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The Emergence of Life: From Chemical Origins to Synthetic Biology (英語) ハードカバー – 2006/7/13
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The origin of life from inanimate matter has been the focus of much research for decades, both experimentally and philosophically. Luisi takes the reader through the consecutive stages from prebiotic chemistry to synthetic biology, uniquely combining both approaches. This book presents a systematic course discussing the successive stages of self-organisation, emergence, self-replication, autopoiesis, synthetic compartments and construction of cellular models, in order to demonstrate the spontaneous increase in complexity from inanimate matter to the first cellular life forms. A chapter is dedicated to each of these steps, using a number of synthetic and biological examples. With end-of-chapter review questions to aid reader comprehension, this book will appeal to graduate students and academics researching the origin of life and related areas such as evolutionary biology, biochemistry, molecular biology, biophysics and natural sciences.
Review of the hardback: 'Charting the successful development of life is certainly a fascinating challenge and one which Luisi addresses head on in this book from both a scientific and philosophical standpoint. … This comprehensive volume will particularly suit those students and academics who wish to delve further into early natural history, either out of an innate curiosity or a more professional approach to unravel one of the true mysteries of nature.' Chemistry & Industry
Review of the hardback: 'This work is a fresh and exciting new look at a now long-established field. Because it is so fascinating to read, it is a work that I feel deserves to be in every library of science.' Chemistry World
Review of the hardback: '… the reviewer recommends this book for specialists in Earth and life sciences.' Zentralblatt für Geologie und Paläontologie
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Therefore, as a result of its small scientific community, contrasted by its large public issue and demand, many books have been published on this topic, a wide range of which present chapters written by the same authors. The results is a great redundancy of information as well as scientific views. If you've read half a dozen books on the origin-of-life and you're looking for something fresher, more vibrant, which presents a new outlook on the subject, then stop looking, this is the book for you!
Pier Luigi Luisi is a chemist who has devoted his scientific carrier to this important question in modern biology. As author of over 400 peer-reviewed publications, he has covered a great deal of various approaches to the origin of life, as well as a multitude of other books on fields directly related to the subject, such as "Giant Vesicles" and "Self-Production of Supramolecular Structures" (also found in Amazon).
Luisi's "The Emergence of Life" is a systematic overview of the field, as seen from an insider. Each part of the big picture, from prebiotic soup to the minimal cell, is thoroughly divided into single chapters and given a critical review, each time carefully pointing out the weakness of our current ideas on the various steps of life evolving from matter. I think even a creationist could greatly benefit from this book as it will give him/her a large variety of arguments to criticize the "non-Intelligent Design approach" to the Origin of Life ;)
Each chapter ends with a few questions for the reader, many of which have a charming balance between philosophy and chemistry put into one sentence. For example, the first question in chapter 5 (which covers the topic of "Self-organization") is:
"Do you accept the idea that self-organization in prebiotic times was the main driving force for the formation of the first living cells? (If not, what would you add to the picture?)"
While his approach leads to more general philosophical problems, Luisi doesn't dodge these topics, rather, he deals with each and every one with great care, as in the case of the importance of the theory of autopoiesis in understanding consciousness (for the author's competance in this field, I would like to mention another book he has recently written: "Mind and Life: Discussions with the Dalai Lama on the Nature of Reality", which just received a positive review in Nature). While most of the book deals with serious chemical problems, philosophical topics are dealt with delicately and in a highly constructed manner, resulting in a book with both a wide range of scientific information as well as an extensive overview of the highly philosophical, ethical nature of this field.
Given this perspective, the book is quite critical of reductionist RNA-world accounts of the origin of life. While self-replicating RNA molecules might sound elegant, as Luisi puts it "in fact, we simply do not know how to make long polypeptides by prebiotic means". Luisi is more favorable towards 'compartmentalist' studies of synthetic biology that focus on micelles, liposomes, and vesicles in an attempt to create a 'minimal cell'. Much of the book is an overview of the research that has been done in this regard. It is full of references, and if you are not particularly keen on learning such details you might find it somewhat dry.
One criticism I had of the book is that it is almost too synthetic in perspective. At many times I got the sense that the argument reduced to what is easier in the lab is a better explanation for the origin of life. Personally, I am not all that interested in these early attempts to create proto-life in the laboratory, and am not convinced that they can tell us all that much concerning the enormous parameter space that must have been available during the Earth's history. Basically, I don't feel that I learned all that much about the origin of life, rather than that it is quite difficult and enormously contentious.
A second minor criticism I have of this book is that it doesn't really do a great job in incorporating fields like physics and information theory. To give just one example, Luisi references Schrodinger's famous book 'What is Life?' but doesn't really talk about the negentropy ('free energy') view of life. This is too bad, as it would have provided a natural bridge between the chemistry and the higher level concepts of autopoeisis. In fact, I will note that neuroscientist Karl Friston has been leading a revival of sorts of Schrodinger 'free energy' view, and it has some pretty clear similarities to the autopoeisis account. This book doesn't get into the physics quite enough for my tastes - for example, I found the chapter on emergence a little weak. However, there is no doubting that Luisi's speciality, synthetic biology, is extensively covered.
We have come along quite a bit since the Urey-Miller experiment and Oparin and now we currently face a complicated and sophisticated understanding of how hard it is for scientists (such as Biochemists and other Chemists) to synthesize fundamental life. This work brings the reader up to date with detailed and technical information from research papers that have been formerly published from all over the world. The Human Genome project and wider studies in Genomics, the rise of Proteomics and Epigentics, along with the ENCODE project which have all added to the real sophistication found in living organisms, by orders of magnitude.
As such, life emerging is definitely no simple matter (life emerged once on Earth - no microfossils of the earliest life forms from 4 billion years ago have ever been found with alternate biochemistries such as non-DNA genetic material, non-carbon based materials). The fact that earth is 35% Iron, 30% Oxygen, 15% Silicon, 10% Magnesium, and 10% all other 80+ elements (including Carbon) adds to the sophistication since Silicon (which has similar properties to Carbon) is way more abundant than Carbon, yet Carbon is what living matter is made from. On top of this, nature seems to posit many biochemical impedance that are pretty important to take into consideration. For example, all chemical reactions and chemical properties and physical properties are influenced or directly affected by changes/effects of: Temperature, Pressure, Density, Viscosity, Thermodynamic Stability (i.e. Gibbs Free Energy considerations), Dilution, Concentration, Purity and Purification processes like Distillation, By-Products, Cross-Contamination, Environmental Contamination, Acidity/Basicity, Chirality, Hydrophobicity/Hydrophilicity, Agitation, Polarity/Nonpolarity, Limiting Reactants (reactions are limited by the molarity of one given reactant), Steric Hindrance (big molecules rotating fast blocking reactants from reacting, thus reaction rates slow down), Vapor/Liquid Equilibria (if these two phases coexist in a given environment), Miscibility/Immiscibility, Crystallization, Diffusion, Oxidation/Reduction, Solubility, Reversibility of chemical reactions, Activation Energies, Entropy, Emergent physical and chemical properties of molecules, Decay, and many other factors.
It gets more sophisticated by the fact that there is research indicating that the 20 amino acid set that life uses is fine tuned and is among the most optimal for exploring chemical space to make life when compared to the potency of random sets of amino acids (Ilardo M, Meringer M, Freeland S, Rasulev B, Cleaves HJ. Extraordinarily adaptive properties of the genetically encoded amino acids. Scientific Reports. 2015. Mar 24;5:9414).
Low entropy (high order and low dissociation) and high energy input from an outside source are two basic necessities for elevate a chemical residue to become "biotic", functional, and autonomous. The prebiotic chemical system that develops to a biotic system, must not be like a general chemical residues which can dissociate, decompose, denature, and break down back to its original components. In other words, chemical irreversibility is necessary for a successful early biotic entity that emerges from prebiotic chemistry. Decomposition of biotic entities is the enemy of every living cell - death. Surely the first life was Built Ford Tough to last and not get annihilated and it was sophisticated too (self-sustainable, energy processing processes, had interdependent parts and systems, was autonomous, had multiple autoregulated and automated processes [control systems] such as self-replicating process, had a development program which required preprogrammed information).
One important point is that the universe is null, void, and has no teleology in and of itself. Just like the common abstracted use of "life" in common language, "nature" should not be treated as if it has notable, reducible, or personified "characteristics" like when people say "nature finds a way to preserve life" or "life finds a way to survive". The natural universe, inherently, has no goals, no aims, no direction, no awareness, no prudence, no capacity to make intrinsic "advancements" nor can it ever detect such a thing, has no control of multiple variables (temperatures, pressures, concentrations. etc.), and no information. It only has regularities and coincidences. If we assume that a sophisticated entity such as a protocell emerged from scratch in the absence of prudence, without the existence of any supervision, then surely after 4.5 billion years of time and chance, some other entity as dynamic as a cell or less that is self assembling, self sustaining, auto-regulating with interdependent parts/systems, with control systems in place, self modifying capacity, and self reproducing capacity (perhaps something like a "primitive" circuit) would have emerged by now from scratch also somewhere at some time. Presumably the emergence of such an alternate entity from scratch would be readily observable today or in the fossil record, in some significant sense. Chance has had many chances already - 4.5 billion years worth. If, with this massive amount of time, cells are the only dynamic entities, by orders of magnitude, that have emerged from scratch compared to all other entities in the natural universe (planets, volcanoes, thunderstorms, rock formations, stars, etc) and nothing else has emerged that even that is even 10% of the compartmentalized sophistication of a cell then it does make one wonder how the first cell could have ever emerged in the first place and why the cell is the only thing in nature ever found that actually has a capacity to adapt, expand, self regulate, and evolve.
Even after +200 years of observing overwhelming abundance of hydrocarbons (more than 20,000 according to BP and Chevron when they gave a talk to our Chemical Engineering classes) in oil from oil fields around the world and rich biochemical residues that have existed for presumably hundreds of millions of years in isolation with literally millions of opportunities to spawn life, we still don't have much at all. Even with our current atmospheric conditions (though probably different from early earth), many organic and biochemical compounds can and do reach stability (amino acids, enzymes, etc) and are used extensively in industry so spawning of *some* independent cellular machinery (proteins, enzymes, etc.) is possible even today, but even in the wild we do not find independent construction of at least some semi-sophisticated cellular machinery. Independent early prebiotic chemical precursors to life, or even cellular machinery, have not been seen or detected on geological strata either. At least, this book will help people see the difficulties on the emergence of life on earth. You'll see what I am talking about. This book will give insights to the limits and capacity of inorganic nature and chance.
Luisi's "Why this...and not that?" approach puts the difficulties and solutions into perspective on the plausible and implausible ways life arose. He also provides many interesting questions for the reader to reflect on at the ends of each chapter. This makes this book more neutral to many controversial issues.
Here is a detailed look by Chapter on stuff that is mentioned and detailed in this text:
Ch 1: Discourse on creationism and science; two main views on the emergence of life: Contingency and Determinism; diverse views on multiple origins of life at many locations and multiple times (11); comments on SETI (Search for Extraterrestrial Intelligence) Institute and panspermia, the Anthropic Principle; it is good to keep a little open door to natural theology, but there are boundaries to keep in mind (13)
Ch 2: Discourse on the difficulties of defining life everywhere as "Darwinian" (22); Intrinsic vs Operational descriptions; more than 30 different models of Origins of Life have been generated thus far (26); popular textbook cliche - 'RNA emerging out of some prebiotic or primordial soup' - lacks evidence and is naive according to Luisi (28); problems in generating RNA; Clay Deposits may have functioned as storage for needed chemical products found in life forms; impedances and improbabilities of prebiotic metabolism (30-40);
Ch 3: Discourse on the Oparin-Miller Soup and the Urey-Miller Experiment; 40,000 tons of stardust settling on Earth per year (47); Polycyclic aromatics found in the Cosmos, hydrocarbons make 10% of Cosmic Carbon, C8's detected in space, what is not found in space: peptides and mononucleotides, chemical extraction from meteorites is difficult (49); why alpha-amino acids formed in the Urey-Miller Experiment 52); chirality (D or L) of amino acids may be nonfunctional for life
Ch 4: Discourse on benefits of enzymes and proteins being long chained entities, proteins and nucleic acids as complementary co-polymers, reaction rates have not been done for amino acids, the problem of peptides as being insoluble and having thermodynamic constraints, weak point of prebiotic chemistry is the weak "prebiotic activation" where activation energy is usually not satisfied to proceed without aid to reaction; chemical reactions for long chain polymers are done on clays since long chain polymers are impeded in reactivity in water (problems of hydrolysis 59-62); volcanic gas (COS) can form some polypeptides, but not long chain peptides with many residues (65); both polynucleotide and polypeptide research is young and self-replicating nucleotides have not been achieved (67); prebiotic pathways for both polypeptides and polynucleotides have not emerged, De Duve's "Sequence Paradox" is mentioned on the sequence order precision that is difficult to acquire with short polypeptide sequences, and why some proteins never formed or did not survive after forming (68-72); he also tried to make light on the frequency of folding that occurs in random sequences of proteins, a model is posited for elongation sequences (72-76); co-oligopepetides and co-oligonucleotides of 30 residues have been produced in "honest" prebiotic conditions, but have not been characterized (83); how probiotc RNA forming (as seen in many textbooks today) is a naïve look at origins of life according to Luisi
Ch 5: Important distinction between "self-assembly" and "self-organization"; discourse on crystallization and surfactant aggregation (surface mixing); interactions under thermodynamic (spontaneous = "free energy change") control and kinetic (non-spontaneous) control
Ch 6: "Emergence" is defined; emergent properties: "the whole is more than the sum of the parts"( Ex: the properties of H20 are not found in H2 or O2 individually); emergent properties in music, geometry, and macro evolution; discourse on reductionism, deducibility, and predictability; Life is seen as an emergent property
Ch 7: Subtle differences between "self-replication" and "self-reproduction"; importance of finding autocatalytic processes that replicate as they reproduce; myths of self-replication (132-133); self-replicating "enzyme-free" systems (134-143); DNA can only replicate with the help of many enzymes, not by itself (134); section on self-reproducing micelles and vesicles (143-152)
Ch 8: "Autopoiesis" defined; discourse on "internal" reproductive systems by the system reproducing itself within the system itself; "auto regulating" processes and "cognition" interactions and "consciousness" ; "enactions" as a process of adaption of environment and at the same time having co-emergence from within the organism.
Ch 9: Surfactant aggregated chemistry and relevant hindrances and occurrences of mixing; micelle compartmentation; solubilation in reverse micellar solutions; prebiotic membranes (non-phospholipids) are hard to generate from basic lipids and fatty acids by meteorites; materials for membrane generation; vesicular structure formation discussed
Ch 10: All about vesicle formation, reproduction, and chemistry; examples of enzyme-catalyzed reactions that have occurred inside lipid vesicles; vesicle competition
Ch 11: Early cells may resemble the simplest cells found today: "Mycoplasma genitalia" and "Buchnera" that have genomes with less than 500 coding regions (244); also there a plausible approach, "roadmap", to making a minimal cell and some requirements needed to generate a minimal cell
Overlook: Here Luisi concludes with his personal view of the Origins of Life and what he thinks can and cannot be achieved theoretically and empirically.
Overall, bravo for Pier Luisi.
For those looking to research the topic further from technical standpoints please look at the Journal:
"Origins of Life and Evolution of Biospheres" where research on this topic may be found. Luisi referenced this Journal many times in the book.
Or look at Life in the Universe: Expectations and Constraints (Advances in Astrobiology and Biogeophysics) by Louis Neal Irwin where the possibility or impossibility life on other planets are discussed in detail. The chemistry of each planet is radically diverse and most planets cannot form life due to their chemical compositions and lack of flexibility in chemical bonds with other non-carbon based compounds. Also read Chemical Evolution and the Origin of Life by Horst Rauchfuss for more on the Origins of Life topic including the diversity of early life. Information Theory is also being applied to biology and the origins of life. Check out Information Theory, Evolution, and The Origin of Life by Hubert P. Yockey and Probability's Nature and Nature's Probability : A Call to Scientific Integrity by Donald E. Johnson for more on Information Theory and the origins of life.
The Minimal Cell: The Biophysics of Cell Compartment and the Origin of Cell Functionality is an interesting read on the likely minimal requirements needed for a cell.
An excellent textbook of the structure, dynamics, and functions of cells (what they do and how they work) is Molecular Biology of the Cell.
For those who want a cheap, lay reader, but technical introduction to the machinery of cells without sacrificing some of the scientific rigor see The Machinery of Life. It sees the cell as nanotechnology - which is exactly what it is. Humans have 200 cell types so there are lots of technology, processes, and equipment to be found. For instance, thousands of reactions can occur in a cell at the same time because of the specificity of enzymes and molecular recognition capacity (26); cells constantly repair themselves without disturbing the ongoing processes of living using limited resources and generating equipment from scratch (30) - a powerful feat of engineering; antibody genes are constantly shuffled daily to create new fine-tuned antibodies (proteins) to attack new infections (35); cells wield many types of energy - chemical, electrochemical, physical motion, light absorption/emission, electron flow (42); ATP synthase is a molecule-sized generator that converts electrochemical energy (stored energy) into chemical energy - has 2 rotary motors connected by an axle (47); transport across cell membranes sometimes involve various equipment like "pumps" (48); several hundred diverse bacterial species live in out gut (67) - some estimate go up to 1,000 species; our own cells generate 30,000 proteins (19); out body is made up of 10 trillion cells that are more complex than bacterial cells (71,83) - however an updated estimate is 37 trillion cells as of 2013; red blood cells are created from stem cells in bone marrow and they carry oxygen fro 4 months (94); blood clotting mechanisms are precise and heavily regulated to heal wounds or ruptured tissue (97-99); all instructions for building a human start in one fertilized egg cell (84); adrenaline (epinephrine) is a hormone (a message carrier to cells) made in the kidney that carries messages that tell cells to focus on energy production (100); programmed cell death (apoptosis) is a systematic activity that could be toxic and messy if it weren't for the mechanisms in cells (109,117); cancer is uncontrolled cellular growth. No wonder cellular research is growing ever more complex rather than simpler as time goes on.
Life emerged 4 billion years ago. About 500 million years were needed for the first life to pop up - might as well look into how it could have happened rigorously. Recent genetic discoveries have led to insights on the emergence of modern humans - which narrows down to one person, a female "Mitochondrial Eve" and one man between 100,000-200,000 years ago.
On a side note on concepts floating around:
From technical books such as this, it is clear why there is ambiguity that there are no intelligent designers (conscious entities like extraterrestrials (panspermia, SETI Institute), cosmic engineers, spirits or even deities, etc). It seems at least one Conscious Biochemist or Engineer would have had to have been involved in the process of generating and synthesizing life indefinitely because of the delicacy and precision needed in generating biochemical machinery from scratch. Information theory makes this almost necessary. Look at Information Theory of Molecular Systems by R. F. Nalewajski, for example, at signals and communication in chemical terms in biology. Thinking of the cell in terms of systems engineering will also be useful since the cell is a complex chemical system with a life cycle (Systems Engineering and Analysis (5th Edition) (Prentice Hall International Series in Industrial & Systems Engineering)). After all there are massive similitudes between nature-made entities and human-made entities. No need to worry that theories of Cosmic Biochemist(s) like the divine or alien life will stop or halt any further science or research, though. Many examples exist from history such as Newton on mechanics, optics,and calculus; Francis Bacon's and his synthesis for the "scientific method(s)"; Hippocrates and his practice of medicine; Pythagoras' geometry and harmonies in music; Lord Kelvin's absolute thermometric scale and the rest of his labors on the age of the earth and physics; Gibbs, Planck, and Joule's work on Thermodynamics; Ibn-Sina and surgery; Mendel's research on genetics via hybridization of peas; Jean-Baptiste Lamarck and the first modern Evolutionary Theory; Carl Linnaeus' foundational work on taxonomic classification of plants and animal species; Robert Boyle's research on "Ideal" gases and elements and chemical analysis; Faraday and Maxwell's work on electromagnetic theory, etc.
Teleological theories that infer some sort of supervision does not result in the "God-of-the-gaps" fallacy as many scientists blindly assume. Historically, scientists from the ancient, medieval, and even modern periods did infer Universal Designers for creating life on other planets and they never stopped at "some powerful being did it and that's the end of that". One can see the complex scientific discourses from historical primary sources found in:
The Extraterrestrial Life Debate, Antiquity to 1915: A Source Book Edited by Michael J. Crowe
General teleological logic is good because it assumes that many things can be done and systematically solved or reconstructed (reverse engineering or retrosynthesis) - we just need to look for the right natural pathways and conditions needed start up a given system (retracing trains of thought). Since designers always use nature as a tool to make and sustain any given design, then agency explanations and natural explanations should not be seen as mutually exclusive. Some scientists generally commit the "Chance-of-the-gaps" fallacy where chance is the explanation given for some phenomenon that "cannot" be explained or falls short in their overall models. "Chance" is a funky word that really means "ignorance" when fellow scientists use it as an explanation for anything. The sciences do not provide 100% certainty in their understandings, but they do not provide 100% uncertainty either so I don't think there is a need to appeal to chance as often in order to avoid dealing with other possible options. One day life will be recreated in laboratory from scratch. That is guaranteed, in my opinion. But the irony, once this does occur, will be that supervision was used to do it. It is likley the only way to do it since 1) no "ponds" of complex cellular machinery forming from scratch have ever been detected anywhere nor have residues of complex cellular machinery been observed at other times in strata and 2) intelligent agents (researchers in origin of life) have been known to actively control multiple chemical variables and generate cellular machinery from scratch. They can replicate many environmental conditions in their labs.
It should be noted that ALL designs are imperfect designs by default in the universe because all things that are engineered (including by humans) can never be designed to last forever since this is not possible under a finite universe with finite but complex chemical parameters and environmental interactions. Clearly designed objects like computers, cars, and ancient artifacts are susceptible to oxidation, fractures, corrosion, friction, and breakdowns through time but one can still tell that these entities emerged in part from teleology. Of course, optimized engineering by default never results in "perfect" designs for the reasons above.
Decide for yourselves.