Title: Life’s Ratchet: How Molecular Machines Extract Order from Chaos
Author: Peter Hoffman
Scope: 4 stars
Readability: 3 stars
My personal rating: 4 stars
See more on my book rating system.

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Topic of Book

Hoffman writes about the connection between physics and biology, particularly about how molecular machines evolve from inorganic matter.

My Comments:

While a challenging book to read, Hoffman’s concept of “molecular machines” creates a conceptual link between quantum physics, biology and technologic innovation. While they are typically viewed as very separate domains, he argues that they share much in common.

Key Take-aways

• Inanimate objects can spontaneously form machines. This is the origin of life.
• The world of sub-atomic particles, atoms and molecules is chaos.
• Cells are molecular machines that spontaneously organize this chaos into a self-sustaining processes by consuming and processing energy.

Important Quotes from Book

 “At the tiny scale of atoms and molecules, chaos reigns, yet at the scale of humans, order prevails (at least for the most part). How does this order arise?”

“I discovered the fascinating science of molecular machines. I realized that life is the result of noise and chaos, filtered through the structures of highly sophisticated molecular machines that have evolved over billions of years.”

“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. 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”

“The reductionist approach of looking at smaller and smaller pieces of living organisms has been a story of continued success. ”

“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?”

“The secret of life’s activity is found at the scale of a nanometer—a billionth of a meter.”

Astoundingly, the force that drives life at the smallest scale is not a mysterious, supernatural force, but it is a surprising one nevertheless. The force that drives life is chaos.”

 “The starting point of our quest must be the molecular scale.”

“Even at the molecular scale, life is incredibly complex; without this complexity, life could not function.”

“As we enter the microscopic world of life’s molecules, we find that chaos, randomness, chance, and noise are our allies. Without the shaking and rattling of the atoms, life’s molecules would be frozen in place, unable to move. Yet, if there were only chaos, there would be no direction, no purpose, to all of this shaking. To make the molecular storm a useful force for life, it needs to be harnessed and tamed by physical laws and sophisticated structures—it must be tamed by molecular machines.

The fruitful interaction of chance and necessity also explains how these chaos-harvesting machines were “designed” by evolution.”

“Where does chaos come from? Why are atoms in perpetual random motion? The random motions of the atoms in our bodies are an afterglow of the creation of the universe, the big bang. The big bang created a universe full of energy, and, eventually, it created stars like our sun. With the sun as intermediary, the energy of the big bang shakes the atoms of our cells—making life on Earth possible.”

“Chaos is the life force. Tempered by physical law, which adds a dash of necessity, chance becomes the creative force, the mover and shaker of our universe. All the beauty we see around us, from galaxies to sunflowers, is the result of this creative collaboration between chaos and necessity. The potential for life was already written into the book of our universe as soon as physical law met the violent motions of elementary particles. For me, this insight makes the story of life a beautiful, even spiritual story.”

“Humans transform energy from food into motion, heat, and thought. Energy is conserved.”

“Once we realize that life is not a thing, but a process, we can begin to scientifically study the process of living. We can make a distinction between living and nonliving. We could even attempt to explain how life’s processes can be the result of molecules.”

 “What distinguishes living organisms is not that they exist outside physics, but is that they are based on a self-organized, dynamic structure that perpetuates the organization of the organism from one point in time to the next. Life sustains itself. Life comes from life.

Every person’s atoms are replaced within seven years, yet we remain the same person. We are not the atoms that constitute us; nor are we our proteins, DNA, or molecular machines. We are, instead, a complex process, a program, as it were, running on chemomechanical hardware.”

“Every person’s atoms are replaced within seven years, yet we remain the same person. We are not the atoms that constitute us; nor are we our proteins, DNA, or molecular machines. We are, instead, a complex process, a program, as it were, running on chemomechanical hardware. ”

“we should be careful not to overuse the computing analogy of life. The “program” that constitutes the process of living is massively parallel, decentralized, self-adaptive, “squishy,” and controlled almost entirely by exchanges of matter… It is also a program that has evolved over billions of years.

Living is programmed molecular dancing.”

“The complicated program of “living” emerges from complicated feedback loops between all these molecules, linking them together in complex networks.”

“But the cell only becomes a cell when these molecules cooperate in a rich network of regulated interactions. This cooperative, self-sustaining, regulated activity is what we call living.”

“Molecular machines are enzymes, first and foremost, and most enzymes in our bodies are regulated by inhibitory binding or allosteric interaction.”

“Medical drugs, with few exceptions, work by inhibiting enzymes or molecular machines and are artificial control molecules.”

“Scientists work their way up from atoms to molecules to proteins to networks to systems, and finally to an entire cell.

“As I hope this book has shown, reductionism is essential if we want to understand life. Without it, scientists would have long ago stopped looking at smaller and smaller scales and would have missed the marvels of molecular machinery. At the same time, molecular machines don’t explain everything… The ultimate goal is always to explain the totality of life’s processes, from molecules to cells to organisms. Having taken the toy apart, we want to put it back together again. This is the way we learn how things work. Thus reductionism and holism are two sides of the same coin—they are both parts of what good science ought to be.”

“To say a cow is explained by what it is made of is to say that bricks explain a house. A better answer is that a cow is the result of evolution—a process made possible by the underlying material reality of particles—but which is essentially unpredictable. If we were to rerun the tape of life, would a cow reemerge? Nobody knows—it is likely that something like a cow could emerge again, but the new being might have six legs and only two stomachs. Thus there is no formula for “cow” based on the laws of particle physics. Particle physics may be necessary to make a cow (because we need atoms and molecules), but it is clearly not sufficient.”

“Science works on many levels. For a living organism, we may start at quarks and electrons. Using these, we can, in principle, predict the properties of nuclei and atoms. Once we have atoms, we can, in principle and with difficulty, explain the properties of molecules. But even at this point, the connection between the level of quarks and that of molecules is weak at best. We can understand many things about molecules by determining their atomic structure, but the quark structure is already too far removed to yield much insight or even a useful explanation for the properties of a molecule.”

“The difficulty in understanding biology is that it operates on many of these levels: from molecules to ecosystems. All of these levels contribute to the understanding of what life (or rather, living) is, and they are all important. As a physicist, I am most fascinated by the levels that connect life to physics, but I am aware that this is just a small part of the complexity of life.”

“To say a cow is explained by what it is made of is to say that bricks explain a house. A better answer is that a cow is the result of evolution—a process made possible by the underlying material reality of particles—but which is essentially unpredictable. If we were to rerun the tape of life, would a cow reemerge? Nobody knows—it is likely that something like a cow could emerge again, but the new being might have six legs and only two stomachs. Thus there is no formula for “cow” based on the laws of particle physics. Particle physics may be necessary to make a cow (because we need atoms and molecules), but it is clearly not sufficient.”

 “Molecular machines tell us more than just how cells work. By their similarity in all life on earth, they tell us of evolution and life’s unity; by their ability to tame chaos, they tell us a creative universe is only possible through chance and necessity; by their ability to be regulated and to regulate, they tell us that life is matter and program; and by their incessant activity, animated by the molecular storm, they tell us that life is a process, not a thing.”

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