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Literature Seminar "Emergent Properties"
Intro: The General Idea of the Seminar
During the winter term 2008/09, I will offer a literature seminar on the topic of emergent properties. Although the seminar is centered around chemistry and biochemistry, it certainly goes beyond these areas and tries to make use of principles from chemistry to explain many other phenomena in nature. The seminar will thus address some general underlying structural patterns which can be found everywhere from molecular self-assembly to the formation of galaxies or from the organization of a living cell to human society. Quite elusive properties such as creativity and intelligence can be explained with similar patterns as an ant nest or the formation of cell membranes. Consequently, the seminar is centered around chemical questions, but shows how we can transfer chemical concepts into the macroscopic world and use them to understand how things work in nature.
A small set of very simple things that interact over time on a short-range scale according to very simple rules can - as a whole - exhibit completely unexpected behavior. Although the same starting point with the same set of rules always results in exactly the same, reproducible behavior, it is extremely difficult to predict what the outcome will be. Changing an extremely small detail, which may seem absolutely unimportant to the whole system may cause extreme changes in the outcome (the "butterfly effect"). The whole system has thus new properties which none of the subunits has. These are the "emergent properties" which we will discuss in the seminar. The whole is more than the sum of its parts; new structural patterns evolve which cannot be examined by studying only the constituing parts of the whole system.
Many people have difficulties to understand why and how this highly complex world has evolved without the help of a higher intelligence. The seminar intends to go one step in this direction and make the power of emergence visible.
Please note: I am currently preparing a book project together with interested students. If you like to join, just have a look at the book project homepage...
Organizational Matters
Participation is not restricted to Masters students. Everyone from Bachelor students to professors is welcome and since at least a larger part of the seminar is not specializing in chemistry alone, we will all be on a non-expert level for some of the topics. For the preparation of your talks, you should take this into account. Some basic knowledge of chemistry certainly helps, though... Interested persons who do not want to contribute a seminar talk are highly welcome to attend the seminar as listeners.
In terms of credit points, you can earn three of them for this seminar, if you a) provide a seminar lecture yourself and b) attend twelve lectures as a listener.
All of the participants, who actively contribute a seminar talk, are invited to actively and freely choose their own topic as long as it fits into the overall theme "emergent properties". I provide a few topics below to give you an impression of the scope and limitations of this seminar. Of course, you are free to use one of these for your lecture. I would like to ask you to discuss the topic you choose with me before starting the preparation - just to figure out how and at what stage it would fit into the seminar.
Those who wish to actively contribute a seminar lecture are asked to register with me so that I can make plans
reliably. Just please send me an email to schalley
chemie.fu-berlin.de with your name, matriculation number and your suggestion for a title of your talk.
Your talk can be in German or English, whatever is more convenient for you. Nevertheless, I strongly encourage talks in English as a preparation for your future work.
Each seminar talk should be ca. 20 minutes long and allow for a detailed discussion.
Although I will be a learner rather than a teacher for many of the topics you may choose, I will offer help for the preparation of your seminars. In order to be able to help, it would be useful, if you would come and see me early on, at least two weeks before the seminar to discuss a concept for the talk. Approximately one week before the scheduled seminar, it would be advisable to briefly discuss your transparencies.
Tips for the Preparation of the Talks
Please make sure that you take into account the following points to make your seminar interesting and beneficial for all others:
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Be absolutely clear: Don't expect your audience to know too much about the topic. In view of the time, reduce the seminar to the really important arguments and concepts. Rather restrict yourselves to a good selection of important points and discuss them in greater detail than trying to make a superficial summery of everything. Choose really illustrative examples. Organize your talks clearly: What argument builds on which other one? How do I introduce each one of them at the appropriate moment? Direct the audience through your talk with (only a couple) of structuring remarks.
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Clarity should also be found in your transparencies: Large enough letter size (usually not below 14 pt), not too much text, easy to grasp graphics, if schematic cartoons help to reduce complexity, you can show a molecule, discuss its properties briefly and then explain the concept using cartoons. Nevertheless, don't forget that we are chemists and need to see how the molecules you discuss look like. A cartoon-only talk would not be sufficient!
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If you want to use a sheet of paper with short remarks to remind you of what you wanted to say, prepare it in a clear way so that you easily find your way through it. My suggestion would be to prepare the transparencies in a way that they also guide you through the talk.
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Use the appropriate scientific language. It is part of your science and you need to be able to use it actively and passively. Name the molecules and things on your transparency by their appropriate names. Reduce for example, IUPAC names to the functional group important in that particular moment. But don't say: "This thing here...", if the molecule can be easily given a more suitable name.
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Restrict yourselves to a small number of well-chosen examples. They should perfectly illustrate your points. Don't try to make the collection complete (even if that would match the Germans' need for "Gründlichkeit"). Your audience will be able to transfer the things learnt with the help of a well-chosen and well-explained example to others they encounter. A too large number of examples reduces the time for going into detail and makes the discussion superficial. You have then seen many examples without really understanding a single one ...
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Prepare a handout for your fellow students. One page is sufficient, if it contains the most important statements of your talk in a very shorrt summary plus the relevant literature you used.
Seminar Topics
When you go through the following list, please keep in mind that we want to keep the seminar within the vicinity of chemistry. You can choose different topics from chemistry and biochemistry, but I would prefer to use the others more in the sense of applying the principles we learnt from molecules. So all those topics which are not primarily focussing on chemistry should appear only once and should be of more general nature. The chemistry and biochemistry talks can thus be more specific and focus on different topics.
I have added a few keywords which hopefully make clear why each individual topic is related to emergent systems. Also, you will find some access to literature concerning the topic. Nevertheless, I do not claim that these literature references are comprehensive. So, please do your own literature search!
Note: You are free to choose your own topic as long as it fits into the overall theme of the seminar. Please talk to me about your ideas early on, so that I can incorporate the new talks into this page. Several other topics are also available from the book project site! Just have a look...
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Mathematics/Informatics: Feedback Loops, Phase Transitions, Bernoulli Shift, Conway's Game of Life and Gödel's Proof of Incompleteness: A Few Food Chunks to Go
Some of the basic ideas will be introduced which we encounter quite often during the seminar. it is interesting to examine the results of feedback loops. They become particularly strange, when they are set up to be self-referring. Paradoxes can easily emerge and Gödel used such a paradox for his proof that any mathematical system is either incomplete or contains a contradiction. Conway's game of life, on the other hand, is a very simple implementation of an emergent system. It may serve as a simple example with which the basic features of emergent systems can be illustrated. Consequently, it is useful for an introductory talk defining what emergence is.
Literature & Links:
- Conway's Game of Life
- Wikipedia info on turing machines
- Lars Burhard's homepage on Turing machines
- In addition, I can provide a Conway's GoL program and highly interesting patterns. Just ask!
- D.R. Hofstadter, Gödel, Escher, Bach, DTV, München 1991
- E. Nagel, J.R. Newman, Der Gödelsche Beweis, Scientia Nova, Oldenbourg, München 2007
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(Astro)physics: Emergence on all time and length scales: From the Standard Model of Particle Physics to the Formation of Galaxy Clusters
Emergence happens on all time and length scales. The formation of stars, galaxies, and even larger structures in the universe depends on small particles that interact through simple rules of gravity. Remember to take a look at the topic of "three-body problems" ("Dreikörperproblem")... An analytical solution is not possible anymore for more than two particles. Consequently, iterative simulations are needed. We will see during the seminar that this is true for emergent systems almost everywhere.
Link to a java applet and to pictures:
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Chemistry: Closed Systems: Self-assembly on a Molecular Level and on Surfaces
Emergent structures can develop in closed systems, which finally end up in the thermodynamic minimum. There are many chemical examples where simple building blocks self-assemble into more complex structures. However, this self-assembly process is completely different from self-organized structures in open systems (see below). The idea of this talk is to analyze the features which are typical for self-assembled systems in order to have a comparison for self-organized ones.
Literature:
- B.J. Holliday, C.A. Mirkin, Angew. Chem. 2001, 113, 2076
- C.A. Schalley (ed.), Analytical Methods in Supramolecular Chemistry, Chapter 10, Wiley-VCH, Weinheim 2006
- S. De Feyter, A. Gesquière, M.M. Abdel-Mottaleb, P.C.M. Grim, F.C. De Schryver, C. Meiners, M. Sieffert, S. Valiyaveetil, K. Müllen, Acc. Chem. Res. 2000, 33, 520-531
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Chemistry: Self-Assembled Architectures Based on Oligonucleotides
Self-assembly is all about programming the building blocks correctly so that they finally collapse into the desired structures. DNA is perfectly suited to be programmed through the base pair sequence. Consequently, quite complex species can be self-assembled from DNA strands. Please also provide some insight into the methods which are used to prove the correct assembly to emerge.
Literature:
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Materials Sciences: Mesoscale Self-Assembly on the Micro- to Millimeter Scale
This talk provides some idea of the fact that self-assembly is not restricted to the molecular level. The concepts learned from chemistry can be analogously applied to much larger objects and again, self-assembly of larger more complex entities from simple building blocks occurs.
Literature:
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Chemistry: Ilya Prigogine - The Thermodynamics of Open Systems
Leaving the self-assembled systems, we need to prepare somewhat for the processes going on in open systems. Ilya Prigogine received the Nobel prize in chemistry in 1977 for developing the thermodynamics of such open systems. With respect to emergence, it is particularly interesting that the energy flow through such an open system can generate quite stable superstructures, which die as soon as the energy flow is shut down.
Literature:
- Ilya Prigogine und Isabelle Stengers: Dialog mit der Natur, Piper, München 1993
- Ilya Prigogine: Die Gesetze des Chaos, Insel, Frankfurt 1998
- Ilya Prigogine und Isabelle Stengers: Das Paradox der Zeit, Piper, München 1993
- Günter Altner (Hrsg.), Die Welt als offenes System. Eine Kontroverse um das Werk von Ilya Prigogine, Fischer, Frankfurt am Main 1986
- H. Joachim Schlichting: Von der Dissipation zur dissipativen Struktur
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Chemistry: Dynamic Self-Organization: The Belousov-Zhabotinsky Reaction
Again, autocatalysis and feedback loops are a topic when the Belusov-Zhabotinski reaction is discussed. As long as chemical energy generated through the individual steps of this reaction flows through the system, patterns are created. When all reactants are consumed and the energy flow stops, the patterns are destroyed through diffusion. This reaction is a great chemical example for pattern generation in open systems. If you like, we can include a demonstration of this reaction on an overhead projector. I need to know that early enough, though...
Links:
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Chemistry: Minimal Replicators as Models for Self-Replication in the Primordial Soup
Emergence occurring in open systems usually comes together with loops. This talk and the next one deal with autocatalytic reactions, in which we can find such loops. Here, a template regenerates itself through molecular recognition of its own subunits which are then connected covalently. Please pay attention to the quite particular kinetic features of self-replicating systems! The focus should be on synthetic minimal replicators. What might Alzheimer's desease have to do with self-replication?
Literature:
- E.A. Wintner, M.M. Conn, J. Rebek, Jr., Acc. Chem. Res. 1994, 27, 198
- L.E. Orgel, Nature 1992, 358, 203
- G. von Kiedrowski, Bioorg. Chem. Frontiers 1993, 3, 113
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Materials Sciences: The Brazil Nut Effect: Why is the Thickest Stuff is always on Top? And: Is it really?
We all know that nuts usually appear on top of the muesli bag, when we buy it in the supermarket. Why is this so? Why does shaking the bag result in such a sorting phenomenon? Again, shaking provides energy whose flow through the system creates a pattern. The talk might also include a hint on other convection processes such as pre-boiling water in a pot that is heated from the bottom, plate tectonics which cause volkanism and earth quakes etc.
Literature & Links:
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Geology: Plate Tectonics: Convection on a Large Scale
In systems in which convection takes place, convection cells emerge. The continetal drift, earth quakes, volcanos and the like are phenomena associated with the convection in the earth mantle. This talk may span from simple convection phenomena (boiling water, the Benard experiment) to the convection in the earth mantle. The major topic is again the formation of dissipative structures in a system which is characterized by an energy flow.
Literature & Links:
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Biochemistry: Peptide Folding: Hierarchical Self-Assembly through Non-Covalent Bonds
With self-assembly and self-organization sorted out, the stage is set to turn to emergent properties in living organisms. The seminar starts this section with two talks on protein structure and cell membrane formation. This talk should discuss how proteins fold. Is it a self-assembly or a self-organization process? Protein folding is a hierarchical process and thus demonstrates how structure creation can occur on different levels of complexity. Please also discuss the Levinthal paradox...
Literature:
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Biochemistry: Formation and Properties of Cell Membranes - A Highly Dynamic Carrier of Biological Function
What are the properties of cell membranes? How are they formed? Why are organisms divided into small compartments? What functions do membranes fulfill?
Literature & Links:
- Biochemistry text books
- Wikipedia pages
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Biochemistry: Regulation of the Metabolism
The metabolism of a living cell is of utmost complexity, but in principle similar to the Belousov- Zhabotinski reaction. Within a small volume, an extreme variety of reactands is converted into intermediates and finally products that the cell needs to get rid of. All these processes need to be balanced. Nature uses (mainly negative) feedback loops in order to keep the metabolism up and running. The talk may focus on few examples, which are discussed in detail, e.g. the regulation of glycolysis.
Literature:
- O. Müller, Grundlagen der Biochemie III: Regulation und Dynamik, Thieme, Stuttgart 1982 (if you can't find it, I can provide you with this book)
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Sometimes, the body uses positive feedback loops, when an emergency occurs such as a wound, which needs to be closed quickly. In a process such as blood clotting, nature uses very fascinating amplification cascades. Other processes, in which they occur, are the energy supply of muscle cells (why do animals use glycogen, while plants use starch for energy storage?), and the process of vision (the amplification factor is high enough that we can in principle see a single photon). So, this talk is about feedback loops again, this time the positive ones!
Literature:
- Biochemistry textbooks
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Biology: Acetabularia acetabulum: Generation of Form from the Interplay of Genetics and Environment
Acetabularia are single-celled algae. However, despite the fact that they are single cells, they go through a quite complex life cycle during which their form changes significantly. It has been well studied, which factors are responsible for the forms the algae can create. Genetics is only one of them, the environment is however important, too. The form of the cells depends much of the calcium concentration around the cell. This talk should make clear how the genetic factors and the environmental conditions cooperate to generate a particular shape.
Literature & Links:
- B. Goodwin, Der Leopard, der seine Flecken verliert, Piper, München 2004 (one chapter only deals with the topic of the talk, but the whole book is interesting with respect to the topics discussed in this seminar!)
- Wikipedia pages (there are great pictures available on the net!)
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Biology: Communication between Cells - How Hormones Exert Control in Feedback Loops
Emergence occurs at higher levels of complexity, not only on the molecular scale. The next talks will emphasize this by using more and more complex examples starting with the hormone control of body functions as a way to organize the interplay of organs in complex living organisms.
Literature & Links:
- Biochemistry text books
- Wikipedia pages
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Zoology: The Organization of Ant Nests - Communication through Pheromones
Instead of hormones which regulate the interplay of organs within a body, ants communicate through pheromones. Ant nests fulfill highly complex functions. For example, some ant species can regulate the temperature inside their nests with great precision - without any ant having a thermometer or giving the command to change the flow of outside air through the nest. How such tasks work is the topic of this talk.
Literature:
- W. Kirchner, Die Ameisen: Biologie und Verhalten, C.H. Beck, München 2001
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Zoology: State-Forming Insects: How Bees Communicate
Like ants, bees are state-forming insects. How do they communicate? How are bee nests organized? How intelligent is the individual bee? Can we consider the nest to be an organism in itself? If so, how intelligent is it then?
Literature:
- J. Tautz, H.R. Heilmann, Phänomen Honigbiene, Spektrum Verlag, 2007
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Zoology: Fish Schools: How do They Know When to Turn Where?
Also, higher animals that live in swarms have efficient communication tools which synchronize the behavior in the swarm. One example are fish schools.
Literature:
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Biology: Symbiosis and Co-Evolution: The Benefits of Cooperation
Symbiotic relationships are almost omnipresent in nature. In analogy to state-forming animals, where kind of a symbiosis exists between individuals of the same species, symbiotic relationships are beneficial for two or more different species. If we think of the emerging system as a more complex organism at a higher level of hierarchy, symbiosis optimizes this organism. Instead of jelly fishes and fishes other examples can of course be chosen.
Literature:
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Biology: Symbiosis - Of Figs and Wasps
As a symbiosis case study, figs and wasps may serve.
Literature:
- B. Goodwin, Der Leopard, der seine Flecken verliert, Piper, München 2004 (one chapter only deals with the topic of the talk, but the whole book is interesting with respect to the topics discussed in this seminar!)
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Neurology: How to Explain Intelligence and Creativity? - Neuronal Nets
The terms "intelligence" and "creativity" are descriptive of the emergent property itself without referring to a "mechanism" which produces them. It is extremely difficult to exactly define what we mean by these terms, although we are probably all able to recognize them, when we encounter them. Maybe, after taking a look at so many examples for emergent systems, we may get a better desciption/definition of intelligence and creativity by trying to explain them as the emergent properties they are plus an idea of the mechanism which creates them. Neuronal nets may be helpful as models.
Literature & Link to Neural Net Simulation Program:
- MemBrain
- H. Cruse, J. Dean, H. Ritter, Die Entdeckung der Intelligenz oder: Können Ameisen denken?, dtv, München 2001
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Neurology: Constructivism: How Real is Reality?
Reality is constructed in a feedback loop between us and the world we live in
Literature:
- P. Watzlawick, Wie wirklich ist die Wirklichkeit? Wahn, Täuschung, Verstehen, Piper, München 1986
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Neurology: When Self-Regulation Fails: Mental Desease as an Emergent Phenomenon
Is it possible that emergence also provides us with a new approach to mental deseases? Maybe psychology which tries to treat the desease on the highest level of complexity would be better off by understanding the mechanisms which cause the deseases and then treating them on the bottom level? Like with the Acetabularia algae, an interplay of predisposition and the environment is probably at work...
Literature:
- P. Watzlawick, Wie wirklich ist die Wirklichkeit? Wahn, Täuschung, Verstehen, Piper, München 1986
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Music: Perception of the Outer World: How Feedback Loops Generate the Meaning of Music
The overtone scale is a physical fact, based on which we understand music (and because of which we all feel similar about the music we hear). The talk is scheduled close to the neurology talks, because I intended to look at how music is heard and processed in the brain. The activity patterns in the brain caused by music are emergent. But, this is not the only connection to the emergent properties seminar. When listening carefully to any music, may it be pop, rock, jazz, or classcal music, we find patterns in it consisting of repetitions and slightly changed repetitions. Repetition creates expectations, the changes destroy it. Listening to music is thus a feedback loop of expectations which are not exactly fulfilled and thus provoke a modified expectation in the listener. Music is ambiguous and this ambiguity produces musical "meaning".
Literature:
- R. Jourdain, Das wohltemperierte Gehirn: Wie Musik im Kopf entsteht und wirkt, Spektrum Verlag, Heidelberg 1997
- L. Bernstein, The Unanswered Question: Six Talks at Harvard, Harvard University Press, 2006
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Geology/Mathematics: Chaos Theory: Can Climate Changes, Earth Quakes, Volcano Eruptions and Tsunamis become Predictable at all?
Many geological and meterological processes can be considered emergent. Convection within the earth mantle, which drives plate tectonics and thus creates mountain ranges, interacts with erosion which finally leads to an enormous variety of structures (nets of rivers, different sorts of soil on which different plants grow etc.). This is nothing else than a large-scale open system. Energy (the sun light and the heat of the earth's interior) drives the creation of structure. The talk should provide some information on how to calculate climate models, on what foundations climate models are based and how precise they are when the conditions change slightly. This talk is intended to provide some of the foundations of the theory of deterministic chaos based on which we may draw conclusions about the predictability of the above mentioned processes.
Literature:
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John Briggs, F. David Peat,
Die Entdeckung des Chaos: Eine Reise durch die Chaos-Theorie, DTV,
München 2006
Gut lesbare Einführung in die Chaos-Theorie mit vielen Anwendungsbeispielen
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John Briggs, F. David Peat,
Die Entdeckung des Chaos: Eine Reise durch die Chaos-Theorie, DTV,
München 2006
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Mathematics: Fractals
Self-similarity on different size scales is the topic of this talk.
Literature:
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System Theory: The Ecosystem - Why Complexity creates Stability
We so far have seen many almost unpredictable results emerging in many different systems. One characteristic feature of emergent systems is that they react with a sometimes extremely different response, when only a marginal change is done initially (the "butterfly effect"). But why is the ecosystem then so stable? How does the complexity of a system relate to its stability? What happens to an emergent system, when a large number of different feedback loops is interconnected? How does such a system deal with distortion?
Links to Java Applets on Different Growth Scenarios:
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Biology: Evolution: Mere Coincidence or Inevitability?
We have seen many examples for complex systems at this stage of the seminar. The question is, however, whether the development of such complexity is a mere coincidence. If we take the biological world as an example, we may ask wheter Darwinists are right (evolution is the accumulation of coincidences) or the creationists (an intelligent designer is necessary who set up the world as we see it). Maybe, there is a better solution to the problem: Evolution may be an emergent property of complex networks. Biological evolution is thus a automatic consequence of chemical networks that are sufficiently complex. The final conclusion is then that evolution must have happened and is by no means just a very improbable coincidence.
Literature:
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Stuart Kauffman,
Der Öltropfen im Wasser: Chaos, Komplexität, Selbstorganisation in Natur und
Gesellschaft, Piper, München 1998
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Stuart Kauffman,
Der Öltropfen im Wasser: Chaos, Komplexität, Selbstorganisation in Natur und
Gesellschaft, Piper, München 1998
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Sociology: Luhmann's Sytem Theory
How does communication work?
Literature:
- to be added
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There has been a long philosophical discussion about how to describe the world around us. Can we do it by studying the individual parts and then conclude that the whole is not more than the sum of them? Can we understand the world without connecting all these parts after we have studied them (reductionism)? Or do we need to look at the world as a whole (holism)? Humans and among them scientists are part of the world as an emergent system. They are entangled in all the loops connecting its parts. Is it appropriate to divide the world into objects to study and subjects which study them? How should we do science? How do we look at the world when we take different points of view (the reductionistic or the holistic one, for example)?
Links:
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Philosophy: The Body-Soul Problem: Does it have an Easy Solution?
One of the questions which philosophers thought about quite much is how the mental regime (the soul) interacts with the body. Does the soul have a materialistic basis? In the early british emergentism, the question of "downward causation" has played a major role: Can an emergent property like the soul cause changes within the body?
Literature:
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Achim Stephan, Emergenz: Von der Unvorhersagbarkeit zur Selbstorganisation, mentis, Paderborn
2007
Zum historisch und philosophischen Hintergrund des Emergentismus und der Kritik daran. Nicht ganz einfach zu lesen. - Wikipedia pages
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Achim Stephan, Emergenz: Von der Unvorhersagbarkeit zur Selbstorganisation, mentis, Paderborn
2007
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Philosophy: The Gaia-Hypothesis: Is there a System Theoretical Definition of Life?
This last talk will summarize and draw conclusions on: (i) what emergent systems are and how we can recognize them, (ii) how emergence creates complexity, (iii) how we describe emergent systems and what implications our way of thinking about them has. The major topic will be the Gaia hypothesis according to which we should consider the planet earth as one big organism, within which we are kind of "organs". If we follow this idea, it is time to rethink human hybris. So, are there even ethical implications connected to the topic of emergence?
Links: