1 Causality in Complex Systems The Probem of Modularity Mt. Tamborine, July 8, 2009 Sandra D. Mitchell Department of History and Philosophy of Science.

Slides:



Advertisements
Similar presentations
Willing to spend the time! Self motivated! Self responsibility! (If you need something Ask For IT!!!!!) Ability to communicate! (Vocabulary) Write,
Advertisements

BEHAVIOR WITHOUT LEARNING Evolution and Development Chaos Theory and Darwins Butterfly The Nature of Evolution Recipes and Blueprints Variation and Selection.
Making Inferences about Causality In general, children who watch violent television programs tend to behave more aggressively toward their peers and siblings.
Evidence for Complex Causes
HOW CAN CT AID IN THE INVESTIGATION OF INDIVIDUAL DIFFERENCES IN ADDITIONAL LANGUAGE LEARNING? Zoltán Dörnyei University of Nottingham.
Causal relations, constitutive relations, and interlevel experiments
Chapter 19 Evolutionary Genetics 18 and 20 April, 2004
AS Achievement Standard.
Constructivism -v- Realism Is knowledge a reflection of an outside reality or constructed by us? MRes Philosophy of Knowledge: Day 2 - Session 3 (slides.
Multiple Realizability, Qualia and Natural Kinds Dr. Andrew Bailey Philosophy Department University of Guelph Guelph, Ontario N1G 2W1, Canada
Robert J. Mislevy & Min Liu University of Maryland Geneva Haertel SRI International Robert J. Mislevy & Min Liu University of Maryland Geneva Haertel SRI.
Chapter 10 Human Resource Management and Performance: a Review and Research Agenda David E. Guest.
Mechanisms versus Difference-Making Examples from genetics and molecular biology Gry Oftedal 2009 University of Oslo.
Dynamic Modeling Of Biological Systems. Why Model? When it’s a simple, constrained path we can easily go from experimental measurements to intuitive understanding.
THE PROCESS OF SCIENCE. Assumptions  Nature is real, understandable, knowable through observation  Nature is orderly and uniform  Measurements yield.
The Once and Future Function: Commentary on Pigliucci and Kaplan Paul E. Griffiths.
Scientific method - 1 Scientific method is a body of techniques for investigating phenomena and acquiring new knowledge, as well as for correcting and.
Changing Directions from the NA Binford’s call for Science resulted in a push in that direction with a focus on ultimate causation Binford’s focus on culture.
1 gR2002 Peter Spirtes Carnegie Mellon University.
Conceptual modelling. Overview - what is the aim of the article? ”We build conceptual models in our heads to solve problems in our everyday life”… ”By.
Chapter 01 Lecture Outline
EL: Reflecting on Unit 3 Biology and Exploring Unit 4 Biology.
Stuart Glennan Butler University September  Terminological Questions: What is history?  A Selective Survey of Models of Explanation – their Problems.
BRS 214 Introduction to Psychology Methodology used in psychology field Dawn Stewart BSC, MPA, PHD.
Qualitative Research.
Paper in “Evolution and Development” The Evolution of Signaling Pathways In Animal Development Andr é Pires-daSilva & Ralf J. Sommer Nature Reviews Genetics,
Pitt-London Workshop in Philosophy of Biology and Neuroscience A meeting held at Birkbeck College London under the auspices of The London Consortium, a.
The Journey Of Adulthood, 5/e Helen L. Bee & Barbara R. Bjorklund Chapter 1 Defining the Journey: Some Assumptions, Definitions, and Methods The Journey.
Bayesian Learning By Porchelvi Vijayakumar. Cognitive Science Current Problem: How do children learn and how do they get it right?
Study Questions: 1) Define biology and science.. Study Questions: 1)Define biology and science. - Biology: The scientific study of living systems - Science:
Selection and Change: Biology and Behavior AILUN – Lecture 4 S. Glenn - AILUN 2008.
Learning Progressions: Some Thoughts About What we do With and About Them Jim Pellegrino University of Illinois at Chicago.
Nature of Science. NOS Card Exchange Step 1: Obtain 8 cards (that are different from one another). Step 2: Trade cards with classmates in order to amass.
Chapter 2 Developmental Psychology A description of the general approach to behavior by developmental psychologists.
Phylogenetic Trees: Common Ancestry and Divergence 1B1: Organisms share many conserved core processes and features that evolved and are widely distributed.
Underlying Principles of Zoology Laws of physics and chemistry apply. Principles of genetics and evolution important. What is learned from one animal group.
Bell-Ringer Activity Danielle Donaldson 10 th Grade Biology.
Copyright © 2011 by The McGraw-Hill Companies, Inc. All rights reserved. McGraw-Hill/Irwin Developing and Evaluating Theories of Behavior.
Mechanisms, Modularity and Constitutive Explanation Mechanisms and Causality in the Sciences University of Kent, Canterbury, UK Jaakko Kuorikoski.
Systems Biology ___ Toward System-level Understanding of Biological Systems Hou-Haifeng.
Chapter 10 Adaptation, Perfection, Function Nicolas Crossley K Sex and Death Summer ‘05 E. Oberheim.
Modularity, Flexibility, and Knowledge Management in Product and Organization Design By Ron Sanchez and Joseph Mahoney SMJ (winter 1996) special issue:
SIMULATIONS, REALIZATIONS, AND THEORIES OF LIFE H. H. PATTEE (1989) By Hyojung Seo Dept. of Psychology.
Descent With Modification: A Darwinian View of Life 30 November, 2005 Text Chapter 22.
Chapter Thirteen – Organizational Effectiveness.  Be able to define organizational effectiveness  Understand the issues underpinning measuring organizational.
Introduction to Physiological Principles
Chapter 3 Behavior Analysis A description of the essential features of behavior analysis as a natural science approach to development.
Single-Subject and Correlational Research Bring Schraw et al.
Evolution Webquest Created by Trina Mitchell Summer 2010.
Theories and Methods in Social Psychology David Rude, MA, CPC Instructor 1.
Essential Questions What is biology? What are possible benefits of studying biology? What are the characteristics of living things? Introduction to Biology.
Chapter 6 Attitudes and Intentions Copyright © 2010 by the McGraw-Hill Companies, Inc. All rights reserved. McGraw-Hill/Irwin.
Ontology and the lexicon Nicola Guarino and Christopher A. Welty(2004). An Overview of OntoClean Weber ( 張澄清 ) 2014/04/23 1.
Ms. Hughes.  Evolution is the process by which a species changes over time.  In 1859, Charles Darwin pulled together these missing pieces. He was an.
Mechanistic explanation and the integration of insights from the humanities and cognitive sciences Machiel Keestra, Institute for Interdisciplinary Studies,
Bringing Diversity into Impact Evaluation: Towards a Broadened View of Design and Methods for Impact Evaluation Sanjeev Sridharan.
Animal Behavior and Evolution (Dunbar Ch 1) Psychologists studied Rats… – And made inferences about humans Biologists studied non-humans… – And didn’t.
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Chapter 1 Lecture Slides.
The Science of Biology Chapter 1. Group #1 The characteristcs that all living things have in common are: 1. Cellular organization- all organisms consist.
Taxonomy & Phylogeny. B-5.6 Summarize ways that scientists use data from a variety of sources to investigate and critically analyze aspects of evolutionary.
The Scientific Method. Scientifically Solving a Problem Observe Define a Problem Review the Literature Observe some More Develop a Theoretical Framework.
Complexity, individuation and function in ecology Part II, sec 4 Ecosystem Functionality Prof. John Collier (Departamento de.
Attitudes and Intentions
System Structures Identification
Comparative Method I Comparative methods deal primarily with finding and/or eliminating necessary and/or sufficient conditions that produce a given outcome.
Free will vs Determinism
Developing and Evaluating Theories of Behavior
Summary and Recommendations
THE NATURE OF SCIENCE.
Neuroscience Needs Behavior: Correcting a Reductionist Bias
Presentation transcript:

1 Causality in Complex Systems The Probem of Modularity Mt. Tamborine, July 8, 2009 Sandra D. Mitchell Department of History and Philosophy of Science University of Pittsburgh

2 Dictyostelium – slime mold life cycle Human Brain Honey Bee Colony DynamicCompositional Evolved

3 Complex Biological Systems Evolved contingency Multi-level organization Multi-component causal interactions Modularity compositional structure Robustness in relation to internal and external changes

4 A manipulationist account of causation Mill’s “Method of Difference” “If an instance in which the phenomenon under investigation occurs, and an instance in which it does not occur, have every circumstance in common save one, that one occurring only in the former; the circumstance in which alone the two instances differ, is the effect, or the cause, or an indispensable part of the cause, of the phenomenon.” (Mill, 1888, page 280). The paradigmatic assertion in causal relationships is that manipulation of a cause will result in the manipulation of an effect. … Causation implies that by varying one factor I can make another vary. (Cook & Campbell, 1979, p. 36, emphasis in original.)

5 What would have happened if X had been different? Jim Woodward Making Things Happen Explanation requires only invariance, not universal truth. Invariance comes in gradations or degrees. Relation between variables F (X,Y) is not universal. Under certain “ideal interventions” where the value of X changes, the function will describe the value of Y. Hence X explains Y for those ranges where the functional relationship is invariant.

6 Features of causality Invariance Relation between dependent and independent variable Relation between purported cause and effect Modularity or Separability Is a relation among multiple functional equations describing a single system i.e. A relation of independent disruptability or contribution to overall effect of casual components Insensitivity Stability of causal relation across variations in background, context, or conditions external to system

7 Modularity essential to Causality “..this is implicit in the way people think about causation…this sort of independence is essential to the notion of causation. Causation is connected to manipulability and that connection entails that separate mechanisms are in principle independently disruptable.” (Hausman and Woodward 1999)

8 Modularity beyond equations Modular equations represent distinct, autonomous, context-insensitive causal mechanisms subject to independent disruptability. Modularity in biology, especially evo-devo is held out as potential theoretical unification.

9 Modularity and Exportation Modularity reflects one form of invariance – distinct, autonomous, internally context- insensitive causal mechanisms subject to independent disruptability. A module’s behavior in one system is sufficiently stable and insensitive to be exportable other systems.

10 Is Modularity essential to causation? Some causal networks have elements that do not behave in modular ways Do we want to infer that the elements are NOT causes? Do we have to move to a finer or coarser granularity to satisfy the modularity/independence required? Do we want to infer that modular causes do not exhaust causality?

11 Genetic knock-out experiments

12 Genetic Knockouts Principle assumption: normal function of a gene can be inferred directly from its mutant phenotype. Results are hard to interpret Sometimes “intervention” on one gene  lethal Sometimes “intervention” on one gene  change in phenotype Sometimes “intervention” on one gene  virtually no change in phenotype

13 Problem of Inference “The big surprise to date is that so many individual genes, each of which had been thought important, have been found to be nonessential for development” Robert Weinberg “I don’t believe in complete redundancy. If we knock out a gene and don’t see something, we’re not looking correctly” Mario Capecchi

14

15 Redundancy and Degeneracy Redundancy When a gene is “knocked out” other elements of the same structure are activated. Built in “fail-safe”. Degeneracy or Robustness When a gene is “knocked out” elements of other structures respond flexibly to issue in a similar functional outcome.

16 What do we say of this system? The causal structure reorganized? With intervention – new causal roles for elements which are non independent or context dependent The initial representation was not complete. Response to intervention indicated that not ALL the causal relations were initially represented. Existing ones became active.

Responses 1. “bite the bullet” strategy the genes in the normal genetic pathways are not causes 2. “make the world fit your theory” redescribe the network in finer or coarser granularity 3. “pluralism of causes” modular causes do not exhaust all the types of causality 17

18 Actual Causes versus Causal Laws Domain of biology is historically and currently existing organic life – not what is possible, or potential given the constraints of physics and chemistry. Biology studies ACTUAL causes i.e. a subset of what is biologically possible. And…actual causes may not behavior modularly

19 Biological Modularity “Speaking loosely, biological modules are consortia that act autonomously to produce a single form or function and are redeployed within and across species, thereby creating novelty and fueling the development and evolution of biological complexity.” Meyers 2004 Nature

20 MODULARITY in biology Apparent paradox: same gene or gene complex  different structures in same organism same gene or gene complex  different structures in different taxa Module is part of a system whose internal constituents are strongly interactive while it is as least partially independent of other modules – weakly integrated.

21 Evolutionary and developmental modularity Evolutionary Modules selectable units, i.e. change can occur in one module without causing disruption in the others, thus increasing viability while permitting adaptive variation in complex organisms. Developmental Modules Morphological units i.e. discrete interactive systems of causes with stable context insensitive effects in contributing to development of an organism.

22 Problem: Modules are system and grain dependent “Although the Notch signaling pathway is context- independent module, in the sense that the molecular interactions between its members are conserved and invariant, the outcome of Notch signaling is highly context dependent” Celis, (produces neuron, hair, dermis) “Shh (super sonic hedghog) signalling is a context- independent module with conserved functon during vertibrate muscle development” Borycki Sometimes – invariance is structure, sometimes function. Evolutionary modules do not necessarily map onto developmental modules

23 Methodological implications Singe perturbation experiments even if they indicate causal contribution of gene, assume a fixed genetic background. If there is interaction with the background genes, the results may not be applicable to other contexts. Multifactorial experiments – use existing variation to generate multiple backgrounds and compare effects of gene perturbation across all realistic genetic variation

24 Conclusion and choices Accept that what is “well-behaved” causally varies with embedded context OR Accept that there are non-modular, context sensitive actual causes that explain the behavior of biological systems. The consequence is that exporting knowledge from one system to another requires more than generalization and instantiation – need to use more local knowledge