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Unicellular Organisms


Origin of Life
Prion and Viruses
Organic Compounds
Amino Acids
Energy Requirement
Proteins and Enzymes
The Y Chromosome
CRISPR Genome Editing
Evolution: Muatation of Gene(s), Natural Selection, and Time
Archaebacteria (Ancient Bacteria)
Protista (Unicellular Eukaryotes)

Origin of Life

Origin of Life There is no unanimous agreement on a theory about the origin of life. Any record would have been erased during the long history of turmoil on the Earth's surface. However, it is known that it must have happened between 4.5 - 3.7 billion years ago when the Earth's crust solidified and flecks of bio-carbon (organisms favor C12 over C13) was found in Isua, Greenland. An artist's impression about the events leading to the origin of life and thereafter is drawn in Figure 11-01.

Some relevant information about this subject is presented in the followings:

  • The Environment - Four and a half billion years ago, the proto-Earth was completing its formation. It was still covered with a thick layer of molten lava. A grazing collision occurred with the subsequent appearance of a transient ring around the Earth that rapidly become the Moon. Small cometary impacts persisted until about four billion years ago. The still dense atmosphere had time to stabilize and slowly cool, above oceans which were at first very hot, then tepid. The number of lagoons and shallows, alternately covered and uncovered by the ebb and flow of the seas, was very great, because the tides were gigantic (with the Moon at least three times closer than at present). Under these conditions of constant, chaotic change, life could not have formed on the Earth's exterior. There was
  • Figure 11-01 Origin of Life
    [view large image]

    only one place of constancy and nourishment - a warm spring in the relative safety of the deep ocean floor. It was the only habitable zone at that time for very simple life.
    Atmospheric Composition Prebiotic Materials
  • The Materials - The raw materials in the atmosphere of early Earth consisted mainly of nitrogen and traces of other molecules as shown in Figure 11-02a. The oxygen concentration started to rise only at about 3.5 billion years ago with the proliferation of life. The composition is markedly different from those exist in the atmosphere of the outer planets (see Table 07-01) and in the inter-stellar molecular clouds where hydrogen is the dominant constituent. Figure 11-02b shows the
  • Figure 11-02a Atmospheric Composition

    Figure 11-02b Prebiotic Materials

    progression from inorganic molecules to simple organic molecules, to more complex organic compounds and eventually toward life.

    Another essential ingredient is water. It is the fluid that transports the molecular components from one place to another and facilitates the chemical reactions that keep life going. Water serves as a supporting and cleansing fluid, bearing nutrients to where they are needed and taking away wastes. Furthermore, water is the general purpose solvent for dissolving organic molecules. If molecules are to be broken down and reconstructed in a controlled way, if information codes are to be translated into working molecules and if information storages are to persist over a long period, only water can satisfy the requirement of providing such a solution in the ranges of temperature and pressure on Earth. Recent researches indicate that the hydrogen bonds in water may play a role on the folding of protein, and the binding of protein to DNA.
    Water The high water content in our body has suggested to many biologists that life on Earth arose in the oceans. In fact, there is a rough correspondence between the content of such elements as calcium and potassium in seawater and in blood and tissues. It is thought that living systems tend to incorporate the primitive environment, so that their internal surroundings would tend to resemble the familiar conditions of the early history of life, a possibility first glimpsed by the 19th century French physiologist Claude Bernard.

    Figure 11-03a Water
    [view large image]

    Prebiotic Chemistry In 1953 Stanley Miller mixed substances such as water, molecular hydrogen, methane, and ammonia in a flask. After passing electrical discharge as input energy to this mixture, the assembly rearranged into a host of organic molecules as shown in Figure 11-03b including amino and nucleic acids - the building blocks of life. However, the result cannot be reproduced if carbon dioxide or molecular oxygen is added to the experiment (more specifically, it requires H/C 4/1). Since the experimental environment is not exactly the same as the atmosphere of the early Earth (note the presence of CO2), it could be that those organic molecules were produced in either localized spots on Earth where the

    Figure 11-03b Prebiotic Chemistry
    [view large image]

    chemical composition may be different from the global environment, or they might come from outer space. For example, the Murchison meteorite1 contains similar organic matter as produced in the
    Astro-Chemicals experiment. Note that glycine and alanine are the most abundant amino acids in both cases. They are the simplest amino acids produced by the most stable codons GGC and GCC (see genetic code). Recent research indicates that they are probably the earliest building blocks for life. Meanwhile, astronomers have detected more than 130 different kinds of organic molecules by 2005 in the giant molecular clouds where stars (and planets) are born. These range from the simple two-atom molecules such as nitric oxide (NO), to the large cyanopentacetylene (HC11N) with chain of 11 carbon atoms. By 2013, the number of molecular species found in space has increased to about 180 by various means of detection (Figure 11-03c). It is not known how some of the more complicated arrangements can be formed in the cold-dark inter-stellar space. One suggestion proposes quantum tunneling to overcome the energy barrier in the process of formation.

    Figure 11-03c Molecules in Space [view large image]

    Hydrothermal Mounds The materials of life can be summarized into one category - the reduced organic compounds. The process of reduction stores energy while the carbon in organic substance provides a versatile building block. There are many theories on the source of such materials, such as lightning in the atmosphere, and delivery by comets as discussed above. Another suggestion is from the hydrothermal vents located near the mid-ocean ridge. Hydrocarbons are produced when CO2 in ocean water meets H2 in the spring water from the mould (Figure 11-03d) according to the formula :

    CO2 (dissolved in water as HCO3-) + [2+(m/2n)]H2 [(1/n)Cn]Hm + 2H2O.

    It might not be coincident that similar kind of chemical process is still running in some modern prokaryotic autotrophs such as the methanogens (see more in "Hydrothermal Vents and the Origin of Life"). A more elaborate formula shows the production of a unit of proto-life as well as voluminous acetic acid and waste water from materials in the ocean and hot spring:

    Figure 11-03d Hydrothermal Mounds [view large image]

    {210CO2 + H2PO4- + Fe, Mn, Ni, Co, Zn2+}ocean + {427H2 + 10NH3 + HS-}hot spring
    {C70H129O65N10P (Fe, Mn, Ni, Co, Zn) S}proto-life + {70H3CCOOH + 219H2O}waste

    The definition of proto-life is : "Complex organic forms thought to represent the stage immediately prior to the evolution of the first living organisms." Accordingly at the very beginning, such entities would incorporate all kinds of chemical elements in the trial and error process until something conducive to life came up. It would be at this point when Darwinian selection took over initiating the evolution toward life.

    By identified 355 protein families from 6 million genes in prokaryotic genomes with LUCA's (Last Universal Common Ancestor), a research article under the title of "The Physiology and Habitat of the Last Universal Common Ancestor" in 2016 provides further support for the idea that it inhabited a geochemically active environment rich in H2, CO2 and iron such as in the hydrothermal setting. The identified genes depicts LUCA as anaerobic, CO2/N2-fixing, H2-dependent and thermophilic.

    The hydrothermal vents provide just the kinds of ingredient for the theory of "Metabolism First" as portrayed in Figure 11-04e. Currently, the theory is championed by Mike Russell (see Figure 11-03e), who is running another "Origin of Life" experiment to investigate the feasibility.
    Mike Russell One of the containers in the experiment holds a liquid that mimics the oceans of the early Earth. The water is rich in carbon dioxide and iron, has a pH of 5.5 and is held at room temperature. The other container is heated to 130oC, and its water is laden with hydrogen and sulphide with a Ph of 11. This second fluid is meant to stand in for the hot waters that spewed out of ocean-bottom springs early in the Earth's history. The liquids mix in a chrome steel pressure barrel containing a catalyst of iron and nickel sulphide. It is supposed to be the pores within the "chimneys" near the ocean hot springs. The gels in the chimneys act as membranes allowing small molecules such as nutrients and wastes to pass through but keeping the macro-molecules such as

    Figure 11-03e Another Origin of Life Experiment

    proteins inside. His goal is to demonstrate that the experiment can produce amino acids and peptides. He has yet to reproduce life's first steps of making simple organic molecules like methane and acetate.

    Now, even if water and the basic organic molecules are somehow available in the early Earth's environment, there were no enzymes (themselves made of proteins) available in the primordial soup. Usually these simple organic molecules cannot be strung together to form biological
    Clay Catalyst Cyclic Nucleotide polymers (such as proteins and nucleic acids) without the assistance from the enzymes. But it has been shown that polymerization of amino acids can occur when exposed to dry heat. Another possible way around this problem is the use of inorganic catalysts such as the surface of some mineral or between layers of clay (Figure 11-03f) to perform the function. A 2010 study indicates that cyclic nucleotides (Figure 11-03g), which are a chemical variation of the nucleotides that make up RNA, will spontaneously link to each other and form viable RNA chains. Thus, if there were cyclic nucleotides in the primordial soup, catalyst was not needed to start life. It is further

    Figure 11-03f Clay Catalyst

    Figure 11-03g Cyclic Nucleotide
    [view large image]

    conjectured that such reactions were more likely to occur in environments like the hydrothermal vents (Figure 11-03d).

    One of the diagrams in Figure 11-04a shows the prebiotic world just before the occurrence of polymerization with pieces of amino acids (in red segments), fatty acids (in green rib-like shapes), ribose sugars (the pentagons), and the nucleotides (the hexagons) mixed together; and occasionally linked up to form primitive polymers. The pre-RNA world in the next diagram shows a short strand of nucleic acids (a nucleotide chain) undergoing binary fission with mutation. However, it is estimated that without the assistance from the enzymes even a short strand will take too long to form with random encounters. The conceptual problem is resolved by the realization that RNA can catalyzes many of the chemical reactions essential to life. RNA enzymes are called ribozymes.

  • Energy Flow - Since process in life is highly non-equilibrium, constant energy input is required to maintain the structures and to support the functions. This is referred to as energy transfers through the redox (reduction-oxidation) gradients as depicted in Figure 11-03j. The redox reactions can occur in many modes as shown in the table below:


    Redox Reaction, H Exchange Redox Reaction, e Transport The oxidation and reduction always run in pair by the conservation of charge. Figure 11-03h shows a typical redox reaction in the form of cellular respiration via hydrogen exchange. Since the electron has higher mobility, it is not necessarily associated directly with the reactants. Figure 11-03i shows a recent study of H2S oxidization by bacteria in marine sediment. This reaction is coupled to the oxygen-reduction in the oxic layer (to form H2O) via rapid electron transfer (instead of hydrogen exchange). It is suggested that the bacteria mediate the electron flow either by the hair-like appendages or by some unknown conducting mechanism. Other

    Figure 11-03h Redox Reaction, H Exchange [view large image]

    Figure 11-03i Redox Reaction, e Transport [view large image]

    examples include the electron transport on cellular membrane, and electrons move through wire in battery even though the electrodes are separated.

    Redox potential is a measure of the tendency of compounds or elements to deliver electrons (and other modes of oxidation). It is defined as the electrode potential on the hydrogen scale (H2 2H+ + 2e-) with a value of E0 = -0.42 volt (V) at pH 7.0 (= 0 at pH 0). Figure 11-03j shows the E0 value for several redox reactions. The free energy G is a measure of the maximum work that can be obtained from a reaction. It is related to the difference in E0 before and after the reaction. Its value is positive for gaining energy in the case of oxidation, and negative implying infusion of energy in reduction such as the processes (1) and (2). The length of the arrows is proportional to G, but the reactions at the end points (of the arrow) are not related.

    Redox Reactions (1) Nitrogen Fixation - N2 + 8H+ + 8e+ 2NH3 + H2, mediated by Azotobacter, and Rhizobium.
    (2) Sulfate Reduction - CH4 + SO42- HCO3- + HS- + H2O, mediated by methanogens etc. The rotten egg odor is from HS- as waste.
    (3) Anaerobic Sulfide Oxidation - 2H2S + O2 2S + 2H2O, mediated by Beggiatoa to yield small amount of free energy (see Figures 11-03i, and i) only suitable for single celled organisms.
    (4) Oxidation of Carbohydrate - CnH2nOn + nO2 nCO2 + nH2O + energy, the respiration process producing large amount of free energy (see Figures 11-03h, and i) used by multicellular organisms. The reversed reaction is photosynthesis to store energy from the Sun.
    (5) Aerobic Sulfide Oxidation - HS- + 2HCO3- + 3H+ SO42- + CH3COOH + 2H+, mediated by sulfur oxidizing bacteria (SOB), of the genus Acidithiobacillus.
    (6) Aerobic Ammonia Oxidation - 4NH3 + 5O2 4NO + 6H2O, mediated by Planctomycetes.
    (7) Aerobic Iron Oxidation - 4Fe2+ + 4H+ + O2 4Fe3+ + 2H2O, mediated by T. ferrooxidans.

    Figure 11-03j Redox Reaction
    [view large image]

    Chemosynthesis Recently (in the 2010s) it is realized that a lot of bacteria live inside animals (such as sponges, nematode worms, clams, ...) symbiotically. The animals provide the hydrogen sulphide (H2S) for the microbes as food via chemosynthesics (Figure 11-03k), the by-products of which supply them with necessary materials for life. It is suggested that our LCA (Last Common Ancestor) started out by utilizing the energy stored in the oxygen when it is combined with hydrogen to form water at the bottom of the redox scale extracting tiny amount of free energy from the environment (see Figure 11-03j, and h). Gradually through these chemical chain, bacteria evolved by taking in various inorganic or organic matters for the maintenance of life. Eventually, photosynthesis was invented to produce a more efficient energy storage via the carbohydrates. The toxic oxygen giving off in this process was finally overcome by oxygen respiration. With the accomplishment of these feats, the dwelling place on Earth is changed forever. Figure 11-03j shows that energy is available for transfer down the redox gradients

    Figure 11-03k Chemosynthesis
    [view large image]

    whenever there is an energy source (such as the hydrothermal mounds or rotting organic matter) to pump the electron up the chain initially, and the materials for life do not depend on oxygen or water or light exclusively. This is especially relevant to the search for life in other planets.

    Loricifera It is discovered in 2010 off the south coast of Greece that there are multicellular animals (metazoans) living all their life in anoxic environments. The species belong to a phylum of tiny bottom-dwellers call Loricifera (Figure 11-03l). Measuring less than 1 mm long, they live at a depth of more than 3000 meters in the anoxic sediments of the Atalante basin - a place seems to be habitable only for bacteria. The Loricifera generates energy from hydrogen sulphide (H2S) using organelles called hydrogenosomes, which it is believed to evolve from mitochondria. Other more primitive bacteria manage to eke out a meagre existence 10 km below sea level on seabed. Their very slow living is maintained by combining sulphate ions (from the rock) with free hydrogen (from water split by uranium decay radiation) through a process called radiolysis§. Such discoveries imply that life could be everywhere in the Solar system and beyond.

    Figure 11-03l Loricifera [view large image]

    § Radiolysis : Radiolysis is the process to split molecules by nuclear radiation. It is the cleavage of one or several chemical bonds resulting from exposure to high-energy flux.

  • The Transition - This is actually a misnomer because it is inherently difficult to define "what is life". It is now understood that life arose as a gradual, sequential process of emergent steps from geo-chemical simplicity to biological complexity. We are poised to reproduce those enigmatic transitional states in the laboratory, and with luck might discover them frozen on other worlds. But picking a step to represent the transition from non-life to life is still intrinsically arbitrary. A "working definition" for life in the context of space exploration states : "Life is a self-sustained chemical system capable of undergoing Darwinian evolution." Thus, any form of life must be a chemical system. Life also grows and sustains itself by gathering energy and molecules from its surroundings - the essence of metabolism. Finally, living entities must be self-replicating and display variation (mutation).
  • Transition Advocates of Intelligent Design used to ridicule evolution theory by the analogy of "tornado in a junkyard" that assembles a 747 airplane from scraps at one fell swoop. However, evolution uses a huge number of incremental steps to go from something simple to something complex as exemplified by the steps in Figure 11-04a in which each step is subjected to natural selection; and while the goal in the

    Figure 11-04a Transition from Nonlife to Life [view large image]

    analogy is to produce a jumbo jet, evolution has no goal - it selects for what's operable now, not for what might become useful in the future. Having said that, although there are plenty of circumstantial
    evidences, scientists have to admit there is no record on Earth for any of those transitional steps from lifeless chemical activity to organized biological metabolism2. It is only known that there are several components essential to the transition: enzymes, genes, and membranes. See "Origin of Life - Self-assembly, Self-organization, and Emergent Phenomena" for concepts that support the spontaneous development of life.

    Mineral Greigite
  • Enzymes - Enzymes are required to accelerate the chemical reactions necessary for organizing the random population of molecules into self-sustaining metabolic cycles. It is suggested that the mineral greigite (Fe5NiS8) could be the very first catalyst. The idea is supported by similar form of chemicals retained in living organisms as enzymes in the form of Fe4NiS5. Figure 11-04b shows the similarity between the greigite and the enzyme acetyl-CoA synthase. Anyway, the most complex chemical reactions would have remained rather arbitrary. There was no consistent ways to produce marcomolecules with specific properties, thus improvements to their design would have been difficult to perpetuate. For Darwinian evolution to begin there had to be some type of natural selection, which implies genetic control, however crude.
  • Figure 11-04b Mineral Greigite [view large image]

  • Genes - RNA molecules capable of replicating themselves have been synthesized in sterilized laboratory. The same process is actually very difficult to achieve in the primordial soup where other closely related nucleotide analogues are present. They tend to join the polymers and
    RNA, Primitive render a cluttered product. The results of thirty years of intensive chemical experimentation have shown that the prebiotic synthesis of amino acids is easy to simulate in a reducing environment (meaning the composition does not contain oxygen or hydrogen is present in the composition), but the prebiotic synthesis of nucleotides is difficult in all environments. It is suggested that the first RNA may be created from the ATP molecules, which were readily available in hydrothermal vents. They linked together to form the very simple genetic code AAA, which still encodes the amino acid lysine today. Figure 11-04c shows the synthesis of peptide chain by a short piece of RNA triplet of A, U, G locating on a mineralized iron sulfide surface in the absence of transfer RNA (the mechanism for specificity in modern organisms). In the diagram, the RNA grips part of the amino acid methionine at the center and offers it to an adjacent amino acid at the left.

    Figure 11-04c Primitive RNA [view large image]

  • Membranes - A space enclosed by a wall is a prerequisite to assemble the necessary chemicals in a confined volume. It would keep the complex molecules inside but allow smaller molecules such as waste and nutrition to pass through. There are some macromolecules such as
    Membrane phospholipid, which can naturally form a tiny sphere bound by a membrane in water (the droplet is called liposome). Various substances can be incorporated into the droplet until the right mixture is acquired to start up metabolism and reproduction. A novel process involves the synthesis of membrane at the inner surface of iron sulfide bubble around alkaline vents. The proteinaceous membrane eventually escaped from the iron sulfide incubator with RNA and peptide inside to become the proto-acetogens and proto-methanogens - the microbes generating waste of acetate (ionic acetic acid) and methane respectively (Figure 11-4d).

    Figure 11-04d Membrane, Primitive [view large image]

    Origin of Life Theories
  • The beginning - Considerable debate in origin-of-life studies has revolved around which of these fundamental components came first - the original chicken-or-egg question. An earlier scenario suggested the cells - enzymes - genes evolutionary sequence. It proposed that life began by the successive accumulation of more and more complicated molecular populations within the droplets (proto-cells). It is a world of little "garbage bags" that only metabolize and reproduce themselves statistically. Once the framework has been established, natural selection will operate to improve the quality of the catalysts and the accuracy of the reproduction. This is the theory of "Metabolism First" in Figure 11-04e, which depicts (1) molecules represented by balls with different symbols, (7) spontaneous formation of compartments, (8) the mixture undergoes cycles of reactions, (9) getting more complicated by natural selection, (10) storing information in polymers. A modern version has the order of the events reversed, e.g., genes - enzymes - cells. It places self-replicating RNA at the beginning, enzymes appearing soon afterwards to start up the metabolic cycles, and cells appearing later to give the process cohesion. This theory is closely related to the concept of "RNA world" (Figure 11-04f, g) and illustrated as the theory of "Replicator First" in Figure 11-04e with the
  • Figure 11-04e Origin of Life Theories

    sequence: (2) the molecules join together by chance in chains, some of which are capable of reproducing themselves, (3) these chains make many copies of themselves, (4) sometimes forming mutant versions that are also capable of
    replicating, (5) mutant replicators that are better adapted to the environment supplant earlier versions, (6) eventually this evolutionary process leads to the development of compartments (cell membrane) and metabolism, in which smaller molecules use energy to perform useful processes.

    The RNA world postulates that in the beginning the RNA molecules also performed the catalytic activities necessary to replicate themselves
    RNA World, Schematic RNA World, Pictorial from a nucleotide soup. The RNA molecules evolved in this self-replicating patterns, using recombination and mutation to explore new niches. They then developed an entire range of enzymic activities. At the next stage, RNA molecules began to synthesize the first proteins, which would simply be better enzymes than their RNA counterparts. Finally, DNA appeared on the scene, the ultimate holder of information copied from the genetic RNA molecules by reverse transcription. RNA is then relegated to the intermediate role it has today - no longer at the center of the stage, displaced by DNA and the more effective protein enzymes. Figure 11-04f is a schematic depiction of the RNA world, while

    Figure 11-04f RNA World, Older Version

    Figure 11-04g RNA World, Updated Version

    Figure 11-04g presents the RNA world evolution in a series of pictures.
    See "RNA folding" for its special characteristic.

    A report in 2009 shows that either cytosine or uracil (known as pyrimi-dines), the building block of RNA, can be synthesized from simple chemicals under conditions that might have existed on the early Earth. The key is to make a molecule whose scaffolding contains a bond that will attract atoms around this skeleton, which unfurls to create the ribonucleotide. The phosphate group acts as a catalyst to guides small organic molecules into making the right connections. This experiment differs from Stanley Miller's in that the nucleotides are produced under controlled and guided process while the latter depends on chance essentially waiting for something to happen.

    Initially, the only safe place for the primitive microorganisms away from the hydrothermal mould was further down through the ocean floor and into the warm, underlying sediments and permeable basalts. Over millions of years, tectonic movement of the Earth's mantle thrust up the ocean floor to form coastal shallows. A few colonies of bacteria must have found themselves in an optimal position: deep enough to be protected from harmful ultraviolet light, but shallow enough to use radiation at longer wavelength to make more organic molecules from carbon dioxide. That's when blue-green algae (cyanobacteria) started the photosynthesis process. The rest is history of other Era.
      Starting in 1991, biochemist Jack Szostak (and his graduate students) has embarked on a project to recreate life in the laboratory from where Stanley Miller left off. Followings is a summary of their accomplishments up till 2004:

    1. By a process of artificial selection, a ribozyme (an enzyme made from RNA instead of protein) was created to copy up to 14 nucleotides from an RNA with an accuracy of roughly 97%. (By 2013 it is reported that the 202 nucleotides long RNA enzyme can produce 206 nucleotides long RNA at -17oC)
    2. Fatty acids were used to form bubbles (for cell membranes) known as vesicles. These vesicles could grow and divide as they were forced through 100-nanometer-wide pores - an "early earth" simulation of the pores in rocks around hydrothermal vents. It is also found that by adding a kind of clay known as montmorillonite to the solution of fatty acids, it sped up the rate of vesicle formation 100-fold.
    3. It was discovered that in a mixture of RNA, fatty acids and clay, the clay can cause nucleotides to spontaneously assemble themselves into
    4. Proto-cell RNA, which is then automatically trapped inside the fatty acid bubbles. The result is something that resembles a cell: It has genetic material and water contained within a waterproof fatty-acid pouch. Figure 11-04h is an image of these makeshift cells taken with an optical microscope and enhanced using fluorescent dye, it reveals yellow bits of RNA inside spherical green vesicles. They have not created life yet. It will be their next step to assemble a system of ribozyme, RNA and vesicle. This system has to grow, divide, and evolve in order to make the transition to life. Once there's one example of a lab system that's evolving by itself, then the challenge is to build systems that can evolve under different conditions such as the high-pressure liquid hydrogen in Jupiter and Saturn. By the summer of 2007, Jack Szostak predicts that within the next six months, scientists will be able to create a cell

      Figure 11-04h Proto-cell
      [view large image]

      membrane using fatty acids. He is also optimistic about getting nucleotides to form a working genetic system. The idea is that once the container is made, if scientists add nucleotides in the right proportions, then Darwinian
      evolution could simply take over. A June 2008 publication by him indicates that early proto-cells with fatty-acid-based membrances could not have been autotrophs (with nourishment generated within). Such early cells were more like the heterotrophic model, which emerged from very simple cellular structures within a complex environment that provides external sources of nutrients and energy.

      In a 2010 NewScientist article, Szostak indicates that the mere presence of RNA could drive vesicle growth by stealing membrane molecules from neighboring vesicles that contain less or no RNA. The physics behind the process is that RNA inside vesicles exerts an osmotic pressure on the inside of these sacs. This internal pressure places tension on the membrane, which grows by absorbing molecules from surrounding vesicles that are less swollen as a consequence of having a smaller cargo of genetic material. Thus protocells with more RNA inside would grow faster. Then it is discovered that when the vesicle has grown big enough (to about 4 micrometers), the spherical vesicle turns into a long, filamentous structure so fragile that it divides into daughter vesicles just by gentle shaking, i.e., the cell has divided. The next step is to check out how a primitive RNA might have catalyzed the synthesis of phospholipids - a class of lipids that are a major component of modern cell membranes.

      Instead of working in a squeaky-clean laboratory, some scientists prefer to investigate the origin of life in mud pools such as those in Bumpass Hell, California (Figure 11-04i). Although there are many differences with the conditions at 4 billion years ago, it is still much closer to the real thing. They found that the cycles of wetting and drying on the edges of boiling mud pools might play an important role in kick-start key
      Origin of Life in Mud Pool Formation of Polymer chemical reactions at the very beginning. As illustrated in Figure 11-04j, synthesis of nucleotide into chain can be destroyed by the reverse reaction of hydrolysis unless the water molecules are removed from the environment. Such environment could be realized exactly with the drying of the clay, while more nucleotides would be added in the wetting cycle. Result on one field trip reveals that chains of RNA may have grown

      Figure 11-04i Life in Mud Pool

      Figure 11-04j Formation of Polymer [view large image]

      wrapped in blankets on concentrated sulphuric acid (in the volcanic mud), which helps to suck water molecules out of the primordial soup.

      Recent research in 2004 suggests that microbes have a better chance to survive (in their cosmic journey) on specks of dust than on boulders or stones. The solar system could be surrounded by a large "bio-sphere" of frozen organisms floating on grains of rock all of which can wander in and out (of the solar system) quite easily. In such scenario, the seeds of life on Earth came from outer space. The idea is similar to a 1969 science fiction: "The Andromeda Strain" (Andromeda stands for "A" - the first case of outer space attack, the microbes are not from Andromeda) in which a satellite brought back deadly microbes from outer space. ... However, the question about the origin of life is still unanswered. It only shifts the problem to somewhere else in the universe.

      D. rad Bacteria Meanwhile on Earth, there are bacteria which can survive very harsh condition on another planet. In an Earth lab, Deinococcus radiodurans (D. rad) can withstand extreme levels of radiation, extreme temperatures, dehydration, and exposure to genotoxic chemicals. They even have the ability to repair their own DNA, usually within 48 hours. Known as an extremophile, bacteria such as D. rad are of interest to NASA partly because they might be adaptable to help human astronauts survive on other worlds. A recent map of D. rad's DNA might allow biologists to augment their survival skills with the ability to produce medicine, clean water, and oxygen. Already they have been genetically engineered to help clean up spills of toxic mercury. Likely one of the oldest surviving life forms, D. rad was discovered by accident in the 1950s when scientists investigating food preservation techniques could not easily kill it. In Figure 11-04k Deinococcus radiodurans grow quietly in a petri dish.

      Figure 11-04k Bacteria,
      D. rad [view large image]

      In early December 2010, NASA announced that bacteria found in the arsenic-filled water of a Californian lake (the Mono Lake, see Figure 11-04l) seems to be able to replace phosphorus P with arsenic As in some of its basic cellular processes. As is in the same group of P in the periodic table. The arsenate ion, AsO43-, has the same tetrahedral structure and bonding sites as phosphate PO43-, which plays several essential
      Arsenic Bacteria roles in cells: it maintains the structure of DNA and RNA, combines with lipids to make cell membranes and transports energy within the cell through the macro-molecule ATP. Many science-fictions portray alternate life-forms using silicon instead of carbon, but this discovery marks the first known case in a real organism. However, rigour scientific method demands that the researchers should demonstrate the presence of arsenic not just in the microbial cells, but in specific biomolecules within them. Such requirement would take much more work to

      Figure 11-04l Arsenic Bacteria

      satisfy. It is also known that arsenate forms much weaker bonds in water than phosphate. It breaks apart on the order of minutes. Thus they should also explain how to stabilize the AsO43- structure in such circumstance.

      Arsenic Vacuoles Further scrutiny of the arsenic data indicates that the microbe is not using the arsenic, but instead is scavenging every possible phosphate molecule while fighting off arsenic toxicity. As shown in Figure 11-04m, the cell's large vacuoles may be their way of sequestering the arsenic. It is also noted that the cells grown in high concentrations of arsenate did not seem to contain any RNA - possibly because RNA production had shut down to conserve phosphate.

      Figure 11-04m Arsenic Vacuoles

      As Christmas 2010 approaching, the authors of the original paper finally response to criticism by posting their supporting evidences online. One of the authors also appears in an interview to express her personal feeling about the pressure created by all the furies.

      After 18 months of controversy, further investigations reveal that the bacteria somehow become arsenate-resistant, and can efficiently extract nutrients from extremely phosphorus-poor environments. But they would not survive without the support of phosphorus. The original author now retorts : "how do these bacteria thrive in lethal concentrations of arsenic? And where does the arsenic go?" (see Arsenic Vacuoles above).

      Life from Ice The experiment of making organic molecules out of inorganic substances in 1953 is not the only origin of life investigation performed by Stanley Miller (Figure 11-04o). He had also filled a batch of vials in 1972 with a mixture of water (H2O), ammonia (NH3) and cyanide (any chemical compound containing the cyano group - CN), chemicals that scientists believe existed on early Earth and may have contributed to the rise of life. He had then cooled the mixture to the temperature of Jupiter's icy moon Europa (~ 170oC). Most scientists believe that it is too cold for much of anything to happen. Examination of the vials in his laboratory at the University of California at San Diego 25 years later in 1997 reveals that the normally colorless mixture had deepened to amber (Figure 11-04n) indicating the presence of complex polymers made up of organic molecules. Tests later confirmed that the mixture had coalesced into the molecules of life: nucleotides, the building blocks of RNA and DNA, and amino acids, the building blocks of proteins. It turns out that the microscopic pockets of liquid within the ice

      Figure 11-04n Life from Ice [view large image]

      increase the concentration of the primordial soup causing the reaction rate to go up. But it was suspected that the "growth" is the result of contamination. Since then other experiments on formation of new strand of RNA, and
      Stanley Miller creating RNA out of individual nucleotides had been successful under such cold environment. Thus, the idea is influencing not just theories about life's origin on Earth but the possibility of life on Europa, Enceladus, and Titan is now more relevant than ever.

      Shortly after Miller finished his 25-year experiment, he suffered a stroke that ended his career. His laboratory, with 40 years of samples, was emptied in 2002 to make way for a building renovation. Experiments that had run for years or decades were discarded without ever being analyzed. Only a few items from the freezer had been rescued, the rest were incinerated for fear of cyanide poisoning. Miller was present for a few hours of this ordeal, struggling to find words to identify the vials that he had known so well. He died on May 20, 2007.

      Figure 11-04o Stanley Miller
      [view large image]

      Ice Catalyst Since then the idea of life starting in ice has inspired further investigations both out in the field north of the Arctic Circle and in the laboratories. These works provide better understandings about chemical reactions within the tiny pockets of water insider the ice (Figure 11-04p). However, this theory should not be considered as the only one in exclusion of the others. Glaciers on early Earth could have scooped up mineral dust; volcanoes could

      Figure 11-04p Ice Catalyst

      have rained ash onto nearby sea ice. Primordial ice must have been full of impurities with some organic compounds already. Followings are some novel properties about the icy environment as published in a special issue (in Summer 2011) on "Evolution" by the Discover Magazine.

      1. Eutectic Freezing - As an ice crystal forms, only molecules of water join the growing crystal, while impurities like salt or cyanide are excluded. These impurities become crowded in the microscopic pockets of liquid within the ice and thus there are more chance for the formation of a variety of macro-molecules such as the nucleotides. The cold environment also stabilize the products by slowing down evaporation.
      2. Frozen Cyanide - It is found that frozen cyanide, in the presence of ammmonia, can form a nucleotide called adenine. This is a more specific macro-molecules related to the formation of life. It is suspected that cyanide was abundant on early Earth, deposited here by comets or created in the atmosphere by ultraviolet light or lightning.
      3. Ice-Water Interface - Studying of ice inside the Arctic Circle reveals that there is strong bonding between the surface of ice and water. This bonding is important for producing long organic chains like RNA. Further study in the laboratory showed that the icy environment can assemble individual nucleotides into long chain of up to 700 bases (with an RNA template). The chain would be about 30 bases long without an RNA template.
      4. RNA Enzymes - At room temperature the RNA enzyme acts like scissors, snipping other RNA molecules into pieces. The process runs in reverse in the icy environment. It is found that short segments of RNA enzyme tend to join just about any kind of molecules producing chains in random sequence (not just the RNA type). The billions and billions of different arrangements eventually generated something meaningful and can replicate itself - the beginning of life.

      1The Murchison meteorite was recovered in Australia in 1969. Analysis of the meteorite found over 90 types of amino acids as well as some left-handed sugar that does not exist naturally on Earth. This rare form of substance tends to prove the extraterrestrial origin of the rest of the contents. The Murchison meteorite contains the same amino acids obtained by Stanley Miller in his laboratory, and even in the same relative proportions

      2Metabolism is the sum of all chemical activities occurring inside a living cell. Metabolic cycle (pathway) begins with a particular reactant and terminate with an end product.

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