Fiziğin Ötesinde Bir Dünya : Yaşamın Ortaya Çıkışı ve Evrimi

by Stuart A. Kauffman, Murat Havzalı (Translator)

Yaşam nasıl başladı? Yaşamın evrimi, fiziktekine benzer yasalarla açıklanabilir mi? Santa Fe Enstitüsü’nde karmaşık sistemler araştırmacısı olarak yaptığı çalışmalarındaki fikirleri ilerleten Stuart Kauffman son kitabında karmaşık kimyası olan bir ortamdan moleküler çoğalmaya, metabolizma ile erken ön-hücrelere ve tanıdığımız yaşama olan evrime ilişkin fizik yasalarının sağlayabileceğinin ötesinde bir açıklama sunuyor. Yaşamın evrimi bilinen evrende var olduğu öngörülen yüz milyar güneş sisteminde kuşkusuz yaygın olmalı. Bu evrim, her örnekte birer “oluş” süreci. Newton’dan bu yana gerçekliği değerlendirmek üzere fiziğe başvuruyoruz. Ancak tek başına fizik, nereden geldiğimizi, nasıl geldiğimizi ve dünyamızın neden tek hücreli organizmaların ötesine geçip son derece karmaşık bir biyosfere evrimleştiğini açıklayamıyor.

Kauffman’a göre canlı sistemlerin ayırt edici özelliği, şimdiye dek yapılan çalışmalarda yeterince ağırlık verilmeyen “örgüt¬lenme” kavramıdır. Hücreler, kendilerini inşa eden öz-yaratım sistemleridir. Evrim, filizlenen bu örgütlenmenin yayılmasını sağlar. Evrimleşen canlı yaratıklar, var olarak, daha da yeni yaratıkların ortaya çıkabileceği yeni nişler yaratır. Evrendeki yaşam, kendi kendini inşa eden, yayılan, artan bu çeşitlilik, tüm biyosferlerde bizi fiziğin ötesine götürür.

“Kauffman, yaşamın doğasını gözler önüne seriyor.” -Scientific American

“Yaşamın en ilkel biçiminin nasıl ortaya çıktığını ve karmaşık organizmalara nasıl evrimleştiğini harika bir şekilde özetliyor.” -Philip Anderson, Nobel Fizik Ödüllü, Princeton Üniversitesi

Genres: Science, Nonfiction, Biology, Physics, Evolution, Philosophy, Audiobook

139 pages, Paperback

First published January 1, 2019

About the author

Stuart Alan Kauffman (28 September 1939) is an American theoretical biologist and complex systems researcher concerning the origin of life on Earth. He is best known for arguing that the complexity of biological systems and organisms might result as much from self-organization and far-from-equilibrium dynamics as from Darwinian natural selection, as well as for applying models of Boolean networks to simplified genetic circuits.

Reviews

[Charlene · Rating 4 out of 5]

This is an important book to read. I disagree with so much of what Kauffman said in this book but, imo, this subject matter is among the most important topics a scientist can study right now. The most intriguing idea to come out of this book and this lecture

https://vimeo.com/246871926

is the idea that first life might have been the result of a phase transition that led to an autocatalytic set. That is to say, whatever process built the first protocell was able to act as catalyst to build its own structure and keep necessary energy cycling in that structure, enough energy to remain alive, repair itself, and replicate itself. 

What is great about this book is Kauffman's focus on the Erdos Renyi Button Thread Phase Transition in which nodes(n) are connected to edges(e). When e/n =0.5 it "passes a threshold where small connected clusters merge into a a giant component of the graph." Kauffman suspected back in the 1970s that molecules could follow this very model for phase transition, where smaller sections end up catalyzing the whole cell so that it can replicate. Interestingly, he was told by some famous biologist not to study something so unimportant. He never mentions the person by name, but it was really great to include this story in the book because moving important scientific ideas along is often a difficult process, which is good because there should be enough debate and fact checking to make sure we are not moving forward toward something scientifically unsound but not so much "debate" that is serves to heavily obstruct progress on an idea that has not yet been falsified. So, I really applaud Kauffman for many things; his gifted story telling ability, his passion that screams at the reader from every single page, his persistence in trying to work out the problem of life (I really dislike calling it "the hard problem of life," as so many people associated with the type of research call it), and his ability and willingness to carefully explain the steps a person needs to take to understand how an autocatalytic set could give rise to first life. In the lecture I posted, he repeated himself a bit when trying to explain, only because it's a difficult concept to convey, but if you read the book, he does a much better job of spelling it out. If you are unfamiliar with constraint closure, Kauffman provided a nice primer in this book. 

Basically, you have 3 non equilibrium processes. and none of them does any work unless they are constrained. The first constraint releases the energy that makes the second constraint, which constrains the second process, which makes the third constraint, which constrains the 3rd process, which makes the first constraint--> Thus it can replicate itself.
Here is a helpful paper on autocatalytic sets

https://www.ncbi.nlm.nih.gov/pmc/arti...

This article puts it even more succinctly than Kauffman's book and lecture. "Simply put, an autocatalytic set is a set of molecules that mutually catalyze each other’s formation through chemical reactions from a basic food source". If you think about this in terms of the laws of thermodynamics for an open system, the protocell takes in a nutrient, uses the energy from that nutrient to remain active and create a product that activates/catalyzes another part of the cell. 

Kauffman explained that if you add together the simple food source with constraint closure, *in which the molecules will not do work unless they are constrained* -- and when constrained, they do the work of building the next structure in the system, then you have a system that built itself and kept itself supplied with the necessary energy needed to remain active and to replicate. When thinking about a system that could generate and cycle this much energy, one that forms a loop of connectedness that keeps cycling that energy, it was hard not to think of Erwin Schrodinger,'s definition of life  in which a piece of matter goes on cycling energy "for a much longer period than we would expect an inanimate piece of matter to 'keep going' under similar circumstance'."

Clearly Kauffman is still working all of this out as he continues to write about it, as are most scientists working in this emerging field.  Kauffman wondered if David Deamer's hypothesis of first life might be the best explanation of how the first protocells might have arisen from an Erdos Renyi Thread Button Model and from Montevil-Mossio's constraint closure. For example, little protocells sitting in hydrothermal fields get dehydrated and rehydrated (spelled out by Deamer in his papers and books. I recommend his newest book Assembling Life). Kauffman thinks this, and not an RNA World, can give rise to cells that are themselves a system constructed of  constraint closure in which molecules build and catalyze the next structure in the system. Through the dehydration and hydration cycles, more of the system is built until it builds a whole system that can sustain itself and replicate. 

Kauffman's criticism of what he calls the lipid world (as opposed to the RNA world) is that the lipid world can only account for the container (the membrane) but not the insides. I think this is only partly true. Metabolism first (lipid world) researchers are trying to figure out how the molecules of life ended up inside a cell. Their guesses are certainly as good as Kauffman's. Curiously, and to my chagrin, Kauffman merely glossed over what an autocatalytic set might look like at hydrothermal vents. He barely even mentioned the vents as a hypothesis. There was so much information about the RNA world, which he thinks implausible and I agree, and so much information about Deamer's hydrothermal fields, but not a word about all that free energy bubbling up from the hydrothermal fields! I mean, it's an embarrassment of riches down there at the white smokers. We already know the black smokers provided too much energy. That much energy would surely kill anything that tried to form into fragile life. But, where is the energy cut off? What is the amount of free energy needed to build but not destroy life? How could there be no discussion of this? It should have been at least covered. 

Kauffman was strangely vocal about Sutherland's RNA world  and Deamer's hydrothermal field hypotheses but absolutely silent on what most researchers call the most plausible scenario, which is Russell, Martin, and Lane's hydrothermal vents (white smokers, not black). So, my brain was left to obsess about this day and night, constantly trying to work out what the energy bubbling up from the vents might look like for building an autocatalytic set. When I read Nick Lane's papers in the past, I was very interested in the physical process by which the container (cell membranes) and the contents inside (all the things that help the cell cycle enough energy to remain active, to repair, and to replicate). Nick lane took great pain to think about how the contents might have evolved/assembled. Very briefly, Lane suggested the rocky protocells were stuck to the pores in the rock (naturally cell shaped). They were unable to make their own channels, and thus could not ingest and cycle energy on their own, without help from the rocks themselves. So, they used the rocks (brilliant) to act as a membrane, generating energy just as cells generate ATP. Over time, they used the energy supplied by the vents to evolve their own  channels (this info is explained so beautifully in Lane's 2012 paper, The Origin of Membrane Bioenergetics. this paper and its illustrations are so beautiful that a print out of them is hanging on my bedroom wall and I had an illustration turned into an iPhone case because I just love it so damned much!!!). But, no matter how much I loved reading Lane's papers, I didn't do so with closure constraint in mind. I didn't read the papers with Erdos Renyi phase transitions in mind. So, I was hoping for at least some discussion of this in Kauffman's books or lecture. You might think it is just a preference for me that Kauffman include hydrothermal vents in his book, but it goes far beyond personal preference. First life at hydrothermal vents is not a fringe hypothesis is dwarfed by Deamer or RNA World hypotheses. Rather, it is the most prominent theory of first life because even if the vents themselves were not where life assembled, it *accounts for the free energy needed to break bonds, free the elements needed to assemble life, and sustain the life of these first protocells. So why no discussion? If you are frustrated like me, you can start with the paper I referenced above. You can also read or reread Lane's 2012 and 2013 papers on bioenergetics with Erdos Renyi, constraint closure, and autocatalytic sets in mind. 

http://nick-lane.net/wp-content/uploa...

I can see areas in which Lane and Kauffman differ, and differ a lot, but Kauffman also differed quite a bit with the RNA world researchers. So why not include anyone working on vents? Before hydrothermal fields, Deamer worked on vents but chose black smokers because that was a reasonable place to look before it was clear that any life assembled would have been destroyed by that amount of energy. 

If Kauffman had been interested in defining life as a quantitative process, and not interested in the way the first cell assembled, then fine, ignoring hydrothermal vents would be a logical choice. When Sara Imari Walker was asked about Jermey England's work, she said she was skeptical about non-equilibrium approaches to life because she thinks it is that plus something else. If Kauffman also believed this, and thought this across the board, that would explain the exclusion of vents. However, the fact that he thinks Deamer's answer to first life aligns with what he is working out, clearly indicates that he thinks non-equilibrium hypotheses can be the answer, when fitted into his framework.He is very upset that Steven Weinberg's suggestion that the universe or life itself is a machine. But if vents or fields built procells-- even if they fit perfectly into Erdos Renyi phase transitions and  Montevil-Mossio's constraint closure, then they are a thermodynamic machine and that machine, even if you cannot predict its outcome from starting conditions is indeed not "beyond physics" as the title suggests. 

Kauffman's need for meaning really drove his thought process. I see this as a huge handicap. In the lecture posted at the beginning of this review, Kauffman doesn't talk so much about meaning, but the book is filled with impassioned discussions about how, if the universe is merely a machine like Steven Weinberg suggests, then the universe and everything in it lack meaning. This is where Kauffman and I part ways. If the universe is a thermodynamic machine (and it is because it has been heading from hot, dense, and fast to cooler, spread out, and will eventually slow down and stop), and if that thermodynamic process leads to the generation of forms ( and it does because the laws of thermodynamics help create all the forms that cycle energy-- including earth and the biological life atop it) and the thermodynamic process leads to the generation of complexity (and it does because it is the thermodynamic process that created more and more complex matter out of energy), then that complex machine -- a physical machine-- does create meaning. It doesn't take away the meaning. 

Kauffman is stuck on the fact that it would take longer than the universe has existed to make all possible proteins. So of all the permutations of proteins, why do things like hearts or tangerines exist?  Since the universe made all possible arrangements of atoms but not of proteins, the universe is non ergodic. If they there are so many possibilities for proteins, then we cannot put to equations to why certain proteins exist and others do not. Since we cannot predict and since we cannot put equations to this process, this process of the emerged heart-- or emergence of any chosen form-- is "beyond physics". I certainly cannot say why, out of all the possible things that could have been made, a heart was made. I actually love thinking about this question. One thing I can say is that we simply do not know enough right not to determine if this process is or is not "beyond physics". I think about how many genes are in the human body and think about the problem of predicting which genes will be expressed and which genes will not. Since we have trouble predicting things like this, we could say that the process is beyond physics. (maybe we guess it's an emergent property or assign some other guess). Along comes a scientist one day and they learn about the master switches. Suddenly we humans come to understand that gene switches are skilled at telling the same genes to do different things. For example, boney fish, humans, and bats all have the same genes that control bone growth. The switch tells the genes, "on, on, on, off" and bam! you have a fin. If the switch tells the genes to turn "on, on, on, off, on, on, off," or whatever, then you get an arm and hand on a human. A different set of instructions will churn out a bat wing. We still can't say why of all the structures, these things were made from the molecules forged in stars  and the explosions of stars, but what is clear is that things that seem beyond our knowledge-- beyond biology, beyond physics, beyond reason-- are slowly figured out by our slow but constantly curious human brains. It seems far too early to say that these processes, of which we know so little, are beyond physics. 

The rest of my review can be found in the comments because it exceeded the character limit.

[Morgan Blackledge · Rating 5 out of 5]

Stuart Kauffman observes that physics often accounts for what is, without accounting for how it got that way.

And how it got that way is actually really really important to account for.

Particularly when you’re talking about the origins of life.

Kauffman posits that life originated as an autocatalytic process, where by each stage enabled the next.

Kauffman argues that in a dead universe, nothing matters. But as soon as something depended on something else for existence, then that something else “mattered” to that something.

And mattering matters.

Kauffman asserts that the language of physics is mathematics, but mathematics can’t actually describe mattering in any kind of useful or meaningful way.

And as soon as you have mattering and enabling, you are in a world beyond physics.

You’re in a world of agency, adaptation and emergence.

Kauffman is a very idiosyncratic thinker and writer.

In fact he’s a total wild man.

The book is short.

It’s very thought provoking.

Full of brilliant energy.

I loved it.

[Rama Rao · Rating 4 out of 5]

The Cosmic Song: Life, matter, energy, order and non-equilibrium thermodynamics

How did matter (non-life), a non-machine-like existence turned into a living cell (life) 3.8 billion years ago? Living cells are "machines" that construct and assemble their own working parts. The emergence of such systems, the origin of life was due to spontaneous phase transition that allowed self-organization in complex prebiotic systems. The protocells were capable of Darwin's heritable variation, hence open-ended evolution by natural selection. Evolution propagates this organization. Evolving living creatures, by existing, create new niches into which yet further new creatures can emerge. Biological evolution is un-predictable, and it has its own growing and subtends to economically possible solutions it is presented with by nature. In this respect living cell operates like the economic web, which is also un-predictable but grows with economic opportunities. There are parallels between biological evolution and evolution of the economy. There are no mathematical models for a predictable evolution, and reductionism which is at the heart of modern science fails to explain the “wholeness” of structure and organization of a biological cell that no one can build. It turns out that life’ is not an objective property of creation, but it’s a very special case made on this planet!

Economics creates our world; it creates wealth, technology and our way of living. Researchers at the Santa Fe Institute in New Mexico where the author is affiliated with have been pursuing a revolution in science and economics. Ignoring the boundaries of disciplines, they are searching for novel fundamental ideas, theories, and practices that integrates a full range of scientific inquiries that will help us understand the complexities of reality. Much of the order and self-building of living cells are being understood by non-equilibrium thermodynamics and negentropy (also referred by terms such as negative entropy or anti-entropy) and phase transitions in early pre-biotic systems rich with a wide varieties of biomolecules.

This is a small book of only 168 pages that reads quickly. It is well described and easy to follow. However, the author proposes that we need new physics to explain the oddities of a living cell: This may be far-fetched!

[AlexBlokhuis · Rating 2 out of 5]

It is quick, concise, with an interesting style to it. It makes difficult concepts more intuitive and elegant. This would normally lead me to give 4 to 5 stars.

Intellectually, I find that the book could use some nuance, be more precise and be a bit more balanced in the representation of the work of authors (e.g. Hume and Dawkins). Most importantly, there are some glaring problems with the discussions on thermodynamics.

The field of nonequilibrium thermodynamics and stochastic thermodynamics has dramatically matured over the last decades. Kaufmann cites some concepts from a popular equilibrium thermodynamics textbook, and then argues how to build on that. Superficially, it leads to frequent misuse of terms like ‘work’ and properties of the second law, although some ideas remain valid and get across.

It is asserted that, regarding some nonequilibrium questions, ‘we really do not know’. A solution is suggested to come from a recent paper in theoretical biology. By presenting himself as an expert, the author is implying the last 40 years of developments in nonequilibrium thermodynamics have not happened. For a book that so heavily relies on thermodynamic concepts, this is a problem that cannot be ignored.

The book makes an interesting, thought-provoking point concerning the limits of physics. It is unfortunate that it mischaracterizes what physicists know. I hope these shortcomings will be addressed in future work.

[Otto Lehto · Rating 4 out of 5]

Brevity matters. You don't need a thousand pages when you write in dense poetry. Kauffman's short book is an accessible and stylistic account of how complexity evolves into self-replicating molecules and ultimately life forms. It serves as a good introduction to complexity biology and to some of the best theories of the biochemical origins of evolution. The short addenda on economics and economic growth are also worthy additions to the overall story because they help 1) to elucidate the interdisciplinary nature of evolutionary thinking and 2) to explain Kauffman's concept of the "adjacent possible" as the constant birthing of new niches and new opportunities.

At the same time, his account has some holes (as well as "Kantian wholes") that make it question begging or idiosyncratic at times. His forays into philosophy are rather crude. He applies Kantian terminology with insufficient justification and he harps on about how Hume was wrong about ethics when he clearly has not understood him. As a result, his functionalist account of purposefulness and "aboutness" leaves something to be desired. In a way, his account of intentionality is the mirror opposite of a "mechanist" like Alex Rosenberg's in The Atheist's Guide to Reality: Enjoying Life without Illusions. The way Kauffman opposes the theory of emergence to the mechanistic worldview of Newton and Laplace is misplaced since it ignores the possibility - I would say likelihood - that emergence is the result of epistemic ignorance. Perhaps we simply do not (yet) have the means of predicting the emergence of novelty. Perhaps a hidden computational process of deterministic complexity underlies all perceived "novelty"?

Overall, despite its lingering problems, I rather liked this book. Kauffman has a knack for simplifying complex matters by translating technical matters into (mostly) understandable prose/poetry. The narrative is concise, beautiful, and full of intuitive examples. His account of how self-escalating evolution emerged from simple beginnings to complex outcomes is speculative but probably close to the truth. Whether the story he provides is true in the particulars it is likely to be true in its broad outlines. Beyond biology, in economics and sociology, he provides an explanation of how the emergence of new niches and creative opportunities (what he calls the emergence of the "adjacent possible") provides endless creative opportunities for diversification. As self-propelling agents we are the children of self-replicating molecules that are destined to evolve and become the self-conscious agents of this evolution: playing "God" since "God" (Nature) gave us that power.

[Peter Gelfan · Rating 5 out of 5]

Is the universe deterministic? Does everything that happens, from the orbits of planets to what you had for breakfast today, stem inevitably from the laws of physics acting on the universe’s initial conditions in invariable lockstep to the end of time? Yes, many would say. It’s a perennial debate. Often this question provokes another: does nothing exist except energy and matter? Materialists say, Right, that’s all. Dualists argue there’s a nonmaterial side to existence, the realm of mind, ideas, spirit, perhaps gods. Free will is up for grabs.

Kauffman takes a different approach. He sets out to prove that the physical universe, at least once life came into existence, is not ruled exclusively by physics. Life forms and our collective evolution are sufficiently complex that future states are impossible to predict from existing states—not because we haven’t yet developed the math, but because the playing field and rules of the game keep shifting. Life not only changes but also, in so doing, changes the environment in which other life forms live, die, or come into existence. To make the process even less predictable, only a minuscule fraction of what could have evolved has evolved, with pure happenstance playing a major role in each step. With that burgeoning, runaway noncomputability, we life forms have left physics and its equations far behind. He briefly speculates on the future of the universe. If there’s life on Earth, it stands to reason that it has arisen elsewhere else as well. What if life, including intelligent life, spreads and evolves throughout the universe?

Kauffman does a good job explaining—of proving—this assertion on two levels. First, he makes the general ideas lucid for any reader. Then he presents hard, scientific arguments for how, specifically, this could have come about: how chemicals could have, and almost certainly would have, randomly come together to form tiny systems that engage in self-organization, reproduction, and evolution. He doesn’t get into arguing about dualism. For scientists, his idea is perhaps even more radical, for he calls into question an assumption intrinsic to much science: that physics is the master key to understanding the universe.

Fastidious readers, please don’t be put off by Kauffman’s writing style: his linguistic flourishes, his exclamation points that swarm like flagellates in a warm pond, his moss-like repetition that creeps into cracks. He nevertheless makes his points clearly, and this book is far too interesting and important.

[Old Man JP · Rating 5 out of 5]

There are several mysteries in science that fascinate me and one of them is the question "what is life?". What makes something alive? When an organism dies what is the difference that occurs that makes it dead because, after all, it is still composed of exactly the same molecules that were present when it was alive. Kauffman's book doesn't really answer these questions but he does bring up several fascinating findings that seem to show that science is coming closer to answers. One of the points that Kauffman makes in the book regards the second law of thermodynamics and how life does not seem to conform to this key principle of physics. Life seems to operate in a completely opposite manner than the law dictates and it is very obvious when you think about it. Only when an organism dies does it go from organization and order into disorganization and decay. To my mind life seems to be connected to the second law as its opposite, like matter and anti-matter.
Much of what Kauffman discusses in the book is about how life may have emerged in a slow step-by-step process from non-living material into something that is recognizable as living. It is a fascinating book and is at times almost beyond the grasp of a non-scientist such as myself but still a wonderful read.

[Jurgen Appelo · Rating 4 out of 5]

I skimmed the molecular biology sections but appreciated the broader message. Emergence brings upward enablement and diversity breeds diversity. But I think we knew that already.

[Vivek Patil · Rating 4 out of 5]

It seems that there are two schools of (scientific) thought when it comes to exploring the origin of life on the earth. One school dominated by theoretical physicists insists that there is no special force that aids the transformation of non-living entities into living species. Everything can be explained by random events with this school of thoughts. The other school of thought, which is less explored than the former one, is dominated by biologists such as Kauffman. They insist that the 'random events' need 'constraints' to go from highly disorganized matter to a living cell. In this book, Kauffman builds on this theory and points out that the creation of these 'constraints', in turn, needs the entities that can only be created in the first place with those constraints.

Probably, this book can fit well as a prologue to Darwin's theory of evolution.

P.S. I just noticed that the cover of this book is strikingly similar to Sean Carroll's 'The Big Picture'. Does anyone know the story behind this?

[Heather-Lin · Rating 4 out of 5]

I truly understood maybe 10%, but I found it fascinating. The thesis that describing life must go beyond physics, beyond mathematics, beyond a machine model is utterly compelling. Furthermore I found the creative, cooperative, opportunistic model of evolving life presented here to be incredibly exciting and compelling.

[Bart · Rating 4 out of 5]

Fascinating idea. Often-clunky read.

[Pooja Kashyap · Rating 3 out of 5]

Stuart Alan Kauffman is not only a complex-systems researcher but he is also a polymath, with a degree in medicine and training in biochemistry, genetics, physics, philosophy and other fields. Very deftly he roams across disciplinary boundaries looking for answers to the riddles that obsess him. In, A World Beyond Physics, he takes up the conundrum of life’s origin.

Boldly Kauffman, in this book, tags the ‘machine theory of the world’ as insufficient. According to which, the world comprises of physical objects that are interacting with each other as per mathematical laws. Early pioneers of this theory were Descartes, Newton, and Laplace.

The theory puts forth two main principles:
1) any macroscopic phenomenon can be directly related to microphysical causes.
2) with enough information regarding position and momenta of particles (along with physical laws) it is very much possible to determine the future trajectory, that is, position as well as momentum of that particle.

This theory according to Kauffman is not complete because it fails to account for the living world. For instance, why do animals have heart? Molecular structure of hearts can never lead us to know why do animals have this organ in the first place.

Therefore, the need is to route the explanatory arrow upwards. Instead of saying that heart exists because it is the result of molecules in action, the appropriate explanation would be – for efficient circulation of blood, which’ll result high chance of survival of organisms, animals have heart.

Kauffman rebuts the second argument of machine theory by saying that for particles, in a closed physical system, the world could be deterministic but biological evolution cannot be determined in advance, take for instance, exaptation.

More from my blog post: A World Beyond Physics by Stuart A. Kauffman

[Daniel · Rating 3 out of 5]

How did life start? Kauffman has a proposal:

1. Lipids form bilayer micelles, able to form an ‘in’-side as against the outside
2. 200 millions ago volcanic hot vents cause waves of hot inorganic stuff to be layered upon rocks, and then dehydration. That is supposed to put stuff inside the micelles, forming proto-cells. He acknowledged that this is building order from disorder. What is to prevent those stuff from being washed out from the proto-cell?
3. Well autocatalysis came to the rescue. Proteins have been shown to catalyse another protein which in turn can catalyse the original protein. Once this is established, they can presumptively self-propagate, supporting the proto-cell which can then develop into real cells by simple evolution. Of course this does not explain how RNA/DNA came into the picture, why genetic material resides in the nucleus, etc.

To develop order from disorder goes against the second law of thermodynamics; as such it is not easy to suggest how life started. In the end, some sort of external input and limitation is necessary. Kauffman makes it sound easy and logical, but to believe thus does take a lot of faith.

[Jiliac · Rating 4 out of 5]

I'm very conflicted on how to rate this book. On the one hand, the content is extremely interesting. Some (foundational) parts of it are very recent (~2015). On the other hand, while the substance is good, the form makes it rough to read. I felt it was it a lot more messy than some of the other books written by academics for a large audience I have read. The author writing could also clearly use a little more modesty. There are several "he is wrong and I'm right" that I found could have been smoother without loss of clarity. That said, it is clear the author has made some effort to make the content accessible, and with some focus, it is understandable. The book is very short.

That's said, I'd still recommend it to anyone interested on emergence (but not as a first introduction to the subject). What a better illustration to emergent process than life itself! I found the proposed hypothesis quite convincing. So, I "only" remove one star b/c I found the read a little rough but the content is very interesting.

[Paweł · Rating 3 out of 5]

Autor na wstępie odrzuca hipotezę panspermii kosmicznej - przez co zmuszony jest brnąć i komplikować wbrew brzytwie Okhama. Jest jakieś prawdopodobieństwo, że ma rację jednak brak tu elegancji. W paru miejscach dziwi mnie brak logiki. Jednak najgorsze dla mnie rozczarowanie nastąpiło po 90 stronach walki z dość abstrakcyjnymi pojęciami fizyki i matematyki (udawadniającymi powstanie życia od warstwy lipidów). Otóż w ostanim akapicie wywodu autor oznajmił, że zdaje sobie sprawę z problemu przejścia do życia opartego na DNA ale, hm, cóż...to się wyjaśni. Jakoś. No, kiedyś. Ja jakoś nie czuję się przekonany jednak może po prostu słaby aparat matematyczny nie pozwala mi tego ogarnąć. Natomiast poruszono sporo innych ciekawych aspektów, jak ewolucja gospodarki, matematyczne ujęcie definicji życia itp. Pozycja warta przeczytania jednak mojego życia nie odmieniła :)

[Franciszek Osiński · Rating 3 out of 5]

Książka ma ogromną wartość naukową i filozoficzną, jednak autor po pierwszych kilkunastu stronach fiksuje się na jednym zagadnieniu, niezbyt istotnym, i kontynuuje je przez kilkadziesiąt stron. Było to przygnębiające i zniechęcało do dalszego czytania, a szkoda, bo przemyślenia i metafory zawarte w tym dziele są pionierskie, unikatowe i niezwykle wartościowe dla każdego.

[Kuba ✌ · Rating 4 out of 5]

kauffman ma ciekawe spostrzeżenia dotyczące powstania życia. nawet jeżeli ktoś się z nim nie zgadza, to mimo wszystko warto przeczytać do końca. mi dał nowy ogląd na genezę życia na ziemii i była to bardzo rozwijająca książka pod względem ekspansywności przemyśleń na ten temat.

[Jacko Cabrera · Rating 2 out of 5]

Se me ha hecho bola.

[Jimi Olivo · Rating 5 out of 5]

At 168 pages or so, this is a short title, but don't let that discourage you. I am currently on my second read-through.

The concept of Constraint-Closure is one of those revolutionary ideas which will reverberate through every scientific field whether its implications about biology and the origin of life prove to be truthful or not. This is a useful thinking model to have access to no matter what field you're operating in. Economics, philosophy, even fiction-writing.

While the concept of autocatalysis has been around since the 1920s, I think we may be entering new territory, at least since Kaufmann's The Origins of Order: Self-Organization and Selection in Evolution (1993).

Note: I am not a scientist or an expert of any kind, just a guy who obsesses on collecting novel ideas, so take my opinion with a grain of your favorite trivializing cliche.

[J TC · Rating 5 out of 5]

Stuart A Kauffman - A World Beyond Physics
No seu livro “A World Beyond Physics” Stuart Kauffman sustenta que no mundo que conhecemos e a sua biosfera não pode ser descrita na diversidade e abundância com base nas leis da física. O mundo da física é um mundo ergódico, um mundo que esgotou as suas possibilidades de combinação. É um mundo que se descreve com duas dezenas de constantes e algumas leis básicas. É um mundo previsível, calculável, um mundo que se sabe de onde se vem e para onde se vai. A biologia não segue estas regras. A biologia existe num patamar Darwiniano, um mundo que pode se pode descrever na retrospetiva, mas cujo futuro nos reserva incógnitas. É um mundo de evolução imprevisível. Se à escala micro as leis da física parecem adequadas para o descrever nessa dimensão, o mesmo não se passa no mundo que vemos, nos rodeia e designamos de “vida”. O mundo não é uma máquina e as leis da física não explicam a vida. A vida emergiu do mundo da física, mas ao emergir deixou de ser regida exclusivamente pelas suas leis.
A vida emergiu do mundo da física e nem esta emergência era expectável (da análise de um rochedo não encontramos nenhuma pista de como desse rochedo se podiam formar protocélulas, bactérias, eucariócitos, e por aí a fora). Nem as leis da física descrevem como a vida emergiu, como funciona ou como pode evoluir.
Talvez a mais importante característica que reconhecemos no fenómeno vida advém do facto de ela ser regida por uma seleção natural, leis de Darwin. Contudo, estas leis fazem-nos luz de que forma a vida evoluiu, mas não nos indicam como surgiu e porque evoluiu. Uma pedra continua a ser uma pedra em tudo igual à primeira que surgiu, enquanto o mundo que dela emergiu perdeu esta imobilidade e adquiriu a possibilidade de evoluir.
Outro aspecto que caracteriza a vida e a distingue do mundo da física, advém do facto da biosfera ser formada por conjuntos que têm um objectivo sendo os seres vivos os agentes desse mesmo objectivo. É isso que caracteriza a vida. O mundo das partículas e dos átomos e das partículas não têm objectivos, nem são seus agentes (as rochas não fazem jogos!).
No livro “A World Beyond Physics”, Stuart A Kauffman propõe-nos um modelo para explicar de que forma foi possível ter emergido um ambiente químico favorável à organização mais complexas, i.e., com replicação molecular, metabolismo, protocélulas e outras formas de maior complexidade ainda, como às que chamamos de vida.
O principal obstáculo para a evolução assenta essencialmente na necessidade de organização, uma característica que para ser atingida tem de contornar a segunda lei da termodinâmica (2LTD).
A 2LTD é uma lei universal segundo a qual se prevê que sem gasto de energia, ou trabalho adicional, os sistemas tendem para um aumento de entropia e a uniformidade global. Ora vida é exactamente o oposto. Vida é um sistema de baixa entropia tanto pela organização que encerra como pela diversidade com que se manifesta.
Assim, a tese central do livro e do seu autor é fornecer-nos uma explicação de que forma um universo não reducionista e não teleonômico, poderia sem a participação de um criador inteligente evoluir de um mundo inorgânico de forma a permitir a emergência de uma biosfera. Qualquer tentativa de explicação que não recorra a conceitos mágicos, terá sempre de abordar de que forma a 2LTD pode ser contornada. Nesta explicação Kauffman remete-nos para o conceito de “constraint closure” (Mael Montévil and Mateo Rossi 2015) – um conceito de organização de sistemas e realização de trabalho, segundo o qual num sistema fechado a realização de um trabalho mediante a imposição de restrições que impeçam a diluição da energia, pode dessa forma contrariar 2LTD e permitir que a energia libertada seja canalizada na elaboração de novas restrições, e actividade autocatalítica.
Daqui resulta um trabalho em que há libertação de energia de forma condicionada, i.e., com vários graus de liberdade. Desta libertação resulta uma dada acção – um trabalho. Sem restrições não há trabalho. Sem restrições não há obstáculos ao aumento de entropia. As restrições permitem ultrapassar a 2ª lei da TD. Sem restrições não há trabalho, e frequentemente sem trabalho não há condições para haver restrições. A estas sequências chamam-se ciclos de restrição-trabalho. Restrições permitem que o trabalho possa ser realizado. Este trabalho vai promover novas restrições e as novas restrições originam novas condições de trabalho. Isto é direcionar as situações de desequilíbrio, é promover uma actividade autocatalítica (AC) e autopoiética (AP) que são característica de seres vivos. As máquinas produzem trabalho, mas não criam restrições que possibilitem novos trabalhos. As máquinas não são seres vivos.
Um trabalho efetuado nestas condições, i.e., num ambiente com restrições permite que a energia libertada seja investida na elaboração de novas restrições e dessa forma sejam criados desequilíbrios no sistema, uma condição indispensável para actividade autocatalítica e autopoiética se instale.
É destes ciclos de trabalho / desequilíbrio, que a evolução é permitida ao permitirem que novos agentes se instalem no desenrolar dos acontecimentos. É esta variação que segundo as leis de Darwin possibilita a evolução por permitir que um sistema com uma variação mais apropriada possa ter vantagem e por isso vingar em detrimento de outras menos adaptadas. Contudo, esta seleção é imprevisível. Olhando de trás para a frente não sabemos qual o caminho que a mesma vai seguir. Olhando-se em retrospetiva o caminho escolhido parecer-nos-á sempre miraculoso.
As espécies quando surgem e/ou evoluem criam condições para o aparecimento de outras espécies. Novas espécies ou variações de espécies já existentes podem encontrar as condições para evoluir, ou não. Mas o ciclo é sempre – são as novas condições que permitem novas oportunidades. Uma oportunidade quando preenchidas resulta numa modificação das condições existentes e no aparecimento de novas condições. Estas novas condições quando surgem permitem que novas variações a ocorrer tenham a oportunidade de ocupar um novo nicho. Não há teleonomia. Este ciclo repete-se e tende a ser exponencial tanto no número de unidades como na complexidade. Criam-se nichos, novas condições que agentes mais adaptados podem preencher, dando origem a novos nichos.
Segundo Kauffman são os ciclos de trabalho em ambientes restritos – Constraint Closure e thermodinamic work cycles de Montévil e Mossios que permitem ultrapassar a 2LTD.
Os sistemas vivos são assim autocatalíticos e autopoiéticos e são-no individualmente, mas também colectivamente. Ao surgirem aproveitam as condições existentes, mas ao ocuparem esses nichos também os modificam criando por isso novos desequilíbrios os quais permitem o aparecimento de potenciais novos ocupantes. Assim o conceito Kantiano de conjunto - no qual as partes existem para benefício do todo, não tendo nenhum significado quando colocadas isoladamente- parece ser apropriado, mas não é a única verdade uma vez que cada conjunto depende de outros para a sua própria subsistência.
Segundo Kauffman, a vida pode ser definida por propriedades autocatalíticas e autopoiéticas num ambiente restrito capaz de originar desequilíbrios e destes evolução. Mas como começou a vida é grande incógnita. Segundo o autor, a vida pode ter surgido em ambientes com restrições iniciais, que facilitaram um trabalho que foi capaz de induzir novos desequilíbrios e de com estes constituir um sistema que em si encerra essas mesmas capacidade AC e AP.
Assim, e de acordo com o autor a vida não emergiu simples e singela, mas múltipla e complexa com múltiplas redes de reacções a catalisarem-se entre si. A vida e o metabolismo resultaram e emergiram da diversidade. Esta diversidade pode estar subjacente ao holismo da vida. A vida é assim fundamentalmente uma interligação de processos de não-equilíbrio e as fronteiras de ambientes com restrições que permitem a libertação de energia em vários graus de liberdade contornando assim a 2LTD. O trabalho e tarefas assim desempenhado produzem peptídeos que são catalisadores de novas reacções e elementos de restrição às mesmas. Um sistema destes é uma “máquina”, mas não apenas de matéria, energia, entropia ou restrições, mas uma feliz combinação de tudo isto.
Mas há diferenças entre a reprodução de máquinas e em biologia. Enquanto as máquinas são capazes de construir cópias de si mesmas, em biologia as cópias não surgem dessa forma. Uma árvore produz sementes e as sementes através de sucessivos ciclos de trabalho levam à formação da árvore. No metabolismo as reacções não aparecem por magia. São necessários reagentes que tenham mais energia, e que esse adicional de energia seja utilizado para numa reacção de onde resulte mais desequilíbrio e novas possibilidades. O metabolismo é assim apenas orientação de energia. Não há finalidade é apenas isso.
Carl Woese mostrou-nos que eventualmente descendemos de uma célula primordial a LUCA, que se eventualmente se dividiu em dois ramos, um a dar origem ao das bactérias e um outros ao das arqueias e os organismos eucariotas. A descoberta de Woese, a das arqueias, veio depois a demonstrar que os eucariotas resultaram da junção de uma bactéria com uma arqueia. Há assim na história evolutiva pelo menos um exemplo de duas linhagens terem convergido para resultar numa nova linhagem. Mas provavelmente as convergências foram muito mais frequentes. Só que da nossa perspectiva, da do resultado fica difícil encontrar essas pistas. Muito provavelmente da “sopa inicial” resultou grande diversidade de protocélulas. O LUCA não foi uma entidade isolada, mas muitas. Somos assim resultado de uma grande diversidade inicial com múltiplas interações e eventuais trocas de capacidades metabólicas. Um florescer de vida que essencialmente era diversa, à escala microscópica e molecular, mas era um mundo em que o que dominava e era importante era a diversidade. E a vida de hoje é o resultado de várias convergências ou fenómenos de seleção. Da nossa perspectiva não é possível ver o que se extinguiu ou o que que convergiu.
Podemos caracterizar a vida por um – conjunto molecular autónomo, capaz de se reproduzir, num ciclo TD, mas tendo sempre um objectivo, optar pelo que é “bom para mim” – a “agency”. Este objectivo em que o agente é simultaneamente agente e objectivo, é seguramente precursor da consciência. Este sentir o mundo – bom ou mau para mim é precursor da sensibilidade. E os nossos objectivos são instrumentais e não morais.
Um importante conceito em biologia é que as características antecedem a função. Ou seja, uma dada característica pode existir, não ter expressão, mas se surgir a oportunidade para ela desempenhar uma qualquer função relevante ela passa a ser importante e passa a desempenhá-las. Não são os genes ou os nichos que determinam a evolução. O que a determina a evolução é o resultado da ocupação de um dado nicho por um dado agente. Ao efectuar esta ocupação o agente altera o nicho e com isso cria condições para que outros agentes possam entrar em cena, ou determinar a sua própria extinção. Neste contexto a evolução em biologia não pode ser reduzida a formulas matemáticas. Não há matemática que possa prever a evolução da vida. Há aproximações estatísticas que nos podem dar uma ideia para onde se caminha. Mas serão sempre probabilidade e nunca certezas. As evoluções permitem adaptações. Não causam adaptações. As evoluções não podem ser previstas. Porque quando ocorrem, modificam o contexto de forma que o que se previu deixa de ser válido. Não sabemos o que pode acontecer e muito menos o que vai acontecer.
A economia tem um comportamento muito semelhante ao observado na diversidade em biologia. Há 15.000 anos existiam, paus, pedras, fogo e caça. Pouco mais haveria. Esta rede de bens com valor económico evoluiu de forma muto semelhante à biodiversidade. Mas há uma diferença entre o mundo biológico e da economia. Enquanto em biologia a evolução precede a utilização, há muito mais tentativa, erro, na economia é a necessidade que gera a oferta, ou seja o nicho cria o agente. Ora nem sempre as ofertas são adaptadas às necessidades e à resiliência da rede. Surgem assim distensões que vão sendo resolvidas com inovações, necessidade de crescimento frequentemente com prejuízo da globalidade tanto da malha (económica) como do template em que se sustenta.
Desde que o homem olha as estrelas que sempre viu o cosmos com um todo em que os humanos, eram partes desse mesmo conjunto. Cumpriam-se assim as quatro causas aristotélicas: formal, final, eficiente e material. A igreja tinha também tinha esta visão do cosmos sendo que para a mesma as causas tinham uma origem divina que variava consoante os seus desígnios. Com a revolução de Newton e o demónio de Laplace as causas de Aristóteles passavam a ser regidas por leis, e a concepção religiosa passou a ver a intervenção de Deus não com um papel teísta, mas antes deísta (Deus já não poderia operar milagres). O mundo era uma máquina previsível, onde se conhecesse a posição de todas as partículas e o seu momento seria possível descrever o passado e o futuro com as mesmas leis. Este mundo seria reducionista. Mas o mundo não é uma máquina! A vida resulta da necessidade de se ter planos e se ser agente deles. É desta interação que surge a complexidade. Ter um objectivo e ser agente do mesmo é uma característica da vida. A bactéria importa-se se no meio há glucose e procura esse meio.
Quanto aos objectivos, considera o autor que há diferenças entre física e vida orgânica no que respeita a função. Diz o autor que o rio corre, mas isso não é uma função; que a borracha é elástica, mas que essa característica não é uma função no sentido em que reconhecemos funções a um órgão como o coração. Não estou de acordo porque mesmo parecendo que a função se confunde com característica (borracha), o que resulta dessas mesmas características é todo um conjunto que não surgiria se essas características não fossem exatamente as mesmas. Acho assim que no mundo macro, mesmo aquilo que é reconhecido como não vida influência a mesma vida. Emissão de gases co m efeito de estufa são bom exemplo. O fluxo de um rio pode não ser considerada uma função e ser apenas uma característica do mesmo. Talvez! Mas se o rio não fluísse isso modificava as caraterísticas que o tornam favorecedor de vida, não participava no ciclo da água, do carbonato de cálcio, toda uma série de ciclos (também eles autocatalíticos porque se alimentam a leles mesmos) e tão importantes são para a vida. Gaia no seu conjunto é ela também um organismo vivo! Para o autor na vida, a função de uma dada parte do todo resulta da sua utilidade para o todo. É o todo que aproveita a função e não uma acção deliberada da parte. Não há reducionismo na função. Eu não posso promover uma função e ter a certeza de como o conjunto reage. Pode seu útil, pode não ser!
Mas não são só os sistemas biológicos que têm capacidade de aproveitar estes desequilíbrios. Também os sistemas “não-vivos” tem a capacidade de o fazer. Os redemoinhos e as Bernard Cells – fluxos de transmissão de calos em superfícies planas; formação das correntes marítimas e alterações na pressão atmosférica. Mas a vida é mais do que fluxos de energia. A vida é AC e AP, e não é sustentável, é evolutiva. Dá-se a oportunidade para surgirem novas formas, e estas alteram o meio e o sistema. A vida não é sustentável é evolutiva!
Mas o que aqui se pretende enfatizar é que na evolução os desequilíbrios criados são geridos pelo conjunto, pelo sistema. É a relação entre inovação e sistema que vai ditar a sua adoção pelo sistema. E isto requere tempo para que haja interface e interação entre novidade e sistema. Só assim o sistema tem capacidade de promover o apropriado e permitir que o sistema se guie no sentido da complexificação. No mundo económico o crescimento, as inovações e os desequilíbrios do sistema funcionam apenas para fomentar novos desequilíbrios, novas oportunidades, sempre no âmbito da economia, não dando oportunidade para o sistema se adaptar, aceitando ou rejeitando o que foi o objecto do crescimento. E isto acontece porque para os economistas o sistema é o sistema económico, a malha da actividade económica, e não reconhecem claramente que qualquer actividade que exercem têm repercussões a montante (disponibilidade de recursos), colaterais (efeitos sobre a biosfera e ecossistemas) e a jusante (resíduos). Não dando tempo a que estes sistemas se adaptem adequadamente à actividade económica e à sua deriva de crescimento contínuo e em crescendo, a actividade económica assemelha-se mais à actividade de células tumorais que crescem exponencialmente, invadem e destroem as estruturas adjacentes sem respeitar a integridade das mesmas. E só por isso determinam a sua própria insustentabilidade.

[Science and Fiction · Rating 4 out of 5]

From the beginning four-page prologue I thought this would be an easy-breezy bit of comfort food suitable for reading before bedtime. But once Chapter One got underway I was wide awake, my synapses firing at full capacity. Kauffman presents an essentially new theory on the emergence of life, and along the way challenges respected scientists like Stephen Weinberg, Richard Dawkins, and Pythagoras. And when I say challenge, I don’t mean a few pot shots here and there. No, Kauffman is going for the knockout punch! There are also some minor corrections to assumptions that Darwin made. This is a book with some very bold assertions! But seemingly backed up by valid evidence.

A major point of the book is that we cannot cite (or ‘prestate’) with deterministic laws, axioms, or mathematical models the specific evolution of the biosphere. This is something that always bothered me about the reductionist approach, that if we could only probe far enough down to the Planck Level we would understand how consciousness emerges from the elemental particles. Since we can’t probe that far, and are not likely to have the technology to do so for the next millennium, this has given philosophers and theologians an invitation to follow Plato’s bad example in the belief that anything can be reasoned and understood if we only think hard enough. So, I was actually quite elated that Kauffman presents a very compelling argument for exactly how life, agency, and self-awareness arose.

Kauffman asks: “How since the Big Bang did the universe get from matter to mattering? What must a physical system be to be an agent – a doer – able to act on its own behalf?” As he explains, there is a “selective advantage of being able to sense one’s world, the presence of food, the presence of poison.” The tactile sense of pain evolved so as to warn of potential danger to the organism, beyond it normal efficient functioning. Then, “once there is food and poison and simple food chains, the prey can mimic being poison to hide from the predator.” Sci-Fi fans take note: This level of agency without yet being self-aware is the concept behind the alien in biologist-author Peter Watts’ Blindsight.

A slight quibble with the book is that, for those of us not directly involved in experimental research, the middle section (chapters three through six) fall prey to Kauffman’s enthusiasm over every minor victory in the laboratory. For me it would have been sufficient to explain the nature of the experiment, say that numerous trials were conducted, and this was the result. I don’t need a blow-by-blow account. Now, I understand why he does this, because sure enough some colleagues or astute reviewers on Goodreads will say that he glossed over the evidence. But, for the average reader, three paragraphs are sufficient and then have a reference number (or hyper-link) to access further details in the index. I recently read a book with sixty pages (in very tiny print) of such information for those who want to go down the rabbit hole.

Anyway, the Prologue and first two chapters were great, and then again from Chapter Seven until the end I couldn’t put it down. There’s a concise and well-written chapter about heritable variation, there’s an entertaining “Interlude” where proto-organisms take on personalities, and there’s even an Epilogue about how this theory relates to global economics.

Given the direct attacks against esteemed evolutionary biologist Richard Dawkins I wondered if Dawkins had rebutted any of Kauffman’s barbs. A search online revealed that Dawkins is indeed very aware of Kauffman’s work. Essentially, Dawkins has some reservations about the modelling as concerns some of the more provocative claims, but on the whole remains intrigued by his work and has hailed Kauffman for the groundbreaking idea of self-organization as being a crucial part of evolution. I then followed up the book by watching an interview with Kauffman on the Closer to Truth podcast and didn’t perceive him as some wild-eyed quack but a serious researcher thoroughly informed and compelling in his ideas.

Biology and the life sciences are outside of my area of study, so I’m hesitant to give five stars, but I’m comfortable with four stars because, right or wrong, it’s been a few years since I’ve read such a thought-provoking new hypothesis. (Not since reading Lee Smolin’s Time Reborn on the nature of space-time.) If you have any interest in the origin of life - and by extension the origin of consciousness - you should check this book out!

[Lee Kuiper · Rating 5 out of 5]

In this fantastic and concise book Stuart Kauffman briefly explains that the world (namely, life) cannot be reduced merely to Physics. He opens up an exciting new space for thinking and scientific discovery.

Physics uses knowable variables to measure and predict outcomes. Picture a billiards/pool table: every possible position and movement of the balls can be predicted if you know the "phase space" which is to say the mass of each ball, the force of the ball being struck, the speed at which each ball moves, the angle/direction of the movement, the resistance/friction of the balls on the surface, and the edges/walls of the table. The reason life is "beyond Physics" is because Biology's phase space cannot be predicted. Unlike in Physics, some of the variables cannot be known (namely the boundary conditions) and, therefore, cannot be predicted.

Biology emerges from Physics but is not bound by the same constraints due to its constant bootstrapping, always building more order and complexity through various cycles and feedback loops, and expanding its boundaries of possibility. Life propagates organization, organization increases efficiency (by slowing the speed of entropy in local and ordered forms/systems), and that expands both complexity and the diversity of possibility. In short, life is always building more life and creating more possible ways to live; it cannot be predicted because it is constantly expanding its boundary conditions. Therefore, there is no possible way to come up with any equation/law regarding the movement or direction of life and evolution.

I found chapters 4-6 to be only tangentially related; dealing with possible origins of life scenarios at a molecular level. Unfortunately, it relied on a fair amount of explaining in terms of equations (my mind just doesn't think well in those terms) and requires a decent amount of knowledge of Molecular Biology (liposomes, peptides, amino acids, polymers, etc) to keep up with. The main idea behind these chapters is about the ability of self-contained feedback loops ("autocatalytic sets") and how they can happen in chemistry: begin to accumulate, remain stable, propagate, and ultimately form protocells... an important steps towards life.

It is self-evident that life builds order. But somehow even before life there is a building towards order. This is a key insight in the author's thinking and exploring. The origins of life are murky and unknown but Stuart Kauffman is a bright light exploring those murky unknowns. He continues his exploration in this book by combining his idea of "autocatalytic sets" with his idea of "the adjacent possible," walking the reader through millions of years on earth, from Chemistry, to Biochemistry, to Molecular biology, to Microbiology, to Physiology, to Ecology, and even to Technology. His conclusions should encourage us to think more deeply with the scientific lens of Complexity/emergence as opposed to the overly-used lens of Reductionism. Life cannot be reduced merely to Physics.

[Philemon - · Rating 3 out of 5]

Stuart Kauffman made a name for himself in his thirties as a main discoverer of autocatalytic sets, and later as a complexity theorist at the renowned and very hip Santa Fe Institute in the 1980s. His aim has been to show that complex structures arise spontaneously in nature and that everything above atomic level is explicable not by physics but as spontaneous creation roughly along autocatalytic lines. Thus everything has a naturalistic origin, such that, as an early book title of his proclaims, we are "At Home in the Universe." Thus there is putatively no need for "mysticism," either at the beginning or the end of the day.

Kauffman's claims have apparently not been borne out by mainstream prebiological research, and autocatalysis is not generally considered adequate to account for the processes leading up to the earliest living cells, including the emergence of complex folding proteins, replication, data correction, energy management, etc. In this book, at age seventy-eight, Kauffman tries to bolster his theory by applying the notion of "constraints," as developed by David Deamer, Bruce Damer, and others, in which autocatalytic reactions not only allow sets of chemicals to reproduce each other, but also to establish and maintain bottlenecks and other types of resistance to encapsulate and give shape (and Kauffman would even add, purpose) to ongoing, self-perpetuating chemical processes. Adding these constraints to autocatalysis produces an engine capable of powering any stage of evolution, the book strongly implies.

Has Kauffman successfully banished what he calls "mysticism," as this book repeatedly claims? Even if his theory could account for the first cells, which appears to be unlikely, we're left with other mysteries of origin, such as the rise of consciousness, which Kauffman scarcely mentions, if at all. He seems to prefer not to widen the field of his argument to include larger-scale cosmological concerns or quantum effects that could have bearing on questions of origin.

Our ignorance, one might argue to all this, is so not easily ignored or waved away. Despite all the grandeur of scientific achievement, humans finally have no way even to estimate how ignorant we collectively are. Our ignorance could be truly vast, even boundless. In the light, or darkness, of that ignorance, we will always and continually brush up against the "mystical," whether we like it or not. The scientific method should probably accept recognition of our immeasurable collective unknowing as part of its process.

[Kevin Prinoski · Rating 4 out of 5]

“A World Beyond Physics: The Emergence and Evolution of Life” (2019) discusses chemical mechanisms that likely led to the spontaneous formation of metabolic pathways and protocells - the precursors of cells and organisms. Using physics as a starting point, the author explains the chemical and mathematical basis of his speculations with reference to existing experimental evidence. Specific additional experiments to gain further confirmation are also mentioned. Kauffman can be regarded as a kind of molecular Darwin. Evolution was posited by Darwin from the perspective of whole organisms. Kauffman, on the other hand, looks at evolution from the perspective of biochemistry leading to required molecules, self-sustaining metabolic pathways, and the first protocells. These were the precursors that led to the development of single and multi-cellular biological organisms. Kauffman is brilliant. Only once previously have I read a book so brief that said so much - only 139 pages, excluding references and index. However, being a brilliant scientist is no guarantee of being an effective communicator of that science to the general public. Therein lies the rub. This book was intended to simplify complex scientific concepts for the general public. It does not. The first two-thirds of this book will be very difficult for anyone to understand without having previously taken an introductory university course in biochemistry. An introductory course each of genetics and cell biology would also be helpful. Surprisingly, the author abruptly changes tack in the last third of the book which is very clearly written and easily understood. Overall, though, this book is more suited as required reading in a university science undergraduate program than it is for the general public who will struggle with some of the concepts. The author also draws interesting conceptual parallels between evolution and niches in biology and those in the economies of goods and services. This is a fascinating book for those with at least a modest formal background in the requisite sciences previously mentioned.

[Lefterisbax · Rating 2 out of 5]

Nothing is beyond Physics

I wanted to like Kaufman and the book, Emergence theory is fascinating, almost bringing back the notions of 'magic' and 'miracles' into the realm of Science. But when he says biology cannot be explained by physics, he lost me.. Biology is chemistry, and chemistry is hydrogen bonds and electrons exchange..
Just because it's too complicated and inconceivable for the human mind to keep track of billions of electrons jumping around at a given instance, does not mean it's not happening.
Reductionism, and I hate to admit that, is alive and well, our limited mind is the problem in comprehending above certain numbers.
The pool table example, with its bounding walls, (used as an example in the book for Newtonian style predictability), has equivalents in biology and the Universe. Auto-catalysts and metabolism do their job because of electrical gradients, proton pumps, electron orbits and quantum energies. The Universe would not exist if any of the bounding 20+ universal constants were slightly different...
That there are so many more combinatorial possibilities in biology, yes, but it is not an open ended system, they always have to play by, and obey, the rules of physics, the universal bounds.

[Stefan · Rating 4 out of 5]

A short book (still I feel could be a bit shorter with good editing) introducing concepts like the "nonergodic world," where complex systems like life cannot explore all possible states within a reasonable timeframe, autocatalytic sets (life emerged from chemical systems capable of self-replication), the idea of "constraint closure," where living systems construct their own constraints and self-organize, arguing that Newtonian, mechanical theory isn't enough to explain life, which requires looking at biological contexts and upward causation, finally getting a bit philosophical on becoming and a process in which life continuously evolves and creates new niches for further evolution.. All good food for the brain, and Kauffman got me on "machinez le truc, trucez le machine" (never herd that elsewhere) and arguing that where laws don't work it's all random, whilst provisorical solutions and emergence needs to be admired for life these created.
On chaos I'm still read a bit more to cast my vote, but I got a sense from other reviews that despite arguing against there is still some reductionisms going on here.. However, it's on so high level and the book is so reach in ideas that's it's definitely worthy these few hours it takes to read.

[Sid · Rating 4 out of 5]

I can't claim to understand everything that has been laid out in this book.

However, this book has introduced some interesting concepts which I was not aware of, one of the more important ones being protocells & constraint closure. Although many scientists point to protocells that's one of the key mysteries in life's origins, a functional protocell has not yet been achieved in a laboratory setting. And only by harnessing energy faster than it disperses through entropy does life arise, multiply and diversify. This in the face 2nd law of thermodynamics, which states that entropy can only increase.

Also, that as diverse as the earth and the universe may be, only the smallest fraction of possible complex molecules ever came into existence (or discovered I presume). And unlike physics, their laws hold sway, no laws at all entail The becoming of the biosphere. No one knows or can know what shall become as the biosphere evolves and shapes its own future in ways we cannot state in advance.

I will probably forget a lot of what I read in this book, but I will keep an eye out for further literature or videos from the author.

[Christopher G. Moore · Rating 4 out of 5]

Why is physics so mathematically precise and biology so mathematically messy?

I found A World Beyond Physics compelling as a good guide to understanding the basic idea of how biological complexity functions. Kauffman demonstrates why messiness of biology sets it apart from physics. He also takes the reader through the process of how a handful of amino acids kick started the enterprise known as 'life'. His conclusion is that Life can't be reduced to physics.

Kauffman draws a distinction between what can be characterised as 'causation' based and that which enables an explosion of emergent, complex becomings. None of which we can anticipate in advance. Biology is a miracle of becomings. Those becomings don't honour the boundaries that contain physics.

Evolution is a complexity producing phenomena that organises ecosystems into biospheres. Further evolution is the handmaiden of entropy by using three closures: constraint, work cycle and catalytic closures harassing thermodynamic work which allow cells to construct themselves.

[John Cumming · Rating 4 out of 5]

After introducing how constraint closure and catalytic task closure contribute to reproduction within systems, the book heads into some hard going biological explanations. I’m reading this to think about organizational complexity and homeostasis - I’m not a biologist!

I emerged from the fog at the ‘Interlude’, a story of four protocells which was both entertaining and brought the remaining 30% or so of the book back to life for me.

Evolution of technology and the economy were covered and now I need to figure out how this all relates to organisational homeostasis.

Something about a stable constraint cycle ensuring entropy does not accelerate. The system stabilising as it grows - resulting in a resistance, maybe even a robustness in the face of change. But all species seem to grow and become too large to survive in a changing environment….

… I’ll keep steering into the fog!

[Phil · Rating 2 out of 5]

Stewart has the large and noble goal of exploring the origins of life, but he doesn’t pull it off here. His discussion of autocatalytic sets is interesting but his descriptions are harder to understand than Wikipedia’s. He claims to disprove Hume’s is-ought problem in two paragraphs, which had me rolling my eyes. I’m open to the idea of evolution working differently from Dawkin’s selfish gene framework, especially early in the development of life, but he doesn’t convince me of anything concrete in this book. It’s clear that Stewart is a smart guy that is willing to challenge widely held ideas. We need more of his kind. But this book had a wild rambling tone that really turned me off. And I didn’t find enough proof for some of his claims.