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Art of Doing Science and Engineering

Gordana Dodig-Crnkovic
Department of Computer Science and Electronic Mlardalen University

Vetenskapsteori och metodik KIN171 Litteraturlista

Marshall, C. & Rossman, G. (2006). Designing Qualitative Research. ISBN 9781412924894. Hansson, S.O. (2003). Konsten att vara vetenskaplig. Filosofi/KTH. Sherlock Holmes. I Doyle, A. Sherlock Holmes ventyr: En studie i rtt. ISBN 91-85267-22-8. Se ven Semmelweiss - du sker sjlv information via internet, bibliotek, artiklar osv. 9

Sherlock Holmes
Sherlock Holmes, huvudpersonen i en serie vrldsbekanta detektivhistorier av sir Arthur Conan Doyle, och prototypen fr en skarpsinnig och inga mdor eller faror skyende yrkesdetektiv. Sherlock Holmes gjorde entr i vrlden 1887 i samband med romanen En studie i rtt, och vann stor ryktbarhet ngra r senare nr de frsta Holmesnovellerna brjade publiceras i tidskriften The Strand Magazine. Holmes karakteriseras av sin imponerande iakttagelse- och slutledningsfrmga vilken han d och d prvar p sin levnadstecknare, och fljeslagare Dr. Watson.

Sherlock Holmes

En studie i rtt (A Study in Scarlet) r den frsta boken om detektiven Sherlock Holmes och r skriven av Arthur Conan Doyle 1887. Det r i denna bok doktor Watson och Sherlock Holmes lr knna varandra och Sherlock Holmes-figuren introduceras fr vrlden. Genast startar en spnnande mordgta som ger prov p Sherlock Holmes skarpsinne.

Deduction-Induction Roller Coaster

general induction particular deduction


Konsten att vara vetenskaplig

Sven Ove Hansson, KTH

Innehll Frord 1 Vilken kunskap vill vi ha? 1.1 Vetande och handlingskunskap 1.2 Vetenskapsbegreppet 1.3 Ren och tillmpad vetenskap 1.4 Generell kontra speciell kunskap 1.5 Handlingskunskapen 1.6 Intersubjektivitet och objektivitet 1.7 Faran med auktoritetstro 1.8 Att utg frn den bsta tillgngliga kunskapen 1.9 Vetenskapen r en mnsklig aktivitet 1.10 Det stora och det lilla tvivlet 1.11 Sinnen och frnuft 1.12 Empirism och rationalism 1.13 Hantverkarnas bidrag 1.14 Episteme och techne nrmar sig varandra igen 6

Konsten att vara vetenskaplig

Sven Ove Hansson, KTH

2 Att resonera frnuftigt 2.1 Det rationella samtalet 2.2 Fora fr vetenskapliga samtal 2.3 Stegvis framlagda argument 2.4 Mngtydighet och vaghet 2.5 Nr behver ord vara vldefinierade? 2.6 Definitioner 2.7 Tre vgar till mer precisa begrepp 2.8 Vrdeladdade ord 2.9 Kreativitet och kritik 2.10 Intuition 3 Att observera 3.1 Sinnenas ofullkomlighet 3.2 Observationer r teoriberoende 3.3 Tekniken hjlper sinnena och minnet 3.4 Utvalda observationer 3.5 Fyra slags observationer 3.6 Nr observationsidealet inte kan uppns 3.7 Observatren sjlv 3.8 Att vara beredd p det ovntade 3.9 Kllkritik att dra slutsatser frn andras observationer 3.10 Mtningar 7

Konsten att vara vetenskaplig

Sven Ove Hansson, KTH

4 Att gra experiment 4.1 Experiment finns av mnga slag 4.2 Att konstruera ett experiment 4.3 Att separera 4.4 Att kontrollera variablerna 4.5 Experiment ska g att upprepa 4.6 Upprepning i praktiken 5 Att pvisa samband 5.1 Att prva hypoteser 5.2 Verifiering eller falsifiering? 5.3 Falsifieringens problem 5.4 Den ndvndiga sammanvgningen 5.5 Kravet om enkelhet 5.6 Slumpens skrdar 5.7 Statistisk hypotesprvning 5.8 All forskning r inte hypotesprvande 8

Konsten att vara vetenskaplig

Sven Ove Hansson, KTH

6 Att anvnda modeller 6.1 Tre slags modeller 6.2 Idealisering 6.3 Om faran med modeller 6.4 Simulering 7 Att frklara 7.1 Vetenskap utan frklaringar? 7.2 Frklaringar och frstelse 7.3 Frklaringsstt som har vergetts 7.4 Reduktioner 8 Att finna orsaker 8.1 Orsak som undantagsls upprepning 8.2 Orsaksbegreppet r antropomorft 8.3 Allt har inte en orsak 8.4 Att faststlla orsakssamband 8.5 Samverkan mellan flera orsaksfaktorer 9

Konsten att vara vetenskaplig

Sven Ove Hansson, KTH

9 Vetenskap, vrderingar och vrldsbilder 9.1 Vetenskapens beslutsfattande 9.2 Att skilja mellan fakta och vrderingar 9.3 Vetenskap och vrldsbild


Gordana Dodig-Crnkovic, Courses

(Follow Open Source Philosophy)

CDT314 - Formal Languages, Automata and Theory of Computation CDT403 - Research Methodology for Natural Science and Technology CDT212 - Vetenskapsmetodik (Scientific Method, in Swedish) CDT409 - Professional Ethics in Science and Engineering Research Ethics and Professionalism (Interdepartmental PhD course) Interdisciplinary Research and Co-Production of Knowledge (NEW! Interdepartmental PhD course) CD5650 - Philosophy of Computer Science, Swedish National Course (2004)

The Art of Doing Science and Engineering: Learning to Learn

by Richard W. Hamming

Highly effective thinking is an art that engineers and scientists can be taught to develop. By presenting actual experiences and analyzing them as they are described, the author conveys the developmental thought processes employed and shows a style of thinking that leads to successful results is something that can be learned. Along with spectacular successes, the author also conveys how failures contributed to shaping the thought processes. Provides the reader with a style of thinking that will enhance a person's ability to function as a problem-solver of complex technical issues. Consists of a collection of stories about the author's participation in significant discoveries, relating how those discoveries came about and, most importantly, provides analysis about the thought processes and reasoning that took place as the author and his associates progressed through engineering problems. Hammings talk on research


Random Notes from R. W. Hamming,

Art of Doing Science and Engineering: Learning to Learn Knowledge also comes from years of study of the work of others. The belief anything can be "talked about" in words was certainly held by the early Greek philosophers, Socrates (469-399), Plato (427-347), and Aristotle (384-322). This attitude ignored the contemporary mystery cults which asserted you have to "experience" some things which could not be communicated in words. Examples might be beauty, gods, arts, and love.


Random Notes from R. W. Hamming,

Art of Doing Science and Engineering: Learning to Learn
Traditional scientific training has emphasized the role of words, along with a strong belief in reductionism, hence to emphasize the possible limitations of language we can take up several places in this book. Style" is such a topic. ..This talking about first person experiences will give a flavor of "bragging," ... Learning from the experiences of others saves making errors yourself, but the study of successes is basically more important than the study of failures. ... there are so many ways of being wrong and so few of being right, studying successes is more efficient, and furthermore when your turn comes you will know how to succeed rather than how to fail! You must think carefully about what you hear or read ...reductionism...


Random Notes from R. W. Hamming,

Art of Doing Science and Engineering: Learning to Learn A simulation is the answer to the question: "what if ...?" 1. cheaper, 2. faster, 3. often better 4. can do what you cannot do in the lab. Why should anyone believe the simulation is relevant? You are responsible for your decisions, and cannot blame them on those who do the simulations, as much as you wish you could. Reliability is a central question with no easy answers. All impossibility proofs must rest on a number of assumptions which may or may not apply in the particular situation. "If an expert says something can be done he is probably correct, but if he says it is impossible then consider getting another opinion."


Det r nstan som under renssansen: mnniskor kan utropa

Ad fontes! Till kllorna, allts. Man behver inte nja sig med en second opinion; man kan frska skaffa sig tusen, och man kan bli odrgligt plst som patient.
Bodil Jnsson, Tnk om det r precis tvrtom!?


Science, Knowledge, Truth, Meaning

WHAT IS SCIENCE? What Sciences are there? What Liberal Arts are there? WHAT IS SCIENTIFIC METHOD? Critique of Usual Nave Image of Scientific Method WHAT IS KNOWLEDGE? SCIENCE, TRUTH AND MEANING


Theory of Science Lectures



Red Thread: Critical Thinking

A red thread in this course: critical thinking. We use critical thinking as method when approaching science. We think (critically!) about critical thinking.


Red Thread: Critical Thinking

Reserve your right to think, for even to think wrongly is better than not to think at all.
Hypatia, natural philosopher and mathematician


What Is Science?

Concentric Rinds (Concentric Space Filling/Regular Sphere Division). Maurits Cornelis Escher



"Scientists are people of very dissimilar temperaments doing different things in very different ways. Among scientists are collectors, classifiers and compulsive tidiers-up; many are detectives by temperament and many are explorers; some are artists and others artisans. There are poet-scientists and philosopher-scientists and even a few mystics." Peter Medawar, Pluto's Republic


Science: Definitions by Goal and Process (1)

Science (Lat. scientia, from scire, to know) is wonder about nature. Like philosophy, science poses questions but also has the specific means to answer them, as long as they concern the state and behavior of the physical world.


Science: Definitions by Goal and Process (2)

Science is the systematic study of the properties of the physical world, by means of repeatable experiments and measurements, and the development of universal theories that are capable of describing and predicting observations. Statements in science must be precise, such that other people can test them (in order to establish universality).


Science: Definitions by Contrast

To do science is to search for repeated patterns, not simply to accumulate facts. Robert H. MacArthur Religion is a culture of faith; science is a culture of doubt. Richard Feynman


Dewey Decimal Classification

000 - Computers, Information & General Reference 100 - Philosophy & Psychology 200 - Religion 300 - Social sciences 400 - Language 500 - Science 600 - Technology 700 - Arts & Recreation 800 - Literature 900 - History & Geography


Dewey Decimal Classification

500 Science 510 Mathematics 520 Astronomy 530 Physics 540 Chemistry 550 Earth Sciences & Geology 560 Fossils & Prehistoric Life 570 Biology & Life Sciences 580 Plants (Botany) 590 Animals (Zoology)


Scientific Comunities as Family Trees

Josh Dever at the University of Texas is compiling a "family tree" of philosophers related by the Ph.D. supervisor relation (or equivalent). The tree is online at


Classical Sciences in their Cultural Context Language Based Scheme

Logic & Mathematics

(Religion, Art, )

Natural Sciences (Physics, Chemistry, Biology, )

Social Sciences (Economics, Sociology, Anthropolog y, )

The Humanities (Philosophy, History, Linguistics )


Critique of Usual Nave Image of Scientific Method (1) The narrow inductivist conception of scientific inquiry 1. All facts are observed and recorded. 2. All observed facts are analyzed, compared and classified, without hypotheses or postulates other than those necessarily involved in the logic of thought. 3. Generalizations inductively drawn as to the relations, classificatory or causal, between the facts. 4. Further research employs inferences from previously established generalizations.


Critique of Usual Nave Image of Scientific Method (2)

This narrow idea of scientific inquiry is groundless for several reasons: 1. A scientific investigation could never get off the ground, for a collection of all facts would take infinite time, as there are infinite number of facts. The only possible way to do data collection is to take only relevant facts. But in order to decide what is relevant and what is not, we have to have a theory or at least a hypothesis about what is it we are observing.


Critique of Usual Nave Image of Scientific Method (3)

A hypothesis (theory) is needed to give the direction to a scientific investigation! 2. A set of empirical facts can be analyzed and classified in many different ways. Without hypothesis, analysis and classification are blind. 3. Induction is sometimes imagined as a method that leads, by mechanical application of rules, from observed facts to general principles. Unfortunately, such rules do not exist!


Why is it not possible to derive hypothesis (theory) directly from the data? (1)
For example, theories about atoms contain terms like atom, electron, proton, etc; yet what one actually measures are spectra (wave lengths), traces in bubble chambers, calorimetric data, etc. So the theory is formulated on a completely different (and more abstract) level than the observable data! The transition from data to theory requests creative imagination!


Why is it not possible to derive hypothesis (theory) directly from the data? (2)

Scientific hypothesis is formulated based on educated guesses at the connections between the phenomena under study, at regularities and patterns that might underlie their occurrence. Scientific guesses are completely different from any process of systematic inference. The discovery of important mathematical theorems, like the discovery of important theories in empirical science, requires inventive ingenuity.


Socratic Method
1. Wonder. Pose a question (of the What is X ? form). 2. Hypothesis. Suggest a plausible answer (a definition or definiens) from which some conceptually testable hypothetical propositions can be deduced. 3. Elenchus ; testing, refutation, or crossexamination. Perform a thought experiment by imagining a case which conforms to the definiens but clearly fails to exemplify the definiendum, or vice versa. Such cases, if successful, are called counterexamples. If a counterexample is generated, return to step 2, otherwise go to step 4.

Scientific Method
1. Wonder. Pose a question. (Formulate a problem). 2. Hypothesis. Suggest a plausible answer (a theory) from which some empirically testable hypothetical propositions can be deduced.

3. Testing. Construct and perform an experiment, which makes it possible to observe whether the consequences specified in one or more of those hypothetical propositions actually follow when the conditions specified in the same proposition(s) pertain. If the test fails, return to step 2, otherwise go to step 4.

4. Accept the hypothesis as provisionally true. Return to step 3 if you can conceive any other case which may show the answer to be defective. 5. Act accordingly.

4. Accept the hypothesis as provisionally true. Return to step 3 if there are predictable consequences of the theory which have not been experimentally confirmed. 5. Act accordingly.


The Scientific Method A Complex Adaptive System




Hypothesis must be redefined Hypotesen Hypothesis mste must bejusteras adjusted



Consistency achieved

4 The hypotetico-deductive cycle


5 The scientific-community cycle


Formulating Research Questions and Hypotheses

Different approaches: Intuition (Educated) Guess Analogy Symmetry Paradigm Metaphor

.... and many more...


Criteria to Evaluate Theories

When there are several rivaling hypotheses number of criteria can be used for choosing a best theory. Following can be evaluated: Theoretical scope Heuristic value (heuristic: rule-of-thumb or argument derived from experience) Parsimony (simplicity, Ockhams razor) Esthetics Etc.


Criteria which Good Scientific Theory Shall Fulfill Logically consistent Consistent with accepted facts Testable Consistent with related theories Interpretable: explain and predict Parsimonious Pleasing to the mind (Esthetic, Beautiful) Useful (Relevant/Applicable)


Ockhams Razor (Occams Razor)

(Law Of Economy, Or Law Of Parsimony, Less Is More!)

A philosophical statement developed by William of Ockham, (12851347/49), a scholastic, that Pluralitas non est ponenda sine necessitate; Plurality should not be assumed without necessity. The principle gives precedence to simplicity; of two competing theories, the simplest explanation of an entity is to be preferred.


What Is Knowledge?
Platos Definition

Knowledge is justified, true belief. The problem with this concerns the word justified. All interpretations of justified are deemed inadequate. These analyses are an excellent example of the critique of theories of knowledge, but do not provide an answer to what knowledge is.


What Is Knowledge?
Platos Definition Gettier Problem

Edmund Gettier, in the paper called "Is Justified True Belief Knowledge? argues that knowledge is not the same as justified true belief.


Knowledge and Objectivity


All observation is potentially contaminated, whether by our theories, our worldview or our past experiences. It does not mean that science cannot objectively [intersubjectivity] choose from among rival theories on the basis of empirical testing. Although science cannot provide one with hundred percent certainty, yet it is the most, if not the only, objective mode of pursuing knowledge.


Perception and Direct Observation


Perception and Direct Observation

"Reality is merely an illusion, albeit a very persistent one." Einstein


Perception and Direct Observation


Perception and Direct Observation



Perception and Direct Observation

Checker-shadow illusion See even: Lightness Perception and Lightness Illusions


Truth and Reality

Noumenon ("Ding an sich") is distinguished from phenomenon ("Erscheinung"), an observable event or physical manifestation, and the two words serve as interrelated technical terms in Kant's philosophy.


Whole vs. Parts

tusk spear tail rope trunk snake side wall leg tree The flaw in all their reasoning is that speculating on the WHOLE from too few FACTS can lead to VERY LARGE errors in judgment.


Science and Truth

Science as Consensus Science as Controversy


Scientific Truth (1)

Physics professor is walking across campus, runs into Math professor. Physics professor has been doing an experiment, and has worked out an empirical equation that seems to explain his data, and asks the Math professor to look at it.


Scientific Truth (2)

A week later, they meet again, and the Math professor says the equation is invalid. By then, the Physics professor has used his equation to predict the results of further experiments, and he is getting excellent results, so he asks the Math professor to look again. Another week goes by, and they meet once more. The Math professor tells the Physics professor the equation does work, but only in the trivial case where the numbers are real and positive."



After: Gdel, Escher, Bach - an Eternal Golden Braid by Douglas Hofstadter.



Gdel theorem is built upon Aristotelian logic. So it is true within the paradigm of Aristotelian logic. However, nowadays it is not the only logic existing!



The term non-Aristotelian logic, sometimes shortened to null-A, means any non-classical system of logic which rejects some of Aristotle's premises.
Related topics: Intuitionistic logic Fuzzy logic General Semantics Meta-systems Multi-valued logic Paraconsistent logic Quantum logic Is logic empirical? Theory of mind


The Limits of Reason - G J Chaitin

The limits of reason Scientific American 294, No. 3 (March 2006), pp. 74-81. Epistemology as information theory: from Leibniz to Collapse 1 (2006), pp. 27-51. Reprinted in Teoria algoritmica della complessit, 2006. Meta Math! first paperback edition Vintage, 2006. Speculations on biology, information and complexity Bulletin of the European Association for Theoretical Computer Science 91 (February 2007), pp. 231-237.


Cybernetics as a Language for Interdisciplinary Communication

Stuart A. Umpleby The George Washington University Washington, DC


How is interdisciplinary communication possible?

We would need to share a common language Perhaps there is a common deep structure which is hidden by our more specialized discipline-oriented terms and theories

Stuart A. Umpleby


What is the origin of the deep structure?

There are at least three possibilities: 1. Common processes and structures in the external world 2. Common human cognitive structures and processes (Mental models) 3. Logic (Mathematics)

After Stuart A. Umpleby


2. Common processes in the external world

General systems theory, particularly James G. Millers living systems theory, claims that there are certain functions that a living system must perform Miller suggested that living systems exist at seven levels cell, organ, organism, group, organization, nation, supranational organization
Stuart A. Umpleby 62

1. Mathematical Isomorphisms

Anatol Rapoport suggested that the aim of general systems theory is to identify mathematical isomorphisms

The word 'isomorphism' applies when two complex structures can be mapped onto each other, in such a way that to each part of one structure there is a corresponding part in the other structure, where 'corresponding' means that the two parts play similar roles in their respective structures." (Douglas Hofstadter, Gdel, Escher, Bach, p. 49)

Not many isomorphisms have been discussed in the literature Their theoretical importance is not clear

After Stuart A. Umpleby


Nineteen critical subsystems in living systems

Matter-energy processing subsystems ingestor, distributor, converter, producer,matter-energy storage, extruder, motor, supporter Information processing subsystems input transducer, internal transducer, channel and net, decoder, associator, memory, decider, encoder, output transducer Subsystems that process both reproducer, boundary

Stuart A. Umpleby


3. Conceptual models
In cybernetics there are basically three conceptualizations Regulation Self-organization Reflexivity

Stuart A. Umpleby


How can these models be used?

To find common ground with a person in a different field, listen to identify which of these models is being used When you have identified which model is being used, cybernetics provides a set of theories and methods to be employed Often more than one, indeed all three, models can be used

Stuart A. Umpleby


1. Regulation
Two analytic elements regulator and system being regulated Engineering examples thermostat and heater, automatic pilot and airplane Biological examples feeling of hunger and food in stomach, light in eye and iris opening Social system examples manager and organization, therapist and patient

Stuart A. Umpleby


The law of requisite variety

Information and selection The amount of selection that can be performed is limited by the amount of information available Regulator and regulated The variety in a regulator must be equal to or greater than the variety in the system being regulated W. Ross Ashby

Stuart A. Umpleby


Methods to use in regulation

Is there requisite (necessary) variety? What is the variety in the system to be controlled? What variety is available to match it? Choose the level of analysis in order to achieve requisite variety Define a model of cause and effect list actions and their expected consequences

Stuart A. Umpleby


Coping with complexity

When faced with a complex situation, there are only two choices
1. 2. Increase the variety in the regulator: hire staff or subcontract Reduce the variety in the system being regulated: reduce the variety one chooses to control

Stuart A. Umpleby


The management of complexity

There has been a lot of discussion of complexity, as if it exists in the world Cyberneticians prefer to speak about the management of complexity Their view is that complexity is observer dependent, that the system to be regulated is defined by the observer This point of view greatly expands the range of alternatives

Stuart A. Umpleby




Definition every isolated, determinate, dynamic system obeying unchanging laws will develop organisms adapted to their environments, W. Ross Ashby Many elements within the system Boundary conditions open to energy (hence dynamic), closed to information (interaction rules do not change during the period of observation) Complex Systems and Self-organization Modelling

After Stuart A. Umpleby


Examples of self-organization 1
Physical example chemical reactions; iron ore, coke, and oxygen heated in a blast furnace will change into steel, carbon dioxide, water vapor and slag Biological examples food in the stomach is transformed into usable energy and materials, species compete to yield animals adapted to their environments

After Stuart A. Umpleby


Digital Video Feedback and Morphogenesis

Video Feedback systems tend toward either stability or chaos. While the stable attractor offers some interest in the subtleties of its decay, the unstable attractor offers an unlimited supply of endless evolving motifs and a window on emergent behaviour. The system can be get into chaotic emergence via camera movement (rotation and positioning). The important thing was to catch the movement of catching a shape in a particular temporal phase to feed back into the system advancing the complexity and initiating lifelike morphogenesis.


Microtubules viewed as molecular ant colonies reactive adaptive self-organizing systems

Populations of ants and other social insects selforganize and develop emergent properties through stigmergy in which individual ants communicate with one another via chemical trails of pheromones that attract or repulse other ants. In this way, sophisticated properties and functions develop. Under appropriate conditions, in vitro microtubule preparations, initially comprised of only tubulin and GTP, behave in a similar manner. They selforganize and develop other higher-level emergent phenomena by a process where individual microtubules are coupled together by the chemical trails they produce by their own reactive growing and shrinking. Viewing microtubules as populations of molecular ants may provide new insights as to how the cytoskeleton may spontaneously develop highlevel functions. It is plausible that such processes occur during the early stages of embryogenesis and in cells.
Microtubules are long tubular-shaped supramolecular assemblies with inner and outer diameters of approx. 16 nm and 24 nm respectively. are a major filamentary component of the cytoskeleton. They have two major roles; they organize the cell interior, and they permit and control the directional movement of intracellular particles and organelles from one part of the cell to another.

Proposed mechanism for the formation of the selforganized structure


Microtubules viewed as molecular ant colonies reactive adaptive self-organizing systems

Self-organization by reactive processes
Normally solutions of reacting chemicals in a testtube do not self-organize. (Kolmogorov et al., 1937; Rashevsky, 1940; Turing, 1952; Prigogine and Nicolis, 1971; Nicolis and Prigogine, 1977) have proposed that some types of chemical reaction might show strongly non-linear reaction dynamics due to being sufficiently far-fromequilibrium. They predicted that in some cases this could result in macroscopic selforganization. Some chemical systems based on reactions originally discovered in the 1920s (Bray, 1921) and 1950s (Belousov, 1951, 1958) have been shown to self-organize this way (Castets et al., 1990; Ouyang and Swinney, 1991). Viewing microtubules as populations of molecular ants may provide new insights as to how the cytoskeleton may spontaneously develop highlevel functions. It is plausible that such processes occur during the early stages of embryogenesis and in cells.

Replication of form


Microtubules viewed as molecular ant colonies

reactive adaptive self-organizing systems
Self-organization by reactive processes
In populations of strongly coupled elements, researchers have progressively discovered that under appropriate conditions new, so-called, emergent phenomena can develop. These phenomena are not the sum of the properties of the individual elements, but on the contrary develop through the non-linear dynamics by which the elements are coupled together and behave as a collective ensemble. In recent years, systems of this type (Gleick, 1987; Nicolis and Prigogine, 1989; Coveney and Highfield, 1995; Camazine et al., 2001) have been termed complex. In many complex systems, self-organization occurs as a major emergent property. A feature of some complex systems is that weak external factors, which at an early critical moment break the symmetry of the process, modify the subsequent collective behaviour and thus trigger or determine self-organization.

Numerical simulations containing only reactive and diffusive terms predict microtubule assembly kinetics and self-organization comparable with experiment


Physical biology of molecular motors involved in intracellular organisation

Motor proteins are key determinants for the spatial organisation of eukaryotic cells. They are thermodynamic non-equilibrium machines playing a crucial role for the dynamic nature of cellular order. In fact, they provide a paradigm for the concept of intracellular order depending on molecular dynamics. How exactly the collective behaviour of various motors with different kinetic properties drives the organisation of the cytoskeleton is not understood.

Network of microtubules and two kinds of motor proteins created by self-organisation in vitro


Origami Programmable Cell Sheet

The objective is to produce a language for describing global shape that can be compiled to local interactions amongst a large number of cells that work robustly inspite of imprecise positioning and individual cell limitations and failures. The long term goal is to contribute to the understanding of engineered self-organisation, i.e. rather than observing emergent global behavior from given local rules, how does one derive local rules for a particular global goal? What are the high level languages for describing global goals, and what are the primitives for constructing local rules? Origami is an example of a language that constructively describes global structures. Using a small set of axioms (called Huzita's axioms) and only two types of folds (mountain and valley), one can construct a very wide variety of complex shapes.The initial conditions are very simple and always the same. The methods of combination are very simple. Axioms generate new creases from existing points and creases and new points can be formed only by the intersection of previous folds. Origami is a scale-independent language - i.e. the sequence of folds for a particular shape is independent of the size of the sheet.


Origami Programmable Cell Sheet

Huzita's Origami Axioms: Given two points p1 and p2, we can fold a line through them Given two points p1 and p2, we can fold p1 onto p2 (make a crease that bisects the line p1p2 at right angles) Given two lines L1 and L2 we can fold L1 onto L2 (crease is a bisector of the angle between L1 and L2) Given p1 and L1 we can make a fold through p1 perpendicular to L1 Given p1 and p2 and line l1, we can make a fold that places p1 on l1 and passes through p2 Given p1 and p2 and lines l1 and l2, we can make a fold that places p1 on l1 and p2 on l2.


Self-Organizing Systems Resources

Archive of papers - adaptation/self-organizing systems EVALife - Self-organisation in life-cycles Extropia - open source software Fractal Structures and Self-Organization - TMR Network One-Over-F Noise - bibliography Scalable Self-Organizing Simulations - DARPA Self-Organising Adaptive Systems - BT Labs Self-Organising Nanopatterns - Sandia National Laboratory Self-organization and fractals - Geodynamics Shalizi's Notebook - self-organization SOS on The Web - small Symbiotic Intelligence Project - self-organizing knowledge Stigmergic Systems - Peter Small The Self-Organization of the European Information Society - EU TSER Project WEBSOM Self-Organizing Maps - web intelligence


Introduction to Complex Systems

by David Kirshbaum

A Complex System is any system which involves a number of elements, arranged in structure(s) which can exist on many scales. These go through processes of change that are not describable by a single rule nor are reducible to only one level of explanation, these levels often include features whose emergence cannot be predicted from their current specifications. Complex Systems Theory also includes the study of the interactions of the many parts of the system. Previously, when studying a subject, researchers tended to use a reductionist approach which attempted to summarize the dynamics, processes, and change that occurred in terms of lowest common denominators and the simplest, yet most widely provable and applicable elegant explanations. But since the advent of powerful computers which can handle huge amounts of data, researchers can now study the complexity of factors involved in a subject and see what insights that complexity yields without simplification or reduction.


Introduction to Complex Systems

by David Kirshbaum

Four Important Characteristics of Complexity: Self-Organization Non-Linearity Order/Chaos Dynamic Emergent Properties Computer Programming approaches used for demonstrating, simulating, and analyzing these characteristics of Complex Systems: Artificial Life Genetic Algorithms Neural Networks Cellular Automata Boolean Networks

Structure and dynamics of animal social networks

Interactions between agents (whatever they may be) can be represented by a network. In animal social systems the nodes represent individual animals and the lines between them social ties. There is a growing interest, among mathematicians, statistical physicists, sociologists and others in understanding and characterizing the structure of such networks, and the dynamics of processes (such as the transmission of disease or other "information") on networks. Algorithms are developed to search a complex animal social network for "communities", or sets of nodes that are better connected among themselves than they are to the rest of the network, and to try to understand what causes the population to contain these structures. Most of the animal social networks constructed so far are built via an accumulation of many surveys of the population. An alternative approach is to monitor interactions in real time, to try to understand not only how information might be transmitted through a network, but also how the nature of the information might be having an effect on the structure of the network. Some of the systems of interest, include tropical fish, Galapagos sea lions, ants and deer.


Examples of self-organization

Large-scale lattice Boltzmann simulations of complex fluids: advances through the advent of computational grids Institute for Computational Physics. Physics on High Performance Computers


Supramolecular chemistry and self-assembling molecules

Supramolecular chemists are now extending their research beyond the design of molecules that can be used for molecular recognition or catalysis. They are actively exploring systems that undergo self-organisation - systems that can spontaneously generate welldefined functional supramolecular architectures by self-assembly from their components. This spontaneous but controlled formation of nanoscale architectures could be used to engineer and process functional nanostructures, offering a powerful alternative to nanofabrication, going from construction to self-construction.

Molecular fragments self-assemble to form a dynamic library of potentially bioactive compounds

"Self-organisation by selection takes advantage of dynamic diversity to allow variation in response to internal or external factors in a Darwinian fashion." "Constitutional dynamic chemistry paves the way towards an adaptive and evolutive chemistry, a further step towards unravelling the science of complex matter." 2007/02/A_natural_selection.asp

Self-reference Reflexivity


Douglas Hofstadters Writings

Self-reference is ubiquitous. It happens every time any one says I or me or word or speak or mouth. It happens every time a newspaper prints a story about reporters, every time someone writes a book about writing, designs a book about book design, makes a movie about movies, or writes an article about selfreference. Many systems have the capability to represent or refer to themselves somehow, to designate themselves (or elements of themselves) within the system of their own symbolism. Whenever this happens, it is an instance of self-reference.
SL #642: My proposal [...] is to see the I as a hallucination perceived by a hallucination, which sounds pretty strange, or perhaps even stranger: the I as a hallucination hallucinated by a hallucination. SL #641: That sounds way beyond strange. That sounds crazy. SL #642: Perhaps, but like many strange fruits of modern science, it can sound crazy yet be right. At one time it sounded crazy to say that the earth moved and the sun was still.... (I Am a Strange Loop, p. 293 )


Self-reference (Reflexivity)
This model has traditionally been avoided and is logically difficult Inherent in social systems where observers are also participants, in individual living organisms Every statement reveals an observer as much as what is observed

After Stuart A. Umpleby


Examples of reflexivity recursive algorithms

This weedlike plant is based on a simple recursive algorithm. Recursion is a popular technique used to describe trees and the like, because of the selfreferential nature of a tree. Basically, you would describe a tree by stating that a branch is something from which smaller branches sprout, and that the root of a tree is a big branch. Self-reference can lead to undecidability (and paradoxes like set of all sets that are not members of themselves)




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Reflexivity in a social system

Stuart A. Umpleby






A reflexive theory operates at two levels

Stuart A. Umpleby


Equilibrium Theory Stock price + Demand Stock + price

Reflexivity Theory + Demand +

Equilibrium theory assumes negative feedback; reflexivity theory observes positive feedback

Stuart A. Umpleby


Equilibrium vs. Reflexivity

A theorist is outside the system observed Scientists should build theories using quantifiable variables Theories do not alter the system described Observers are part of the system observed Scientists should use a variety of descriptions of systems (e.g., ideas, groups, events, variables) Theories are a means to change the system described

Stuart A. Umpleby


Adaptation/Reactivity/Regulation, Self-organization, Self-reference/Reflexivity/Recursiveness Models of regulation, self-organization, and reflexivity can be used in two ways Either to develop descriptions of some system (develop interdisciplinary models) Or to guide efforts to influence some system

Stuart A. Umpleby


Overview of cybernetics
The focus of attention within cybernetics has changed from engineering to the biology of cognition to social systems Ideas from cybernetics have been used in computer science, robotics, management, family therapy, philosophy of science, economics and political science Cybernetics has created theories of the nature of information, knowledge, adaptation, learning, self-organization, cognition, autonomy, and understanding

Stuart A. Umpleby



First Order Cybernetics

Second Order Cybernetics

Von Foerster Pask Varela Umpleby Umpleby

The cybernetics of observed systems The purpose of a model Controlled systems Interaction among the variables in a system Theories of social systems

The cybernetics of observing systems The purpose of a modeler Autonomous systems Interaction between observer and observed Theories of the interaction between ideas and society

Definitions of First and Second Order Cybernetics

Stuart A. Umpleby


Engineering Cybernetics The view of epistemology A realist view of epistemology: knowledge is a picture of reality Reality vs. scientific theories

Biological Cybernetics A biological view of epistemology: how the brain functions

Social Cybernetics A pragmatic view of epistemology: knowledge is constructed to achieve human purposes The biology of cognition vs. the observer as a social participant Explain the relationship between the natural and the social sciences How people create, maintain, and change social systems through language and ideas Ideas are accepted if they serve the observers purposes as a social participant By transforming conceptual systems (through persuasion, not coercion), we can change society

A key distinction

Realism vs. Constructivism

The puzzle to be solved

Construct theories which explain observed phenomena How the world works

Include the observer within the domain of science

What must be explained

How an individual constructs a reality

A key assumption

Natural processes can be explained by scientific theories Scientific knowledge can be used to modify natural processes to benefit people

Ideas about knowledge should be rooted in neurophysiology. If people accept constructivism, they will be more tolerant

An important consequence

Three Versions of Cybernetics

100 Stuart A. Umpleby

The cybernetics of science

NORMAL SCIENCE The correspondence principle Incommensurable definitions

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The Correspondence Principle

Proposed by Niels Bohr when developing the quantum theory Any new theory should reduce to the old theory to which it corresponds for those cases in which the old theory is known to hold A new dimension is required

Stuart A. Umpleby


New philosophy of science Old philosophy of science

Amount of attention paid to the observer

An Application of the Correspondence Principle

Stuart A. Umpleby



Logic & Mathematics

Natural Sciences (Physics, Chemistry, Biology, )

Social Sciences (Economics, Sociology, Anthropology, )

The Humanities
(Philosophy, History, Linguistics )

Kultur (religion, konst..)



Our scheme represents the classical groups of sciences. Modern sciences are stretching through several fields of our scheme. Computer science e.g. includes the field of AI that has its roots in mathematical logic and mathematics but uses physics, chemistry and biology and even has parts where medicine and psychology are very important. Examples: Environmental studies, Cognitive sciences, Cultural studies, Policy sciences, Information sciences, Womens studies, Molecular biology, Philosophy of Computing and Information, Bioinformatics, ..



Disciplinary change is a present day phenomenon. The discovery of DNA in the 1970s was a cognitive revolution which refigured traditional demarcations of physics, chemistry and biology. New fields of application arose. New discoveries, tools, and approaches change the way that research is conducted at empirical and methodological levels.





Development Science Technology


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Preface Part I 1 2 3 4
5 1


The Simple and the Complex Prologue: An Encounter in the Jungle Early Light Information and Crude Complexity Randomness A Child Learning a Language Bacteria Developing Drug Resistance The Scientific Enterprise The Power of Theory What Is Fundamental? 3 11 23 43 51 63 75 89 10 7

5 6 7 8 9


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Part II

The Quantum Universe

5 C h i l d L e a r n i n g a L a n g u a g e


Simplicity and Randomness in the Quantum Universe



A Contemporary View of Quantum Mechanics: Quantum Mechanics and the Classical Approximation



Quantum Mechanics and Flapdoodle


a c t e r i a D e v e l o p i n g D r u g R e


Quarks and All That: The Standard Model



Superstring Theory: Unification at Last?



Time's Arrows: Forward and Backward Time



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Part III

Selection and Fitness


Selection at Work in Biological Evolution and Elsewhere From Learning to Creative Thinking

23 5 26 1 27 5 29 1 30 7

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Superstition and Skepticism


Adaptive and Maladaptive Schemata


Machines That Learn or Simulate Learning

Part IV

Diversity and Sustainability


Diversities Under Threat

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a c t e r i a D e v e l o p i n g D r u g R e


Transitions to a More Sustainable World







Scientific Worldview: the Structure of Matter


DNA - Deoxyribonucleic Acid

DNA is the primary chemical component of chromosomes and the material of which genes are made











From the mid 1970s to the late 1990s a cluster of anti-rationalist ideas became increasingly prevalent among academic sociologists in America, France and Britain. Those ideas have formed following fields
- Deconstructionism - Sociology of Scientific Knowledge (SSK) - Social Constructivism or - Science and Technology Studies (STS).

The umbrella term for above movements was Postmodernism.



All forms of post-modernism were anti-scientific, anti-philosophical and generally highly skeptic about rationalism. The view of science as a search for truths (or approximate truths) about the world was resolutely rejected. According to postmodernists, the natural world has a small or nonexistent role in the construction of scientific knowledge. Science was just another social practice, producing ``narrations'' and ``myths'' with no more validity than the myths of pre-scientific peoples.



``The dictum that everything that people do is 'cultural' ... licenses the idea that every cultural critic can meaningfully analyze even the most intricate accomplishments of art and science. ... It is distinctly weird to listen to pronouncements on the nature of mathematics from the lips of someone who cannot tell you what a complex number is!'' Norman Levitt, from "The flight From Science and Reason," New York Academy of Science. Quoted from p. 183 in the October 11, 1996 Science)



Modernism has provided the philosophical foundation for much of Western culture since the Enlightenment. Modernism reaches its highest form in science although this approach arguably influences all of Western culture. Inherent in modernism is the notion of an essence: the truth behind the appearances we see around us. Science is about discovering these essences as science slowly reveals the truth about the world around us. Postmodernist attacks on essentialism have taken aim at this modernism version of essentialism.



Third, postmodernists assert that because no interpretative framework can be objectively shown to be true or false, the choice of interpretative framework is purely relativist and subjective. We are in the world of subjective values. That is, anything goes. This postmodern perspective provokes astonishment among those working within a modernist framework. For the most part, such people merely scoff at postmodernist attacks and believe no response is neededor possibleto what is seen as irrational anti-scientism.


Objectivity and Values

Postmodernisms attack on modernism has undercut modernisms pretension to scientific objectivity. Yet postmodernisms success is actually very narrow and their devastating critique of modernism does not carry over to non-modernist perspectives on essences. Despite the great confidence of many postmodern thinkers, postmodernism makes sense as a general critique only if you accept two flaws of logic. Postmodernist values appear to be the following: people have a right to decide what to believe, oppression is bad, and diversity of interpretive frameworks is good.


An Alternative Resolution

Both modernism and postmodernism subscribe to the false dilemma discussed above: we face a starkand necessarychoice between the correspondence theory of truth and the subjectivist approach.

But in time, both in philosophy and politics, new ideas become old ideas; what was once challenging, becomes predictable and boring; and what once served to focus attention where it should be focused, later keeps discussion from considering new alternatives. This has now happened in the debate between the correspondence views of truth and subjectivist views. Hilary Putnam Reason, Truth and History, Cambridge University Press, 1981, page x.


AFTER POSTMODERNISMS DEATH ... Interdisciplinarity and Complexity

Relationships between economy, politics, law, media, and science Emergent phenomena with nonlinear dynamics. Effects have positive and negative feedback to causes, uncertainties continue to arise, and unexpected results occur. Reality is a nexus of interrelated phenomena that are not reducible to a single dimension (Goorhuis, 2000; Egger & Jungmeier, 2000; Caetano, et al., 2000).


Interdisciplinarity and Complexity

The new discourse centers on problem- and solution-oriented research incorporating participatory approaches:
problem-oriented, beyond disciplinarity, practice-oriented, participatory, and




Interdisciplinarity and Complexity

Interdisciplinarity is necessitated by complexity. The nature of complex systems, provides a comprehensive rationale for interdisciplinary study, unifies the apparently divergent approaches, and offers guidance for criteria in each step of the integrative process. The ultimate objective of any interdisciplinary inquiry becomes understanding the portion of the world modeled by a particular complex system. (William Newell)