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This Concept Map, created with IHMC CmapTools, has information related to: n2. The Origen of Life, Catalysts, of which protein enzymes and ribozymes are examples, can speed up both the forward and reverse reactions by the same amount. The equilibrium between A and B is not altered. Enzymes simply hasten the rate at which this state of balance is reached. ???? There is an intermediate state between A and B called the “transition” state, in which one or more of the bonds among the atoms of the molecules are severely strained and distorted. The measure of this strain is given by the energy of the molecule., In a sense, life, complex, whole, and emergent, is simple after all, a natural outgrowth of the world in which we live. Life emerges as a natural phase transition in complex chemical systems. ???? At its heart, a living organism is a system of chemicals that has the capacity to catalyze its own reproduction., The secret of life is to be found in the achievement of collective catalytic closure. The roots are deeper than the double helix and are based in chemistry itself. ???? In a sense, life, complex, whole, and emergent, is simple after all, a natural outgrowth of the world in which we live. Life emerges as a natural phase transition in complex chemical systems., A collectively autocatalytic system is one in which the molecules speed up the very reactions by which they themselves are formed. A makes B; B makes C; and C makes A again. There is a whole network of these self-propelling loops. Given a supply of food molecules, the network will be able to recreate itself. It will be alive. ???? Catalysis alone, however, is not sufficient for life. All living systems “eat”; they take in matter and energy in order to reproduce themselves, and the emit waste. This means that they are open thermodynamic systems., The emergence of the giant cluster is natural. The analogue in the origin of life theory is that when a large enough number of reactions are catalyzed in a chemical reaction system, a vast web of catalyzed reactions will suddenly crystallize. Such a web is almost certainly autocatalytic and almost certainly self sustaining, or alive. ???? The emergence of autocatalytic sets is almost inevitable., There is an intermediate state between A and B called the “transition” state, in which one or more of the bonds among the atoms of the molecules are severely strained and distorted. The measure of this strain is given by the energy of the molecule. ???? Cells have proofreading enzymes, as well as editing enzymes which act on the RNA to snip out entrons and splice them with exons. The RNA itself acts as an enzyme cutting out its own introns. In fact a variety of ribosomes can catalyze themselves or other RNA sequences., Emil Fischer – In the mid nineteenth century synthesized urea, demonstrating that organic molecules could be made of inorganic chemicals. This was a major step in the reduction of biology to chemistry and physics. Life had come from non-life in spontaneous generation. ???? Mendel, 1902 – Formulated the basic laws of heredity. Chromosomes were so named because of the color when stained., The emergence of life is an expected property of the physical world. ???? If all this is true, life is vastly more probable than we have supposed. Not only are we at home in the universe, but we are far more likely to share it with as yet unknown companions., These reactions have two parameters, M (the number of molecules) and P (the probability of one chemical catalyzing another). As either parameter increases, at first nothing happens in the dead soup; then suddenly it springs to life. ???? Life crystallizes at a critical molecular diversity because catalytic closure itself causes crystallization., When the number of catalyzed reactions is about equal to the number of chemical nodes, a giant catalyzed web forms and a collectively autocatalytic system snaps into existence. Life emerges as a phase transition. ???? Each molecule must play two roles in creating the autocatalytic set. It can serve as an ingredient or a product of the reaction, but it can also catalyze other reactions., Catalysis alone, however, is not sufficient for life. All living systems “eat”; they take in matter and energy in order to reproduce themselves, and the emit waste. This means that they are open thermodynamic systems. ???? At chemical equilibrium, in which chemical reactions move forward and then reverse, such reactions occur thousands of times per minute, and are only statically in equilibrium. Minor fluctuations occur all the time., There is an intermediate state between A and B called the “transition” state, in which one or more of the bonds among the atoms of the molecules are severely strained and distorted. The measure of this strain is given by the energy of the molecule. ???? Low energy corresponds to unstrained molecules and high energy to strained molecules. Enzymes work by binding to the transition state and stabilizing it. This makes it easier for A and B molecules to jump to the transition state, thus increasing the rate at which the equilibrium ratio of A and B concentrations is reached., Imagine enzymes which have only two states, on and off, and that they can switch between them. At each moment, each enzyme is either active or inactive. The rate of reactions depends on the concentrations of enzymes and substrate, which can vary swiftly from high to low in complex reaction networks. ???? The range of possibilities for autocatalytic sets is vast, and is called the state space. This is the mathematical space in which the system is free to roam., A phase transition occurs when the ratio passes 0.5. At that point a giant cluster suddenly forms. ???? When the number of catalyzed reactions is about equal to the number of chemical nodes, a giant catalyzed web forms and a collectively autocatalytic system snaps into existence. Life emerges as a phase transition., Each molecule must play two roles in creating the autocatalytic set. It can serve as an ingredient or a product of the reaction, but it can also catalyze other reactions. ???? Ribosomes are RNA molecules that can act as enzymes on other RNA molecules. All kinds of organic molecules can act as substrates and products of reactions, and simultaneously act catalytically to hasten other reactions., A phase transition occurs when the ratio passes 0.5. At that point a giant cluster suddenly forms. ???? As the giant cluster grows larger, the rate of growth slows as the remaining isolated nodes and isolated small components decreases., Life, at its root, lies in the property of catalytic closure among a collection of molecular species. Alone, each of these molecules is dead. Jointly, once the catalytic closure among them is achieved, the collective system of molecules is (springs to) alive. ???? Catalysis alone, however, is not sufficient for life. All living systems “eat”; they take in matter and energy in order to reproduce themselves, and the emit waste. This means that they are open thermodynamic systems., Kaufmann – Spontaneous order has been as potent as natural selection in creation of the living world. We are the children of twin sources of order, not a single source. ???? Life crystallizes almost inevitably in sufficiently complex mixtures of molecules. Life may be an expected emergent property of matter and energy., n2. The Origin of Life see also m9. Evolution, Autocatalytic metabolism arose spontaneously in primal waters, from a random conglomeration of whatever happened to be around. ???? Molecules can catalyze formation of another molecule, but can also inhibit each other’s formation.