måndag 22 november 2010

Evolution is a process.

On Physics arXive Blog they talked about biology and evolution, the possibility that life as it has evolved on Earth is but a local minima in a vast landscape of evolutionary possibilities. If that's the case, biologists are studying a pitifully small fraction of something bigger. Much bigger. Then the charachter of Life could also look very much differently from what we see on Earth? Already here we have such a diversity of life forms. Take nanobacterias for instance. And yet many are undiscovered, also in the human body.

Usually biological evolution stops at the emergence of Life and the cosmical evolution starts, but there is no essential difference between the two concepts. There was a wast evolution also before Life was created on Earth. The RNA World is much about that pre-biological evolution.

As I see it Life is a phase of intermediate matter, where the quantum world is very much ruling. The Schrödinger cat is both dead and alive. It is not about chemistry, because also chemistry is ruled by the same quantum world. Merely you can see ordinary matter and living matter as two different paths of realisation. For living matter the governing rule is the capacity to react on surroundings and change the surroundings in own favor. Ordinary matter is bad at that. Essentially Life is about consciousness and qualias, which requires self-awareness and memory.
Today, we get an important insight into this state of affairs thanks to a fascinating paper by Nigel Goldenfeld and Carl Woese at the University of Illinois. Life Is Physics: Evolution As A Collective Phenomenon Far From Equilibrium. Goldenfeld is a physicist by training while Woese, also a physicist, is one of the great revolutionary figures in biology. In the 1970s, he defined a new kingdom of life, the Archae, and developed a theory of the origin of life called the RNA world hypothesis, which has gained much fame or notoriety depending on your viewpoint.
They suggest that biologists need to think about their field in a radical new way: as a branch of condensed matter physics. Their basic conjecture is that life is an emergent phenomena that occurs in systems that are far out of equilibrium. Goldenfeld and Woese say that biologists' closed way of thinking on this topic is embodied by the phrase: all life is chemistry. Nothing could be further from the truth.

And they take the example of superconductivity. No wonder.

The real explanation is much more interesting and profound. It turns out that many of the problems of superconductivity are explained by a theory which describes the relationship between electromagnetic fields and long range order. When the symmetry in this relationship breaks down, the result is superconductivity. And it doesn't just happen in materials on Earth. This kind of symmetry breaking emerges in other exotic places such as the cores of quark stars. Superconductivity is an emergent phenomenon and has little to do with the behaviour of atoms.

Life is like superconductivity. It is an emergent phenomenon and we need to understand the fundamental laws of physics that govern its behaviour. Consequently, only a discipline akin to physics can reveal such laws and biology as it is practised today does not fall into this category.

In the paper they point to some crucial facts:
- we have too little genes to encode for all that is needed, brain only would need them all. The collapse of the doctrine of one gene for one protein, with one direction of causal flow from basic codes. The key to complexity is not more genes, but more combinations and interactions generated by fewer units of code and many of these interactions (as emergent properties) must be explained at the level of their appearance, for they cannot be predicted from the separate underlying parts alone. Genes need to be treated collectively.
- majority of signaling is microbial also in the body, with coordinated division of labor, cellular differentiation and cooperative defense
- evolution was equal to 'natural selection', and relegated to a peripheral role during the development of molecular biology and high-tech biophysic. Collective phenomena are important also in microbiology etc.
- biology may extend the frontier of non-equilibrium physics, revealing principles of self-organization that seem absent in purely physical processes such as pattern formation
- sexual reproduction, fitness, growth rates

I could add to that list a lot.

What about death then? What brings the flow to cease?

The main problem with Life is its coherence and synchrony and that is not "far from equilibrium" - on the contrary, it is very much about equilibrium, but as a "bubble in bubbles", a phase transition. Energetically life is an open system, though, and requires an energy flow going through the ecosystem. Maybe, if you take entropy as the leading star but Life is about negentropy. A maximation of negentropy, (or a minimal decoherence) that is collected from environment by the superconductive nerves, perception organs, and at the far end the carbon networks. It is no random chance Life is based on carbon. This year the Nobel prize in physics went to graphene, a very interesting material in the science of what Life is, although arbitrary.
To the biologist interested in practical issues, we ask that you do not dismiss the seemingly useless and na¨ıve issues that we necessarily raise. On the one hand, a fundamental understanding of evolution may not seem to offer immediate benefits in terms of finding the next wonder drug; on the other hand, the lack of appreciation for the rapidity and pervasiveness of evolution has, within a lifetime, destroyed the effectiveness of numerous antibiotics, and probably is responsible for the limited success of the treatment of cancer. The biomedical-industrial complex cannot afford to ignore the need to create a fundamental science of biology.
That is true. Physical texts about biology often seems so naive, but they are looking for the similarities, the first principles.
The lack of structure in the way that biology is traditionally presented reflects the field’s unavoidable focus on a single sample path; however, the underlying evolutionary process itself is surely one with deep mathematical structure, capable of expression and elucidation in unifying terms based on emergent physical laws. This is a true frontier of physics, but one that will require a great deal of what has been termed (in another context of non-equilibrium physics) “open-minded spadework” to unearth.
Superconductivity is best understood as arising from the breaking of the global U(1) gauge symmetry in the effective field theory that describes the interaction between offdiagonal long-range order and the electromagnetic field. It is not about chemistry. There is nothing fundamental about the atoms or molecules. Examples are topological insulators, other examples of major significance include the Aharonov-Bohm effect, the quantum spin Hall effect, localization, and the renaissance in atomic, molecular and optical physics provided by the experimental realization of atomic Bose-Einstein condensates.

It certainly is not a microscopic theory, because it lacks a biochemical level of description, and it is certainly an effective theory, valid only when there is a separation of scales between ecosystem dynamics and gene mutation dynamics.
First, the very existence of the phenomenon of life needs to be understood.
Second, the realization or instantiation of it, on Earth, for example, needs to be understood. For the most part, it is fair to say that the discipline of biology has neglected the first condition, and in pursuit of the second, has confused understanding of the realization with understanding of the phenomenon. This has had a number of unfortunate consequences, which arguably have hindered both the conceptual development of biology and the proper application of foundational understanding to societal applications.
Perhaps the primary shortcoming of the biological enterprise is the manifest failure to account for the phenomenon of the existence of life. Without doubt, this failure reflects not only on biologists, but also on physicists. Biology is a big anomaly, echoes in my brain. Said by Matti Pitkänen.

At last something begins to happen.

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