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Life's Ratchet: How Molecular Machines Extract Order from Chaos
Life is an enduring mystery. Yet, science tells us that living beings are merely sophisticated structures of lifeless molecules. If this view is correct, where do the seemingly purposeful motions of cells and organisms originate? In Life’s Ratchet, physicist Peter M. Hoffmann locates the answer to this age-old question at the nanoscale.
Below the calm, ordered exterior of a living organism lies microscopic chaos, or what Hoffmann calls the molecular storm—specialized molecules immersed in a whirlwind of colliding water molecules. Our cells are filled with molecular machines, which, like tiny ratchets, transform random motion into ordered activity, and create the “purpose” that is the hallmark of life. Tiny electrical motors turn electrical voltage into motion, nanoscale factories custom-build other molecular machines, and mechanical machines twist, untwist, separate and package strands of DNA. The cell is like a city—an unfathomable, complex collection of molecular workers working together to create something greater than themselves.
Life, Hoffman argues, emerges from the random motions of atoms filtered through these sophisticated structures of our evolved machinery. We are agglomerations of interacting nanoscale machines more amazing than anything in science fiction. Rather than relying on some mysterious “life force” to drive them—as people believed for centuries—life’s ratchets harness instead the second law of thermodynamics and the disorder of the molecular storm.
Grounded in Hoffmann’s own cutting-edge research, Life’s Ratchet reveals the incredible findings of modern nanotechnology to tell the story of how the noisy world of atoms gives rise to life itself.
Below the calm, ordered exterior of a living organism lies microscopic chaos, or what Hoffmann calls the molecular storm—specialized molecules immersed in a whirlwind of colliding water molecules. Our cells are filled with molecular machines, which, like tiny ratchets, transform random motion into ordered activity, and create the “purpose” that is the hallmark of life. Tiny electrical motors turn electrical voltage into motion, nanoscale factories custom-build other molecular machines, and mechanical machines twist, untwist, separate and package strands of DNA. The cell is like a city—an unfathomable, complex collection of molecular workers working together to create something greater than themselves.
Life, Hoffman argues, emerges from the random motions of atoms filtered through these sophisticated structures of our evolved machinery. We are agglomerations of interacting nanoscale machines more amazing than anything in science fiction. Rather than relying on some mysterious “life force” to drive them—as people believed for centuries—life’s ratchets harness instead the second law of thermodynamics and the disorder of the molecular storm.
Grounded in Hoffmann’s own cutting-edge research, Life’s Ratchet reveals the incredible findings of modern nanotechnology to tell the story of how the noisy world of atoms gives rise to life itself.
288 pages, Hardcover
First published January 1, 2012
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July 7, 2015
Hoffmann, in Life's Rachet, sets out for himself a substantial task: to explain the emergence of life, along with its relentlessly growing complexity over time. He does neither, and gloriously. Or as the brilliant Wolfgang Pauli would say of his students' poor answers, "It's not even wrong."
Hoffmann is a physicist. It is that bag of talents that he brings to bear on the perennial questions of evolutionary biology. He sees his background in material sciences as an asset in the problem of life, a misplaced hubris to be sure. His solutions to those evolutionary questions, surprise surprise, are to be found in the physical sciences, the bump and clang of molecules in motion, oozing energy and possibility captured by molecular machines that build forward their own sophistication. He profits a great deal by not understanding the most basic challenges facing those who are seriously addressing the problems of life's origins and evolution. Hoffmann makes a parody of life's origins, and something less flattering of its evolution. As Charles Darwin himself aptly put it, "Ignorance more frequently begets confidence than does knowledge."
On life's origins, he throws his hat casually into the ring with the lipid vesicle theory as the birthplace, presenting origins here as though it were as certain as bad days and sex scandals:
"If we place different chemicals inside the vesicle, we create an isolated, nanosize reaction chamber. All kinds of interesting things could go on inside this tiny chamber -- life, for example" (p.106).
And with that, Hoffmann has effortlessly brushed aside a hailstorm of problems with the lipid vesicle theory of life's origins.
That's the most attention Hoffmann gives to life's origins. For good reason, because appeals to physics and chemistry alone in explaining life's origins will get him about as far as a lit match in a sandstorm. It is a magic trick that many of our patients have been performing for decades prior to seeing us clinically: a problem ignored is - voila - not a problem at all. But for heartburn and bad theories both, problems ignored have a tendency to just get worse.
Cells, as we know, are built of proteins. And not just any ol' proteins but functional proteins. The landscape of *possible* proteins is ginormous, say, the size of Texas. And the landscape of *biologically functional* proteins is, in this example and relatively speaking, the size of a dime. And how does Hoffmann's slosh of substrates in this vesicle pouch find that dime as his physics and chemistry go randomly searching the terrain of Texas? Well, here's how:
"Cells take advantage of ... *entropic forces* to assemble a variety of molecular structures, including collagen, actin, and microtubule filaments." He's talking about these molecular structures exactly two pages after he even *proposed* the idea that a lipid vesicle could bring together chemical reactions that form life! The organizational expanse between a theoretical lipid vesicle with some chemicals in it and a metabolically stabilized cell is something like the difference between random letters lined up on a scrabble rack and the collected works of Shakespeare, though that very dramatically understates the case. And how did the cells stumble upon collagen and actin and microtubule filaments? Well, Hoffmann doesn't tell us, so apparently they just did.
Here's a quick sampling of what Hoffmann is glossing over. Let's assume that all bonds between any two amino acids are equally probable (all evidence suggests they are, which is why their arrangement is arbitrary, not patterned), and that we have a mix of amino acids randomly bumping into each other. Since there are 20 amino acids involved in the building of a protein, and since the primary structure of actin is 374 amino acids in length, we now can calculate that the probability of building actin through a process driven by nothing but thermodynamics is 20^-374 (or, 1 in 20 raised to the 374th power). And that's just to build actin. Of course a cell can't do much with just actin, so each *individual protein* must be subjected to the same constraints.
Hoffmann's treatment of his subject gets no more sophisticated as he plows through explanations of information and its accrual, the building of complex structures, and even the whole of evolution itself. For him, it is just balancing an equation: random molecular events stumble some parts into more order, which leads to a greater amount of disorder elsewhere. That disorder increase (increased entropy) not only keeps the thermodynamic scale in balance, but is the playground for more order to happen. Problem solved. Of course Hoffmann hopes you didn't notice that life is not ordered, it is *organized*, and he has given not a whit of insight into the source of its organization.
I have been amazed in reading reviews of this book. The broad consensus is that it is a solid, scientific, *plausible* explanation for the things he is explaining. On the back cover, a blub by a Professor of Biology states, "Life's Rachet is one of those rare books that pay off one of science's central promises: reductionism can explain higher-order phenomena."
And herein lies the value of Hoffmann's book. Readers get insight into how thoroughly implausible and even cartoonish ideas can dress themselves up in scientific language and be received as compelling proposals. So long as books like this are accepted uncritically, reductionism will stand protected. It is a testament to the mind-numbing power of faith in materialism that the absurdities of this book are not roundly critiqued rather than praised.
Hoffmann is a physicist. It is that bag of talents that he brings to bear on the perennial questions of evolutionary biology. He sees his background in material sciences as an asset in the problem of life, a misplaced hubris to be sure. His solutions to those evolutionary questions, surprise surprise, are to be found in the physical sciences, the bump and clang of molecules in motion, oozing energy and possibility captured by molecular machines that build forward their own sophistication. He profits a great deal by not understanding the most basic challenges facing those who are seriously addressing the problems of life's origins and evolution. Hoffmann makes a parody of life's origins, and something less flattering of its evolution. As Charles Darwin himself aptly put it, "Ignorance more frequently begets confidence than does knowledge."
On life's origins, he throws his hat casually into the ring with the lipid vesicle theory as the birthplace, presenting origins here as though it were as certain as bad days and sex scandals:
"If we place different chemicals inside the vesicle, we create an isolated, nanosize reaction chamber. All kinds of interesting things could go on inside this tiny chamber -- life, for example" (p.106).
And with that, Hoffmann has effortlessly brushed aside a hailstorm of problems with the lipid vesicle theory of life's origins.
That's the most attention Hoffmann gives to life's origins. For good reason, because appeals to physics and chemistry alone in explaining life's origins will get him about as far as a lit match in a sandstorm. It is a magic trick that many of our patients have been performing for decades prior to seeing us clinically: a problem ignored is - voila - not a problem at all. But for heartburn and bad theories both, problems ignored have a tendency to just get worse.
Cells, as we know, are built of proteins. And not just any ol' proteins but functional proteins. The landscape of *possible* proteins is ginormous, say, the size of Texas. And the landscape of *biologically functional* proteins is, in this example and relatively speaking, the size of a dime. And how does Hoffmann's slosh of substrates in this vesicle pouch find that dime as his physics and chemistry go randomly searching the terrain of Texas? Well, here's how:
"Cells take advantage of ... *entropic forces* to assemble a variety of molecular structures, including collagen, actin, and microtubule filaments." He's talking about these molecular structures exactly two pages after he even *proposed* the idea that a lipid vesicle could bring together chemical reactions that form life! The organizational expanse between a theoretical lipid vesicle with some chemicals in it and a metabolically stabilized cell is something like the difference between random letters lined up on a scrabble rack and the collected works of Shakespeare, though that very dramatically understates the case. And how did the cells stumble upon collagen and actin and microtubule filaments? Well, Hoffmann doesn't tell us, so apparently they just did.
Here's a quick sampling of what Hoffmann is glossing over. Let's assume that all bonds between any two amino acids are equally probable (all evidence suggests they are, which is why their arrangement is arbitrary, not patterned), and that we have a mix of amino acids randomly bumping into each other. Since there are 20 amino acids involved in the building of a protein, and since the primary structure of actin is 374 amino acids in length, we now can calculate that the probability of building actin through a process driven by nothing but thermodynamics is 20^-374 (or, 1 in 20 raised to the 374th power). And that's just to build actin. Of course a cell can't do much with just actin, so each *individual protein* must be subjected to the same constraints.
Hoffmann's treatment of his subject gets no more sophisticated as he plows through explanations of information and its accrual, the building of complex structures, and even the whole of evolution itself. For him, it is just balancing an equation: random molecular events stumble some parts into more order, which leads to a greater amount of disorder elsewhere. That disorder increase (increased entropy) not only keeps the thermodynamic scale in balance, but is the playground for more order to happen. Problem solved. Of course Hoffmann hopes you didn't notice that life is not ordered, it is *organized*, and he has given not a whit of insight into the source of its organization.
I have been amazed in reading reviews of this book. The broad consensus is that it is a solid, scientific, *plausible* explanation for the things he is explaining. On the back cover, a blub by a Professor of Biology states, "Life's Rachet is one of those rare books that pay off one of science's central promises: reductionism can explain higher-order phenomena."
And herein lies the value of Hoffmann's book. Readers get insight into how thoroughly implausible and even cartoonish ideas can dress themselves up in scientific language and be received as compelling proposals. So long as books like this are accepted uncritically, reductionism will stand protected. It is a testament to the mind-numbing power of faith in materialism that the absurdities of this book are not roundly critiqued rather than praised.
February 21, 2017
5-star thesis, 2.5-star presentation. Does a good job of explaining the thermodynamic basis for the operation of biomolecular machines, but some of the intuition pumps are weak, the personal touches stand out awkwardly, and there are several misleading or outright false statements (including the classic "all your atoms are replaced every 7 years").
February 17, 2013
If you only read one book concerning the significance of the second law of thermodynamics to life itself, this would be a good one.
July 13, 2020
The first 100 pages or so rated two stars, as it seemed a history on physics and probablity theory to lead up to "legitimizing" the nefarious Charater 8. The next hundred pages were more illuminating and I'd rate as four stars. It was interesting to learn about molecular transport motors: Kinesin, Dynein and Myosin. There are over a hundred in the Myosin family.
In Chapter 8 the author suggests that Myosins and Kinesins probably had an elusive common ancestor but doesn't prrovide a possible staging sequence. He doesn't even offer up a pair of Myosins that may have branched from one another, although from the diagram on pages 190-191 offer potential candidates.
The author then uses a Flavobacterium strain that breaks down nlyon as an example of evolution in action (page 217) that would have gone through 87,600 generations of gazillions of bacteria to devise three enzymes. Coming up with an enzyme no way compares with devising a new gene, yet thousands of new ones exist in the hominid line in less than 87,600 generations without the benefit of gazillions of reproductive pairs. It's like saying after decades of avalanches you find three examples of two rocks atop each other that you could expect throwing piles of construction iron together and the Eiffel Tower will appear.
And if natural selection is such an efficient process why hasn't it weedled down those hundreds of Myosins down to just a few? Perhaps Hoffman should stick to Physics.
In Chapter 8 the author suggests that Myosins and Kinesins probably had an elusive common ancestor but doesn't prrovide a possible staging sequence. He doesn't even offer up a pair of Myosins that may have branched from one another, although from the diagram on pages 190-191 offer potential candidates.
The author then uses a Flavobacterium strain that breaks down nlyon as an example of evolution in action (page 217) that would have gone through 87,600 generations of gazillions of bacteria to devise three enzymes. Coming up with an enzyme no way compares with devising a new gene, yet thousands of new ones exist in the hominid line in less than 87,600 generations without the benefit of gazillions of reproductive pairs. It's like saying after decades of avalanches you find three examples of two rocks atop each other that you could expect throwing piles of construction iron together and the Eiffel Tower will appear.
And if natural selection is such an efficient process why hasn't it weedled down those hundreds of Myosins down to just a few? Perhaps Hoffman should stick to Physics.
August 5, 2014
Carl Sagan opened our minds to the vastness of the universe, Peter Hoffmann helps us peer into the incredibly small.
December 11, 2014
This is a popularization in the sense of intended for non-scientists, but it's fairly complex in a couple of ways so that it's not a simple read. First, it covers a lot of ground that you might or might not be interested in, from history of science to creationism to lots of technical detail -- piconewtons, equivalent temperature gains from the chemical reaction of single molecules, and much more. I personally found the breadth to be too much, though only by a little. Second, some of the technical material is pretty technical. We work through gentle introductions to statistical mechanics, what the second law of thermodynamics really means, introductory chemistry and biochemistry, atomic force microscopy, and quite a selection of other topics, before getting to what seems to be the heart of the book, explanations of the molecular machines that make life work, whose structure and workings we're just starting to understand. We also get quite a bit of detail along the way about the clever experimental techniques that scientists have invented to figure these things out.
So it's not very everyone, but if you're up for it and interested in such things, this book is well worth your time. The best thing about it for me as a science popularization was the vivid way he helps you understand what it's like in the nano world, and how different it is -- the world of what he calls the "molecular storm", the world of life at the level of the cell. This is critical to his narrative, because it turns out that the molecular machines that make life work are actually coming as close as possible to cheating the second law by exploiting the highly disordered energy in the molecular storm to drive things forward and then click the "ratchet" forward when random forces push things in the wanted direction. Although less vivid, a philosophical theme of the book is that the roles of chance (randomness) and necessity (physical law) are exquisitely balanced in the universe generally and the workings of life in particular.
Hoffmann is an excellent writer, and many of the technical descriptions are quite masterful. For example, the description of the machine in mitochondria that recharges ATP from ADP is spine tingling. In addition, Hoffmann is very well read: in science, in the history of science, and even in matters philosophical that go beyond science. (His knowledge of popular culture isn't too shabby either -- one of the chapters is named "Twist and Route" for example. One would never suspect his native language is not English.) Different parts of the book discuss works I knew about by famous scientists (Schrodinger, Monod, D'Arcy Thompson), and some I hadn't heard of (Smoluchowski, Delbruck, and more). In the age of the web, one can follow many of the references in the book. For example, on page 123 Hoffmann has a fascinating diagram about why different kinds of energy "converge" at the nanoscale, but his explanation is in this case not very good. Fortunately, it's easy to find the article where the diagram was originally published and the explanation there is better. Hoffmann's affection and enthusiasm for his subjects is infectious. Although some of the philosophical and historical parts can come across as a bit unfocused, I really appreciated the path he takes from physics through biology to help his readers understand at a deeper level what life is like in the cell, how it works energetically, and how a fairly large selection of the most important molecular machines do what they do.
So it's not very everyone, but if you're up for it and interested in such things, this book is well worth your time. The best thing about it for me as a science popularization was the vivid way he helps you understand what it's like in the nano world, and how different it is -- the world of what he calls the "molecular storm", the world of life at the level of the cell. This is critical to his narrative, because it turns out that the molecular machines that make life work are actually coming as close as possible to cheating the second law by exploiting the highly disordered energy in the molecular storm to drive things forward and then click the "ratchet" forward when random forces push things in the wanted direction. Although less vivid, a philosophical theme of the book is that the roles of chance (randomness) and necessity (physical law) are exquisitely balanced in the universe generally and the workings of life in particular.
Hoffmann is an excellent writer, and many of the technical descriptions are quite masterful. For example, the description of the machine in mitochondria that recharges ATP from ADP is spine tingling. In addition, Hoffmann is very well read: in science, in the history of science, and even in matters philosophical that go beyond science. (His knowledge of popular culture isn't too shabby either -- one of the chapters is named "Twist and Route" for example. One would never suspect his native language is not English.) Different parts of the book discuss works I knew about by famous scientists (Schrodinger, Monod, D'Arcy Thompson), and some I hadn't heard of (Smoluchowski, Delbruck, and more). In the age of the web, one can follow many of the references in the book. For example, on page 123 Hoffmann has a fascinating diagram about why different kinds of energy "converge" at the nanoscale, but his explanation is in this case not very good. Fortunately, it's easy to find the article where the diagram was originally published and the explanation there is better. Hoffmann's affection and enthusiasm for his subjects is infectious. Although some of the philosophical and historical parts can come across as a bit unfocused, I really appreciated the path he takes from physics through biology to help his readers understand at a deeper level what life is like in the cell, how it works energetically, and how a fairly large selection of the most important molecular machines do what they do.
October 23, 2014
Well, this is the first popular book which I have read about molecular machines. It is well written and joy to read. I admired clear style of Hoffmann throughout the book while conveying important and complex ideas on chance and necessity in emerging life. As a physicist, I liked the chapters on Entropy and Maxwell's Demon the most where a basic statistical and thermodynamical picture of life process was sketched.
Maybe only caveat was the long introduction of vital forces and lengthy debates between different schools of ideas at the ancient era.However, I think it is a legitimate approach to show the reader what old guys were contemplating while trying to elucidate life's machinery.
I highly recommend the book if you want to look closely to the self-sufficient mechanism of life at the smallest scale.
Maybe only caveat was the long introduction of vital forces and lengthy debates between different schools of ideas at the ancient era.However, I think it is a legitimate approach to show the reader what old guys were contemplating while trying to elucidate life's machinery.
I highly recommend the book if you want to look closely to the self-sufficient mechanism of life at the smallest scale.
no
May 20, 2016I gave up after about 10%.
Big excitement/discovery of the millennium is pronounced at the very beginning. And then the author bores you to tears with Aristotle's birth year, death year and his arguments with his contemporaries.
Seriously, any popular science book starting with a history chapter should be banned! It reflects a lazy habit of the author carried from their academic publishing career. A writer needs to spend at least 5 minutes on the organization and structure of a book before typing away! Chronology is the laziest and most boring way to organize a book!
Big excitement/discovery of the millennium is pronounced at the very beginning. And then the author bores you to tears with Aristotle's birth year, death year and his arguments with his contemporaries.
Seriously, any popular science book starting with a history chapter should be banned! It reflects a lazy habit of the author carried from their academic publishing career. A writer needs to spend at least 5 minutes on the organization and structure of a book before typing away! Chronology is the laziest and most boring way to organize a book!
June 2, 2019
"Here be dragons!" - finger-pointed Fermi on hazy shadowy picture of nucleus.
Nowadays by using our AFM's, we can wander way down across atomic scale with our quantum theory, and we have no doubt that Mr. Fermi was not far from the truth, in some sense.
In the summary of the book it is explained what the "Life's ratchet" is all about, thus I would rather avoid tauthology any of kind...however, the future reader must have some basic knowledge of particle physics, chemistry, cellular biology, evolution theory, genetics, because here you gonna meet a lot of scientists from the past, even Mr. Cardano! He is obviously one of the main players in Life's Ratchet, not because of his invention of Cardan-shaft, but because of the probabilistic theory that is a tool for statistical mechanics. Don't worry, the author will make his best to you understand the statistical mechanics.
The "Life's ratchet" once it's unfold in full before your eyes and start sink into your mind, in some people, depending on their global worldview, may cause anger, disappointment, sadness, depression, or just doubt.. or, sweet epiphany, happiness, and other good sensations.
The impact on me was fantastic: my knowledge on all fields mentioned is deepened, especially I've got a sufficient dose from the II. Law of thermodynamics and quantum. However, I must admit that one of my favorite fields of interests is a Chaos Theory and Particle Physics, thus it's very difficult for me to predict how will readers with just a basics cope with a challenges of vital part of this book. I hope everything's gonna be just fine.
If to make some brief presentation, I'd describe Mr. Hoffmann's "Life's Ratchet" as a ribosome, the protein maker in living cell! Imagine that your knowledge is a final product, say the Knowledge protein, and the amino acids that are the constituent parts of your knowledge protein are the belonging knowledge contents from all the fields from cosmology, through physics, chemistry, cellular sciences, way until to the genetics - and the ribosome is there for you to link all these parts of knowledge amino acids and fold them in one Knowledge Protein that is projecting into your very mind a picture about the "origins of life". But, will you get a full understanding of the origins? If we found the "élan vital" in the energy of of a cosmic explosion aftermath, does that mean, that we gonna see answers unfolding on all the, until now, our unanswered questions?
Generally, the book is written on reader friendly way, the language is rich and clear with utmost hygiene.
Thank! Cheers!
Nowadays by using our AFM's, we can wander way down across atomic scale with our quantum theory, and we have no doubt that Mr. Fermi was not far from the truth, in some sense.
In the summary of the book it is explained what the "Life's ratchet" is all about, thus I would rather avoid tauthology any of kind...however, the future reader must have some basic knowledge of particle physics, chemistry, cellular biology, evolution theory, genetics, because here you gonna meet a lot of scientists from the past, even Mr. Cardano! He is obviously one of the main players in Life's Ratchet, not because of his invention of Cardan-shaft, but because of the probabilistic theory that is a tool for statistical mechanics. Don't worry, the author will make his best to you understand the statistical mechanics.
The "Life's ratchet" once it's unfold in full before your eyes and start sink into your mind, in some people, depending on their global worldview, may cause anger, disappointment, sadness, depression, or just doubt.. or, sweet epiphany, happiness, and other good sensations.
The impact on me was fantastic: my knowledge on all fields mentioned is deepened, especially I've got a sufficient dose from the II. Law of thermodynamics and quantum. However, I must admit that one of my favorite fields of interests is a Chaos Theory and Particle Physics, thus it's very difficult for me to predict how will readers with just a basics cope with a challenges of vital part of this book. I hope everything's gonna be just fine.
If to make some brief presentation, I'd describe Mr. Hoffmann's "Life's Ratchet" as a ribosome, the protein maker in living cell! Imagine that your knowledge is a final product, say the Knowledge protein, and the amino acids that are the constituent parts of your knowledge protein are the belonging knowledge contents from all the fields from cosmology, through physics, chemistry, cellular sciences, way until to the genetics - and the ribosome is there for you to link all these parts of knowledge amino acids and fold them in one Knowledge Protein that is projecting into your very mind a picture about the "origins of life". But, will you get a full understanding of the origins? If we found the "élan vital" in the energy of of a cosmic explosion aftermath, does that mean, that we gonna see answers unfolding on all the, until now, our unanswered questions?
Generally, the book is written on reader friendly way, the language is rich and clear with utmost hygiene.
Thank! Cheers!
June 3, 2015
Peter Hoffman is one of the many physicists who straddles the line between physics and microbiology. In this book, he does that quite successfully. His aim is to show that what we see and call life can be identified by the actions of certain molecules that in aggregate drive the activity of cells. The overriding principle governing the emergence of these molecules is chaos and necessity. The author admonishes those who claim that the complexity of life requires an autonomous life force, a divine aspect or intelligent designer. Hoffman makes a convincing argument for the inevitability of life given the nature of particles at the molecular level and the growing complexity of life given the power of evolution. Reading the book should provide you with the understanding that science has been the most successful human endeavor in answering the question of who we are.
April 3, 2017
- Great book highlighting one of the biggest success stories of reductionism.
- A few key takeaways:
(1) It is only at the nanoscale that different forms of energy (electrical, chemical, mechanical) can be easily interchanged and utilized effectively. This means that most of life in the physical Universe likely follows a similar evolutionary path. At least in terms of deploying a large/varied factory of molecular machines to build life.
(2) If reductionism can be brought upon such an ambitious question, we should not get discouraged in pushing this path all the way up to behaviors. New kinds of sciences will have to be developed to explain different levels of emergence but it is not hopeless
- A few key takeaways:
(1) It is only at the nanoscale that different forms of energy (electrical, chemical, mechanical) can be easily interchanged and utilized effectively. This means that most of life in the physical Universe likely follows a similar evolutionary path. At least in terms of deploying a large/varied factory of molecular machines to build life.
(2) If reductionism can be brought upon such an ambitious question, we should not get discouraged in pushing this path all the way up to behaviors. New kinds of sciences will have to be developed to explain different levels of emergence but it is not hopeless
August 13, 2017
Wow, that's the first time I enjoyed molecular biology, and I am a biologist. Awesome, quite thorough but yet simple introduction into molecular machines as the basis for life, perfect explanation of the 2nd law of thermodynamics for all those pesky creationists (in case any of them reads it, he will never mention it again as an argument; too bad they read just that one stupid book). Don't worry if your are not much into (bio)chemistry and such - it's not my cup of tea either. This book is enjoyable anyway.
February 1, 2016
Filled with simple analogies and clear language, along with bits of interesting history behind each concept. I normally devour books, but with this one I took my time, savouring Hoffmann's vision of life and the universe. Got a feeling this book is going to be a classic.
May 20, 2014
Don't miss time. This is the book you are looking for. Believe me. Five stars.
February 2, 2025
An exploration of life at the smallest scale, and the science explaining its function.
This book tells the story of a big idea: that life is not driven by some supernatural outside force, but that it is something that normal matter spontaneously does when organized in the right way. It explores the physics of atoms, molecules, and living matter, the history of those ideas, and the scientists that refined them. From there, it explores what the world of the very small is like, and the sorts of molecular machines we see there, the unfamiliar ways in which they work, and how they relate to life itself, which is made of and by those machines. The first two thirds of the book gives the background you need to understand chapter 7, where the design and function of several specific molecular machines are described in detail.
Part of what makes this book so enjoyable is how excited the author is about his research. He clearly feels as if his field is uncovering the secrets of life, the universe, and everything and wants to share his wonder and excitement with the world! He does a good job telling the story, and makes a strong case for why this is so important. On the other hand, he may be overselling what we know. In the introduction, he makes it sound like we've "figured it all out" when it comes to how cells function, but by the end the truth becomes clear: there are a handful of these biological mechanisms that we've started to explore and only sorta understand. It really is quite extraordinary that these machines work, that we can observe and understand them at all, and that what we're learning suggests new general principles for how life works. But we've only just scratched the surface here.
This book does an unusually good job of reconciling science with philosophy and religion. It's clear that science is the author's focus, but he knows the philosophy well enough to avoid many large pitfalls, and to successful describe the meaning and significance of this work. Religion is barely mentioned, but given the subject matter, this book can't help but touch on questions about the origins of life, evolution, and intelligent design. Mostly, it argues firmly against intelligent design, but in a way that doesn't present science and religion as fundamentally incompatible. Importantly, he makes it clear that knowing how cells function or evolve does not explain their origins, and that cells are built of and by molecular machines does not mean that life is a machine.
This is a fantastic book that makes the mysteries of life just a little bit less mysterious. It's well written and suitable for all audiences. It helps bring the microscopic world to life, and reveal the masterpiece of evolutionary engineering which is the living cell.
This book tells the story of a big idea: that life is not driven by some supernatural outside force, but that it is something that normal matter spontaneously does when organized in the right way. It explores the physics of atoms, molecules, and living matter, the history of those ideas, and the scientists that refined them. From there, it explores what the world of the very small is like, and the sorts of molecular machines we see there, the unfamiliar ways in which they work, and how they relate to life itself, which is made of and by those machines. The first two thirds of the book gives the background you need to understand chapter 7, where the design and function of several specific molecular machines are described in detail.
Part of what makes this book so enjoyable is how excited the author is about his research. He clearly feels as if his field is uncovering the secrets of life, the universe, and everything and wants to share his wonder and excitement with the world! He does a good job telling the story, and makes a strong case for why this is so important. On the other hand, he may be overselling what we know. In the introduction, he makes it sound like we've "figured it all out" when it comes to how cells function, but by the end the truth becomes clear: there are a handful of these biological mechanisms that we've started to explore and only sorta understand. It really is quite extraordinary that these machines work, that we can observe and understand them at all, and that what we're learning suggests new general principles for how life works. But we've only just scratched the surface here.
This book does an unusually good job of reconciling science with philosophy and religion. It's clear that science is the author's focus, but he knows the philosophy well enough to avoid many large pitfalls, and to successful describe the meaning and significance of this work. Religion is barely mentioned, but given the subject matter, this book can't help but touch on questions about the origins of life, evolution, and intelligent design. Mostly, it argues firmly against intelligent design, but in a way that doesn't present science and religion as fundamentally incompatible. Importantly, he makes it clear that knowing how cells function or evolve does not explain their origins, and that cells are built of and by molecular machines does not mean that life is a machine.
This is a fantastic book that makes the mysteries of life just a little bit less mysterious. It's well written and suitable for all audiences. It helps bring the microscopic world to life, and reveal the masterpiece of evolutionary engineering which is the living cell.
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December 16, 2024This book examines the physicists’ quest to understand living systems and how they do not violate the second law of thermodynamics. Yes, thermal motion, “the molecular storm” randomly and inexorably pushes life’s constituent molecules around in a chaotic entropic dance. But ATP is used by molecular “machines” to harness the push of water molecules in the molecular storm. I particularly liked hearing about ATP synthase that sits in the mitochondrial membrane and has component parts with a central shaft which rotates to add P ions to ADP and produces 3 ATP’s per 360deg rotation of a molecular motor similar to how an armature works. The discussions of kinesin /microtubules and myosin/ actin and how these molecules walk down the fibers while using ATP to release their alternating grips but the translation of motion is a result of the molecular storm not some allosteric pushing along the fiber is fascinating. The author lays out that life is a convergence of chance (evolution) and necessity (chemical/physical laws of molecules) at the nanoscale. You need both to define life. At the nanoscale (1-10nm) the activation energy for all types of energy are similar and thus conversion between thermal, electrical, chemical, and kinetic energies is facilitated making molecular machines, self-assembly and life possible. I think I am getting this correct. Very well written explanation of life’s thermodynamics. The description of kinesin-1 carrying a vesicle and walking down a microtubule track appearing to look like someone walking with their pants down around their ankles was humorous. If you think life can’t be explained by chemical and physical properties, this book will explain why you’re wrong.
March 22, 2017
Hm... don't even know what to think. It was interesting, but without clearly expressed one subject. Or rather expression of it in just a few sentences wasn't enough for me. OK, I clearly understand the concept that people are rarely interested in complex things and as a consequence don't see how evolution (or anything) works (as I'm saying in these cases =you can't get the information [edge] when being in the game), but explaining it in one sentence "if you thought about it..." does nothing. On the other hand, I should admit I am not interested in explaining complex things for others either, so book was good for me just fro few sentences I didn't thought before. For ex., molecular evolution, when proteins seek low energy states. Years ago participated in World Community Grid, but didn't fully understood wtf is that low energy state.
October 30, 2020
Kitabın Türkçe başlığı biraz yanıltıcı olmuş. Ancak bunun dışında çok iyi bir kitap.
May 21, 2021
A thoroughly fascinating look at how life works, told in deep, gentle detail. We find that inside of us are tiny molecular machines pumping ions through cell walls, manufacturing proteins, moving muscles. After listening to this well written book I understand how life works at the molecular level. Life is no less miraculous for understanding this physical mechanism.
May 19, 2020
Life's ratchet
The first chapter deals with how scientists and philosophers went about reasoning the source of "living-ness" of living beings. From Aristotle's times to post-Renaissance, multiple hypotheses were proposed. Many involved the existence of a "vital force". The author introduces Lavoisier, Laplace and Helmholtz among others while narrating the various theories that were put forth to explain life.
The second chapter is dedicated to the nature of chance and statistics as a tool to nevertheless exploit the resulting uncertainty. There is a description of Gauss' contributions and the nature of the bell curve which for me personally is some sort of sacred symbol of the nature of our reality. "In the limit of large numbers, Pascal's triangle could be approximated by a formula describing a curve that looked like a bell. This bell curve, or normal distribution, is what Gauss found in errors of astronomical data." This then gives way to discussions on the contributions of chance to the origin of life. A number of thinkers are discussed. Johnson, Chardin and Monod.
There is discussion of Godfather Schrodinger's views on life and how amazingly accurate he had come to describe how heredity comes to be. He was however incorrect about one aspect. It is here that the author starts to put forth the thesis of the book. That life exists not in spite of the random chaotic thermal noise of the atoms and molecules, but because of it.
Thermodynamics emerges from the averaging and statistical analyses of the random motions of atoms and molecules. The tragic story of Boltzmann whose ideas were ahead of his time was quite sobering.
The concept of entropy has been wonderfully explained and it builds a really good foundation on which the book progresses to explain higher concepts. I was amazed at how the author explained the second law of thermodynamics. And at each step of his explanation he is careful to completely clarify all the impositions that need to be applied for the law to held, otherwise creationists would use some loophole to claim that life cannot emerge because of this second law. He in fact says that within cells, several proteins and other molecules are created spontaneously while entropy still increases. The stuff of life happens by maintaining a position quite close to this equilibrium and by harnessing the relentless molecular storm that surrounds it.
The author himself got into this exciting field as a physicist by being involved in the various tunneling microscopes that have helped demystify life since their invention. He gives an introduction about these and says that the nanoscale is a sweet spot between being affected by thermal motion and macroscopic forces.
Explanations of the physics and chemistry of everyday things like snowflakes, detergents and cheese were very entertaining and educational. This made me want to understand so many more chemicals that we take for granted every moment of our lives!
The book then covers how all these ideas come together to form life.
Simply phenomenal book and I am so glad that I back to reading some good science non-fiction after the Gene.
The first chapter deals with how scientists and philosophers went about reasoning the source of "living-ness" of living beings. From Aristotle's times to post-Renaissance, multiple hypotheses were proposed. Many involved the existence of a "vital force". The author introduces Lavoisier, Laplace and Helmholtz among others while narrating the various theories that were put forth to explain life.
The second chapter is dedicated to the nature of chance and statistics as a tool to nevertheless exploit the resulting uncertainty. There is a description of Gauss' contributions and the nature of the bell curve which for me personally is some sort of sacred symbol of the nature of our reality. "In the limit of large numbers, Pascal's triangle could be approximated by a formula describing a curve that looked like a bell. This bell curve, or normal distribution, is what Gauss found in errors of astronomical data." This then gives way to discussions on the contributions of chance to the origin of life. A number of thinkers are discussed. Johnson, Chardin and Monod.
There is discussion of Godfather Schrodinger's views on life and how amazingly accurate he had come to describe how heredity comes to be. He was however incorrect about one aspect. It is here that the author starts to put forth the thesis of the book. That life exists not in spite of the random chaotic thermal noise of the atoms and molecules, but because of it.
Thermodynamics emerges from the averaging and statistical analyses of the random motions of atoms and molecules. The tragic story of Boltzmann whose ideas were ahead of his time was quite sobering.
The concept of entropy has been wonderfully explained and it builds a really good foundation on which the book progresses to explain higher concepts. I was amazed at how the author explained the second law of thermodynamics. And at each step of his explanation he is careful to completely clarify all the impositions that need to be applied for the law to held, otherwise creationists would use some loophole to claim that life cannot emerge because of this second law. He in fact says that within cells, several proteins and other molecules are created spontaneously while entropy still increases. The stuff of life happens by maintaining a position quite close to this equilibrium and by harnessing the relentless molecular storm that surrounds it.
The author himself got into this exciting field as a physicist by being involved in the various tunneling microscopes that have helped demystify life since their invention. He gives an introduction about these and says that the nanoscale is a sweet spot between being affected by thermal motion and macroscopic forces.
Explanations of the physics and chemistry of everyday things like snowflakes, detergents and cheese were very entertaining and educational. This made me want to understand so many more chemicals that we take for granted every moment of our lives!
The book then covers how all these ideas come together to form life.
Simply phenomenal book and I am so glad that I back to reading some good science non-fiction after the Gene.
February 7, 2020
Aside from the amount of space the author devotes to science history, and how we got to where we are now (which in my opinion mostly helps to understand the huge amount of effort and difficulty that preceded major scientific advancements), the main point of the book is in the word 'ratchet', and specifically, in the 'reset mechanism', which is how molecular motors can extract energy out of chaos, and which explains away how the infamous Maxwell's demon, and biological systems, do not violate the 2nd law (Entropy).
There is an eerie feeling with a graph that he shows from Physics Today showing the correlation between spatial dimensions and transformation between different forms of energy, including thermal 'useless' energy, which shows that this is optimally accomplished at the nanoscale (10E-9m), i.e. molecular level, bonds breaking and forming, etc., which rings a bell as another Goldilocks principle, for Life itself ...
As Democritus said, everything is a fruit of Chance (chaos, noise, mutations, molecular storm) and Necessity (universal laws), so Life consists of tiny machines converting chaos into temporal and spatial dynamic processes.
Of course, this, or any other book, does not explain the WHYs, just the HOWs - the mechanisms..
An excellent book overall for the general public, but of course these concepts are difficult to grasp for anybody, due to the levels of complexity and depth of information. 3D graphic simulations really help, and there are some
on you tube, relevant to the book,such as a kinesin protein walking on a microtubule, and an actual AFM video of the same thing.. There's also a presentation by Peter on his book, but you won't understand much unless you read the book :)
There is an eerie feeling with a graph that he shows from Physics Today showing the correlation between spatial dimensions and transformation between different forms of energy, including thermal 'useless' energy, which shows that this is optimally accomplished at the nanoscale (10E-9m), i.e. molecular level, bonds breaking and forming, etc., which rings a bell as another Goldilocks principle, for Life itself ...
As Democritus said, everything is a fruit of Chance (chaos, noise, mutations, molecular storm) and Necessity (universal laws), so Life consists of tiny machines converting chaos into temporal and spatial dynamic processes.
Of course, this, or any other book, does not explain the WHYs, just the HOWs - the mechanisms..
An excellent book overall for the general public, but of course these concepts are difficult to grasp for anybody, due to the levels of complexity and depth of information. 3D graphic simulations really help, and there are some
on you tube, relevant to the book,such as a kinesin protein walking on a microtubule, and an actual AFM video of the same thing.. There's also a presentation by Peter on his book, but you won't understand much unless you read the book :)
August 29, 2018
I am thrumming with excitement in my cell biologist soul over this nano-scale synthesis of physics, chemistry, and molecular biology. This is 100% my jam, folks! Will it be yours? A little hard to say. I would call this “intermediate” level, in that you don’t have to be an expert as long as you aren’t put off by protein jargon and some math. This is definitely a scientist writing as opposed to a science journalist, but I still think it is accessible.
The topics fit so well with the discussions I had recently with my Dept Biology and Chemistry colleagues, talking about entropy and thermodynamics and how to accurately describe them for students. The later 1/3 was less novel for me (any of my students can tell you how excited I already am by ATP synthase and molecular motor proteins) but I did enjoy thinking about these marvels in light of the earlier technical discussions. Good explaining power for evolutionary biology, too.
I’ll put it this way: I liked this audiobook so much I am planning to buy it again IN HARDCOVER to sit in my office and perhaps lend out.
NB: If you do pick this up, please be advised, in a way the audiobook’s narrator was not, that the 5’ and 3’ ends of a nucleic acid molecule should be read as “5 prime” and “3 prime.” There is not a 5 inch and 3 inch side of a DNA molecule.
The topics fit so well with the discussions I had recently with my Dept Biology and Chemistry colleagues, talking about entropy and thermodynamics and how to accurately describe them for students. The later 1/3 was less novel for me (any of my students can tell you how excited I already am by ATP synthase and molecular motor proteins) but I did enjoy thinking about these marvels in light of the earlier technical discussions. Good explaining power for evolutionary biology, too.
I’ll put it this way: I liked this audiobook so much I am planning to buy it again IN HARDCOVER to sit in my office and perhaps lend out.
NB: If you do pick this up, please be advised, in a way the audiobook’s narrator was not, that the 5’ and 3’ ends of a nucleic acid molecule should be read as “5 prime” and “3 prime.” There is not a 5 inch and 3 inch side of a DNA molecule.
November 1, 2019
Peter Hoffman, who is the founder and director of Wayne State University's Biomedical Physics program has written a fascinating book on molecular machines and how they extract order from choas. Hoffmann reviews the ancient concepts of atomism and vitalism and shows the subsequent scientific history that reflects those debates. Hoffmann then reframes those debates as being between reductionism and emergence. Along the way we discover that complex order can indeed come from chaos, that molecular machines cannot form and do their work without entropy, and all without violating the second law of thermodynamics. Indeed such complexity in the form of evolution requires entropy. Life, it turns out, is a balance between chance and necessity. In light of these discussions Hoffmann shows that creationism and intelligent design are wrong in their approaches.
I highly recommend this book to anyone who's interested in biology, the interplay between biology and physics, molecular machines, and biological evolution.
I would also recommend this following video:
https://www.microsoft.com/en-us/resea...
I highly recommend this book to anyone who's interested in biology, the interplay between biology and physics, molecular machines, and biological evolution.
I would also recommend this following video:
https://www.microsoft.com/en-us/resea...
August 12, 2017
This is a modern day equivalent to Schrödinger's "What is Life?", although it substantiates on how life originated and obviously has more solid science. This is a book, about a physicist's journey through the history of how we defined life in antiquity, to how we define life in modern day science. This book is chalk full of information on how this definition has changed throughout the ages at first. Although, I felt like this book started out strong, that momentum slowly decreases overtime. I do not think he explained some of his reasoning to well, although I have a bachelor's in Molecular Biology I had trouble trying to understand some of the concepts he was putting forth. I eventually put the book down as the information presented builds on itself, and I felt like I missed to much already to catch up. However I plan on reading his suggested reading, and hopefully that will clear up a lot of the . Btw, if you are reading this and want to suggest a book that is in the same genre of this book I'm all ears. But as of now I felt like the author didn't not even try to explain his ideas in a way that a dilettante can understand, and honestly I would consider a textbook more comprehensible than this book.
June 29, 2020
This book sparked my interest in understanding biology. I had just a single class in high school on biology and it felt like just memorizing names of glands and organs. Everything felt like magic and nothing was explained (I'm more of a physics guy). Luckily, so is Hoffman. He explains the world of biology in a way I could wrap my head around. Nothing about biology seems like magic to me anymore - it's just really, really, incredibly complex.
March 29, 2021
Life is about molecular machines. This is the main idea of this book and it goes into significant details on this topic. But before it, the author gives us a historical context of a scientific search in undertanding life. This jump from science history to molecular biology of a physicist is a bit strange, but you get used to it in the end.
Interesting and a kind of unusual book that I liked a lot. Recommended!
Interesting and a kind of unusual book that I liked a lot. Recommended!
May 11, 2019
Fantastic book, describes the building blocks of the cell(mitochondria, nucleus, etc), their functions and how they are built, the proteins, dna and the other various structures in a cell. Starts off with the physics base needed to understand this (like entropy). All this in a clear and understandable language. No math needed, the book also uses a clear and easy to read language.
December 15, 2016
One of the most inspiring, clear, well structured and informative science books I have read.
It is a sensational introduction to the smilingly incompatible relationship between chaos, structure and function.
A fascinating read.
It is a sensational introduction to the smilingly incompatible relationship between chaos, structure and function.
A fascinating read.
July 11, 2017
Peter Hoffman writes very well, and conveys complex ideas in an understandable light. The ideas are conveyed with the appropriate excitement, and it is really fascinating to envision "walking" proteins, self-assembling machines, and atomic force microscopes.
November 23, 2019
One of the best science books I've read in years. Thought-provoking and awe-inspiring. When I hit one of the "wow" moments in the book, I just broke into a huge grin on the subway in the middle of the morning commute.
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