Short works

Books : reviews

Alan S. Perelson, Stuart A. Kauffman, eds.
Molecular Evolution on Rugged Landscpaes: proteins, RNA and the immune systems.
Addison Wesley. 1991


Richard G. Palmer. Optimization on rugged landscape. 1991
C. Amitrano, L. Peleti, M. Saber. A spin-glass model of evolution. 1991
Daniel L. Stein. What can physics do for biology?. 1991
Peter Schuster. Optimization of RNA structures and properties. 1991
Herman N. Eisen. Affinity maturation: a retrospective view. 1991
C. Berek, M. Apel. Maturation through hypermutation and selection. 1991
Catherine A. Macken, Alan S. Perelson. Affinity maturation on rugged landscapes. 1991
Tim Manser. Maturation of the humoral immune response: a neo-Darwininan process?. 1991
Stuart A. Kauffman, Edward D. Weinberger. The NK model of rugged fitness landscapes and its application to maturation of the immune response. 1991
William V. Williams, Thomas Kieber-Emmons, David B. Weiner, Mark I. Greene. Use of antibodies as molecular mimics to probe intermolecular interaction landscapes. 1991
Gerard Weisbuch, Alan S. Perelson. Affinity maturation and learning in immune networks. 1991
Gregory W. Siskind. Auto-anti-idiotype and antigen as selective factors driving B-cell affinity maturation in the immune system. 1991
Richard G. Weinand. Somatic mutation and the antibody repetoire: a computational model of shape space. 1991
Wlodek Mandecki. Evolution of proteins from random sequences: a model for the protein sequence space and an experimental approach. 1991
Marshall S. Z. Horwitz, Dipak K. Dube, Lawrence A. Loeb. Studies in the evolution of biological activity from random sequences. 1991
Debra L. Robertson, Gerald F. Joyce. The catalytic potential of RNA. 1991
Peter Schuster. Dynamics of autocatalytic reaction networks. 1991

Stuart A. Kauffman.
The Origins of Order: self-organization and selection in evolution.
OUP. 1993

Stuart A. Kauffman.
At Home in the Universe: the search for laws of complexity.
Viking. 1995

rating : 2 : great stuff
review : 1 March 1996

Being a physicist by training, I understand reductionism -- it's a natural way for me to think. I've been reading about complexity and self-organisation for a while now. It's certainly saying something very important, but I've been struggling to fit its emergent, holistic approach into a scientific world with 'real' laws. After reading At Home in the Universe, I think I see that it might be possible.

We can never hope to predict the exact branchings of the tree of life, but we can uncover powerful laws that predict and explain their general shape.

I find the prose a bit purple in places, especially the introductory and concluding chapters. But in between there is an excellent discussion of the inevitability of spontaneous emergent self-organisation. The exposition is structured around several simple models used to 'train your intuition' about optimisation and evolution.

Networks in the regime near the edge of chaos --- this compromise between order and surprise --- appear best able to coordinate complex activities and best able to evolve as well.
Life ... is an emergent phenomenon arising as the molecular diversity of a prebiotic chemical system increases beyond a threshold of complexity. ... No vital force or extra substance is present in the emergent, self-reproducing whole.

p236. The size of the avalance is unrelated to the grain of sand that triggers it. The same tiny grain of sand may unleash a tiny avalanch or or the largest avalanch of the century. Big and little events can be triggered by the same kind of tiny cause. Poised systems need no massive mover to move massively.

Stuart A. Kauffman.
OUP. 2000

rating : 1 : unmissable
review : 3 June 2001

I have been reading this book slowly over the past few weeks. Slowly, because it is so densely full of new and wonderful insights that I needed time to absorb them, and slowly, because I simply didn't want it to finish. And now I have finished it, I have to review it. But how to review a book like this? It is so marvelously original and stunningly imaginative, and so full of profound ideas, that a short review cannot possibly hope to do it justice. Go and read it yourself.

In his previous book, At Home in the Universe, Kaufmann discusses spontaneous emergent self-organisation. Here he takes his ideas, I was going to say a step, but actually it is a giant leap, further forward, covering life, evolution, and the universe itself. And fortunately his prose style, although still slightly over-poetic in places for my personal taste, is a lot less purple than before.

He starts small, with a definition of life suitably broad enough for a general biology (that is, one not constrained merely to the contingent developments of life on earth).

An autonomous agent is a self-reproducing system able to perform at least one thermodynamic work cycle. ... An autonomous agent is a physical system ... that can act on its own behalf in an environment. ... I suspect that the concept of an autonomous agent ... defines life.

The quoted definition may look rather bald, but he discusses each of the aspects -- self reproducing autocatalytic systems, work, and work cycles, in fascinating detail. [But I do wonder if self-reproduction is a necessary condition for life -- maybe it is simply one possible mechanism?]

... work is the constrained release of energy. ... it typically takes work itself to construct the constraints on the release of energy that then constitutes work.

Chapter 2 comes as a bit of a shock after the readily readable chapter 1 -- it assumes rather more detailed biochemistry than I have -- but keep courage and keep reading -- there's lots of explanation, with lots of different examples.

There is a lot of discussion on how life is necessarily a non-equilibrium system, and how non-equilibrium systems can (self-)organise to do the work required for life.

In a nonequilibrium setting, measurements can be ... used to extract work from the measured system. ... only some features of a nonequilibrium system, if measured, reveal displacements from equilibrium from which work can, in principle, be extracted. ... there remains the issue of how the [agent] knows to measure those features rather than other useless features

We get discussions of systems building themselves recursively. To survive, systems like cells need to be close to, but on the stable side of, the edge of chaos, lest they lose their identity under the onslaught of novelty. They operate recursively, reaching some kind of 'fixed point', or attractor. Kauffman wonders if Category Theory, with the elements recursively constructing themselves, might be a suitable mathematical basis for these systems. On the other hand, evolving things like ecosystems are 'supercritical', constantly generating new kinds of members, with a generative, non-convergent, open-ended, forever growing recursion. Current computer models seem to be able to generate at most a few levels of novelty, and have not yet demonstrated ever increasing novelty.

But simply getting a good definition of life isn't enough for Kauffman. He goes on to describe how life evolves and coevolves, how complexity necessarily flows into the "adjacent possible" (the states a single step away from the system's current state), and why the science of this kind of evolution is qualitatively different from "classical" science: because it is impossible even in principle [I am not sure I agree with that "in principle", but I do with the sufficient "in practice"] to finitely prespecify the state space [Cohen and Stewart also make this point -- their favourite examples are oxygen and grass], and because the evolution of the universe is so vastly non-ergodic, so vastly contingent. He discusses that the contingent evolution of the world is confined not just to the species level, but is present in the molecules that go to make up life on earth, and maybe even the fundamental laws of nature themselves.

... autonomous agents forever push their way into novelty---molecular, morphological, behavioural, organizational. I will formalize this push into novelty as the mathematical concept of an "adjacent possible", persistently explored ... Biospheres, on average, may enter their adjacent possible as rapidly as they can sustain; so too may econospheres. Then the hoped-for fourth law of thermodynamics for such self-constructing systems will be that they tend to maximize their dimensionality, the number of types of events that can happen next.

... this nonequilibrium flow into a persistent adjacent possible may be the proper arrow of time, rather than the more familiar appeal to the second law of thermodynamics in closed thermodynamical systems.

Having covered life, and how it evolves, he next goes on to asking why evolution works. Macready and Wolpert's "no-free-lunch" theorem tells us that there is no one search algorithm better than any other when its performance is averaged over all search landscapes. Random search is as good as any other on average. So how come the search algorithms evolution uses just happen to be ones that work well on the evolutionary fitness landscape? Coincidence? No. The creatures and the fitness landscapes co-construct each other:

If organisms are sexual because recombination is a good search strategy, but recombination is only useful as a search strategy on certain classes of fitness landscapes, where did those fitness landscapes come from? ... The ways of making a living presenting fitness landscapes that can be well searched by the procedures that organisms have in hand [mutation, recombination, selection] will be the very ways of making a living that readily come into existence.

Kauffman doesn't like anything to be coincidence. In his final chapters he leaves biology, and ventures into economics and fundamental physics.

In an evolving economic world, where new goods and services are forever coming into being, where the future goods available cannot be prespecified, the old ideas of equilibrium economics and clearing markets cannot hold. He shows that economic agents on coevolving fitness landscapes must necessarily have bounded rationality -- they can use only recent data in building predictive models of other agents, data from when the landscapes were roughly as they are now, and they can devise only simple theories, to avoid overfitting the sparse data. Ironically, in periods of relative stability, the available data increase and the theories can get more sophisticated, but hence more fragile, until a small change in reality can cause catastrophic failure of the now fragile models, and result in an avalanche of new behaviours and consequently requirements for new models: hence cycles of stability and rapid change. [Here, for Kauffman's argument to work, the economic fitness landscape must be of a sort readily searchable by the search procedures the economic agents have to hand -- but he doesn't say what these procedures are -- mutation and selection, clearly -- but what is the economic analogue to biology's sexual recombination?]

Finally, Kauffman considers the universe itself, and has a dislike for even the weak anthropic principle -- he wants to explain why the universe has to be the way it is, or at least, close to the way it is. He uses quantum decoherence (covered in some detail in The Quark and the Jaguar) to explain why the universe is getting more complex. Bigger systems, more complex systems, decohere more rapidly, and hence preferentially come into classical existence. He then applies Feynman's idea of sums over histories and constructive quantum interference to explain why the universe has the laws and geometry it does. Nearby histories constructively interfere when they are similar -- when small changes to whatever is being measured lead to small changes in the outcomes -- which might help explain our smooth and flat space-time: the irregular ones have destructively interfered themselves out of existence. [I admit to having missed the point here -- Kauffman seems to be saying that the universe gets ever more complex because the complex co-observing systems decohere -- become classical -- fastest, whilst we get flat space-time because that is the geometry that decoheres slowest. But maybe I can be excused this lapse in understanding: the writing is at its densest here, with whole new cosmologies packed into a few spare paragraphs. I would love to see this chapter expanded into a whole book of its own. Some of it can be found in The Life of the Cosmos, but most goes beyond that.]

In all, this is a glorious, mind-expanding book. My attempts at summarising Kauffman's many rich, diverse arguments cannot possibly do them justice. I have just skimmed the surface of his thesis here. There are many more fascinating details and arguments in the book. Read it. And if its ideas are not yet in your own adjacent possible, go and do some background reading (not helped by the rather sparse bibliography herein), then read it.

Stuart A. Kauffman.
Reinventing the Sacred: a new view of science, reason, and religion.
Basic Books. 2008

Stuart A. Kauffman.
Humanity in a Creative Universe.
OUP. 2016

In the hard sciences, which can often feel out of grasp for many lay readers, there are “great thinkers” who go far beyond the equations, formulas, and research. Great minds such as Stuart A. Kauffman think about the functions and nature of the universe, the implications of our living existence, and other impossibly fascinating, yet difficult questions. He has dedicated his lifetime to researching “complex systems” at prestigious institutions and now writes his treatise on the most complex systems of all, the creative universe, the limits of scientific laws, and the role of the mind.

Grounded in his rigorous training and research background, Kauffman is interdisciplinary in every sense of the word, sorting through the major questions and theories in biology, physics, and philosophy. Best known for his philosophy of evolutionary biology, Kauffman coined the term “UNprestatabilitys” to call into question whether science can ever accurately and precisely predict the future development of biological features in organisms that cannot even be prestated. If not, he argues, no laws will entail biological evolution. As evidenced by the title’s mention of creativity, the book stunningly argues that our preoccupation to explain all things with scientific law has deadened our creative nature. In this fascinating book, Kauffman concludes that the development of life on earth is not governed by law, because no theory could ever fully account for the unprestatable emergence of new functional variations of evolution. This book reframes our view of reality, challenges the next generations of great thinkers, and will be discussed for years to come.

Stuart A. Kauffman.
A World Beyond Physics: the emergence and evolution of life.
OUP. 2019

How did life start? Is the evolution of life describable by any physics-like laws?

Stuart Kauffman’s latest book offers an explanation—beyond what the laws of physics can explain—of the progression from a complex chemical environment to molecular reproduction, metabolism and to early protocells, and further evolution to what we recognize as life. Among the estimated 100 billion solar systems in the known universe, evolving life is surely abundant. That evolution is a process of “becoming” in each case. Since Newton, we have turned to physics to assess reality. But physics alone cannot tell us where we came from, how we arrived, and why our world has evolved past the point of unicellular organisms to an extremely complex biosphere.

Building on concepts from his work as a complex systems researcher at the Santa Fe Institute, Kauffman focuses in particular on the idea of cells constructing themselves and introduces concepts such as “constraint closure.” Living systems are defined by the concept of “organization,” which has not been focused on enough in previous works. Cells are autopoietic systems that build themselves: they literally construct their own constraints on the release of energy into a few degrees of freedom that constitutes the very thermodynamic work by which they build their own self-creating constraints. Living cells are “machines” that construct and assemble their own working parts. The emergence of such systems—the origin of life problem—was probably a spontaneous phase transition to self-reproduction in complex enough prebiotic systems. The resulting protocells were capable of Darwin’s heritable variation: hence, open-ended evolution by natural selection. Evolution propagates this burgeoning organization. Evolving living creatures, by existing, create new niches into which yet further new creatures can emerge. If life is abundant in the universe, this self-constructing, propagating, exploding diversity takes us beyond physics to biospheres everywhere.