Astrobiology_A Very Short Introduction

by David C. Catling

  Oparin and Haldane also proposed that gases in Earth’s early atmosphere would have been converted by ultraviolet sunlight or lightning into organic molecules. In the 1950s, such ideas were tested when Stanley Miller, a student of the Nobel Prize-winning chemist Harold Urey, devised an experiment at the University of Chicago. A blend of ammonia, methane, hydrogen, and water vapour was put in a flask and electric sparks passed through the gas to simulate lightning. Miller found that yellowish water condensed out at the bottom of the flask. This dark residue contained organic molecules, including various amino acids—the building blocks of proteins. At the time, the Miller–Urey experiment was trumpeted in the media as virtually solving the problem of the origin of life. Life was said to start in a ‘primordial soup’ generated by atmospheric chemistry. In 1953, when Miller wrote up his results, a common view (dating back to Oparin and Haldane) was that genetic material was protein, but a month before Miller’s paper came out, DNA was identified as the real basis of heredity. Subsequently, experiments in the Miller–Urey genre have also produced molecules containing hexagonal rings of carbon, nitrogen, and hydrogen atoms, which are the kind of rings found in DNA.

  However, geochemists have raised doubts about the Miller–Urey experiment because they argue that the Earth’s early atmosphere was probably not as hydrogen rich as Miller assumed. Volcanoes supply the Earth’s atmosphere with gases over long timescales but most volcanic gas is steam, i.e. water vapour (H2O), with an average of less than 1 per cent hydrogen (H2). Similarly, volcanic carbon comes out as carbon dioxide (CO2) rather than the hydrogenated form of methane (CH4), while nitrogen is emitted as dinitrogen (N2) instead of ammonia (NH3).

  It is thought that the atmosphere in the Hadean was mostly maintained from gases released through volcanism, so the air should have consisted predominantly of CO2 and N2. Of course, it depends on how far back you go. When the Earth was forming, the vaporization of large impactors would have produced hydrogen-rich atmospheres if impactors were sufficiently rich in iron to provide the right kind of chemistry to stabilize hydrogen in the impact explosion. Early on, most of the atmosphere was steam and oceans had not yet condensed. After oceans formed, atmospheres produced by impact vaporization would have been ephemeral. Because of uncertainties about the composition of the Hadean atmosphere, astrobiologists have proposed sources of organic carbon other than that presumed by Miller and Urey.

  One alternative is that organic carbon came from space. Some carbon-rich meteorites contain amino acids, alcohols, and other organic compounds that perhaps could have seeded Earth with the materials needed for prebiotic chemistry. For example, the Murchison meteorite, which fell on Murchison, Australia, in 1969, contains over 14,000 different molecules. Also, micrometeorite particles that are 0.02–0.4 mm in size currently bring about 30 million kg of organic carbon to the Earth per year. Organic carbon can fall intact to the Earth’s surface because tiny particles don’t necessarily burn up in the atmosphere. Furthermore, the interiors of comets are rich in organic material and may have played a similar role to meteorites in getting life started if the organic material survived cometary impacts on the Earth.

  Another possible source of organic carbon is deep-sea hydrothermal vents. A hydrothermal vent is a spot where hot water emerges from the seafloor. New seafloor is created at mid-ocean ridges, where the Earth’s tectonic plates separate and magma rises up from the mantle, filling the void. Seawater flows down through cracks near the ridges, is heated by the hot magma, and rises, picking up substances produced by chemical reactions between the water and rocks, such as hydrogen, hydrogen sulphide, and dissolved iron. When the hot acidic water hits cold (2°C) ocean water, it produces a plume of precipitated particles containing dark-coloured pyrite, an iron sulphide mineral (FeS2, where Fe is iron and S is sulphur). That is why these hydrothermal vents are called ‘black smokers’. One hypothesis suggests that life originated on the surface of such pyrite minerals. However, black smokers are very hot, around 350°C, so most researchers who favour a deep-sea origin of life have focused on vents that are cooler, around 90°C, alkaline rather than acidic, and located further from the mid-ocean ridges.

  Beneath alkaline vents, hydrogen released in reactions between water and rock can combine with carbon dioxide to make methane and bigger organic molecules. In the Hadean, tiny pores in the mineral structures that grew up from vents could, in principle, have contained and concentrated simple molecules to allow them to react and make more complex prebiotic molecules.

  Also, in alkaline vents, because the fluid emerging is more alkaline than seawater, there is a natural gradient in pH that is similar to that in cells. If life originated in such an environment, it might explain why energy production is intimately tied to pH gradients.

  Life generates energy from microscopic electrical motors that are embedded in cell membranes and run off electrical currents driven by pH gradients across the membranes. It is impossible for words to do justice to these amazing molecular machines, so I suggest that the reader search the Internet for ‘ATP synthase animations’. Essentially, metabolic energy is used to create a different pH on each side of a cell membrane with the outside usually more acidic than the inside. This differential is a proton gradient, because pH is an inverse measure of the concentration of positively charged hydrogen ions (protons) in solution—the greater the concentration, the lower (and more acidic) the pH. The proton gradient is essentially a battery. When discharged, electrical current flows through the molecular turbine in the cell membrane and generates molecules that store energy. These molecules of adenosine triphosphate or ‘ATP’ are the energy carriers in all cells. For example, a human typically contains 250g of ATP and uses up a body weight’s worth of ATP every day as ATP is made used, and remade.

  The above process of generating ATP is called chemiosmosis, which contains the word ‘osmosis’, meaning water moving across a membrane, because the proton movement is analogous. Chemiosmosis is so weird compared with the familiar idea of generating energy from chemical reactions that when it was proposed in 1961 by British biochemist Peter Mitchell most biochemists were hostile. Eventually, Mitchell was vindicated with a Nobel Prize in 1978. Given that chemiosmosis is universal to terrestrial life and presumably related to its origin, it is interesting to wonder whether ion gradients might be fundamental for life anywhere.

  Currently, the source of the organic carbon that led to the origin of life—the atmosphere, space, or hydrothermal vents—is unresolved. Given such a source, however, organic compounds must have been concentrated for chemical reactions to happen, which could have occurred when films formed on mineral surfaces, perhaps arising from drying or coldness. Then the simple organics could join up to make more complex molecules. But chemical systems need several other features before they can be considered ‘alive’. The main ones are a metabolism, enclosure by a semi-permeable membrane, and reproduction that incorporates heredity with a genome.

  With regard to the last characteristic, a more tractable issue for laboratory experimentation than the origin of life itself is a hypothesized stage of very early life, called the RNA World, in which RNA preceded DNA as the genetic material. In modern cells, DNA (deoxyribonucleic acid) provides an instruction set that is transcribed into RNA (ribonucleic acid) molecules that carry the information needed to make specific proteins. DNA is similar to RNA but more complicated, so it is logical that RNA evolved first. Moreover, in the 1980s it was discovered that some RNA molecules, known as ribozymes, can act as catalysts. So it is plausible that RNA once catalyzed its self-replication and assembly from smaller molecules. At the next stage, RNA would begin to make proteins, some of which would be better catalysts than RNA itself. Eventually, DNA would replace RNA because it is more stable and can be larger, both of which confer reproductive advantages.

  Another critical feature in the origin of life was the encapsulation of a genome in a cell membrane. This was beneficial for a couple of reasons: first, to increase rates of reaction by conc
entrating biochemicals; and second, to give an evolutionary advantage to self-replicating molecules. For example, an RNA genome that produced a useful protein could keep it to itself inside a cell, thereby favouring its progeny.

  So-called ‘pre-cell’ structures have been made in the lab. Spherical structures form spontaneously when oils are mixed with water, which is something we’re all familiar with in the kitchen. Such oily or fatty membranes plausibly led to the membranes that surround modern cells and were surfaces for prebiotic chemistry.

  Subsequent events may have occurred as follows. RNA took up residence in pre-cells, cells with an RNA genome evolved, and then modern cells with a DNA genome took over from RNA. At some point, metabolism also evolved, perhaps after RNA World. However, there remains an ongoing debate about which came first, metabolism or genetic replication. Also, the actual location, conditions, and evolutionary steps for the origin of life remain uncertain and are an area of research ripe for significant progress.

  Chirality (or the art of clapping with one hand)

  A description of life’s origin would be incomplete without mentioning a related aspect of biochemistry: for biomolecules that come with two mirror-image structures, life on Earth uses only one of the structures, not both. The property of having mirror-image symmetry is called chirality, which comes from the Greek cheir for ‘hand’, given the fact that a person’s hands are mirror images and cannot fit on top of one another (the same way up). If you’re not convinced that a left-hand structure is truly different from a right one, try wearing your shoes on the wrong feet all day!

  Chirality arises in biomolecules if a central carbon atom is surrounded by four different groups of atoms. The groups naturally arrange themselves in a tetrahedron, which is a pyramid with four triangular faces. If we number the groups with a ‘1’ at the top of the tetrahedron, the three tetrahedral feet can be numbered clockwise or counterclockwise as shown:

  The two molecules in the picture are ‘handed’ because one cannot be superimposed on top of the other. Such molecules are called enantiomers from the Greek enantios morphe, for opposite shape. Let’s consider a specific enantiomer, the amino acid alanine. It would have ‘1’ as a hydrogen atom, ‘2’ as a carboxyl group (COOH), ‘3’ as an amine group (NH2), and ‘4’ as a methyl group (CH3). By convention, with the clockwise numbering of groups 2 to 4, alanine is said to be in the right-handed or D-form after the Greek dextro for right. With the counterclockwise arrangement, alanine is in the L form from the Greek laevo for left. Remarkably, life on Earth uses L-amino acids in proteins, almost entirely, and D-sugars almost exclusively as well whether in DNA, cell walls, or synthesis. (A handy mnemonic is ‘lads’ for left amino, dextro sugars). However, when a chiral substance is made in the laboratory, equal proportions of left- and right-handed forms are usually produced, called a racemic mixture.

  Chiral molecules can have very different effects despite their identical chemical formulae. An example is the infamous drug thalidomide. The right-handed form cures morning sickness in pregnant women, but the left-handed version induces severe birth defects. A more pleasant example is the flavouring limonene: the D-form tastes like lemons but the L-form is orange-flavoured.

  What caused the common chirality, or homochirality, shared by all life? There are two general hypotheses. One is that the organic molecules from which life started had a slight excess of one enantiomer that was subsequently amplified. Physical processes invoked to induce this excess include polarized light from stars that might cause organic molecules that seeded the Earth to develop a chiral bias during their synthesis in space; alternatively, polarized radiation from radioactive decay might generate an enantiomeric excess. A problem with such radiation-related ideas is that the excess is often small, less than 1 per cent. The second hypothesis is that prebiotic chemistry preferentially assembled only one of the enantiomers. For example, adsorption on a mineral surface might have chiral selectivity. Chemical kinetics is generally more efficient for a pure substance than a mixture, so this might cause further amplification. One biological process—reproduction of a genome—may require homochirality. Homochirality was probably needed for the replication in the RNA World model because only replicated RNA strands of the same chirality would line up with an RNA template strand.

  Signs of the earliest life

  Although the origin of life remains obscure, in the oldest sedimentary rocks on Earth we find possible signs of life. Perhaps it’s no coincidence, but these rocks (mixed with volcanic flows) date from the end of the Late Heavy Bombardment, around 3.8 Ga. They are found in Isua, in the interior of south-west Greenland. They form a dark, foreboding landscape that looks something like Mordor, albeit icy, and they are remarkable for telling us much about the early Earth. There is gravel that was rounded by the action of water. Also, some sediments that were laid down under the sea contain flakes of carbon in the form of graphite. Isotopic analysis suggests that this carbon was once part of microbes living in the oceans. Carbon has two stable isotopes, carbon-12 and carbon-13. Life tends to concentrate a few per cent more carbon-12 atoms in its tissues than carbon-13 because molecules containing lighter carbon-12 atoms react faster in biochemistry. The graphite in Isua is enriched in carbon-12 by about 2 per cent, which is similar to the proportion in marine microbes. So the inference is that marine microbes died and sank into the sediments where the carbon was subsequently compressed and converted into graphite.

  Better preserved evidence for early life is found in north-west Australia and dates from about 3.5 Ga. In the 1980s, my colleague Roger Buick found fossil stromatolites of this age near North Pole in north-western Australia (Fig. 2). An Aussie joker named the place ‘North Pole’ because it is one of the hottest, most sun-baked locations on Earth. Stromatolites are laminated sedimentary structures made by photosynthesizing microbial communities in water that is shallow enough to receive sunlight. Often stromatolites take the form of domes of wrinkly laminations. These domes are built up from trapped sediment as sheets of microbes, called microbial mats, growing upwards towards sunlight. On modern stromatolites, the living part—the mat—is just a veneer about a centimetre thick with a texture like tofu that sits atop accumulated mineral layers. If you could travel back to the Archaean Earth, you would see coastlines covered in stromatolites all over the world. Today, stromatolites are rare because certain fish and snails (which didn’t exist in the Archaean) feed on the microbial mats that make them. Consequently, modern stromatolites are found only in lagoons or lakes where the water is too salty for such voracious animals.

  2. Left: Cross-section of the world’s oldest fossil stromatolites in the Dresser Formation, North Pole, Australia. Right: A plan view of the bedding plane of the stromatolites, showing their tops. The lens cap is 5 cm diameter for scale

  Some sceptics wonder if the North Pole structures could have formed without life and so are not really stromatolites, but most astrobiologists accept their organic heritage because they have various features we expect of biology. The fossil stromatolites have laminations with extremely irregular wrinkles that are difficult to explain as folds created by purely physical processes. Also, the laminations thicken at the top of convex flexures, which is just what happens when photosynthetic microbes grow where there is more sunlight. In troughs between flexures there are fragments that are plausibly interpreted as pieces of microbial mat that were ripped up by waves in the sea. The fragments contain thin, wrinkly layers that incorporate organic carbon. The combination of such observations suggests that the North Pole stromatolites are indeed the oldest fossil structures visible to the naked eye.

  To find evidence for past life, we can also look for individual dead bodies of single-celled organisms, since only microbes existed so far back in Earth history. Such microfossils, which can only be seen with a microscope, are found in sedimentary rocks such as chert (a fine-grained silica-rich rock; flint is a familiar example) and shales, which are fine-grained sedimentary rocks that were once muds.


  Geologists who study microfossils take rock samples from likely settings back to the lab where they slice them up and hope that something shows up under the microscope. It’s a hit-and-miss affair. The problem of distinguishing life from non-life also rears its ugly head again because mineral grains sometimes look like fossil cells. Consequently, microfossils are more convincing if they show signs of cell division, colonial behaviour, or filamentous structures that occur when cells join up in a line. Microfossils can also be tested to see if they contain organic carbon.

  The oldest incontestable microfossils occur in South Africa from 2.55 Ga. They are convincing because they are found in fossilized mats of filaments that contain organic carbon and include some microbial forms immobilized in the act of cell division. There are older possible microfossils in South Africa dated at 3.2–3.5 Ga that are spheroidal, contain organic carbon, and appear to show cell division, but have no other biological attributes. Similar microfossil colonies in 3.4 Ga sandstone of the Strelley Pool Formation in north-west Australia also possess organic carbon with isotopes characteristic of life.

  The world’s most controversial microfossils come from the Apex Chert rock formation in north-west Australia, with an age of 3.5 Ga. These were identified as the ‘world’s oldest microfossils’ in the 1990s by Bill Schopf, of the University of California, Los Angeles. The structures appear as black to dark brown streaks that appear to be partitioned into cell-like sections. Schopf gave them Latin names implying that they were extinct cyanobacteria, which are photosynthetic bacteria. In 2002, a rancorous dispute arose when Martin Brasier of Oxford University re-examined the samples and showed that they didn’t look like microbial filaments in three dimensions. Brasier also noted that the chert was not sedimentary but a type produced in a hydrothermal vent, which is an unlikely place to find cyanobacteria that need sunlight. Since then, further investigation has suggested that the filaments are really fractures that are partially filled with haematite, an iron oxide, which provides the dark colour. However, organic carbon is dispersed in the chert outside the filaments and the controversy continues.