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- DON MIKULECKY
- PROFESSOR EMERITUS OF PHYSIOLOGY AND SENIOR FELLOW IN THE CENTER FOR THE
STUDY OF BIOLOGICAL COMPLEXITY-VCU
- http://www.people.vcu.edu/~mikuleck/
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- IF THE SYSTEM IS CORRUPT THEN HOW CAN A PERSON WHO WANTS NOT TO PARTICIPATE IN CORRUPTION BE A
PARTICIPANT?
- HE MUST REDUCE THE SYSTEM TO UNRELATED ENDEAVORS SO THAT HE CAN ESCAPE
RECOGNIZING HIS PARTICIPATION IN THE CORRUPT WHOLE
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- REQUIRES A CIRCLE OF IDEAS AND METHODS THAT DEPART RADICALLY FROM THOSE
TAKEN AS AXIOMATIC FOR THE PAST 300 YEARS
- OUR CURRENT SYSTEMS THEORY, INCLUDING ALL THAT IS TAKEN FROM PHYSICS OR
PHYSICAL SCIENCE, DEALS EXCLUSIVELY WITH SIMPLE SYSTEMS OR MECHANISMS
- COMPLEX AND SIMPLE SYSTEMS ARE DISJOINT CATEGORIES
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- Von NEUMAN THOUGHT THAT A CRITICAL LEVEL OF “SYSTEM SIZE” WOULD
“TRIGGER” THE ONSET OF “COMPLEXITY” (REALLY COMPLICATION)
- COMPLEXITY IS MORE A FUNCTION OF SYSTEM QUALITIES RATHER THAN SIZE
- COMPLEXITY RESULTS FROM BIFURCATIONS -NOT IN THE DYNAMICS, BUT IN THE
DESCRIPTION!
- THUS COMPLEX SYSTEMS REQUIRE THAT THEY BE ENCODED INTO MORE THAN ONE
FORMAL SYSTEM IN ORDER TO BE MORE COMPLETELY UNDERSTOOD
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- AHARON KATZIR-KATCHALSKY (died in terrorist massacre in Lod Airport
1972)
- LEONARDO PEUSNER (alive and well in Argentina)
- ROBERT ROSEN (died December 29, 1998)
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- FOR A BIBLIOGRAPHY OF ROSEN’S WORK: http://views.vcu.edu/complex/
- Pusner, Leonardo: Two books on network thermodynamics
- My book: Application of network thermodynamics to problems in biomedical
engineering, NYU Press, 1993
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- New review:The Circle That Never Ends: Can Complexity Be Made Simple? In
Complexity in Chemistry, Biology, and Ecology Bonchev, Danail D.;
Rouvray, Dennis (Eds.) 2005
- New Book: Into the Cool: Energy Flow, Thermodynamics and Life by: Eric D. Schneider and Dorion
Sagan, University of Chicago Press, 2005
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- ALLOWS US TO ASSIGN MEANING TO THE WORLD AROUND US
- STANDS FOR OUR THINKING PROCESS
- CAUSALITY IN THE NATURAL SYSTEM IS DEALT WITH THROUGH IMPLICATION IN A
FORMAL SYSTEM
- THERE IS AN ENCODING OF THE NATURAL SYSTEM INTO THE FORMAL SYSTEM AND A
DECODING BACK
- WHEN IT ALL HANGS TOGETHER WE HAVE A MODEL
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- THE FORMAL SYSTEM DOES NOT INCLUDE INFORMATION ABOUT ENCODING AND/OR
DECODING
- THEREFORE MODELING WILL ALWAYS BE AN ART
- ONLY IN THE NEWTONIAN PARADIGM DOES THE FORMAL SYSTEM BECOME THE NATURAL
SYSTEM (ENCODING AND DECODING ARE AUTOMATIC) AND ALL THAT IS LEFT TO DO
IS TO MEASURE THINGS
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- THE FORMAL SYSTEM DOES NOT AND CAN NOT TELL US HOW TO ENCODE AND DECODE.
(MODELING IS AN ART!)
- THE FORMAL SYSTEM DOES NOT AND CAN NOT TELL US WHEN THE MODEL WORKS,
THAT IS A JUDGEMENT CALL EVEN IF OTHER FORMALISMS ARE ENLISTED TO HELP
(FOR EXAMPLE: STATISTICS)
- MODELS EXIST IN A CONTEXT: A FRAME
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- WE ARE TOO AFRAID OF “BELIEFS” (SCEPTICISM IS “IN”)
- WE DEVELOPED THE MYTH OF “OBJECTIVITY”
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- Based on the work of George Lakoff
- Cognitive Linguistics
- Frames are the mental structures
that shape the way we see the
world
- Facts, data, models, etc. only have meaning in a context
- Leads us to a scientific application of framing: Rosen’s theory of
complexity
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- Don’t think of an elephant
- Impossibility of avoiding the frame
- In science the dominant frame is reductionism and the associated
mechanical thinking
- The dominant modern manifestations include molecular biology and
nonlinear dynamics
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- SCIENTISTS FOCUS ON THE FORMAL DESCRIPTION RATHER THAN THE REAL WORLD
- THE REAL WORLD IS COMPLEX
- FORMAL SYSTEMS COME IN VARYING SHADES AND DEGREES OF COMPLICATION
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- Rather than change methods we have
the changed names for what we do
- The consequences are significant
- It is impossible for you to believe what is being taught in this lecture
and to then simply add it to your repertoire
- The reason is that in order to see the world in a new way you have to
step out of the traditional frame and into a new one. Once done, you can never go back. The ability to reframe a question is
the basis for change and broadening of ideas.
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- WE MORE OR LESS FORGOT THAT THERE WAS AN ENCODING AND DECODING
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- THE “REAL WORLD” REQUIRES MORE THAN ONE “FORMAL SYSTEM” TO MODEL IT
(THERE IS NO “UNIVERSAL MODEL”)
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- The map is not the territory
- An equation is just an equation without interpretation
- This means we use formalisms in a context
- This context dependence also exists in nature
- This is one reason why there can never be a largest model
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- A process happens in a context
- The process usually changes that context
- If the context changes the process usually changes as a result.
- Living systems are replete with examples of this
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- IT HAS BEEN TRIED
- IT FAILED
- THE ALTERNATIVE IS TO “GO AROUND” IT – THAT IS TO IGNORE CASES WHERE IT
POPS UP
- WHAT IF IT IS VERY COMMON?
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- TOO MANY DEFINITIONS, SOME CONFLICTING
- OFTEN INTERCHANGED WITH “COMPLICATED”
- HAS A REAL MEANING BUT AFTER THE QUESTION IS REFRAMED
- THAT MEANING ITSELF IS COMPLEX(THIS IS SELF-REFERENTIAL: HOW CAN WE
DEFINE “COMPLEX” USING “COMPLEX”?)
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- Complexity is the property of a
real world system that is manifest in the inability of any one formalism
being adequate to capture all its properties. It requires that we find
distinctly different ways of interacting with systems. Distinctly
different in
- the sense that when we make
successful models, the formal systems needed to describe each distinct
aspect are NOT
- derivable from each other
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- COMPLEX
- NO LARGEST MODEL
- WHOLE MORE THAN SUM OF PARTS
- CAUSAL RELATIONS RICH AND INTERTWINED
- GENERIC
- ANALYTIC ¹ SYNTHETIC
- NON-FRAGMENTABLE
- NON-COMPUTABLE
- REAL WORLD
- SIMPLE
- LARGEST MODEL
- WHOLE IS SUM OF PARTS
- CAUSAL RELATIONS DISTINCT
- N0N-GENERIC
- ANALYTIC = SYNTHETIC
- FRAGMENTABLE
- COMPUTABLE
- FORMAL SYSTEM
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- What is life?
- Why is an organism different from a machine?
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- Rosen used relational ideas to
apply category theory to living systems
- These were called “Metabolism/Repair” systems oo M-R systems
- Causal mappings were diagramed a syntax involving category theory
mappings and the semantics were used along with this to apply the causal
interpretaion
- The result was a clear demonstration that the machine and the organism
are disjoint in this context
- An organism is closed to efficient cause while a machine is not
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- Since machines are causally impoverished, they lead to an infinite
regress of causes.
- Descartes led us to use the machine metaphor for organisms
- In so doing he made a concept of God necessary
- Today, “Intelligent Design” is based on this erroneous Cartesian
metaphor: The Machine Metaphor
- Real orgainisms are closed causually and escape this fallacy
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- HAS MANY DEFINTIONS
- SOME OF THESE ARE IN CONFLICT
- SCIENCE IS A BELIEF STRUCTURE
- SCIENCE OF METHOD VS SCIENCE OF CONTENT
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- WHY IS THE WHOLE MORE THAN THE SOME OF THE PARTS?
- SELF-REFERENCE AND CIRCULARITY
- THE LIFE/ORGANISM PROBLEM
- THE MIND/BODY PROBLEM
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- I AM A CORINTHIAN
- ALL CORINTHIANS ARE LIARS
- OR
- “THE STATEMENT ON THE OTHER SIDE IS FALSE”-ON BOTH SIDES
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- DNA?
- GENES?
- PROTEINS?
- OTHER CELLS?
- SPONTANEOUS GENERATION?
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- CELLS COME FROM OTHER CELLS
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- THE MACHINE METAPHOR TELLS US TO ASK “HOW?”
- REAL WORLD COMPLEXITY TELLS US TO ASK “WHY?”
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- MATERIAL: THE STUFF IT’S MADE OF
- EFFICIENT: IT NEEDED A BUILDER
- FORMAL: THERE WAS A BLUEPRINT
- FINAL: IT HAS A PURPOSE
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- BECAUSE REDUCING A REAL SYSTEM TO ATOMS AND MOLECULES LOOSES IMPORTANT
THINGS THAT MAKE THE SYSTEM WHAT IT IS
- BECAUSE THERE IS MORE TO REALITY THAN JUST ATOMS AND MOLECULES
(ORGANIZATION, PROCESS, QUALITIES, ETC.)
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- THE “LAWS” OF NATURE THAT TRADITIONAL SCIENCE TEACHES ARE ARTIFACTS OF A
LIMITED MODEL
- THE REAL “RULES OF THE GAME” ARE CONTEXT DEPENDENT AND EVER CHANGING-
THEY MAKE THE CONTEXT AND THE CONTEXT MAKES THEM (SELF-REFERENCE)
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- LIFE IS CONSISTENT WITH THE LAWS OF PHYSICS
- PHYSICS DOES NOT PREDICT LIFE
- LIVING CELLS COME FROM OTHER
LIVING CELLS
- AN ORGANISM MUST INVOLVE CLOSED LOOPS OF CAUSALITY
- LIFE DOES INVOLVE PURPOSE: See Into the cool
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- Thermodynamics is an example of how attempts to remove complexity from
reductionist thought can not succeed
- The nature of thermodynamic reasoning had resisted this tendency very
well and we will look at why this is so
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- REDUCTIONISM DID SERIOUS DAMAGE TO THERMODYNAMICS
- THERMODYNAMICS IS MORE IN HARMONY WITH TOPOLOGICAL MATHEMATICS THAN IT
IS WITH ANALYTICAL MATHEMATICS
- THUS TOPOLOGY AND NOT MOLECULAR STATISTICS IS THE FUNDAMENTAL TOOL
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- CAROTHEODRY’S PROOF OF THE SECOND LAW OF THERMODYNAMICS
- THE PROOF OF TELLEGEN’S THEOREM AND THE QUASI-POWER THEOREM
- THE PROOF OF “ONSAGER’S” RECIPROCITY THEOREM
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- THERMODYNAMICS IS ABOUT THOSE PROPERTIES OF SYSTEMS WHICH ARE TRUE
INDEPENDENT OF MECHANISM
- THEREFORE WE CAN NOT LEARN TO DISTINGUISH MECHANISMS BY THERMODYNAMIC
REASONING
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- NATURE EDITORIAL: VOL 234, DECEMBER 17, 1971, pp380-381
- “KATCHALSKY AND HIS COLLEAGUES SHOW, WITH EXAMPLES FROM MEMBRANE
SYSTEMS, HOW THE TECHNIQUES
DEVELOPED IN ENGINEERING SYSTEMS MIGHT BE APPLIED TO THE EXTREMELY
HIGHLY CONNECTED AND INHOMOGENEOUS PATTERNS OF FORCES AND FLUXES WHICH
ARE CHARACTERISTIC OF CELL BIOLOGY”
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- THE NATURE OF THERMODYNAMIC REASONING
- HOW CAN LIFE FIGHT ENTROPY?
- WHAT ARE THERMODYNAMIC NETWORKS?
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- ENTROPY MUST INCREASE IN A REAL PROCESS
- IN A CLOSED SYSTEM THIS MEANS IT WILL ALWAYS GO TO EQUILIBRIUM
- LIVING SYSTEMS ARE CLEARLY “SELF - ORGANIZING SYSTEMS”
- HOW DO THEY REMAIN CONSISTENT WITH THIS LAW?
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- DISSIPATION AND THE SECOND LAW OF THERMODYNAMICS
- PHENOMENOLOGICAL DESCRIPTION OF A SYTEM
- COUPLED PROCESSES
- STATIONARY STATES AWAY FROM EQUILIBRIUM
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- WE CHOSE TO LOOK AT FLOWS “THROUGH” A STRUCTURE AND DIFFERENCES “ACROSS”
THAT STRUCTURE (DRIVING FORCES)
- EXAMPLES ARE DIFFUSION, BULK FLOW, CURRENT FLOW
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- KEDEM AND KATCHALSKY, LATE 1950’S
- J1 = L11 X1 + L12 X2
- J2 = L21 X1 + L22 X2
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- T Ds/dt = J1 X1 +J2 X2 > 0
- EITHER TERM CAN BE NEGATIVE IF THE OTHER IS POSITIVE AND OF GREATER
MAGNITUDE
- THUS COUPLING BETWEEN SYSTEMS ALLOWS THE GROWTH AND DEVELOPMENT OF
SYSTEMS AS LONG AS THEY ARE OPEN!
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- LIKE A CIRCUIT
- REQUIRE A CONSTANT SOURCE OF ENERGY
- SEEM TO BE TIME INDEPENDENT
- HAS A FLOW GOING THROUGH IT
- SYSTEM WILL GO TO EQUILIBRIUM IF ISLOATED
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- High potassium
- Low Sodium
- Na/K ATPase pump
- Resting potential about 90 - 120 mV
- Osmotically balanced (constant volume)
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- ELECTRICAL NETWORKS ARE THERMODYNAMIC
- MOST DYNAMIC PHYSIOLOGICAL PROCESSES ARE ANALOGS OF ELECTRICAL PROCESSES
- COUPLED PROCESSES HAVE A NATURAL REPRESENTATION AS MULTI-PORT NETWORKS
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- RESISTANCE IS ENERGY DISSIPATION (TURNING “GOOD” ENERGY TO HEAT IRREVERSIBLY - LIKE FRICTION)
- CAPACITANCE IS ENERGY WHICH IS STORED WITHOUT DISSIPATION
- INDUCTANCE IS ANOTHER FORM OF STORAGE
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- START WITH KINETIC DESRIPTION OF DYNAMICS
- ENCODE AS A NETWORK
- TWO POSSIBLE KINDS OF ENCODINGS AND THE REFERENCE STATE
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- ONE CAPTURES THE UNCONSTRAINED BEHAVIOR OF THE SYSTEM AND IS GENERALLY
NON-LINEAR
- THE OTHER IS ONLY VALID WHEN THE SYSTEM IS CONSTRAINED (IN A REFERENCE
STATE) AND IS THE USUAL THERMODYNAMIC DESRIPTION OF A COUPLED SYSTEM
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- SR (BRIGGS,FEHER)
- GLOMERULUS (OKEN)
- ADIPOCYTE GLUCOSE TRANSPORT AND METABOLISM (MAY)
- FROG SKIN MODEL (HUF)
- TOAD BLADDER (MINZ)
- KIDNEY (FIDELMAN,WATTLINGTON)
- FOLATE METABOLISM (GOLDMAN, WHITE)
- ATP SYNTHETASE (CAPLAN, PIETROBON, AZZONE)
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- THE REAL WORLD IS COMPLEX
- THE WORLD OF “SIMPLE MECHANISMS” IS A SURROGATE WORLD CREATED BY
TRADITIONAL SCIENCE
- WE ARE AT A CROSSROADS: A NEW WORLDVIEW IS NEEDED
- THERE WILL ALWAYS BE RISK ASSOCIATED WITH ATTEMPTS TO PROGRESS
- YOUR CRYSTAL BALL MAY BE AS GOOD AS MINE OR BETTER
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- WE LIVE IN A WORLD DOMINATED BY COMPUTERS
- MOST COMPLEXIFIERS BELIEVE THAT COMPLEXITY IS SOMETHING WE CAN DEAL WITH
ON THE COMPUTER
- THIS NOTION OF COMPLEXITY FOCUSES ON THE MECHANICAL ASPECTS OF THE REAL
WORLD
- WHAT MAKES THE REAL WORLD COMPLEX IS ITS NON-COMPUTABILITY
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