Understanding Complex Ecosystem Dynamics: A Systems and Engineering Perspective

Yackinous

Preface

Look deep, deep into nature, and then you will understand everything better.

Albert Einstein¹

I have had a 34-year professional career as a systems engineer at Bell Laboratories. Originally, The Bell Telephone Laboratories was the research and development arm of the Bell System in the United States. From the 1920s to about 2000, Bell Labs was acknowledged by many to be the premier R&D labs in the world. The term systems engineering was coined at Bell Laboratories in the 1940s. Throughout my career, I worked to solve systems problems for Bell Labs and for its clients across the United States and around the world. During that time, I acquired a very significant set of skills and perspectives with respect to the practice of systems engineering and the systems approach. In my Bell Labs work, I focused on building human-made systems (some would say artificial systems). I have always thought, however, that this same set of skills and perspectives could be applied very beneficially to understanding natural systems—specifically natural ecological systems. After taking early retirement from Bell Labs in 2001, I began to do just that. I began to follow Einstein’s admonition (above) in earnest.

My first task was to explicitly define and describe the systems and systems engineering skill set that I had acquired during my career. The science and engineering working environment at Bell Labs was outstanding and full of opportunities. Over the years, I was fortunate² to be in a position to earn every major Bell Labs technical award and honorarium including the highest and most prestigious—Bell Labs Fellow. As a result, I frequently had the opportunity to give talks and seminars on systems engineering both inside Bell Labs and at major universities. I gave presentations, on behalf of Bell Laboratories, to graduate engineering and computer science students and faculty at Stanford University, UC Berkeley, Cal Tech, UCLA, University of Arizona, University of Texas, Purdue University, and Oxford University. My objective in these various talks was to describe my view of the required skills and perspectives necessary for the successful practice of systems engineering. Beginning with the material comprising the talks, I have developed A Systems Engineering Skills Framework. We will discuss that in Chapter 1.

My next task—and my primary ongoing work objective—was the application of those systems and engineering skills to increase understanding of complex natural systems. Given the state of our planet’s environment, I decided that the most important and relevant natural systems for me to consider were ecological systems. I needed to engage, therefore, in very substantial ecological system study and research. To that end, I pursued a PhD in Ecology at the University of Georgia’s Eugene P. Odum School of Ecology. Dr. Eugene Odum was a very influential ecologist, a pioneer in the area of systems ecology, and a founder of the ecology program at the University of Georgia. Dr. Bernard C. Patten was my PhD major professor and my doctoral committee chairperson. He is a systems ecologist and is recognized as one of the premier ecological system modelers and ecological network analysts in the field. I studied with Dr. Patten and the Systems and Engineering Ecology group—an interdisciplinary group of professors and graduate students at the University of Georgia. I received my PhD degree in Ecology in December 2010. My doctoral research and dissertation on Emerging Principles of Ecological Network Dynamics are prominently reflected in this book.

As I have explained, the systems and engineering skills and perspectives that I acquired at Bell Labs are absolutely essential to my ecosystem research. My related systems and engineering academic background also plays an important role. My early degrees—bachelors and masters—are in electrical engineering. My master’s degree work (and early Bell Labs work) included the areas of communications theory, signal processing theory, information theory, control theory, and network theory. My more recent PhD academic work has enhanced my understanding of the various important subsets of complex systems theory. All of these scientific disciplines and their associated methods and tools contribute to my current complex system dynamics work. You will notice that throughout the book.

Highly complex systems (including ecosystems) take the form of networks. My work addresses challenging and open issues of complex system network dynamics. It pushes boundaries and explores frontiers. Thus far, mainstream network science has focused primarily on understanding network structure. Network dynamics is a much tougher issue. Melanie Mitchell, in her book on complexity, has said, To understand the dynamics … network science will have to characterize networks in which the nodes and links continually change in both time and space. This will be a major challenge, to say the least (Mitchell, 2009). Duncan Watts has said, Next to the mysteries of dynamics on a network … the problems of networks that we have encountered up to now are just pebbles on the seashore (Watts, 2003). In this book, we take on the challenge of understanding complex system network dynamics—specifically complex ecosystem network dynamics.

The complex system dynamics research described in the book is innovative and unique in many respects. The full set of experiences, approaches, methods, and tools employed here have never before been applied to ecological systems (or to complex systems in general). The work represents a fresh look at ecological network dynamics. I have begun with substantial systems and engineering experience and knowledge; combined that with PhD-level study of ecology; and further, have supplemented those resources with additional study of complex systems theory in the areas of networks, nonlinear dynamics, cellular automata, and roughness (fractals). I have assimilated, extended, and combined all of these resources in new ways to create a fresh view of complex system dynamics. That process is the working definition of innovation and creativity. Creativity is the ability to discover new relationships, to look at subjects from new perspectives, and to form new combinations from two or more concepts already in the mind (Evans, 1991). Scientific discovery often arises from picking up the stick from the other end (Butterfield, 1960). The other end, in this case, is the systems and engineering perspective.

This book clearly takes an interdisciplinary perspective and contains many new ideas that sometimes do not represent merely small, incremental changes to existing scientific paradigms. Although such new perspectives and ideas are often necessary to push research boundaries, they are not always easily accepted by natural science investigators who prefer more traditional approaches and paradigms. (Thomas Kuhn (1996), in his classic book The Structure of Scientific Revolutions, comprehensively describes these effects.) Some of the ideas and hypotheses in the book, therefore, may be controversial. That circumstance may generate an increased focus on important complex system issues and motivate scientists across disciplines to ponder and explore these issues. In my view, that would be a very desirable outcome of the book. It would help to further our collective understanding of complex system dynamics.

Throughout this book, I reference and quote a lot of very smart people. Except for a few, I know these people only by their work. Their work has been exceedingly helpful. I quite agree with the sentiment that Thoreau³ expressed long ago in his Journals: He who speaks with most authority on a given subject is not ignorant of what has been said by his predecessors. He will take his place in a regular order, and substantially add his own knowledge to the knowledge of previous generations. I certainly do not claim that I speak with most authority—but I am pleased to have the opportunity to express my views in this book.

We began this preface with some advice from Albert Einstein. I have attempted to look deep into nature. I think that now I really do understand everything better. I’m still working on it ….

Bill Yackinous

November 2014

References

Butterfield H. The Origins of Modern Science. New York, NY: Macmillan; 1960.

Evans JR. Creative Thinking in the Decision and Management Sciences. Cincinnati, OH: South-Western Publishing; 1991.

Kuhn TS. The Structure of Scientific Revolutions. third ed. Chicago, IL: The University of Chicago Press; 1996.

Mitchell M. Complexity: A Guided Tour. New York, NY: Oxford University Press; 2009.

Watts DJ. Six Degrees: The Science of a Connected Age. New York, NY: W. W. Norton; 2003.

¹ Albert Einstein, in The Quotable Einstein, Princeton University Press, 1996, p. 32.

² I have found that such opportunity and good fortune is directly related to having very good bosses. They were plentiful at Bell Labs. I’ve had some of the best.

³ Henry David Thoreau, Journals, December 31, 1859.

Introduction

The primary purpose of my work in this book is to increase the understanding of complex system dynamics—in particular, complex ecological system dynamics. My systems and engineering perspective is foundational to this effort. I begin by defining and describing pertinent systems and engineering skills and practices, including an explanation of the systems approach and its major elements. Consistent with the systems approach, I then formulate an ecosystem dynamics functionality-based framework to guide my investigations. Complex systems theory, across many subject matter areas, is crucial to the work of this book. I cover relevant network theory, nonlinear dynamics theory, cellular automata theory, and roughness (fractal) theory in some detail. This material serves as an important resource as we proceed in the book. Next, in the context of all of the foregoing investigation, I construct a view of the characteristics of ecological network dynamics. This view, in turn, is the basis for the central hypothesis of the book, i.e., ecological networks are ever-changing networks with propagation dynamics that are punctuated, local-to-global, and perhaps most importantly fractal. To analyze and fully test this hypothesis I define, design, and develop an innovative ecological network dynamics model. The modeling approach seeks to emulate features of real-world ecological networks. The approach does not make a priori assumptions about ecological network dynamics, but rather lets the dynamics develop as the model simulation runs. Model analysis results corroborate the hypothesis. Additional important insights and principles are suggested by the model analysis results and by the other supporting investigations of this book—and may serve as a basis for going-forward complex system dynamics research, not only for ecological systems but also for complex systems in general.

Map of the Book

The book has six major parts comprised of nineteen chapters. There is also an appendix. An overview of each of the book’s components follows.

Part I The Systems and Engineering Perspective

Part I (Chapters 1 through 4) provides a comprehensive look at the systems and engineering perspective that is foundational to the work of this book. Chapter 1 describes my view of systems engineering skills, the systems approach, and the associated systems perspectives that can be beneficially applied to understanding highly complex natural systems. Chapter 2 discusses additional views on systems thinking from the scientific community—as well as more of my own views. In Chapter 3, I detail three important concepts that I consider to be major elements of the systems approach. They are: a blend of synthesis and analysis; network thinking; and the systems triad. Note that traditional scientific research (including ecological research) is most often conducted using a reductionist approach rather than a systems approach. Chapter 4 addresses a significant potential problem with the indiscriminate use of reductionism, i.e., reductionism can isolate the target of investigation from the larger system in which it resides and thereby cause information loss.

Part II A Function-Structure-Process Framework for Ecological System Dynamics

In Part II (Chapters 5 through 7), I construct and describe a functionality-based framework that provides a unifying context for exploring principles of ecosystem dynamics. In systems engineering, I have found that such a framework is essential for specifying and guiding the design and development of artificial (human-made) systems. In systems ecology, such a framework is equally essential for understanding natural systems. Chapter 5 provides an overview of this ecosystem dynamics framework—which consists of operational, developmental, and core functional tiers. In Chapter 6, one of the core ecological system functions, regulation/adaptation, is discussed in detail. Chapter 7 addresses the developmental tier. I make the case that the species evolution function provides the basis for a universal development model. The operational tier becomes our focus in Parts IV and V of the book. (All of the elements of the framework are discussed, to varying degrees, throughout the book.)

Part III Complex Systems Theory: Networks, Nonlinear Dynamics, Cellular Automata, and Fractals (Roughness)

In Part III (Chapters 8 through 12), we conduct an extensive review of the pertinent extant complex systems theory. Chapters 8 and 9 cover network theory. Those two chapters address the structure aspects and the dynamics aspects, respectively, of complex networks. Chapter 10 reviews nonlinear dynamics theory. Chapter 11 is about cellular automata investigations and associated emerging complex system principles. Chapter 12 addresses fractals (roughness theory). In some areas, I provide additional commentary based on my systems, engineering, and ecological perspectives. The material of Part III serves as a valuable and necessary resource for our work. Application and, in some cases, extensions of the theory contribute to a synthesis of ideas that is pursued in the subsequent parts of the book.

Part IV A View of the Characteristics of Ecological Network Dynamics

Based on knowledge of the systems approach (Part I), the ecosystem dynamics framework (Part II), and applicable complex systems theory (Part III), a view of the characteristics of ecological network dynamics is constructed in Part IV (Chapters 13–15). First, we do a bit more investigation to properly set the stage. Chapter 13 addresses the human perceptual context in which we are working, especially the human tendency to see smoothness, stability, and continuity in the natural world—even when they are absent. Chapter 14 considers the nature of order and complexity in ecological systems—and their relationships—to gain additional insights into the behavior of highly complex systems. Now we are ready to proceed with the dynamics characteristics. Chapter 15 describes a comprehensive view of the behavioral characteristics of ecological network dynamics, which is the basis for the central hypothesis of the book: ecological networks are ever-changing, flickering networks with propagation dynamics that are punctuated, fractal, local-to-global, and enabled by indirect effects.

Part V Modeling Ecological Network Dynamics and the Generation and Analysis of Results

In Part V (Chapters 16–18), I describe the development of an innovative ecological network dynamics model, the generation of results, and the analysis of those results in order to test our central characteristics hypothesis. Model requirements are the subject of Chapter 16. Model software design and development are covered in Chapter 17. The software implements the ecological network operational model, the required analysis activities, and the needed graphics capabilities. Chapter 18 is all about results. Ecological network dynamics results are generated, displayed, and analyzed. The specific dynamics results categories are: operational propagation flow; network propagation events; propagation path length; indirect effects; and network connectivity. The characteristics hypothesis is fully tested—and corroborated.

Part VI Pulling It All Together

In Part VI (Chapter 19), we pull everything together. The chapter begins with a brief summary of the key aspects of the work covered in the book. We then take a broader and more interpretative look at the work with respect to the perspective taken, what we have found, what it means, and its potential influence on work in this area going forward. We see that, although our focus has been ecological systems, there are implications for all complex systems.

Appendix

Complex system dynamics modeling is an important part of my work and an important part of this book. I have developed the software that implements my complex ecosystem dynamics model using the MATLAB¹ programming environment and language. I want readers to have access to the model and the complete MATLAB programming code. Readers are invited to explore, run, and experiment with the model software in order to enhance their understanding of complex system network dynamics—as well as to develop and test their own ideas. The full complex ecosystem dynamics model code is available on the book’s companion website.² The programming code is heavily commented to explain and describe the software.

In the appendix to this book, I provide selected excerpts of the model programming code. I refer to this material as I discuss the model in the main body of the book. These excerpts provide the reader with easy access to examples of the software without having to navigate through the full set of MATLAB m-files while reading the book. There are nine code excerpts ranging from code that establishes the model network structure and relationships, to code that describes and implements propagation process flow, to code that describes and implements ecosystem dynamics analysis activities.

A Fresh Look at Complex System Dynamics

The book takes a fresh, interdisciplinary look at complex system dynamics and contains many new ideas, perspectives, and areas of emphasis. Here are a few examples. (1) In complexity theory, the emphasis is often on chaotic systems. While chaotic systems are complex, they are not the most complex. They do not exhibit coherent process-over-structure flow that delivers meaningful function. I focus on the most-complex systems, e.g., highly complex ecological systems. (2) Extant work on fractals typically emphasizes static spatial fractals (also called structure fractals). Even Benoit Mandelbrot (the originator of fractal geometry) dealt primarily with structure fractals. I, on the other hand, focus on dynamic process fractals—which have both spatial and temporal aspects. (3) Although most of the extant research efforts on networks have dealt with network structure rather than network dynamics, I have taken on the challenge of complex system network dynamics in this book. (4) I have found that traditional ecosystem models do not adequately represent the real-time ecological system dynamics that I wish to represent. Therefore, I have developed a new innovative modeling approach that does so. (5) Finally, much of the writing on systems thinking is limited to discussion of broad generalizations. My view of the systems approach focuses on tested and proven elements that I have applied successfully in my work for years—and have applied throughout this book as well.

¹ MATLAB release R2009a, The MathWorks, Inc., February 12, 2009.

² To access the companion site, go to http://booksite.elsevier.com/9780128020319.

Part I

The Systems and Engineering Perspective

Introduction

This part provides a comprehensive look at the systems and engineering perspective that is foundational to the work of this book. My views as well as other views from the scientific community are addressed. The systems approach and the reductionist approach are compared and contrasted.

Chapter 1

A Systems Engineer’s Perspective

Abstract

This chapter describes my view of the systems engineering skill set, the systems approach, and the associated systems perspectives that can be very beneficially applied to understanding highly complex natural systems. The vehicle for accomplishing this is my systems engineering skills framework. The framework defines the systems engineering domain, and then addresses the four key skill areas: engineering technical methods, system development skills, systems thinking, and communication skills. Engineering technical methods include mathematical methods, empirical methods, and computer simulation. System development skills include system design, system modeling, and system architecting. The major elements of systems thinking are iterative synthesis and analysis, network thinking, and the systems triad. Necessary communication skills are also discussed. Application of these skills to ecological systems is not a giant leap. In the spirit of the systems approach, it is a reasonable and prudent pursuit.

Keywords

Systems engineering

Systems engineering skills

Engineering technical methods

System development skills

System design

System modeling

Systems thinking

Reflective rationality

1.1 Introduction

As I discussed in the Preface to this book, I had a 34-year career as a systems engineer at Bell Laboratories. During that time, I acquired a very substantial set of skills and perspectives with respect to the practice of systems engineering and the systems approach. I frequently had the opportunity to give talks and seminars on systems engineering both inside Bell Labs and at major universities. The university audiences were composed of graduate engineering and computer science students and faculty. My objective in these various talks was to describe my view of the required skill set necessary for the successful practice of systems engineering. It is these same skills and perspectives that I endeavor to apply to ecological systems in this book.

I have explicitly defined and described the systems and systems engineering skill set that I acquired during my career. Starting with the material comprising my Bell Labs and university talks, I have developed a systems engineering skills framework. In this chapter, I’ll provide an overview of the skills framework and discuss my systems engineering perspectives. Areas requiring further elaboration regarding their application to ecological systems are discussed in more detail in subsequent chapters.

1.2 Definitions

Let’s begin with a few definitions and then get right to the framework. The Merriam-Webster online¹ definition of system includes 1: a regularly interacting or interdependent group of items forming a unified whole … as (a): a group of interacting bodies under the influence of related forces … (b): a group of body organs that together perform one or more vital functions … (c): a group of related natural objects or forces … (d): a group of devices or artificial objects or an organization forming a network. The etymology is given as late Latin and Greek with origins from synistanai, to combine. The Next Generation Education Project² provides a concise and useful definition of system: A group of interacting, interrelated, or interdependent elements that together form a complex whole.

Systems engineering can be defined as an interdisciplinary approach and means:

1. To enable the realization of successful human-made systems.

2. To increase understanding of natural systems.

The first part of this definition is from INCOSE (The International Council on Systems Engineering).³ I added the second part.

The term system(s) engineer has been used rather loosely by the technical community over the years, and has been given very different meanings in different contexts. For example, the title Microsoft Certified Systems Engineer⁴ referred to someone who knows something about Microsoft computer operating systems and has passed some related exams. That usage of the term systems engineer has little to do with what I am talking about here. I consider a much broader context.

1.3 Systems Engineering Skills Framework

The systems engineering skills framework is depicted in Figure 1.1.

Figure 1.1 The systems engineering skills framework.

Application of these skills to ecological systems is not a giant leap. In the spirit of the systems approach and systems thinking, it is a reasonable and prudent pursuit. The five framework components—systems engineering domain, engineering technical methods, system development skills, systems thinking, and communication skills—are described in Sections 1.3.1–1.3.5, respectively.

1.3.1 Systems Engineering Domain

As shown in the center of Figure 1.1, traditional systems engineering activities include

• Articulating needs and stating the problem.

• Defining requirements.

• Designing and specifying a system solution.

All of these more traditional activities pertain to building human-made systems. I want to expand the systems engineering domain and activities to include understanding natural systems.

So we want to apply systems engineering skills and techniques to increase understanding of natural systems. Which natural systems in which natural science disciplines can best be addressed by the systems approach and systems engineering? The answer is the most complex systems in the most complex natural science disciplines. Ecosystems and the ecological sciences are in this group.

Consider the complexity spectrum of the natural sciences. Proceeding from least complex to most complex, we find physics and then chemistry at the lower end, and ecological sciences and social sciences at the higher end. Scientific disciplines in the physics realm focus on systems that are (relatively) less complex and more well defined. The system problems that are addressed are known to or expected to have solutions (if only we are clever enough to find them). The many-body problem, for example, seems too complex. Herbert Simon (1996) points out that since the time of Newton, a comprehensive solution to the many-body problem has never been found. Simon states, Since Newton, astronomers have been able to compute the motion of a system of two bodies that exercise mutual gravitational attraction on each other. With three or more bodies, they have never obtained more than approximations to the motion. The n-body problem with n ≥ 3 is too complex for the methods of physics. The physical sciences, of course, have made tremendous progress in understanding systems that do reside in their limited domain. Progress is much more difficult in the ecological sciences.

The ecological sciences do not have the luxury of addressing less-complex systems. All of the most important ecological systems are highly complex. In my view, the systems approach and systems engineering are essential for understanding complex ecological systems. These are among the most complex systems in the most complex natural science disciplines. That’s where the most help is needed. Ecology is an especially fertile application area for systems and engineering approaches.

1.3.2 Engineering Technical Methods

Traditionally, we have usually thought of two general categories of technical methods: theoretical and empirical. Now, of course, computers are an important part of the technical methods across all of the sciences and engineering. Melanie Mitchell (2009) explains the situation this way: The more mathematically oriented sciences such as physics, chemistry, and mathematical biology have traditionally concentrated on studying simple, idealized systems that are more tractable via mathematics. However, more recently, the existence of fast, inexpensive computers has made it possible to construct and experiment with models of systems that are too complex to be understood with mathematics alone. … The traditional division of science into theory and experiment has been complemented by an additional category: computer simulation.

My categorization of engineering technical methods is shown in Figure 1.1. There are three broad categories:

Mathematical methods

Empirical methods

Computer simulation

The effective systems engineer is proficient in all three.

The three categories are not mutually exclusive and, in my view, all three can have theoretical aspects. Additionally, the first two categories very often employ the third. For example, regarding mathematical methods, in some cases we can write mathematical equations for a system (e.g., a differential equation description of a simplified dynamical system), but cannot solve the equations in closed form. We need to use a computer-based numerical approach (computer simulation) to obtain a solution. In other cases, except perhaps for some specific aspects of a given highly complex system, we cannot even write (let alone solve) mathematical equations that describe the system. Computer simulation of an appropriate system model can provide a means for us to make progress in understanding the complex system. All three of these technical method categories are used extensively in the work described in this book. For the moment, I’ll comment further on mathematical methods and then empirical methods. Computer simulation of a cellular automata model of complex ecosystem dynamics is the subject of Part V of the book.

1.3.2.1 Mathematical Methods

Mathematics is very important in all of the natural sciences. Mathematics-based methods are rigorous, objective, and definite—and appealing for those reasons. They work well for less-complex systems, and can also work well for certain aspects of highly complex systems. In my systems engineering work, I use mathematical methods whenever they are helpful and appropriate. For complex systems, I find that mathematics is necessary but not sufficient.

To better understand my view of mathematical methods, let’s consider a specific engineering example, that is, mathematics-based optimization theory, which is often used in engineering system design. As we proceed, I think you’ll see both the benefits (for simpler systems) and the significant limitations (for complex systems) of this approach.

We’ll use Jasbir Arora’s (1989) description of optimization theory in system design.⁵ Perhaps the first thing that should be mentioned is that Arora does not discuss how to create a system design. (I’ll touch on that topic later in this chapter and in Part II of the book.) Rather, Arora addresses the details of optimizing an already-proposed design: It is assumed that various preliminary analyses have been completed and a detailed design of a concept or a subproblem needs to be carried out. Arora’s stated objectives are to provide mathematical foundations for engineering design (It is my sincere belief that methods of optimum design will form a core for the engineering design process) and to provide a means of systematizing the engineering design practice (Optimization is viewed as a tool for the systematic design of engineering systems). Arora’s key areas of coverage are

• Mathematical formulation of design problems

A proper mathematical statement of the problem is critical for designing workable systems.

• Solution methods (usually computer-based)

Many optimization problems must be solved using numerical algorithms because they are difficult to solve by analytical procedures.

Optimum design … requires sophisticated computer programs.

• Dealing with nonlinearity

Solutions of many optimization problems are the roots of nonlinear equations.

Let’s discuss the first of Arora’s key areas—design problem formulation—in more detail. The goal is to transcribe the design problem into a well-defined mathematical formulation where a measure of performance is to be optimized while satisfying all the constraints. This approach forces the designer to identify explicitly a set of design variables, a cost function to be minimized [or an objective function to be maximized], and the constraint functions for the system. This rigorous formulation of the design problem helps the designer to gain a better understanding of the problem. Proper mathematical formulation of the design problem is a key to good solutions. The steps in the procedure are

• Analyze the design problem.

(Generate pertinent mathematical expressions that describe the design problem.)

• Identify and define the design variables.

(Design variables are parameters chosen to represent the design.)

• Specify an objective function or cost function.

(This is a function of some or all of the design variables that provides a criterion to measure the performance of candidate designs. Either an objective function or a cost function can be used. An objective function is to be maximized while a cost function is to be minimized.)

• Identify the system constraints.

(The constraints specify limits on the values that design variables can take. Express the constraints in terms of some or all of the design variables and identify a resulting feasible region. This region specifies the set of feasible designs, i.e., designs that satisfy all of the constraints.)

Figure 1.2 provides a very simple design problem formulation example: optimizing the design of a beverage can.