Life's Ratchet: How Molecular Machines Extract Order from Chaos (Anglais) Relié – 15 novembre 2012
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For millennia, there has been a sense that living matter is somehow different from ordinary matter. There had to be some kind of vital force, something outside the well understood laws of physics and chemistry. For centuries, the challenge stood, even as scientists discovered cells, organic synthesis, genes and protein structure.
Then science reached the nanoscale. In the late 1980s and early 1990s a new class of microscope opened up the world of the nanometer. Individual molecules could be viewed, first statically, then in motion. New techniques could mark individual molecules and tweezers made of light beams opened a new area to experimentation and measurement. At the nanoscale biology, chemistry and physics converge. Living creatures are made of tiny machines.
These machines are made of molecules. They operate in a veritable storm of random motion and random collisions, and it is this storm that provides the energy for living motion - cellular motion, genetic manipulation and chemical transport. The second law of thermodynamics has this random motion effectively useless, unable to drive directed activity, but there is a loophole. Energy can be used to destroy information, to forget and reset molecular state. In cells, this energy is provided by ATP losing a phosphorous atom and converting to ADP. It seems insignificant, but at the nanoscale this minuscule jump burns at 7000 degrees. It is these fiery sparks of forgetfulness that drive life's ratchet and make life possible.
This book is a biophysicists manifesto. There has been a critical convergence in our understanding of living systems. We can look at the mysterious vital force up close and understand it. We can go to Youtube and watch a myosin molecule walk its track, buffeted by the invisible storm. It's an amazing story, and this book does a wonderful job of bringing this story to anyone with even a basic scientific background. I cannot recommend this book highly enough. We truly live in amazing times.
In this book by a physicist (who admits to having no biological training), Peter Hoffman finds the answer to this most forbidding of all of mankind's questions. According to him, the answer lies not in deep philosophical or religious speculation, but in Darwin's natural selection and the intricacies of the second law of thermodynamics as they combine and work together at the atomic, molecular and cellular levels. He discovered that amid the storm of chaos that goes on at the atomic level, there emerges from colliding water molecules, machine-like components capable of spontaneously converting one form of energy into another.
These components are tiny machines (nano-machines, as it were) that act like nano-scale electrical motors, operating on electrical voltages found in water, and which, in addition to being able to change one form of energy into another, are also capable of rendering order to the chaos we find at the atomic level. Our cells are filled with these tiny molecular machines that ratchet up the process of transforming random motion into hierarchically ordered cellular activity.
They do this by first operating on electrical voltages, and then by turning those voltages into collections of machines (like themselves), and them into hierarchies of nano-scale factories. These factories go on to custom build other molecular level machinery that together have proceeded down a long evolutionary path, and through many very complicated processes involving natural selection, to produce and package enzymes, peptides, amino acids, and even strains of DNA.
Thus, what emerges from this book is a scientifically testable set of conjectures about the creation of life, namely that: life has emerged from the ability to self-order random chaos in water by filtering the motion of atoms through sophisticated structures of our evolving cellular machinery.
According to Professor Hoffman, the cell is like a complex city of molecular machines and factories working together to produce order, and then inexorably (and purposefully?), to produce something bigger than themselves. Using Darwin's insights about how natural selection helped resolve the split between reductionism and vitalism, Hoffman shows us how order can be created from a chaotic storm of thermal energy, and then with the process of natural selection, can produce all of the ingredients necessary to sustain cellular life.
And while it is true that for the moment some of this is what one might at best call "strategic speculation," especially the teleological aspects about the purposeful nature of the cell's activity, it is still the kind of "experimentally guided speculation" that leaves the door wide open for later scientific verification, testing and validation.
I love this book because for the first it gives us a framework for generating testable scientific hypotheses that may be able to stand as viable alternatives to the Creationists' Intelligent Design and other Biblical Genesis creation myths: This chain of logic that links atomic activity, the second law of thermodynamics, thermal, electrical and chemical energy, and Darwin's theory of evolution, contains all of the seeds of the always suspected root cause ingredients of life, and does so in the correct logical and epistemological proportions. By my way of thinking, this framework alone is a giant step in the direction of a more solid and scientifically correct understanding of how life began. Ten Stars
The book starts out with some history of science that while interesting seems tangential to the main idea in the book. But it soon got going with that idea - that the process of life is driven by molecular machines. And that these machines harvest the random motion of atoms and ratchet into work that drives the cellular processes that constitute life. This was all excellent. This is a rather profound idea and it is persuasively argued in the book. I loved it.
However a good chunk of the second half of the book was taken up with much too detailed descriptions of examples of these processes. While I found the initial examples interesting it just went on too long and got too technical. It's possible to understand it with careful reading but I found myself wondering why? I already got the point. At this point the book became too specialized.
I found the last couple of chapters inspiring and an excellent summary of the main idea without all the technical details.
So, I think this book deserves very high marks for its insights, but tried to be too much for the general reader. You can have a fairly technical book or a popular book but it's hard to mix the two and I think in this case the author tried and failed.
However, I still strongly recommend this book with the above warning in mind. If you don't like technical explanations you will be very frustrated with parts of this book. On the other hand the ideas and insights related to the main thesis are brilliantly argued.
Life's ratchet is split into 9 chapters. It starts by introducing life from a historical understanding of what people have thought was behind the force of life. It goes through Greek ideas like atomism and vitalism and goes through Aristotelian concepts of purpose that defined humanities views on life and science for so long. The chapter goes on to discuss the enlightenment and life as a machine as physics and math evolved and science became more rigorous. The author shows how irrespective of time period, the same fundamental questions are re-asked using different language and more precise argument. The author then moves onto on determinism and probability. The author discusses some basic ideas in chance and combinatorics and the author discusses the philosophically loaded issue of how much in life is chance versus a natural consequence of background conditions. The author plots how different philosophies can be seen as relative combinations of a two dimensional space of life being defined by necessity --> chance as one dimension and vital forces --> physical forces as the other. The author introduces entropy. He starts out by considering an analogy of energy with money and how money spent gets quickly dispersed within an economic system such that recollecting is much harder than initially disbursing. This constant increase in dispersion is the authors neat representation of how entropy increases in a physical system. The author discusses statistical mechanics and thermodynamics in particular the second law and the concept of free energy and the rule of thumb that a system is always trying to reduce its available free energy (which is defined as Energy - temperature*entropy). The author familiarizes the reader with the nano-scale and how small that is relative to our sense of physical size. He discusses the engineering miracles of recent history and the new microscopes used to probe the atomic level to allow us the investigations to follow. The author discusses some physics as well introducing mediums like mayonnaise to discuss how biology and chemistry can be combined to understand many phenomenon. The author reintroduces thermodynamics and how order can be created within the second law in open systems. He starts with discussing the famous Maxwell's Demon, a hypothetical creature who through a clever thought experiment can reduce entropy in a closed physical system The author discusses some basic biology including proteins, how they fold and the enzymes involved, the role of DNA. The way that chemical reactions are happening across an energy landscape and the designs are there to help navigate this background landscape. One starts to get a sense of the immense complexity and subtle beauty of what is happening at the nano-scale in our cells. The author begins to introduce molecular machines and in particular kinesin. The author discusses the mechanics and conveys to the reader much of what modern investigations of come to conclude about the molecule and how it works. The author moves on to fully starting to look at molecular machines and the forefront of what people are working on by looking at more molecular machines, like kinesin (again, but more varieties), myosin, dynein, the way ATP cycles work, DNA, RNA- there is a lot of material in the chapter "Twist and Route" and a full appreciation is beyond possibility for the non-expert. The author moves on to investigate the ribosome. He discusses evolution and how it works at the cellular level and how irreducible complexity is a poor argument as its premise can often shown to be false. This chapter ties a lot of the mechanics back to investigating the philosophy of life and where it "really" is when looked at on the determinism vs chance, and vitalism vs physical forces. It reinforces the idea of the selfish gene and how natural selection is such a powerful idea. The author in the last chapter takes a step back and discusses reductionism and holism and how one can think about physics and biology. These are all opinions about the nature of science and life. The reader is left with a lot to think about...
Life's Ratchet is an excellent book. It started out a bit slow for me as i am relatively familiar with the history of science and basic physics and as a result was wondering where the main subject matter would be introduced. That being said, the way the author constructed his book led to a deeper appreciation of his core material when he got there. One really gets a view from above as well as at the microlevel of what is happening in the author's field and life sciences in general. Highly recommend reading this.
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