I liked the first, historical part of the book, but later chapters, in my view, lacked cohesiveness and struggled to provide proofs to the quote by Democritus after which this article is named. It is obvious that we are not marionettes and that life forms are governed by laws of thermodynamics, but what is less obvious is the force that set these laws in motion. I do not allude to God as a creator for a simple argument that a creator would also require a creator ad infinitum, but I share some of the views of Carl Sagan. I would like to quote Newton:
“Gravity explains the motions of the planets, but it cannot explain who sets the planets in motion.”
― Isaac Newton
Albert Einstein once said the following:
“Everyone who is seriously involved in the pursuit of science becomes convinced that some spirit is manifest in the laws of the universe, one that is vastly superior to that of man.”
There is still too much we do not know about ourselves and the universe, there is still so much to learn.
Here are the quotes and notes from the book…
That crude matter should have originally formed itself according to mechanical laws, that life should have sprung from the nature of what is lifeless, that matter should have been able to dispose itself into the form, of a self-maintaining purposiveness—that [is] contradictory to reason.
Physics is the only real science; all else is stamp collecting.
What is life? Scientists have tried to answer this question for as long as science has existed. For Aristotle, the body was matter, but a soul was needed to give the body life. Even today, such views are common in the general public. Books like The Secret tell us we have vast untapped reserves of “life energy” that can help us attract riches and happiness. Yet, a special life force has never been detected. If we look at the balance sheet of energy intake (food) and output (motion, heat) of any living organism, there is no missing energy or untapped energy source.
The microscope was invented in the late 1500s in the Netherlands by two Dutch spectacle makers, Zacharias Janssen and his son Hans. Improvements to the microscope were completed by Galileo (1609) and Cornelius Drebbel (1619). In 1614, Galileo observed that flies had “fur.” Others observed mites and studied the structure of a fly’s eye.
Beginning in the seventeenth century, with the invention of the microscope, scientists searched for the secret of life at ever smaller scales. Biological cells were first described in Robert Hooke’s Micrographia in 1665 which became the most famous early book on microscopic observations. Robert Hooke (1635-1703), a master experimenter, used his homebuilt microscope to look at everything from flees to “gravel” in urine. The early microscopists discovered what Hooke called “small machines of nature,” from the legs of flees to single-celled animals. Hooke was the first to see cells in cork. The first animal cells, red blood cells, were discovered shortly thereafter by Antonie Philips van Leeuwenhoek (1632-1723), but neither he nor Hooke realized that these cells were the smallest units of all living beings.
It took until 1902 for chromosomes to be identified as carriers of inheritance. The structure of DNA was deciphered in 1953, and the first atomic-scale protein structure was obtained in 1959.
What creates “purposeful motion” in living beings? This was one of the original mysteries of life, formulated by Aristotle more than two thousand years ago. Aristotle assigned this motion to purpose. But today, having penetrated into the realm of molecules, we do not find purpose. Instead, we find random motion. Today, this great question has morphed into another question: How can molecules create the “purposeful” action that characterizes cells and bacteria? How do we go from assemblies of mere atoms to the organized complex motions in a cell?
Humans transform energy from food into motion, heat, and thought. Energy is conserved. The energy we expend during a day comes from the food we eat. A typical energy intake from food is 2,500 food calories per day. One food calorie is equal to 4,184 joules of energy. A human consuming 2,500 food calories takes in approximately 10.5 million joules (2,500 calories x 4,148 joules) in energy from food a day. This sounds like a lot. However, a day has 86,400 seconds, and therefore the rate at which our bodies transform this energy is 10.5 million joules divided by 86,400 seconds, or about 120 watts (where 1 watt = 1 joule per second). A human being has about the same power rating as one light bulb.
After receiving his medical doctorate from the University of Rheims, La Mettrie (1709-1751) had served as medical officer to the French Guards and participated in a number of bloody battles. Through this experience, he developed a profound distaste for the slaughter of war and saw what savagery and injury could do to the human mind. He came to realize that reason and emotion, supposedly part of the soul, could be thoroughly altered by injury. Didn’t this clearly show that Descartes’s last refuge of soul—the mind—could ultimately be explained by pure mechanism?
La Mettrie’s denial of the soul led to his being charged as an atheist (the standard charge for all philosophers who spoke out against Church doctrine). But he was more of a sincere agnostic: “I [do not] question the existence of a supreme being; on the contrary, it seems to me that the greatest degree of probability is in its favor. But that doesn’t prove that one religion must be right, against all the others; it is a theoretical truth that serves very little practical purpose.” For him, metaphysical and theological speculations about the soul served little purpose when a meal could make the “soul” happy and content and when we could see “to what excesses cruel hunger can push us.” La Mettrie, tongue-in-cheek, observed that “one could say at times that the soul is found in our stomach.” Observing that hunger, injury, drugs, and sleep affected people’s minds, he felt certain that the soul was just part of the body, even if he could not explain in detail how it worked: “It is folly to waste one’s time trying to discover its mechanism. . . . There is no way of discovering how matter comes to move.”
La Mettrie concluded that the “soul’s abilities” clearly depend on the “specific organization of the brain and the whole body.” Man a Machine by La Mettrie can be found here.
In the first set of experiments, Helmholtz set out to prove that motion in muscles is caused by chemical processes, that is, that animal motion is a physicochemical process and is not related to any mysterious vital force. To prove this, he irritated frog legs several hundred times by passing electrical currents through them, just as Galvani had done. He then made several chemical extracts of the irritated frog legs and compared the extracts with extracts from non-irritated frog legs. He found that if the muscles had been irritated, a “water-based extract lost mass and an ethanol-based extract gained an equivalent amount of mass. Clearly, some chemical compound in the muscles had been changed from a water-soluble to an alcohol-soluble form through the action of the muscles. This proved that the motion of the muscles caused a chemical change in the muscles, and Helmholtz concluded that muscles were machines that converted chemical to mechanical energy. To establish that this energy was purely chemical, he next compared the heat that can be released upon chemical breakdown of food, called the latent heat, with the latent heat of excreted substances in animals. This was Lavoisier’s experiment. However, since the time of Lavoisier, more refined experiments had improved on Lavoisier’s guinea pig. Helmholtz reviewed these experiments and concluded that the difference in energy between food and excrement accounted well for the observed animal heat.
Everything existing in the universe is the fruit of chance and necessity.
We believe that God created the world according to his wisdom. It is not the product of any necessity whatever, nor of blind fate or chance. We believe that it proceeds from God’s free will.
— Catechism of the Catholic Church, Article 295
Statistics has been called the theory of ignorance. It’s an apt description. Statistics is what we do when we face complex situations with too many influencing factors, when we are ignorant of the underlying causes of events, and when we cannot calculate a priori probabilities. In many situations, from the motion of atoms to the value of stocks, patterns emerge when we average over a large number of events—patterns not obvious from looking at individual events. Statistics provides the clues to understanding the underlying regularities or the emergence of new phenomena arising from the interaction of many parts.
In his book The Drunkard’s Walk, Leonard Mlodinow reproduces Graunt‘s life table for London in 1662. In the late 1600s, 60 percent of all Londoners died before their sixteenth birthday. Such an awful statistic makes modern-day Afghanistan look like paradise. There, the death rate of 60 percent is close to age sixty. By comparison, the 60 percent death rate in Japan is around ninety years old.
Mathematician Francis Galton, Charles Darwin’s cousin, was one of the first to apply Quetelet‘s ideas to a wide range of biological phenomena. He found that the normal distribution governed almost every measurement of an organism: heights, masses of organs, circumferences of limbs. One of his most important discoveries was regression toward the mean: Galton found that any offspring of a parent who was at the outer ranges of a distribution, for example, a very short man or a very tall woman, generally tended to “regress” toward the mean of the distribution. In other words, the son of an exceptionally short man tended to be taller than his father, and the daughter of an extremely tall mother tended to be shorter than her mother. Mozart’s children were not geniuses like their father; neither were Einstein’s. And parents of below-average intelligence often have smarter children. In the long run, we all tend toward the average. In some sense, this is a good thing. Genius is unpredictable—which makes it all the more puzzling that Galton became one of the founders of eugenics, the idea that selective breeding of humans could improve humanity. Beyond the obvious human rights issues with this awful idea, Galton’s own “regression to the mean” suggested that the prospect of success would have been highly questionable.
Physicists best remember Brown for a discovery he made in the safety of his own home. Brown observed that pollen grains suspended in air or liquid perform a jittery dance, as if pushed by an invisible, random force. Today we call this dance Brownian motion. In some sense, Brown really only rediscovered what Democritus had observed two thousand years earlier—the “motes in the air” that were “always in movement, even in complete calm.”
By one definition, entropy is the amount of unknown information about a system or, in other words, the amount of information we would need to fully describe the microstate.
The second law of thermodynamics: There can be no process whose only result is to convert high-entropy (randomly distributed) energy into low-entropy (simply distributed, or concentrated) energy. Moreover, each time we convert one type of energy into another, we always end up overall with higher-entropy energy. In energy conversions, overall entropy always increases. The same applies to how life works: Life uses a low-entropy source of energy (food or sunlight) and locally decreases entropy (creating order by growing) at the cost of creating a lot of high-entropy “waste energy” (heat and chemical waste).
A biological system can be exceedingly small. Many of the cells are very tiny, but they are very active; they manufacture various substances; they walk around; they wiggle; and they do all kinds of marvelous things—all on a very small scale.
— Richard Feynman, “There’s Plenty of Room at the Bottom,” Lecture at American Physical Society Meeting, 1959
When you defend your Ph.D. at the University of Oxford, you’d better know your stuff. Examiners are brought in from other universities, preferably from outside the country. They don’t know you, but are there to ensure you’re no slacker. When my friend Steve got his Ph.D. at Oxford from his work with atomic force microscopes (AFMs), his examiners were two of the best-known AFM experts in the world: Christoph Gerber, who together with Nobel Prize-winner Gerd Binnig, had invented and built the -world’s first AFM in 1986; and Ernst Mayr, who runs one of the largest and most successful AFM groups in the world. Gerber, who works for IBM, is a technical genius. When he visited Oxford in 2000 to be an examiner for Steve’s Ph.D. defense, he told us about a new AFM spinoff: an artificial nose. This nose works by coating tiny cantilevers (micrometer-long beams of silicon) with different substances that absorb airborne chemicals. When the chemicals are absorbed, the substance on the cantilever expands, and the cantilever bends. Using an array of differently coated cantilevers, each sensitive to different types of chemicals, this mechanical nose can be trained to distinguish many different smells. Gerber, a connoisseur of Scottish whiskeys, was excited to find that his mechanical nose had no problem distinguishing a Craigellachie from a Laphroaig, but he was even more surprised when the nose told him that one of his whiskeys had a hint of cherry. He called up the distillery in Scotland, and, indeed, the whiskey had been aged in cherry wood casks.
In our lab we can measure the mechanical properties of much smaller numbers of water molecules. We can squeeze water between an AFM tip and a surface until the water layer between the tip and surface is a single molecule thick (however, since the tip has an area of about 50 nanometers by 50 nanometers, the single molecule layer under the tip contains about 25,000 molecules). Now, adding or subtracting single layers of molecules makes a huge difference to the mechanical properties of the liquid. As a result, when we push from a layer 6 molecules thick to one 5 molecules thick, and then from 5 to 4, and so on, the stiffness and the apparent viscosity of the layers alternate between high and low values.
When we make something smaller, its surface to-volume ratio increases. A golf ball has a greater surface-to-volume ratio than does a bowling ball. Shrunk to the nanoscale, this ratio “would be more extreme. As volumes become small, surfaces start to dominate and the forces that are important at the macroscale become irrelevant at the nanoscale, and vice versa. At the macroscale, forces associated with mass, such as gravity and inertia, dominate. Surface forces, such as stickiness, are usually unimportant, unless specifically engineered, as in a glue. For example, in a baseball game, inertia (when the bat hits the ball) and gravity (when the ball comes back down) dominate. But, typically, the baseball does not stick to the bat. In a game of nanobaseball, however, inertia would be unimportant, as the ball would weigh next to nothing. Ditto gravity. But the relatively large surface area compared with the tiny bulk of the nanobaseball would make it difficult to get the nanobaseball off the nanobat. This is an example of one peculiar property of nanoscale systems: profound changes in behavior depending on the size of the system.
A common fallacy that people hear over and over is that our DNA contains all the information needed to make a human being. Nonsense! The amount of information contained in our DNA is staggering, but it is not nearly enough to specify each molecule’s or cell’s location, or even the shape of an organ. Rather than being a blueprint (as DNA is often mistakenly called), DNA is more like a cooking recipe. When I make a cake, I don’t have to specify where each starch or sugar molecule goes. I just follow the instructions, and the molecules go where they are supposed to. Much of the information to make a cake or a human being is contained in the laws of physics and chemistry. Molecules “know” how to put themselves together.
The growth of a snowflake shows how complexity and beauty can arise from cold physical principles (no pun intended). Freezing is accompanied by a release of heat. This heat has to be removed (increasing the entropy of the environment) to allow the water to freeze. Thus ice crystals will grow fastest at those places where heat is removed the fastest, namely, at the endpoints of any spiky features. Spikes, however, are already the result of rapid growth. This creates positive feedback: The locations on a crystal that grow the fastest become spiky, which allows better heat transfer from these locations, which makes them grow faster, and so on. The result is what physicists call an instability, leading to the formation of long, spiky features. But there is an opposing force as well: The local temperature also depends on the spikiness of the crystal; spikier parts (those with higher curvature) melt at lower temperatures, thus reducing the temperature difference between spiky parts and the environment. This reduction in temperature difference slows heat transfer, counteracting the effect of the exposure of the spikes. Once a spike becomes too pointy, growth will slow down—a negative feedback that counteracts the positive feedback. When this happens, the crystal develops branches. The combination of these two tendencies, to become spiky and to develop branches, leads to the dendritic growth of snowflakes.
Cells are incredibly crowded places, stuffed full of large proteins, DNA and RNA molecules, sugars, lipids, ions, and innumerable water molecules. It has been estimated that the average space between proteins in living cells is less than ten nanometers. Since proteins are between ten and one hundred nanometers in size, this is equivalent to a crowded parking lot with just a foot or less between each car. When things are this tight, it becomes tricky to maneuver past each other. In addition to this crowding, every space between proteins is filled with water, ions, sugars, and other assorted small molecules. You now have an idea of what a crowded mess a cell is. This crowding has consequences, many of which are not well understood, because when we do experiments on proteins, the steps are usually conducted outside the cell in a test tube, where proteins have plenty of space.
While solids, in the form of crystals, have long-range order (atoms are arranged in an orderly pattern over large distances throughout the crystal), liquids have short-range order: If you were sitting on a “water molecule in a pool of liquid water, you would see neighboring molecules at an average distance of 0.25 nanometer (nm). These neighbors would move around, but on average, there would be a cloud of “water molecules surrounding you at this distance. Beyond this distance, the next nearest neighbors would feel the presence of your neighbors, and you would see an excess of molecules at an average distance of 2 x 0.25 nm = 0.5 nm. However, because of the incessant motion of all molecules, this excess of molecules at 0.5 nm would be a little bit more smeared-out than the excess of molecules at 0.25 nm. Going even further, there would be an even more smeared-out excess at 0.75 nm and so on, until at a distance of five to six molecular diameters, thermal motion would have smeared out any semblance of order, and water molecules could be found with equal probability at just about any distance.
Intriguingly, only at the nanoscale are many types of energy, from elastic to mechanical to electrostatic to chemical to thermal, roughly of the same magnitude.
Lavoisier, Helmholtz, and many others determined that our bodies do not create energy, but rather waste energy. The efficiency of a human body (i.e., the amount of physical “work obtained compared with the food energy intake) is about 20 percent. The rest (80 percent of food energy intake) is either directly turned into heat through friction or serves to maintain basic metabolic processes in our cells.
The DNA in our cells is rolled up—and then the rolls, in turn, are rolled up again—into compact DNA-protein structures called chromosomes. This packaging of DNA into chromosomes is performed by molecular machines. DNA contains the information both to make proteins and to regulate the making of proteins. It does not contain the information of how to make a human—at least not directly. There is no gene for a toe or an eye. There are genes to make protein components of toes and eyes. The actual development of a human is a complicated process and involves the accurate timing of the synthesis of many proteins, their interaction, their regulation, and the movement of molecules by molecular motors.
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This is an annotated list of books for further reading. They may help clarify topics mentioned in the book, or continue a topic where the book left off.
- Greenblatt, Stephen. The Swerve: How the World Became Modern. New York: W. W. Norton, 2011. Delightful reading about impact of ancient Greek and Roman atomistic ideas on modern science.
- Kauffman, Stuart. At Home in the Universe: The Search for the Laws of Self-Organization and Complexity. New York: Oxford University Press, 1996. Thought-provoking ideas about self-organization, complexity, and the origin of life, from one of the best-known complexity theorists.
- Waldrop, M. Mitchell. Complexity: The Emerging Science at the Edge of Order and Chaos. New York: Simon & Schuster, 1992. A highly readable, almost journalistic account of the early days of complexity research. Although the book is older, the topics discussed are just as relevant today as they were in the early 1990s.
- Carroll, Sean. Endless Forms Most Beautiful: The New Science of Evo Devo. New York: Norton, 2005. This book and Carroll’s The Making of the Fittest, below, provide a superb introduction into evolutionary development (“evo devo”) — the theory of how bodies get their shapes and how these shapes evolve.
- Carroll, Sean. The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution. New York: W. W. Norton, 2006. See notes on Endless Forms Most Beautiful, above. 259
- Dawkins, Richard. The Ancestor’s Tale: A Pilgrimage to the Dawn of Evolution. New York: Houghton Mifflin, 2004. My favorite Dawkins book (but all his books are recommended). A travel back in time, species by species, to the origin of life.
- Fallen, Mark. The Rough Guide to Evolution. New York: Penguin Books, 2009. A quick, but surprisingly detailed introduction to evolution. A fun read.
- Zimmer, Carl. Evolution: The Triumph of an Idea. New York: Harper Collins, 2001. A companion book to the highly recommended PBS TV series. Superb explanations, good writing, and many, many illustrations.
- Ridley, Matt. Genome: The Autobiography of a Species in 23 Chapters. New York: Harper Perennial, 2000. A great introduction to the human genome. Each chapter covers a chromosome. The writing in this book is excellent.
- Harold, Franklin M. The Way of the Cell: Molecules, Organisms, and the Order of Life. New York: Oxford University Press, 2003. A very readable, popular introduction to cell biology.
- Hoagland, Mahlon, and Bert Dodson. The Way Life Works. New York: Three Rivers Press, 1995. This book is also listed in sources, but I list it here again because I believe that everybody who has any interest in biology must have this book. It is a unique combination of humor and cartoons and a serious introduction to molecular biology. This is the best book to get you up to speed.
- Lane, Nick. Power, Sex, Suicide: Mitochondria and the Meaning of Life. New York: Oxford University Press, 2005. A detailed, but very readable account of how energy is generated in cells, but it also branches out into many fundamental questions, such as why there are two sexes.
- Rensberger, Boyce. Life Itself: Exploring the Realm of the Living Cell. New York: Oxford University Press, 1996. A well-written, popular introduction to cell and molecular biology.
- Jones, Richard. Soft Machines: Nanotechnology and Life. New York: Oxford University Press, 2007. Covers ground similar to Life’s Ratchet, but with less emphasis 0n the physics and more emphasis on nanotechnology. A good read.
- Nelson, Philip. Biological Physics: Energy, Information, Life. New York: Freeman, 2008. Although I already listed this book in my sources, I list it here again because of its importance to Life’s Ratchet. This book inspired me to write the book in the first place. Biological Physics is the most interesting and well-written textbook I have ever read. However, it is quite technical, so buy it only if your calculus and physics are solid.
Origin of life
- Davies, Paul. The Fifth Miracle: The Search for the Origin and Meaning of Life. New York: Simon & Schuster, 2000. A very readable introduction to theories about life’s origin.
- Hazen, Robert. Genesis: The Scientific Quest for Life’s Origin. Washington, D.C.: Joseph Henry Press, 2007. A very readable, personal account of an origin of life researchers. Up-to-date.
Self-Organization and Patterns in Nature
- Ball, Philip. The Self-Made Tapestry: Pattern Formation in Nature. New York: Oxford University Press, 2001. A detailed and beautifully illustrated account of the spontaneous formation of patterns in nature. A modern update of D’Arcy Thompson’s Growth and Form.
Thermodynamics and Life
- Brown, Guy. The Energy of Life: The Science of What Makes Our Minds and Bodies Work. New York: Free Press, 1999. A popular account of how thermodynamics plays into human life, from the thermal motion in our cells to losing weight.
- Kurzynski, Michal. The Thermodynamic Machinery of Life. The Frontiers Collection. Berlin and New York: Springer, 2006. A very technical, but profound discussion of thermodynamics and life.
- Schneider, Eric. Into the Cool: Energy Flow, Thermodynamics, and Life. Chicago: University of Chicago Press, 2006. Discusses not only how life and the second law of thermodynamics are compatible, but how the second law is necessary to explain life.