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MCS Process

 

by MCS

version 1.4: 27 June 2019

 

 

Introduction to the MCS Process

The MCS process is a sequence of activities designed to help people solve problems that arise in the context of complex systems. The process is divided into a number of steps which we will describe here. For an overview of the process please refer to the following figure.


Figure: MCS Process


Identify the problem areas of interest

These depend on the interests and goals of the reader be they student or researcher. By student, we mean a person who has little or no knowledge of the problem areas. By researcher, we mean someone who may be familiar with the problem areas, but is looking to acquire a broader educational background than they already possess.

 

Note: For the remainder of this discussion about the MCS Process we will use concrete examples to illustrate the points we wish to make. The reader can freely substitute their own interests and goals as necessary. In fact, building your own learning process infrastructure lies at the heart of the MCS Process.



Select the problem areas

We are going to select four:

  1. cancer
  2. immunology
  3. aging
  4. nutrition.

 

All of these problem areas arise in the category of environmental systems that we have termed biosystems. Choosing a related set of problem areas will help focus our search for resources.



Describe in general the problems of interest and the desired solutions

We associate with each of these problem areas our general goals:

  1. Predict and mitigate the side effects of cancer related therapeutics.
  2. Improve the application of immunotherapies in the treatment of disease.
  3. Improve the quality of aging through better understanding of aging mechanisms.
  4. Create the means to optimize personal nutrition guidelines



Determine the required resources 

To understand the nature of the problems of  interest we need to discover the resources that will help provide that understanding, and which will help us learn the skills necessary to proceed. This information will be the basis of the foundation program of study.



The discovery process

The process of uncovering primary and secondary resources is ongoing. We will discover new ones even while we are studying the ones we have already uncovered. Thus the MCS process includes a feedback loop between the implementation of the foundation program and the determination of resources (see Figure: MCS Process).

 

The discovery process requires a significant amount of work on the part of the student. It is not a skill that is learned in school where all the discovery has been done by the people who write curricula and those who teach it. The typical end result of the discovery process in school—as far as the student is concerned—is a course number, a teacher and a textbook. By contrast, outside of a traditional learning environment, executing the discovery process will be the full responsibility of the student.



Discovering biosystems resources

Biosystem resources are any resources designed to improve our understanding of the nature and function of a biosystem. We define a biosystem as any system that exhibits the characteristics of a life form. That last definition doesn't tell us much since there is so much debate about what constitutes a living system, but we are happy leaving it at that. Nature, of course, doesn't spend any time worrying about the issue either.

 

In our own opinion, life is simply a matter of degree, that is, some things are more alive than others. There is no simple set of criteria that can be used to draw a line between living and nonliving entities. We do know that carbon based molecules have a lot more capability for adding variety to life forms, and therefore we tend to think of life forms as being composed primarily of carbon based molecules. But even this notion is suspect  because animals are mostly water. Human beings are approximately 60 percent water by weight. Even our bones are watery (about 31 percent). We suppose that this is an artifact of our watery origins.

 

The task of a student of biosystems is to put together a list of resources that they can use to gain a better understanding of the nature of a biosystem. The fact that we are talking about a complex system makes the task at least an order of magnitude more difficult than if we were talking about a simpler system. Add to this that we would like to solve problems that affect human beings, and we are tasked to describe the most complex system that we are aware of in this universe.

 

As we mentioned in another section, organizing the information that we gather is going to be a difficult problem to solve of itself.  By organization we are implying not only listing the resources we discover, but finding the relationships and dependencies that exist between the various resources.

 

The question then becomes, how or where does the student begin when they are unfamiliar with the subject matter that describes the problem areas of interest?



Selecting resources

One thing to keep in mind is that many people have already attempted to solve this problem of resource identification: the problem is not without existing solutions. Any college catalog will show a four year undergraduate program for any field of study that is offered by that school.

 

In addition, there are many professionals who are teaching and doing research who would probably be more than willing to share their expertise in this matter. Keep these and other resources in mind. What we are asking of the student is to spend some time wrestling directly with the problem before trying to sort out the opinions or regimens recommended or dictated by others.

 

Let's start by looking at our problems of interest and the desired solutions. In one of our goals we stated that we would like to be able to

 

"Predict and mitigate the side effects of cancer related therapeutics."

 

Perhaps we came to this conclusion by witnessing the effects of cancer related therapies on individuals we have known personally, and witnessed first hand the side effects of chemotherapy, radiotherapy, or surgery. In any case we have expressed an interest in learning how to predict and mitigate these side effects.

 

The first step we recommend is to look at a good textbook on cancer, and determine what it is we need to learn in order to bring ourselves up to date on the nature and treatment of cancer.

 

As of this writing (27 December 2018) if you type the terms "textbook" and "cancer" into the Amazon.com primary search field you will see a list of textbooks related to cancer. The  fourth in the list that we are looking at is titled Cancer Immunotherapy Principles and Practice by Lisa Butterfield et al., and the fifth is called simply The Biology of Cancer by Robert A. Weinberg. The surrounding titles are not nearly as compelling.

 

Of the two we have cited, Weinberg's book seems to be the most relevant at this time; Butterfield's looks like something we might want to take a look at when we address the subject of immunotherapies.

 

Using the Look Inside feature of Amazon's webpage for Weinberg's book we can read the entire Preface, a section called a Note to the Reader, the full Table of Contents, the complete contents of chapter one: The Biology and Genetics of Cells and Organisms, and about half of chapter two: The Nature of Cancer. The Glossary and Index are not available for viewing as a Look Inside feature for this book.

 

In addition, it is often possible to download the same information (more or less) from the book publisher's website as a set of PDF files. This is sometimes more convenient for reading and marking up then starting with the electronic version on Amazon's site.

 

Note: Having purchased this book for our library in 2016 we would like to apprise the reader that the original publisher of this book—Garland Science—is no longer in business and that the rights to the book have shifted to W.W. Norton & Company.

 

Now that we have some sample text in hand, we can read through that text and use it to determine what we need to learn in order to understand the topic that we are reading about.

 

Let's start with the Preface. Here is a list of potentially unfamiliar terms and phrases that we think will prove useful in helping us uncover additional resources.

Table: Unfamiliar Terminology

Based on the terminology we've obtained from the Preface and entered into the table, we can proceed to find resources that will explain that terminology.

 

The first term in our list is biology. Using Amazon as our database let's take a look at existing biology textbooks. We will enter the keywords textbook and biology into the primary search field.

 

As you can see there are quite a few listed. In the list we are looking at, it appears that the most popular text is Campbell Biology, 10th ed.  Peter Raven's book, Biology, gets a lot of nice reviews. Both are books for biologists to be; both are in the 11th edition; both have 1400 plus pages. Read through some of the text that is available, as well as the TOC, and select one or the other of these books as a resource.  Now add an additional column to the Unfamiliar Terminology table and label it Resources.

 

Note: We suggest that you build tables using either Microsoft OneNote, or Excel. You will be manipulating tables a lot and you will want to be able to reformat them easily.

 

By repeating the search process just described, we can fill in resources for many of the terms in the list . This takes time, but by proceeding slowly you will find many relationships between the textbooks or other resources being added to your list. Besides Amazon, you may want to check out what's available on YouTube, DVD video, or one of the many MOOC platforms such as Coursera, MIT OpenCourseWare, Stanford Online, or the commercial outfit The Great Courses. We've added a DVD biology resource from The Great Courses repertoire to our list. Our completed resource list for the entire Preface appears in the following table.

Table: Terminology Plus Resources

 

Additional primary resources

Based on our own research,  we recommend continuing the resource discovery search in the other problem areas with the following textbooks.

 

Immunology:

Author: Judith Owen

Title: Kuby Immunology, 7th ed.

 

Aging:

Author: Roger B. McDonald

Title: Biology of Aging

 

Nutrition:

Author: Sareen S. Gropper

Title: Advanced Nutrition and Human Metabolism, 5th ed.

 

The advantage of using textbooks as primary resources is that they summarize the research taking place in the subject area of interest to the date of publication, and they include a comprehensive list of additional resources on which that research was based.  This gives the reader a research audit trail that makes it easier to find the resources they will need to bring them up to date on the subject .

 

The resources discovered using the primary resources utilized above are necessary but not sufficient to provide the information and  develop the skill sets necessary to solve the problems of interest. Our technique of problem solving involves modeling the system of interest until we are able to reproduce the problem in the system context, and then modify that system to eliminate or at least mitigate the problem to the best of our ability.

 

Developing our modeling skills will require familiarity with subjects such as mathematics and engineering including many topics in computer science.

 

In addition to the biological sciences we will find ourselves in need of the physical sciences to come to an understanding of the nature of matter at the molecular, atomic, subatomic and quantum levels.

 

Furthermore, we need to understand how the environmental systems that we have described elsewhere in this presentation will  influence the behavior of our system of interest.

 

Finally, even if a solution to a difficult problem is found, people  other than the researcher or research team will need to communicate that information to convince  an often skeptical audience. For that we need to develop our understanding of the social sciences in order to communicate our results as a policy that people will be willing to accept. Our solutions may not simply be drug interventions, but require significant changes in human behavior be it social or economic.



Practical considerations

The problem of creating a resource database is not completely solved by simply creating a list of resources based on unfamiliar terminology. Organizing that information into some coherent schema will be necessary in order to make efficient use of it. In addition, the student will need to convert that information into a viable sequence of studies. We will examine the organization problem in the following section.



Design and implement a Foundation Program

The Foundation Program is an umbrella term used to denote the activities for acquiring the knowledge and skill sets required to build a Research Program for the problem area of choice. The activities associated with the Foundation Program are listed here.

 

  • Construct a schema for our discovered resources.
  • Populate the schema with the discovered resources.
  • Use the resources database to construct a studies curriculum.
  • Master the resource topics detailed in the studies curriculum, while building an ontology of the resource topics and their associated resources.


Note: We assume that the discovery of resources is taking place throughout the execution of the Foundation Program. This means that the studies curriculum will normally be generated on the fly rather than having it laid out for the student from the start as we have shown here. We have shown a full curriculum at the start in these pages in order to illustrate the scope of the topics that can arise in the solving of problems as complex as those that are found in biosystems. We did not want the reader to have to hang around for six years to see the results of the discovery process.

 

We have found that the discovery process very quickly leads to those topics which need to be mastered from the start. The first year of the biosystems Foundation Program curriculum includes just such topics. The sooner those studies begin the better as they will certainly assist in the ongoing discovery process. Thus the MCS Process figure shows a feedback loop connecting resource discovery with what are essentially studies activities.


Construct or select a schema

The business of constructing a schema for organizing our resources could be a long and arduous task requiring months of work. A simple example will suffice to illustrate our premise. Suppose you own a rather large collection of books and would like to organize them in some fashion to make each and every one of them easy to locate in your personal living space. What organizational schema would you use to do that?

 

You might say that you would simply assign each book a number and store the books throughout your personal living space in labeled bookshelves: something like they do in brick and mortar libraries. So on the spine of each book you paste an unsightly label with a number on it and put the book in numerical order in the bookshelf you have designated for that  sequence of numbers. You store the pertinent information about this book in a retrievable fashion on your computer. Using a keyword search you are able to locate the book by author or title, retrieve the ID number, and by an additional search retrieve the bookshelf where it is located.   Problem solved, or is it?

 

Suppose you have a favorite author or subject and would like to group all of the books in this collection together next to one another in a prominent location for all to see. Now what? Suppose you keep adding to this collection over time as the author continues to publish new works. Does the numerical labeling scheme still make sense? What if you want to group your books by subject. What would be your subject name schema? What if a book's contents spanned several subjects?

 

We have a similar problem in trying to organize our discovered resources. We will simply offer up  our solution rather than go through any long winded explanation at how we arrived at it. In reality, you the reader are free to build your own schema and use it as the basis for the rest of the activities in the Foundation Program.

Table: Biosystems Resources Schema

 

Biosystems resources schema

Our Biosystems Resources Schema begins with five column headings listed in the following order: Field, Subject, Topic, Principal Resources, Supporting Resources.

 

We promote the following field types in row order: Mathematics, Natural Sciences, Engineering, Environmental Systems, and Social Sciences

 

Under each field type we promote a number of subject types. For example: under the Engineering field type we promote the following subject types: Computer Science, Control Systems Engineering, Electrical and Electronic Engineering, Operations Research, and Systems Engineering. Notice that a large number of engineering disciplines are not included. The reason for the exclusion is that we have not found it necessary to do so at this time. Our discovered resources do not include what we would typically call civil engineering topics.

 

Under each subject type we promote a number of topics. Referring to the subject of computer science in the table indicates the number of topics comprised by this subject. These include Java Programming language, Programming in Java, Python, MATLAB, Graphics, Algorithms, … and a host of others.

 

Associated with each topic are the Principal Resources and Supporting Resources. These fields will contain references to the actual resources.

 

Although this schema appears at first glance to be hierarchical—that is, constructed in a top down fashion—the category identifiers were derived from the bottom up based on the nature of the discovered resources. The topics are the rallying points for this schema. You can think of the field and subject headings as simply prefixes for a given topic which allow for the unique identification of a topic. Each topic with its field and subject prefix identifies a unique collection of references to principal and supporting resources.

 

In our schema, a resource can be a member of more than one topic collection.

 

Note: We will refer to the entries in the principal and supporting resource fields as "resources" when  in fact they simply refer to the object. That is, an entry in a resource field  only references a resource object; the entry is only a pointer to an actual object.



Populate the schema with the discovered resources

Actually the title of this section is somewhat misleading. The discovered resources themselves have suggested the topic names we have chosen, and we merely join the resources with a topic name to form a collection. The same goes for the subject identifiers as they relate to various topics: the nature of a group of topics suggests a subject heading. In addition, the field identifier serves to collect subject identifiers in a homogeneous collection. But as we have stated above, there is in reality only one type of collection in this schema, the topic; both the field and subject types serve to uniquely identify a given topic.

 

Note: We have overloaded the term field in our discussion here. We use the term in two ways. In one instance we use the term Field to mean a major branch of knowledge, using it as the heading of our first column in the Biosystems Resources Schema table. In another instance we use it to mean a cell in the same table. The context in which we use the term should be sufficient to distinguish which meaning we have in mind. We will sometimes capitalize the former but never the latter unless it is the first word in a sentence. Blame the semantics of our language for this anomaly.

 

Although this business of referring to topics as identifiers of collections seems intuitively obvious, it will become more of an issue in our future work when we are building computer assisted databases in a network fashion. Topics at that time will represent nodes in a system network, and it will prove to be a nice way in which to organize information. In fact, an ontology of our resources will be organized in just such a fashion. An ontology—according to a definition found in Wikipedia—"may be considered as dealing with what entities exist or may be said to exist and how such entities may be grouped, related within a hierarchy, and subdivided according to similarities and differences".

 

It will turn out that when we have completed the Foundation Program, the most important result leading to the development of a research program will be our ontology of the problem area. This ontological network will illustrate all of the important relations (a term which we have yet to define) needed to solve the problem of interest.

 

In any case we give you the results of no small amount of work in discovering, collecting, organizing and placing our discovered resources into a table we call simply Biosystems Resources. When necessary for clarification, we will refer to this table formally as our Biosystems Resources Database. At some point in the future this table will be generated by a MySQL database which will be an integral part of this website for information storage and retrieval.

Table: Biosystems Resources

 

How to construct a biosystems curriculum

Now that we have the information needed to acquire a foundation of learning in the problem areas we have chosen to explore, we need to develop a plan of action. First, we need to develop a biosystems curriculum.

 

There are a number of approaches to this problem. The traditional way, that is, the way most college curricula are organized and taught, is by determining the prerequisites for each course in a given curriculum. Students start at the bottom of this predetermined curriculum and work their way to the top, i.e., the course with the most prerequisites. This approach is really a matter of determining the dependencies that exist among the various topics that form the curriculum.

 

Using this approach  it takes literally years to begin to tackle the problems, which the student thought they were most interested in solving. It's akin to climbing a mountain by scaling directly up the face. This is usually not the best route, and the student often loses sight of their educational goals, just as they would when climbing a mountain in this manner.

 

Another approach, which we favor for its motivational aspects, is to endeavor to keep the goal in sight throughout the learning process.  While this approach may be best for the student, it would be difficult to implement in a traditional manner. The coursework would need to be organized differently in order to accommodate the needed flexibility. Courses would be an amalgam of  topics that would not lend themselves to oversight by individual departments: if indeed departments existed at all.

 

Nature is like that, as well as human activities. Any natural process is a combination of all the topics (and more) in our list for the natural sciences. And, if the reader needs convincing about human activities being an amalgam of topics, well, just pick up a newspaper.

 

Our recommendation for a curriculum designed for understanding the human biosystem, and solving its related problems, will be a combination of the approaches suggested above. We will define a curriculum that continually seeks to keep the end result  in sight. By that we mean we will constantly be asking how the particular topic that we are studying will help us improve our ability to solve the problems in the areas of cancer, immunology, aging and nutrition. These will provide much needed motivation when the going gets intellectually rough.

 

In addition, we will not attempt to cram a topic into an arbitrary fixed time frame for the sake of continuity of "teaching". We will add material to a given topic, from a variety of resources, when it makes sense from a problem solving  perspective in order to enhance learning.

 

As we proceed through our ersatz curriculum, we will build an ontology in the form of a dependency network as we discover a clear relation between any two topics. This network would obviously be our curriculum map if it were available, but unfortunately it never is. It can only be drawn by jumping into the pool of topics we have uncovered, and diving deep enough to see those relations from a three dimensional perspective (literally, as the student of this site will discover).  Of utmost importance to the MCS Process, this three dimensional map will provide the initial directions to the source of the problems we wish to solve. As a result, this resource map will also serve as the foundation for planning our research program.



Construct the biosystems curriculum

We begin by looking at the domain of  subjects that we have determined will be necessary and sufficient to provide us with an appropriate range of topics to solve the problems of interest.

Figure: Biosystems Curriculum Subject Map

Remember that our search for resources has yielded the topics and the associated subjects which will be discussed and mastered throughout this program. It's been a bottom up approach. Not the other way around. On the other hand it is difficult for us, having been raised academically in a traditional manner, not to have been influenced by a top down approach. So the reader should be alert for our biases, as much as we try to avoid them.

 

A look at the Biosystems Resources table will reveal a number of subjects which we portray in a circular fashion in our Subject  Map. In scope, we have broadened our search to include all biosystems because human beings are at the end of a long evolutionary chain. We should probably begin our studies at the beginning of this chain for a complete understanding of how we got where we are. It will probably provide us a better understanding of where we are headed as well.

 

The subject headings could easily be names of departments within any college. This results from a contemporary view of  higher education: that is, a search for a degree in any one of these subjects. Our contemporary higher educations at the undergraduate level are not problem focused but subject focused, regardless of how many homework problems one is required to solve along the way.

 

We could conceivably (we won't at this time) overlay rings on the map representing different years. The outermost ring would represent the time we started our studies of the biosystems curriculum, and the center of all these concentric circles would represent the time we concluded our studies. We have estimated the total time horizon for the foundation program to be six years: thus six rings could be used to represent the curriculum on an annual basis. Of note is that some of the paths (arrows) would begin at the outermost ring and others would begin later in time. This picture is very much a traditional approach to higher education: beginning a new subject only when all the prerequisites for it have been met. Thus some of the arrows in the map (or directed graph) would be  shorter than others. We propose that the reader reconstruct this diagram in this fashion. It is a nontrivial exercise.

 

What is different about our "curriculum" from most biosystems oriented curricula at the college level is the sheer number of subjects required of the student. That plus the fact that it is a six year program as opposed to a four. And the school year is presumed to be year round as opposed to having a long (summer) break between two adjoining semesters. Not shown explicitly is the development or design of the Research Program in the sixth year. The implementation of the Research Program would most likely be a  Ph. D. level program at a university for a student, or the execution of a research grant for those already working at the Ph. D. or equivalent level.

 

It turns out, however, that it is not necessary to stay strictly within the limits of a prerequisite determined curriculum. All of these subjects could  be started at the same time, or at least introduced long before they would be in a traditional curriculum. This is what we will attempt to do in the MCS Process. These early introductions are not shown in this diagram, but will occur during program implementation, and be included in the Biosystems Studies description for each year of studies. This approach to learning is more in sync with  our need for a systems approach to problem solving. In the real world we get into trouble by excessive compartmentalization of analysis and labor. In our opinion health care delivery is particularly prone  to errors in judgement because of its high degree of specialization.



The biosystems curriculum

We now want to introduce you to the Biosystems Curriculum. All of the subject headings and topics in this table are based on the information contained in the Biosystems Resources table.

Table: Biosystems Curriculum

We estimate that a chronological year will be the amount of time necessary to master the topics shown in this table for a given year. We will be using that amount of time to generate the accompanying material for the topics shown for a given year.



Biosystems studies: first year

Now we would like present the complete list of topics and their associated resouces that we will attempt to master during that first year of studies.

Table: Biosystems Studies Year 1

A much more complete analysis of our choices for this first year is given in the Description page for the Studies by Year One. See the TOC for the appropriate link.

 

 

Our approach

We will provide an analysis of each of the resources listed in the Biosystems Studies plan. These analyses will not "cover" the material associated with a resource or set of resources in the way that a typical lecture might, but will attempt to provide further insight into the material. That insight will be focused on how this material can be of use in building models for solving problems associated with these topics. We will also discuss the relations of the topics with one another in the pursuit of building an ontology that encompasses all of the topics in the resource database.

 

In addition we will pose problems associated with the resources that we are studying. Most of these problems will be of our own creation and require the construction of a static or dynamic model to solve the problem.

 

Our analyses and problems can be found in the Studies by Subject and Studies by Year pages listed in the TOC. Possible approaches to problem solving can be discussed and posted on the Forum. We will look at and comment on any of the proposed solutions using the Forum. We will post our own solutions to each problem following the problem statement. Questions about our solutions should be posed in the Forum pages.



Studies: following Years

As we complete a given year, we will introduce the studies for the following year. As in Year 1 we will post  the analyses and problem sets as we progress through that year, until we complete the full six year MCS process.  If the reader is coming to this site at a later date than the date at which we actually began this program (approximately February of 2019)  the studies material already presented can be found organized by year in the order in which it appeared.



Identify a research problem

During the sixth year of the Foundation Program we will identify a research problem. The problem will be a more specific statement of one of the problems of interest that we stated early in the MCS Process.

 

Note: Those already possessing the needed expertise, normally obtained by participating in the Foundation Program, can begin the MCS Process here. We estimate that it may take up to a year to complete the activities associated with developing and writing a research proposal.

 

In addition to identifying a research problem in the sixth (or first) year, we will execute the following activities.


Determine the required resources

We will use that problem description to determine the required resources needed to understand the nature of that problem. Media resources will be drawn primarily from the currently available literature. We will specify the modeling environment needed to understand the problem and effect a solution. We will also specify the biotechnology (or technology of your choice based on your problem statement) needed in the course of the research in order to parameterize the model or models to be used.

 

Design a Research Program

We will design a Research Program to solve the problem of interest. The Research Program will include the construction of a networked ontology illustrating the literature pathways and the additional bioresearch needed. The design will also include the specifications of a model or models needed to reproduce the problem within the context of the system of interest. We will assert that this model or models will provide an understanding of how the system may be modified to solve or mitigate the problem of interest.

 

Write a research proposal

Based on our research program design we will write one or more research proposals. The proposals will be directed at specific funding organizations. The student of this website will then have in hand a research proposal that they can use when applying as a Ph. D. candidate to an institute of higher learning.  Anyone who already holds the necessary qualifications to submit a research proposal to a funding organization will be able to utilize that proposal directly in their application for funding.