TIME AND PLACE: March 28**-April 28, 2001; MWF 9-9:50pm; Hibbs 428.


INSTRUCTOR: D. C. Mikulecky, Professor of Physiology, Affiliate Professor of Biology,

Office: 3-012E Sanger Hall, East Campus, Office phone : 828-4500,


web: and



This time around, with the breaking of the humane genome project, we will focus on Rosen's criytical analysis of the gene/phenotype relation as a way of getting the idea.

This module is one of three that also include "Vitalism Old and New" and "Neural Networks/Artificial Intelligence". It traces some exciting changes in our models of reality including catastrophe and bifurcation theory, the theory of chaos, and fractal theory. These honors modules started out having a tentative tone and seeming somewhat speculative when they were introduced over a decade ago. Today, they are at the center of a revolution in science that has been the subject of numerous volumes on "complexity" and "artificial life" in the lay press. We will focus on the meaning of this change and its impact on science as well as on society in general.

In a real sense, things have come full circle. Nicholas Rashevsky was the father of modern biological modeling (mathematical biology). In 1954 he was "visited on the road to Damascus" and completely changed his approach from a very traditional, mechanistic one to a forerunner of modern complexity theory called "relational biology". His student, Robert Rosen, one of the leading pioneers of complex systems theory, further developed his ideas. Robert Rosen died from complications of long term diabetes in December, 1998. His last book, Essays on Life Itself , Columbia University Press, 1999, will furnish most of our material.

In this book, the central ideas stem from Rosen's recent writings, especially those recently expressed in his penultimate book, "Life Itself", which, among other things, seeks to define life and talks about the possibility of the fabrication of living things.

TEXT: Robert Rosen’s book: Essays on Life Itself, Columbia University Press, 1999 [Available in bookstore]

PREVIOUS TEXT: Turbulent Mirror, by John Briggs and David Peat, Harper & Row, 1989

READING ASSIGNMENTS: Since we will be making our classroom discussions a central part of the course, you will be pressed to finish the text assignments before you come to class. Each assignment should be read and ready for discussion at the beginning of the session mentioned below. The readings in Rosen’s book can be difficult. They are not meant to be tedious or overwhelming. Please read/skim them for ideas and things that may help you write your paper and participate in class discussions. In addition to readings in Rosen’s book, you can become much more familiar with the concepts and terms we will be trying to master by looking at the following material on Dr. Mikulecky’s Website:

ISSS paper -Robert Rosen: the well posed question and its answer-why are organisms different from machines?

The Murkywaters discussions

Definition of complexity

Chaos paper

Introduction to chaos

Introduction to Fractals

In addition, please familiarize yourself with the terms in the appendices of this syllabus. Thank you.


Session Reading Assignment The first week we will have no class.   Be prepared to discuss the first weeks reading assignments when we meet for the first time on Wednesday, April 4.


1. (March 28)-Essays….The Preface and Introduction to Part I: On biology and physics

2. (March 30) and 3. (April 2)   Essays.....Chapter 1: The Schrödinger Question, What is Life?

4. (April 4 First Meeting) & 5 (April 6)  Essays….Chapter 3: What is Biology?

6 (April 9)Essays….Introduction to Part III: On genericity

7 (April 11) & 8(April 13) Essays….Chapter 13: Some Random Thoughts about Chaos and Some Chaotic Thoughts about Randomness

9 (April 16) & 10(April18)  Essays….Chapter 14: What Does It Take to Make an Organism?

11 (April 20)  & 12 (April 23) Essays….Introduction to Part IV: Similarity and Dissimilarity in Biology & Chapter 17: What Does It Take to Make an Organism?

13 (April 25)  & 14 (April 27)  Essays….Chapter 21: Cooperation and Chimera

15  (April 30) Recapitulation.  PAPERS DUE May 7 NO EXCEPTIONS!!!



Students will be asked to choose topics for a short (5 to 15 pages) paper due at the end of the course. Class participation in discussions and the paper will be the main evaluation tools. Each will count 50% One goal of the essay will be the integration of the course material into other aspects of the student's work. Another will be to try to write as an integral member of the class as a group. This may be significantly different from expectations in other courses, so please try to understand these guidelines. A full 15% of the evaluation of the paper will be based on how well each paper is part of a composite whole. This can be achieved in a number of ways. ] This is one class where collaboration and working together with one or more of your classmates will be recognized! Some considerable notice will be given to material used from the internet. The remainder of the grade for your paper will be distributed as follows:

quality 25%

understanding of concepts in text and on the internet 25%

organization 10%

use of references and the internet 15%



[These are suggestions, but if you choose something else, check it out with Dr. Mikulecky, please. Any topic in the reading assignments will be ok.]

The human genome project: What it has promised vs what it can deliver

The relationship between genotype and phenotype

The role of Eastern thought in Science

The relationship of physics to biology

Is an organism a machine?

The Role of Fractals and Chaos in [my field]

The relation of Fractals and Chaos to Reductionist thought

Self Organization in living systems

How the educational system is responding to holistic thinking (If at all)

Fractals and Chaos in life and disease

A Review of Michael Chrichton's novel: Jurassic Park

The implications of Fractals and Chaos on predictability

The implications of Fractals and Chaos on the distinction between determinism and randomness

The distinction between realizable and non realizable models in science fiction

The effect of culture and/or gender on one's approach to science

The role of ideology in science

Methodological, ontological, and epistemological reductionism.

Appendix A: Definitions, And other matters.

The modeling relation. Was consciousness our first modeling attempt?

A. The Modeling Relation: How we deal with the world outside ourselves.

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Some things to note about the modeling relation:

It is basically inescapable. You either use it consciously or unconsciously.

It is only a working model of the "real world" if it commutes, in other word if going by arrows 2 + 3 + 4 gets you essentially the same result as arrow 1. If that is not so, you basically have a fantasy or even less.

The encoding and decoding steps are not obtainable from the formal system. They must be supplied independently. In general, they are not even easily spelled out as a stepwise procedure. Thus, one could safely say that there is always some art involved in the modeling process. This is minimized by the reductionist approach that reduces all systems to simple physics and chemistry and therefore uses an predetermined encoding and decoding as a recipe.

The Newtonian Paradigm and the Modeling Relation:

The early successes of Newtonian mechanics and its close relation with Cartesian Reductionism and Dualism led to the modeling relation becoming



What is implied by the above  is that over the past few hundred years, this one way of looking at the world has become so well accepted and so dominant, that we no longer realize we are doing the encoding and decoding. They have become implicit. The Newtonian paradigm with all its reductionist baggage and Cartesian dualism have become synonymous with science. Further, to the extent that biology, sociology, psychology and other fields are not able to successfully conform to this paradigm, they are considered "soft" science and therefore less valid.


Discussion questions:

Why is a "soft" science less valid than physics, for example?

Which is more general and which is more special, physics or biology?

Can you think of reasons or examples that would suggest that the Newtonian paradigm is not always going to make the modeling diagram commute when used as the formal system?


Appendix B: Aristotelian Causality

In Aristotle's epistemology, the question of cause was central.. It arose from asking the question "why?". In modern science, we are taught never to ask "why?" but rather to ask the positivist "how?". This distinction is one important result of our objectification of nature and our selves and is closely related to Cartesian reductionism and dualism. The causalities Aristotle invoked are neither unscientific nor illogical. Let us examine them in the context of answering the question: "why a house?" The causal answers would be:

Material cause: Because there are bricks, lumber, glass, iron, etc. that make up the material aspects of the house.

Efficient cause: Because there are builders who constructed the house.

Formal cause: Because there was a plan or blueprint.

Final cause: Because there was a need for a dwelling place for someone.

It is easily shown that the Newtonian Paradigm incorporates the first three causes in a natural way that is relatively unique in that they appear distinctly and separately:

Material cause is a set of initial conditions for a dynamic system.

Efficient cause is the set of equations of motion generated by Newton's Second Law (f = ma) or its equivalent.

Formal cause is the trajectories obtained by integrating the equations of motion.

There is no Final Cause in the Newtonian Paradigm!

In complex systems, especially living systems, all four causes appear and are usually not easily separated as in the Newtonian Paradigm.

Appendix C: The three forms of reductionism (see Peacoke 1985).

Methodological reductionism: Breaking a system down into constituent parts to better study them apart from the whole.

Ontological reductionism: Seeing a system as the parts.

Epistemological reductionism: Using theory from one level of a hierarchical system to explain events at another level.

Methodological reductionism is generally inescapable. In biology, it is often overdone. Some writers claim that biologists are not happy until their object of study is dead. One reason for this is the lack of emphasis on theory in biology. The Newtonian paradigm seems adequate, but this is because of having reduced the living system to simple physical and chemical systems.