## lördag 20 augusti 2011

### Topi Sorsakoski - Olet kaikki

This remarcable man died of cancer in relatively young age. His voice isn't beautiful, nor his person, and still he sings like few. With such big feeling. I have met him 'Live' on a dance once. This song is so special, and I always think of a very special person when I hear it :)

A truly finnish song.

There is no Death, only a transmission. Like a phase shift. A beautiful place. Green flowering meadows.

## fredag 19 augusti 2011

### A Priori

Today I left some dishes dirty,

The bed got made around 3:30.

The diapers soaked a little longer,

The odor grew a little stronger.

The crumbs I spilled the day before

Are staring at me from the floor.

The fingerprints there on the wall

Will likely be there still next fall.

The dirty streaks on those windowpanes

Will still be there next time it rains.

Shame on you, you sit and say,

Just what did you do today?

I held a baby till she slept,

I held a toddler while she wept.

I played a game of hide and seek,

I squeezed a toy so it would squeak.

I pulled a wagon, sang a song,

Taught a child right from wrong.

What did I do this whole day through?

Not much that shows, I guess that's true.

Unless you think that what I've done,

Might be important to someone

With deep blue eyes and soft blonde hair,

If that is true...I've done my share.

I am very much of the same mind - lovely

## onsdag 10 augusti 2011

### Inertia - change I. Of what?

Why are there balance and counteraction? Life creates unstabilities, noise, change? Actions that requires an reaction. Stress and adaption. Homeostasis.

We all know that living structures are reactive, flexible, often formable, soft = NOT descreate and determined. But also that it need some fixed structures like bones, or cytosceletons. Hardness and flexibility. Is Life always enclosed in structure?

The Dynamic Process of Communication:

Demonstrations of impossibility, whether in relativity, quantum mechanics, or thermodynamics, have shown that nature cannot be describedThis is at the heart of Einsteins problem with quantum gravity. Inertia - change. Which takes us immidiately to the second law of thermodynamics. It works differently for living and ordinary matter? Why? And has it anything to do with the first law and the E=mc2? Energy is the interesting part, not only mass? Gauge fields and matter fields counterinteract. The fluctuation-dissipation theorem, or mass compressability*, says Radoslav Bozov."from the outside", as if by a spectator. Description is a dialogue, communication, and this communication is subject to constraints that demonstrate that we are macroscopic beings embedded in the physical world. We are evolved dissipative structures. The time symmetry is broken in the following way: the existence of irreversible processes on the microscopic level through kinetic equations violates the symmetry of the canonical equations. And dissipative structures may, in turn, break the symmetries of space-time.

The conservation of mass is a fundamental concept of physics, as is the conservation of energy. Within some problem domain, the amount of mass remains constant; mass is neither created or destroyed. The

**mass**of any object is simply the volume that the object occupies times the density of the object. For a

**fluid**(liquid or gas) the density, volume, and shape of the object can all change within the domain with time and mass can move through the domain.

*in the boson case, the connection between density fluctuations and compressibility was used to study

**superfluidity in a two-dimensional system**.

In addition to gauge fields, in nature there also are matter fields. The matter fields describe things such as electrons, neutrinos, quarks, and possibly Higgs particles. Gauge fields mediate “forces” between particles described by matter fields (and between additional particles described by the gauge fields themselves). Edward Witten 2009.The great insight was "Do not quantize", tells us Matti Pitkänen. No supergravity for him.

What really IS the secret with Life?

Prigogine has been one of my leading stars through my Journey. 1980 he wrote From Being to Becoming: Time and complexity in Physical Sciences. He has three main theses:

(1) irreversible processes are as REAL as reversible ones.

(2) irreversible processes play a fundamental CONSTRUCTIVE role in the physical world.

(3) irreversibility is deeply rooted in dynamics.

Most of the directional processes are irreversible or hypercyclic. Very few are totally reversible,and they are not at equilibrium. He adds, "This formulation leads to a unified picture that enables us to relate many aspects of our observations of physical systems to biological ones.

"Biological order is both architectural and functional; furthermore, at the cellular and supercellular levels, it manifests itself by a series of structures and coupled functions of growing complexity and hierarchical character. This is contrary to the concept of evolution as described in the thermodynamics of isolated systems, which leads simply ... to 'disorder.' ... The unexpected new feature is that nonequilibrium may ... lead to a new type of structure, the DISSIPATIVE structures, which are essential in the understanding of coherence and organization in the nonequilibrium world in which we live."Again structure and function, inertia and change.

Order out of

*Chaos, Prigogine 1984*in his intellectual odyssey from classical thermodynamics, through linear nonequilibrium thermodynamics, and finally to his holy grail of nonlinear nonequilibrium thermodynamics, and how the processes of entropy and energy scattering can lead a system open to its environment to evolve greater complexity.

Open systems evolve complexity! Seen in structure of proteins? Molecular machines? But if we look only at complexity, then we forget the open system.

The irreversibility (not invariant) in non-equilibrium thermodynamics, leading both to structure and function change. Take only the example with diffusion over a membrane.

The End of Certainty, 1997.

How is it, for instance, that basic principles of quantum mechanics-which lack any differentiation between forward and backward directions in time-can explain a world with an "arrow of time" headed unambiguously forward? And how do we escape classical physics' assertion that the world is deterministic? Prigogine explores deterministic chaos, nonequilibrium thermodynamics, and even cosmology and the origin of the universe... There is a way in which biology could be "reduced" to physics, but only if we learn to define "physics" very differently than we do today.Prigogine's explanation of Henri Poincaré's proof that contemporary physics' belief in reversible, closed-system, deterministic modeling actually precludes the arrow of time, obviates self-organization, and prohibits the existence of life itself. In short, Prigogine shows that Poincaré proved that biology CANNOT be reduced to contemporary physics, and he even proved why (the existence of Poincaré resonances). It's an exquisitely beautiful insight.

Ironically, when the problems of biology has again and again been said to be the determinism and decoherence, seen from the light of Schrödinger and the double-slit experiment. Something is simply WRONG here, Lubos. Where is the build-up?

Points toward a revolutionary realignment of fundamental physical principles, theoretical perspectives, and even scientific methodology - a coherent major shift in the foundational paradigms of physical science. Both Einstein and Schrödinger knew that contemporary physics is inadequate to explain more complex phenomena... like biological life.Newton's laws were once considered to be final.

Prigogine 1997, Non-linear Science and the Laws of Nature: Simple examples such as the Bernouilli shift and the anharmonic lattice are studied. It is shown that instability as well as the thermodynamic limit lead to a new formulation of laws of nature in terms of probabilities (instead of trajectories or wave functions), following the realization that large classes of systems may exhibit abrupt transitions, a multiplicity of states, coherent structures or a seemingly erratic motion characterized by unpredictability often referred to as deterministic chaos. Distance from equilibrium, and therefore the arrow of time, plays an essential role in these processes, somewhat like temperature in equilibrium physics. Time is an operator.

The 19th century has left us with a conflicting heritage. On one side, there are the 'laws of nature' such as Newton's law which relates acceleration to force. This law is time reversible and deterministic. If we know the initial condition of a dynamical system, we can predict its state at an arbitrary time, be it in the future or in the past. There is no distinction between past and future. These characteristics remain true in relativity and quantum mechanics, as the Einstein or Schrrdinger equations are also reversible and deterministic. On the other hand, the famous 'second law' of thermodynamics, associated with the increase of entropy, expresses the arrow of time.

Stuart Kauffman has a probalistic approch in his "The origin of order."

"Is the moon there when nobody looks", asked Einstein. The observer - effect and consciousness. Are there consciousness outside living matter? The Anthropic effect simply cannot be true.

What if we shift the focus from matter to waves, or probabilities, uncertainty? We start to explain our Universe in waves? Is the Universe Analog or Digital, asked FQXI in a contest last year, where I contributed. Maybe the answer is neither, but a TRINITY (particles-strings-waves) or (by replacing 1-dimensional strings with 3-dimensional light-like surfaces = self-containing = observer)? Or even a quartett? A tangent on a tangent? A quantized gauge theory with a mass gap? Maybe a superposition of many kinds (7 trees in one), so there are no definitive answer (E8?)? Also the fact that matter is only about 5% of total energy budget in Universe tells a lot. Dark matter is much more, about 20%. In which part is Life? WHAT is Life?

"One can best feel in dealing with living things how primitive physics still is," said Einstein.

If the equations of evolution are non-linear we observe, in general, bifurcations which lead to new spatio-temporal structures. The 'dissipative structures' achieved in this way are therefore the consequences of non-linearity. In this sense we may even consider life, with its essential non-equilibrium properties, as the manifestation of non-linearity. Close to equilibrium, entropy is maximum or free energy minimum. Free energy is reaction energy. To keep the reactivity negentropy must be maximized in living structures.

"Laplace's demon", cannot be true. Laplace's demon was based on the premise of reversibility and classical mechanics. Invariance? Causal or scientific determinism, if someone knows the precise location and momentum of every atom in the universe, their past and future values for any given time ... killed by irreversibility (time?) and quantum world? Einsteins problem again. With a note, There has recently been proposed a limit on the computational power of the universe, i.e. the ability of Laplace's Demon to process an infinite amount of information. The limit is based on the maximum entropy of the universe, the speed of light, and the minimum amount of time taken to move information across the Planck length, and the figure was shown to be about 10

^{120}bits. Accordingly, anything that requires more than this amount of data cannot be computed in the amount of time that has elapsed so far in the universe. The Lambda-cosmological constant-dark energy problem.

Wolpert’s results (acc. to Binder) are particularly compelling because they are totally independent of both the details of the laws of physics and the computational characteristics of the machines. Wolpert, D. H. Physica D 237, 1257–1281 (2008). A prescription for deriving the laws of nature was proposed by Roy Frieden 2004. Science from Fisher Information: A Unification (Cambridge Univ. Press). Producing multiple solutions, as in M-theory-landscape?

Non-linear time? Non-linear information? Through the attractor reconstruction method, in which a time series is converted into a geometrical trajectory in higher-dimensional spaces? Kantz, H. & Schreiber, T. Nonlinear Time Series Analysis (Cambridge Univ. Press, 2004). Sounds very TGD'ish, in light-like CD-diamonds and zero energy ontology.

One can also know more than everything (superpositions of states). Quantum walk is another example (scattering?), as in photosynthesis or massively parallel computers (right brainhalf?), touching at a distance and Bells inequality, lattice with different spins where forward and backward propagating fields pick up polarization rotations in opposite senses, and may even reverse time... Quantum thermodynamics?

Undoing a quantum measurement, quantum phase transitions... (non-local PDE's) How does a bosonic system store information about the Fermi energy, show how this fractal behavior would influence the thermodynamic response functions of liquid

^{3}He, a fermionic fluid. The results could potentially be applied to understanding quantum critical behavior in heavy-fermion metals and high-temperature superconductors.

The Yang-Mills equations are analogous to the vacuum Einstein equations Rμν = 0 (where R is the Ricci tensor). They are nonlinear hyperbolic wave equations. Most applications of partial differential equations involve domains with boundaries and periods, and use matrices (for scattering waves). Asymptotic charachter and resonance are other nonlinear equations. See Schrödinger eq. book.

Is Future Given? 2003, when Prigogine died. No fate, the future has not been determined.

He has consistently held that nature is probabilistic. Much of his motivation seems to have been in sorting out why Boltzman and Gibbs failed to satisfy the science community that their statistical physics explained the 2nd law, due to reversible classical equations and Poincare recurrences. However in order to make his probabilistic argument he may have created a loophole. He points to the Langevin equation as an irreversible equation with noise (friction) and he says Poincare should have connected nonintegrability with irreversibility and most dynamics are nonintegrable. However everyone agrees some (simple) systems are reversible (pendulums etc) so how can all of nature be stochastic? Maybe because the noise terms tend to but never go to zero?'The rate of change of entropy with time for a nonequilibrium stochastic process is always positive = the arrow of time.'

In this case Poincare recurrence maybe a mere statistical fluctuation with no actuality. (Prigogine says it is false because he introduces new microscopic dynamics, the irreversible processes. At the website secondlaw.com the thermodynamic explanation of entropy is fundamental as it is a measure of energy diffusion, and not randomness or uncertainty, as the tool of statistical entropy would imply. In this way the 2 approaches are not contradictory; the statistical is merely a measurement tool for observers while the thermodynamic is real dynamics requiring no observers (ice melts, water crystalizes etc long before man was around). If anything this should be viewed as fundamental as it is a direct measurement of the physical movement of heat.

One should not confuse information theory and measurement techniques with real underlying dynamics. When some authors say 'entropy is not a property of a system, it is a property of our description of the system. The quantum measuremental tools are badly developed.

Non-linearity is also fractals, hierarchy, self-assembly. Infinity. No zero, no end.

The importance of the individual's actions implies a reflection of each person on the responsibilities that each one assumes when taking or acting upon a decision. This responsibility is associated with the freedom of thought as well as a critical analysis of fashions, customs, preconceived ideas, and ideologies, externally imposed: exactly contrary to the ideas of those who wish us to be "perfect consumers" in a world dominated only by monetary wealth.

Such self-organization patterns are not a feature of living systems solely; they occur in many physical and chemical systems composed for instance of molecules that are amphiphylic (both hydrophylic and hydrophobic), leading the way from simple material to the construction of biomimetic and microrobotic systems.

Adaption relaxes stress. Energy is 'chrystallized', fixed. Movement diminished. Determinism and decoherence increased. Consequently coherence must be increased when the free energy is increased.

And synchrony?

"Maybe the details of the neurons are completely irrelevant. Maybe it is only a property of oscillators." says Babette K. Dellen. Neurons are composed of many elements and are typically nonlinear and, for example, have been modeled as interconnected, or "coupled", oscillators because of the way they interact with one another. Coupled oscillators can be imagined as being tethered to their nearest neighbor, thus influencing their movement. Neurons, on the other hand, may display repetitive electrical activity that can be influenced by the activity of neighboring neurons. Sebastian F. Brandt et coll. January 2006 Physical Review Letters.

The origin of life was marked by the transition from chemical reactions to self-replicating molecular entities capable of evolving by natural selection. The structure and function of many biological molecules and supramolecular assemblies are today accessible in simulated “prebiotic’’ conditions; nevertheless we are still unable to establish a link between these structures and the complex metabolisms at work in living matter.

**Maryvonne Gérin et Marie-Christine Maurel.**

To have 'a jump and a consciousness', says Matti Pitkänen..

To Prigogine, irreversibility is a fundamental property of physics. Prigogine proposes that entropy production is part of an operator (operators map functions onto functions), and time is an operator. And that the time that we are all familiar with from classical mechanics is just an ensemble average of this operator with a state vector. I.e. "ordinary" time is an average over his new time operator. And that "age" is dependent of the distibution.

So what does that mean about operators..? Let's say that we wish to know the time evolution of a system. In both quantum mechanics and classical mechanics, the Hamiltonian operator determines how the system will evolve in time. The evolution that we are all familiar with is a reversible and deterministic evolution (We can say that the reversible change of a wave function that represents the quantum system corresponds to a reversible motion along a trajectory that represents the classical system.) The wave function or trajectory represents the maximum knowledge of the system.Prigogine has incorporated reversible and irreversible parts into a new microscopic equation/description. The equation contains an operator analogous to the Hamiltonian, that is a new "time evolution operator" that now can drive the system to both equilibrium or nonequilibrium states. Entropy is produced by the even part of the new time evolution operator and he has defined an operator for that.An example that Prigogine gives looks at the conventional and his unconventional determination of energy levels in a quantum system. In the conventional quantum mechanics, both the energy levels and the time evolution of them are determined by the same quantity: the Hamiltonian operator. Prigogine's method allows him to use two different operators: the time operator for time evolution and another operator (a "superoperator" that can act on other operators) to determine the energy levels. So in this way, instead of having the "particle" and the "interaction" (conventional view), we have the physical process that contains electrons, photons, etc. that drive the total system. This process is "real" and cannot be "transformed" away by any change of representation.Or another way to look at it: the classical order says particles come first and the Second Law of Thermodynamics comes later, while Prigogine says that we mustfirstintroduce the Second Law before being able to define the entities.Another one of Prigigine's main themes is that nonlinear interactions frequently lead to order (which he calls "dissipative structures") through fluctuations. A dissipative structure is order visible on a macroscale which can exchange energy with the outside world. In particular, if the system is in a far-from-equilibrium-state this can happen.

...the increase of entropy can be far more accurately described [than simply disorder] using terms such as ‘dispersal of energy,’ ‘spreading and sharing of energy,’ and ‘spatial and temporal spreading.’ In decoherence theory, a similar metaphor is used to describe the phenomena involved with quantum non-locality, superposition, and entanglement. Specifically the wavefunction of a quantum entity, such as a sub-atomic particle or photon is not seen to collapse but rather is transferred through interactions to a system and/or its environment. This suggests there may be a common basis for entropy and non-locality.Prigogine is primarily a chemist. As I understand it, his main discovery has been the discovery of

*"chemical clocks."*These are chemical reactions that oscillate in a very regular and precise way. Prigogine predicted that they should exist from a theoretical chemistry standpoint several decades ago. In the late 1950's, one of his research group came back from a visit with a colleague in Russia, announcing that they had a chemical reaction that did just what Prigogine predicted. The reaction is now known as the Belousov-Zhabotininskii reaction and it is the oxidation of citric acid by potassium bromate catalyzed by the ceric-cerous ion couple.

## fredag 5 augusti 2011

### Artificial life conference, Paris.

Next week it’s the European Artificial Life Conference (ECAL) 2011 in Paris.

**Artificial Life** is an interdisciplinary undertaking that investigates the fundamental properties of living systems through the simulation and synthesis of biological entities and processes. It also attempts to design and build artificial systems that display properties of organisms, or societies of organisms, out of abiotic or virtual parts.

**ECAL**, the European Conference on Artificial Life, is a biennial event that alternates with the US-based *Alife* conference series.

**Download the complete PDF program booklet**(53-page, includes all the abstracts)

I borrow this!

# So what is life?

Posted by STEEN RASMUSSEN 5.8. on steennewmexicoThis question, of course, has to be addressed, if you want to create life from scratch. At our FLinT center in Denmark we study and implement life-like and minimal living processes in a variety of materials and systems. In particular we seek to assemble a minimal protocell, a minimal physicochemically based cell.

First a little history:

Von Neumann, the inventor of the modern computer, realized that if life is a physical process, it should be possible to implement life in other media than biochemistry. He was one of the first to propose the possibility of implementing genuine living processes in computers, robots and other media. This perspective, while still controversial, is rapidly gaining momentum in many science and engineering communities and it is the basis for our work. Ilya Prigogine reemphasized and clarified the importance of utilizing free energy fluxes to generate order in physicochemical systems through self-organization. The metabolic processes in our protocells utilize free energy to maintain local order. Our metabolism is a thermodynamic engine that locally drives our system away from equilibrium. Manfred Eigen pointed out that autocatalysis between functional physicochemical components could be a mechanism for the emergence of early life and that autocatalysis can enhance a systems ability to maintain information. All our protocellular components are autocatalytically coupled.

Now, what is minimal physicochemical life then?

There is not a generally agreed upon definition of life within the scientific community, as there is a grey zone of interesting processes between nonliving and living matter. Our work on assembling minimal physicochemical life is based on implementing systems that meets three criteria, which most modern biological life forms satisfy.

In my opinion, and from a practical point of view, a minimal living physicochemical system needs to:

- use free energy to convert resources from the environment into building blocks so that it can grow and reproduce,
- have the growth and division processes at least partly controlled by inheritable information, and
- allow the inheritable information to change slightly from one generation to the next, thereby permitting variation of the growth and division processes and thus allow selection and hence evolution.

How difficult can that be? Implementing these three simple criteria?

Well, I’m telling you, it’s *not* easy. It’s very complicated, as it takes many components to fall into place at the same time, and these components are not only of scientific nature.

For me personally, it took many years to convince any funding agency (peer review committee), that this kind of work is even possible. Secondly, we had to convince the committees that this work is worthy to spent tax payers money on: “In which sense will assembling minimal life benefit society?” Very important question, which I’ll get back to in some later blog. Only very few funding agencies give you money for basic, or curiosity driven, science.

I’ll say, getting continued funding for our activities is still, and has been, the hardest part of creating life. It’s certainly more complex than doing the science.

Secondly, due to the necessary complexities of the involved physicochemical systems, this kind of science is not a one-man activity. It takes a small village of skilled scientists from different disciplines, which gets us back to the previous point about money, as well as being able to host an exciting research environment.

Finally, and of course most importantly, it takes human wondering and amazement about why things are the way they are, as well as the courage to dream about how things could be. And it takes very good people. Without good people nothing moves. And then it takes tenacity. A dedicated effort day after day (and sometimes nights), month after month, year after year.

So don’t become a scientist unless you can’t help it. It consumes too much of you. But if you can’t help it, playing with your imagination and dreaming up new stuff, I believe is one of the most exhilarating things you can do as a human being. However, fundraising, writing grants, doing budgets, paying bills, dealing with whatever organization you are a part of, managing very smart people (herding cats), teaching, correcting exams, etc., is exhausting and can take some of the fun out of it. But that’s how it is. There are no free lunch.