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The Emergence of Life: From Chemical Origins to Synthetic Biology

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The Emergence of Life by Pier Luigi Luisi is a thoughtful book. It is not a book where to find easy answers on how the life appeared on Earth. Rather, on the contrary. The author scholastic and erudition is impressive on subjects from fundamental physics and chemistry up to polictics and language. Luisi included topics as difficult to define as self-organization and emergence, not only in the biological and biochemical context, but also in social behaviour and economics, for example. The text is crystal-clear, based mostly on arguments from others, but also by the author's personal thinkings based on a life long scientific carreer (over 300 scientific publications), first at the ETH-Zurich (Switzerland) then at Rome 3 (Italy). The book is strongly based on scientific support and thoroughly referenced (over 500 scientific references, including papers of scientific journals and books), and includes an excellent subject index. Graphs and figures are of good support to understand the text. I really recommend it for readers interested on the non-trivial hypotheses of life arousal on Earth. A point (?): Luisi does not include any religious discussion in his book. I was very pleased with his well balanced way of thinking.

How could life emerge from unanimate matter? Despite the importance of this question and its broad public interest, the field of research in origin-of-life is relatively undermined in the scientific community. This field doesn't offer a promising carrier for a young scientist, mainly because of its slow development and the fact that it doesn't benefit from recent technical progress, as is the case with other fields,

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.

I found this book to be an excellent review of the scientific literature that relates to the chemistry of the origin of life. The author brings forth the concepts and the relevant experiments to those concepts. His diagrams and graphs are a great help towards understanding. I used it as a textbook this past year for an introductory course in which one has at least a college sophmore's knowledge of chemistry and biology. I will be using it again. The more valuable aspect for me was the review of the literature.

Pier Luisi has done an excellent job in bringing in many relevant viewpoints, methods of approach, and the current standing of Origins of Life research as of 2006. Not much has changed up to 2011. This book is aimed towards Biochemists, Physical Chemists, and Molecular Biologists, etc. but there are sections where a lay reader will understand easily.

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 (mainly 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. For this work, it is very much recommended for people to familiarize themselves a little with either Biochemistry, Organic Chemistry, Physical Chemistry, or Molecular Biology to get the most out of this technical book and to understand some of the significance of the information presented, for example, basic understanding of what chemical pathways are and concepts like hydrolysis would definitely help.

With the overwhelming abundance of hydrocarbons found in oil (more than 20,000 according to BP and Chevron when they gave a talk to our Chemical Engineering classes) and rich biochemical residues that have existed for presumably hundreds of millions of years in isolation with millions of opportunities to spawn life in these oil fields from all around the world, it sure feels pretty nonsensical that life could really from by nature alone since early prebiotic chemical precursors to life have never been found despite the interest in oil fields or other biochemically rich environments on earth, for more than a 200+ years. Life should have formed and should STILL be forming today (carbon atoms are very flexible under many conditions, but maybe they are too flexible to form anything as big as a cell without careful control), especially in places with abundance of biochemical materials such as hydrocarbons in oil fields, for example. Truly, life forming is a ridiculously rare event since it only happened once on this planet. Life hasn't been observed to spawn on its own by any scientist despite the rigorous search and attempts at prebiotic synthesis. If you want to see more on the difficulties of spawning life step into the biochemical universe of how to potentially generate simple life forms. You'll see what I am talking about more clearly. This book will give insights to the limits and capacity of Nature and Chance.

Life emerging is definitely no simple matter and nature seems to posit many biochemical impedances 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.

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.

Stuff like this makes for Origins of Life research so interesting and sophisticated.

Luisi's "Why this...and not that?" approach puts the difficulties and solutions into perspective on the plausible and implausible ways life arose.

Here is a detailed look by Chapter on stuff that is mentioned and detailed in this textbook:

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); SETI (Search for Extraterrestrial Intelligence)Institute, the Anthropic Principle

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 "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 function 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 (is 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) 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 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 and Probability's Nature and Nature's Probability : A Call to Scientific Integrity for more on Information Theory and the origins of life.

For a better look at the complex interactions in biology and sophisticated gene networks found in current cells please research "systems biology" to get an idea of interactions in a cell in:

"An Introduction to Systems Biology: Design Principles of Biological Circuits (Chapman & Hall/CRC Mathematical & Computational Biology)".

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.

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On a side note:

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 in generating biochemical machinery from scratch. Information theory makes this almost necessary. Look at Information Theory of Molecular Systems, for example, at signals and communication in chemical terms. No need to worry that theories of Cosmic Biochemist(s) like gods or extraterrestrials will stop or halt any further science or research, though. Many examples exist. Newton's theism didn't stop or impede his work on mechanics, optics,and calculus, nor did Francis Bacon's theism impede his synthesis for the "scientific method(s)", nor did Hippocrates views of gods impede his views of illnesses as having most origins in nature and not by the will of the gods nor did it affect his practice of medicine, nor did Pythagoras' theism impede his views on geometry and harmonies in music, nor did Lord Kelvin's theism impede his work on the absolute thermometric scale and the rest of his labors on the age of the earth and physics, nor did Gibbs', Planck's, and Joule's theism impede their work on Thermodynamics nor did Ibn-Sina's theism impede his research on how to do surgery and create surgical instruments in the Middle Ages, nor did Gregor Mendel's theism impede or substitute his research on genetics via hybridization of peas, nor did Jean-Baptiste Lamarck's view of God impede him from making the first modern Evolutionary Theory, nor did Carl Linnaeus' theism impede or substitute his foundational work on taxonomic classification of plants and animal species, nor did Robert Boyle's theism impede or substitute his research on "Ideal" gases and elements and chemical analysis, nor did Faraday's and Maxwell's theism impede their work on electromagnetic theory. One can see this is the case if one actually reads the very words these men and other giants wrote in their primary documents as is found even here A Sourcebook in Medieval Science (Source Books in the History of the Sciences). Scientific advancements go a long way even from ancient times.

Theories of conscious interference like Intelligent Design does not result in the "God-of-the-gaps" fallacy as many scientists blindly assume by their stereotypical and often unanalyzed and unverified views of historical scientists or the history of science. All of the previous theists and many more never stopped at "some powerful being did it and that's the end of that". They asked about how things were done and how could it have been initiated in the first place and tried to seek for explanations for these phenomena just like anyone else. If designers create, we can try to replicate that which was created since if it was done before, then we should be able to do it again (reverse engineering or retrosynthesis), technically.

This is the general designer logic, which is good because it assumes that many things can be done and systematically solved or reconstructed - we just need to look for the right pathways and conditions to start up a given system (retracing trains of thought). If anything, some scientists generally commit the "Chance-of-the-gaps" fallacy where chance is the best explanation given for some natural phenomenon that they themselves cannot explain 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.

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 chemical parameters and finite environmental interactions. Clearly engineered objects like computers and cars are susceptible to non-optimized designs, fractures, corrosion, friction, and breakdowns but one can still tell that these are engineered. Of course, optimized engineering by default never results in "perfect" designs because there are many finite interactions that interfere and affect the designed object at all times since no designed objects, at least by humans, exist in vacuums, especially not life forms.

Decide for yourselves.