Bio101 Ecology and Evolution

Vivid Cave drawing like animations, generated by Jianfei with the aid of AI Tool StableFusion.

Hi students, always be curious about the things around you. Why not start this first with the course name, "Bio101L: Ecology and Evolution"? 

Have you ever wondered why we put these two subjects, "Ecology" and "Evolution", together into a single course? 

Have you ever considered why this combined course "Ecology and Evolution" is introduced in your freshman/sophomore year in college, instead of during your junior/senior year?

Please keep these questions in mind while you read along, and I'll shared my thoughts on these two questions at the end of this page.

To answer these questions, let's start with how the concept of ECOLOGY was developed and changed over time...

Imagine a world that was untouched by technology, where every rustle in the grass could signify danger, and every changing season brought new challenges. In this harsh environment, there was a small tribe of cave men and women found their home. They just set their foot on this new vast yet uncharted continent after their long march from Africa. 

To these ancient souls, upon their stepping on the new soil, every sunrise brought forth not just a new day, but a renewed test of their mettle, a battle with the nature, also a delicate dance with the new environment. The seasons were constantly changing, not only the temperature and the rainfall, so were all their surroundings. The migration of animals, the flowering of plants, even the flow of the rivers and creeks, all were puzzle pieces that these early humans had to start to understand. So, they watched, learned, and adapted. In the cave, the wise elders of the tribe, they decided to find a way to record this sacred knowledge, in which we must celebrate the newborn of ECOLOGY :) With pigments made from earth and charcoal, the wise began to paint on the walls. Just like the three pictures (see above) that I used the AI tool to make. Each stroke was a symbol, each image was a lesson, each painting is a hope. Gradually, the cave became a living textbook, also a guide to survival. 

Every night the younger generation of cavemen and women would gather around the flickering firelight, eyes wide with wonder, as the elder cavemen/women told stories of the previous great hunt, the changing seasons, the dance of life and death, and their hope for the next hunt and its captures. The paintings on the cave were more than art. They were the collective wisdom of the tribe, a visual encyclopedia of their ECOLOGICAL understanding of how to adapt to the environment. They started to know when the Bisons would pass through their valley, when the berries would ripen, and where to find shelter when the winter storms came. Decades and centuries passed by, as the tribe's descendants continued to learn from the cave's teachings and added new generalizations. The tribe thrived because they strived to be in tune with their environment. They respected the delicate balance of nature and knew that their survival depended on such expanding knowledge.

Their brains expanded, thoughts sharpened, and hands mastered the art of intricate tasks. The thriving tribe soon branched out, exploring and conquering various terrains, with the lessons learned from the cave walls. As they settled, they wisely handpicked plants that thrived in their new homes, be it teosinte, sorghum, millets, wheat, rice, cassava, etc. Fast forward a few centuries, there came the mighty Greeks, ingenious Romans and wise Chinese, they observed, wondered, and realized the deep relationships between living beings and their environments. Socrates, and his student Plato, and Plato's student Aristotle, the trio of ancient intellectuals debated under the olive trees, wandered around, trying to figure out why certain plant species only grew well in certain places. Leap forward to the Renaissance, then came the Leonardo da Vinci, with his vivid imaginations and artistic strokes, depicting explorers globe-trotting and finding strange, exotic flora and fauna. This global show-and-tell demands order, some serious organizing. That's where Carl Linnaeus came in. His classification system finally outcompeted its peers and he is the brain behind the species classification system, like a librarian who organized nature's vast library. Time flashed again, came Charles R. Darwin who took a boat trip around the world, from the jungles of Brazil to the Galagapos Islands, and Alfred R. Wallace, who trekked through Amazon and Malay Archipelago, together developed the hottest science theory of the 19th century: natural selection, the nature's version of talent hunt, where only the best-adapted species become celebrities. This concept they developed were greatly inspired by Thomas Malthus's book, "An Essay on the Principle of Population". In it, this English economist posited that populations expand more rapidly than their essential resources, invariably resulting in rivalry. Therefore, nature crowns the fittest with survival. This was exactly the concept as ancient as the tribes, adapt and thrive. Only the tribes that could adapt to their environment would finally grow and prosper. Wallace further recognized the intricate web of life in various ecosystems. Jean-Baptiste Lamarck also proposed his view of evolution, posits that characteristics acquired or lost during an organism's lifetime can be passed on to its offspring. While the Lamarckism was not primarily supported by current evidence, his merits relied on his recognition of the dynamic nature of life and re-emerged with epigenetic inheritance nowadays. Remember how we use the 3D printed DNA Double Helix set to demonstrate the epigenetic modification to the bases? Remember the Methyl group addition?

The turn of the 20th century marked a significant advancement in the field of Ecology, becoming more than just a qualitative discipline, but embracing systematic and quantitative approaches to understand the Earth's systems and processes. Sergei Winogradsky, a Russian microbiologist, and Martinus Beijerinck from the Netherlands are considered the towering figures in environmental microbiology. Their research together unraveled the mysteries of the microbial world. Winogradsky's work on the sulfur cycle led him to the discovery of chemosynthesis, where organisms can obtain energy without sunlight. He also isolated the first known nitrogen-fixing bacteria, highlighting microbes' crucial role in soil fertility. Beijerinck, on the other hand, made revolutionary findings in the study of nitrogen-fixing organisms and was the pioneer in the enrichment culture technique, a method used to isolate microbes in their natural environment.

While Winogradsky and Beijerinck dived deep into the microscopic, the understanding of broader ecological systems had its foundations in the 18th century. Joseph Priestley, an English polymath, and Antoine Lavoisier, the French "Father of Modern Chemistry", were instrumental in identifying the process of photosynthesis. They recognized plants' pivotal role in consuming carbon dioxide and producing oxygen, hence laying the groundwork for the study of carbon fixation.

Building upon their findings, Jean-Baptiste Boussingault, a 19th-century French agricultural chemist, was one of the first to quantify the carbon exchange between plants and the atmosphere, highlighting the importance of plants in the carbon cycle. Then, in the latter half of the 20th century, Charles D. Keeling further amplified our understanding by developing precise methods to measure atmospheric carbon dioxide. His meticulous observations, known as the Keeling Curve, showcased the rise of CO2 in the atmosphere, bearing evidence to the increasing anthropogenic impact.

Our first Ecology session will take a deeper dive into the pivotal role of forests in the carbon cycle. Forests, being the planet's lungs, play an instrumental role in regulating atmospheric CO2, not just through photosynthesis, but also through intricate processes involving soil carbon storage, respiration, and decomposition. This deeper understanding of both the microscopic and macroscopic aspects of ecology has enabled humanity to appreciate the delicate balance of our environment and the critical role of various organisms in maintaining the Earth's health. People started to develop mathematical models to explain the environment, the "ecosystem", to whom Arthur Tansley provided pioneering conceptualization (see his 1935 paper). His revolutionary view was that sunlight, soil, microorganisms, plants, and animals - all became inherent parts of a beautiful, interconnected dance. His 1935 "ecosystem" paper laid the groundwork for almost all subsequent ecological research. The novel "Silent Spring" by Rachel Carson marked the Green Movement that signals the awakening of global environmental consciousness and a pivotal call to action against the unchecked use of synthetic chemicals, propelling society towards a more sustainable future. 

Skyscrapers rose, cities expanded, the realities of Climate Change turned Ecologists to use everything, from ice cores in Antarctica to sediment in lake beds, to piece together Earth's climatic past in order to predict its future. As we stand here today, in a world vastly different yet inherently connected to the above-mentioned ancient time, the stories and lessons from the cave still resonate. Just like the cavemen, our ancestors, we must carefully observe our ever-changing environment. 

The studies of Ecology are gradually changing to a gene centric perspective. When I was a graduate student, I came across a book with the title "The Selfish Gene"

As a young generation transcended from the cavemen and women, we have our responsibilities not only to pass the knowledge to the next, but also to observe the changing environment now and take actions to ensure human continuous survival on this lonely blue planet. We must observe, learn, adapt and find our place within the ECOSYSTEM that sustains us. The cave paintings are vivid reminders that our survival, our very existence, is intertwined with the world around us. They are a call to look beyond ourselves and keep a keen eye on the intricate web of life that we are all part of.

Just as our ancestors adapted and changed, so did the plants and animals that co-exist with us. As the cavemen observed, evidenced by the fossils, some species, once vibrant and numerous, find themselves unable to keep up with the ever-changing dance. Whether through shifts in climate, the arrival of new competitors, or the loss of vital resources, they slowly fade away. At the same time, new species emerge, each one is a testament to the incredible power of adaptation and survival. Here, EVOLUTION is not just a concept; it is a living, dynamic breathing process. 

In ancient Greek, Philosophers, like Anaximander and Empedocles, have already proposed that the idea of life changing into complex forms with simple origins. However, the idea of species fixity taught by religious teachings suppressed in the Middle Ages. It was the vast arrays of previously unknown plants, animals and cultures triggered the idea of life being far more diverse than previously taught. The indefinite changes powered by genetic variations promoted plants and animals more fitted with changing traits into the ever-changing environment. 

In our class, we will routinely refer to the term, "Genetic Variation". In Campbell Biology (12th edition), it is defined as "Differences among individuals in the composition of their genes or other DNA sequences". It refers to the differences in the genetic makeup among individuals within a population or between populations. It is the Genetic Variation that provides the raw material upon which natural selection can act. Ronald A. Fisher further proposed that even small genetic variations within a population could result in evolutionary changes and the rate of increase in the mean fitness of any organisms is equal to its genetic variance in fitness. Together with John Haldane and Sewall Wright, they proposed population genetics, which serves a major step towards modern synthesis theory combining both genetics and evolution. Over generations, some plants grow taller, seeking the sun's nourishing rays; while some insects evolve intricate patterns to blend into the foliage, hiding from watchful predators. A finch bird with a beak perfectly shaped to reach nectar deep within a flower, a fish that can survive in the harshest salt flats, and a tree that grows in the arid dissert - each one is a marvel of EVOLUTION, a product of the never-ending dance with their environment. 

Gradually the evolution studies changed to a Gene-Centric perspective. It was started with Gregor Mendel, the father of genetics, whose work on pea traits inheritance patterns laid the foundation or the field of genetics. We have mentioned the following three scientists in the previous paragraph. Ronald A. Fisher emphasized the importance of continuous variation (as opposed to discrete Mendelian traits) in evolutionary processes. John Haldane's work, A Mathematical Theory of Natural and Artificial Selection, linked Mendelian genetics to the evolutionary theory. Sewall Wright further introduced the ideas of Genetic Drift (Random fluctuation in allele frequencies within a population due to change events) and Adaptive Landscape (visualization of fitness values for various genetic combinations in evolution). Additionally, Theodosius Dobzhansky's work directly pointed out the critical roles of genetic variation and its essence for the adaptability of populations (I encourage you to read his 1937 book, Genetics and the Origin of Species, link 2). The title of his book already suggested the linkage of Genetics with Evolution. In this book, Dobzhansky introduced the theory of how genetic mutations feeding into natural selection and speciation and how evolution as a whole process changes the diversity of all living organisms on earth in a genetic content.

Then it comes my favorite part. The seminal work later laid by Peter Grant and Rosemary Grant proposed groundbreaking insights into the speed of evolutionary changes in response to environmental changes (Link). Contrary to the traditional belief that evolutionary changes happen over long periods, they have conducted decades-long field studies to suggest a rapid speed in the speciation event, especially how the hybridization between different species of finches resulted in a speciation event within just a matter of years. 

Now you may get an idea that Ecology shapes fitness in response to evolving environmental conditions; and in doing so, it drives the Evolutionary process over vast stretches of time. At the same time, Evolution provides the genetic and phenotypic changes that drive the structure, function, and dynamics of ecosystems. Therefore, Ecology and Evolution are tightly interconnected with each other. This is the main reason that we integrate these two subjects into a single cohesive course. 

In a nutshell, Evolution feeds into Ecology, Ecological pressures and interactions also drive evolutionary processes.

To give you a sense on how biologists study Evolution, I will list the following long-sought questions that the work of Peter Grant and Rosemary Grant actually aimed at answering: 

• Can Evolution be observed in Real-Time?

Evolution has been considered as a grand process that happened on vast timescales and it could not be observed directly in nature unless using fossils as evidences. The work done by the Grants spanned decades and demonstrated that evolutionary changes, driven by natural selection, can indeed be observed within human lifetimes (see this link). This dramatically shifted the perspectives on the pace at which evolution can occur under specific circumstances. 

• How does Natural Selection operate on Traits (Finch beak morphology here)?

The Grants used the traits of finches on the Galapagos Islands, specifically on Daphne Major island, as an isolated natural laboratory to delve deep into the intricacies of evolution in real time. Over several dacades, they meticulously documented changes in beak size and shape, directly linking these morphological shifts to environmental factors, such as varying rainfall patterns and food availability. Their seminal work showcased how swift and responsive natural selection can be, especially when species face significant ecological challenges with REAL examples.

• Is Hybridization (interbreeding between species) Evolutionarily Significant? *In my humble opinion, this is primarily why Mendel did his pea crossings at the VERY VERY VERY (yes, 3x very) beginning.

Hybridization, the interbreeding between species, has been observed historically over and over again. However, its significance in evolutionary biology and its role in speciation were less known. The Grants observed finch hybridization and the subsequent success of some hybrid lineages in Daphne Major island highlighted the potential evolutionary importance of such events. 

• How does Speciation Event occur in Nature?

Do you know that they actually witnessed the rise of new species through hybridization? Super cool, right? If time allows, I will tell this story in class. The role of geographic isolation in speciation is a central theme in evolutionary biology. The finches are distributed across different islands in Galapagos with occasional contact. They studied the hybridization, gene flow and reproductive isolation among different finch species to understand the complex processes that eventually lead to new species formation.

• Can Evolutionary Changes be Reversible?

An understanding of Evolution would help you to predict that the evolutionary changes in morphologic traits should be reversible upon selection pressures since genetic variation is un-directional. However, real world examples are lacking. Through their long-term studies, Grants were able to provide evidences to show that evolutionary changes are not always unidirectional. Depending on the changing selective pressures, populations can evolve in one direction and then reverse. They measured the beak size of finch populations, finding the size could increase in one generation due to specific selective pressures and then decrease in another when the previous selective pressures change.

I enjoyed reading their books and seminar research articles. You may find details in the Evolution section.

INTERESTING STORY! EVOLUTION in ACTION!

Let's get back to the Darwin's finches at the Galápagos Islands archipelago. Finches on these isolated islands have adapted to each of their unique environment. Known as "Adaptive Radiation", each species of finch can sing their unique songs and has evolved distinct beak shapes and sizes that are suited to their specific diets and the unique environments of the individual islands they inhabit. 

Do you know that despite its isolated islands, why the Galápagos Islands archipelago is a perfect place to study the evolution processes? Think about this, to observe evolution, in other words, is to observe fitness changes in the ecosystem in a grand time scale. However, you better prefer to observe the evolution within a lifetime, therefore, you need to be in an isolated ecosystem with a dramatic changing environment. This is exactly the Galápagos Islands archipelago. It has extreme climate, drastic changes from periods of severe drought to huge rain precipitation. Check the Big Bird story, a distinct species formed within just decades as a process of evolution by natural selection.

As the second part of BIO-101L, the EVOLUTION section, we must embrace the beauty of EVOLUTION, as we explore the intricate world of ECOLOGY. It is a story not just of survival but of innovation and transformation. It is a story that connects us all, a shared journey between both ECOLOGY and EVOLUTION that shaped every living thing on this lovely blue planet.

The cave paintings of our ancestors are a window into the past, but they are also a mirror reflecting our present and future. So let us begin this exciting journey, discovering how ECOLOGY and EVOLUTION dance together in this delicate ballet that has been performing for billions of years. (note: This is indeed a research subject wth the name Evolutionary Ecology.)