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Unicellular Organisms

Contents

Origin of Life
Prion and Viruses
Organic Compounds
Carbohydrates
Lipids
Nucleotides
Amino Acids
Energy Requirement
DNA
RNA
Proteins and Enzymes
Cells
Mitochondria
The Y Chromosome
Genomes
CRISPR Genome Editing
Evolution: Muatation of Gene(s), Natural Selection, and Time
Microbiology
Archaebacteria (Ancient Bacteria)
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 progression from inorganic molecules to simple organic molecules, to more complex organic compounds and eventually toward life.

    • Figure 11-02a Atmospheric Composition

    Figure 11-02b Prebiotic Materials


    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

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

    		produced in either localized spots on Earth where the 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 experiment.
    Astro-Chemicals 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
    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.

    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.
    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
    Clay Catalyst Cyclic Nucleotide biological 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 11-03e) to perform the function. A 2010 study indicates that cyclic nucleotides (Figure 11-03f), 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 conjectured that such reactions were

    Figure 11-03e Clay Catalyst

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

    		 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 11-03i. 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 11-03g 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 11-03h 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 examples include the electron transport on

    Figure 11-03g Redox Reaction, H Exchange

    Figure 11-03h Redox Reaction, e Transport

    		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 11-03i 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 11-03h, 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 11-03g, and i) used by multi-cellular 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 11-03i Redox Reaction
    [view large image]

    		 These reactions (except #4) are referred to as chemosynthesis used by primitive bacteria.



    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 11-03j), 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 11-03i, 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 11-03i shows that energy is available for transfer down the redox gradients whenever there is an energy source (such as the

    Figure 11-03j Chemosynthesis
    [view large image]


    		 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 11-03k). 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 11-03k 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 analogy is to produce a

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

    		 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
    RNA, Primitive polymers and 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 phospholipid, which can naturally form a tiny sphere bound by a membrane in water (the droplet is called liposome).
    Membrane 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 sequence:

    • Figure 11-04e Origin of Life Theories

    		(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.

    RNA World, Schematic RNA World, Pictorial The RNA world postulates that in the beginning the RNA molecules also performed the catalytic activities necessary to replicate themselves 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

    Figure 11-04f RNA World, Older Version

    Figure 11-04g1 RNA World, Updated Version

    		enzymes. Figure 11-04f is a schematic depiction of the RNA world, while Figure 11-04g1 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.

  • Experiments :

    (a) Hydrothermal Vents -

    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 11-04g2), who is running another "Origin of Life" experiment to investigate the
    Mike Russell feasibility. 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 proteins inside. His goal is to demonstrate that the

    Figure 11-04g2 Origin of Life Experiment

    		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.

      (b) RNA World -

      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
      4. Proto-cell themselves into 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 membrane using fatty acids.

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

      		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.

    In 2017, Szostak has to retract a paper on RNA replication, which is an important step from non-life to life (see "Nobel Laureates Make Mistakes Too: Jack Szostak Retracts Nature Chemistry Paper"). Although disappointed that the approach does not work, he is returning to the drawing board to look at alternative ways to overcome this roadblock.

    (c) Icy World -
    Life from Ice The experiment of making organic molecules out of inorganic substances by Stanley Miller in 1953 is not his only origin of life investigation (Figure 11-04j). 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 11-04i) 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 increase

    Figure 11-04i Life from Ice

    		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 creating RNA out of individual nucleotides had been successful under such cold environment.
    Stanley Miller 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 11-04j 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 11-04k). 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 have rained ash onto nearby sea ice. Primordial ice must have been full of impurities with some organic compounds already.

    Figure 11-04k Ice Catalyst

    		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.

    (d) Minimal Genome - See "Minimal Genome courtesy of JCV".

    (e) Mudpool -

    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 11-04l). 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
    Origin of Life in Mud Pool Formation of Polymer in kick-start key chemical reactions at the very beginning. As illustrated in Figure 11-04m, 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 11-04l Life in Mud Pool

    Figure 11-04m 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.

    (f) Plucky Microbes -

    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. 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 11-04n Deinococcus radiodurans grow quietly in a petri dish.

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

    (g) Plucky Tardigrades -

    Tardigrade is Multicellular Organism with ~ 40000 cells belonging to the phyla of Arthropods. They are usually about 0.5 mm long when fully grown and can be found everywhere on Earth because they can withstand extreme levels of radiation, extreme temperatures, very high/low pressure and dehydration. Their chubby appearance (Figure 11-04o,a) is due to the absence of some Hox genes. The body is essentially the extension of the head in segments. The missing Hox genes are also implicated in eyeless or near eyeless with sensory bristles on the head and body as replacement. See "Tardigrades=Water Bears=Moss Piglets" for details.

    Interest in this tiny animal is minimal for most people until one day in April 11, 2019 when it acquired cosmic significance involving an outer space misadventure. It all started by a generous donation to Arch Mission Foundation which has this big idea of creating multiple redundant repositories of human knowledge around the Solar System. The funding enables them to assemble the Lunar Library consisting 30 million pages of information in 25 nickel nanofiches about human on Earth. At last minute before delivering the package to the Beresheet Lunar Lander, they decided to add some organic samples including human hair, blood, DNA, ... and some dehydrated tardigrades inside epoxy resins between the disks and on the Kapton tapes for good measures (Figure 11-04o,b,c). Beresheet was launched from Cape Canaveral on a used SpaceX Falcon 9 rocket on Feb. 21, 2019. It reaches the moon on time but the landing failed with the fate of tardigrades in question (see crash site in Figure 1104o,d).

    Tardigrade on Moon According to Arch Mission, there would be no chance for the tardigrades to contaminate the Moon since it has no water to revive the little bugs even if they manage to get out of the enclosure somehow. That could be exactly the situation with the Beresheet crash-landing although they maintain that the library should be intact. An interesting case arises if in the next million or billion years, an ice-bearing comet hit the Moon near the crash site. The impact will melt the epoxy resins releasing the plucky tardigrades which will then flourish and turns into some kind of indestructible monster ...

    Figure 11-04o Tardigrades on Moon
    [view large image]

    		It is a nice plot for science fiction or is it how multicelluar life began on Earth? i.e., via delivery from another world triggering the Cambrian Explosion.

    Tardigrade, Protection by Dsup Analysis of tardigrade's genome in 2016 reveal an unique sequence expressing the Damage suppressor protein (Dsup), which is present only in tardigrades. Further research indicates that Dsup binds to nucleosomes and protects DNA from hydroxyl radicals as well as high energy radiation. Genetically modified human cells to express Dsup also safeguards against damage from X-rays (Figure 11-04oa). It turns out that the Dsup forms a cloud-like structure; the cloud surrounds the DNA's chromatin envelope, blocking hydroxyl radicals and preventing them from disrupting cellular DNA (see insert), it works on free DNA as well. Computer simulation of Dsup in complex with DNA shows that it is an intrinsically disordered protein. Its flexibility and electrostatic charge helps it bind to DNA and from aggregates.

    Figure 11-04oa Tardigrade, Protection by Dsup [view large image]

    		Right now, the main applications are in pharmaceuticals and crop plants. Other possibilities include cancer treatment, and space traveling.

    [2024 Update]

    Tardigrade, Protection by Dsup

    Figure 11-04ob Tardigrade

    		See

    According to ChatGPT (in Italic) :

    Tardigrades can survive extreme environments thanks to unique adaptations, but their success at this comes down to specific evolutionary trade-offs and a few powerful mechanisms that aren't common in more complex animals:

    1. Cryptobiosis: Tardigrades can enter a state of cryptobiosis, essentially "shutting down" almost all biological processes when conditions are unfavorable. In this state, they lose almost all body water and enter a form of suspended animation, protecting them from extreme temperatures, radiation, and lack of oxygen. Larger animals can't achieve cryptobiosis to the same extent because it would require shutting down complex systems that need constant energy and maintenance, like the brain and heart.
    2. Trehalose Sugar and Proteins: When desiccating, tardigrades produce trehalose (a type of sugar) and specific proteins that protect their cells from damage. These form a glass-like structure around their cells, preserving cellular integrity in ways larger animals haven't evolved. Complex organisms would need significant molecular changes to mimic this effect, which likely hasn't developed because the payoff isn't as beneficial in environments where water is more consistently available.
    3. DNA Repair Mechanisms: Tardigrades have unique DNA repair abilities, helping them recover from radiation damage. While other animals do have some repair mechanisms, they're usually geared toward managing smaller, more common stressors, like UV exposure, rather than the extreme levels tardigrades endure.
    4. Metabolic Constraints: Larger animals have high metabolic needs that prevent complete shutdowns. Maintaining heart and brain functions requires constant energy, meaning animals like mammals can't simply turn "off" during extremes without fatal consequences.
    5. Ecological Niche Specialization: Tardigrades are micro-animals with niche adaptations allowing them to endure "uninhabitable" places without competing with larger organisms. Complex animals evolved differently, adapting to survive within stable ecological niches that don't require the level of resilience that tardigrades need.

    Tardigrades' diets are highly adaptable to their environments, allowing them to thrive in various habitats, from the deep ocean to mountain ranges and even extreme conditions in space.

    In short, tardigrades' microscopic size, simple physiology, and unique biochemical adaptations allow them to handle extremes, but larger, more complex animals evolved to maximize survival in more predictable environments.

    More complex animals have intricate body systems and specialized cells that make adapting to extreme changes more challenging. Here's why:

    1. Genetic Complexity: Complex animals have much larger genomes and more interdependent genes regulating everything from metabolism to nervous system functions. Adaptation often requires coordinated changes across multiple genes to produce a viable response to new or extreme conditions. For simpler organisms like tardigrades, fewer genetic changes are required for resilience because they have fewer interdependent biological systems.
    2. Cell Specialization and Interdependence: In complex animals, cells are highly specialized (e.g., muscle cells, nerve cells, blood cells) and often can't function independently. These cells rely on stable, specific conditions to keep the whole system working. Rapid adaptation to extremes-like a lack of oxygen or water-is more challenging because it would require coordinated, system-wide responses.
    3. Metabolic Demands: Larger, more complex animals need continuous energy to maintain essential systems, like the brain, circulatory system, and immune system. Sudden changes in the environment can disrupt these energy flows, which is why they're more vulnerable to starvation, dehydration, or rapid temperature shifts than simpler organisms that can shut down almost completely.
    4. Slower Reproductive Cycles: Complex animals often have longer lifespans and slower reproductive rates, so genetic adaptations can take many generations to become widespread. In contrast, simpler organisms with rapid reproduction can evolve and adapt more quickly, sometimes within just a few generations, when exposed to new environmental pressures.
    5. Lack of Extreme Survival Mechanisms: Most complex animals didn't evolve mechanisms like cryptobiosis (which allows tardigrades to essentially "pause" life) because they typically inhabit stable environments where such adaptations aren't necessary. This limits their ability to withstand conditions that differ too much from their original habitats.

    In essence, complex animals evolved for stability within specific environments rather than versatility in extreme conditions. Adaptations are possible, but they require coordinated changes that don't occur as easily as they do in simpler organisms like tardigrades.

    Tardigrades' ability to endure extreme conditions has helped them to survive numerous mass extinctions and other catastrophic events since they first appeared around 500 million years ago.
           

    [End of 2024 Update]

    (h) Another Misadvanture -

    In early December 2010, NASA announced that bacteria found in the arsenic-filled water of a Californian lake (the Mono Lake, see Figure 11-04p) 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
    Arsenic Bacteria several essential 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 satisfy. It is also known that arsenate forms

    Figure 11-04p Arsenic Bacteria

    		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 11-04q, 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 11-04q 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).

    (i) Synthetic Life (2018 Update) -

    Investigation of the "Origin of Life" usually adopts a top-down approach starting from a known process and searching for the parts that make it tick. The other methodology is bottom-up by running experiments to see "How Life can be Created from Non-living Matter". This is called "Synthetic Life" (Figure 11-04r).
    Synthetic Life Synthetic Membrnace Incorporation of Proteins Such field is thriving with more funding from various agents. The Synthetic Biology Journal started publication in 2016, and researchers from 17 laboratories in the Netherlands formed the group Building a Synthetic Cell (BaSyC), which aims to construct a “cell-like, growing and dividing system” within ten years.

    Figure 11-04r Synthetic Life
    [view large image]

    Figure 11-04s Synthetic Membrance [view large image]

    Figure 11-04t Incorporation of Proteins [view large image]
    See "How biologists are creating life-like cells from scratch"

    The research to synthesize life would offer a peek on the possibility of life in other planets. However, it also brings up the nightmarish scenario of strange life form (e.g, the Medusa-like creature in Figure 11-04y) running amok. The public is assured that
    Crossota Millsae Crossota Millsae controls can easily be incorporated into the process or a kill switch can be installed to render the things harmless. Anyway, Figure 11-04z shows the trailer of a 1969 movie: "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 ...

    Figure 11-04y Crossota Millsae

    Figure 11-04z Andromeda Strain
    [view large image]

    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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