CANCER – A SYSTEMATIC VIEW

CANCER – A SYSTEMATIC VIEW Author: Herbert James Spencer, PhD, DIC, BSc © H. J. Spencer (21 June 2016) [48.3K words; 80 pages] V0.85

TABLE OF CONTENTS 1.0 INTRODUCTION .............................................................................................................................................................. 1 1.1 Preface ............................................................................................................................................................................................ 1 1.1.1 Framework ...................................................................................................................................................................................................... 1 1.1.2 Audience ........................................................................................................................................................................................................... 1 1.2 What is Cancer? ............................................................................................................................................................................ 2 1.3 Motivation ...................................................................................................................................................................................... 2 1.3.1 Personal ............................................................................................................................................................................................................ 2 1.3.2 Dedication ........................................................................................................................................................................................................ 3 1.4 Author’s Qualifications .............................................................................................................................................................. 3 1.5 Summary ........................................................................................................................................................................................ 4 2.0 SYSTEMS ............................................................................................................................................................................ 6 2.1 Language and Natural Philosophy ......................................................................................................................................... 6 2.1.1 Life Forms as Systems ................................................................................................................................................................................ 6 2.2 General Systems .......................................................................................................................................................................... 6 2.2.1 Background ..................................................................................................................................................................................................... 6 2.2.2 Holons ............................................................................................................................................................................................................... 7 2.2.3 Systems Theory ............................................................................................................................................................................................. 7 2.3 Living Systems .............................................................................................................................................................................. 7 2.3.1 Overview .......................................................................................................................................................................................................... 8 2.3.2 Biology .............................................................................................................................................................................................................. 9 2.3.3 Objectives & Strategies .............................................................................................................................................................................. 9 2.4 Vital Subsystems ........................................................................................................................................................................ 10 2.4.1 Boundaries & Functions ......................................................................................................................................................................... 11 2.4.2 Global Systems ............................................................................................................................................................................................ 11 2.4.3 Internal Systems ........................................................................................................................................................................................ 12 2.5 Organs and Components ......................................................................................................................................................... 15 2.5.1 Tissues & Cells ............................................................................................................................................................................................ 15 2.5.2 Biochemistry ............................................................................................................................................................................................... 16 2.5.3 Molecular Biology ..................................................................................................................................................................................... 16 2.6 Cells ................................................................................................................................................................................................ 17 2.6.1 Cell Types ...................................................................................................................................................................................................... 18 2.6.2 Cell Structure ............................................................................................................................................................................................... 18 2.6.3 Cell Processes .............................................................................................................................................................................................. 21 2.7 Summary ...................................................................................................................................................................................... 21 3.0 NORMAL GENETICS ..................................................................................................................................................... 24 3.1 Heredity ........................................................................................................................................................................................ 24 3.1.1 Family Heredity ......................................................................................................................................................................................... 24 3.2 Molecular Genetics ................................................................................................................................................................... 24 3.2.1 Watson and Crick ...................................................................................................................................................................................... 24 3.2.2 Genetic Code ................................................................................................................................................................................................ 25 3.2.3 Genes .............................................................................................................................................................................................................. 25 3.2.4 Gene Expression ........................................................................................................................................................................................ 25 3.2.5 Human Genome .......................................................................................................................................................................................... 26 3.2.6 Epigenetics ................................................................................................................................................................................................... 26

3.3 Making Cells ................................................................................................................................................................................ 27 3.3.1 Entity Life Cycle ......................................................................................................................................................................................... 27 3.3.2 Germ Cells ..................................................................................................................................................................................................... 28 3.3.3 Stem Cells ...................................................................................................................................................................................................... 29 3.3.4 Normal Cellular Replication ................................................................................................................................................................. 29 3.3.5 Cellular Suicide (Apoptosis) ................................................................................................................................................................. 31 3.4 Process Controls ........................................................................................................................................................................ 32 3.4.1 Bypass Checkpoints .................................................................................................................................................................................. 32 3.4.2 Repair/Suicide ............................................................................................................................................................................................ 32 3.5 Summary ...................................................................................................................................................................................... 32

4.0 CANCER ........................................................................................................................................................................... 34 4.1 History .......................................................................................................................................................................................... 34 4.1.1 Overview ....................................................................................................................................................................................................... 34 4.1.2 Types of Cancer .......................................................................................................................................................................................... 36 4.1.3 Cancer Science Milestones .................................................................................................................................................................... 39 4.2 Tumors .......................................................................................................................................................................................... 40 4.2.1 Malignancy ................................................................................................................................................................................................... 40 4.2.2 Stages .............................................................................................................................................................................................................. 40 4.2.3 Grading Tumors ......................................................................................................................................................................................... 40 4.2.4 Aggressive Cancers ................................................................................................................................................................................... 41 4.2.5 Metastasis ..................................................................................................................................................................................................... 41 4.2.6 Angiogenesis ................................................................................................................................................................................................ 41 4.2.7 Clonality ......................................................................................................................................................................................................... 42 4.2.8 Genetic Cell Phases ................................................................................................................................................................................... 42 4.2.9 Mutations are Genetic Failures ........................................................................................................................................................... 42 4.3 Carcinogenesis ........................................................................................................................................................................... 43 4.3.1 Overview ....................................................................................................................................................................................................... 43 4.3.2 Oncogenes .................................................................................................................................................................................................... 43 4.3.3 Repair Failure ............................................................................................................................................................................................. 44 4.3.4 Suicide Failure ............................................................................................................................................................................................ 44 4.3.5 Suppressors ................................................................................................................................................................................................. 44 4.3.6 p53 Failure ................................................................................................................................................................................................... 45 4.3.7 Wound Failure ............................................................................................................................................................................................ 45 4.4 Causes of Cancer ........................................................................................................................................................................ 45 4.4.1 Risks ................................................................................................................................................................................................................ 45 4.4.2 Viral ................................................................................................................................................................................................................. 46 4.5 Eight Key Cancer Properties .................................................................................................................................................. 46 4.6 Mistiming ..................................................................................................................................................................................... 46 4.6.1 Mutation Timing ........................................................................................................................................................................................ 46 4.6.2 Development Mistiming ......................................................................................................................................................................... 47 4.6.3 Stem Cell Theory ........................................................................................................................................................................................ 47 4.7 Summary ...................................................................................................................................................................................... 47 5.0 CANCER TREATMENTS .............................................................................................................................................. 49 5.1 History .......................................................................................................................................................................................... 49 5.1.1 Overview ....................................................................................................................................................................................................... 49 5.1.2 Epidemiology .............................................................................................................................................................................................. 49 5.2 Surgery .......................................................................................................................................................................................... 49 5.3 Radiation ...................................................................................................................................................................................... 50

2

5.4 Cytoxic Chemotherapy ............................................................................................................................................................. 50 5.4.1 Drug Types .................................................................................................................................................................................................... 51 5.4.2 Side Effects .................................................................................................................................................................................................... 51 5.5 Targeted Therapy ..................................................................................................................................................................... 52 5.6 Immunotherapy ......................................................................................................................................................................... 53 5.6.1 Monoclonal Antibody Therapy ............................................................................................................................................................ 53 5.7 CAT/PET Scans & MRIs ............................................................................................................................................................ 53 5.8 Summary ...................................................................................................................................................................................... 54

6.0 TREATMENT FAILURES ............................................................................................................................................. 55 6.1 Disappointments ....................................................................................................................................................................... 55 6.1.1 Cancer as Black Box .................................................................................................................................................................................. 55 6.2 Surgery – too Late ...................................................................................................................................................................... 55 6.3 Radiation Problems .................................................................................................................................................................. 55 6.4 Chemotherapy Problems ........................................................................................................................................................ 55 6.5 Intrinsic Problems .................................................................................................................................................................... 56 6.5.1 Chemo & Radiation are too Indiscriminate .................................................................................................................................... 56 6.5.2 One Disease .................................................................................................................................................................................................. 56 6.5.3 Tumors as Diverse Cell Colonies ........................................................................................................................................................ 56 6.5.4 Treating Tumors often changes its DNA ......................................................................................................................................... 56 6.5.5 Microscopic Scale ...................................................................................................................................................................................... 56 6.5.6 Non-Mathematical Knowledge ............................................................................................................................................................ 57 6.5.7 Uniqueness ................................................................................................................................................................................................... 57 6.5.8 Mystery of Metastasis .............................................................................................................................................................................. 57 6.6 Institutional Problems ............................................................................................................................................................ 58 6.6.1 Surgery/Oncology Rivalry ..................................................................................................................................................................... 58 6.6.2 Science/Oncology Rivalry ...................................................................................................................................................................... 58 6.6.3 Big Pharma & the FDA ............................................................................................................................................................................. 59 6.6.4 Drugs Only .................................................................................................................................................................................................... 59 6.6.5 Endemic Mutagens ................................................................................................................................................................................... 59 6.7 Human Genome Project .......................................................................................................................................................... 60 6.8 Summary ...................................................................................................................................................................................... 60 7.0 NEW RESEARCH DIRECTIONS ................................................................................................................................. 61 7.1 Basic Research ........................................................................................................................................................................... 61 7.1.1 Common Functions ................................................................................................................................................................................... 61 7.1.2 Cancer Genome Atlas ............................................................................................................................................................................... 61 7.1.3 Cancer Stem Cells ...................................................................................................................................................................................... 62 7.1.4 Anti-Inflammatory Targeting ............................................................................................................................................................... 62 7.2 Therapies ..................................................................................................................................................................................... 62 7.2.1 Cancer Vaccines ......................................................................................................................................................................................... 62 7.2.2 Viral Infections ........................................................................................................................................................................................... 62 7.2.3 Immune Reactivation .............................................................................................................................................................................. 63 7.3 Directions ..................................................................................................................................................................................... 63 7.3.1 Detection ....................................................................................................................................................................................................... 63 7.3.2 Repair ............................................................................................................................................................................................................. 63 7.3.3 Avoidance ..................................................................................................................................................................................................... 64 7.3.4 Context ........................................................................................................................................................................................................... 64 7.3.5 Timing ............................................................................................................................................................................................................ 64

3

7.4 Diet ................................................................................................................................................................................................. 65 7.4.1 Processed Foods ........................................................................................................................................................................................ 65 7.4.2 Organic Foods ............................................................................................................................................................................................. 65 7.4.3 Anti-Cancer Foods ..................................................................................................................................................................................... 66 7.4.4 Supplements ................................................................................................................................................................................................ 67 7.5 Alternative Medicine ................................................................................................................................................................ 68 7.5.1 Natural Therapies ..................................................................................................................................................................................... 68 7.5.2 Oncothermia ................................................................................................................................................................................................ 68 7.6 Summary ...................................................................................................................................................................................... 69

8.0 OVERALL SUMMARY & CONCLUSIONS .................................................................................................................. 70 8.1 Summary ...................................................................................................................................................................................... 70 8.2 Conclusions ................................................................................................................................................................................. 70 8.2.1 Prognosis ...................................................................................................................................................................................................... 70 8.2.2 Outlook .......................................................................................................................................................................................................... 71 8.2.3 Systematic Biology .................................................................................................................................................................................... 72 8.2.4 A Frankenstein? ......................................................................................................................................................................................... 72 APPENDIX A. GLOSSARY .................................................................................................................................................. 73 APPENDIX B. BIBLIOGRAPHY ........................................................................................................................................ 74

4

CANCER – A SYSTEMATIC VIEW

1.0 INTRODUCTION 1.1 Preface 1.1.1 Framework This book provides a unique view on the modern scourge of cancer by organizing the vast amounts of genetic discoveries on this disease using a Systems Theory approach, rather than the more usual historical viewpoint. Although Systems Theory is often presented as a mathematical scheme, this is not the approach used here. Recognizing that social understanding requires natural languages, the emphasis here is on the organized presentation of concepts and their key relationships, especially when viewed from a systems perspective. Since cancer has primarily been investigated from a scientific perspective and as science (especially physics) operates mainly through the Materialist Hypothesis (“Nature only consists of Matter”), this framework will be presented from a purely materialist perspective (which is difficult enough, without adding any further factors). Cancer is seen here as molecular level mistakes that cause cells to regress to the wrong phase in their normal evolution, when their re-activated processes are inappropriate. Time is therefore a key organizing principle that is often overlooked when traditional (reductionist) approaches to cancer are used. Time is also the implicit dimension in all dynamical systems and encourages focus on processes, rather than timeless structures.

1.1.2 Audience There is a growing curiosity in the general public in reading about scientific advances, especially when presented without reliance on mathematics. Since cancer now impacts so many families, there is a widespread interest in understanding more about this disease. The prime audience here are people with a general interest in the science of cancer. The approach used here might also prove useful as an introductory book for both high school and first-year university students, who are thinking of careers in medicine, biochemistry or genetics. Since cancer is now known to be a problem at the cellular level, we approach the human cell in its full biological context (the lowest form of living systems), by placing it within all the other vital systems needed to keep each one of us alive. This key context is arrived at by a fast journey that covers much information that is often presented in a non-systematic manner; often overwhelming the reader with vast amounts of data, presented usually in a simple hierarchical manner. Although much information is available on the Web (especially Wikipedia), it is organized as a network, not a linear narrative. After following only a few links (starting with ‘cancer’), one can very quickly get lost in the “Wiki Wilderness”. There is a need for an organized approach – this is the thrust behind this book. There is quite a bit of science in this book (by design) but it is presented in as easily a digestible manner as possible. If a potential reader is seeking a more people-oriented history of cancer, then they should definitely read the superb book by the oncologist, Siddhartha Mukherjee: a magnificent book[1], worthy of its Pulitzer Prize (The Emperor of all Maladies). Unfortunately, Mukherjee deliberately embeds his scientific information on cancer much too deeply within his historical narrative for the general reader. Meanwhile, textbooks assume the reader already understands the science of cancer, so they discuss it at a level that already needs an undergraduate degree in biology to follow. The novel perspectives presented here may also prove useful to some professional cancer specialists, who are being overwhelmed by the vast number of uncoordinated discoveries being announced almost daily and need a broader framework to integrate new knowledge as it appears; hence the systems approach. The key idea of cancer “timing” or when a gene mutates becomes a critical event, may prove useful.

1

1.2 What is Cancer? We now know that cancer is a multiple set of accumulated failures in several systems in an animal. These failures occur in the cell’s nucleus, so are accumulated and endlessly passed on genetically to each descendant cell of every subsequent generation (“the cancer family”). The most critical failures occur in a single cancer family within the family’s cell-reproductive system. Each cancerous cell is immortal and continues to multiply until collectively they create complex tumors, which escape the animal’s defense systems and ultimately cause the host creature to die.

1.3 Motivation Cancer has become the second most common cause of death in North America, after heart disease. Now, for every twelve people who die, three will die of cancer of one form or another while four will die of circulatory problems, such as a heart attack or (brain) stroke depending where the blood blockage occurs. It is a rare family today that does not know of one of their members, who has died of cancer - a disease that has engendered a terrifying reputation. Many people will not want to know any facts about this disease, leaving it to the medical specialists (“oncologists”), who attempt to treat this disease. As we will see, their attempts have been extensive and dramatic but have largely remained unsuccessful. Some non-medical people wish to understand more about cancer but its complexity has made it far too difficult to comprehend. Even most cancer researchers are so specialized today that few have built up a comprehensive perspective. There have been some who have tried to enlighten the general public but these are either mainly narrative (such as Mukherjee’s monumental cancer biography or too narrow, such as Armstrong’s recent best-seller [2] on the “P53” gene or perhaps, too old, like Weinberg’s 1998 classic [3], “One Renegade Cell”). Since even most oncologists rejected the major role of genes in cancer as late as 1970, there are few (if any) books dedicated to presenting a systematic overview of cancer from a genetic perspective. Even now, graduate students face enormous challenges trying to gain a comprehensive understanding from recent genetic texts, such as the 300 page text [4] : “Next Generation Sequencing” by L-J C. Wong (editor), published in 2013. The present book will introduce quite a lot of biological information but it is not a textbook on physiology or on total cellular biology (texts [5-8] covering these vast fields cost well over $100 and span at least 1,000 pages). The information introduced here is believed necessary to understand the fundamental processes of cancer. There are several marvelous books already written on the biology of cancer, such as Bob Weinberg’s classic[9] but this is not inexpensive ($200) and, at 900 pages, is only written for experts.

1.3.1 Personal My own life was radically impacted when my wife of over 50 years, Eileen was diagnosed in 2011 with a rare form of pancreatic cancer. Pancreatic cancer is usually such a virulent form that few victims survive six months after the initial diagnosis. In this case, it was the neuro-endocrine variety (PNET) that only occurs about 5% of the time with a much higher survival rate. In fact, the surgeon, who received the initial biopsy, after suspecting pancreatic cancer that had migrated to the liver, first said to us: “Congratulations, you have just won the lottery.” As it was, Eileen was ‘adopted’ by a research oncologist, who persuaded her to participate in a new study of a recently announced PNET chemotherapy drug, instead of surgery. This began a new phase in our lives of monthly medical visits (to several experts), a series of chemo treatments as each drug only seemed to ‘work’ for a limited time (9 months) until it was too late for surgical intervention and we were faced with accepting the “last drug” on the shelf (ironically one of the oldest chemotherapies). We declined this offer as it had poor outcomes and very savage side effects. My wife died soon after; luckily peacefully in a superb local hospice, staffed with very caring people. This four-year journey exposed me to the personal side of cancer, while my scientific mind led me to undertake wide readings into all aspects of this dreadful disease. It was a great shock to realize how little our ‘experts’ knew about this problem and to eventually realize how little progress had been made winning the “War on Cancer”, declared by American President Richard Nixon in December 1971, when he signed the National Cancer Act. I have continued to research this topic ever since and wish to share my insights and understanding now with a much wider audience. 2

1.3.2 Dedication This book is dedicated to my beloved wife, Eileen Spencer (née Horrigan), who demonstrated exemplary courage, fortitude and good spirits in resisting the disease (pancreatic cancer) that eventually (after 4 years) killed her.

1.4 Author’s Qualifications I believe the only effective way to understand complex systems, such as cancer, is to adopt a scientific approach that tries to organize the vast amounts of information in a systematic manner. I have had to use this technique several times throughout my varied career. Firstly, in 1964, I had to rapidly learn the latest ideas in advanced quantum physics when, at 21, I was accepted for a three year PhD program in theoretical physics at Imperial College, London University after a three-year Bachelor of Science (BSc) honors degree at the same institution. I had picked Imperial College after winning a UK-wide national scholarship to study science as, at that time, Imperial had more Nobel Prize winners in physics than any other educational institution in Britain. As one of the few students to gain a First-Class degree, I was keen to pursue a career in academic research. My thesis was entitled “Many Body Problems” but this was not about cancer (or Hollywood actresses!) but a new opportunity to extend the recently developed techniques of Quantum Field Theory to complicated situations in solid materials. Within two years, I had invented a new quantum representation of magnetic interactions that could be used immediately with previous known methods for quantum fields in empty space that was being used in high-energy physics. I was able to publish several papers in the new area of Solid State theory, so that in 1967 my PhD thesis was readily accepted by the two external doctoral examiners, one of whom went on to be awarded the Nobel Prize in physics, for his own work in Solid-State theory. I was soon offered several challenging opportunities as a post-doctoral student at various prestigious institutions but I had reached a major decision point in my life (after marrying a lovely young ‘Arts’ student). I realized that I was becoming bored with the type of research I was doing and furthermore realized that once one started down the academic career path one was effectively locked in for life. So I began a search for alternatives and was fortunate to get an offer of a job as a systems-analyst with a new computer company opening in London. I accepted their offer (even though I knew little about this challenging new technology). Fortunately, my new boss was looking for people who could learn quickly as there were no schools of Computer Science in those days. My own head of department at Imperial was furious when I announced my irrevocable decision to leave: in fact, he refused to ever speak to me again. This turned out to be a good decision for me, as my physics education had taught me how to approach novel situations in a systematic manner. Later, I became a professional management consultant with international firms in London and Vancouver, Canada. In these situations, I pioneered the new techniques of Information Technology and eventually became the senior IT Partner of a national firm. About ten years later, my feet began to itch again, so I resigned to create my own software development company. Initially, our firm would commit to building new, online information systems for a broad range of companies across diverse industries. Unusually, we would offer a fixed price and give the client the final decision on when the contract was complete. Luckily, I had developed some new techniques for analyzing companies and systems to always deliver “on time”. Eventually, I created one of the largest information systems for the Property & Casualty insurance industry, so I could afford to retire and (recycle my life) return privately to fundamental physics research, supplemented by wide reading in Natural Philosophy and History. I have applied this lifelong experience and knowledge to understanding the disease that destroyed our lives. In trying to understand cancer, I have applied my personal approach to new information systems and the new research expertise known as General Systems Theory as it has been specialized to biology, where it is known as Systems Biology. A non-mathematical approach will be taken here that emphasizes concepts, especially those of entities and processes (relationships). We will organize our current knowledge of cancer in a systematic manner for the general reader who wishes to understand the science of cancer but it will not be presented at a deep technical level that only a cancer specialist may be seeking. 3

1.5 Summary This book was written to provide a firm scientific perspective on human cancer in a readable form. There is an enormous amount of technical knowledge on the ‘modern plague’ being published every year and with research emphasis on specialization, it has become increasingly difficult to get the ‘Big Picture’, especially for interested people who do not have a deep medical education. In the last fifty years, there is a growing consensus that cancer is a genetic problem that involves mistakes in the natural processes that happen all the time in most cells in every human being. Huge amounts of detailed medical information are available in excellent texts and on the Web, particularly in the ever-expanding Wikipedia. However, these sources will overwhelm all but the most motivated reader, especially online where information is organized in thousands of fragments, which are networked together. This book cuts this Gordian knot by using the insights of systems theory to impose a traditional linear narrative on all this massive volume of technical information. It may come as a surprise to many but biology uses little mathematics while still being critically dependent on technology. This will be the approach adopted here where the philosophical tradition of verbal analysis and description to enhance understanding will still be followed. Information is translated from the language of medical experts into normal terms, while still linking back to the esoteric terminology developed in any scientific field. The narrative will be offered in a hierarchical approach with chapters, sections, subsections, etc. labeled in a decimal manner to aid cross-referencing and the linkage of key ideas, using the symbol §n. A glossary of key terms and a bibliography are also included at the end of the book. Chapter 2 introduces the idea of life forms as systems, emphasizing their parts and functions, which transform into a focus on processes when the functions interact amongst them selves. This chapter is built on the innovative ideas found in James Miller’s influential book [10] Living Systems, which directed attention to the necessary subsystems, needed to preserve all life forms. Key concepts discussed here are matter transformations and the difficult idea of information. These ideas lead naturally to the science of biology that underlies all research into cancer. The main ideas of animal physiology are presented through the lens of vital subsystems, needed to maintain the existence of any human. This review inevitably introduced the principal organs that make up each one of us. From here, it is only a small step to the introduction of the central actors in our cancer story: cells and tissues. This journey is briefly interrupted to bring in the foundational science of biochemistry and its major focus – the macromolecules that form proteins and DNA. Continuing this microscopic journey leads to the major parts of human cells, where cancer originates. Like one of the pioneer pathologists, Sidney Farber, who made major discoveries about cancer by first studying the normal processes of the body, we too first review the major systems that keep people alive. The next chapter reviews the important ideas of genetics, as cancer is known to be an abnormality of the multiple generations of cell errors. This is where the idea of genes is discussed and their unique collection per individual known as the genome. The heart of this chapter is the explanation of the universal process of ‘Making Cells’ that includes the current understanding of the central process of cell division, where errors may lead to cancer. Finally, in the fourth chapter we review the foremost characteristics of human cancer, with a major focus on tumors. The emphasis here is on the deadly process of secondary tumor generation or metastasis. These fatal processes are re-examined in terms of cancer systems biology. Great attention is made here to explicate the latest ideas in carcinogenesis and epigenetics, where process-control errors are seen as the major drivers of tumor growth. The chapter introduces the seminal ideas in a famous cancer review paper on the “Six Hallmarks of Cancer”, which did much to focus scientific thinking on the universal characteristics of most malignant cancers. Cancer treatments are examined in chapter five. The focus here is on the traditional techniques, summarized in the phrase: “Cut, Poison and Burn” because these are still the basis of most of contemporary cancer treatments that still do not reflect the insights gained from the huge cancer-science efforts over the last forty years. The side effects of 4

these traditional treatments are reviewed for the benefit of future patients who are not told the full story of these drugs. Two of the latest methods for treating cancer (Targeted Therapy and Enhancing the Immune System) are also examined in more detail as these do rely on modern cancer-science understandings. Chapter six covers the author’s response to the information uncovered in this investigation; especially an analysis of why there has been such disappointing progress in the treatment of cancer over 40 years. The various treatment modalities are examined, including those on the horizon, based on the latest scientific research into cancer. Some authorial license is also taken in chapter seven, where some new directions for cancer scientific research and therapies are made. A plea is also entered here to expand beyond the traditional medical model and begin serious investigation of alternative possibilities involving diet (for prevention) and natural alternatives, such as plant-based therapies that cannot be monetized through patents under our present commercialized approach. The final chapter summarizes the author’s conclusions to this investigation of cancer from a system’s viewpoint. The sad conclusion is that although there has been impressive scientific knowledge about the cellular processes involved in understanding carcinogenesis, developed over the last fifty years, there has been little progress in getting this to appear as effective clinical therapies: “Cut, poison and burn” still seem the standard treatments being offered to many cancer patients today. Unless major changes are made in how the research is conducted and then transferred to oncologists, we may still be facing further grim defeats by this “Emperor of All Maladies”. This part of the book recommends a more focused and holistic approach with greater attention on the processes involved in the sub-system, known as inflammation, which is one of the body’s own systems that get hijacked by cancer. In the meantime, individuals who are still cancer-free should review their life-style choices (especially the foods they eat), to minimize their risk of becoming stricken with cancer, while existing cancer patients would also improve their survival by adopting similar strategies. Avoiding good advice because it “has not been scientifically verified” is not a wise strategy. The book concludes with a possible “Wolstencroft Warning” about what might transpire should humans ever “cure cancer”. Ironically, the fact that malignant cancer hijacks many of our body’s basic techniques (which were developed to preserve the collective good of the multi-cellular organism, called a person) for its own selfish purposes (that it then passes genetically down to all its subsequent descendants) seems to be mirrored at the level of human societies. Some selfish families (the aristocracy) hijack our social institutions simply for their own private desires. History shows that societies that do not correct these selfish impulses ultimately collapse over time just as cancer ultimately kills its own host. A final note for those who find their lives too busy to even read a short book like this: try just a quick review of each chapter’s separate short summary. This might encourage reading the full text – the price is just your life.

5

2.0 SYSTEMS 2.1 Language and Natural Philosophy Philosophy was developed by the Ancient Greeks to create a verbal method for understanding the world around us. These early ideas still pervade western civilization and form the foundation for much of how we view the world, even though most people are unaware of these implicit links. One of the most original of these thinkers was Aristotle (c. 350 BC), who rejected the over emphasis on mathematics of his own teacher (Plato); since Aristotle was fascinated by the world of living things, he became the ‘Father of Biology’ [11]. While Plato focused on timeless concepts, such as truth and mathematics, Aristotle recognized that time was a critical part of reality, especially for living things. Unlike Plato, who tried to arrive at verbal definitions to describe the world, Aristotle saw that most of us came to understand the meaning of words by noting the commonalities of similar examples; meaning was reached by pointing out examples and intuitively noting similarities and differences. Although there were very many men, each unique; one could point out the similarities (and differences with other creatures) and generate the concept of MAN; emphasizing certain differences led to the concept of WOMAN, while both could be combined together to create the new concept of HUMAN (or PEOPLE). Similarities with other creatures can be identified to generate a new, higher level concept: ANIMALS. This illustrates how many languages organize their concepts into hierarchies of ideas. Analyzing many European languages also demonstrates that most of them are structured around the concepts of nouns and verbs or more generally as objects (things) and relationships (between objects). Importantly, some relationships are timeless, (such as mother to son), while others are quite varied across both space and time (e.g. marriage). Abstract concepts mainly rely exclusively on verbal definitions.

2.1.1 Life Forms as Systems Aristotle was the first intellectual to analyze living objects in terms of parts and functions. He realized that the whole could be thought of (or analyzed) into separate parts but these had to be well organized and co-operate together appropriately if each life form was to continue to exist (a universal purpose that he saw as fundamental to life). Unlike the non-living parts of nature (like rocks) that could just ‘sit there’ (unconditional existence), the vital parts of life-forms had to continue to interact together in well defined but complex processes, where the parts moved around in space over time (an ongoing real existence contingent on the parts remaining in place and moving together correctly). These movements were neither random nor without pattern; they were critical to ‘the Dance of Life’. Each group of parts behaved like a minor life form in its own right, with its own objectives and purposes. This idea of analyzing time-based patterns of the world into collections that persist for an extended timeframe leads intuitively to the idea of any such dynamic collection as a system. Only when complex ideas are given in terms of natural languages can many people agree on their validity and value: necessary first steps on the road to becoming widely accepted through empirical evidence and eventually becoming a science.

2.2 General Systems 2.2.1 Background A system is any set of interacting (or interdependent) component parts forming a single object. Every system is described by its structure and purpose and defined in terms of its functioning. It is delineated by its spatial and temporal boundaries, separating it from its environment, which if permeable further influences it and making it an ‘open system’. The word “system” itself comes from the Latin word systema, derived in turn from the similar Greek word meaning: “a whole thing compounded of several parts or members”, implying the idea of “composition”. All the parts must eventually interact; otherwise, they do not form a singular system but two or more distinct systems. Usually, this implies that the parts must have some commonality to interact.

6

2.2.2 Holons Since the parts of systems (except at the lowest level) are themselves systems, then a part (or component) may be viewed from the larger perspective as simply a part or it may be “opened up” and viewed (or analyzed) in terms of its own component systems. This two-way perspective was first introduced by Arthur Koestler in his book “The Ghost in the Machine” (1967); he called such parts ‘holons’ and this has proved a powerful technique for understanding complexity. Complex systems cannot be analyzed into the sum of several independent activities (like the linear systems popular in physics); new paradigms, like system theory, must be added to old ways of thinking. Some properties (like life) emerge from all the interactions and are not found at the deepest system level.

2.2.3 Systems Theory Systems theory is the study of systems in general, with the goal of discovering overall similarities (or patterns) and generating principles that can be discerned from, and applied to, all types of systems at all nesting levels in all fields of research. Systems theory can be considered a specialization of all forms of system thinking, with an emphasis on generality, useful across a broad range of systems compared with the particular models used within individual fields. A major objective in this approach is to achieve scientific (non-subjective) understanding of how systems influence each other within one larger system. Ideas in this area can be traced back to Ludwig von Bertalanffy in the 1940s, which evolved into the field of cybernetics in the 1950s. This new view of problem solving tries to balance synthetic and analytic (reductionist) thinking, which has unfortunately characterized too much of the scientific approach since Descartes but, in fact, only succeeded in identifying the parts of complex objects but failed to understand how the parts came together (i.e. interacted) to produce the larger object or unexpected functions (socalled “emergent properties”). The challenge in understanding complexity is to appreciate why a part or process persists (continues to exist over time). The synthetic view of systems thinking arises from the view that a system’s component parts can best be understood in the context of their relationships (interactions) with each other and with other systems rather than in isolation (the analytic view). This often exposes cyclical and non-linear patterns that historically have not presented easy mathematical representations, which often rely on linear models (implying simplistic assumptions of linear cause and effect). This integrated perspective shows why even small changes or localized events can ‘trigger’ significant changes in large, complex systems. One of the most important characteristics that needs to be determined for any system (or sub-system), once its boundary has been identified, is whether the parts of the system communicate (or interact) across the boundary or not. If there is no communication across the boundary then it is classified as a closed system, which is often the case for manmade (or mechanical) systems, which are much easier to analyze. However, when communication does occur, they are classified as open systems and these are much more of a challenge to understand. Viewing life forms as machines has been one of the greatest mistakes of western, scientific thinking.

2.3 Living Systems In the last few decades, several scientists have proposed that a general living systems theory is required to explain the nature of life. Such a general theory, arising out of the ecological and biological sciences, attempts to map general principles for how any living system functions. Instead of examining phenomena by attempting to break things down into just timeless components, a general living systems theory explores natural phenomena in terms of dynamic patterns of the relationships of organisms and organs within their external and internal environments. This is the philosophy adopted in this book, where the central focus is the animal cell: the foundational component of all living systems. Since change is always present in living systems, then time becomes the fundamental dimension. Even a single cell has resisted the best attempts at understanding it in isolation; its tissue context is very important.

7

Life forms are open, self-organizing living things (collections of matter) that interact from time to time with their environment. As systems, they appear to share one common purpose: the absolute need to continue to stay alive. Therefore, these systems remain alive (i.e. maintain their existence) by flows (or exchanges) of information and matter/energy. When the flow of matter is itself complex, then its spatial arrangement or its internal motion can be a local source of change when this matter-object interacts with other matter-objects. Such transfers of potential for change are referred to as energy.

2.3.1 Overview Living systems theory is a general theory about the existence of all living systems, their boundaries, their structure, interactions, behavior and development. This theory was created by the famous academic and scholar, James Grier Miller (1916-2002), who wished to formalize the concept of life. According to his views, as spelled out in his 1,100 page 1978 magnum opus [10] “Living Systems”: “each living system has to consist of all twenty ‘critical’ subsystems” - themselves defined by their functions and illustrated in numerous examples, from simple cells to organisms, countries and societies. In this influential book, he provides a detailed examination of a number of systems in order of increasing size while identifying his subsystems in each. Living systems can be as ‘simple’ as a single cell or as huge and as complex as a supranational organization such as The United Nations. Regardless of their complexity, each depends upon the same essential twenty subsystems (or processes) in order to survive and to continue the propagation of their species or types beyond a single generation. Complexity usually occurs when a system has memory (an “adaptive” system) and/or feedback flows from earlier times. Most machines made by humans (before the invention of computers) were not adaptive systems. Viewing animals as machines, like Descartes, was always a gross simplification, erroneous and quite unjustified outside his theological motivations.

2.3.1.1 Key Concepts We agree with Miller that the concepts of space, time, matter and information are essential to a broader understanding of living systems because all living systems exist in space and are viewed as made of matter organized by information. His theory of living systems employs two sorts of spaces: physical (or geographical space) and conceptual (or abstracted spaces); since we are presenting a physical theory here we will limit our discussion to real, three-dimensional space – the one we all exist in and are somewhat familiar with. We also agree that the cell is the best starting point to study life (Grier begins with this and spends over 100 pages on it) but we do not agree that all his 20 sub-systems are the clearest way to understand the cell; they seem far too technical. Grier does emphasize the overwhelming complexity of the processes in living cells, especially animal ones. 2.3.1.2 Information Here it is also useful to clarify the abstract and central concept of information. At its most physical level of generality, information is just the response of a material part of nature to only the fact of existence of another material part, at other locations in space. If the motions of these parts are altered by this interaction event then we say that energy has also been exchanged. Thus, patterns of matter in space may influence or transform other patterns of matter in space, usually at a later time. If the source (original) pattern changes over a given time span, then the response of the “receiver” may also change. It was Gregory Bateson who usefully defined information as: “the difference that makes a difference”. Below the human cognitive level, it is important here to generalize the notion of information to extend beyond our own ideas of data and knowledge. For example, at the lowest level of nature (outside the atomic nucleus) an electron “knows” about and reacts to (i.e. is influenced by) the existence of another electron with which it interacts. Reaction/response is more general in nature than communication or representation and is more useful when thinking about biological systems in general, when future action (or processes) may be selected (or determined) by the information received.

8

2.3.1.2 Processes A process is viewed here as the central focus of analysis of a system (or subsystem). It defines the spatial arrangements of the parts over time and which internal parts interact with other internal or external parts. Material flows are many parts moving and interacting in a similar manner. Some events may introduce irreversible changes.

2.3.2 Biology

2.3.2.1 Taxonomy It was almost 2,000 years before western intellectuals began to study nature after Aristotle, theology was the subject of choice amongst educated men and even the study of mathematics languished for almost 1,500 years in Europe (although it still fascinated Arabic scholars for most of this period.) The word “biology” was coined in 1736, by the Swedish Natural Philosopher, Carl Linnaeus in his book “Bibliotheca Botanica”, one year after publishing his ground-breaking book “Systema Naturae”, where he created a taxonomy of life by attempting to classify or group all known life-forms by their external appearances or observable, shared gross characteristics (‘morphology’). His hierarchical scheme began with Aristotle’s major separation of the physical world into animals, vegetables and minerals. Linnaeus divided living things into two Kingdoms: animals and plants based on the ability of animals to generate self-movement. Biology began to quickly develop and grow with Anton van Leeuwenhoek’s dramatic improvement of the optical microscope in 1674. Using this new technology, scholars discovered a new world of living creatures. Major discoveries included the motile life-forms: spermatozoa, bacteria (oldest, unicellular life) and minute aquatic creatures (designated infusoria) and a vast diversity of microscopic life, never previously imagined when humans had been limited to their own unaided senses and the arrogant view that only objects that could be seen directly could exist. New, high technology advances in microscopy (like electron microscopes) have shown us even smaller objects than bacteria, especially the parasitic life forms, known as viruses. Since our focus here is on human cancers, we will mainly restrict ourselves to large, live-birthing creatures such as mammals.

2.3.2.2 Systems Biology Along with these innumerable discoveries of new life forms (now usually called organisms, for self-organizing beings capable of growth and reproduction), biology divided into several sub-disciplines. These were defined by the kinds of organisms studied and the methods used to study them. It is estimated that less than 1% of all species that ever existed on Earth still exist: the number of current species is thought to be about 10 million. Botany studies the biology of plants; evolutionary biology examines the processes that produced the diversity of life; while ecology examines how organisms interact together in their environment. A principal need of the new biology, especially after powerful microscopes (literally) exposed a whole new world, was to go beyond a simple, physiological reductionist approach to understanding biological structures; historically, this had followed the analysis of observable organs, such as heart and lungs – while occasionally integrating them into a combined heart/lung ‘system’. This new microscopic world, led to many new scientific specialties. This science explosion makes the need for an integrative view, such as Systems theory even more important. Particularly, from 2000 onwards, biology begins to use the term ‘systems biology’ widely.

2.3.3 Objectives & Strategies Although there may be deeper and more mysterious metaphysical objectives across all living systems, it is possible that all life forms simply manifest an urge to continue to exist for as long as possible; an idea that might be called vitalism (not some magical substance or ‘non-physical entity’ that makes us ‘organic’). We shall focus on this common objective and examine it in terms of its possible strategies that may be grouped as higher concepts, such as survival of each example across time, thriving (dynamic positive changes across space) and common solutions to achieve the goals.

9

2.3.3.1 Survival Strategies 2.3.3.1.1 Species Survival When discussing survival, it is important to realize that Nature takes the long view – it is the species that seems to be the unit of survival across time, not the individual organism and not even the unique cell. Life has discovered that making copies (new examples) is the easiest strategy to follow but this can only occur at the level of the individual organism. The optimum strategy for a species to survive across time is for it to maximize its variety; it can do this by getting its exemplars to gradually change over time to manage unexpected situations (evolution). This is easiest to achieve when many species use the same processes and structures as each other; this implies the appearance across many species of similar systems, organs, cells and processes, especially deep at the cellular level; this also accounts for the universality of the same molecules occurring at the foundational level of life (e.g. proteins, nucleic acids, etc.). Over any short time period, a species can expand its chances for survival by spreading its exemplars across as much space as possible seeking out all kinds of environments that prove more beneficial (i.e. geographical dispersal). We will use the term entity when referring to one example of a type (species) of organism. 2.3.3.1.2 Entity Survival Humans, with their consciousness of the world, may realize Nature’s strategies intellectually but their desperate, personal strategies to avoid dying indicate that the pull of vitalism still operates within most individuals. This is because only individuals actually exist and they must create progeny for the species to survive and this process must occur before it is too late. Individual organisms must possess useful subsystems that help each example (entity) to survive to maturity, create copies and, if necessary, help the new young to survive to maturity. This requires that they each possess vital sub-systems: these are described next. Another useful strategy appears to be to develop cooperative behaviors, where needed tasks may be shared among many exemplars and new techniques passed down through time (learning). Cancer illustrates the urge to survive at the level of a single cellular family. Indeed, cancer may be an example of what happens in a multi-cellular organism when a single cell ‘forgets’ that its role is to just play its part contributing to the whole organism; localized damage to this one cell makes it regress to an earlier, single cell model when living just for itself was sufficient as a unicellular organism. In this sense, cancer is a suitable metaphor for when sociopaths ignore the fact that humans thrive collectively in multi-person societies.

2.4 Vital Subsystems We shall approach our investigation of cancer through one of the major areas of biology and medicine, namely physiology as this focuses principally at the level of organs and systems. Most major aspects of human physiology have close correspondences in animal physiology, especially mammals. This is why animal experimentation has provided so much of the foundation of physiological knowledge and why much medical research is conducted upon animals. So much of new cancer research is conducted on mice; it is often referred to as Animal Models. Mice are particularly well suited for helping us with cancer research as their genetics are quite similar and they breed another generation every nine weeks. Anatomy and physiology are closely related fields of study: as anatomy is the study of form while physiology is the study of function; they are intrinsically related and are usually studied in tandem as part of a medical education. Anatomy may be viewed as the static forms and structures of a given organism (e.g. head, feet, etc.), while physiology can then be seen as the time-based, changing view of its functions and activities, organized into systems, such as the immune system. Human gross anatomy is the study of human structures, which can be seen by the naked eye. Physiology, human anatomy and biochemistry (the chemical processes) are basic sciences, generally introduced to students in their first year at medical school. A single example of a living organism (called an entity) consists of many interacting systems, each helping to maintain the stable existence (homeostasis) of itself, the other sub-systems and the entire organism. Death is the failure of a vital subsystem. 10

2.4.1 Boundaries & Functions When investigating living systems, it is often simplest to define each system boundary in terms of its special membranes: the physical material defining the outer limits of a particular example. This same perspective will be adopted in examining each smaller sub-system (or organ) in each person. Rather than look at static structures of animals, a systems view focuses on functions and tries to identify particular organs that exhibit these functions; working backwards, one can identify the major systems needed in normal human bodies. However, there are some systems that span the whole animal – these we will call global systems, as their purpose is to manage the whole organism as a single unit; they often have components that operate at the surface and internally (usually across the whole entity).

2.4.1.1 Integumentary Systems This term is used to define the organ system that protects the complete organism from environmental damage, such as external abrasion or internal losses (especially water). It is our first line of defense. It is usually the location for external sensory organs to detect extreme pressure and temperature. In humans, the outer boundary of a person is referred to as the skin; it is actually the largest organ (15% by mass) in everyone. The outermost layer of the skin or epidermis contains no living tissue; it acts as a simple, passive first line of defense.

2.4.2 Global Systems

2.4.2.1 Movement Systems Unlike plants, animals must change their location to find nutrients to sustain them. This implies that their ongoing survival depends on suitable actions occurring (contingent existence). When the entity (i.e. organism itself) is totally responsible for making the decisions on which actions to take, one can readily see how important good decisions are to an entity’s long-term survival. Key to these decisions is moving the entity around threedimensional space. This requires that organisms have the ability to move their complete body from one spatial location to another; this implies that they must possess one or more movement systems, for travelling on the ground or flying above it. Thus, they must possess a suitable Muscular/Skeletal System, consisting of contractible muscles (which can contract and relax) attached to bones that keep all the parts of the organism moving together in a synchronized manner. Additionally, the muscular system may only move a significant part of the whole structure (e.g. hand) relative to all the other parts; as such, it may perform important functions within other organs, as with the heart muscles, where the rhythmic (oscillatory) motions or beating are involuntary.

2.4.2.2 Information Systems As movement is vital and requires energy, it is important that such movement is non-random or purposeful (i.e. intelligent); this requires that the organism know where it is, where it has been and when it has achieved its relocation. All of these activities require information; this is the role of the Nervous System. The originators of new external information are referred to as our senses; they transcribe excitations into electro-chemical changes in the sense organs (located near our surface) and transmit these signals via specialized physical connections, known as nerves. All higher animals have a major nerve pathway, called the spinal chord, connecting to the principal information processing organ (brain); together these two major organs form one vital system: the Central Nervous System (or CNS). In vertebrates, the brain is protected by the skull, while the spinal chord is protected by the vertebrae. Reactions of the body (either by the brain or via reflex shortcuts at the spinal chord) are relayed back to the muscles for appropriate responses, sometimes along their own dedicated nerve paths or motor nerves; some distant peripheral nerves can be over one meter in length. Since similar processes occur when internal changes require action, a similar system is used for controlling internal changes. Some of the internal nerve paths are vital to the entity’s survival, so they respond very fast and automatically (autonomic nervous system). 11

The primary input-transformation organs of the gastro-intestinal system [GI] – see later) are also vitally important to survival, so they have their own set of nerves, called the enteric nervous system (ENS), with its own nerve structures (embedded in the lining of the GI duct) and with its own independent reflex activity. All nerve functions may send signals from one part of the body to others when decisions must be made.

2.4.2.3 Circulatory System Every part of a living organism requires nutrients to sustain its existence, so there must be a global system that brings material to every part of every organ at the lowest level of life (called cells – see later); this is known in animals as the circulatory or vascular system. The principal fluid medium in which this distribution occurs in animals is called blood (which is mainly plasma), which consists of several vital components. Blood is so vital to animals that it is reused as much as possible (forming a closed system); so after it is created in the core of bones it is pumped around the body by a major organ (the heart); the average human body contains about five liters of blood. The blood circulates through dedicated channels, called arteries (from the heart) and veins (back to the heart), interconnected by the narrowest blood vessels (capillaries). Breaks in these channels are so life-threatening that special cells, called platelets, are always circulating to immediately plug any small leaks.

2.4.2.3.1 Respiratory System Since blood reaches every cell in the body, it is also used to carry other components both to and from every cell. The most critical blood component is oxygen, which is transported in red blood cells and is converted in each cell into energy that drives all the local activity. As oxygen only exists outside the organism, there must be a large subsystem to bring it inside the body: this is known as the respiratory system. In air-breathing mammals, like humans, air has to reach a major organ, called the lungs. Oxygen molecules diffuse passively into the blood through tiny air sacs across the lungs, reached by moving down the trachea, into wide passages (bronchi) and finally very narrow tubes (bronchioles). Once a cell has processed its oxygen, its bi-product (carbon dioxide) diffuses back into the blood where it is returned to the lungs and eventually exhaled by the same pathways as the oxygen entered, usually relying on the natural elasticity of the muscles surrounding the lungs. The whole input/output gas exchange system is controlled by the autonomic system (using blood pH levels) as oxygen deprivation can quickly kill most cells.

2.4.2.4 Entity Reproductive System All families of similar organisms (i.e. each species) maximize their overall viability by generating wide variations across all examples; this variability allows for surviving unexpected changes in their own environment. Most animals use a set of special genital organs, known as the reproductive system. Unlike most organ systems, the sexes of differentiated species usually have significant differences, both in form and in function: a process known as sexual reproduction, in contrast to asexual methods used by less complex organisms. Since this process is a special variant of the major process of replication, its description will be deferred until later (see Making Cells).

2.4.3 Internal Systems 2.4.3.1 Energy Systems Living organisms are dynamic systems, which are continuously changing over time; all of this activity requires supplies of energy to maintain its processes. The major source of energy is driven by oxygen conversion (as introduced in the respiratory system, above). Other sources of energy are derived from chemical changes of various materials brought in (or ingested) from outside the organism. Other types of materials, such as proteins, must also be ingested to provide raw materials for biochemical processes, like replication.

12

2.4.3.1.1 Digestive System The principal system for importing chemical materials is called the digestive system, which begins with the oral cavity (mouth) and its local systems, which breakup the food into smaller pieces and mix with saliva to make a bolus, which is swallowed down the esophagus (throat) and into the gastro-intestinal system, where many important molecules are absorbed. The six-carbon sugar, called glucose or (CH2O)6 , plays a central role in most cell’s energy processes. The recent book [12] Gut gives an excellent description of this little known but vital part of our bodies.

2.4.3.1.2 Gastro-Intestinal System The largest structure of the digestive system is the gastro-intestinal (GI) tract: beginning at the mouth and ending at the anus, a distance of about nine meters in adult humans. The largest part of the GI tract is the large intestine (colon), where waste matter is stored prior to final ejection. This is also the area, where much of the water is reabsorbed. Most of the food digestion occurs upstream in the small intestine, after breakdown in the initial large organ of the stomach. Biochemically, much of the digestive process is assisted by products of the accessory digestive glands, such as the organs of the liver, gall bladder and pancreas, which help convert many carbohydrates into glucose. The liver is the second largest organ in the human body and plays a key role in our overall chemical transformations (metabolism).

2.4.3.1.3 Excretory System Most of the waste passed out of a human body consists of digested materials that are not required. Many metabolic processes generate dangerous waste products that must also be removed, along with dead material that is no longer of value. Blood’s waste removal role forms a key part of the excretory system. In most mammals, much of the waste is transported away by the urinary system (or renal system). The critical organs here are the kidneys (doubled to reflect their importance), with extensive blood links to the circularity system. Most of the fluid waste (called urine) is temporarily stored in the bladder before being finally discharged through the urethra - up to two liters of urine are produced daily in a healthy human adult. The kidneys also regulate the critical acid/alkali (pH) levels of the blood. The spleen is another important organ in most vertebrates; it plays useful roles in removing old (dead) red blood cells (to recycle iron) and holding a supply of reserve red and white blood cells (see later).

2.4.3.2 Defense Systems 2.4.3.2.1 Immune System Since organisms are open systems, whose ongoing existence is not guaranteed, there is always the possibility of external threats to each example (or entity). There is thus an existential need to defend against these threats (or diseases); this is the vital role of the immune system. In order to function correctly, an entity’s immune system must detect a wide variety of threat-agents, called pathogens; these may take many forms from viruses, through bacteria to parasitic organisms, such as worms. In many cases, physical barriers prevent some pathogens (like viruses and bacteria) from entering the organism but if these barriers are breached then the innate immune system provides an immediate (but non-specific) response. A central feature of the immune system is to recognize foreign organisms, i.e. to know that they are non-self or not part of the principal entity. In going to every cell, blood plays a key role in the organism’s defense system. A large class of non-self molecules is antibody generators (antigens), which bind to specific immune receptors and generate an immune response. Advanced life forms, such as vertebrates, have also evolved adaptive immune systems, which can remember defeating previous examples of pathogens (using ‘signature’ antigens) so they respond even faster to repeated threats. Disorders of the immune system can result in autoimmune diseases, inflammatory diseases and cancer. Researchers were shocked when it was discovered that enormous numbers of unicellular bacteria, (2 ~ 10 x more numerous than our own cells) reside in and on each human (called the microbiome). This discovery has meant that our older knowledge of our immune system has been dwarfed by the realization that this huge symbiotic ecosystem (perhaps, almost 1,000 species) 13

makes major contributions to our ongoing health by playing vital roles in our immune system. It is believed presently that these are implicated in about 20% of human cancers, with 10 microbes currently designated as human carcinogens damaging DNA but only for some genetically susceptible individuals.

2.4.3.2.2 Lymphatic System The open, lymphatic system is a vital part of the immune system that interfaces with the circulatory system. It consists of special glands that generate a clear fluid (called lymph), which is stored in lymphatic areas (lymph nodes) around the body, as well as in the spleen and the thymus gland. About 15% of the blood’s plasma remains between cells, where it is called interstitial fluid, bathing every cell in the body. Constituents of the blood diffuse through the interstitial fluid on their journey to normal cell tissue. One of the main functions of the lymph system is to provide an extra return route for the interstitial fluid. Lymph contains special defense cells called lymphocytes and other white blood cells; it also contains helpful bacteria and proteins. These are all critical parts of the adaptive immune system. It is important for one’s own health to realize that lymph has no pumping system of its own: muscular contraction squeezes lymph from its nodes into the blood, which then transports it around the rest of the body. This is why injured people must have some exercise to keep their immune system primed with lymph.

2.4.3.2.3 Natural Killer Cells Since tumor cells are the body’s own cells, with mutations deep in the inner nucleus, they are ignored by the adaptive immune system, which relies on ‘markers’ on the problem cell’s surface, like antibodies or the major histocompatibility complex (MHC), which is the cell’s mechanism for raising an ‘emergency’ flag on its surface. Thus, the universal (innate immune system) must be activated; this is the key role of the Natural Killer (NK) cells, including its defense against cancer. They are called NK because (unlike the white T-lymphocyte cells) they do not need to be activated by other cells in the immune system. NKs mature in bone marrow, lymph nodes and spleen, where they then enter into circulation. NKs respond to the balance of their received activating/inhibiting signals. When NKs need to kill a cell, they release two proteins: perforin makes a hole in the target cell’s membrane and then a destructive granzyme molecule is injected, which induces apoptosis (see later). They also release messenger molecules (cytokines), especially a vital pro-inflammatory called ‘nuclear factor – kappa beta’ (or NF-κB).

2.4.3.2.4 Inflammation System When tissue is damaged, the body activates its inflammation process to try to repair the wound. This is detected by special white blood cells that release a signaling molecule, called a platelet-derived growth factor (PDGF), which alerts other white cells in the immune system to co-ordinate the repair operations, including triggering similar tissue cells to start dividing. Unfortunately, tumor cells (being ‘self’) do not trigger any inflammation, so they often avoid immune responses. Inflammation is a protective response that involves immune cells, blood vessels, and molecular mediators. The objectives of inflammation are to eliminate the initial cause of cell injury, clear out any dead cells and tissues (damaged from the original insult and the inflammatory process) and to finally initiate new tissue repair. Acute inflammation is the initial response of the body to harmful stimuli and is achieved by the increased flow of plasma and white blood cells from the blood into the injured tissues. A series of biochemical events propagate and sequence the inflammatory response, involving the local vascular system, the immune system and various cells in the injured tissue. Inflammation describes purely the body's immune-vascular response, whether the problem was a microbial infection (the commonest reason) or not. Inflammation is usually located by adding –itis to the organ’s name, so that appendicitis is inflammation of the appendix (usually an infection).

2.4.3.3 Internal Information Systems In addition to external information systems, which inform an organism about changes in its external environment, there is also a need to co-ordinate purely internal systems about changes that occur within the entity itself. Information signals move both remotely, through the blood stream (hormones) or between nearby cells or even

14

within cells. These signals are chemical only, so they move much more slowly (but often have a global impact) than the fast electro-chemical signals of the nervous system but while hormones’ effects are slow to initiate their effects can be quite extended, lasting from hours to days.

2.4.3.3.1 Endocrine System The endocrine system is based on specialized glands that secrete special molecules, called hormones, directly into the circulatory system to be carried to distant target organs. There are several such glands, each producing unique hormones; they include: the pancreas, the gonads, hypothalamus, pineal, pituitary, thyroid and adrenal glands plus several specialized glands in the GI tract. Neuroendocrine hormones may be triggered by neural activation, especially in the brain through the hypothalamus. A number of glands trigger each other in sequence, called an axis, such as the hypothalamic-pituitary-adrenal axis. The pancreas is a very active gland (a mixocrine gland) as it produces both the insulin hormone (at a few Islet sites) for controlling the use of glycogen (sugar) in every cell’s basic energy process as well as continuous quantities of digestive chemicals for the stomach and liver.

2.4.3.3.2 Exocrine System The exocrine system is similar to the endocrine system but here the glands (such as salivary and sweat glands) secrete their hormones only to the outside (or surface) of the entity using local, dedicated tubes or ducts.

2.4.3.3.3 Localized Hormone Systems Some hormones are very short-range; sometimes, they act on the same cell (autocrine) or local organs or similar tissue (paracrine) and sometimes on physically adjacent cells only (juxtacrine).

2.4.3.3.4 Cellular Information Systems Co-ordination of activity is often critical at all levels of living systems, especially within the smallest biological systems (i.e. cells themselves). Such intra-cell signaling is vital to most cellular processes, where it uses very specialized small molecules, called cytokines, which are produced by many cells in the immune system. Cytokines often act in concentrations 1000 times less than hormone signaling. Their special 3D shapes mean that they act like very specific ‘keys’ that fit only a few cellular ‘keyholes’ or surface receptors. Cytokines play major roles in health, disease and reproduction. This why now, cytokines are an active focus in cancer research.

2.5 Organs and Components 2.5.1 Tissues & Cells The above systems review of organisms demonstrated that processes occur in organs. This level of life appears as tissues, which are collections (from the same origin) of similar cells (see later) that all together carry out a specific function. Organs are formed by the required groupings together of multiple tissues. There are four basic animal tissue types: connective, muscle, nerve and epithelial. This latter type lines the cavities and surfaces of blood and lymphatic vessels, glands and organs throughout the body. The linings of blood and lymphatic vessels form a subtype, known as endothelium cells. All epithelia have no blood supply of their own but rely on diffusion from the underlying connective tissue through the surrounding basement membrane (the fibrous layer of the extra cellular matrix or ECM). The epithelia are the cells, which are most constantly exposed to the outside world, so that they need a much higher replacement rate than those in protected regions. It is not surprising that they are found to be the commonest sources of most cancers. Connective tissues (including blood) may be fibrous, skeletal or fluid and give shape to organs by holding them in place. Acting in a structural role, the fibrous cells are called the stroma and they keep the functioning cells of the organs (called the parenchyma) separated.

15

2.5.2 Biochemistry Since 1900, scientists have been convinced that the material world is made of atoms – the smallest unit of matter: all atoms are incredibly small with sizes of about one millionth of one mm. There are only 92 different kinds (elements) but they define all of chemistry (interactions between atoms). Only six types of atoms (elements) make up 99% of the mass of a human body, they are: carbon, hydrogen, nitrogen, oxygen, calcium and phosphorus; trace amounts of another 18 elements are also needed to sustain human life. However, atoms also combine together, via their vastly smaller electrons, into uncountable varieties and combinations, but all known as molecules. Most molecules are fairly simple, consisting of only a few or perhaps dozens of atoms. However, living systems require giant molecules, consisting of up to tens of thousands of atoms; these are known as macromolecules. The most common macromolecules in biochemistry are proteins and nucleic acids, which play key roles in the structure of cells and their vital processes. The chemistry of the cell also depends on the reactions of smaller molecules and charged atoms (ions). Smaller organic molecules, such as amino acids, are used to synthesize proteins. The commonest biomolecules are carbohydrates; they are used to store energy (often in the form of sugars) and genetic information as nucleic acids. Most human cells contain about 30,000 different types of proteins.

2.5.3 Molecular Biology Molecular biology is concerned with the molecular basis of biological activity between biomolecules in the various systems of a cell, as well as the detailed regulation of these interactions. Atomic physicist, Erwin Schrödinger is often credited with initiating the interest in molecules and the biology of life with his 1943 lecture series in Dublin, entitled “What is Life?” that was published in the following year as a book [13] with the same title. Most of our current knowledge of biochemistry arises from the study of single-celled creatures, like E-coli and yeast. Our knowledge of multi-cellular life (like humans and animals) is based on broad studies of mice and fruit-flies.

2.5.3.1 Biomolecules As biology has increasingly taken on the Materialist Hypothesis, pioneered by physics, it has become necessary to link the lowest levels of matter to biochemistry. This step requires a review of certain types of molecules (biomolecules) that are found everywhere in living systems. Understanding cancer requires us to follow this connection. It is incredibly complex but several general rules (luckily) seem to apply to simplify the task.

2.5.3.2 Amino Acids An amino acid is a universal, small biomolecule of a single carbon atom bound to a single hydrogen atom and three other atomic groups (peptide bond). One end is an amino group (a nitrogen atom with two attached hydrogen atoms = NH2); the other end is a carboxylic acid group (a carbon atom attached to a single oxygen atom plus a hydroxyl group of an oxygen atom with its own hydrogen atom = CO-OH). To complete the central carbon atom’s four bonds, there can be attached any one of 500 other groups of atoms, called the side-chain. Only 20 of these are found within cells; these are called the canonical amino-acids, 10 of them must be ingested, so are called essential; all of them are used to make vital proteins in humans while determining (in a very complex way) the overall 3D shape of the protein. The digestive system can break down complex proteins into needed amino acids. The seven critical amino-acids, along with their single letter codes are: histidine(H), isoleucine(I), lysine(K), methionine(M), phenylalanine(F), tryptophan(W) and valine(V). The remaining ones are: alanine(A), arginine(R), asparagine(N), aspartic acid(D), cysteine(C), glutamic acid(E), glutamine(Q), guanine(G), proline(P) and tyrosine(Y). Amino acids are the universal molecules of all life systems. Understanding amino acids makes one realize how they are the simple, chemical ‘Lego’ bricks of life and how easily they can be altered (mutated) to produce massive changes in critical life systems, such as cancer.

16

2.5.3.3 Proteins Proteins are very large molecules made from many repeating units of amino acids. Gigantic numbers of different proteins can be made from only a few hundred amino acids. The structure of proteins is viewed at four levels. The primary level is simply the linear sequence of amino acids, such as: G-W-P-E-D-G- etc. The second level describes the local shape, which could be a helix (‘alpha’) or a sheet (‘beta’). The tertiary structure is the entire 3D complex shape (‘conformation’) of the protein (determined by the total sequence of amino-acids, i.e. the primary level). The fourth-level structure describes the number (and arrangement) of peptide subunits, like the hemoglobin protein (carries oxygen in red blood cells), with four subunits or ‘domains’. Proteins can have tens of thousands of atoms in each molecule; some large proteins may have over 50 domains, each with several hundred amino acid units. They vary considerably in size: from 30 to 34,000 amino acid units; on average, they are a thousand times smaller than a cell. Proteins constitute most of each cell’s mass and are very dynamic: they execute most of the cell’s functions. They are (by far) the most structurally complex and functionally sophisticated molecules yet discovered. Proteins are not just rigid lumps of matter (like a stone) but active chemical participants, which can even generate mechanical action (movement); this coupling of chemistry and movement drives the dynamic processes of all living cells. The selective binding between molecules enables proteins to act as catalysts (enzymes), switches, signal receptors, motors and tiny pumps. A protein’s interactions with other molecules (‘ligands’) determine its biological contributions. This binding is very specific, often tight but sometimes loose and very temporary. Many of these bonds are quite weak but the protein’s shape means that many bonds arise simultaneously and can effect where in the cell the protein is most active. However, a small change of a few atoms can radically alter its conformation.

2.5.3.4 Enzymes Huge protein molecules are formed by the repetitive linking of the amino group of one amino-acid to the carboxyl group of another amino-acid (a peptide bond). The number of permutations of these peptides is gigantic. The most important proteins act as enzymes, which speed up the joining of pairs of biomolecules by a billion times. A cell interaction that might take 3,000 years, waiting for random collisions, can complete in less than a second if a suitable enzyme is present; most importantly, the enzyme is not changed in the process and is available for re-use many times. Enzymes of have a metal ion (like zinc or magnesium) close to their most active site that boosts its catalytic action. Sometimes a small organic molecule, called a coenzyme, serves a similar activity-boosting role. Many thousands of different proteins are usually found (and made!) within cells that may be viewed as protein factories. Some enzymes can cut other proteins at certain locations; these molecular ‘scissors’ are often given a name ending in –ase, like protease. All of this molecular activity is the veritable “Dance of Life”.

2.6 Cells Most plant and animal cells are visible only under the microscope, with dimensions between 1 and 100 micrometers (1/10,000th of a cm or about 60,000 on a pinhead), humans contain about 100 trillion (1014) living cells at any time. Advances in microscopy have had a profound impact on biological thinking. In 1665, the cell was discovered in plants by Robert Hooke, who named the biological unit for its resemblance to the study-cells inhabited by monks in a monastery. In the early 19th century, a number of biologists pointed to the central importance of the cell. It was not until the 1860s that most biologists appreciated the universal significance of the cell, when Remak and Virchow proposed the three primary tenets of what came to be known as “cell theory”. These tenets are: 1) the basic unit of all organisms is the cell; 2) individual cells are the ‘building blocks of life’; 3) all cells come from the division of other cells. By implication of cell theory, all living things are composed only of one or more cells or the secreted products of those cells (e.g. shells, hairs and nails etc.). The specialized study of cells is called cell biology (cytology) – it has become one of the most active areas of biology today all around the world, including cancer research. Since cancer is a cellular failure, we then will focus increasing attention on this part of animal organisms. However, it is always important to understand the context of any system, including nearby other cells (tissues). 17

2.6.1 Cell Types All life forms are constructed from cells; even single cell bacteria use a similar set of biomolecules to move, to eat, to breathe and reproduce. Organisms are often divided by the nature of their cell type; there are two fundamental types, the first type, found in all animals, is called eukaryotic, and contains organized components; the other type (often found in bacteria) are called prokaryotic, they do not have these complicated internal structures. Every organ has its own cell types, reflecting the organ’s functions; humans have about 210 different cell types; this fact has been misinterpreted to imply that there are hundreds (273) of forms of human cancers. All distinct cell types in a single entity arise from the first fertilized egg (see Growth §3.3.4). Multicellular organisms develop two classes of cell: somatic cells (majority and structural) and germ cells (used to create the next generation of the species). Within any creature, the various cell types differ by making selective use of their shared genetic instructions following the cues received from their surroundings. Reacting to contextual signals, different sets of genes are triggered into action according to the sequence of received signals, as in embryonic development. Somatic cells form the organs of the entity from three main layers: ectoderm, mesoderm and endoderm varying with their depth from the outer surface of the entity. Once a cell is in a given layer, it will normally continue to specialize into its organ type where it is very resistant to changes in cell type. Somatic cells are the commonest source of most human cancers. All multi-cellular organisms use eukaryotic cells; in fact, cancer occurs because a damaged cell operates as if it were no longer part of a larger collective – it becomes a selfish renegade trying to survive forever, along with its immortal, selfish descendants; the whole family ignoring their primary role as tissue members contributing usefully to the survival of the whole organism.

2.6.2 Cell Structure Understanding the structure of cells is an essential prerequisite for learning how cell functions. 2.6.2.1 Organelles As the smallest example of any living system, every cell is enclosed by its own membrane, which keeps all its components together within a jelly-like fluid called the cytoplasm, which is actually 80% salt water. The cells are the myriad sites where the deepest processes of life occur. Certain cellular functions are further localized within the cell in specialized structures, called organelles – a name chosen to reflect the analogy that organelles are to cells as organs are to organisms. Definitions vary: some biologists limit this term to those containing their own DNA (like mitochondria), on the assumption that long ago these distinct subunits had an independent existence until they were absorbed into larger cells to play a symbiotic role. Many of the organelles have their own surrounding membrane, which resembles each cell’s own outer membrane; in fact, some organelles even have double membranes. The major animal organelles are: the nucleus, mitochondria, the Golgi apparatus, the endoplasmic reticulum, vacuoles. The minor animal organelles are: vesicles, lysosomes and proteasomes. However, there are some organelles without any membrane at all; these are sometimes called biomolecular complexes, as they are usually just large assemblies of macromolecules that carry out specialized functions. Some of the more important membrane-less cell complexes are: ribosomes, proteasomes, nucleosome and the centrioles. The primary functions of all these components are described in regular biological texts on physiology but we will only focus on those components that play a major role in human cancers, especially in the largest organelle in animal cells – the nucleus of the cell. The nuclear envelope (a double membrane) allows the nucleus to control its contents and separate them from the cytoplasm when needed. This also allows control of regular cellular processes (such as glycolysis in energy metabolism) by keeping key enzymes within the nucleus. The nuclear envelope acts as a barrier that prevents both DNA and RNA viruses from entering the nucleus. Cells are 1000 times more efficient at energy production than gasoline engines.

18

2.6.2.2 Cell Nucleus Eukaryotic cells have a complex nucleus that has two major functions: storing the cell’s hereditary (genetic) material (DNA) and coordinating all the cell’s activities, such as: growth, metabolism, protein synthesis and cell division. The main function of the cell nucleus is to control the creation of sub-lengths of genetic molecules (genes) and mediate the replication of DNA during the cell cycle. As the cell’s nucleus is impermeable to large biomolecules, there are thousands of dynamical channels (called nuclear-pores, consisting of special proteins) that regulate the needed transport of some important biomolecules by protein carriers across the envelope, while allowing free movement of ions and small molecules. Regulated movement through the pores of large biomolecules, like proteins and RNA, is needed for both gene expression (protein manufacture) and the maintenance of the chromosomes. Failure in this regulation can be a significant cause of cancer. 2.6.2.2.1 Nuclear Components The fundamental components of each cell’s nucleus are nucleic acids and ribosomes; these are found in several forms (all related) and in large collections, such as chromosomes and the nucleolus (see §2.6.2.2.2 and §2.6.2.2.3). 2.6.2.2.1.1 Ribo Nucleic Acid (RNA)

Ribo Nucleic Acid (RNA) is not as famous as its related molecule, DNA but it is simpler to understand and comes in several forms. RNA plays major roles in the cell’s protein synthesis processes and in the management of genes themselves. RNA is always assembled as a single chain of repeating nucleotides (see later). It occurs in one of three forms, according to its principal function: these are “messenger RNA” (written as ‘mRNA’), the second form is called “transfer RNA” (‘tRNA’), while the third form (the commonest) is called “ribosomal RNA” (‘rRNA’). The tRNA delivers amino acids to the ribosomes, where the rRNA then links the amino acids into proteins. The mRNA directs the cell’s transfer of genetic information from the genes to make genetic proteins. 2.6.2.2.1.2 Genetic Nucleic Acid (DNA)

All eukaryotic cells contain hereditary information, which is passed from cell to cell during cell division; it is present in the form of stable macromolecules (two meters long in humans) with the chemical name: “DeoxyriboNucleic Acid” that is always abbreviated to the famous 3 letters: DNA. Even school children now know that DNA occurs in two strands, like a twisting ladder, popularly known as the “Double Helix”. Each strand is formed from units called nucleotides (see next). The DNA structure is very stable and because of the “Base-Pair” rule, the two strands actually store the same biological information but running in opposite directions (‘anti-parallel’). The steps of the DNA ladder are weakly interacting hydrogen bonds (two for the GC base pair; three for the AT pair). These are readily opened (‘unzipped’) during transcription by the mRNA molecules and then closed back together. 2.6.2.2.1.3 Nucleotides

All nucleic acids are made (in the liver) from multiple repetitions of short molecules called nucleotides, each made from a 5-carbon sugar, a small phosphate group and one nitrogen-containing nucleobase (or simply ‘base’) – either cytosine (C), guanine (G), adenine (A) and thymine (T) [in DNA] or uracil (U) [in RNA]. If the sugar is ribose the nucleic acid is RNA, if it is deoxyribose, the nucleic acid is DNA. These nucleotides are joined to one another in a long sequence by electronic interactions (covalent bonds – shared electrons) between the sugar of one and the phosphate of the next, making an alternating sugar-phosphate ‘chain’. These chains make DNA the longest molecule known (billions of atoms) with one human chromosome containing 247 million base pairs. Base-Pairing Rule: In the DNA double helix, each type of nucleobase on one strand only links to (or bonds) with just one type of nucleobase on the other strand (its ‘complement’). The two types of base pairs are: AT and GC. In addition to acting as building blocks in nucleic acids, nucleotides also act as energy packets, playing a central role in cell metabolism. 19

2.6.2.2.2 Chromosomes A chromosome is a packaged and organized structure within each cell nucleus, containing most of the DNA of a living organism. A chromosome is not usually found by itself but rather it is structured by getting itself wrapped around protein complexes called nucleosomes, which consist of eight proteins, called histones. These compact structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are copied (‘transcribed’). Most of the time, a chromosome exists as one long DNA molecule but during the metaphase step, in the synthesis phase of the cell cycle (see §3.3.4.2) the chromosome takes on its more recognizable X-shaped form. Each human cell has about 2 meters of DNA but when wound into the nucleosomes, it is reduced to a more manageable one millimeter. Human cells have 22 pairs of somatic (body) chromosomes and one pair of sex chromosomes (the gender defining X and Y chromosomes). The number of chromosomes varies by species; the fruit fly has eight, chimpanzees have 48 and the goldfish has 100. 2.6.2.2.2.1 Ribosomes

Ribosomes are the cell’s protein synthesis sites (or ‘protein factories’) found in all living cells. Ribosomes are large, complex structures of rRNAs and dozens of distinct proteins. Ribosomes have two linked units: a small part that ‘reads’ a mRNA (telling it what protein to make) and a larger part that actually builds the required protein from amino-acids brought to it by the tRNAs (see RNA above), one for each coding triplet found in the mRNA. Ribosomes (along with molecular chaperones) build and fold the growing protein chains. There are usually millions of ribosomes in a single cell. 2.6.2.2.3 Nucleolus The nucleolus is a sub-organelle (within the nucleus but with no membrane of its own), which assembles ribosomes from RNA and proteins, once created these are transported to the cytoplasm where they translate mRNA.

2.6.2.3 Cytoplasmic Components 2.6.2.3.1 Mitochondria Mitochondria are the energy producing organelles found in most eukaryotic cells; they are enclosed by their own double membrane. These subunits generate most of the cell’s chemical energy from ATP (§2.6.3). They are also involved in cell signaling, differentiation and even the cell’s death, as well as control of the cell cycle and cell growth. Their number varies by cell type: from zero (red blood cells) to over 2,000 in each liver cell. Hundreds of different proteins arise in cells of various species and tissue type, with over 600 distinct types found in humans. The mitochondria have their own ribosomes and DNA, which shows substantial similarity to the bacterial genome. Since 100% of every cell’s mitochondria are passed directly through the female (ovum) without change, female hereditary can be traced over thousands of generations. 2.6.2.3.2 Vesicle A vesicle is a small container of fluid enclosed by its own local membrane, which sometimes may merge with other organelles in the cell or even the cell’s own membrane to release its own specialized contents in a highly localized manner. Dysfunctions in a cell’s vesicles may contribute to some cancers and several other disease conditions. 2.6.2.3.3 Golgi This organelle is vital to the life of most animal cells, as it groups proteins into small collections (vesicles), which are then sent together to their final destination (especially if they are to be excreted from the cell). Depending on the cell type, these extracellular proteins may form antibodies for the immune system or neurotransmitters for the

20

nervous system; many secreted proteins become digestive enzymes or membrane proteins. In mammals, there is only one Golgi structure per cell and it is located near the cell nucleus and adjacent to the endoplasmic reticulum exit sites. There are extensive (and varied) protein modifications performed here that form a signal sequence (the first 5 to 30 amino acids) that determines the final destination of the protein. 2.6.2.3.4 Endoplasmic Reticulum Some vesicles entering the Golgi are produced by the rough endoplasmic reticulum (ER), whose outer membranes (studded with ribosomes) are continuous with the outer nuclear membrane. There also exists a smooth ER that lacks ribosomes but is mainly involved with lipid manufacture and carbohydrate metabolism, production of steroid hormones (in endocrine tissue §2.4.3.3.1) and detoxification of natural metabolic products. This smooth version is abundant in mammalian liver and gonad cells. When the vesicle contains destructive enzymes (from the rough ER), it is called a lysosome; it is used in the process of autophagy to destroy defective or damaged organelles, as well as almost all kinds of biomolecules. Lysosomes are the cell’s ‘waste disposal/recycling’ system. The ER, with its network of membranes, plays a major transportation role in eukaryotic cells.

2.6.3 Cell Processes Every cell, as a living system, has three major processes, divided into catabolic (breaking down) and anabolic (creating or synthesizing) molecules. The most important anabolic process is the creation of proteins (see later) and the most vital catabolic process is metabolism, where the cell needs to generate energy and new materials to maintain itself, using critical chemical reactions. Secondly, it must deliver material and/or information to other cells forming the organs of the entity; here the most important materials are proteins (protein synthesis – was described above in the section on ribosomes). Finally, the cell must create and maintain the tissues in the organ, in which it is a member. Since this process is a special variant of the major process of replication, its description will be deferred until later (see Making Cells §3.3). Metabolism is the set of vital chemical transformations that take place within the cells of living organisms. The chemical reactions of metabolism are organized into metabolic pathways, in which one chemical is transformed through a series of steps into another chemical, by a sequence of enzymes. Enzymes are crucial to metabolism because they allow organisms to drive desirable reactions that require energy that are too slow if left to random collisions between molecules; they also permit reactions to occur that need extra energy. The activation or suppression of enzymes also allows the control of metabolic pathways in response to changes in the cell’s environment or to signals from other cells. Some enzymes are quickly transformed vitamins (small molecules that cannot be made in cells). Metabolism involves a vast array of chemical reactions, but most fall under a few basic types of reactions that involve the transfer of functional groups of atoms and their bonds within molecules. This common chemistry allows cells to use a small set of metabolic intermediates to carry chemical groups between different reactions. These group-transfer intermediates are called coenzymes. Each class of group-transfer reactions is carried out by a particular coenzyme, which is the substrate for a set of enzymes that produce it and another set of enzymes that consume it. These coenzymes are therefore continuously made, consumed and then recycled. One key coenzyme is adenosine triphosphate (ATP), the universal energy currency of cells. This small molecule is used to transfer chemical energy between different chemical reactions. There is only a small amount of ATP in cells but as it is always being continuously regenerated, the human body can use about its own weight in ATP per day.

2.7 Summary This chapter sets the scene for the remaining parts of this book as it describes the system of a human being in terms of its own biological subsystems that are needed to keep each one of us alive and in good health. The approach here is to follow the path of traditional medical anatomy by introducing the major components, but not from a static perspective, rather in terms of how the systems perform, i.e. in terms of their functions and relationships. However,

21

before going straight into biology, the historical context is set by introducing Aristotle, the ‘Father of Biology’, who unlike most of the other famous ancient Greek philosophers knew that verbal theorizing (philosophy) had to be grounded in a thorough study of reality that he believed was based on time, especially for living things. His method was to examine many examples and draw out the differences and similarities in arriving at a clear idea of a concept, not just attempt purely verbal definitions, like his mentor, Plato. Aristotle, as the son of a physician, was obsessed with living creatures, which he studied in terms of parts and functions. These parts could not stay alive unless they all got to interact together in suitable ways: a result we now call a process. This led to the idea of time-based patterns of real things, co-operating together to achieve shared objectives: an idea we call a system. This idea is then further developed around the powerful concept of holons: viewed as parts of other systems or as a sub-system itself. Comparing many different systems resulted in an abstract set of common principles, called Systems Theory. It is a pity that too many ‘scientists’ stop after just identifying the parts of a system (analytic reductionism), without going further into the complexity of trying to understand the functions and processes of the discovered parts. Unfortunately, this is the stage that much of cancer-science is still at; the result is not surprising: a disappointing lack of useful therapies. It was obvious that the system view would eventually focus on living systems. Miller wrote a huge book on this subject that identified twenty major subsystems needed for a living system of any size: from animal cells to large, multi-person organizations. This required a deeper understanding of a few foundational concepts, such as space, time, matter and information. Like Miller and most biochemists, the restriction is towards a materialist view. None-the-less, the driving purpose in living systems, from cells to organizations, is the internal perception that the need to survive (at any time) and persist (across time) is the ultimate imperative: the central objective that spans all other motivations; additionally, most organized systems wish to do well at all times. We have called this urge to thrive and survive: “vitalism” as it seems the common objective of all living systems. This term should not to be confused with a similar ancient word that took on an erroneous meaning, in the Greek style of ‘substance’ thinking, to distinguish a magical, organic ingredient from the vast array of inert (or inorganic) substances. We have retained this word to emphasize that living systems are organized fundamentally differently from non-alive material. In this model, the two inter-related ideas of interaction and information become central. Most of us have an intuitive idea of interaction (although physics has confused this by assuming they are always continuous i.e. the concept of ‘force’) but information is a much newer and nebulous idea, so a discussion of this powerful idea was included at this point. This is the point where the foundational science of biology is introduced as the organized investigation of living systems. Biological science progressed rapidly after the invention of the microscope (interestingly, a similar impulse motivated cellular biology in the late 20th century when advances in physics led to even more powerful technologies to study the vastly smaller world of the cell’s nucleus. We approach vital systems from the outside: in terms of their boundaries (or membranes). Moving an example of an organism (called here: an entity) leads immediately to the importance of information and the central role of the nervous system. The circulatory system is also discussed in terms of its global transportation functions, bringing nutrients to all cells and helping remove waste products, via the excretory subsystem. Since the ongoing existence of a living system is not guaranteed, there is a need for several defense systems. The most important component is our immune system that has been optimized to destroy external threats (pathogens). A key function of the immune system is to recognize ‘non-self’ objects; failure in this activity can result in harmful autoimmune reactions, where a person’s own immune system attacks his own cells. Unfortunately, this loophole allows most cancer cells to survive because their errors usually lie deep in the nucleus of the cancerous cell, so they escape this feature of the immune system that operates primarily at the surface of the cell. This is also the point where the key role of information appears when the function of internal information systems is introduced. Global

22

signals, such as hormones, are distinguished from information messaging, both between and within cells; these material messages trigger actions when and where needed; good co-ordination is vital to successful systems. Once the major systems have been reviewed, chapter two continues to analyze the organs and components, starting with an examination of human tissues and the cells they are made from. Modern biochemistry must be viewed from the perspective of atoms (the tiniest form of eternal matter) and their stable collections, called molecules. Most molecules in nature consist of only a few atoms (like H2O with 3 atoms) but living creatures are the exception, as they contain giant numbers of atoms: thousands or millions (called macromolecules) forming proteins and nucleic acids. These macromolecules are constructed from unique combinations of repetitions of very simple atoms, such as amino acids and carbohydrates; these cellular ‘Lego’ structures are readily explained herein. This chapter is concluded with a concentrated discussion of biological cells: the locus for all human cancer. We then describe the functions of the major organelles in a cell, with a focus on those involved in the cell-division mechanism (like the nucleus) that play a crucial role in cancer when mistakes occur. The focus here is on the nucleus where the cell’s information on how to make its needed proteins (and when to make them) is stored in its unique DNA, which alone determines all the other molecules in the cell. These manufactured molecules (mainly proteins) each have their own role to play in each cell as they interact together as they are buffeted around by the many tiny water molecules. Proteins are the most useful molecules in the cell, each specific protein performs one of the five major functions: they provide structures, they move material around, they provide protection, they signal critical events and trigger key activities and play a vital role, as enzymes, in speeding up or blocking molecular interactions. The important role of DNA is to store the information needed to manufacture all of the proteins needed in the organism. This incredible but almost invisible world has been visualized in a magnificent book by a professor of molecular biology, Dr. David S. Goodsell in his “The Machinery of Life” [16]. This chapter also introduces the principal player in this story: the living cell, where all the mystery of life is focused. Animals are multi-cellular creatures and (by analogy) the body of an animal operates as a single society, wherein its members are cells that reproduce by cell division and organize themselves into collaborative assemblies (tissues and organs). These multi-cellular societies do NOT operate on the competitive principle: “survival of the fittest” but on the co-operative principle: “self-sacrifice for later generations on behalf of the whole collective”. The vast majority of the organism’s cells (the somatic ones) are destined to die, leaving no progeny; instead, they dedicate their existence to support the few germ cells, which alone have a chance of ongoing survival. Ultimately, all the somatic cells are clones of the first fertilized egg (zygote). Since all the entity’s cells share the same genome, this self-sacrifice of the somatic majority helps propagate copies of their own genes. In order to achieve this overall aim, every cell co-ordinates its behavior across the collective by sending, (and receiving) signal molecules that act as social controls. All of this complicated sequences of interactions within the 200+ human cell types is occurring at an incredibly high rate, such that about 10 million cell birth and death events are occurring in most human adults every second. It is not surprising to read the confession of one of the world’s leading experts in human cancer biology admit that: “we still possess an incomplete understanding of how genotype influences phenotype.” Ironically, this was the initial motivation for introducing the idea of genetics, so long ago. None-the-less, we will now turn to the science of genetics as this eventually leads to the modern focus of cancer research.

23

3.0 NORMAL GENETICS 3.1 Heredity The modern study of genetics evolved from our long obsession with heredity: the passing of traits (such as eye color) from parents to their offspring. The study of heredity in biology is called genetics, which now plays a major role in the study of cancer. These traits arise from the interaction of an organism’s inherited genetic material (genotype) with its environment. The complete set of observable traits (structure and behavior) of an organism is called its phenotype – a distinction made to emphasize major differences between what is inherited and what that heredity produces. Most traits are quite complex; they are thought to be determined by multiple, interacting genes (see later) within and among organisms. In fact, the actual correspondence of observable traits (even race) and genes still remains a mystery, which will surprise many, who watch TV police detective programs that use DNA.

3.1.1 Family Heredity Most human societies have obsessed about passing on desirable traits to their offspring; perhaps the cultural belief in immortality of the family’s aristocratic bloodlines playing a role here. Two of the major contributors to the ideas of hereditary were the Moravian monk, Gregor Mendel and the English naturalist, Charles Darwin.

3.1.1.1 Darwin When in 1859, Charles Darwin published his revolutionary theory of evolution one of its major problems was the lack of an underlying biological mechanism for heredity. He really offered a theory of ‘Variety within Species', driven by natural selection. Theories of the origination of species remain a contentious challenge.

3.1.1.2 Mendel It was Mendel, who first proposed in 1866 (after a seven year study of pea plants) a biological scheme for trait inheritance with his ideas of information packets – a concept that was way beyond its technical exposure at that time or even in 1900, when it became much more widely known, after its rediscovery. Although Mendel did not use the word ‘gene’, he explained his plant results in terms of tiny (invisible) discrete, inherited material units that give rise to observable physical characteristics, such as plant height, seed shape and color, flower position and color, pod shape and color. Until the 1950s, most of the thinking on Medelian hereditary and genetics remained purely theoretical, with a large component (especially the study of population genetics) pioneered by the Cambridge mathematician, R. A. Fisher. It needed the invention of new technologies to actually study them, as genes are far too small to be seen with a light microscope, while changes to genes are even very much smaller.

3.2 Molecular Genetics In the early 1950s, experiments pointed to DNA (see above) as the biochemical component of chromosomes that held the trait-carrying material units that had become known as genes (see below). A focus on new kinds of invisible (i.e. model) organisms, such as bacteria and viruses, along with the discovery of the double helical structure of DNA, marked the transition to the era of molecular genetics.

3.2.1 Watson and Crick The molecular structure of DNA was first identified in 1953 by James Watson and Francis Crick, whose modelbuilding efforts were guided by X-Ray diffraction pictures made by graduate student, Rosalind Franklin; the two strands of DNA were a key clue. In 1962, Watson and Crick were together awarded the Nobel Prize in physiology/medicine, along with Franklin’s supervisor, Maurice Wilkins (omitting Franklin was a controversial decision) as Nobel prizes are limited to three winners. 24

3.2.2 Genetic Code After Watson and Crick’s proposal for the structure of DNA, the race was on to determine how genetic information was encoded therein, especially the rules (called the Genetic Code) for generating proteins from the DNA. All the properties of an organism depend either directly or indirectly on proteins (lipid or carbohydrate syntheses are the result of protein enzymes). By 1961, it was guessed (and then soon proved) that it was triplet sets of three consecutive DNA bases (or nucleotides), called codons that specify a single amino acid. Much later, it was demonstrated that mRNA is needed to translate this DNA information (occurring within the ribosomes). This scheme mathematically can create 64 (43) amino acids but only 20 are used biologically, multiple codons can code for the same amino acid. However, the model is so powerful that it is used by most of the living systems on Earth.

3.2.3 Genes Each segment of DNA that codes for a protein (or RNA) is called a gene - it is the molecular unit of heredity. Since a triplet depends on where the sequence starts; this is indicated by the triplet AUG on the mRNA (or ATG on the DNA). Similarly, a ‘stop’ protein sequence is signified by one of three codons: UAG, UGA or UAA. These special codes play the role of blank spaces in removing ambiguity if written sentences were just continuous sets of letters (as they once were). While the genetic code determines the protein sequence for a given coding region (structural), other DNA regions can influence when and where these proteins will be produced (regulatory). Mitochondrial DNA uses a slightly different set of protein-coding rules. There can be distinct variants of a gene, known as alleles, competing in any population. Alleles at a locus may be dominant or recessive: dominant alleles give rise to their corresponding phenotypes when paired with any other allele for the same trait, whereas recessive alleles give rise to their corresponding phenotype only when paired with another exact copy of the same allele. Genes act like a recipe to dictate how cells function and what traits they express. A signal (environmental or internal) first stimulates certain receptors on the outside of the cell. These receptors then cause biochemical changes within the cell, which are usually carried out by proteins and enzymes responsible for initiating specific functions. Cells have various signaling pathways that carry out these responses and genes ultimately control these pathways, in complex networks that work forwards and backwards over time (feedback). These pathways resemble a subway system. It is interesting that each human being only differs from another by one or two codons per thousand (1/10 of 1%). It is disappointing that most multi-cellular genomes appear to be remarkably “disorganized” – increasing the puzzle.

3.2.4 Gene Expression The regulation (or control) of gene expression refers to many techniques for increasing (‘up regulating’) or decreasing (‘down regulating’) the production of the cell’s genetic products, such as RNA or proteins; it is often informally called ‘gene regulation’ but these methods do not alter the genes or genome itself. There are several techniques for impacting gene expression, such as initiating developmental pathways, responding stronger to the cell’s environmental stimuli or adapting to new food sources. Almost any step of gene expression can be internally modulated; from converting DNA to RNA (transcriptional initiation), to when and how much RNA are copied and to the chemical modification of proteins by adding/removing standard functional groups like phosphates, acetates, amides and methyl groups that dramatically alter the actions of 3D protein shapes. Transcription of DNA is dictated by its structure. In general, the density of its packing is indicative of the frequency of transcription. Nucleosomes (see §2.6.2.2.2) are responsible for the amount of super-coiling of DNA, and these complexes can be temporarily modified by processes such as phosphorylation or more permanently modified by processes such as methylation. Such modifications are considered to be responsible for more or less permanent changes in gene expression levels. Up-regulation is any process that occurs within a cell triggered by a signal (originating internal or external to the cell), which results in increased gene expression and, as a result, the protein(s) encoded by those genes. Downregulation is any process resulting in decreased expression of a gene and corresponding protein expression.

25

3.2.5 Human Genome Genetic information is organized as genes; the complete set of this information in a species is called its genotype. The complete set of genes (in a given cell) makes up its genome. All cells in one entity contain exactly the same genome; different cell types express different proteins to exhibit their distinct functions. In 1990, the Human Genome Project (HGP) was launched with the goal of mapping the general genome across humanity. This project was first declared complete in 2003. The estimated number of genes has changed over time, as definitions of genes and the methods of detecting them have been refined. Everyone’s human genome has about three billion base pairs of DNA, all arranged into 46 chromosomes. In most species, only a small fraction of the total DNA encodes for protein, called exons; these are retained in protein synthesis but other segments (called introns) are discarded. This is a clever method for ‘splicing’ together different sequences of several proteins from one common DNA segment, using another recently discovered RNA variant called ‘pre-mRNA’, sometimes joining remote exons together. Most human genes are spliced in more than one way, perhaps helping with species evolution, but splicing makes it even harder to predict protein sequences purely from knowledge of the genome sequence. The human genome is neither the largest, nor does it possess the greatest number of genes but our proteins seem to be the most complex producing many more protein-protein interactions. Even though most vertebrate genes seem to be inherited from invertebrates, the function of at least 10,000 human genes still remains a mystery. Only about 1.5% of the human genome consists of protein-coding bases, with over 98% of human DNA consisting of noncoding repetitive and regulatory sequences, non-coding DNA and RNA. With our usual human arrogance when presented with a mystery, we dismissed this anomaly by calling the non-gene 98% “junk DNA”. The current consensus is that humans carry about 24,000 protein-coding genes; about 40% (i.e. 10,000) have been assigned to known protein structures, belonging to about 500 different protein families. Across all species, the 3D shapes (conformations) of about 20,000 proteins have been identified.

3.2.6 Epigenetics Epigenetics is the study of the regulation of gene expression through chemical, non-mutational changes in DNA structure. While genes play a direct role in the manufacture of proteins within a cell (see §3.2.4), the focus here is on making biomolecules from these ‘other’ sections of the genome that will directly control or regulate the proteinmaking process itself. The discovery of epigenetics solved the mystery of the ‘missing genes’ (or ‘Junk DNA’) in the genome but at a high cost of a 50-fold extra degrees of complexity in understanding the control mechanisms for expressing proteins at the cellular level. This level of difficulty confounds and overwhelms our ability to understand the biological complexity occurring in cancer, as earlier science (especially physics) made great strides by making hugely simplifying (linear) approximations of nature. Epigenetic alterations refer to functionally relevant modifications to the genome that do not involve a change in the nucleotide (base) sequence. Epigenetics can be used to describe anything other than the DNA sequence that influences the development of an organism. Useful examples of such modifications are changes in DNA methylation (more or less), adding phosphate groups to serine, threonine or tyrosine amino acid sections (‘phosphorylation’) or adding many types of complex ‘sugar trees’ to proteins (‘glycolation’) or even directly modifying the histones (§2.6.2.2.2) and changes in chromosomal architecture. Each of these epigenetic alterations serves to regulate (how and when) gene expression, without altering the underlying DNA base sequences. Although initiated by external factors, these changes may remain through the cell division process (lasting through several generations); they may be considered to be epimutations (equivalent to DNA mutations), particularly the ‘silencing’ of mitogenic quality control genes that play a major role in tumors. Genes could be viewed as the information about which instruments are to be used (and how to make them), while epigenetics could then be viewed as the orchestral score of when these instruments are to be played. Even worse, single mutations can create novel splices adding further complexity to decoding the “Genetic Puzzle”.

26

3.3 Making Cells Since timing issues are regarded here as central to cancer, it is important to view the serial, consecutive phases of an organism across time (known as its ‘Life Cycle’).

3.3.1 Entity Life Cycle 3.3.1.1 Overview

As a living system, every example of an organism (each entity) first comes into existence at birth, grows to full size (‘youth’), continues to reach maturity (when the next generation is created), decays in old age (senescence) and finally dies. This life cycle for every member of the species, repeats endlessly, creating new individuals over and over again. Nature prefers the survival strategy of New Versions rather than immortality (variety minimizes risk).

3.3.1.2 Embryonic The embryo is the earliest stage of every organism; in animals, it is too helpless to survive on its own and needs to grow in the uterus of its mother, who supplied the first egg – the majority of the mass of the initial cell. In humans, the embryo is considered to have transitioned at 10 weeks to a fetus when the organs start becoming fully formed. The fetus has a 50% survival chance at 24 weeks and most human live births occur after between 40 and 47 weeks.

3.3.1.3 Youth Young animals are theoretically viable but often stay with their own family as they continue to grow and learn the skills of their group to become independently viable. In humans, youth is a very culturally determined concept.

3.3.1.4 Maturity Mature entities can sometimes exist alone but social animals benefit from being with others of their kind. This helps with subsequent sexual reproduction, task sharing and the accumulation of knowledge exhibited by the group. At the cellular level, maturity defines the final stage of the cellular differentiation of organs, tissues and cells themselves. At this stage, they are fully contributing members of the collective (tissue) to which they belong.

3.3.1.5 Senescence Senescence derives from the Latin word ‘senex’ for old. In biology, it is used to define the penultimate life stage when the necessary functions for sustaining life gradually deteriorate, increasing the probability of death. Most biologists believe that cellular senescence underlies the senescence of the whole organism. Senescence can be delayed or slowed but cannot be deferred forever. Senescence is the leading (indirect) cause of death of all humans – about 2/3 (or 150,000 daily) at the moment. Cellular senescence occurs when a cell can no longer divide; usually they have reached their telomere limit (see §3.3.4.2). Senescent cells can provoke inflammation: a condition that underlies almost all age-related disease. Overall, senescence is characterized by lower ability to respond to external stimuli (stress, in particular), increased homeostatic imbalance and succumbing to age-associated diseases, including cancer, possibly because they seem to have shut down the cell-suicide mechanism (apoptosis: §3.3.5).

3.3.1.6 Death Death is the termination of all biological activity and the functions that sustain the active, independent existence of an organism. It is the natural complement of the process of origination; it allows for another example of life to run its natural cycle. Like the initial process, where materials are aggregated to begin a new individual, now is the time to return the immortal raw materials back to the universe. It is atoms that are eternal, not people. Human death is today defined as the irreversible loss of all brain function.

27

3.3.2 Germ Cells All sexual animals reproduce sexually, so they must create both germ cells and body (somatic) cells, determined by the presence or absence of zygotic genes. In mammals, a few cells of the early embryo are induced by signals of neighboring cells to become primordial germ cells, which divide continuously for about 4 weeks. The germ cells develop in the sexual organs (gonads), where they undergo meiosis, followed by cellular differentiation into mature gametes (either a sperm or an ovum – egg). Once an ovum is fertilized by a sperm, it becomes a zygote: the first cell possibly of the next generation. The zygote's genome is a combination of the DNA in each gamete and contains all of the genetic information necessary to form a new, unique individual, although newly ‘mixed’ for greater variety. Both zygotes and somatic cells replicate by the growth process of cell division (mitosis).

3.3.2.1 Meiosis All multi-cellular organisms, such as animals, use a specialized type of cell division during the sexual reproduction process. The genetic materials are deliberately mixed when combined by halving the genetic complement of each parent’s sex cells: a process called meiosis. Errors in meiosis are the leading known cause of miscarriage and the most frequent genetic cause of developmental disabilities. Meiosis eventually reduces the chromosome number by half, after two rounds of cell division to produce four child cells, each with half the number of chromosomes as the original parent cell. The first round deliberately exchanges genetic information between each pair of chromosomes to generate variety. Normally, after the second round there is only one survivor (the zygote) of the four child cells.

3.3.2.2 Embryonic Development There is much commonality of developmental processes across the animal kingdom: using similar stages, signaling and similar genes. This is fortunate as it allows animals to be used in researching this field, as human-based research here would present insurmountable ethical barriers. Once created, the zygote begins continuous cell division until, after about four days, there are 128 copies contained in the original cell membrane; at this point specialization starts with separation into the three principal cell layers or types: ectoderm, mesoderm and endoderm. Groups of these cells then start forming the major organs as well as the overall shape of the animal embryo. The three major processes of embryonic development are cellular morphogenesis, cell differentiation and cell growth.

3.3.2.2.1 Morphogenesis Morphogenetic processes define the growing shape of the embryo; many of these processes rely on special control molecules (acting on specific protein receptors) managing cell differentiation in a concentration-dependent manner. During this stage, cells sort themselves into clusters that maximize contact between cells of the same type.

3.3.2.2.2 Cell Differentiation Cellular differentiation is the universal process of a cell changing from one cell type to another type, usually a more specialized type. Differentiation occurs many times during the development of a multicellular organism, such as a human. This process must occur as mature organisms all begin as a single cell (zygote). Differentiation dramatically changes a cell’s size, shape, metabolic activity and both generation/response to biochemical signals but nearly never involving a change in the cell’s DNA sequence. These changes are due to highly controlled modifications in gene expression, as in epigenetics. Most cells exist in communities of healthy tissue that take their behavior from signals from their neighbors. Many of the signal molecules conveying information between cells are called growth factors (GFs). These GFs attach to special receptors on the cell surface, which transmit the ‘go’ message, via complex protein intracellular pathways, to promote or inhibit the expression of specific genes. Embryo cells grow because there is insufficient ‘stop’ messages from nearby cells, so continue to divide by the ‘go’ signal. Signaling cascades are inter-connected RNA and enzymatic pathways. A cell that can differentiate into all cell types is known as a stem cell. 28

3.3.3 Stem Cells Stem cells are proto-cells at a very early stage in their individual life; at this stage they have yet to take on the unique characteristics of a given tissue in the body (a critical transition known as differentiation); in other words, they are cells that have yet to differentiate themselves from generality to specific type. At this stage, stem cells can divide continuously (through mitosis – §3.3.4.2) to produce whole new generations of stem cells. In multi-cellular organisms, such as mammals, there are two types of stem cells: embryonic and adult. In a developing embryo, stem cells can eventually differentiate into all the specialized cells found later in adult entities. Adult stem cells are found in all the normal tissues, where they begin the repair process replenishing lost adult (or infant) tissues. They can be quite readily found in bone marrow and blood and exclude sourcing from an embryo (still controversial); since these cells can also be obtained from the eventual recipient they avoid the risk of rejection. Most adult stem cells are restricted to their own lineage (‘multipotent’). Some stem cells form tumors after transplantation – this is an important clue to cancer progression.

3.3.4 Normal Cellular Replication Each example of an organism (i.e. each entity) grows continuously in size from its initial appearance as a single cell (zygote §3.3.2) until it reaches it normal adult size for its species. Initial growth of the entity in animals is a specialized process and usually occurs in the protective organ of the female (uterus), where it is called an embryo. Once an embryo matures and emerges into world as an infant, it continues to grow and repair itself after injuries.

3.3.4.1 Independent Entity Growth Early emphasis in hereditary studies focused on passing some key traits from parents to children (a process that is dominant during the development of the embryo – see §3.3.2.2). The major activity in transmitting identical characteristics is found at all later stages in an organism when one tissue cell in an organ must be exactly replaced, (i.e. preserving 100% of the required DNA information and the type of cell that must be regenerated). It is failure in this universal process of cell division that is the most common source of human cancers.

3.3.4.2 Cellular Replication System Since every organ in humans is made from various types of cells, which have both a finite life (by design) and die from a variety of actions, there is an ongoing need to replace each cell at some time or another. The normal reason for replication is that some other (nearby) cells in the organ have disappeared, either dying from disease or physically removed by an unexpected accident (e.g. cut). In these circumstances, a surviving cell realizes, probably by a drop in the quantity of intra-cellular signals, that the organ needs some more cells of the same type. This triggers the survivor’s cell division process, where one cell (the ‘parent’ cell) divides into two ‘children’ (or ‘next generation’) cells. This division is just one stage (or phase) in the complete cell cycle. Each phase is separated by a triggered event. In nucleated cells, there are three stages: the interphase, the mitotic phase (when the parent actually splits itself into the two child cells with identical genetic material, called mitosis) and cytokinetic phase (when control processes validate the overall success of the division process). During the interphase (the longest stage, lasting 90% of the full cycle), the cell grows as it accumulates needed material for the next stage. The heart of this phase is synthesis when the nuclear DNA (see §3.2.2) is replicated with duplication of the chromosomes; this process is preceded by the growth G1 checkpoint, which ensures that synthesis can begin. Synthesis is also ended by the genetic G2 checkpoint, which checks that synthesis went well (and stopped) so the interphase phase can start. This same ‘doubling’ process for renewing/repairing internal organs (somatic cells) and creating short-lived cells (e.g. blood cells) is also used (as this results in exponential growth) in creating a mature (adult) organism from a single fertilized egg, as described above in the Entity Reproductive System. Actually, in higher animals there is a secondary process, called meiosis (see §3.3.2.1), where the number of chromosomes in the children cells is reduced 29

by half to produce sex cells (or gametes). Since mitosis is a universal process, occurring across the whole organism, it sometimes fails and can result in cancer, this process will be explored later in a lot more detail. Once a new cell has been formed, it can contribute to the local tissue community a small amount of the growth/stop signals until the local target quantities have been achieved. Local cell division will continue as necessary.

3.3.4.2.1 Telomeres In most animals, somatic cell division eventually stops; in humans, this occurs (on average) after 52 divisions when the cell enters its final senescent phase. This cell division ‘halting’ occurs because key base pair endings on each chromosome (called telomeres), needed for division, shorten by one unit with each copy. Telomeres are special six codon sequences, which in humans are marked by the sequence: TTAGGG. Cancer cells defeat this limitation by deliberately creating an enzyme called telomerase, which rebuilds the telomeres allowing cellular division to continue indefinitely. 90% of all cancers have active telomerase, an enzyme, also found in embryonic stem cells.

3.3.4.3 Cell Cycle All cells follow the same sequence of events during the process of cell division, which after it completes, is ready to begin again, i.e. it is a cyclic process. In the eukaryotic cells of animals, there are two major phases: the interphase and the mitotic phase. During the interphase, taking the majority of the time (90%), the target cell grows as it accumulates the materials needed for the next mitotic phase, when the cell splits itself into two distinct child cells. To ensure that this process has proceeded correctly, there are two major checkpoints: before and after mitosis.

3.3.4.4 Mitosis Mitosis is the critical part of the cell cycle in which the chromosomes in the cell nucleus are separated into two identical sets so that each set results in its own nucleus; this is vital to normal cell division. In animals, the nuclear envelope (surrounding the nucleus itself and separating the DNA from the cytoplasm) disintegrates along with the nucleolus. Microtubules appear at opposite ends of the cell and align the chromosomes before pulling one copy of each to opposite ends of the parent cell, as it elongates. A new nuclear membrane then forms around the separated child chromosomes. The mitotic stage is a relatively short period of the cell cycle, alternating with the much longer interphase, when the cell prepares itself for cell division by producing many proteins and cytoplasmic organelles.

3.3.4.5 Cytokinesis Once the mitotic stage is complete, the cytokinetic stage can begin. This is the process whereby all the remaining parts of the parent cell, such as the cytoplasm, organelles and even the cell membrane, are divided equally between the two child cells. Finally, the cell membrane pinches inward between the two developing nuclei to produce two new distinct cells. Mitosis and cytokinesis together define the mitotic phase of the cell cycle in an animal – the division of the single parent cell into two children cells, both genetically identical to each other and the parent cell. During the mitosis step, the already duplicated chromosomes condense and attach to spindle fibers that pull one copy of each chromosome to opposite sides of the cell. Sometimes, three child copies occur as well as other types of replication error. Various types of cancers can arise from these failures if the ‘failed’ cell is not self-destructed.

3.3.4.6 Regeneration Unlike a few other creatures (e.g. hydra, salamanders), humans are quite limited in their capacity for reparative regeneration, in response to injury. One of the rare exceptions is liver regeneracy, which can be exploited in cancer surgery. After the removal of part of the liver, the original mass of the liver is re-established in direct proportion to the amount of liver removed, indicating that signals from the body precisely regulate liver mass. This process is controlled by growth factor and cytokine regulated pathways. Some renewal has also been found in the brain (in the hippocampal neurons) and in the heart muscle (myocyte renewal) but only about 1% - usually not enough. In contrast, none of the 7000 earing (hair) cells ever are replaced when they die.

30

3.3.4.7 Growth Factors A growth factor is one of a family of specialized proteins or steroid hormones, which are capable of stimulating cellular growth, cell proliferation, cellular differentiation and maturation; they are obviously very important for regulating a variety of critical cellular processes. Growth factors usually act as signaling molecules between cells; common examples are cytokines and hormones that bind to specific receptors on the surface of their target cells. The term ‘growth factor’ has sometimes been used interchangeably with the older term ‘cytokine’ (see §2.4.3.3.4), which was used to describe certain processes in blood and lymph cell (see §2.4.3.2.2) production. Recently, it was realized that some of these earlier cytokines (acting in picomolar – trillionth – concentrations) were also being used by many sorts of other cells and tissues, during development and in the mature organism. Unfortunately, the term ‘growth factor’ implies a positive effect (growth) on cell division; while some cytokines do act as growing factors (increasing cell type populations); there are others that can have an inhibitory (or negative) effect on cell growth or proliferation. Indeed, some cytokines can act as ‘self-destruct’ signals to cause programmed cell death. These signaling proteins can participate in complex, multiple-event sequences triggering other proteins (cascades or pathways). Many of these small molecule proteins (cytokines) have a matching cell-surface receptor that must function properly for the programmed action sequence to complete successfully. Errors, particularly in their protein forms can often lead to cancer. This is a very active area of so-called “targeted cancer therapies”.

3.3.4.8 Controls: Kinases and Phosphorylation A central topic of systems theory is self-regulating systems, i.e. systems self-correcting controls through feedback. Self-regulating systems are widely found in nature. The primary control mechanisms are found in the normal cell cycle, especially in the G1 and G2 checkpoint stages. There are two classes of related, regulatory molecules (generated from the cell’s DNA): cyclins and cyclin-dependent kinases (CDKs). The four cyclin proteins combine with their related kinases to form key maturation-promoting factors. Protein kinases are enzymes that catalyze the transfer of phosphate groups (PO3-OH) from high-energy, phosphate donating molecules to specific substrates (always called phosphorylation). This is one of the most critical, universal mechanisms by which proteins are activated or silenced in cells, as the phosphate groups newly attached to some of the amino groups (defining the protein) can utterly alter the stable shape of the enzyme that determines its biochemical properties. Thus, the phosphorylation state of a molecule can affect its activity, reactivity and its ability to bind to other molecules. This makes kinases critical in many cellular processes, such as metabolism, signaling, regulation and many other pathways. Many of their source genes in the DNA are labeled as ‘cdcN’, for ‘cell division cycle #N’ (e.g. cdc25). MTOR is a critical kinase that senses cellular, nutrient, oxygen and energy levels to determine if the synthesis phase in the cell cycle can begin. This extremely important action may be triggered by several molecules, which are then referred to as mitogens. Mutation errors in some genes produce mitogens that often trigger cancer in humans. Methylation is a similar process involving methyl (CH3) groups. Note: many enzymes are given names that end with the letters ‘-ase’, such as ‘protease’ – an enzyme that breaks up proteins and useful in digestion.

3.3.5 Cellular Suicide (Apoptosis) Cell division is a physiological process that occurs in almost all tissues and under many circumstances. Normally, like most living systems a cell eventually reaches the end of its useful life and must then die. Nature has anticipated this need and established a normal biochemical process, called apoptosis, to accomplish this ‘programmed cell death’ at the end of each cell’s natural life cycle. Once started, destructive apoptosis cannot stop, so it is a highly regulated process. The start may be triggered internally because of self-regulatory detectors or it may respond to commands from other cells. In either case, the process requires the activation of special proteases, enzymes (called caspases; understandably, an abbreviation for cysteinyl aspartate serine proteases) that degrade other proteins. This is a two-step technique, where initiator-caspases are first activated, which then generate executioner-caspases that kill the cell by degrading proteins indiscriminately. The resulting cell fragments are then neatly digested by 31

phagocytic cells that recycle all the dead cell’s material. Unlike necrosis, in this cleanup process there is no spillage of cell contents, which usually provokes the body’s inflammatory reaction. Approximately 60 billion cells die each day due to apoptosis in the average human adult. For a healthy child between the ages of 8 and 14, approximately 25 billion cells die every day. Failure of the cell’s apoptosis mechanism is a major factor in the development of cancer, especially through disruption of the p53 cellular checking mechanism (see later).

3.4 Process Controls There are many processes, which occur in a living cell, but some of the most complicated (and important from a species – temporal perspective) are those involved in cell division. Mutations in DNA repair genes can be inherited or acquired. Although suitable DNA is needed to make the appropriate proteins, this requires fine-tuning across space (enzymes) and when a necessary step is activated (time). The critical steps are those associated with starting and stopping the cell cycle. It is changes at these stages, destroying the planned control actions, which allow cancer to start/continue its horrible journey. If genetic errors occur here, the cell will try to fix these problems (so it can survive) through using DNA repair proteins (produced from their associated genes) after the DNA is copied. Any failure to repair these dangerous errors must be followed by programmed cell death (apoptosis) or cancer results.

3.4.1 Bypass Checkpoints The regular cell-division process lies at the very center of living systems, so it is important that it operates properly. This is especially true for the post-mitosis checkpoint (G2). However, this process, like all cellular actions, is built around the correct actions of proteins occurring but unfortunately they too may be damaged over time; when this damage occurs on the genome then it will be passed on lethally to all of its subsequent descendants.

3.4.2 Repair/Suicide The first response that a cell makes when it detects a problem with cell division is to try to repair the damaged DNA in its genome: if successful then the cell can survive. However, if repair attempts fail, then for “the greater good” (since each cell is part of a larger multi-cellular collective), it must commit suicide by apoptosis (§3.3.5).

3.5 Summary This chapter examines the biological bases of hereditary to gain an understanding of the normal processes of cell division that keep multi-cellular creatures alive for so many years. The eventual focus here is on the foundational process of cell division because it is errors at this deep level that lead to cancer. The chapter begins with a very brief introduction to hereditary, which was the scientific area that eventually led to the modern science of genetics. Ironically, our study of the human genome (after spending billions) has not led us to link genes back to the observable traits that initiated the interest in genetics. It is also unfortunate that our modern knowledge of cellular genetics has shown us just how vastly complicated this area of life really is, so that we will see that there are still massive areas of ignorance remaining about cancer. It was the discovery of the double helical structure of DNA in 1953 that marked the transition to the era of molecular genetics. It was soon realized that finite lengths of DNA, containing thousands of amino-acid bases, could play the role of Mendel’s genes. We soon discovered that matching lengths of DNA with proteins was a very simplistic (static) view of how proteins were produced in the cell. This ‘expression’ of a gene was a complex, multiple gene process spread across time that needed contributions from other structural components in the cell – particularly in and near its nucleus. Scientists were shocked by the early results of the Human Genome Project which not only showed that less than 2% was used for coding proteins but that the remaining huge fraction was involved with regulating protein expression: a process now recognized to be impacted by the organism’s environment – a new specialty, known as epigenetics.

32

The heart of chapter 3 is the section entitled: Making Cells – the essence of staying alive and where mistakes occur that can result in cancer. There are actually two occasions when an animal makes cells; the obvious one is when a new example is generated, this is the one-time stage when an embryo develops. The second stage occurs throughout the life of the organism, as the tissues need to repair and replace themselves; mix-ups of processes between these two stages (mistiming) create cancer. Old age and death are reviewed here as natural parts of all living lifecycles. There is increasing interest today in stem cells. We introduce them here as part of normal embryonic development, where they first appear before they start their journey evolving into a specific tissue component, in a process known as differentiation. Adult mammals also invoke stem cells as part of their long-term survival strategy; however, they also seem to play a critical (but mysterious) role in carcinogenesis. We will return to this important topic later. The growth of new cells is vital to the normal evolution of an organism during both the embryonic stage of life and also to maintain organs and tissues in a mature entity. During this latter phase, growth is normally regulated (started and stopped) by reacting to messages from surrounding cells of the same type. When this communication fails, particularly when DNA mutations lead the cell to react as if it had received a start message (oncogenes) or the genes that ensure success or halting (tumor suppressor genes) are damaged, the uncontrolled growth will result. The majority of the effort in this chapter is still focused on normal cell replication. This universal and continuous process must be understood to appreciate how mistakes here (especially in the cell-duplicating phase or mitosis) can lead to cancer. Discussion of this key process is used to introduce a new form of proteins, called growth factors that act as critical messengers throughout all this. This is another ‘hot’ area of cancer research. This is also a suitable time to discuss a new word that is appearing more frequently in advanced chemotherapy: this is the special class of proteins called kinases, that act as major switching molecules in the cell division processes. One of the most important steps in cell division occurs after mitosis, once a cell fails its examination as a successful splitting; this dangerous possibility has been anticipated and the failed cell instructs itself to commit programmed cell death: a process given the fancy (Greek) name ‘apoptosis’. Failure of apoptosis usually leads to deadly cancers. It can be seen that there are many complex processes at work in a normal cell, so it is important that there are many mechanisms to ensure that they all proceed correctly; this why the idea of process control is so critical in cancer research. The hidden dimension, associated with the notion of a process, is time. Each protein is created for a given task and they must be eliminated once the task is complete. In a typical cell, almost half the newly synthesized proteins will be destroyed in less than one hour. In particular, some proteins are deeply involved in time-critical processes, such as cell division, so they only survive for a few minutes at most. It can be readily seen that this whole dynamic set of interactions must occur in a finely regulated manner across space and time. Mutated proteins that outlast their designated survival span can cause devastation in the cell’s lifecycle: errors that accumulate over several generations when produced in mutated DNA – a catastrophe called cancer that can destroy the organism. Since a cell is itself a living system, it sometimes ‘forgets’ that it is a ‘team-player’ or just another member of some tissue group and starts acting like a single-celled organism in its own right: trying its hardest to stay alive itself and only care about passing on its own characteristics to its cellular progeny. Unfortunately, it is unaware that it is itself seriously damaged (as it passed – mistakenly – all its cell checkups), so it transfers these genetic mistakes along with its ability not to commit suicide. This is why one of the top cancer researchers labeled his early books [3] on cancer: One Renegade Cell, when it appeared in 1989. In this regard, cancer is a suitable metaphor for breakdowns of society by certain sociopaths and their selfish families; their ongoing existence indicates we have failed also to solve our ‘social cancers’ after thousands of years, as they pursue only their ends of ‘surviving and thriving’ with no regard for the vast number of other people in their societies.

33

4.0 CANCER 4.1 History 4.1.1 Overview 4.1.1.1 Ancient Evidence Egyptologists have found descriptions of cancer in a few papyrus documents that are almost 4,000 years old, such as those from one of the oldest known physicians, Imhotep, who after an accurate diagnosis of breast cancer even then admitted: “there is no known therapy”. Cancer rightly paled in comparison to ancient plagues, like typhus and smallpox, which raged through whole populations. With its non-infective impact limited to individuals, cancer did not surface again in written texts until the Greek historian Herodotus described the suffering of a Persian queen about 400 BC. There is other archeological evidence from Africa to suggest that cancer is as old as humanity.

4.1.1.2 Origin of the Name It was Hippocrates (c. 450 BC), the “father of Greek medicine”, who first distinguished benign from malignant tumors. He said the deadly malignancy spreads to other parts of the body from the initial site that often included new blood vessels, which resembled the claws of a crab (karkinos in Greek or cancer in Latin). Progress began about 1760, when the English physician, Dr. John Hill noticed a correlation between sniffing tobacco (snuff) and nasal cancer. Soon after, another English doctor suggested a similar link between cases of scrotum cancer in young chimney sweeps and the coal dirt in the chimneys they climbed up to clean. Our understanding of the link between cancer and cells arose only slowly after the German pathologist Rudolf Virchow proposed his cell theory (§3.6). It required the explosion of molecular biology (§2.5.3.1) before the cellular basis of cancer became widely accepted.

4.1.1.3 The Modern Plague Evidence of bone and abdominal tumors has been uncovered in Egyptian mummies although experts believe that cancer remained extremely rare in ancient times, as so few civilizations had a word for it; perhaps because other causes of death were so common or that few lived long enough to exhibit this age-sensitive disease. This illustrates why cancer is sometimes referred to as ‘the modern plague’ because we have made major inroads in reducing other major causes of (early) death, like malnutrition, tuberculosis and pneumonia, and we are now much better at cancer diagnosis. However, the commercial pressures for many people to take up smoking and the widespread addition of thousands of chemicals into manufactured foods may both be introducing new sources of cancer in the 20th Century. The failure to find effective treatments for malignant cancers meant that cancer had achieved its infamous position as the second major cause of death in North America after heart disease by 1926. This sad fact still faces many today.

4.1.1.4 Genetic Mutations Cancer is fundamentally a disease of tissue growth regulation failure. In order for a normal cell to become a cancer cell, its genes that regulate cell growth and differentiation must be altered. Gene changes that start in a single cell, at anytime over the course of a person's life, cause most cancers. All our cancers are now believed to be due to permanent alterations in genes (perhaps a few thousand in total). When genes themselves are damaged and not repaired, they can develop changes called mutations, which involve permanent changes in the nucleotide sequence of the cell’s genomic DNA (see §2.6.2.2.1.2). Cancer almost certainly involves multiple gene mutations.

34

Many mutations are quite harmless but when mutations occur in the growth and damage-controlling genes themselves, cells can grow out of self-control and cause cancer. For most unfortunates who develop cancer, the cancercausing gene mutations often accumulate over the course of a whole lifetime, resulting in cancer often appearing later in life. Mutations that kill children are fortunately rare as they usually kill the victim before they themselves pass on the corrupted genes for another generation. Despite all that is known about the different ways cancer genes work, many cancers still cannot be linked to a specific gene. Mutations happen often, and the human body is normally able to ignore or correct most of them. Depending on where in the gene the change occurs, a mutation may be beneficial, harmful, or make no difference at all. One mutation alone is unlikely to lead to cancer. Usually, it takes multiple mutations over a lifetime to cause cancer. This is why cancer occurs more often in older people, who have had more opportunities for mutations to build up. A further mutation in signaling machinery of the cell might send error-causing signals to nearby cells. Small-scale mutations include point mutations, deletions, and insertions, which may occur in a gene's coding (base) sequence and alter the function or stability of its protein product or it may occur in the promoter region of a gene and affect its expression. Disruption of a single gene may sometimes result from integration of foreign bases from a DNA or retrovirus, leading to the expression of viral oncogenes in the affected cell and its descendants.

4.1.1.4.1 Genome Instability Genome instability (also “genetic instability”) refers to a high frequency of mutations within the genome of a cellular lineage, sometimes reflecting a high rate of externally caused DNA damage, especially with DNA repair genes, or worse: the disappearance of such genes. In persons without cancer, there is a very low rate of protein coding mutations (about 70 per generation).

4.1.1.5 Cancer Epigenetics A variety of epigenetic mechanisms (§3.2.6) can be perturbed in different types of cancer. Epigenetic alterations of DNA repair genes or cell cycle control genes are very frequent in sporadic (non-germ line) cancers, being significantly more common than germ line (familial) mutations in these sporadic cancers. Tumor suppressor genes are often disabled by cancer-promoting genetic changes. Epigenetic alterations are sometimes more important than genetic mutations in a cell’s transformation to cancer, particularly since the epigenetic DNA methylation process differs between normal and tumor cells in humans. Genes commonly found to be transcriptionally silenced due to promoter hyper-methylation include: the cyclin-dependent kinase inhibitor p16 (a cell-cycle inhibitor - §3.3.4.8); the family of DNA-repairs (MGMT-glioblastomas, MLH1-colon and BRCA1-breast cancer genes). Cancer incidence in only one of a pair of identical twins (with identical genomes) indicates the powerful role of epigenetics in the occurrence of cancer as one’s epigenetic impact reflects the unique biological history of each individual.

4.1.1.6 Germ Line Mutations Germ line mutations, which are less common, are passed directly from a parent to a child. In these situations, the mutation can be found in every cell of a person’s body, including the reproductive sperm cells in a boy’s body and egg cells in a girl’s body. Because the mutation affects reproductive cells, it passes from generation to generation. Cancer caused by germ line mutations is called inherited cancer, and it makes up about 5% to 10% of all cancers. It is ironic that a science based on ideas of familial transmission (genetics) plays such a small role in the ultimate disease of genetics.

35

4.1.2 Types of Cancer Cancers are characterized by the organ in which it first appears in a person. The incidence of cancer varies with a person’s gender; the most common cancers in males occur in the lungs, the prostate, the colon and stomach. As expected, in females, the commonest cancers originate in the breast (25%), colon, lung and cervix. By 2012, over 14 million new cases of cancer occurred globally; cancer (including melanomas) caused about 40% of all human deaths. Lung cancer is the commonest type of cancer: killing 1.6 million people worldwide, with a 90% eventual death rate, although 17% of US victims are still alive 5 years after diagnosis, while 85% of cases are believed to be due to cigarette smoking. The risk of cancer increases significantly with age and many cancers occur more commonly in developed countries, except for lung cancer, as smoking is less restricted in poorer countries. In 2012, about 165,000 children under 15 years of age were diagnosed with cancer. Unfortunately, brain tumors are one of the commonest childhood cancers, along with certain forms of white-blood cell cancers (leukemia).

4.1.2.1 Carcinomas Since the location of the first cell that goes cancerous (leading to a possible solid tumor cluster) determines the nature of the cancer (whether it subsequently spreads or not) then cancers can be categorized by the nature of the first tissue in which they occur. Cancers are named by adding ‘oma’ to the Latin word for their location; so ‘hepatoma’ is cancer of the liver (hepato). Outer-surface organs, consisting of epithelial cells (§2.5.1) that start the cancer-chain, will result in carcinomas, which are found in about 85% of cases as these are the most rapidly dividing cells because these cells need to be replaced quickly in order to withstand the ‘many blows from the outside’. There are more chances of errors happening when cells divide more frequently.

4.1.2.2 Sarcomas Organs in connective tissue (endothelial - §2.5.1) that become cancerous will generate sarcomas but usually since these are slowly dividing cells, they only contribute about 1% of cancer cases in humans. The commonest locations for these cancers are bone, cartilage, fat and muscle tissues as well as the linings of blood and lymphatic tissues.

4.1.2.3 Adenocarcinomas Glandular tissue that becomes cancerous will create adenocarcinomas. As glands are continuously active (as in the pancreas, lung and prostate), they usually contribute 15% of human cancers – many often fatal. Several, deadly breast cancers could also be called ‘invasive ductal carcinomas’. The remaining cancers do not form solid tumors.

4.1.2.4 Lymphomas These are all the cancers that develop from lymphatic cells; very active in all animals (see §2.4.3.2.2). Since this area is a major part of the immune system, cancers here can generate many other disease problems. These types of cancer now represent about 5% of all American cancers (or 55% of blood cancers).

4.1.2.5 Leukemia Leukemia is a group of cancers that originate in the bone marrow and manifest as too many immature white blood cells and too few red blood cells. There are five main sub-types: acute lymphoblastic leukemia (ALL), acute myeloid leukemia (AML), chronic lymphocytic leukemia (CLL), chronic myeloid leukemia (CML) and acute promyelocytic leukemia (APL). ALL was so deadly that some children were dead within three days of initial diagnosis. Leukemia is the commonest form of cancer in children but 90% of leukemia (usually AML and CLL) is found in adults; leukemia accounts for about 3% of American cancers (or 30% of blood cancers).

36

4.1.2.6 Inherited Cancers Inherited genetic mutations only play a minor role in most cancers (about 5 to 10 percent of all cancers). Extensive research has associated mutations in specific genes with only about 50 inherited forms of cancer, which sometimes may predispose individuals to developing certain cancers. However, cancers that are not caused by inherited genetic mutations can sometimes appear to “run in families.” For example, a shared environment or lifestyle, such as tobacco use, can cause similar cancers to develop among family members. Importantly, certain patterns in a family—such as the types of cancer that develop, other non-cancer conditions that are seen, and the ages at which cancer develops—may suggest the presence of a hereditary cancer syndrome. Some rare types of cancer actually do run in certain families, but overwhelmingly, most cancers are not clearly linked to the genes we inherit from our parents. Genetic testing can be useful for people with certain types of cancer that seem to run in their families. Even if a cancer-predisposing mutation is present in a family, not everyone who inherits the mutation will necessarily develop cancer. Cancer remains very much a personal “Death Lottery”.

4.1.2.6.1 Genetic Testing The term cancer syndrome is used whenever it is discovered that there exists a genetic disposition in a family towards developing cancer. Common examples of inherited cancer syndromes are hereditary breast-ovarian cancer and hereditary colon cancer (Lynch syndrome). Genetic tests can tell whether a person from a family that shows signs of such a syndrome has one of these mutations. These tests can also show whether family members without obvious disease have inherited the same mutation as a family member who carries a cancer-associated mutation. Many experts recommend that genetic testing for cancer risk be considered when someone has a personal or family history that suggests an inherited cancer risk condition.

4.1.2.7 How Cancer Kills Solid tumors kill their host in a different manner than leukemia, which usually reduces the volume of red blood cells, depriving all cells everywhere of sufficient oxygen. Solid tumors kill either by damaging vital organs or by cachexia.

4.1.2.7.1 Damaging Organs Most organs are surrounded by a fairly inflexible membrane, which defines how many cells may contribute to that organ. When a tumor grows in an organ, it competes with the good cells for inputs such as nutrients, blood, etc. If it grows too large, it may physically block resource flows (e.g. blood flows in the brain, blocking the GI tract) and today will often be removed surgically. Since all organs are inter-connected then damage to another organ can have a secondary impact on other organs, such as damage to the lungs (oxygenated blood) or liver (vital bio-chemicals) or lymph nodes (immune cells).

4.1.2.7.2 Cachexia Typically, a cancer patient may suffer from “wasting” — this may be due to toxins that get released into the body: either from the tumor cells or in response to the tumor cells. This loss of body mass cannot usually be reversed by increasing nutrition. This pathology is very common (80%) with terminal cancer, especially with pancreatic and GI tumors but can occur from other pathological conditions, like congestive heart failure. Cachexia is found to be the immediate cause of death of between 20 and 40% of all cancer fatalities. It is initially suspected if there is a greater than 5% weight loss within six months of any diagnosis. The exact mechanism of this failure is still poorly known but problems with inflammatory cytokines (like TNF-alpha, IGF-1 and IL-6), originating in the tumors, are suspected. Cannabinoids and omega-3 fatty acids have been found to be somewhat helpful.

37

4.1.2.8 Death Rates # 1 2 3 4 5 6 7 8 9 10 11

System Reproductive Digestive Glandular Respiratory Circulation Disposal Misc. Integum. Oral Commun. Structural

Organ Genital GI tract Breast Lungs Blood Urinary Various Skin Throat Nerves Connect.

Cancer Cervical Colorectal Breast Lung Leukemia Bladder Misc. Melanoma Larynx Brain Muscle

Incidence {1} 320 260 220 180 120 100 60 60 40 12 8 1380

Mortality {2) 60 140 50 160 60 80 50 5 5 8 5 623

Lethality{3} Survival {4} 19 5.3 54 1.9 23 4.4 90 1.2 50 2.0 80 1.25 83 1.2 8.3 12 13 8 75 1.5 63 1.6 45 2.2

Key: {1} new cases/thousand {2} ann. Deaths/100,000 {3} mortality/incidence (%) {4} incidence/mortality (yrs) US data drawn from American Cancer Society for 2004 Since few cancers are currently cured, the most popular medical measure of treatment success is called the “Five Year Survival Rate”, which calculates the percentage of patients (of those diagnosed with a particular cancer) are still alive after five years, including all those undergoing therapy. This is usually called the ‘absolute’ rate when only cancer patients are considered but the ‘relative’ rate can be used when the total number (divisor used in the calculation) is the percentage of the general population of corresponding sex and age are also alive after five years. Five-year survival rates can be used to compare the effectiveness of various treatments. Use of 5-year survival statistics is often more useful in aggressive diseases that have a shorter life expectancy following diagnosis (such as lung cancer) and less useful in cases with a long life expectancy, such as prostate cancer. The chance of survival depends on the type of cancer and the extent of disease at the start of treatment. In children under 15 at diagnosis, the five-year survival rate in the developed world is on average 80%. For cancer in the United States, the average five-year survival rate is 66%. Unfortunately, earlier diagnosis (‘lead time bias’) can “improve” these statistics.

4.1.2.9 Dying Well Since most terminal cancer victims will die of their disease it is important to know that today this “final act” can be managed humanely, particularly with modern pain management medications and the growing number of hospice facilities that provide excellent ‘final care’. It is also good to know that most people will be unconscious when they die. Death can even be dignified if family members are present to provide reassurance and help calm anxieties as the final moments arise. The end-stage symptoms appear universal for most people, with the following symptoms occurring: reduced activity, dry mouth but little appetite, falling blood pressure and body temperature, cold hands and feet, abnormal breathing (rapid breaths with extended gaps) and loss of consciousness (coma).

38

4.1.3 Cancer Science Milestones This section will establish the major breakthroughs that have defined the evolution of the scientific understanding of cancer over the last 100 years. Each entry will identify the principal contributors, along with a brief description of their major discoveries and will use the notation {N:19yy} to indicate the year they were awarded the Nobel Prize in Physiology or Medicine (if this has already happened). These milestones usually illustrate how often major breakthroughs take so long to be recognized in science, while remaining unknown to oncologists for several years.

4.1.3.1 Cancer causing Viruses Francis Peyton Rous {N:1966}, a young researcher at the Rockefeller Institute in New York, discovered in 1910 that a few viruses (e.g. RSV) could induce tumors in live chickens. This led to the genetic focus in cancer research.

4.1.3.2 DNA James Watson and Francis Crick {N:1962}, postdoctoral researchers in 1953 at Cambridge University, proposed a model for the molecular structure of deoxyribonucleic acid (DNA), which focused genetic research on the cell.

4.1.3.3 Retro-Viral Disease Howard Temin {N:1975}, a postdoctoral researcher in 1958 at Caltech showed that RSV could be cultivated in the laboratory (in vitro), later he proved that a copy of this virus’s genes could structurally attach itself to a target (normal) cell’s genes. This theory reversed the widespread view that DNA only made RNA (transcription).

4.1.3.4 Oncogenes J. Michael Bishop and Harold Varmus {N:1989} were both recent converts to virology research, coming from Arts backgrounds before setting up a laboratory at the University of California in San Francisco. In 1976, together they discovered that a modified gene (called src – for sarcoma – pronounced ‘sark’) was found in the cancerous cells of many animals as well as RSV. Subsequent research uncovered that this gene was a regular kinase (§3.3.4.8) that fired up many other messenger molecules in the cell-division process (§3.3.4.2). The mutated form was a key mitogen (§3.3.4.8) triggering cell division. So, RSV could be seen as altering normal genes (‘proto-oncogenes’) that already played a useful role in cells.

4.1.3.5 Anti-Oncogenes Robert Weinberg, at the Whitehead Cancer Institute (at MIT), not only discovered another major oncogene (ras – see §4.3.2), but worked with other cancer researchers near Boston that in 1986 uncovered the first anti-oncogene (rb), or tumor-suppressor genes (see §4.3.5). It is the presence of the normal Rb protein that usually shuts off the cell-division process but when mutated allows its ‘locked-up’ mitogenic proteins to continue the cell-division process unchecked. Ras has proved to be one of the most common and deadly causes of cancer.

4.1.3.6 Chimeras Janet Rowley was a geneticist in Chicago, who uncovered in 1972 the genetic basis of leukemia, when she found that two misplaced pieces of human genes on chromosomes #22 and #9 had incorrectly combined to form a chimera-gene subsequently called bcr-abl from the two fragments of separate genes, in a rare genetic event called translocation. That contributed to CML; Rowley also uncovered another leukemia chimera from chromosomes #21 and #8 that contributed to ALL; she also showed that linking chromosomes #15 and #17 caused APL.

39

4.2 Tumors The correct medical term for any abnormal growth of tissue is neoplasia; such a growth sometimes reaches a size visible to the unaided eye. When these neoplasms are malignant, they are simply called cancers or tumors. The term ‘mass’ is used when the tumor exceeds 2 cm (0.8") in size, while the word ‘nodule’ is used when smaller.

4.2.1 Malignancy The most important fact for people when first informed that they have a tumor is whether it is benign or malignant. As we shall see: it is the degree that the cancer may spread around the body (medically called metastasis) that is critical. For anyone diagnosed with cancer, the most important medical decision is to define what stage the cancer has reached; this will usually determine the prognosis and type of treatment. Not all tumors are cancerous; when tumors do not spread to other parts of the body, they are called benign or “non-cancerous”. Most benign tumors are surrounded by an outer fibrous sheath; common examples are moles and uterine fibroids but these must still be checked regularly to ensure that they have not transformed into cancerous forms through a process known as ‘tumor progression’. Biopsies are vital to determine if a tumor is malignant and needs early intervention. None-the-less, some initially benign tumors may still grow sufficiently large to cause dangerous local conditions, such as tissue compression leading to organ damage or even cellular death (necrosis). For all these reasons, many benign tumors are surgically removed. In some cases, over-growths of normal tissue, such as skin tags or polyps of the colon or vocal chords may be mistakenly called benign tumors; these may be determined as safe by local biopsies and microscopic cell examination. As we shall see, it is the presence of metastasis that usually makes a cancer malignant and therefore, potentially fatal.

4.2.2 Stages Cancer staging is the process of determining the extent to which a cancer has developed by spreading from the original site. Contemporary practice is to assign a number from I to IV to a cancer, with I being an isolated cancer (“simple”) and IV (“advanced”) being a cancer which has spread to the limit of what the assessment measures. The stage generally takes into account the size of a tumor, whether it has invaded adjacent organs (see §2.4), how many regional (nearby) lymph nodes (§2.4.3.2.2) it has spread to (if any), and whether it has appeared in distant locations (metastasized). The pathological determinations are made by distributed biopsies, whereas clinical determinations are made while the tumor is still in the body. However, pathological estimates may be lower if some treatments have occurred with partial success. Staging systems often vary with the specific type of cancer. Another coding technique uses letters and numbers, where the three letters represent T (tumor), N (node) and M (metastasis) with each letter followed by an Arabic number, perhaps preceded by c (clinical) or p (pathological); e.g. pT2N2M1.

4.2.3 Grading Tumors As we have seen in examining embryology (§3.3.3), cells can begin their life in a non-specialized form but at some time must transform into a specific type of cell – a process known as differentiation. This process usually occurs in most cancers but in reverse (called anaplasia). The cells in a cancer tumor most closely resemble those in their parent tissue at the start of their lives but over the generations may become less specific (or undifferentiated). This is a poor indication, as these undifferentiated cells are more likely to ‘take root’ after they have spread to other parts of the body. The technical term for this degree of abnormality is the ‘grade’ of the tumor, indicated as Gn, where n is a number from 1 (low) to 4 (high). The Gleason system for grading prostate tumors ranges from 2 to 10. A highscoring grade (very poorly differentiated or undifferentiated) is sometimes called anaplastic.

40

4.2.4 Aggressive Cancers Normal, healthy cells in regular tissue divide at fairly well defined rates, which vary by tissue type. Unfortunately, cancerous cells, especially in malignant tumors, can divide much faster than normal, implying that their tumors will grow at dangerous speeds. Some notoriously aggressive cancers include: basal-cell carcinomas (skin), non-smallcell lung carcinomas, pancreatic adenocarcinomas, squamous-cell carcinoma (neck), acinic-cell carcinoma (breast), B-cell lymphomas (blood) - the prognosis for people found with these types of cancer is very poor, with few (5%) surviving five years. The cells in a benign tumor have a slower growth rate than those in malignant tumors.

4.2.5 Metastasis Metastasis is the spread of a cancer to other, remote locations in the body. The new tumors are called secondary or metastatic tumors (or metastases), while the original is called the primary tumor. Almost all types of cancer can metastasize. In fact, this is the most deadly feature of cancer, as most (90%) cancer deaths are due to a tumor that has spread from its primary site to other organs. However, there are a few exceptional cancers, like basal cell carcinoma, which are malignant but still mostly non-metastatic. Mysteriously, about 5% of metastatic cancer cases have no identifiable primary tumor when first diagnosed, perhaps because the primary tumor has been successfully regressed. Fortunately, the most common cancer of the skin rarely metastasizes except for the deadly melanoma. Metastasis is common in the late stages of cancer, and it can occur via the blood or the lymphatic system or both. Most sarcomas appear to spread via the lymphatic system, while carcinomas usually spread via the blood. The typical steps in metastasis are: local invasion, breakthrough into the blood or lymph systems (intravasion), extended circulation through the body, exiting capillaries into the new tissue (extravasion), proliferation and tumor-genesis. Different types of cancers tend to metastasize to particular organs, with the nearby lymph nodes being frequent targets but overall the most common places for solid metastases to occur are the lungs, liver, brain and bones. It only takes a few cells to break away from the primary tumor to initiate metastasis; when this capacity repeats at secondary sites then there is no cure. Once a patient has been treated for a primary tumor and a remote secondary is later discovered it is usually a metastasis. Fortunately, humans have evolved about a dozen special proteins, called metastasis suppressors, which resist metastasis. This offers a very promising possible cure for cancer. Luckily, most initial secondary tumors are very tiny (less than a pinhead), called micro-metastases; they are not life threatening until they grow larger to a stage known as macro-metastasis (a step called “Colonization”) that requires the necessary process of angiogenesis.

4.2.6 Angiogenesis As discussed above, every cell in an organism must be in communication with the blood of the circulatory system. This process of linkage occurs in two stages: the first vessels in the developing embryo form through the normal cell differentiation-process called vasculogenesis, when early endothelial precursor cells transform into blood vessels. Later, the process of angiogenesis takes over and extends the pre-existing blood network to the full adult extent; it is also needed for wound healing. Although angiogenesis is a normal and natural process, it also occurs abnormally when cancerous cells metastasize to remote parts of the body. Once the required blood vessels have grown sufficiently, normal cells produce the enzyme ‘protein kinase G’ (PKG), which suppresses any additional angiogenesis. The growing, secondary tumor needs extra nourishment (especially oxygen) to thrive above and beyond that already established for the normal cells already present in this new tumor site. Without angiogenesis, a microtumor cannot grow beyond a very limited size (about 0.2 mm). Malignant tumors carry mutations that can secrete several growth factors (§3.3.4.7), such as ‘vascular endothelial growth factor’ (VEGF), that can induce capillary growth into the tumor. Worse, cancerous cells stop producing PKG, which acts by blocking the VEGF protein. Presently, there is much cancer research in the area of angiogenesis, where attempts are being made to

41

slow or even stop the process through use of localized angiogenesis inhibitors, using natural and synthetic proteins, like endostatin and canstatin. The origin of the theory of angiogenesis illustrates some of the professional jealousies confounding cancer research. A US navy surgeon invented the theory of angiogenesis in 1971, risking his career for daring to propose such a biological theory of cancer; until in 1994 his hypothetical chemical, angiostatin was discovered, which blocked the growth of new blood vessels. Since then, several synthetic drugs similar to angiostatin have been developed by the pharmaceutical companies – the most famous being Avastin. Once again, cancer had been caught red-handed, as it hijacks another of the body’s basic processes for its own purposes.

4.2.7 Clonality Unfortunately, a visible tumor may contain many cancer-gene families that have taken different evolutionary paths over extended time periods before discovery. These cancer-clusters often contain more than one type of cell but usually there is a sub-population of super-aggressive types of cell, which are assumed to all derive from a single ancestor (the “renegade” cell) i.e. they are clonal or belong to the same genetic family, reflecting many generations of cell division (§3.3.4.4). Each family is a collection of similar (sub-species) of the same cell type, which have evolved in slightly different ways. Lethal cancers retain the malignant mutations but often add many harmless types of genetic variations.

4.2.8 Genetic Cell Phases Each genetic cell phase is defined by its particular pattern of regulated gene expression. This reflects the capability of a cell to create families of proteins as needed; normally a cell has reached a stage when a given set of proteins are being expressed because various biomolecules are present at that time and the cell’s genome is in a given state (under epigenetic controls) for allowing these expressions. The initiating event (resulting in a change in gene expression) includes activation or deactivation by ligands of proteins in the cell’s membrane (receptors). Each receptor is linked to a specific biochemical pathway in the cell. The ligand may activate or suppress the pathway. Cell differentiation (§3.3.2.2.2) is thus a transition of a cell from one genetic cell type to another and it involves a switch from one pattern of gene expression to another (i.e. switching protein production rules).

4.2.9 Mutations are Genetic Failures Since cancer usually gets progressively worse over time, there must be a genetic feature involved, which passes the accumulating problems through the many generations of cells created over a person’s lifetime. The numbers involved are almost astronomical; it has been estimated that, on average, each human creates about one million trillion (1018) cells over a normal life span and 10 million cells are replaced every second. Each replacement event can potentially introduce an error, leading finally to cancer. It was not until as late as 1969 that most experts began to accept that cancer had a genetic basis; even then, this was falsely thought to be limited only to inherited (family) forms of cancer. Only approximately 5~10% of cancers are due to genetic defects inherited from a person's parents, including the infamous breast cancer genes (BRCA1 & 2 that give an 80% lifetime risk). Indeed, most of the genes (§3.2.3) leading to inherited (family) cancers have now been identified. As shown earlier, genes control how all cells work by making proteins that have specific tasks and act as messengers for the cell. Therefore, each gene must have the correct instructions or “code” for making its related protein. However, there are many steps required (§3.2.4) to produce a protein from the protein’s structure-information in the gene (“expressing the gene”); most of these other steps themselves require the presence of other proteins (each having itself to be properly expressed) – all together forming complex processes or pathways. All cancers begin when one or more genes in a cell are first mutated, or changed. This creates an abnormal protein or no protein at all. An abnormal protein provides different information than a normal protein, which can cause cells to multiply uncontrollably and become cancerous. These mutations are an inevitable consequence of DNA replication; given enough time everyone would get a tumor.

42

4.3 Carcinogenesis 4.3.1 Overview Regulation of the cell cycle involves processes crucial to the survival of a cell, including the detection and repair of genetic damage as well as the prevention of uncontrolled cell division. The molecular events that control the cell cycle are ordered and directional across time; that is, each process (as a series of protein ‘expressions’) occurs in a sequential fashion and it is impossible to ‘reverse’ the cycle. The existence of a protein is sufficient to trigger the next step in the pathway of the cell. The two principal processes that contribute to cancer when they go wrong are cell division and process (timing) signals; both of these are critical to the survival of the cell itself and failures may multiply so extensively as to threaten the very existence of the host organism. Tumors are formed by a process (called carcinogenesis) in which certain cellular alterations lead to the formation of cancer. Multi-generational carcinogenesis involves the sequential genetic (or epigenetic) changes to a cell's DNA, where each critical step produces a more advanced tumor. The process is characterized by a progression of changes at the cellular, genetic and epigenetic level that ultimately reprograms a cell to undergo uncontrolled cell division and other lethal changes, thereby forming a malignant mass. This extended process is often broken down into three stages; initiation, promotion and progression; several mutations may occur at each stage. Initiation is where the first dangerous genetic mutation occurs in a cell. Promotion is the clonal expansion (repeated division) of this transformed cell into a visible tumor that is usually benign. Following promotion, progression may take place where more genetic mutations are acquired in a sub-population of tumor cells. Progression usually changes the benign tumor into a malignant tumor. Cancer-causing genetic changes can also be acquired during one’s lifetime, as the result of errors that occur as cells divide during a person’s lifetime or exposure to substances, such as certain chemicals in tobacco smoke or radiation (X-rays or ultraviolet rays from the sun) that can readily damage DNA. The number of cells in the body that carry such changes depends on when the changes occur during a person’s lifetime. In general, cancer cells have more genetic changes than normal cells. However, each person’s cancer has a unique combination of genetic alterations. As the cancer continues to grow, additional changes will occur. Even within the same tumor, cancer cells may have different genetic changes. Genetic changes that occur after conception are called somatic (or acquired) changes. They can arise at any time during a person’s life. Cancer is fundamentally a disease of regulation of tissue growth. In order for a normal cell to change into a cancer cell, genes that regulate cell growth and differentiation must be altered. Moreover, serious deficiencies in any of the 34 DNA-repair genes allow more damaged DNA to accumulate, increasing the cancer risk, especially p53 and MGMT mutations.

4.3.2 Oncogenes Mutated genes that trigger the start of the cell division cycle are called oncogenes (from the Greek word onkos – for mass). As long as they are active (being ‘expressed’), they will continuously (and mistakenly) compel the cell to keep dividing. Often, oncogenes are the mutated derivatives of normal cellular genes (called proto-oncogenes) that once mutated then stimulate normal cell division to be overactive. Some of these oncogenes may produce hormones (chemical messengers) between cells that encourage mitosis (§3.3.4.4). When a hormone receptor on a recipient cell is stimulated, the signal is moved from the surface of the cell to the cell nucleus to affect some change in gene transcription regulation at the nuclear level. Some oncogenes are part of the signal transduction system itself, or are even the signal receptors in cells themselves, thus controlling the sensitivity to such hormones. Oncogenes make cancer cells independent of the normal growth signaling factors (effectively, they return the cell to embryo stage). One of the first oncogenes to be identified was the ras oncogene in 1982, in the Harvey sarcoma virus genome. Mutations in the ras family of proto-oncogenes (H, N and K) are very common, being found in about 25% of all 43

human tumors (and 90% of all pancreatic tumors), as the ras gene family makes several proteins involved in cell communication pathways, cell growth, and cell death. Another common oncogene is the her2 that determines cancer growth and spread; it is often found in breast and ovarian cancer cells.

4.3.3 Repair Failure A majority of somatic cancers has a deficiency in DNA repair due to epigenetic alterations that reduce or silence DNA repair gene expression. When expression of DNA repair genes is reduced, DNA damage accumulates in cells at a higher than normal level and these excess damages cause increased frequencies of mutation and/or epimutation. Once a cancer is formed, it usually has an increased rate of future mutations (genome instability). This instability is likely due to reduced DNA repair or excessive DNA damage. Because of such instability, the cancer continues to evolve and to produce sub-clones. There are some individuals, who are at increased risk of cancer because they have an inherited (germ line) mutation causing a deficiency in any of the 34 DNA repair genes. Some germ line mutations in DNA repair genes generate an up to 100% lifetime chance of cancer (e.g. p53 mutations). There is evidence that more than 80% of the somatic mutations found in certain human colorectal tumors occur before the onset of terminal clonal expansion. Other researchers point out that more than half of somatic mutations identified in tumors occurred in a preneoplastic phase, during growth of apparently normal cells. Likewise, many epigenetic alterations present in tumors may have occurred in pre-neoplastic defects. It is combinations of bad mutations that are lethal.

4.3.4 Suicide Failure As we saw earlier, there are built-in checkpoints (§3.3.4.2) in the normal cell cycle to ensure only one good cell is produced from one cell-division cycle. A critical pathway here is to shutdown the mitotic cycle (in effect, acting like a ‘brake’ on the process). Another critical step is to ensure that the newly created cell is fit to deserve all its own future descendants because otherwise any genetic errors, including cancerous ones, will propagate across very many cells. A failed copy will have to be destroyed through cell suicide (see apoptosis §3.3.5).

4.3.5 Suppressors Tumor-suppressor genes (or anti-oncogenes) are cellular protective genes. Normally when undamaged, they limit cell growth by monitoring how quickly cells divide into new cells, repairing mismatched DNA and controlling when a cell dies. When a tumor-suppressor gene is mutated, cells grow uncontrollably and may eventually form a tumor. BRCA1, BRCA2, and p53 are examples of tumor suppressor genes. Germ line mutations in BRCA1 or BRCA2 genes increase any woman’s risk of developing breast or ovarian cancers but this is only a small effect, accounting for about 2 to 3 percent of all breast cancers, so that cancer may not be inevitable for all carriers of BRCA1 and BRCA2 mutations. About half of hereditary breast/ovarian cancer syndromes involve unknown genes. Unlike oncogenes, which are usually ‘dominant’ and so need only one copy for activation, suppressor-genes are usually ‘recessive’ and need both copies to exist for activation. This implies that both copies need to be damaged (Knudson’s “two-hit” theory) before “the brakes fail”: a rarer event that is also reflected in modern car design. The first tumor-suppressor protein (pRb) was discovered by Knudson in his analysis of the childhood cancer, retinoblastoma (a nasty eye tumor). Functioning rb genes stop cell division but when ‘double-hit’, they fail to perform this critical function, unleashing ongoing cell proliferation.

44

4.3.6 p53 Failure The most commonly mutated gene in people who have cancer is p53. In fact, more than 50% of all cancers (and 80% of squamous-cell carcinomas) involve a missing or damaged p53 tumor-suppressor gene, as the failed cell is not detected and destroyed; its failures are passed on to the subsequent generations. Unfortunately, some of the p53 mutations are single-hit that over-ride the remaining ‘good’ gene. Its normal function is so important that it has been given the nickname: “Guardian of the Genome”, as its principal role is as a DNA damage sensor. This gene was given its name in 1979 as it produces a giant protein (called p53) with a mass of 53 kilodaltons (i.e. about equal to the mass of 53,000 hydrogen atoms). It is found in humans on chromosome 17; it contributes to over 30 cellular tasks. Most p53 gene mutations are acquired (somatic) mutations; germ line p53 mutations are rare. Importantly, it was realized that damaged p53 was almost never found in leukemia cells but p53 was needed at the G1 checkpoint. Many mutations destroy the protein’s ability to bind to its many target DNA sequences, which are important in apoptosis, inhibition of angiogenesis (§4.2.6), genomic repair and stability (§4.3.3) and most importantly, it no longer triggers the production of the p51 protein that is the actual “stop signal” of cell division. Interestingly, while humans have only one p53 gene, some species, like elephants have 20 copies each: with much lower rates of cancer. There are many mutagens causing cell failure and each has its own pathway to activating the cell’s p53.

4.3.7 Wound Failure Cancer hijacks the inflammation process that is normally invoked for wound repair. Virchow suggested in 1863 that cancer was a wound-repairing attempt that had failed. This ideas was ignored until 1986, when a pathology professor at the Harvard Medical School published his research that strongly supported this old idea by showing the similarities between the processes involving normal inflammation and the generation of cancer tumors – this paper was titled: “Tumors – Wounds that do not Heal”. Just like the immune cells repairing wounds, cancer cells need to produce inflammation to sustain their growth. By adopting similar techniques, cancer cells trigger inflammation to infiltrate neighboring cells, slip into the bloodstream, migrate and establish new remote sites (metastases). Key to these activities is the production of the inflammatory factor NF-κB (see §2.4.3.2.3) by the tumor cells themselves. Subsequent research in 2005 has shown that almost every cancer preventive is an inhibitor of NF-κB, as this prevents them from creating metastases, while neutralizing natural killer (NK) cells and other vital white blood cells of the immune system. Cancer has hijacked the carefully balanced and self-limiting tissue repair process for its own selfish needs. This theory was reinforced by research in Scotland in the following year, when it was shown that patients with various cancers with the lowest blood levels of inflammatory markers (such as C-reactive protein) were twice as likely to live through the next several years compared with those with high levels.

4.4 Causes of Cancer 4.4.1 Risks Most cancers are related to ‘external’ or lifestyle exposures. External here means any substance or interaction originating outside a human being; it includes tobacco (30% of all cancer deaths), infections (20%), radiation (10%) and pollutants, like asbestos. Obesity provides more cells as possible cancer sources while offering more nutrients. Lifestyle would include diet, obesity, alcohol, stress, lack of exercise and some jobs. Aging is often considered a ‘risk factor’ but is unavoidable, like one’s parents (for some hereditary cancers). Most sources of an individual’s cancer are almost impossible to identify. A very few cancers are known to be caused by certain bacteria and oncoviruses. Diet must be a factor because deadly cancers (breast, colon, prostate) are 7 to 60 times more prevalent in North America than in Asia. Immigrants from other, simpler cultures soon manifest similar cancer rates to longtime Western residents as the newcomers adopt ‘modern’ western diets. Twin studies also show life-style is more critical than hereditary.

45

4.4.2 Viral Before 1970, many scientists believed that cancer was caused by viruses. Ironically, this scientific myth was quite productive, as the study of cancers caused by viruses led directly to the realization that cancer is a problem found at the cellular level of all animals. The godfather of this viral theory was Peyton Rous, who in 1910 began researching sarcomas in chickens by injecting tumors between chickens; this effect still propagated a cancer even after the finest efforts at filtering the ground-up tumor. He had found the Rous sarcoma virus (RSV). Other cancer causing viruses were found later in other animals. In 1958, the Epstein-Barr virus was shown to cause human cancers. Panic set in: were cancer patients infectious? Indeed, subsequent research showed that only a very few viruses (7 for humans) did have a simple genome that could cause a tumor; still accounting for an estimated 12% of human cancers.

4.5 Eight Key Cancer Properties Two of the leading genetic researchers in cancer, Robert Weinberg and Douglas Hanahan published a highly influential review paper in the journal Cell in 2000. They argued that all cancers shared six common traits (or ‘hallmarks’) that determine whether a normal cell eventually produces cancerous descendants. These carcinogenic characteristics were: 1) stimulate their own growth; 2) resist stopping cell division; 3) resist programmed cell death; 4) immortality; 5) stimulate angiogenesis; 6) metastasize. In 2011, they added two more features: 7) abnormal metabolism; 8) evade the immune system. There are many genes, whose failures contribute to these features but ‘switching off’ the mighty p53 gene (§4.3.6) contributes to 4 of the 6; hence it’s role in so many human cancers.

4.6 Mistiming It can be readily seen that it would be massively unlikely that a single cell in one generation (i.e. single cell cycle) could suffer all the mutations implied by the ‘Hallmarks of Cancer’ above. Once a cell survives one of these mistakes then its descendants can eventually accumulate all of them, if the host body survives long enough. As we have seen from our survey, all of these features are anomalies from normal processes that occur in healthy cells. All of these anomalies are failures in the process control mechanisms, especially in the foundational cell division cycle. These critical control mechanisms involve several proteins, so that a vital protein must malfunction in each of these mechanisms. These ‘failed’ proteins become genetically propagated when their corresponding genes are also damaged through inherited or somatic mutations. They also share the common feature that an anomaly has appeared at the wrong time in the life history of the cancer cell family, often regressing to an embryological stage.

4.6.1 Mutation Timing Whenever a normal cell first suffers damage to one of its initiator or terminator genes the undamaged monitor gene will be activated and cause the damaged cell to destroy itself. Even if one of the monitor genes in a normal cell is damaged, apoptosis will still occur as every cell has two monitor genes. Only when both monitor genes, in a single cell first become damaged (a very rare pair of events) will the proto-cancer cell enter a state of enhanced risk. This damaged cell will generate generations of descendants without problem even if an initiator gene subsequently is damaged because the remaining normal terminator gene will continue to switch off divided cells. Alternatively, once both monitor genes are ‘broken’ and the terminator gene is damaged, then the cell will only divide if it continues to receive ‘start-division’ messages from nearby cells of the same type. This will result in a growing localized tumor (or produce an excessive quantity of distributed cell products, such as red or white blood cells) – its growth rate will depend on how much the damage to the initiator gene has lowered the threshold sensitivity to the start-division messages. This state of the cell may be referred to as the ‘omega-minus’ state. However, if now an omega-minus cell descendant suffers one final, complementary gene mutation (e.g. if first initiator then terminator or vice-versa) then this cell becomes the parent cell of a deadly, omega clonal family. Almost all cells can be picked up by the blood system and dispersed around the body. If the cell is in an omega-minus state the dispersed 46

cell will not likely divide as it needs appropriate cell-divide signals from its neighbors, which are now remote in most cases; the exception occurs when the dispersed omega-minus cell ends up near similar damaged cell types in certain key organs, like the liver with good blood supplies. When omega cells are dispersed then the cancer tumor has metastasized and it becomes lethal if the initiator damage is severe enough.

4.6.2 Development Mistiming One of the central ideas presented here is that cancer is a mistiming phenomenon when a cell reverts to an earlier stage in the organism’s evolution. Instead of simply replacing lost, similar cells, the mistaken cell behaves as if it were still at the early growth stage (like in an embryo – §3.3.1.2) of the organism, when almost ‘unlimited’ growth is the desirable goal for the cell. This radical proposal will be expanded here. When we reviewed the cellular activities at the embryo stage, it was important to note all the different stages where new cells appear and replicate vigorously in an organism. Normally, a mature cell divides when it gets a growth signal from similar cells in it’s nearby tissue group; this triggers the ‘start’ dividing process but if another gene (oncogene) mutates to one of these initial ‘start’ proteins then the cell can keep dividing as long as the ‘stop’ proteins is absent or switched off. If the aberrant cell has regressed to its embryonic stage, not only will it divide but the number-of-division controls (telomeres – §3.3.4.2) no longer apply (like the cell suicide process) at this stage. As we saw earlier, also during the embryonic stage, new blood vessels are growing and cells are migrating to many different locations.

4.6.3 Stem Cell Theory During this embryonic stage, cells are characterized as being stem cells, this suggests the Stem Cell theory of cancer. There is increasing new evidence that tumors usually arise from the group of stem cells in a tissue that are responsible for the repair and replacement of cells as part of routine maintenance. Additionally, most cancers are diagnosed in older people implying that our cells accumulate critical damage during our whole life, while stem cells are the only cells that can transmit DNA throughout our whole life. The cancer stem cell hypothesis proposes that the different kinds of cells in a heterogenous (or mixed) tumor arise from a single cell, termed the cancer or Tumor Stem Cell (TSC). Cancer stem cells may arise anomalously from the transformation of adult stem cells (differentiated, dividing cells). These cells persist as a subcomponent of the tumor and retain key stem cell properties, such as homeostatic control and periods of vigorous growth, as well as giving rise to a variety of cells, including dividing into many ‘child’ stem cells. These TSCs are hypothesized to persist in tumors as a tiny (2%) distinct population and become the principal cause of the relapse of cancer and the emergence of metastasis by alone producing new secondary tumors. It is suspected that conventional chemotherapy drugs kill differentiated but not stem cells, which have a slower rate of cell division and they can remain dormant (and safe!) for long periods. This is a very grim discovery as almost all anti-cancer chemo drugs are measured by how effectively they reduce the size of tumors and the tiny number of TSCs indicates that not only are they much more difficult to identify but their mutation rates must be much higher than ever suspected. Carcinogenesis (§4.3) then becomes a very non-linear (tree-like) explosion

4.7 Summary This chapter is the principal heart of this small book as it attempts to convey our current scientific knowledge about cancer to the interested reader. It begins with setting the historical context for this disease that appears to be as old as humanity itself; the latest science of cancer appears to confirm this view as its mechanisms simply appear to be random errors in the natural processes of every mammalian living cell. With hundreds of trillions of cells, millions of mistakes (mutations) occur daily and these are mostly managed effectively to keep the whole collective viable.

47

Sometimes, a rare mistake may occur that gives one cell a preferential advantage allowing it to survive more readily than its neighbors. These errors are captured in the DNA of the cell (mutations) so they are spread through all the cells descended from the damaged ‘Father of the Rebellion’. Worse, further mutations may be later added, so the rogue clan carries its expanding set of mistakes throughout the life of the owner of these cells until a cancer is formed that is sufficiently severe to kill the victim. These errors in the genes are changes (including point flips, deletions and insertions) that are usually passed to the next generation of cells in the normal cell division process, unless fixed by the cell’s repair processes. Epigenetic alterations of DNA repair genes or cell cycle control genes are very frequent in sporadic (non-germ line) cancers, being significantly more common than germ line (familial) mutations in these sporadic cancers, which are passed between an adult parent and their child. Cancers are characterized by the organ in which it first appears in a person; this originating location determines how the cancer will be treated, even after it spreads to other sites in the body; e.g. it is still a lung cancer after it has spread to the bones. Unfortunately, brain tumors are one of the commonest childhood cancers, along with certain forms of white-blood cell cancers (leukemia). Outer-surface organs, consisting of epithelial cells that start the cancer-chain, will result in carcinomas, which are found in about 85% of cases. Mammalian organs in connective tissue (mesodermal) that become cancerous will generate sarcomas but usually, since these are slowly dividing cells, they only contribute about 1% of cancer cases in humans. Other types of common cancers are the deadly adenocarcinomas, lymphomas and leukemia, all reflecting their tissues of origin. This chapter also includes a short list of the major milestones in the science of cancer along with their contributors and references to possible Nobel Prizes in Physiology or Medicine. The primary focus of this chapter is the cancer tumor as it is usually in this form that cancer most frequently occurs and mutates into its most deadly stage, which is defined here along with the oncological concept of tumor grading. We expend a major effort exploring the concept and mechanisms of secondary or metastatic tumors, as this is the stage that will usually result in death from cancer. It is a complex distortion of the natural processes that occur at various times in a person’s life, especially right at the beginning when one first appears as an embryo or when a body must try to heal (repair) a flesh wound. Another stage in the deadly career of fatal tumors is known as angiogenesis, which often begins after a new tumor colony has been created at a remote secondary site (i.e. after metastasis) and these ‘wandering rogues’ need their own access to the body’s blood system in order to keep growing. Without angiogenesis, a tumor cannot grow beyond a very limited size (about 0.2 mm). Thus, it is the deadly combination of metastasis/angiogenesis that kills. The biochemical processes involved in the evolution of cancer in a cell are known as carcinogenesis; they have all been found to be associated with errors introduced in the universal action of cell division. The major area of research into the genetic origins of cancer has resulted in the discovery of so-called oncogenes. As long as they are active (being ‘expressed’), they will continuously (and mistakenly) compel the cell to keep dividing. As complex systems, cells have built in controls to try to keep processes within acceptable, narrow ranges. After the critical process of cell division, a new cell is checked to see that its OK, if not, then repairs are attempted – but if these fail then the cell should instruct itself to commit suicide. However, this control too can fail – with cancer resulting. The most important controls are tumor suppressor genes; these are discussed in considerable detail. We also introduce the recent discovery of Tumor Stem Cells, which appear to play a major role in the recurrence and eventual death from cancer. Their characteristics make most anti-cancer treatments even more difficult than we ever imagined.

48

5.0 CANCER TREATMENTS 5.1 History 5.1.1 Overview Cancer has been such a deadly disease to the few people who have been overwhelmed by its awesome power. It is fortunate that it is so rare amongst the sources of sickness that strike down humanity because so little has been known about it throughout history. Even today, our medical responses to its expanding encroachments are still mainly limited to those techniques that were pioneered in the Nineteenth Century (namely, surgery and X-rays) and derivatives of the killing chemicals invented in the Great War of the early Twentieth Century (i.e. chemotherapy). Recently, some of the new scientific insights into cancer’s cellular mechanisms are being used to produce more powerful drug therapies but most of them, like the older chemo treatments, are so unfocused that many healthy cells are still being destroyed as undesirable side effects. The latest targeted therapies offer the potential for improved treatments but the results are still disappointing, in spite of the apparent statistical improvements. An analysis of the problems found with treatments to date against cancer is reserved for the next chapter.

5.1.2 Epidemiology When Dr. Pott suggested a link between filthy flue-ash and scrotal cancer in chimney sweeps (see §4.1.12), he was not only suggesting a material cause for certain cancers but taking a first step into investigating cancer’s epidemiology: the study and analysis of the patterns, causes and effects of disease. If cancer is caused by natural substances then it is potentially preventable; humans can avoid these substances (carcinogens) as much as possible. This was the case with scrotal cancer that almost completely disappeared soon after using young chimney sweeps was abolished. The major problem with identifying these correlations occurs when both the cause of the disease and the disease itself are common: the patterns are hard to distinguish – this was the case with the widespread use of tobacco and lung cancer, whose incidence became suspected soon after 1945. Unfortunately, the new science of epidemiology was first grounded in the study of infectious diseases, whose ‘pathogen carriers’ could be identified. Ironically, the causal link between smoking and tobacco was greatly helped by tracking British medical doctors, who died of lung cancer. None-the-less, the enormously profitable (and powerful) tobacco industry resisted this link, first adding filter-tips and then hiring pliable “scientists” to confuse the issue, eventually (and reluctantly) allowing warning messages on cigarette packages; eventually in 1971, cigarette advertising was stopped on television in the USA. In 1994, the state of Mississippi sued several tobacco companies to recover over one billion dollars of health-care costs incurred by the state from smoking-related illnesses – especially lung cancer. Clever lawyers suggested a Master Settlement Agreement, which was eventually signed by over 50 tobacco companies; it has allowed these “purveyors of death” to continue their extremely profitable activities in their now legal drug addiction business. The purpose of conducting epidemiological studies into any disease is to suggest clues as to broad classes of causes of the disease; in the case of cancer, the most famous success was to identify cigarette smoking with extensive lung cancer. Unfortunately, this has not been repeated against the food manufacturing companies, who continue to add tens of thousands of ‘mysterious’ chemicals to our daily diet.

5.2 Surgery Surgery is one of the oldest medical interventions, perhaps invented to address non-fatal body wounds inflicted in battles. There is evidence of sutures to bind wounds done over 3,500 years ago in Egypt. The Greek doctor Galen is credited as being one of the great surgeons of Rome around 150 AD, who (it is claimed) performed brain and eye surgery. Vesalius was a well-known Italian Renaissance professor of anatomy, who improved his skills by direct dissection. Modern surgery did not get put on a scientific footing until Scottish surgeon John Hunter reconstructed 49

surgical knowledge from first principles in the 18th century, after spending some years as an army surgeon. Once surgeons began to specialize in removing tumors, it became known as surgical oncology. In the nineteenth century, with the introduction of ether anesthesia in 1846, there were few alternatives. All surgery was usually fatal because of subsequent bacterial infections that were not reduced until Lister’s introduction of his radical antiseptic carbolic interventions, noted by the removal of a breast tumor from his sister in 1869. In 1885, this approach to breast cancer was an accepted procedure with increasing amounts of chest tissue being removed. By 1900, many early primary tumors were being removed successfully by surgeons. Unfortunately, overly aggressive surgery was attempted long before the danger of metastasis (§4.2.5) was understood. Even today, one of the best approaches in the treatment of localized tumors is still surgical removal; this is why knowing the stage of the tumor (§4.2.2) is critical.

5.3 Radiation X-rays were discovered accidentally by the German physicist, Wilhelm Roentgen in 1895. Madame Curie spent many months extracting 1/10th of a gram of radium from several tons of radioactive ore called pitchblende. This new element emitted so many X-rays that it glowed in the dark. These powerful rays could also transmit energy deep within tissues as well as illustrating bones on photographic plates. Unfortunately, Marie Curie was initially unaware of this characteristic until it badly burned her hand, damaged her bone marrow and eventually killed her. Many years later, biologists discovered that X-rays could seriously damage DNA, which is usually a very stable molecule. However, as early as 1896, attempts were being made to treat cancer with X-rays. Again, it was soon realized that the treatment could only be successful with localized primary tumors that had not yet metastasized. Even worse, by 1930 it was realized that X-rays could also induce cancer in healthy tissue. The limited use of Xrays still continues to be widely used in medicine for diagnostic purposes (e.g. broken bones), when its use is called ‘radiology’. When X-rays are used for therapy the treatment is known as ‘radiation oncology’; it is still sometimes used for palliative treatments, especially in hard to reach areas of the body, such as in the brain. In order to spare intervening tissue then, several shaped radiation beams are used to concentrate the effects on small volumes. The specific radiation approach depends on the location of the tumor and its type and stage. Some cancers and cell types are more sensitive to radiation, such as leukemia and lymphomas. Some cells are considered highly resistant against radiation, such as renal cell cancer and metastatic melanoma. Large tumors also respond poorly to radiation but some cancers can be made more radiation sensitive by giving drugs like cisplatin or cetuximab during treatment. Sometimes, low-dosage radiation (normally painless) is applied after surgery but even then, it is of limited value; for example, the difference between breast cancer recurrence, in patients who receive radiotherapy compared to those who do not, is seen mostly in the first two to three years while no difference is seen after five years. Side effects are not usual and often associated with treatments of the stomach or head. A tiny minority (1 in 1000) of radiated patients actually develops new tumors after radiation treatment but usually not for several years.

5.4 Cytoxic Chemotherapy Chemotherapy (often abbreviated to ‘chemo’) is a popular form of cancer treatment that uses chemical substances. Chemo was accidentally discovered in 1943 when a US cargo ship, secretly carrying illegal mustard-gas bombs, was sunk in Bari, Italy by German planes. This released a toxic gas that spread over the whole city killing nearly 100 people. The subsequent autopsies on these victims revealed that the normally fast-dividing cells of the lymph glands and bone marrow had been suppressed. This gave experts the idea that these types of chemicals could be used to kill rapidly dividing cancer cells. These chemicals are cytotoxic: they act by killing cells that are in their mitotic cell division phase, so are more likely to target those that are dividing rapidly, one of the main properties of cancer cells (see §3.3.4.4). There is a growing list of chemo drugs, as pharmaceutical companies continue to spend large amounts investigating this growing ‘market’. Most of these drugs are targeted at cancers impacting selected organs. Adjuvant chemotherapy is given after another local treatment (radiotherapy or surgery). It can be used when there is little evidence of cancer present but there is a risk of possible recurrence. 50

It is also useful in killing any cancerous cells that may have spread invisibly to other parts of the body (micrometastases), which can be treated with adjuvant chemotherapy or radiation and can reduce relapse rates caused by these disseminated cells. Neo-adjuvant chemotherapy is given prior to a local treatment, such as surgery and is designed to shrink the primary tumor. It is also given to cancers with a high risk of micro-metastatic disease. Palliative chemotherapy is sometimes given without curative intent but simply to decrease tumor load (and associated pain) and increase life expectancy. The efficacy of chemotherapy depends on the type of cancer and the stage. The overall effectiveness ranges from being curative for some cancers (such as some forms of leukemia) to being quite ineffective, such as in some brain tumors, to being no value in others (like most non-melanoma skin cancers). There is a real art in estimating the appropriate dosages for chemo because the original formula was developed in 1916 and only varied with a patient’s weight and height, producing a 10 fold variability for many drugs (i.e. the same quantity of drug could produce a 10 times difference in blood concentration between two patients). Dose limits of most cell-killing treatments (like chemo and X-rays) are normally set by the sensitivity of the bone marrow: too high dosages will kill off the blood forming cells – it is referred to as the ‘red ceiling’.

5.4.1 Drug Types There are four main families of chemotherapy drugs that have appeared over the years; they include: a) Alkylating Agents (all derived from WW-I mustard gas), such as: chlorabucil, mustine, dacarbazine, cysplatin. b) Antimetabolites (including anti-folates), such as: capcitabine, gemcitabine, methotrexate, fluorouracil. c) Plant-based Agents such as: tubulin, vincristine, paclitaxel and etoposide. d) Topoisome Inhibitors like: irinotecan, teniposide and doxorubicin. Different drug families are targeted at different type of cancer; oncologists are trained to know this information.

5.4.2 Side Effects Almost all these drugs are explicitly designed to disrupt the cell division cycle and as they are so powerful, are mainly delivered intravenously, although some are now being taken orally. Chemotherapeutic techniques have a range of side effects that depend on the type of medications used. The most common medications (as expected) affect mainly the fast dividing cells of the body, such as skin and blood cells and the cells lining the mouth, stomach and intestines. In contrast, muscle cells (making up about 50% of a human body) are not constantly dividing so that muscle cancer is very rare. Most cells are ‘stable’, which means that they only divide when they get a suitable message from their neighboring cells. Some of the most stable organs are the liver and the kidneys. There are actually some cells (such as neurons and heart cells) that are incapable of division once they mature; primary cancers never arise in these cell types.

5.4.2.1 Nausea & Vomiting Nausea, vomiting, constipation and diarrhea are common side effects of chemotherapeutic medications that kill fast-dividing cells. Nausea and vomiting are two of the most feared cancer treatment-related side effects for cancer patients and their families. Some studies have found that patients receiving chemotherapy ranked nausea and vomiting as the first and second most severe side effects, respectively. There are therefore several drugs specifically designed to minimize vomiting and nausea (called anti-emetics). These have been developed to manage these symptoms in a large portion of patients, becoming a nearly universal standard in chemotherapy regimens. Unfortunately, many of these well-acting drugs (like ondansetron) are quite expensive.

51

5.4.2.2 Hair Loss Since most chemotherapy kills rapidly dividing cells, systemic treatment can also cause hair loss due to the high mitotic rate of hair follicles. Chemotherapy induces hair loss in women more often than in men. These are usually temporary effects: hair usually starts to regrow a few weeks after the last treatment but can sometimes change color, texture, thickness and style. This type of hair loss is more reversible than male baldness, although permanent cases can occur.

5.4.2.3 Fatigue Cancer-related fatigue is a subjective symptom that may be a consequence of the cancer or its treatment; it can last for months to years after treatment. It is almost universally experienced by patients undergoing chemotherapy as it is often caused by anemia – the killing of blood-producing cells. Its degree is found to range from mild to severe.

5.4.2.4 Nerve Pain Up to 40 percent of patients undergoing chemotherapy experience chemotherapy-induced peripheral neuropathy (CIPN) — a progressive, enduring and often irreversible condition — causing pain, tingling, numbness and extra sensitivity to cold; beginning in the hands and feet and sometimes progressing to the arms and legs. Chemotherapy drugs associated with CIPN include ixabepilone, bortezomib, vincristine, paclitaxel, docetaxel and the platinumbased drugs (cisplatin, oxaplatin and carboplatin). CIPN often follows the first chemotherapy dose and increases in severity as treatment continues but this progression usually levels off at completion of treatment. The platinumbased drugs are the exception; with these drugs, sensation may continue to deteriorate for several months after the end of treatment. Some CIPN appears to be irreversible. Pain can often be managed with drug or other treatment but the numbness is usually resistant to treatment.

5.5 Targeted Therapy Some newer anticancer drugs are not indiscriminately cytotoxic but (based on new cancer research) simply target specific proteins that are being abnormally expressed in cancer cells and that are essential for their growth. Such treatments are often referred to as targeted therapy, as distinct from classic (or standard) chemotherapy. As a form of high-tech, molecular medicine, targeted therapies are a relatively new class of small molecule, anti-cancer drugs that can overcome many of the side effects seen with the use of cytotoxic drugs, which have poor specificity to only attacking cancer cells. Standard chemo drugs will kill any rapidly dividing cell: tumor or normal. Targeted therapies are designed to affect cellular proteins or processes that are only used by the cancer cells. This allows a high dose to cancer tumors with a relatively low dose to other tissues. As different proteins are used by different cancer types, the targeted therapy drugs are used on a cancer type specific, or even on a patient-specific basis. One of the most successful molecular targeted therapeutics is the commercial drug “Gleevec”, which is a kinase inhibitor (§3.3.4.8) with a strong affinity for the protein BCR-Abl (a major contributor in producing chronic myelogenous leukemia and gastro-intestinal stromal tumor). There are targeted therapies for some breast cancers and lymphomas, leukemia, multiple myeloma and prostate cancer, as well as non-small-cell lung cancer. One of the earliest targeted therapy drugs was sunitinib (widely marketed – and expensively – as Sutent) that is taken orally and has been used against renal cancer and (disappointingly) against pancreatic neuroendocrine tumors. Everolimus (marketed as Afinitor) is a similar drug that has disappointed in trials against neuroendocrine tumors of the pancreas and GI tract. Although the side effects are often less severe than that seen with cytotoxic chemotherapeutics, serious lifethreatening effects (such as cytokine storms) can still occur, while fatigue is still common.

52

5.6 Immunotherapy Immunotherapy is any treatment of disease that is based on enhancing the positive actions of the immune system. In practice, it is increasingly seen as one of the new approaches associated with ‘targeted cancer therapy’ (see above), so they usually have fewer (and milder) side effects than traditional chemo drugs. The explicit design goal is to force cancer specific molecules (antigens) to appear on the surface of cancer cells, when the normal elements of the immune system can recognize the ‘target’ and destroy it. In theory, it is possible to create a mAb specific to almost any cell surface target (see next). Originally, in the late 1980s, pioneering immunotherapy treatments involved the administration of natural cytokines, such as interleukin. Blood was extracted, lymphocytes removed and grown externally with a tumor antigen before being transfused back into the patient’s own body. In some cases, tumors shrank to an undetectable size.

5.6.1 Monoclonal Antibody Therapy Most cancers develop defense mechanisms against the body’s immune system detecting and destroying cancer cells; each defense is called a checkpoint. The tumor’s microenvironment also prevents the recruitment of T-cells, which would normally spearhead the immune system’s attack on the tumor. Recently, antibodies have been used to bind to molecules involved in T-cell regulation removing (cancer cell generated) inhibitory pathways that block the immune system’s T-cell action. An exciting form of immunotherapy involves creating multiple copies of an antibody targeted against specific cancer features. Since these are all identical copies, this method is referred to as Monoclonal Antibody (mAb) therapy; most commercial drugs that use this technology have names that end in – mab. It is now possible to create human monoclonal antibodies (drugs use the suffix –umab), using transgenic mice, by transferring human immunoglobulin genes and vaccinating the mouse against the desired antigen. Three new drugs are undergoing extensive testing against specific cancers: alemtuzumab (B-cell leukemia), rituximab (non-Hodgkin’s lymphoma) and trastuzumab (selected breast cancers). Almost half of the best-selling biotechnology drugs in the USA are therapeutic monoclonal antibodies.

5.7 CAT/PET Scans & MRIs The ‘T’ in the names of these machines refers to tomography – a mathematical technique to produce cross-sectional images (‘virtual slices’) from a body exposed to X-rays taken from many different directions; this allows medical personnel to gain detailed views of the insides of human organs, particularly when subjected to cancerous tumors. A CAT scan involves taking images from all around the long Axis of a human body; hence called “Computerized Axial Tomography”. One of the great advantages of CT images is the high-contrast resolution; CT can especially distinguish tissues with about 1% in density. This technique currently involves quite moderate to high radiation exposures (about 100 to 1,000 times higher than conventional X-rays), so CT imaging is often limited to once every three months. It has been estimated 1,800 CT scans might cause one extra cancer; this risk diminishes with age. A more sophisticated technique is Positron Emission Tomography (PET scans), which detects gamma rays emitted indirectly by positron (positive-electron) transformations from radioactive tracer solutions. The PET technique is mainly used to observe metabolic processes in the body but is also used in diagnosing lymphomas and lung cancer; however, it is more expensive and delivers about twice the radiation exposure as CAT scans. The final diagnostic technique involves magnetic resonance imaging (MRI). As this method uses strong magnetic fields and radio waves, there is minimal risk of ionizing radiation exposure. Although safer, these machines are much more expensive than CT scanners but cannot be used with patients using cardiac pacemakers. Their higher resolution means that they are often used for neurological cancers and in the pre-operative staging of rectal and prostate cancers. Although painless, MRI scans can be unpleasant for those who are claustrophobic, especially on older machines that may take 40 minutes per session. 53

5.8 Summary This chapter reviews the various treatments of cancer; most of this information is known to oncologists (doctors who specialize in cancer) but unfortunately this is not always shared with patients and their families. It is included here because of the authorial belief that “information is power” and patients need as much information as possible to make informed decisions. It is also a pity that many recently notified cancer victims are in shock for quite a while after the initial announcement and they need an informed advocate to ensure that they get the best treatment. This chapter starts with putting cancer treatments in their historical context, which only goes back to the nineteenth century when surgery was the only option. Fortunately, the absolutely vital inventions of anesthesia and anti-sepsis were introduced around 1850 because otherwise all forms of surgery before then were both frightful and deadly. Even the discovery of X-rays only added destruction to the technique of removal of the tumor but both approaches were defeated if the tumor had already spread around the body (metastasized). Before starting a detailed review of cancer treatments, a rapid review of cancer’s epidemiology is included to illustrate how difficult it has been to find ‘causes’ of cancer so that better preventive measures may be taken. In the near future (say, the next 25 years), it is only by improving preventative measures that the incidence of cancer is likely to decrease. Since the vast majority of cancer patients are only offered the three traditional treatments, ironically summarized as: ‘Cut, Poison or Burn’ then most of this chapter describes the popular chemotherapy treatments. Unfortunately, this dominant approach uses very little of the scientific understanding about cancer gained in the last 40 years. Almost all traditional chemotherapy drugs are cytotoxic – they are designed to kill cells, particularly if a cell has started its division cycle, as most cells do at some stage in their life, although cancer cells do this more frequently. Most chemo today is given for palliative purposes to decrease tumor size temporarily and thereby increase life expectancy, as cures are very rare. Dosage levels for drugs are sometimes based on old formulae and these levels depend critically on the skill and art of the attending oncologist. Since a cytoxic approach inevitably kills many healthy cells, there are substantial side effects generated when using traditional chemotherapy drugs. These are examined here. Several of these effects are not life threatening but they are extremely unpleasant for many people. The discovery of oncogenes (§4.3.2) has resulted in a new generation of anti-cancer drugs that are aimed at specific molecules, mainly found in cancer cells. This new approach is called ‘targeted therapy’ to distinguish it from the classic or traditional chemotherapy; it has the great benefit of reducing the unpleasant side effects from chemo. Another new treatment, sometimes seen as a form of targeted therapy, is known as “immunotherapy”. The design goal here is to defeat the very clever strategy of most cancer cells in escaping from the body’s own immune system. Artificial antibodies are created that can attach to cancer cells and attract the body’s own ‘killer cells’ to eliminate the cancer targets. The observation that immune-compromised people experience higher levels of various cancers implies that the immune system is continuously scanning body tissues for tumors and is actually quite effective for most people. It also suggests that helping one’s immune system, at all times, through good diet and supplementation is a wise strategy. Natural antibodies (immunoglobins) are Y-shaped proteins binding to uniquely shaped antigens. This chapter concludes with a brief description of the most popular hi-tech imaging machines used in diagnosing and tracking the growth of tumor cells. CAT scans are given the most attention and then contrasted with PET scans and MRI machines. Some problems with these imaging technologies are briefly discussed. Although these new therapies are built on sound scientific discoveries, they are still proving to be a disappointment when viewed from the perspective of cancer cures – this unfortunate perspective is covered in the next chapter.

54

6.0 TREATMENT FAILURES 6.1 Disappointments It was as recent as 1940 that there were only two medical approaches to cancer: surgical removal of the tumor or burning it with radiation (X-rays): the “cold knife or the hot ray” – ‘cut or burn’ were the only options. By 1980, only cell-killing (cytotoxic) poisons had been added to the “War against Cancer”. Rarely, do any of these produce a cure; nor do many of the newer “targeted therapies” based on the latest scientific insights. Cancer still kills 90% of its victims. This is a very disappointing conclusion after all the massive efforts expended on a worldwide basis. The reasons for this disappointing but hugely expensive rebuff to conventional research will be explored here.

6.1.1 Cancer as Black Box Even by 1978, oncologists and researchers had no idea how cancer acted – it was a total mystery (“a black box”). Forty years of scientific investigation has since given us a clearer idea of what is happening inside the cancer cell but metastasis still kills over 90% of cancer victims. A leading cancer researcher has sadly admitted: “We still do not understand how cancer cells learn to invade and create metastases. We have only a very imperfect understanding of the role of the immune system in preventing cancer development.” There is now a much greater need to ‘defocus’ our research and look outside

the single cell at its surroundings to see how a cancer spreads around the body (metastasis). Too much of the past research seems to have been aimed at solving the easy but less critical problems.

6.2 Surgery – too Late Only surgery on primary tumors offered a cure but even here, micro-metastases (too small to detect, even with CAT scans) could still eventually emerge to threaten the patient’s life again. None of the known anti-cancer techniques at present even promise a cure – at best, they are palliative (making the patient more comfortable) or extending the average life span by a few (usually less than 12) months. Earlier detection is distorting the survival statistics.

6.3 Radiation Problems As we saw earlier (§5.3), radiation oncology offers no better outcomes than surgery – both can be effective against primary tumors but are always eventually defeated when tumors finally metastasize. Worse, careless use of X-rays can even create new cancers (unlike expert surgery) by damaging the DNA of any healthy cell.

6.4 Chemotherapy Problems Chemotherapy-related toxicities can occur acutely after administration (within hours or days) or chronically from weeks to years afterwards. The major problem facing all chemo approaches is that each cell wishes to survive, so it has built-in solutions to being chemically poisoned. The cleverest approach, discovered in 1971, is to create protein molecules (such as p-glycoprotein) that penetrate the cell’s membrane to pump intrusive chemicals from within the cell to outside it. This cellular technique is called “resistance” and is a widespread cancer-cell strategy as it is so generally successful. Chemotherapy rarely works, and even when it is useful, it usually does not completely destroy the cancer. Patients frequently fail to understand its limitations. In one study of patients, who had been newly diagnosed with incurable, stage 4 cancer, more than two-thirds of patients with lung cancer and more than fourfifths of patients with colorectal cancer still believed that chemotherapy was likely to cure their cancer. Many oncologists fail to tell their patients of the probable poor prognosis. This sad situation reminds one of the challenge facing physicians before antibiotics were discovered. Even new drug technologies, such as monoclonal antibodies, have been found to have serious problems (death and disability); for example, rituximab has induced cardiac arrest and renal failure, as well as dangerous cytokine storms. 55

6.5 Intrinsic Problems There are many problems associated with ‘winning the war against cancer’. Some are organizational (group-think) and some reflect the intrinsic complexity of the problem (which humans are, as yet, too unsophisticated to resolve). This section will analyze some of these problems and suggest some possible solutions. The next section will review some of our institutional problems.

6.5.1 Chemo & Radiation are too Indiscriminate Chemo poisons any cell that has entered its Divide-Phase (see Cell-Cycle: §3.3.4.3); although this is a feature of all cancer cells at some point; it is, unfortunately, part of the natural cycle of all normal cells. Thus, these lethal chemicals kill far too many healthy cells, not just the cancer ones. This widespread, indiscriminate cytotoxicity accounts for most of the nasty side effects of chemotherapy. A similar level of indiscriminate ‘slaughter of the innocents’ occurs with radiation treatments, whose beams are too broad to just kill the cancer cells in a tumor. This lack of ‘cancer specificity’ is the major challenge facing developers of all cancer therapies; if only cancer cells could be made to mark themselves as different from their healthy neighbors, especially on their outer surfaces, then the body’s own immune system could be readily trained to eliminate them.

6.5.2 One Disease Contrary to popular opinion, such as: “Cancers are a large family of diseases …” (Wiki – cancer). This is a confusion about the many sites in humans where cancer might occur. Each of the 210 different cell types in the human adult can potentially go wrong at the DNA level and start on its noxious cancer journey. Most cells share common functions, especially in the cell-division process; they may differ in which growth signals they respond to but once they start dividing they follow common sequences. It is these commonalities that must be identified so that universal cures may be pursued. Society cannot afford to develop 210 specific cancer cures. This would be like calling burns a widely diffuse disease because burns may occur anywhere on one body. Even one mutation in any one part of a cell-division pathway is enough to inactivate the whole pathway and promote cancer.

6.5.3 Tumors as Diverse Cell Colonies Many descriptions of cancer talk about the many forms of this disease – even just for human victims. As we have seen, it is only the surrounding tissue of the cell’s original location that determines which type of growth factor might be mutated. Once this has triggered, the renegade cancer family then starts accumulating further mutations that eventually result in a tumor sharing many of the same characteristics – so, in fact, there really is only one type of disease process at work here. The critical transition is when a cell metastasizes. This should give more focus to cancer research. Even in a visible tumor (at least 1 cm in size), there are many cancer families as different changes have occurred in similar families (cousins) so evolution leads to even more powerful survivors in these families.

6.5.4 Treating Tumors often changes its DNA Gross cancer treatments, such as chemotherapy and radiation, have been found to alter the DNA of surviving cancer cells in the tumor; in other words, these treatments are themselves mutagenic. Although the risk of new tumors is now small, it could well indicate that these are not likely to prove to be successful strategies.

6.5.5 Microscopic Scale One of the unspoken challenges facing cancer researchers is that cancer occurs at the microscopic scale, which is far too small to see with the human eye. This limits the power of imagination to create possible new ideas, as our imagination is closely related to our powerful visual system, which operates on the macroscopic scale. This very small scale makes it difficult for an innovator to convince other researchers of his new ideas; this was illustrated 56

historically by Pasteur’s revolutionary suggestion that much disease was due to germs – too small even to see with most microscopes of his time. This submicroscopic scale also means that by the time a tumor is usually detected it is several millimeters in size, so that it contains tens of thousands of cells, not all of which are cancerous. This late detection means that there are few long-term survivors. Indeed, at this scale only a single cell with a metastatic defect is sufficient to wander off and start a new set of tumors. Even advanced technology, such as the electron microscope, finds it difficult to capture information on the timescales that characterize subcellular processes that can fail and then lead to cancer. Indeed, at this scale, attempts to extract data may also introduce new changes in the cell that were only introduced by the attempts at energetic observations. Many of the chemical interactions, which are occurring in cellular proteins, are actually taking place at the level of atoms (or even electrons); usually a single protein will interact with about 5 to 15 other proteins presenting a ‘complexity network’ that swamps understanding At this level we are not seeing what is happening when we are not watching but at a blended level where our own instruments are part of the drama (a well-known atomic problem, called the Heisenberg Uncertainty principle).

6.5.6 Non-Mathematical Knowledge Historically, science made the most dramatic progress when it could study large systems, such as astronomy, where timescales were large and insensitive to the observational efforts (in contrast to atomic systems that are impacted directly, as in the Heisenberg Uncertainty principle). A further characteristic of ‘classical’ systems is that they are simple; there are few interactions occurring at any one time, so simple mathematics can be used to make linear, although still accurate enough, approximations. This is not the case in cellular processes, where many actions are occurring at the same time, many determined by earlier events (i.e. adaptive systems). It is a major error to view cells as “machines” – this will only lead to simplistic assumptions. This is not a plea for using a lot more mathematics to try to understand cancer processes: quite the opposite, mathematics would introduce too many hidden simplifying assumptions in its attempts to import the art of arithmetic symbol manipulation into an area where deep complexity and uniqueness are dominant. Mathematics was invented at the human scale, such as counting pebbles; it is an unproven assumption that this kind of mathematics works at all scales of the universe.

6.5.7 Uniqueness Historically, science has done well when it studied collections of similar objects; or, at least, samples from identical collections (e.g. all hydrogen atoms are identical) so examining any one provides insights into any other. This is not the case with living creatures when examined at the scale of genetic information. Each of us is truly unique, not just superficially (observable differences) but deeply within each of our cells – our genomes are unique. Not only is the information unique between us, but it is vastly large in absolute terms. This implies that the traditional methods of extracting information (based on statistics) may only be useful, on the average or at the herd-level. Thus, the standard approach of ‘double-blind’ studies of new drugs could prove to be worse than useless for an individual patient; the required results for an individual may be easily lost in the outliers of a study involving hundreds of unique strangers. Even the basic scientific idea of causality may be readily lost when large numbers of cases are compared to an individual situation. Indeed, the whole idea of a species genome, with its billions of components subject to vast numbers of combinations, may prove to be far too premature for our present understanding.

6.5.8 Mystery of Metastasis Readers who have been paying attention will have noticed that metastasis (§4.2.5) is the critical problem with cancer. It is only when tumors have migrated to form new colonies (secondary tumors) that cancer has reached its deadly stage: survival after this point almost never occurs. Unfortunately, this is the most complicated situation and there has been minimal progress in this area; perhaps, this is why cancer scientists have been investigating simpler areas – it is easier to get results elsewhere.

57

6.6 Institutional Problems Institutions are the attempt by societies to construct organizations, which combine the efforts of many people to solve human problems that extend beyond the life (or impact) of a single person. Unfortunately, they often succumb to the psychological failing of the ‘need to belong’ and so create an institutional orthodoxy (sometimes called ‘group-think’) that can over-ride personal responsibility, originality/creativity and block new innovative ideas. Contrary to the (carefully cultivated) view that most cancer research is undertaken by the pharmaceutical industry, most funding for cancer research comes from taxpayers and charities. In the US, less than 30% of all cancer research is funded by commercial researchers, such as pharmaceutical companies. As a percentage of GDP, the non-commercial funding of cancer research in the US was four times the amount dedicated to cancer research in Europe. Half of Europe's non-commercial cancer research is funded by charitable organizations. We can do better. Since 1971, the U.S. has spent over $200 billion on cancer research, including resources from the public and private sectors and foundations. There are numerous organizations interested in both conducting research and/or treating patients. The major institutions are pharmaceutical companies, universities, large hospitals and cancer agencies. It is likely that there are probably, at least five million people worldwide making their living from the “cancer industry”, including 25,000 oncologists. Other consequences of the highly pressured competition for research resources appear to be a substantial number of research publications whose results cannot be replicated and perverse incentives in research funding that encourage grantee institutions to grow without making sufficient investments in their own faculty and facilities. As well as providing most of the investment in basic cancer and drug research, publicly funded medical research is the major source of innovative drugs; including sixteen of the seventeen key scientific papers leading to the discovery and development of the five top-selling US drugs in 1995. Too many publications can mask any significant new discoveries or ideas.

6.6.1 Surgery/Oncology Rivalry By 1965, there was a serious professional rivalry developing between radical breast surgeons and oncologists, who were pushing chemotherapy. In particular, most breast surgeons viewed chemotherapists as estranged rivals, who could not be trusted with anything, least of all improving surgical outcomes. Even with stable, slow-growing tumors that had metastasized only into the liver (a renewable organ), oncologists were still pushing drug therapies when surgery (by top liver surgeons) could safely remove the only known tumors. It might be years before any tumors grew back or even if other micro-metastases grew to life-threatening size. First-hand experience confirms that this rivalry was still present in 2015, even in a country where doctors did not operate as private businesses.

6.6.2 Science/Oncology Rivalry Even as early as 1950, when Temin discovered the role of retroviruses in inducing cancer – a discovery accepted by many cancer scientists as a possible mechanism for cancer, this significant discovery was mainly ignored by clinical oncologists. Indeed, there are still huge professional rivalries between these two large groups of cancer experts; each group has their own specialized journals and hold separate massive annual conferences where they only hear from people within their own specialty. It appears that even when some oncologists participate in major (Phase III) drug studies, they are listening more to the pharmaceutical companies than to the objective scientists, who usually have no financial stakes in the outcomes. Indeed, oncologists still reject much science, based on animal models; they still rely (almost exclusively) on large-scale, phase-III studies conducted by and for pharmaceutical companies.

58

6.6.3 Big Pharma & the FDA Worldwide, the largest multi-national pharmaceutical companies (“Big Pharma”) dominate the commercial research into cancer therapies, leaving universities to undertake fundamental scientific research. Even when new research companies (often based on university research spinoffs using publicly-funded breakthroughs) focus on the latest high technology, such as genetic engineering, the largest pharmaceutical companies will avoid the high-risk, early stage research; waiting for proven success before taking over the smaller companies. Genentech, one of the first and most successful of the genetic engineering companies was nervous about investing further in cancer therapies. In 1995, Genentech’s executives were reluctant to put their revolutionary, anti-breast cancer drug Herceptin into Phase III trials, as just enrolling 500 women was going to cost them almost $15 million. Before 1962, the US Federal Drug Administration (FDA) used to verify all new cancer drug trials, now they just accept the published results from the clinical trials conducted for the pharmaceutical companies, as they follow the guidelines called the New Drug Application (NDA). This involves three sets of trials (phases); the most expensive is the double blind, placebo-controlled, phase III trials. These are so expensive to conduct that only major pharmaceutical companies can afford to go through this process, giving them a virtual monopoly. The FDA will now authorize a new anticancer drug if it shows at least a three-month extension in average survivability compared to others in the control group. New cancer drugs may be approved under the NDA process in about six months.

6.6.4 Drugs Only In the pharmaceutical industry, the patent protection of drugs and medicines is accorded a particular importance, because drugs and medicines can easily be copied or imitated (by analyzing a pharmaceutical substance) and because of the claimed high cost of research and development (R&D) spending and the high risks associated with the development of a new drug. Clever patent lawyers try to get valuable extensions to keep out lower cost generic drug manufacturers. In consequence, new possibilities, such as plant-based chemicals do not get approved, as the phase III trials are too costly, while no patents can be issued on such natural ‘products’. Some have raised ethical objections specifically with respect to pharmaceutical patents and the high prices for medication that they enable their proprietors to charge, which poor people in the developed and developing world cannot afford. Critics also question the rationale that exclusive patent rights and the resulting high prices are required for pharmaceutical companies to recoup the large investments needed for R&D. One study [14] concluded that marketing expenditures for new drugs often doubled the amount that was allocated for research and development (R&D). Worse, experts are now suspecting that, like antibiotics, cancer may require combinations of agents rather than mono-therapies, which is the present legal and commercial approach to investigating new drugs. One has stated: “At present, the choice of drugs to be used is inspired by biological intuition or inspired guesses. Both the patent system and the FDA both emphasize single agents, so perhaps some in the past have been dropped when their combo utility might have been important.

6.6.5 Endemic Mutagens By 1981, Doll and Peto had conducted an epidemiological study in which they compared cancer rates for 37 specific cancers in the United States to rates for these cancers in populations where the incidence of these cancers is low. The populations compared with US populations included Norwegians, Nigerians, Japanese, British and Israeli Jews. Their conclusion was that 75 - 80% of the cases of cancer in the United States were likely avoidable. The avoidable sources of cancer included tobacco, alcohol, diet (especially meat and fat), food additives, occupational exposures (including aromatic amines, benzene, heavy metals, vinyl chloride), pollution, industrial products, UV light from the sun, exposure to medical X-rays and infection. Many of these sources of cancer are DNA damaging agents. The tragedy is that in a civilization obsessed with money, it is difficult to see how widespread sources of mutagens, such as some food ingredients, can be eliminated when epidemiology cannot extract the ‘signal’ from the background ‘noise’ to “prove” that certain food additives are dangerous. This is a major problem when rich, powerful companies wish to maintain their profits by getting the FDA to ‘grand-father’ their products as ‘safe’. 59

6.7 Human Genome Project The Human Genome Project (HGP) was introduced earlier (§3.2.5); it was the largest collaborative biological project ever undertaken in the world, costing over $3 billion. It was designed to determine the sequence of the three billion chemical base pairs making up human DNA. Its goal was to identify and map all of the human genes from both physical and functional perspectives. It is disappointing to inform readers that these objectives were not achieved. It certainly identified all the bases but failed to uncover their physiology. Contrary to common belief, the genome published by this project does not represent the sequence of every individual's genome. It is the combined mosaic of a small number (~12) of anonymous donors, all of them of European origin. The HGP genome is seen as a ‘scaffold’ for future work to identify differences among individuals. Subsequent projects sequenced the genomes of multiple distinct ethnic groups, though as of today there is still only one “reference genome”. It is not known which parts of the genome apply to every human and which vary by race, family, individual or even organ. Police usage of DNA can only compare two samples, with one taken from the crime scene; without such comparisons, the process has minimal forensic value. Fortunately, President Clinton announced that the human genome sequence would not be allowed to be patented. This undercut the share value of the HGP’s principal commercial competitor (Celera Genomics) as its CEO, Craig Venter had planned to patent thousands of genes, although only his own genes had been examined; - this in spite of the US Patent law that “natural products cannot be legally patented”.

6.8 Summary The sixth chapter is short and sad. This is because it reviews the failures of treatments, which have now been used for over one hundred years, in trying to rid patients of cancer. Surgery is the oldest method and when used early enough, it can eliminate 100% of the cancer; like ionizing radiation, it only ultimately fails if the tumor has already spread to other sites in the body. The greatest disappointment is with chemotherapy, which is still the most popular method for attacking cancer today but due to its lack of specificity to only cancer cells it usually causes more harm to the patient than the initial tumor, which is often only reduced in size for a few months. Other problems in fighting cancer center on our institutions that we have given the task of understanding and then killing this subtle and tenacious foe. We have not been helped by commercializing our approach to both cancer research and prevention. Large pharmaceutical companies only want profits from their research while food manufacturers still add thousands of unknown chemicals into our daily diets with unknown consequences. Allowing university research groups to take their publicly funded research to the market may help with government budgets in education but transfers the costs of expensive therapies to the nation’s Health and Hospital sectors. Even when facing a single tumor, we are actually looking at thousands of cells: some good, some bad and some very ugly. The small size of single human cells makes it very difficult to imagine the incredibly small scale that the fight must be carried out. What is microscopic for us is the normal scale of the biochemical mistakes that must be corrected. For most of the last 400 years, during which we have made great technical advances in our civilization, we have relied on sciences and mathematics that were developed at our usual human (macroscopic) scale. At this level, ‘first approximations’ (and relying on time-averaged values) have often worked quite well for us; these tricks will not work at the atomic scale that cellular processes occur. Even the existence of a single molecule can trigger a life threatening change. Assuming ‘life is like machines’ was a huge error and was only inspired by the invention of clockwork mechanisms in medieval times. There are no simple systems to rely on to build useful analogies for life itself; it is the ultimate level of complexity in the universe. Since cancer occurs at the level of individual cells and as each cell is as unique as each one of us (coded as only 0.1% of the human genome), then we must now learn to develop a science oriented to uniqueness. Neither our existing medical approaches nor statistically based experimentation (e.g. Phase III trials) has yet to face up to this challenge of uniqueness.

60

7.0 NEW RESEARCH DIRECTIONS 7.1 Basic Research 7.1.1 Common Functions In reviewing the history of mankind’s quite successful attacks on the many diverse forms of bacteria, one can see a possible broad path forwards for cancer research: find the commonalities of cancer failures, such as identifying the common mutations with which no tumor can survive. Trying to personalize cancer treatment will prove impossibly expensive and too broad a challenge. A biological solution must be sought for the biological problems of cancer: not customized pharmaceutical treatments. We must find solutions that enhance the body’s own defenses to identify and kill only cancer cells, leaving normal cells alone – not treat them as necessary collateral damage, as has been the approach to date. Several scientists are suspecting that cancers share certain common signatures and traits no matter where in the body they originate. A study reported in Nature validated this assumption and leads to the hope that if genetic changes are similar between cancers, then therapies designed to target specific genes and molecular pathways could affect multiple types of cancer. One such human ‘needle’ was discovered at Columbia in the form of melanoma differentiation associated gene-7 (mda-7), also known as interleukin (IL-24). This gene has been shown now as not normally expressed in a variety of cancers including breast, prostate, colorectal, ovarian, pancreatic, brain and lung cancers, which is common for genes that suppress cancer. When forcibly expressed in these cancers, it directly impacts two forms of cell suicide known as apoptosis and toxic autophagy, regulates the development of new blood vessels and plays a role in promoting cancer cell destruction by the immune system. In any event, the drug developers usually do not know which types of tumors will respond to the new drug, so the choice of patients recruited into expensive phase III trials are often arbitrary and sub-optimal.

7.1.2 Cancer Genome Atlas The Cancer Genome Atlas (CGA) project was begun in 2005 to catalogue genetic mutations responsible for cancer using techniques similar to those developed for the HGP. Initially, the focus was on three cancers: glioblastoma, lung and ovarian cancers. After 2009, the project expanded its target list to 33 cancers, although ten of them are regarded as rare. The results are derived from about 20,000 bio-specimens collected from about 500 patients, so are (at best) only of statistical significance. It is estimated that this project will cost US taxpayers about $150 million. Indeed, the intrinsic difference between individuals is reflected in their unique DNA. Comparison of strangers’ DNA seems to be of little value since “every patient’s cancer is unique because every cancer genome is unique” (Mukherjee page 452). So, only by comparing the DNA from a single individual’s own infected organ, comparing the tumor’s DNA with that from healthy tissue in the same organ can one be assured that the cancer genes for that person have been identified. Perhaps, the prevalence of ‘herd-medicine’ has been extended to cells. None-the-less, the scientists have concluded that in individual specimens: about 80 genes are mutated in breast and colon cancers and about 60 in pancreatic cancer. Fortunately, most of these gene mutations are ‘passive’ and do not contribute to the cancer; the active cancer mutations (sometimes called ‘driver’ genes, damaging oncogenes and tumor suppressors) only occur in small numbers (less than 200). These driver genes (like ras, pRb, p53, hTERT), or rather their mutated proteins, can be organized into cancer pathways that define the cellular processes. The best estimates to date are that there are only about 15 critical cancer pathways. There is a deep, common genetic unity, which promises hope for future cancer research, since there are still dozens of malfunctioning proteins (involved in cancer), which can become targets for new anti-cancer agents. Unfortunately, there is growing awareness of the role of promoters of cancer, rather than initiators (even some of the human initiators may function more as nonmitogenic promoters) especially in the inflammation processes. At the very least, this new view will complicate any epidemiological search for cancer-causing agents.

61

7.1.3 Cancer Stem Cells There are two distinct populations of cancer cells in the tumors of most cancer victims: 99.9% of the cells are the rapidly replicating cancer cells (and these can readily be killed by cytotoxic chemo drugs). However, there are also a few undifferentiated stem cells (§4.6.3) in the tumor that are not actively dividing so they are resistant to normal chemo drugs. They only become active when the metastatic stage is reached. A cancer stem cell (CSC) is capable of dividing by mitosis to form either two stem cells (increasing the size of the stem cell population) or one daughter cell that goes on to differentiate into a variety of cell types, and one daughter cell that retains stem-cell properties. This means CSCs are tumorigenic (tumor-forming) and should be the primary target of cancer treatment because they are capable of both initiating and sustaining cancer. They are also increasingly being recognized as the cause of relapse and metastasis following conventional cytotoxic chemotherapy. Unfortunately, most cancer treatments have been developed in animal models, where the goal has been to shrink a tumor but mice only live for less than two years, making tumor relapse (and metastasis) very difficult to study. The tragedy here is that normal chemotherapy only kills a fraction of the tumors after each treatment, so that multiple treatments (sometimes with several different drugs) are needed to shrink the observed tumor. Cellular evolution then ensures that it will be the most drug-resistant cancer cells which will survive and thrive (fewer competitors); CSCs are the most durable of all the cancer cells, so (ironically) it seems that standard chemotherapy is making the cancer more malignant. Radiation and other insults to the body’s own immune system only seem to accelerate the degree of malignancy. Innovative research by a few investigators (see below) has shown that there are several plant-based chemicals targeting cancer stem cells. Unfortunately, it seems there are too many mainstream scientists, who do not wish to risk their regular funding sources by elaborating on these “alternative” types of non-toxic chemotherapy – ‘groupthink’ has been the bane of institutional thinking in many professions (see §6.6).

7.1.4 Anti-Inflammatory Targeting One of today’s sad lessons about cancer research is that the pharmaceutical industry is looking for drugs that would inhibit NF-κB, while there are thousands of natural substances but these are not patentable. Locked into their money-mindset, these profit hungry corporations are scrambling to find a suitable synthetic form they can patent.

7.2 Therapies 7.2.1 Cancer Vaccines Vaccines have been developed that prevent infection by some known carcinogenic viruses. Vaccines, like Gardasil and Cervarix, for use against HPV (human papilloma virus), have been shown to decrease the risk of developing cervical cancer. The National Cancer Institute (NCI) expects that widespread use of these vaccines could reduce worldwide cancer deaths (270,000 in 2002) by as much as two-thirds. One concern with this approach is that we may end up with thousands of vaccines to prevent every virus that can change our cells. Viruses can have different effects on different parts of the body. It may be possible to prevent a number of different cancers by immunizing against one viral agent. It is likely that HPV, for instance, has a role in cancers of the mucous membranes of the mouth.

7.2.2 Viral Infections It has also been discovered that adenoviruses (like the one for the common cold) could selectively attack a cell missing its active p53 protein, as is often the case with cancer cells. When such a virus invades this type of cancer cell, it grows and multiplies until the cell bursts, but the virus dies if it invades a healthy cell with functioning p53. However, care is needed to ensure that the infected patient’s immune system does not begin over-reacting.

62

7.2.3 Immune Reactivation One of the most promising therapies being investigated at the moment is known as ‘active immunotherapy’. This involves the selective removal of immune cells, which are re-activated externally, cultured (to multiply them) and then re-injected into patient with a custom-built virus when these invigorated immune cells attack the tumor. It was discovered that some cancers were blocking the normal immune system’s attack (using T-cells) on cancer cells through the surface CTLA4 protein. Ipilimumab (‘Yervoy’) is a new drug, (approved in 2011), which uses the human IgG1 (immunoglobulin G1) antibody to bind specifically to the CTLA4 molecule. This allows active melanoma-specific cytotoxic T-cells to generate effective anti-tumor responses, with very dramatic positive effects on previously deadly metastatic melanoma. Recently, the first FDA-approved therapy targeted at angiogenesis in cancer came on the market in the US. This is bevacizumab, a monoclonal antibody (§5.6.1) directed against a form of VEGF, commercially called Avastin. It has been found that this drug acts as an inhibitor of angiogenesis, especially against metastatic colon cancer, it was initially hoped that it would be effective against breast cancer but it proved otherwise, even though it was the bestselling cancer drug in the world in 2010. Concern has been expressed that non-specific anti-angiogenesis drugs may interfere with normal wound healing (needing new blood vessels) and with overall circulation, thereby worsening conditions like coronary and peripheral heart diseases. Even powerful drugs like this can delay the regrowth of tumors (this is medically known as ‘progression-free survival time’) without reducing overall survival time (when death occurs). It has been estimated that this drug costs about $100,000 per year of life extension.

7.3 Directions 7.3.1 Detection The only problem with surgical treatments of cancer is that they may be too late; some rogue cells may have already wandered off to other sites in the body. This means that early detection is critical when surgery is being considered. Searching for genes in body fluids is a ready test to assist early detection. Moreover, the body fluid where the biomarker is found is a good indicator of where the tumor is developing (e.g. urine for bladder cancer). Although most tumor types, such as breast, colon, pancreas and lung, can be readily detected in the blood this is often too late, as this only occurs at the 90% level with advanced cancers. Since certain organs, like the liver, are closed interior organs, only connected with the outside world indirectly, such as via the bloodstream, then traces of all their DNA eventually ends up in the blood where it can be tested for. P53 and ras proteins may prove useful early markers. Unfortunately, it is still the case that biopsy remains the only definitive diagnostic test for cancer.

7.3.2 Repair Several promising viral gene therapies utilizing certain genes have been shown to kill cancer cells at the original tumor site and also in distant metastases. Engineered viruses (adenoviruses) are also being modified to seek out and replicate only within cancer cells. When these adenoviruses infect the cancer cell, they deliver immunemodulating and toxic genes, such as mda-7/IL-24. Current studies are also exploring the potential of directly delivering purified mda-7/IL-24 protein as a cancer therapeutic. Additionally, new strategies involving viruses, therapeutic proteins or chemotherapeutic agents with ultrasound-targeted micro-bubble destruction technology, which uses microscopic gas bubbles that can be combined with these therapies. The bubbles are treated with special molecules known as complement to place them under the immune system's radar. Small molecules (or drugs) may be developed that block an oncogene from working. This is the case with another gene, mda-9/syntenin. It was also found that this gene is directly responsible for metastasis in a variety of cancers.

63

7.3.3 Avoidance Now that it is known that strong sunlight can activate deadly melanomas, then people who live in areas of strong sunshine, such as Australia, can take suitable precautions, like getting all school children to wear broad-brimmed hats. Unfortunately, such widespread prevention measures have not yet been taken against banning thousands of powerful chemicals, such as pesticides and other chemicals regularly added to manufactured (processed) foods that seem likely to be carcinogens but researchers seem adverse to threatening these popular and profitable products.

7.3.4 Context Gerard Evan, now Professor of Biochemistry at Cambridge University, has emphasized that a cell should not be viewed in isolation, particularly if it arises in a multicellular organism. Not only are the cells in a tumor interacting with one another but they are also in two-way communication with normal cells in the rest of the organism. In other words, a cell’s context is also important in understanding its actions. Evan drives his research from this perspective and the need to understand, not simply measure and discover. Science is becoming aware that systems, like living organisms (or cancerous cells), cannot be understood by analysis; processes need to be understood. As Fran Visco, founder of the National Breast Cancer Coalition has admitted: “We cure cancer in animals all the time, but not in people.” This is a recognition of the limits of mouse models, whose life-cycles are dramatically shorter than humans.

7.3.5 Timing Experiments have demonstrated that as long as the p53 suppressor gene (§4.3.6) is present after the DNA is damaged then cancer will be suppressed; it does not have to be present when the cell damage actually occurs. In the normal life of a cell, time moves forward – once a cell has reached a later stage it does not normally regress to an earlier stage; this is also one of the responsibilities of the normal p53 gene. Timing is also critical in some cancers when the p53 mutation occurs early in the tumor’s evolution while in other types, like colon cancer, it does not happen until late when it marks the switch from local growth to metastasized malignancy: this is a very important clue. Perhaps it is time to return to an earlier hypothesis: that cancer begins when a cell regresses to an earlier stage in its life history; when mutations cause it to resemble embryonic or fetal cells with unrestricted growth. The following schematic, called a “Temporal Interaction Diagram” (or TID) is offered as an aide to visualizing when proteins come together (+), start to interact (#) and separate (-). It suggests a musical score of the Cell Dance. The usual pathway diagrams are too static as a metaphor and ignore the importance of time correlations. This figure illustrates two proteins (P1 & P2) being converted by enzyme E1 into a new protein P3, over time (t5 – t1) proteins P3 P2 P1

(+)

(#) (+)

(#)

t1

t2

t4

(-)

E1 t3

t5

time 64

7.4 Diet 7.4.1 Processed Foods A nutritionist from the Boston-based, world-famous Dana-Farber Cancer Institute (a major research establishment) defines a processed food as: “A food that has undergone a transformation from the raw form either to extend shelf-life — such as freezing or dehydration of fruits and vegetables —to improve consumer palatability of raw commodities — like transforming grain and animal products into bakery and meat products.” This seems a far too broad and cautious definition; a more useful one for

cancer purposes might be to focus on manufactured foods as: “A natural, edible product that has manmade chemicals added to it prior to purchase.” Apparently, the US FDA has allowed over 80,000 manmade chemicals in circulation (including foods) on the grounds that they have not been proven harmful. However, in 2015, the International Agency for Research on Cancer (IARC - the cancer agency of the World Health Organization) announced that it has classified processed meat as a colorectal carcinogen (some thing that increases the risk of getting cancer); it also classified red meat as a probable- carcinogen (something that probably causes cancer). Processed meat includes hot dogs, ham, bacon, sausage, and some deli meats. It refers to meat that has been treated in some way to preserve or flavor it. Processes include salting, curing, fermenting and smoking. Red meat includes beef, pork, lamb, and goat. Meanwhile, the Canadian Cancer Society (CCS) has publicly stated that: “Food additives are chemicals that help preserve, color and flavor our food. It is very unlikely that food additives cause cancer.” Indeed, the

American Cancer Society (ACS) writes on its website that: “NEW food additives must be cleared by the US Food and Drug Administration (FDA) before being allowed into the food supply, and thorough testing is done in lab animals to determine any effects on cancer as part of this process.” The ACS makes no mention of foods given a “grand-fathered” pass by the FDA or

that most safety testing is done on mice with only a short, two-year life; too short to exhibit cancer. One never hears about the “Fat Fiasco”. This was the erroneous advice [15] recommended to Americans to eliminate natural (animal) fats from their diets and replace them with saturated fats, based on a false connection with cardiovascular disease. Worse, this was accompanied by the secret addition of “trans fats” in commercial foods and eating establishments. “Butter is bad” and “vegetable and manmade fats are good” became the accepted expert opinion pushed on the public. Most margarine contains minimal healthy omega-3s but huge amounts of omega-6s. Soy and canola farmers loved these recommendations and planted huge acreages of these source crops. Processed foods also switched to these cheap ingredients without any negative comments arising from the medical profession. Trans fats are additionally ‘hydrogenated’ fat molecules that make them even more indigestible and more inflammatory than unadulterated omega-6 molecules. These oils have the added benefit for industry that they do not go stale, so the foods made from them have a longer shelf life. In 2004, the Dutch Ministry of Health calculated that more people in Holland were dying from trans fats annually than were killed in automobile accidents. All of these processed oils have been proven to be linked specifically to cancer, as shown in a 2008 French study of breast cancer. This appalling state of affairs has been made worse by the very limited education in nutrition received by people pursuing a career related to medicine, that concentrates only on the (oil-based) pharmaceutical model.

7.4.2 Organic Foods When it comes to Organic Foods, the American Cancer Society (ACS) also says on their web site that: “Concern about the possible effects of food additives on health, including cancer, is one reason that many people are now interested in organic foods. Organic foods are often promoted as an alternative to foods grown with conventional methods that use chemical pesticides and herbicides, hormones or antibiotics. These compounds cannot be used for foods labeled as “organic”. Organic foods, as defined by the US Department of Agriculture (USDA), also exclude “genetically modified foods or foods that have been irradiated”. At the very least,

this implies that the ACS believes that “chemical pesticides, herbicides, hormones and antibiotics” should be considered only as “food additives”. They do add the cautionary note: “Whether organic foods carry a lower risk of cancer because they are less likely to be contaminated by compounds that might cause cancer is largely unknown.” 65

Astonishingly, the CCS still gives the artificial sweetener, aspartame (“Nutrasweet”) a cancer-free pass even though initial FDA research banned it in 1974 after demonstrating that it caused brain cancer in rats. Aspartame was manufactured when Donald Rumsfeld was CEO of G.D. Searle. He later joined the government of George Bush as Secretary of Defense, when the ban was rescinded by the FDA Commissioner (Arthur Hayes), who then left for a position with G.D. Searle's public relations firm. G.D. Searle was later taken over by Monsanto. The CCS website states: “there is no proven link between these substances and cancer in humans.” It is these types of ‘business-

before-health’ statements and the earlier reluctance of these major cancer societies to link tobacco and cancer that generate deep suspicions of their motivations, loyalties and intentions. Money still plays a major role in the cancer epidemic.

7.4.3 Anti-Cancer Foods Anthropological research has concluded that humans spent hundreds of thousands of years living as hunter-gathers but we have only cultivated grains and husbanded animals for the last 10,000 years. It is therefore logical that since our biology only changes slowly that humans need to follow a diet more like our ancient ancestors than ‘modern’ ones. This implies that fruit and vegetables should be the major part of our diet, supplemented by eggs and sometimes meat. It is unlikely that our bodies were ever exposed to rich sources of calories, such as sugar and (sugar-generating) grains. These long-range views of human diet have been confirmed by modern dietary research [15] ; this means that today all humans should consume more of the following natural foods:Berries (like strawberries, blueberries, blackberries and cranberries) contain several helpful anti-cancer molecules; these promote the elimination of a range of carcinogenic substances and inhibit angiogenesis or promote apoptosis. Citrus fruits are known to contain anti-inflammatory flavonoids; they have been shown to stimulate the liver to rid the body of carcinogens. Cruciform vegetables (such as cabbages, Brussels sprouts, broccoli and cauliflower) are some of the best foods to consume on a regular basis. These contain the anti-cancer molecules: sulforaphane and indole-carbinols, which prevent precancerous cells mutating into malignant tumors; they also promote apoptosis and suppress the action of angiogenesis. ‘Exotic’ herbs (such as garlic and green tea) are also beneficial as complements to one’s consumption. Garlic is one of the oldest medicinal herbs (with evidence going back over 5,000 years); Pasteur observed its anti-bacterial features. Its sulfur compounds promote apoptosis in leukemia and in colon, breast, lung and prostate cancers. Some studies have also suggested a reduction in kidney and prostate cancers in people who regularly consume the most garlic. Green tea contains several polyphenols, called catechins, which is a nutritional molecule that blocks the growth of new blood vessels by cancerous cells (see angiogenesis – §4.2.6). Unfortunately, these molecules are removed in the production of black tea. Tests show that green tea slows the tumor growth and metastases of breast, kidney, prostate, skin and mouth cancer, while also slowing leukemia. There are many more foods that will help promote a healthy life – it is also likely that they also reduce the risk of cancer; there is certainly no harm from emphasizing all these foods in one’s diet. The same cannot be said for two of the worst ingredients in the modern diet: sugar and carbohydrates. Everyone should consume very much less of these. Refined sugar did not enter the western diet until about 1810; it is now found in most manufactured foods and it has got to the level where its average consumption has reached about 150 pounds (70 kg) per person per year. The famous German biologist, Otto Warburg won the Nobel Prize in medicine (1931) for his discovery that malignant tumor metabolism is largely dependent on glucose (the form of digested sugar in the body) consumption. Western diets have gone totally in the wrong direction in the last sixty years with the massive liquid consumption of highfructose corn syrup (fructose and glucose), produced by subsidized corn farmers. Both diabetes and cancer rates have rocketed over this same time frame. Perhaps, it is only a coincidence but it is far better to be safe than sorry.

66

Carbohydrates have become the primary source of calories in the modern diet; they are cheap, readily available and advertised to the maximum on television as “snack foods”. White bread (hamburger buns) and pizza are the most readily consumed sources of carbohydrates. Corn has also become the primary input for industrially farmed animals. Unlike pasture-fed animals, which get high quantities of omega-3 fatty acids, corn is only high in omega-6 fatty acids. Both of these are ‘essential’ as humans cannot produce them our selves. These two forms compete with each other inside us. Omega-6 is stored as fat cells and promotes rigidity in cell walls as well as being much more sensitive to inflammation. In contrast, omega-3 fats develop the nervous system, make our cell membranes more flexible and reduce inflammation. Chickens have also had their diet fundamentally changed over these last 50 years so their eggs and meat contain less helpful omega-3s. Farm animals are also subject to powerful (growth) hormones and antibiotics, which all eventually migrate into humans after eating these animals with unknown consequences. High glycemic materials (like sugar and white flour) rapidly raise the blood levels of glucose, causing the pancreas to secrete higher levels of insulin and insulin-growth factor (IGF). Both of these molecules stimulate cell growth and tissue inflammation. Tumor cells can hijack the cellular processes of tissue healing triggered by inflammation. Extra inflammatory molecules in nearby cells block apoptosis (the body’s natural defense against over-production of tissue); they also neutralize key components of the immune system (NK and other white blood cells) giving an easy pass to any tumor cells in the vicinity. As we saw (§4.3.7): “cancer cells act as a wound that does not heal”. Cancer victims found with high blood markers for inflammation (C-reactive protein) die faster than those with low levels of these markers. Anti-inflammatory medications (cox-2 inhibitors) reduce victims’ cancer vulnerability but, unfortunately, they have soon increased their cardiovascular risk.

7.4.4 Supplements There has been a long-running debate about the value of certain vitamins and minerals to either minimize the risk of being struck down with cancer or even reducing its impact, once hit. The following list of standard vitamins has been considered for these roles: vitamin C, vitamin D, vitamin E, vitamin A and vitamin B. A research study in India indicated that both vitamins C and A reduced the number of mice who succumbed to induced breast cancer, especially when used together. Skin cells produce vitamin D when directly exposed to sunlight; many people do not get sufficient exposure to trigger enough of this vital reaction, particularly when living far from the Equator in the winter. A small study in Canada showed that a daily intake of 2000 units of vitamin D3 for eight months dropped the PSA levels on patients with prostate cancer. Other recent studies also showed the positive effects of vitamin D3 on breast cancer, non-small-cell lung cancer, colon cancer, colon cancer and prostate cancer; oily fish (such as salmon, tuna, sardines and cod) are excellent sources of vitamin D. These fish contain valuable amounts of long-chain omega-3 fatty acids, which reduce inflammation and have reduced cancer cell growth in a large number of tumors (breast, lung, colon, prostate, kidney). However, note that larger fish contain larger quantities of the neurotoxin mercury. Vitamin E is a powerful anti-oxidant that was shown by Dr. Dean Ornish to have useful effects on prostate cancer. Certain minerals, like selenium and magnesium, are increasingly deficient in foods grown in over-used soils. They have also been shown to be vital together in helping resist cancer growth.

67

7.5 Alternative Medicine 7.5.1 Natural Therapies Although many drugs originate from chemicals first discovered in plants, all pharmaceutical companies are only interested in these chemicals if they can make a synthetic version that they can patent. As a result, it is believed that there are over 3,000 plants that appear to promise powerful therapies against cancer (and are not cytoxic); almost none of these are being investigated by these companies or even university researchers, who hope to “go public” at some future date with a patented drug. This is unfortunate as there are already several plants that seem to offer exciting avenues for in-depth investigation, these include: cannabinoids, curcumin, berberine (‘Oregon grape’), milk thistle, sulforaphane (from broccoli) and parthenolide (feverfew). Curcumin (the main ingredient of the spice turmeric) is being investigated by a few brave researchers; it has been found that it induces apoptosis of cancer stem cells through linkage to the immune system’s CD44 markers. Other studies showed that curcumin inhibits release of certain cancer-associated cytokines (IL-6 and IL-8), resulting in the suppression of cancer stem cells. Most exciting is the discovery that curcumin blocks key pathways (Wnt and Ntch) that cancer stem cells try to use as they emulate replication processes during the embryo stage of cell evolution. Remarkably, curcumin molecules only target cancer stem cells (enhanced uptake) and they have no negative effects on normal stem cells. It has also been reported that curcumin down-regulates the Cyclin D1 gene in mantle cell lymphoma (MCL), again inducing apoptosis, while leaving normal cells alone: exactly the desirable characteristics of a non-toxic targeted therapy. It is not surprising to realize that cancer rates (lung and colon) are eight times less in India and one fifth fewer breast cancers for people of the same age as in North America since people in India consume about 2 grams a day of turmeric in their regular diet. A 2009 study of pancreatic cancer showed that the small molecule sulforaphane targets the NF-κB induced antiapoptotic signaling molecule by dramatically decreasing levels of the β-catenin proteins. Another study in 2011 also demonstrated that sulforaphane increased cell death in colon cancer cells, which had low levels of p53 suppressor molecules. It is significant that these studies are not being conducted by pharmaceutical companies.

7.5.2 Oncothermia Oncothermia is targeted heat treatment for cancer (sometimes called “loco-regional hyperthermia”) that can be a powerful tool when used in combination with chemotherapy (thermo-chemotherapy) or radiation for the control of a variety of cancers, such as gynecological (breast, ovarian, cervical), pancreatic, prostate, lung and liver tumors, skin and brain. This therapy was developed in Europe over 20 years ago but it is only slowly entering North America. This is not a standalone technique but it is used to enhance standard therapies to achieve reduction in tumor burden, improve quality of life and even improve survival. Documented results show survival times increased from 50% to 250% (based on different organs) compared with the US standard mono-therapies. In oncothermia, focused and controlled microwave energy is sent directly to the area containing the tumor, which preferentially absorbs this energy because their disorganized and compact vascular structure poorly dissipates heat; this increases apoptosis, especially as the higher temperature (above 42°C) thins the tumor cells’ membranes, allowing entry of higher intracellular drug concentrations and improved immune system responses. Oncothermia is minimally invasive (harmless to healthy cells) and it has also been shown to help prevent or reverse chemoresistance; it may also activate the p53 tumor suppressor gene. Even if cancerous cells are not killed directly by oncothermia treatment, they seem to become more susceptible to subsequent chemotherapy or ionizing radiation.

68

7.6 Summary This section reviews topics that are not given much coverage by conventional scientists and oncologists, as many of them do not fit well into the Western scientific worldview but since sixty years of research from that singular view has not produced any serious reductions in deaths from cancer, it suggests that a wider perspective be adopted. One of the major changes needed is to adopt a more holistic (systems) approach; this worked well for our attacks against bacterial infections but cancer research is terribly fragmented. Since cancer seems to have hijacked the body’s own natural processes then a biological, rather than pharmaceutical, approach seems to offer better prospects for success. However, the failure of the much-hyped Human Genome Project to deliver any promised anti-cancer therapies has not stopped Big Science from pursuing another of its mega projects, as cancer scientists attempt to ‘map’ all the genes suspected of contributing to cancer in the Cancer Genome Atlas. On the smaller scale, there appears to be promise of major progress by investigating cancer stem cells, particularly as they are capable of both initiating and sustaining cancer. Short summaries are included here on various new therapies, such as cancer vaccines and active immunotherapy. More attention is focused in this section on possible new directions for improving cancer outcomes by better detection, improved cellular repairs, minimizing environmental hazards and taking broader spatial and temporal contexts of tumor cells. This section also focuses on anti-cancer foods (and their opposite: unhealthy foods); it was added deliberately, since food is the widest exposure of every human to both positive and negative components of good health. As Richard Béliveau, professor of molecular biochemistry at Montreal University (and a specialist in cancer biology), has said: “If I had to design a diet today that promoted the development of cancer to the maximum, I would recommend the present (Western) diet.” A critical analysis of ‘manufactured’ (not simply ‘processed’) food is included here, with an emphasis on chemical food additives. This is contrasted with the proven benefits of organic foods and the impact of fruits, vegetables and supplements in resisting cancer growths versus the demonstrated, negative effects of sugar and carbohydrates. Information (based on personal knowledge) of complementary heat treatment (oncothermia) wraps up this section on new directions. It is humbling to recall that the US Government’s oldest cancer research organization (the National Cancer Institute) set itself the goal (almost fifty years ago): “of eliminating the suffering and death due to cancer by 2015.” This short book has been written to help as many people as possible to understand why cancer still defeats all these gigantic efforts made on a worldwide basis, by meeting a challenge written in the preface of a major text [17] that has gone through four editions (and now reached over 550 pages): “Perhaps the most difficult aspect of modern biology is the complexity of current knowledge that seems to defy simplifications to the level of the ‘non-expert’.” So, if the reader here is a ‘non-expert’ and has not grasped everything presented herein then do not despair; you are now more knowledgeable about the science of cancer than 95% of the human population. If the reader feels that they are now comfortable with this subject, they may wish to study a highly readable book [18] written as an introduction (400 pages) for non-science (Liberal Arts) undergraduates. Readers who have readily understood all that has presented here may wish to study a more difficult introductory text [19] on cancer biology, which was published in 2013. Readers who really wish to be intellectually challenged should consider reading one of the bibles of cellular biology [5].

69

8.0 OVERALL SUMMARY & CONCLUSIONS 8.1 Summary Although this book is not based on personal laboratory research into cancer, it has attempted to summarize much of the relevant research that has occurred in the last fifty years. The information described here (in a non-technical way, as much as possible) does rely on many other books, journals and articles. Even today, too many people are afraid to even talk about cancer, while some people refrain from mentioning this as a cause of death in obituaries. It is hoped that this book might remove some of the darkness from this fearsome disease. Atomic physics came to realize, at the beginning of the 20th century, that the old (Cartesian) reductionist way of viewing the world no longer made sense when the interactions between objects became as powerful as the observations being made on the objects. Indeed, particles had to be seen in terms of their interactions with each other, not as isolated things. These views were the first clues that the western, mechanical model of science was deeply flawed in its very foundations. Unfortunately, this mechanical viewpoint has been adopted by too much of medical research. Analysis of parts is still the basic assumption and simplistic models of causality still applied to living systems, such as drug testing. The ability of cells to regress to out-of-order stages in their life cycle (particularly the embryonic phase) might just prove a more helpful clue in understanding the ability of cancer cells to survive and thrive when their very existence puts the whole organism at risk. The systems perspective requires that it is not enough to simply identify the parts of a complex system (e.g. proteins and molecules) but the real need is to understand the processes (interactions and timings involving the components); understanding the living cell is the ultimate scientific challenge.

8.2 Conclusions 8.2.1 Prognosis It cannot be denied that there is a cancer epidemic; there have been explosive increases in internal cancers (such as leukemia and those of the breast, lungs, brain, pancreas) since 1945. Since then, our civilization has changed very dramatically with huge increases of sugar in our diet, factory farming and massive additions of manmade chemicals. Cancer has a valid reputation as a deadly disease. Taken as a whole, about half of people receiving treatment for invasive cancer (excluding non-tumorous neoplasms and non-melanoma skin cancers) die from cancer or its treatment. The survival rates vary dramatically by type of cancer, and by the stage at which it is diagnosed, with the range running from the majority of people surviving to almost no one surviving as long as five years after initial diagnosis (pancreatic). Once a cancer has metastasized (spread beyond its original site), the prognosis normally becomes much worse. Those who initially survive cancer are at greater risk of developing a second primary cancer at about twice the rate of those never diagnosed with cancer. Predicting either short-term or longterm survival is difficult and depends on many factors. The most important factors are the particular kind of cancer and the patient's age and overall health. Older, frail people (with many other health problems) will have lower survival rates than otherwise healthy people (2/3 of cancer deaths occur in people over 65). People who report a higher quality of life tend to survive longer. People with lower quality of life may be affected by major depressive disorder and other complications from cancer treatment and/or disease progression that both impairs their quality of life and reduces their quantity of life. Additionally, patients with worse prognoses may be depressed or report a lower quality of life directly because they correctly perceive that their condition is likely to be fatal. Unfortunately, even some of the top cancer researchers remain pessimistic after 40 years of intensive investigations about making much positive progress in the near future (50 years?). The ability of cancer cells to survive is quite astonishing. Weinberg has written[9]: “It remains unclear whether we will be able to devise treatments which will allow us to develop life-long cures of malignancies.” Even developing drugs that kill malignancies while having minimal side effects on normal tissue still remains a pipedream; the exceptions form rare but desirable breakthroughs. 70

8.2.2 Outlook As one of the world’s leading cancer researcher wrote[9]: “The deeper we probe into the cell, the more we realize how much remains to be understood. … Genome sequencing gives us a molecular parts-list but we have only the most primitive grasp of the dynamics of biochemical systems.” There is a drastic need to refocus our efforts in cancer research; our present reductionist approach has identified over 200 human mutated genes, which represents “a bewildering complexity”. Most

of the encoded, mutant proteins still contribute in obscure ways to the neoplastic growth of various types of human cancer cells. Our current methods, after nearly 50 years, of organizing and integrating data on human cancer cell genomes and cell-signaling pathways are not up to the task. Weinberg believes that: “even the genetic, biochemical and cellular information gained since 2000 about cancer development exceeds the capacity of any human mind to assimilate and comprehend.” We do not understand how cancer cells learn to handle and create the metastases that are responsible

for 90% of cancer mortality. We have still only a very imperfect understanding of the role of the immune system in preventing cancer development. The “good news and the bad news” is that we now recognize that there is only one stage in the life cycle of cancer that is critical – ‘colonization’ (metastasis/angiogenesis). The bad news is that until we solve this complex riddle, cancer will continue with its deadly victories. The good news is that we need only focus on the actions of this one area, since tumor progression to date has shown that it is the transition to the stage of metastasis (§4.2.5) that is the most deadly. This implies that most of the scientific research into cancer must be concentrated in this area; this will require that cancerous cells be studied in the context of their surrounding, living tissue over realistic time frames. There is also a powerful need to develop biochemical ‘autopsies’ to determine the degree of metastasis (the real cancer killer). This is not easy and perhaps may explain why progress in this area has been so frustrating. Indeed, cancer experts have admitted that our knowledge of metastasis is still largely a mystery; worse, it is not even clear at this time, what properties a cancer cell must acquire to turn metastatic. One of the most troubling recent discoveries is the major role played by the tiny number of Tumor Stem Cells; they are not only difficult to kill (impossible with conventional chemo) but probably are central to metastasis as they seem to have all the power and capabilities of Embryonic Stem Cells for restarting new growth everywhere. Perhaps, they too illustrate the mistiming problem that characterizes the cancer processes as they mimic previous natural characteristics: maybe, every cell has a ‘clock’ that prevents regression but gets damaged in cancer cells? None-the-less, the rewards from being able to minimize metastatic transitions would do much to reduce the death rates from cancer. The link to inflammation is a major insight, as metastasized micro-tumors only become a life threat after they have successfully linked into the blood system to feed their future growth (angiogenesis – §4.2.6). Early detection can be a huge boost in reducing the destructiveness of cancer. The detection, using colonoscopy, of benign, colon growths (polyps) and their ready removal by the age of 50 can reduce the incidence of colorectal cancers by 75%; this would be an excellent public-health intervention in the current battles against cancer. Since there is no guaranteed cure for cancer today, except surgical removal of localized, early tumors then there is a critical need to identify the location of tumors as early as possible so that surgery can eliminate them before they metastasize; relying on visual cues or patient symptoms has failed to achieve this goal. There is a desperate need for better blood tumor markers to begin the hunt for tumor sites as early as possible. Further basic research into suppressing the deadly inflammatory factors is also important; this must involve objective studies of many natural plant substances, such as turmeric that will not be patentable. In fact, a revolution in the way drugs and other cancer therapies reach the clinic, is desperately needed. The commercial pharmaceutical model has shown it to be a failure compared to publicly-funded basic research. The best scientists are not motivated by money but by the

71

technical challenges themselves and (perhaps) by the urge to help humanity. Most treatments to date appear to be acts of desperation in that they do as much harm (or even more so?) to healthy tissue as they briefly slow the progression of the tumors themselves. This is because the “target characteristics”, such as rapid cell division, apply to normal tissue. This is like bombing Berlin (and its civilians) because Hitler’s bunker was known to lie down there, somewhere. This implies that cancer research must focus strongly on identifying only the cancer cells as suitable targets; killing good tissue (“side effects”) to gain a few more months of (miserable) life is not good enough. It is improving the quality of the life of the patient that must become the primary medical objective, not the reduction in tumor size per se. Patients must be told the real risks of certain therapies so they can make informed choices – perhaps, choosing increased risk of cardiac problems for better results on the cancer tumors. Dietary components, including vitamins and mineral supplements, need to investigated objectively so, that at a minimum, cancer victims can extend the survival time naturally without any devastating ‘side effects’. Furthermore, most treatments ignore cancer stem cells (§7.3.2), which seem to lie at the heart of deadly metastasis. This implies that future treatments need to emphasize the following characteristics: A) Increase Selectivity – only kill cancer cells; B) Boost the immune system – mark the cancer cells as different; C) Preferentially, destroy cancer stem cells – minimize metastasis. It is likely that research in natural, plant-based chemicals must be the focus of future chemotherapy; the fact that these chemicals cannot be patented is irrelevant to humanity’s need for a cure for cancer. Low cost would be an added benefit to everyone: except multinational pharmaceutical companies, who have had their chance - and failed! The Bad News maybe is that the cancer epidemic is the Natural World’s reaction to the bad choices being made by our super organization (society). The Good News is that we can change our ideas: but only with great difficulty, as we are intrinsically conservative, social creatures, who too often break the rules of good social behavior for private advantages.

8.2.3 Systematic Biology It appears that, like the present author, many cancer researchers today would like to understand the entirety of a biological system, such as a living cancer cell, rather than just identify its individual functional components. The current reductionist approach has collected vast amounts of information on the individual, isolatable components so that now may be the time to attempt to integrate this information into complex, interacting systems. The systems background of this book’s author’s has emphasized the key role of time when taking a systems view, so he would not encourage too much reliance on the hopes for automated, mathematical techniques (called “bioinformatics”) as mathematics has only been successful when time is ignored. The short-term goal of totally curing many kinds of deadly tumors may well be quite unreachable, so a better short-term goal may be just to reduce cancer to a chronic but bearable disease for most patients.

8.2.4 A Frankenstein? When conducting research at the very foundations of life, there is always the risk that the discovery of a ‘cure’ may be worse than the disease. Understanding the atomic nucleus brought us vast amounts of low cost electrical energy but it also unleashed the threat of worldwide nuclear war. For example, understanding the deepest processes of the cell might well lead to a cure for cancer but it might also provide techniques for offering immortality that only the rich in society could afford, with radical consequences.

72

APPENDIX A. GLOSSARY Angiogenesis: Apoptosis: Carcinogen: Chromosome: Cytotoxic: DNA: Enzyme: Gene: Genome: Kinase: Metastasis: Mitosis: Mutation: Oncogene: Protein: Proto-Oncogene: RNA: Tumor: Tumor-Suppressor:

The process of generating new blood vessels, especially to a tumor (§4.2.6) The programmed process of cell death by biochemical interactions (§3.3.5) Any cancer-causing agent (§5.1.2) The sub-structure within the cell nucleus storing a part of the DNA (§2.6.2.2.2) A substance (usually chemotherapy) that kills cells (§5.4). Deoxyribonucleic acid, the giant molecule carrying genetic information (§2.6.2.2.1.2) A protein that accelerates a biochemical reaction (§2.5.3.4) The unit of genetic inheritance – a section of DNA coding for a protein (§3.2.3) The total set of all genes in an organism, found in almost all cells (§3.2.5). An enzyme that attaches phosphate groups to other proteins (§3.3.4.8). The process of creating secondary, remote tumors (§4.2.5) The normal process of duplicating a cell by division (§3.3.4.2) A permanent alteration in the chemical structure of DNA (§4.1.1.4) A cancer causing gene, after it is mutated (§4.1.3.4) A molecular chain of amino acids – made in a cell when a gene is expressed (§2.5.3.3) A normal gene that is converted by mutation into an oncogene (§4.3.2) Ribonucleic acid molecule that acts on a gene to make a protein (§2.6.2.2.1.1). An abnormal mass of tissue due to excessive cell growth (§4.2). A gene that when mutates no longer stops the cell division process (§4.3.5).

73

APPENDIX B. BIBLIOGRAPHY [1] “The Emperor of All Maladies”, Siddhartha Mukherjee, Scribner, (2010) [2] “P53: the gene that cracked the cancer code”, Sue Armstrong, Sigma Books, (2014) [3] “One Renegade Cell”, Robert A. Weinberg, Basic Books, (1st Ed. 1999) [4] “Next Generation Sequencing”, Lee Jun C. Wong (ed), Springer, (2013) [5] “Molecular Biology of the Cell”, Bruce Alberts et al, Garland Science, (5th Ed. 2008) [6] “Molecular Biology of the Gene”, James Watson et al, Benj. Cummings, (7th Ed. 2013) [7] “Molecular Cell Biology”, Harvey Lodish et al, W.H. Freeman, (7th Ed. 2012) [8] “Molecular Biology: Principles of Genome Function”, Nancy Craig et al, Oxford Univ. Press, [9] “The Biology of Cancer”, Robert A. Weinberg, Garland Science, (2nd Ed. 2013) [10] “Living Systems”, James G. Miller, McGraw-Hill Books (NY), 1978 [11] “Aristotle: A Very Short Introduction”, Jonathan Barnes, Oxford Univ. Press, (1982) [12] “Gut”, Giulia Enders, Greystone Books, (2015) [13] “What is Life?”, Erwin Schrödinger, Cambridge University Press, (1943) [14] “The Truth About the Drug Companies: How they deceive us”, Marcia Angell, Random House, (2004) [15] “AntiCancer: A new way of life”, David Servan-Schreiber, Viking, (2009) [16] “The Machinery of Life”, David S. Goodsell, Springer, (2010) [17] “Introduction to Cellular & Molecular Biology of Cancer”, M. A. Knowles & P. J. Selby, OUP (4th ed 2005) [18] “Cancer: Basic Science and Clinical Aspects”, C. A. Almeida & S. A. Barry, Wiley-Blackwell (2010) [19] “Introduction to Cancer Biology”, Robin Hesketh, Cambridge University Press (2013)

74