The Law of Entropy II:

Assembling the Molecules of Life

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    If a hurricane blasts through an auto wrecking yard, we do not expect to see it leave a fully functional automobile in its wake. And yet the theory of evolution claims that the chemical maelstrom swirling in the seas of pre-biotic Earth produced a fully functional life-form, the simple single-celled creature from which all subsequent life evolved.

    Ironically the hurricane itself gives us an excellent example of a self-assembling dynamic structure. How does it increase entropy?

    A hurricane begins when wind blowing west from North Africa passes out over the Atlantic Ocean and, under the influence of the Coriolis effect due to Earthís rotation, begins to spin. The centrifugal force exerted by the air mass, small though it is, creates a zone of low pressure at the center of the growing storm. Water vapor rises from the warm tropical water under the air mass and condenses into clouds, releasing heat as it does so, which makes the air expand, become less dense (lighter), and rise, lowering the pressure at the center of the storm further. Air gets drawn in toward the center of the storm and spins faster (due to conservation of angular momentum), which further lowers the pressure at the center. As long as the storm hovers over warm water it will be locked into a positive feedback process (the infamous vicious cycle) and can develop winds moving in excess of one hundred miles per hour. The laws of physics, especially as expressed in thermodynamics, have created a natural steam turbine.

    The master equation of thermodynamics tells us that in an isolated system at a given absolute temperature the change in the entropy of the system comes from a change in the heat content of the system plus a change in the volume of the system at a given pressure. Any arbitrarily defined mass of air, perhaps kilometers in extent, is effectively an isolated system over a period of hours or days. It expands and contracts adiabatically, which means that heat does not flow into or out of the mass. As moist air at the center of the hurricane rises, it expands and becomes cooler. The water that gives it its humidity condenses and falls as rain. When the water condenses, it releases heat into the air, thereby making the air expand and rise faster. Thereís no net change in the amount of heat we would measure in that mass of air, but its expansion due to condensation heating increases the massís entropy. The hurricane produces a net increase in entropy, as the second law of thermodynamics requires, so the laws of physics allow the existence of self-assembling structures.

    The laws of chemistry also allow for self-assembling structures - molecules. We have already seen how ammonia, methane, carbon dioxide, and water vapor can self-assemble into amino acids. Astronomers have also detected the presence of organic molecules in deep space through the spectra in the light that they emit. Experiments have shown that even ribose, a key ingredient in life, can self-assemble in space in the ices that coat grains of dust when those grains are bathed in ultraviolet light.

    We know that Earthís primordial oceans were a thin broth of organic chemicals. The famous Urey-Miller experiments showed that they certainly contained amino acids. Other organic chemicals of the simple species were present as well. Those molecules consist of atoms of various kinds held together by electric forces.

    A full and proper treatment of the physics behind the chemistry would oblige us to make a foray deep into the scary black jungle of quantum theory. Let it suffice to say that when atoms approach each other the distribution of electric charge around them shifts, producing imbalances in the electric fields that envelope the atoms, which imbalances enable the atoms to cling to each other. Some atoms cling very tightly: in the water molecule it takes 1.23 electron volts of energy (equivalent to a temperature of 14,275 degrees Kelvin) to remove the hydrogen atoms from the oxygen atom. Some atoms or molecules cling loosely to each other: water molecules, at normal room temperature and air pressure, form chains that break apart, reform, break apart again, and so on. With the addition of 0.42 electron volts of energy per molecule at 373 degrees Kelvin (100 Celsius, 212 Fahrenheit) and normal atmospheric pressure the chains break apart completely and water becomes a gas (steam). If we take enough thermal energy out of the water at 273 Kelvin (0 Celsius, 32 Fahrenheit), the chains lock up and water becomes a solid (ice).

    The second law of thermodynamics (the law of entropy) tells us that in the absence of opposing forces particles will spread evenly throughout the space that they occupy. Those particles can be atoms or molecules and the rule will apply separately to each separate species. Thus, the complex chemicals, such as amino acids, being washed out of the atmosphere by rain got distributed by currents, turbulence, and diffusion more or less uniformly throughout the oceans. There, dissolved in water, they could interact as they couldnít in air.

    Now we turn our attention to continental drift, which carried out the next stage in the creation of life. As the continents drift across Earthís surface, ocean basins expand and contract. On the bottom of an expanding ocean, where Earthís crust is relatively thin, there are lines where opposite sides of the basin pull apart. Magma rises into those cracks and forms new ocean bottom. At those places volcanic heat and abyssal cold drive chemical reactions.

    Heat makes weakly bonded chemicals come apart and cold allows them to come back together, perhaps in different patterns. When Earth first formed, its atmosphere contained large quantities of methane, ammonia, and carbon dioxide, among other gases. Lightning and ultraviolet radiation from the sun created amino acids in that atmosphere as the Urey-Miller experiments indicated (and the like of which we see in the colors displayed by the clouds of Jupiter). But the atmospheric gases also dissolved in the oceans, so the Miller processes also occurred around hydrothermal vents.

    Chemical syntheses could go further near hydrothermal vents than they could in the atmosphere. The precursors of amino acids that were made in the Miller experiments fell out of the gas and deposited on the wall of the flask in which the experiment took place. As a consequence, the synthesis went no further. In a denser solvent, such as water, the products of the synthesis remain dissolved and, thus, remain available to participate in further syntheses. In water we get a much wider array of molecules.

    The basic idea behind the doctrine of Irreducible Complexity tells us that the difference between chemistry and biology comes at a threshold that natural processes alone cannot cross, that there is a discontinuity, like a cliff that blocks a path, that something must help chemistry get over before it can become biology. People commonly believe that the second law of thermodynamics is the cliff, that creating a living being, even the simplest, requires that something reduce the entropy of some system without producing and equal or greater increase in entropy in a neighboring system.

    Again we come back to probability and the ways in which Nature loads the dice in favor of increasing complexity. Imagine a wide, flat box divided into cells. Inside each cell we see a die sitting with a six showing on its top face. A sheet of glass or transparent plastic covers the box so that the dice cannot come out of their cells. There is only one way to set the dice so that each and every one of them shows a six (or any other number that we choose), so we have the dice in a state that corresponds to the lowest entropy of the system; that is, the system resides in its simplest possible state.

    Now so shake the box that the dice jump and bounce around in their cells. When you stop shaking the box, the dice will settle into the most probable arrangement. You know that, more or less, one sixth of the dice will display any given number (one through six), but you will not be able to predict which dice display that number. With that image you can see the distinction that physicists make between a macrostate and a microstate: the macrostate describes how many dice show a given number for the six available numbers and the microstate describes which dice display the given numbers. There are many different ways in which you can arrange the dice in the box with one sixth of them showing a given number, so there are many microstates that correspond to a given macrostate.

    Naturally a system will evolve toward a macrostate with the largest number of microstates corresponding to it. Itís simply a matter of probability. Each and every possible microstate has the same probability of being manifested when we stop shaking the box, so the macrostate with the greatest number of microstates corresponding to it has the greatest probability of being manifested.

    When we start considering systems with a large number of components, the numbers of microstates become extremely large. For convenience, physicists use the natural logarithms of those numbers and they discovered, in the latter half of the Nineteenth Century, that those logarithms stand in direct proportion to the entropies of the macrostates. Thus, our shaking the box shifted the dice from a macrostate with zero entropy to a more probable macrostate, which is more probable because it has a higher entropy.

    In chemistry we shake up molecules instead of dice. If we have atoms of hydrogen, carbon, and oxygen instead of dice and put them into boxes labeled water and methane, heat will shake up that macrostate and put the atoms into a macrostate in which some of the atoms go into boxes labeled methanol (three hydrogen atoms and a hydroxyl radical bonded to a carbon atom), formaldehyde (two hydrogen atoms and an oxygen atom bonded to a carbon atom), and formic acid (one hydrogen atom, one oxygen atom, and one hydroxyl radical (a water molecule missing one hydrogen atom) bonded to a carbon atom). That latter state has a larger entropy than the former state does, so weíre more likely to see it manifested when we have methane dissolved in water.

    Of course, thatís a vast oversimplification. We would get more species of molecules than the ones I listed. And if we add ammonia (with its nitrogen atom) and carbon dioxide to the mix, we get even more species of molecules. Each species achieves a concentration that marks an equilibrium between the rate at which the molecule is being produced and the rate at which it is being destroyed or removed from the solution (such as by being made into a different molecule). Two molecules in particular are important to the story of the creation and evolution of life.

    Phosphorus is one element found in Earthís crust, where it has an abundance of about one-tenth of a percent. At undersea hydrothermal vents it emerges, in part, as phosphoric acid, whose molecule consists of one phosphorus atom with one oxygen atom double bonded to it and three hydroxyl radicals each single bonded to it.

    We can think of ribose as starting with five methanol molecules stuck to each other by their carbon atoms so that the carbon atoms form a short chain. Each carbon atom has one hydroxyl radical and one or two hydrogen atoms stuck to it. The chain bends so that the hydroxyl radical on the second carbon atom meets the hydroxyl radical on the last carbon atom and sheds a water molecule, leaving one oxygen atom bonded to each of the second and last carbon atoms. In this way the ribose molecule is manifested as a ring.

    In solution a phosphoric acid molecule can approach a ribose molecule and touch one of its hydroxyl radicals to the hydroxyl radical jutting from either the third or fourth carbon atom in the ribose ring. A water molecule emerges and the phosphate molecule is bound to the ribose by the remaining oxygen atom. Using one of its remaining hydroxyl radicals, the phosphate can touch a second ribose and bind itself to it. A second phosphate can then bind itself to that second ribose and then bind itself to a third ribose. That process can continue, producing a chain that consists of ribose - phosphate - ribose - phosphate - ribose - phosphate and so on. Such chains are the foundation of ribonucleic acid (RNA).

    On those chains, on the fifth (last) carbon atom on each ribose ring, one of four basic components attaches to the chain. Those four basic components are: the pyrimidines (uracil and cytosine) and the purines (adenine and guanine), with thymine replacing uracil in DNA. The Fischer-Tropsch process using carbon monoxide, hydrogen, and ammonia will produce small quantities of all four bases, so we expect that we would find some of those bases around hydrothermal vents in Earthís primordial oceans. Thus, we also expect that RNA existed there as well.

    The free ends of the bases on a strand of RNA are chemically active and will bond weakly to certain other base molecules. In coming together to form RNA, adenine only bonds to uracil and cytosine only bonds to guanine, so we get A-U and C-G pairs in the RNA molecule. When a strand of RNA has attracted other base molecules, those molecules attach themselves to ribose-phosphate molecules to create a second strand of RNA, a kind of mirror image of the first. If it doesnít attract base molecules, the RNA strand can attract amino acids to each trio of its bases and hold them loosely until they attach to each other and form a protein.

    Thus we see that all of the molecules needed by living beings existed in Earthís early oceans. Starting from simple molecules, thermodynamic processes transformed a simple solution into a complex one, in accordance with the law of entropy. If a process is energetically possible, it will find a way to obey the second law, just as water flowing downhill will find a way over any obstacle. But a thin broth of organic molecules is not a living thing. The next step in the creation of life had to be the organization of those molecules into the first cell. The next essay in this trio will examine that process.

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