methane, ethane and propane. Other work suggests that the reactions at Lost City also produce small organic acids such as formate and acetate. Together these findings confirm that the reduced conditions at the Lost City vents could support the types of chemical reactions necessary to create organic compounds from inorganic compounds—a simple but critical step in prebiotic chemistry. This new work establishes that some hydrothermal vent environments are able to produce at least simple organic compounds, possible ingredients for life. But Lost City is not a perfect setting for testing such ideas, because the carbonate towers are not sterile chemical reactors. In fact, they teem with microbial life, which raises the possibility that these microbes could be contributing to the formation of organic compounds in the vent fl uids. To resolve this puzzle, we must take a closer look at the microbes themselves.

No Sun Needed 

Many microorganisms have evolved the ability to consume the abundant energy contained in hydrogen. Methanogens constitute one such group. As their name suggests, methanogens generate methane: the natural gas that many of us use to heat our homes and cook our food. It turns out that up to one third of the microbes at Lost City are methanogens belonging to the family Methanosarcinales. Their presence is not surprising given the abundance of hydrogen in the vent fluids. What is remarkable is that the Lost City methanogens operate independently of the sun. Virtually all life on Earth depends on solar energy—be it humans, who rely on photosynthetic organisms for food, or plants and algae serpentinithat photosynthesize. Even at black smokers, in the darkest depths of the oceans, life depends on the sun. The microbes that support the growth of the giant tube worms, for example, require both sulfide and oxygen. The ultimate source of the oxygen is photosynthetic organisms far above.

In contrast, all that the Lost City methanogens need to survive is carbon dioxide, along with liquid water and peridotite, which react to form the raw ingredients they require. Investigators have found that both geochemical reactions stemming from serpentinization and the activity of biological methanogens contribute methane to the Lost City ecosystem. This simultaneous generation of methane may not be a coincidence. In a series of studies over the past few years, biochemist William Martin of Heinrich- Heine University in Germany and geochemist Michael Russell of the NASA Jet Propulsion Laboratory in Pasadena examined the precise chemical steps required to produce methane abiotically, that is, without living organisms in environments such as that in Lost City. They found that each step is replicated in the biological pathways of organisms that generate methane. From this work, Martin and Russell proposed that on the early Earth, sites like Lost City produced methane geochemically and that primordial lifeforms may have simply co-opted each of the chemical steps for themselves, leading to what might have been the origin of the first biochemical pathway. Martin and Russell are not the first scientists to suggest that life might have arisen at a hydrothermal vent. That idea has been around for a number of years. Support for it comes not only from the advantageous chemistry at hydrothermal systems but also from the evolutionary record found in the genetic material of all living organisms.

The study of ribosomes—biological machines that the cell uses to translate the information encoded in nucleic acids (DNA and RNA) into proteins— has proved especially enlightening in this regard. The ribosomes are themselves built of both RNA and protein. By comparing the sequences of the ribosomal RNA building blocks, or nucleotides, scientists have constructed a family tree that shows the relationships of all life on Earth. Many of the organisms that reside on branches near the root of the tree consume hydrogen and inhabit high-temperature hot springs, either on land or on the seafloor, indicating that the last universal ancestor of all life on Earth may also have inhabited a hot spring, possibly in an environment resembling that of the Lost City Hydrothermal Field. Geologists have reason to suspect that ecosystems like that of Lost City may have once been relatively common. Peridotite is among the most prevalent types of rock in the solar system. On Earth, it makes up the bulk of the upper mantle. Although newly formed peridotite is rarely found on the terrestrial surface today, it was abundant three billion to four billion years ago. Back then, the planet was much hotter, and increased volcanism transported more of the molten mantle to the surface. In fact, peridotite probably made up most of the rock on the seafloor of the early Earth. This rock would have reacted with water then just as it does now. Warm, alkaline settings akin to Lost City may have thus nurtured the first life-forms. Fiery, acidic conditions similar to those found at black smokers, in contrast, would probably have been too hostile to foster the emergence of life.

The findings from Lost City also bolster hypotheses about where else in our solar system life might exist or have existed in the past. Any planet or moon containing both peridotite and liquid water—the ingredients necessary for serpentinithatzation—could conceivably support life-forms analogous to microbes at Lost City.

Evidence of these components is strongest on Mars and on Jupiter’s moon Europa. Indeed, researchers have already detected methane in the modern Martian atmosphere. Whether it comes from microbes or chemical reactions in the planet’s rocks—or both—remains uncertain, however. That determination may turn out to be harder than scientists had envisioned. Most of the organisms on the tree of life are microbes. Although we can study the DNA and RNA sequences of such organisms, finding a fossil record of small creatures with ambiguous shapes is difficult. To that end, in the past few decades researchers have developed techniques that permit investigation of the evolutionary history of microbes by combing the geologic record not for physical fossils but for chemical ones. Chemical fossils are molecules that can be traced to living organisms and can be preserved as fossils in rocks over millions or even billions of years. Most chemical fossils are derived from the lipids that make up cell membranes. Although lipids do not hold as much information as DNA or a physical fossil does, they are reliable indicators of life and can carry structures diagnostic of the organisms that produced them. Moreover, the carbon that constitutes the lipids is itself informative, because it contains a marker that reveals how an organism extracted carbon from its environment. That marker is carbon 13, a relatively rare form of the element that does not degrade over time. The carbon in most organisms includes between 1 and 3.5 percent less carbon 13 than does the carbon in the carbon dioxide dissolved in seawater. Scientists have thus assumed that carbon in ancient rocks that is depleted by this amount derived from living organisms. And as a corollary to that rule, carbon from ancient rocks that is not depleted comes from abiotic processes. But Lost City puts the lie to that notion. My work with a team of scientists at the Massachusetts Institute of Technology and at Woods Hole has shown that some of the most abundant lipids found in the carbonates at Lost City are from methanogens. Yet these lipids exhibit no carbon 13 depletion whatsoever. Instead their carbon 13 contents are what one would expect from material that did not derive from living organisms. How can this be? The use of carbon 13 as a tracer of life rests on the assumption that more carbon dioxide is available in the environment than can be used. As long as there is a surplus of carbon dioxide, organisms can incorporate lighter carbon 12 molecules, which they prefer, and discriminate against the heavier carbon 13. But if carbon dioxide were somehow scarce, organisms would scrounge for every available carbon molecule that they could get, be it the lighter variety or the heavier one. And if that were to occur, the relative abundance of carbon 13 in the organisms would be no different from that in the environment. The chemical tracer of life would be invisible. This process is exactly what is happening at the Lost City vents. Unlike nearly every other environment on Earth, where carbon dioxide is always available, at Lost City hydrogen predominates and carbon dioxide is scarce, in effect forcing organisms there to extract carbon isotopes indiscriminately. The invisibility problem applies to methane, too. Usually methane produced by organisms shows an extreme depletion in carbon 13, in contrast to methane from geochemical reactions. But in serpentinizing systems, this difference does not always appear. The methane in the Lost City vent waters lacks the telltale carbon 13 depletion. Researchers know from observation that this methane is a mixture of geologic and biological products. Carbon isotopes alone are incapable of making the distinction, though.

If life has evolved elsewhere in our solar system, the best bet may be that it consists of microbial methanogens living in sites where rock is being serpentinized. We know that methane is somehow being produced on Mars. NASA plans to launch the Mars Science Laboratory in 2011, and one of its missions will be to determine the carbon isotope ratio of that methane. A strong depletion in carbon 13 would be an indication that organisms inhabit the Red Planet. Yet Lost City demonstrates that failure to find that signal can hardly be considered evidence of absence. Indeed, the discovery of microbes thriving in this previously unknown type of ecosystem provides yet more reason to expect that scientists will one day find signs of life beyond Earth.

http://www.nytimes.com/2009/06/16/science/16orig.html?_r=2 via http://richarddawkins.net/article,3953,n,n

New Glimpses of Life’s Puzzling Origins

Janet Iwasa

A START In one view of the beginnings of life, depicted in an animation, carbon monoxide molecules condense on hot mineral surfaces underground to form fatty acids, above, which are then expelled from geysers.

By NICHOLAS WADE

Published: June 15, 2009

Some 3.9 billion years ago, a shift in the orbit of the Sun’s outer planets sent a surge of large comets and asteroids careening into the inner solar system. Their violent impacts gouged out the large craters still visible on the Moon’s face, heated Earth’s surface into molten rock and boiled off its oceans into an incandescent mist.


Yet rocks that formed on Earth 3.8 billion years ago, almost as soon as the bombardment had stopped, contain possible evidence of biological processes. If life can arise from inorganic matter so quickly and easily, why is it not abundant in the solar system and beyond? If biology is an inherent property of matter, why have chemists so far been unable to reconstruct life, or anything close to it, in the laboratory?

The origins of life on Earth bristle with puzzle and paradox. Which came first, the proteins of living cells or the genetic information that makes them? How could the metabolism of living things get started without an enclosing membrane to keep all the necessary chemicals together? But if life started inside a cell membrane, how did the necessary nutrients get in?

The questions may seem moot, since life did start somehow. But for the small group of researchers who insist on learning exactly how it started, frustration has abounded. Many once-promising leads have led only to years of wasted effort. Scientists as eminent as Francis Crick, the chief theorist of molecular biology, have quietly suggested that life may have formed elsewhere before seeding the planet, so hard does it seem to find a plausible explanation for its emergence on Earth.

In the last few years, however, four surprising advances have renewed confidence that a terrestrial explanation for life’s origins will eventually emerge.

One is a series of discoveries about the cell-like structures that could have formed naturally from fatty chemicals likely to have been present on the primitive Earth. This lead emerged from a long argument between three colleagues as to whether a genetic system or a cell membrane came first in the development of life. They eventually agreed that genetics and membranes had to have evolved together.

The three researchers, Jack W. Szostak, David P. Bartel and P. Luigi Luisi, published a somewhat adventurous manifesto in Nature in 2001, declaring that the way to make a synthetic cell was to get a protocell and a genetic molecule to grow and divide in parallel, with the molecules being encapsulated in the cell. If the molecules gave the cell a survival advantage over other cells, the outcome would be “a sustainable, autonomously replicating system, capable of Darwinian evolution,” they wrote.
“It would be truly alive,” they added.

One of the authors, Dr. Szostak, of the Massachusetts General Hospital, has since managed to achieve a surprising amount of this program.
Simple fatty acids, of the sort likely to have been around on the primitive Earth, will spontaneously form double-layered spheres, much like the double-layered membrane of today’s living cells. These protocells will incorporate new fatty acids fed into the water, and eventually divide.

Living cells are generally impermeable and have elaborate mechanisms for admitting only the nutrients they need. But Dr. Szostak and his colleagues have shown that small molecules can easily enter the protocells. If they combine into larger molecules, however, they cannot get out, just the arrangement a primitive cell would need. If a protocell is made to encapsulate a short piece of DNA and is then fed with nucleotides, the building blocks of DNA, the nucleotides will spontaneously enter the cell and link into another DNA molecule.

At a symposium on evolution at the Cold Spring Harbor Laboratory on Long Island last month, Dr. Szostak said he was “optimistic about getting a chemical replication system going” inside a protocell. He then hopes to integrate a replicating nucleic acid system with dividing protocells.

Dr. Szostak’s experiments have come close to creating a spontaneously dividing cell from chemicals assumed to have existed on the primitive Earth. But some of his ingredients, like the nucleotide building blocks of nucleic acids, are quite complex. Prebiotic chemists, who study the prelife chemistry of the primitive Earth, have long been close to despair over how nucleotides could ever have arisen spontaneously.

Nucleotides consist of a sugar molecule, like ribose or deoxyribose, joined to a base at one end and a phosphate group at the other. Prebiotic chemists discovered with delight that bases like adenine will easily form from simple chemicals like hydrogen cyanide. But years of disappointment followed when the adenine proved incapable of linking naturally to the ribose.

Last month, John Sutherland, a chemist at the University of Manchester in England, reported in Nature his discovery of a quite unexpected route for synthesizing nucleotides from prebiotic chemicals. Instead of making the base and sugar separately from chemicals likely to have existed on the primitive Earth, Dr. Sutherland showed how under the right conditions the base and sugar could be built up as a single unit, and so did not need to be linked.

“I think the Sutherland paper has been the biggest advance in the last five years in terms of prebiotic chemistry,” said Gerald F. Joyce, an expert on the origins of life at the Scripps Research Institute in La Jolla, Calif.

Once a self-replicating system develops from chemicals, this is the beginning of genetic history, since each molecule carries the imprint of its ancestor. Dr. Crick, who was interested in the chemistry that preceded replication, once observed, “After this point, the rest is just history.”

Dr. Joyce has been studying the possible beginning of history by developing RNA molecules with the capacity for replication. RNA, a close cousin of DNA, almost certainly preceded it as the genetic molecule of living cells. Besides carrying information, RNA can also act as an enzyme to promote chemical reactions. Dr. Joyce reported in Science earlier this year that he had developed two RNA molecules that can promote each other’s synthesis from the four kinds of RNA nucleotides.

“We finally have a molecule that’s immortal,” he said, meaning one whose information can be passed on indefinitely. The system is not alive, he says, but performs central functions of life like replication and adapting to new conditions.

“Gerry Joyce is getting ever closer to showing you can have self-replication of RNA species,” Dr. Sutherland said. “So only a pessimist wouldn’t allow him success in a few years.”

Another striking advance has come from new studies of the handedness of molecules. Some chemicals, like the amino acids of which proteins are made, exist in two mirror-image forms, much like the left and right hand. In most naturally occurring conditions they are found in roughly equal mixtures of the two forms. But in a living cell all amino acids are left-handed, and all sugars and nucleotides are right-handed.

Prebiotic chemists have long been at a loss to explain how the first living systems could have extracted just one kind of the handed chemicals from the mixtures on the early Earth. Left-handed nucleotides are a poison because they prevent right-handed nucleotides linking up in a chain to form nucleic acids like RNA or DNA. Dr. Joyce refers to the problem as “original syn,” referring to the chemist’s terms syn and anti for the structures in the handed forms.

The chemists have now been granted an unexpected absolution from their original syn problem. Researchers like Donna Blackmond of Imperial College London have discovered that a mixture of left-handed and right-handed molecules can be converted to just one form by cycles of freezing and melting.

With these four recent advances — Dr. Szostak’s protocells, self-replicating RNA, the natural synthesis of nucleotides, and an explanation for handedness — those who study the origin of life have much to be pleased about, despite the distance yet to go. “At some point some of these threads will start joining together,” Dr. Sutherland said. “I think all of us are far more optimistic now than we were five or 10 years ago.”

One measure of the difficulties ahead, however, is that so far there is little agreement on the kind of environment in which life originated. Some chemists, like Günther Wächtershäuser, argue that life began in volcanic conditions, like those of the deep sea vents. These have the gases and metallic catalysts in which, he argues, the first metabolic processes were likely to have arisen.

But many biologists believe that in the oceans, the necessary constituents of life would always be too diluted. They favor a warm freshwater pond for the origin of life, as did Darwin, where cycles of wetting and evaporation around the edges could produce useful concentrations and chemical processes.

No one knows for sure when life began. The oldest generally accepted evidence for living cells are fossil bacteria 1.9 billion years old from the Gunflint Formation of Ontario. But rocks from two sites in Greenland, containing an unusual mix of carbon isotopes that could be evidence of biological processes, are 3.830 billion years old.

How could life have gotten off to such a quick start, given that the surface of the Earth was probably sterilized by the Late Heavy Bombardment, the rain of gigantic comets and asteroids that pelted the Earth and Moon around 3.9 billion years ago?

Stephen Mojzsis, a geologist at the University of Colorado who analyzed one of the Greenland sites, argued in Nature last month that the Late Heavy Bombardment would not have killed everything, as is generally believed. In his view, life could have started much earlier and survived the bombardment in deep sea environments.

Recent evidence from very ancient rocks known as zircons suggests that stable oceans and continental crust had emerged as long as 4.404 billion years ago, a mere 150 million years after the Earth’s formation. So life might have had half a billion years to get started before the cataclysmic bombardment.

But geologists dispute whether the Greenland rocks really offer signs of biological processes, and geochemists have often revised their estimates of the composition of the primitive atmosphere. Leslie Orgel, a pioneer of prebiotic chemistry, used to say, “Just wait a few years, and conditions on the primitive Earth will change again,” said Dr. Joyce, a former student of his.

Chemists and biologists are thus pretty much on their own in figuring out how life started. For lack of fossil evidence, they have no guide as to when, where or how the first forms of life emerged. So they will figure life out only by reinventing it in the laboratory.

Life's First Spark Re-Created in the Laboratory

source: http://richarddawkins.net/article,3845,n,n

http://www.wired.com/wiredscience/2009/05/ribonucleotides/

A fundamental but elusive step in the early evolution of life on Earth has been replicated in a laboratory.

Researchers synthesized the basic ingredients of RNA, a molecule from which the simplest self-replicating structures are made. Until now, they couldn’t explain how these ingredients might have formed.

“It’s like molecular choreography, where the molecules choreograph their own behavior,” said organic chemist John Sutherland of the University of Manchester, co-author of a study in Nature Wednesday.

RNA is now found in living cells, where it carries information between genes and protein-manufacturing cellular components. Scientists think RNA existed early in Earth’s history, providing a necessary intermediate platform between pre-biotic chemicals and DNA, its double-stranded, more-stable descendant.

Continue reading:
http://www.wired.com/wiredscience/2009/05/ribonucleotides/

Also see:
RNA world easier to make - Nature
Molecule of life emerges from laboratory slime - New Scientist
HOW RNA GOT STARTED - Science News
Found: the origin of life - The Independent
Chemist Shows How RNA Can Be the Starting Point for Life - NY Times

Inspirational Orbits - Astronomers are finding new planets

source: Scientific American, June 2009 by John Rennie, Editor-in-Chief

The year 1609 was noteworthy for two astronomical milestones. That was when Galileo built his first telescopes and began his meticulous study of the skies. Within months he discovered the four major satellites of Jupiter, saw that Venus (like our moon) has illuminated phases and confirmed earlier observations of sunspots—all evidence that undermined the Aristotelian model of an unchanging, Earth-centered cosmos.

During that same year, Johannes Kepler published Astronomia Nova, which contained his detailed calculation of the orbit of Mars. It also established the first two laws of planetary motion: that planets follow elliptical orbits, with the sun at one focus, and that planets sweep through equal areas of their orbits in a given interval.

Small wonder, then, that when the United Nations General Assembly declared an International Year of Astronomy to promote the wider appreciation of the science, it selected 2009, the quadricentennial of those standout accomplishments (among many) by Galileo and Kepler that informally founded modern astronomy.

Currently astronomers can look beyond the familiar planets and moons to entirely new systems of worlds around other stars. As I write this, the tally stands at 344 known extrasolar planets. Only a handful of these bodies were found by telescopic means that Galileo or Kepler would have recognized, but each one owes its discovery to their work. A recent and surprising trend is the apparent abundance of planets turning up close to very small stars—suns that may not be much larger than the planets circling them.

Astronomers Michael W. Werner and Michael A. Jura have more in their article starting on page 26, including why the existence of these unlikely planetary systems might imply that the universe is chockfull of planets.

New, improved recipe cooks up life molecule

• 13 May 2009 by Kate Ravilious
• Magazine issue 2708. Subscribe and get 4 free issues.

CREATING life in the primordial soup may have been easier than we thought. Two essential elements of RNA have finally been made from scratch, under conditions similar to those that likely prevailed during the dawn of life.

The question of how a molecule capable of storing genetic information - even DNA's simpler cousin RNA - could ever have arisen spontaneously in the primordial cooking pot has perplexed scientists for decades. RNA consists of a long chain composed of four different types of ribonucleotides, which each consist of a nitrogenous base, a sugar and a phosphate.

Most people assumed that these three components first formed separately, and then combined to make the ribonucleotides. The only trouble was that it seemed impossible that two of the four bases with particularly unwieldy chemistry ever reacted spontaneously with the sugar.

To tackle this problem, John Sutherland from the University of Manchester, UK, tried to work out a new recipe for RNA that gets by without forcing isolated bases and sugar molecules to react. His team experimented by cooking up ribonucleotides from five small molecules thought to be present in the primordial soup. "We started with the same building blocks as others, but take a different route," Sutherland says.

And this time the cooks seem to have got it right. The recipe and conditions that they came up with to mix the five ingredients - including a good blast of UV light - produce ribonucleotides via a joint precursor molecule that contains both the base and the sugar instead of making each in their free form (Nature, DOI: 10.1038/nature08013).

This package deal sidesteps the problem of getting two unwilling partners to react, but only thanks to another trick, say the researchers. The reaction worked only when phosphate was present right from the start, although it does not react with the mixture until near the final stages. It turns out it is needed as a catalyst and as a chemical buffer early on.

"We don't use any way-out scenarios - all the conditions are consistent with what we know about early Earth," says Sutherland. William Scott, from the University of California in Santa Cruz agrees: "It's a great leap forward that demonstrates how prebiotic RNA molecules may have assembled spontaneously from simple and presumably relatively abundant constituents."

It's a great leap forward that demonstrates how prebiotic RNA molecules may have assembled

The need for UV light suggests life didn't begin in a submarine vent, one possible scenario. Instead, it points towards a warm pond - an idea first mooted by Charles Darwin, who knew nothing of RNA.

Complex molecules (Ethyl formate & Propyl Cyanide) seen in space

By Paul Rincon Science reporter, BBC News, Hatfield

A model of Ethyl formate: Complexity can be built up step by step

Astronomers have detected two of the most complex carbon-rich molecules ever found in interstellar space.

Their models suggest even more complex await to be discovered, including amino acids - which are essential for life.
The results were presented at the European Week of Astronomy and Space Science meeting being held in the UK.
Researchers detected the organic molecules in the star-forming region of space known as Sagittarius B2, close to the centre of our galaxy.
Large carbon-rich molecules of many different types have been seen in this cloud in the past, including alcohols, aldehydes, and acids.
The two new molecules - ethyl formate and n-propyl cyanide - were found in a hot, dense cloud of gas which contains a luminous newly formed star. They represent two different classes of molecule: the esters and alkyl cyanides.
Atoms and molecules emit radiation at different frequencies, which appear as characteristic lines in the light "spectrum" from an astronomical source.

The IRAM 30m Telescope at Pico Veleta in southern Spain

"The difficulty in searching for complex molecules is that the best astronomical sources contain so many different molecules that their 'fingerprints' overlap, and are difficult to disentangle," says Arnaud Belloche, from the Max Planck Institute for Radio Astronomy in Bonn, Germany.
"Larger molecules are even more difficult to identify because their fingerprints are barely visible: their radiation is distributed over many more lines that are much weaker," adds Holger Mueller, researcher at the University of Cologne.
Out of 3,700 spectral lines detected with the IRAM telescope in Spain, the team identified 36 lines belonging to the two new molecules. The astronomers then ran computational models to understand how molecules like these form in interstellar space.
They could be built up atom-by-atom via collisions of gaseous particles. Alternatively, atoms could meet and react on small grains of dust suspended in the interstellar gas.

n-propyl cyanide: Large molecules can sometimes be hard to disentangle

As a result, the grains build up thick layers of ice, composed mainly of water, but also containing a number of basic organic molecules like methanol, the simplest alcohol.
Their computational models suggest the largest molecules form section-by-section, using pre-formed building blocks already carried by the dust grains.
The new molecules seem to be "born" in this way, via a series of short steps that build up long-chain molecules.
"There is no apparent limit to the size of molecules that can be formed by this process - so there's good reason to expect even more complex organic molecules to be there, if we can detect them," says Robin Garrod, an astrochemist from Cornell University in Ithaca, New York, US.
Astronomers believe it could only be a matter of time before amino acids are found in interstellar space. This class of molecules is needed for the production of proteins, and are therefore essential for life.
In the past, researchers have looked for the simplest amino acid, glycine, without any luck.

Change of Name of Blog

Today the name of this blog has changed from "Search for ET" to "Search for ET and the Origin of Life" to reflect my dual interests.

Second Genesis: The search for shadow life

• 13 March 2009
• Magazine issue 2699. Subscribe and get 4 free issues.
• For similar stories, visit the Astrobiology Topic Guide

See a gallery of possible forms of shadow life

While some researchers are attempting to create brand new life in the lab, others are searching for alien life on Mars and, eventually, elsewhere in the solar system. This burgeoning field of astrobiology has a less well-known offshoot right here on Earth: the search for a "shadow biosphere"- a second, independent form of life unrelated to sort we know (Astrobiology, vol 5, p 154).

After all, many astrobiologists now think that given the right conditions any sufficiently complex molecular soup has a good chance of generating life if it simmers long enough. If that's so, it seems plausible that life may have arisen on Earth not once, but several times. New origins of life are unlikely today, because existing life would gobble up any aggregations of prebiotic molecules before they could edge over the threshold. However, opportunities for the origin of life may well have existed for long periods on the early Earth. Some of these origins may have been dead ends, out-competed by other life forms - but others could still be living among us, unnoticed.

As big as Darwin

"I think if we found a second sample of life on Earth, it would be as big as Darwin's theory of evolution," says cosmologist and astrobiologist Paul Davies at Arizona State University in Tempe. "It would answer the most fundamental question we can imagine, which is: are we alone in the universe?"

Sceptics might scoff that shadow life could pass unrecognised for so long, but Davies and his collaborators have a simple rejoinder: we've never looked properly. Such life would probably take the form of single-celled microbes, so we would not expect naturalists to spot it casually like some rare parrot. And the techniques microbiologists use to detect life - staining for DNA, sequencing DNA, and culturing microbes in the lab - assume that the target microbes have the normal biochemistry.

"They couldn't detect an alternative form of microbial life," says Carol Cleland, a philosopher of science and astrobiologist at the University of Colorado in Boulder. Given that fewer than 1 per cent of microbes have been cultured and described, there is plenty of room for shadow life to be living right under our noses.

However, the task of searching for shadow life on Earth is much tougher than looking for life on other planets. "This planet is heavily contaminated with life as we know it," says Shelley Copley, a biochemist at the University of Colorado. That means researchers can't just look for evidence of metabolism or the presence of large biopolymers, because ordinary life would swamp any signal from shadow life. Instead, shadow-stalkers have to get more creative.

One promising avenue is to explore extreme environments that are beyond the reach of conventional life, such as ultra-dry deserts, ice sheets, the upper atmosphere or the hottest hydrothermal vents (see The most extreme life-forms in the universe)

Another is to devise ways of detecting alternative biochemistries. In the first and so-far only experiment of this kind, Richard Hoover, a microbiologist at NASA's National Space Science and Technology Center in Huntsville, Alabama, went looking for "mirror life". Normal organisms use right-handed sugars and left-handed amino acids almost exclusively, and eschew their mirror-image equivalents. But what if shadow life developed the opposite preference? Hoover and his colleague Elena Pikuta created nutrient broths containing only left-handed sugars and right-handed amino acids, inoculated them with unusual extremophile microbes and waited to see if anything grew.

"Much to our great astonishment, we found that we did have some microorganisms that were capable of growing," Hoover recalls. But on closer examination, the shadow microbes turned out to be ordinary bacteria with unusual metabolisms.

Cleland thinks there are other places to look. "What I think we should do is go out looking for anomalies," she says. For example, some researchers have reported nanobacteria which show some of the characteristics of life but are too small to be ordinary cells.

An even more promising anomaly, Cleland says, is "http://www.imperial.ac.uk/P7911.htm desert varnish" - a thin, manganese-rich layer that forms on the surface of rocks, especially in hot, dry places. "Everyone thinks they know what desert varnish is, but everyone disagrees," says Cleland. "There is no agreement on whether it is produced by living or nonliving processes." The layered varnish looks a lot like the primitive microbial mats called stromatolites, but for the most part, microbes are absent. Bacteria-like objects are occasionally present, but have never been fully characterised. "What they really are, I have no idea," says Ronald Dorn, a who studies rock varnish at Arizona State University.

In September 2008, Cleland and her colleagues took samples of desert varnish. They hope to find unusual ratios of elements that might point to some sort of metabolic process, but with a signature that differs from that of familiar life. They hope to have some results later this year.

Not likely, says Norman Pace, a microbiologist at the University of Colorado who is one of the researchers Cleland has recruited to examine the desert varnish. "The only reason to invoke [shadow life] is that we don't know what causes desert varnish," he says. Still, he's willing to have a look.

Davies hopes that more researchers will start looking for shadow life. Even if they don't find it, the search could turn up previously unknown branches on the familiar tree of life. "So it's worth doing anyway," he concludes, "even if you've convinced yourself that we're alone in the universe."

Galaxy has 'billions of Earths'

via http://richarddawkins.net/article,3606,n,n

The number of stars points to there being many rocky planets

There could be one hundred billion Earth-like planets in our galaxy, a US conference has heard.

Dr Alan Boss of the Carnegie Institution of Science said many of these worlds could be inhabited by simple lifeforms.

He was speaking at the annual meeting of the American Association for the Advancement of Science in Chicago.

So far, telescopes have been able to detect just over 300 planets outside our Solar System.

Very few of these would be capable of supporting life, however. Most are gas giants like our Jupiter, and many orbit so close to their parent stars that any microbes would have to survive roasting temperatures.

But, based on the limited numbers of planets found so far, Dr Boss has estimated that each Sun-like star has on average one "Earth-like" planet.

This simple calculation means there would be huge numbers capable of supporting life.

"Not only are they probably habitable but they probably are also going to be inhabited," Dr Boss told BBC News. "But I think that most likely the nearby 'Earths' are going to be inhabited with things which are perhaps more common to what Earth was like three or four billion years ago." That means bacterial lifeforms.

Dr Boss estimates that Nasa's Kepler mission, due for launch in March, should begin finding some of these Earth-like planets within the next few years.

Recent work at Edinburgh University tried to quantify how many intelligent civilisations might be out there. The research suggested there could be thousands of them.

Did lack of comet impacts help life evolve?

• 28 November 2008 by David Shiga
• Magazine issue 2684.

IT SEEMS we got off lightly in the cosmic lottery. Deadly comet impacts may be much rarer in our solar system than in others nearby.

We can't directly measure the rate of comet collisions in other solar systems but we can detect signs of the dust that such smashes kick up because the dust gets warmed by the star and so gives off infrared radiation. That radiation shows up as extra infrared in the spectrum of light coming from the star. Because such dust should dissipate quickly, it is thought to provide a good snapshot of the recent collision rate.

Jane Greaves of the University of St Andrews, UK, analysed observations by the Spitzer Space Telescope and found that

the vast majority of sun-like stars near us have more dust than our solar system does and therefore have had more collisions in their vicinity. Our solar system may be one of the few that have been safe for life.

Greaves presented her results at the Cosmic Cataclysms and Life symposium in Frascati, Italy, this month.

more...

Exoplanets finally come into view

source: BBC

Three exoplanets orbiting the same star have been imaged directly

The first pictures of planets outside our Solar System have been taken, two groups report in the journal Science.

Visible and infrared images have been snapped of a planet orbiting a star 25 light-years away.

The planet is believed to be the coolest, lowest-mass object ever seen outside our own solar neighbourhood.

In a separate study, an exoplanetary system, comprising three planets, has been directly imaged, circling a star in the constellation Pegasus.

While several claims have been made to such direct detection before, they have later been proven wrong or await confirmation.

It's a profound and overwhelming experience to lay eyes on a planet never before seen Paul Kalas, University of California

The search for exoplanets has up to now depended on detecting either the wobble they induce in their parent star or, if their orbits are side-on to telescopes, watching them dim the star's light as they pass in front of it.

Being able to directly detect the light from these planets will allow astronomers to study their composition and atmospheres in detail.

Ring cleaning

The difficulty for astronomers imaging exoplanets is that their parent star's light swamps them - like trying to spot a match next to a floodlight at a distance of a mile.

The light from the star Fomalhaut was blocked to spot the planet Enlarge Image

But advances in optics and image processing have allowed astronomers to effectively subtract the bright light from stars, leaving behind light from the planets. That light can either come in the infrared, caused by the planets' heat, or be reflected starlight.

Paul Kalas of the University of California, Berkeley, led an international group that used the Hubble Space Telescope to image the region around a star called Fomalhaut in the constellation Piscis Austrinus.

The star has a massive ring of dust surrounding it that appears to have a cleanly groomed inner edge.

That is in keeping with what is known as accretion theory - that young planets gather up dust and matter as they orbit - and prompted the team to begin looking for the suspected planet in 2005.

The team estimates that the planet, designated Fomalhaut b, is some 18 billion kilometres (11 billion miles) away from its star, about as massive as Jupiter and completes an orbit in about 870 years. It may also have a ring around it.

"I nearly had a heart attack at the end of May when I confirmed that Fomalhaut b orbits its parent star," Dr Kalas said. "It's a profound and overwhelming experience to lay eyes on a planet never before seen."

An artist's concept of the star Fomalhaut and the planet observed by Hubble

Christian Marois of the Herzberg Institute for Astrophysics, Canada, and his team used the Keck and Gemini telescopes in Hawaii to look near a star called HR 8799, which is just visible to the naked eye.

The team studied light in the infrared part of the spectrum, hoping to spot planets that were still hot from their formation.

What they found in 2004, and confirmed again this year, are three planets circling the star.

According to a theoretical model that accounts for the light coming from the planets, they range in size from five to 13 times the mass of Jupiter and are probably only about 60 million years old.

The trio have similarities with our own Solar System. Their orbits are comparable in size to those of the outer planets, and the smaller planets are those closest to the Sun - again suggesting a system that formed through accretion.

Dr Marois points out that the current methods used in the exoplanet hunt are sensitive primarily to Jupiter-sized planets and larger.

"We thus do not have a full picture," he told BBC News. "The detection of the three planets around HR 8799 does not mean that no planets are orbiting at smaller separations. Other gas giant or even rocky planets could reside there."

A to-scale comparison of the HR 8799 system and our own

The study of the light directly from the planets will yield information about their atmospheres and surfaces that is impossible to collect from planets discovered indirectly.

Further, the current results will also support theories of how planets form from the grand discs of dust and material around stars, and lead to better estimates of how many Earth-like planets are likely to exist.

These latest claims are both based on observations that were well-spaced in time, allowing the researchers to apply a rigorous test for direct detection.

"You see an object next to a star and you might think it's a planet," commented Mark McCaughrean, an astrophysicist at the University of Exeter, UK.

"But you have to watch it for several years and make sure that it moves around the star and with the star as it moves across the sky. Though I've been very sceptical in the past, these ones all seem pretty real to me," he told BBC News

"It's like a London bus - you've been waiting for one for ages and suddenly four come along at once.

Cassini might hold secrets to life on Saturn moon

Cassini might hold secrets to life on Saturn moon

• 18:17 03 November 2008
• NewScientist.com news service
• Rachel Courtland

Enlarge image

Jets of fine, icy particles erupt from the south polar region of Enceladus (Image: NASA/JPL/Space Science Institute)

Habitable worlds may hide in gas giants' wake

Habitable worlds may hide in gas giants' wake

• 01 November 2008

HABITABLE planets may be lurking in the wake of Jupiter-like planets as they orbit distant stars.

When a gas giant coalesces from the swirling nebula of gas and dust surrounding a young star, the planet's gravity forms a wake ahead and behind it, concentrating enough matter there for it to clump together and form smaller, rocky planets like Earth. That's according to simulations led by Wladimir Lyra of the Uppsala Astronomical Observatory in Sweden. Objects born in Jupiter's wake may have merged to form the planet Saturn, which was then nudged into its current position by the gravity of other planets, the team says (www.arxiv.org/abs/0810.3192).

Outside our solar system, some gas giant planets have been detected in the habitable zone of their stars. Their wakes may harbour rocky, Earth-size worlds. "It's an exciting possibility," says Sara Seager of MIT. She notes that such planets could be found by the small gravitational tugs they exert on their larger, known siblings, an idea supported by recent calculations by Nikku Madhusudhan and Joshua Winn, also of MIT.