Perspectives on Living Systems Student Module 1 PDF

Module 1 PERSPECTIVES ON LIVING SYSTEMS Marie-Sol O. Hidalgo 1.1. INTRODUCTION Welcome to SCIENCE 11, Living Systems: Concepts and Dynamics. This semester, we shall embark on a journey that will give us a glimpse of...

Module 1 PERSPECTIVES ON LIVING SYSTEMS Marie-Sol O. Hidalgo 1.1. INTRODUCTION Welcome to SCIENCE 11, Living Systems: Concepts and Dynamics. This semester, we shall embark on a journey that will give us a glimpse of the intriguing concept that is Life. This course will take us from the energy and matter from our environment and how they become part of the molecules that make up our smallest cells. We shall study how cells organize into tissues, organs, and organisms. We shall then look at how organisms relate to each other as populations and ecosystems, and how all of these affect us, human society, and how human society affects these in turn. We offer this course to introduce you to the world of Living Systems seen from the eyes of a Biologist, and to give you insights on how you can take your place in living mindfully and meaningfully, aware of the effects and ramifications of the choices that you make in school, in your chosen profession, and in everyday life. Science 11 may look a lot like your high school Biology class, and to a certain extent, it is. We will be reviewing a lot of what you have studied in High School, but with a new twist: we will look at them from a complex systems perspective. As you will see later, this perspective is both as old as antiquity and as new as cutting-edge Science of the 21st Century. 1.2. LEARNING OUTCOMES At the end of this module, you would have: 1. explored biocultural expressions of knowledge on living systems (1.3) 2. gained an appreciation of the changing paradigms about living systems from antiquity to the Renaissance (1.4); 3. reviewed the content of High School Biology in the context of the History of Biology (1.5); and 4. gained a substantive introduction to SCIENCE 11. 1.3. LIVING SYSTEMS IN ORAL TRADITIONS In your High School science classes, you have studied Biology concepts and principles that operate within the physicality and materiality of living systems. However, our appreciation of living systems has not always been thus. Indeed, Biology reflects our efforts to answer questions we humans have asked since time immemorial, and how we figured out means of answering them, and the answers we have given. Questions such as: where have we come from? what is our relationship to the world around us? Answers to these questions guide how we perceive ourselves and our place in the world, and how we should act in accordance to the order that we see in our environment. Let us go back to the age when learning something new entailed more than opening a book or connecting to the Internet. When there were no books, in fact, there was no written word. Let us go back to the tribes of our ancestors, to times long, long ago, and ask: How did our ancestors understand Living Systems during their time? And how do we know them now? From the dawn of humanity, we humans have been dependent on our immediate environment for all our needs: for water, food, shelter, and clothing. An intimate knowledge of our environment, gained through systematic observations, was a matter of life and death for an individual and the tribe. It is equally important to share and pass on this knowledge to the next generation. With the absence of writing, this knowledge was transmitted orally, through telling of stories, chanting and music, and the creation of visual arts. It is also transmitted experientially, through direct teaching of the younger generations in hunting and gathering expeditions, and by experiencing living systems both physically and metaphorically in nature walks, rituals, and dream journeys. Elders are esteemed for their knowledge, and the knowledgeable among them are required to perform special roles. The Storyteller, with the ability to tell stories in a memorable, engaging way, performs an important teaching function in the life of a tribe; for stories, myths, and legends are how experiences of the tribe, especially of catastrophic events, are recorded and stored. The Hunter, whose knowledge of wildlife, capacity to read the slightest of signs, and the capability to create tools and weapons, teach the knowledge of the environment without words; the same holds true for the Gatherer, who has knowledge of fruits, animals, and herbs and their uses; and the Farmer, who has knowledge of the seasons and the signs of the wind and sky. All have a role to play in the creation, recording, and teaching of knowledge for the survival of the group. In these myths, legends, folklore, art, and in all their activities, the tribe communicates their holistic appreciation of their place in the living system: “The natural world - the land, plants, animals, seasons and cycles of nature - has been a central tenet of their lives and worldviews since the dawn of time. Their understanding of the natural world is sophisticated and comprehensive… (It) is not viewed as a separate entity but one, interconnected aspect of the whole. This interconnectedness equates to a moral responsibility to care for, live in harmony with, and respect the natural world” (Joseph, 2016). 1.3.1. Indigenous Knowledge, Systems, and Practices Myths and legends and folklore are a part of what we call Indigenous Knowledge Systems and Practices (IKSP). These are traditional knowledge passed on through traditional means for many generations. A product of careful and methodologically sound observations of the natural world, IKSPs have been tested and re-tested for thousands of years in the most rigorous real-life laboratories for survival and well-being. This knowledge affects not only their forms of art and oral literature but includes all aspects of life: from knowledge of geography and climate that allow them to “read” signs from nature—the wind, animal behavior, and the appearance of indicator plants’ leaves and flowers—to predict future environmental conditions as accurately as any barometer or weather gauge. This has allowed them to create many inventions and technologies that relate to domestication of food, storage, and preparation; herbal-based medicines; forms of clothing and transportation; astronomy; sustainable  agricultural and industrial practices, etc. The intimate knowledge of the interplay among elements in the local living systems give rise to many applications which have been validated by indigenous knowledge systems as well as modern scientific methods. This knowledge is called biocultural knowledge: knowledge that is rooted both in the natural environment and what is readily available, at the same time grounded on the culture—values and norms—of the people who hold it. 1.4. LIVING SYSTEMS FROM ANTIQUITY TO THE RENNAISSANCE It was not only in indigenous cultural communities that subscribed to the holistic worldview. The earliest material evidence in civilizations that used the written word showed that societies kept track of their livestock and grains, made bread, wine, and cheese, and recorded astronomical data to keep time and predict the weather. However, the need for myths and legends were still strong, as heavenly bodies were still attributed to gods. The human connection to the gods – the Priestly Class – were the sole interpreters of the gods’ desires, such that, they had exclusive access to the stored knowledge, and they were the only ones authorized to interpret them. Thus, knowledge was in the hands of the priests, and they controlled much political power, including the surplus production. What is noteworthy is the invention of the written word and its relationship to knowledge production, transmission, and storage. Whereas in oral cultures, the Storyteller was the keeper of knowledge, in literate cultures, knowledge was stored and thus transmitted through the clay tablets of the Sumerians, the papyrus scrolls of the Egyptians, the bamboo, bone or wood of the early East Asians, the animal hide of the Mayans, the wax tablets of the Romans, the parchment that pervaded most of medieval Europe, and the paper that held the records of the Chinese empire and copies of the Qur’an. It follows that literacy allowed for the expansion of collective knowledge beyond the Storytellers’ collective memories, however well-developed those memories were. It allowed for the development of more complicated trains of logic, of more abstraction and thus analytical knowledge, reflection, and introspection, which were very difficult to keep track of in story, song, or art. 1.4.1. Sumerians and their Knowledge of Biology (4500 – 1750 BCE) The knowledge held by the Sumerians was kept in clay tablets written in cuneiform. The Sumerians were faithful in their recording of the medical lore of their time, particularly in the treatment of disease, the use of herbs and animal material as materia medica, dentistry, endocrinology, histology, health, and sanitation, among many other subjects. The Sumerian belief system encompassed both empirical and the magical, for example, in the treatment of disease. Some diseases were attributed to demon possession, and it was believed that the sacrifice of animals would cure this possession through the transmission of the demon from the afflicted person to the lamb as a sign of compassion to the family. Historians of Science argue that these early attempts at explaining causes can be considered scientific, to wit: “While this may seem laughable in light of today’s learning, the  “demon” idea really was scientifically sound – in this sense: In the absence of a scientific canon, all ancient civilizations sought to fathom the workings of the universe in some other manner. Very often, they attributed commonplace events to demons, witches, and so forth… They were speculating in a theoretical manner, and the demon supposition was at least an attempt to explain the transmission of illness” (Serafini, 2013). 1.4.2. Greek Philosophers and their Theories (800 – 300 BCE) The History of Biology usually traces the beginnings of abstract scientific thought to the Greek Philosophers. The written transcripts of the lectures of these learned men being transmitted through the years by translators and scribes from the Roman times, then transmitted by the Islamic translators and scribes, and the Christian monks and learned men. The reasons for expanding this effort through the centuries is clear: the legacy of Greek philosophical inquiry resonated with the most important questions of human existence: What is Man? What is the world? These men of learning were not connected to the priesthood but rather affianced to the political powers of the time. The Greek philosophers were noted for the treatises that eloquently explain not only their observations, hypotheses, and conclusions about the world and Man’s place in it, their works also show in detail the methods by which they obtained these insights. There has, therefore, been an exposition of their ontology and epistemology, something that has been similarly present in ancient and indigenous (oral) knowledge but not described in an abstracted and detailed manner. In the Box below, we read about Aristotle and his lectures about his research in various topics in living systems. We find that his curiosity about the natural world, and his methods of studying them, still hold true to this day, even though his theories do not. 1.4 BOX: Aristotle The most influential Greek thinker was born at the end the Greek era. Aristotle (324-322 BC), a student of Plato, and the teacher of Alexander the Great, was a philosopher whose works have been the backbone of philosophical studies from this era until the European Renaissance. He may be said to be the first biologist in the Western tradition, and a significant portion of his work devoted to the study of living systems. In the study of living systems, he explained the distinction between the specialist -- one who has a considerable body of experience in practical fieldwork – and the generalist -- one who knows many different areas of study, when he wrote: In all study and investigation, be it exalted or mundane, there appear to be two types of proficiency: one is that of exact, scientific knowledge while the other is a generalist’s understanding. Indeed, Aristotle practiced both specialist and generalist modes of study, and has clearly and eloquently outlined his reasoning in his lectures. He is credited for expounding on levels of organization (“the more and the less”), systematics or the relationship of species of plants and animals, reproduction, and embryology, among many others. He was a very avid observer of life, particularly of fishes. Based on his close study of animals, Aristotle defined a species: a breeding group of particular animals or plants that can breed and produce offspring that eventually could reproduce. He then concluded that species  were fixed, immutable, and that they have always existed. Later Christian philosophers tried to integrate Genesis with Aristotle. They typically viewed each species as created by God in the beginning, in a hierarchical fashion from the inanimate, animate, to the spiritual beings as a “Great Chain of Being”. Reference: Boylan, n.d. Aristotle: Biology. In Internet Encyclopedia of Philosophy. https://www.iep.utm.edu/aris-bio/ Shields, Christopher, "Aristotle", The Stanford Encyclopedia of Philosophy (Winter 2016 Edition), Edward N. Zalta (ed.),. The methods used by these philosophers are similar to that used ancients and indigenous people in that they use their experience, meditation, and learned intuition in trying to understand what they believe is the nature of things. Thus said, there is little actual experimentation other than what is done while healing and surgery. These studies in natural sciences were much utilized in practical ventures such as medicine, astronomy, and engineering. 1.4.3. Medieval Europe and the Golden Age of the Islamic Civilization Medieval European society is commonly characterized as feudal and hierarchical. In those agrarian societies where surplus was few, most of the population was concerned in the production of food and of goods that were used in the local communities. The business of seeking and using knowledge was relegated to a select few who knew how to read and write. Thus, knowledge and its interpretation were prescribed by a ruling class; the Monarchies and the Church were very powerful. In early Medieval Europe, the monastic schools were important in terms of education, governance, and practical applications of astronomy and medicine. The Church had great reach in terms of territory and ideological influence. It was the sole interpreter of the Holy Texts, and the arbiter of the appropriate knowledge and use of knowledge, as it was responsible for its flock not only in this life but also the next. Thus, individuals, philosophies, and discoveries had to pass through the censure of the Church. That which did not conform to the erstwhile view of Truth were regarded as heresy, and those who tried to explain miracles and other matters of faith faced harsh punishment. However, outside of the Church’s purview are the practical arts; and thus, metallurgy, navigation, agriculture, and engineering continued to flourish following the collapse of the Roman Empire. The exposure of Europe to Near Eastern culture was inevitable, due first to trade via the Silk Road, then the Crusades, and then the colonial expansion. This contact led to the transmission of the combined knowledge from the Arabic, Byzantine, Persian and Indian cultural traditions from the Golden Age of the Islamic Civilization in the 12th century onwards. Thus, European scholars and scribes were exposed to very different ways that the history of the Earth, natural sciences, and philosophy were understood outside of the constraints of the Catholic Church.  “Students in the 12th century were eager for knowledge and sought it out with enthusiasm. They read the Latin classics, analyzed the texts of Roman law, they read and commented on the works of the Church Fathers. The most advanced scholars knew that the Muslims of Islamic civilization had great storehouses of knowledge, so they traveled to Spain to tap these new sources of information. Others went to Constantinople to obtain translations of Greek manuscripts. In the end, these scholars renewed western knowledge of Greek science and philosophy and to this added the treasures of Arabic mathematics and medicine” (Kreis, 2004). In many instances, Islamic scientists and mathematicians developed criticisms of Greek assertions, refined the theories of the classical philosophers to conform to current empirical information, significantly modified Aristotelian ideas, invented Algebra and Trigonometry as new fields of mathematics, and improved on Indian numeral system to include the zero, in what we now know as the Arabic number system (Whitney, 2004, p. 12). A resurgence of interest in gaining knowledge in Europe helped in advancing the creation of centers of learning outside the monasteries: the University. While not the first universities in the world, these early European institutions of learning were open to scholars, mainly male feudal lords those who can afford the high fees, but who are neither clerics nor monks. This level of democratization of education came with a challenge: throughout Europe, traditional authority was questioned, and the new scholars embraced the notion that humanity could be improved not only through prayer and good works, but through rational change. 1.4.4. The European Enlightenment: The hypothetico-deductive method and democratizing knowledge Aristotelian thought was the dominant view for a millennium in the West. Aristotle’s “Great Chain of Being”, as a classification system, was the major organizing principle and foundation of the emerging science of biology until the 18th century. Even with the many different theories available in the 16th – 17th century, only the Aristotelian worldview was taught in all the leading universities of the time. However, this changed in mid- 17th century, when the arguments of Descartes proved to be most convincing in the European continent. Cartesian metaphysics, the mechanistic worldview, the duality between matter and mind, and the Cartesian hypothetico-deductive methodology became accepted by the community of scholars at the time. It may sound surprising to many modern-day scientists that the beginnings of the current agnostic, materialistic epistemology in science was a train of reasoning deeply grounded in seemingly disparate threads of methodological skepticism and an inherent assumption of the existence of God. The zeitgeist of the era being one of change and progress, the long th 18 century brought about a spate of different, divergent, and conflicting theories on the origins and purposes of living systems. Questions on the age of the earth, a subject broached by the exposure to non-Christian doctrine  as well as archeological discoveries, were debated. Evolution of living things were considered with the increasing tolerance for questioning long- established dogma and the discovery of fossils, as well as an openness to test theories by experimentation. The Experiments on the Generation of Insects, written by Francesco Redi in the late 17th century (who, at that time, was the court physician to the Grand Duke of Tuscany), served to disprove a once-held notion of spontaneous generation of living things. Much later, the theory on the Transmutation of Life was raised by Lamarck in the early 1800s. This theory argues for the evolution, the main argument being that species change as individuals relate to their environment. Thus, were new ideas more freely discussed, and hypotheses on phenomena and their underlying mechanisms were tested not only based on the train of logic and reasoning, but based on actual, physical experimentation. Advances in optics allowed for the visualization and discovery of microscopic entities and paving the way for the study of anatomy in greater detail. Moreover, advances in chemistry eventually allowed for analytical studies of phlogiston (thenceforth purified to what we know now as oxygen gas) and to look into what was once thought of as a metaphysical vital substance that animated living organisms, now conceptualized as proteins called enzymes. Slowly, and with much labor from scholars and philosophers of the time, the understanding of mechanisms of living systems—very much independent of the need for spiritual and magical causes—unfolded into the one we accept today. 1.5. LIVING SYSTEMS IN THE 19TH AND 20TH CENTURY 1.5.1. Reductionist Science and the growth of Biology The acceptance and eventual dominance of the hypothetico- deductive method as the Scientific Method, with its materialist, mechanistic, and reductionist philosophy which analyses a larger system by breaking it down into pieces and determining the connections between the parts. It became clear that the reductive study of organisms, alongside the development of specialized equipment, afforded more and more powerful means for analysis. The elegance of classical experiments of the time, with the method of controlling conditions to minimize variables, brings into focus the definitive relationships among two variables, highlighting a direct relationship between a given cause and a given effect. This capacity to put forward and test various new theories allowed for the growth of the field of Biology, and its benefits spread greatly through medicine, food, and agriculture, among others. It was through this methodology that Biology, not quite a field of study until the 18th century (for before, it was called natural history), branched into sub disciplines including Anatomy, Microbiology, Genetics, Taxonomy, Cell Biology, Embryology, Biochemistry, Physiology, and Molecular Biology. Following the development of chemistry, and the increase in analytical power of the X-ray crystallography, the chemical composition of cells became an object of study, a feat anticipated since the age of Alchemy. Thus, with increasing analytical power, the unit of analysis moved from organism to organ to tissue to cell, and even further within the cell, to its organelles, and later to the macromolecules and smaller molecules that have physiological effects. The increase in exposure of the Europeans to the knowledge and the vastly different environments of their colonies in the 16th to 17th centuries led to the increase in interest in collecting, cataloguing, and studying different kinds of organisms in the different kinds of environments. During this period, Darwin published his theory of evolution. In the 18th and 19th century, scientific expeditions were conducted by trained naturalists. Ecology was established by the late 19th century, and the concept of ecosystems emerged in the mid-20th century, fusing matter and energy flows into the study of ecology. This then became the basis of systems ecology, which began circa 1960s to 1970s. With the threats to the environment becoming evident in this period, within the scientific community and communicated to the public through books like Carson’s The Silent Spring (1962). The interdisciplinary field Environmental Science includes traditional science disciplines such as biology, ecology, geology, and chemistry and combines in issues such as environmental ethics and social issues. Thus, it is the gains of reductionist biology of the 20th century that forms the content and the context of most High School Biology courses. 1.5.2. Limits of mechanistic and reductionist paradigms In the two hundred years of Cartesian and thereafter Newtonian science, abstract and practical scientific knowledge has increased by leaps and bounds. The analytical power of the human senses has been extended by the creation of tools developed precisely to study various physical phenomena. Energy available to do work has also been increased beyond biological sources such as human and animal power, with the development of machines fueled by coal and then by petroleum, and then through electricity. The accumulation of knowledge and the culture of rational skepticism has allowed for scientific communities to abrogate models that are not backed by current state of data or have been disproved by experimentation. The Cartesian framework uses its analytical power and focus on how to control conditions to maximize gains, a useful tool for industrial and economic growth. Moreover, the exploration of many frontiers in knowledge were mainly utilitarian in objective and were not held back by issues of tradition, balance, ethics, or reciprocity. The Cartesian analytical framework has led to the use of industrial practices that were very efficient in bringing forth its desired outcomes. However, the singular focus on desired outcomes has led to many unforeseen consequences to the environment and to human societies. These severely lack safeguards that maintain balance and ensure the sustainability of the industry and the environment of which it is a part. For many advocates, it is this utilitarian view of Nature that has led to the environmental crises that we experience today. Indeed, they believe that the framework from which these problems arose cannot be the same framework that will give rise to solutions:  “Cartesian science believed that, in any complex system, the behaviour of the whole could be analysed in terms of the properties of its parts. Systems science shows that living systems cannot be understood by analysis. The properties of the parts are not intrinsic properties but can be understood only within the context of a larger whole” (Capra, 1996). The study of Living Systems has grown in such a way that it now seeks to predict and mitigate the current environmental crisis that the human society seems to be moving towards. Reductionist science has given us the concepts and tools with which to analyze parts of the living system, but a new perspective and thus new tools are needed to make sense of the whole. 1.6. OVERVIEW OF SCIENCE 11 Our course is divided into four units. Unit 1 (Modules 2 through 7) discusses the Attributes and Properties of Living Systems, which looks a concept you have studied in High School but through a complex systems perspective. Unit 2 (Module 8) uses these concepts to frame a discussion on Biodiversity, issues, and challenges. Unit 3 takes on resource conservation and management (Module 9) as a way towards Sustaining Living Systems. Lastly, Unit 4 (Module 9) discusses issues and challenges on Health and Wellness through the concept of ecosystem services. 1.7. SUMMARY In this module, we discussed how Nature and the origins of Life were perceived by human communities over time: from indigenous and traditional ways of viewing nature to the analytically powerful western Enlightenment paradigms, to the complex systems perspective we have today. We started with myths and legends and how orality brings metaphorical and embodied forms of knowledge and transmission. With the creation of the written word, the compilation of knowledge changed not only in form but also in content: abstraction and longer philosophical reasoning could be reproduced with great fidelity over time and space. It is through written documents transmitted by ancient scribes and translators that we know of the great Greek Philosophers and their theories today. Over time, technology developed and greater reliance on mechanical means extending human senses to verify information were found, leading to changes in paradigms and ways by which humans perceive themselves with respect to Nature. Accelerated advances in understanding discrete processes of nature led to greater capacity to change the environment. However, the loss of balance and reciprocity with the (re)generative forces of nature led to the current environmental crises. Present day environmental consciousness in this historical context can be seen as a cyclical return from holistic to mechanistic paradigms and back again. Human communities will always endeavor to create and refine models for understanding the processes of nature, and it is the hope of this course that we can use our understanding to further increase not only our conceptual knowledge of how we fit in the cycles of living systems. We are then called on to recognize, respect, and care not only for our limited selves in our limited space/time, but for the whole of the living system of which we are a part. We need to consider our increased capacities to influence the environment, learn from the lessons of the past, and work towards our common future. 1.8. REFERENCES Arrows, F. Cajete, G. & Lee, J. (2010) Critical Neurophilosophy and Indigenous Wisdom. Sense Publishers. Capra, F. & Luisi, P. (2014). The Systems View of Life: A Unifying Vision. Cambridge: Cambridge University Press. doi:10.1017/CBO9780511895555, p. 1-16. Elise Huffer, E. and Rakuita, T. (2008) Land and people as the measure: A Pacific ethic of place and prudence. Asia Pacific Perspectives on Environmental Ethics, UNESCO Bangkok. Joseph, B. (2016). What Is The Relationship Between Indigenous Peoples And Animals. https://www.ictinc.ca/blog/what-is-the-relationship-between-indigenous-peoples-and- animals. King, DNT & James Goth, J. (2006). Māori environmental knowledge in natural hazards management and mitigation. NIWA, Aukland, NZ. Accessed from : https://niwa.co.nz/sites/niwa.co.nz/files/niwa_report_akl2006-055.pdf. Piccardi, L. & Masse, W.B. (2007). Myth and Geology Geological Society of London, 350 pages. Serafini, A. (2013) The Epic History of Biology. Springer, 395 pages. Shields, C. "Aristotle", The Stanford Encyclopedia of Philosophy (Winter 2016 Edition), Edward N. Zalta (ed.), Accessed from: https://plato.stanford.edu/entries/aristotle/. Sumingit, 2005, in: WIPO (2006). Protecting traditional knowledge and cultural expressions: The experience of indigenous peoples in the Philippines. http://www.wipo.int/edocs/mdocs/tk/en/wipo_grtkf_ic_9/wipo_grtkf_ic_9_inf_7_c.pdf). Tebtebba Foundation, 2010. Traditional management & enhancement of Carbon stocks. In: Indigenous Peoples, Forests & REDD Plus: State of Forests, Policy Environment & Ways Forward. (pp. 217- 221) https://www.tebtebba.org/index.php/resources-menu/publications- menu/books/96-state-of-forests-policy-environment-and-ways-forward/file. UN/ISDR Press release (2008) “Traditional knowledge can save lives when disaster strikes.” Bangkok, Thailand 19 September 2008. http://www.unisdr.org/files/5438_pr200809Indigeneousknowledge.pdf, accessed January 13, 2018. Whitney, E. 2004. Medieval Science and Technology. Greenwood Publishing Group, 258 pages.