1.1: Introduction to Molecular Biosciences

Biology

Biology is the scientific study of life. Studying biology is an opportunity to ask exciting questions about the world that surrounds us. It is an opportunity to probe humanity's deepest questions about our origins, our planet's history, and our connections to other living beings (big and small/extant(opens in new window) or extinct(opens in new window)). It is also an opportunity to dive into a world of problem solving and to think hard about solutions for improving health care, maintaining sustainable food supplies, and producing renewable energy technologies.

Studying biology also helps us to understand and solve everyday problems. For instance, understanding the biochemical reactions that transform your food into something useful for your body, how energy is stored within food items, and how this energy transfers from your food to your body, teaches you about how your diet and exercise influence your health. Understanding what the microbes which live in, on, and around us, do may help you decide whether to buy products labeled "antimicrobial" or "probiotic". Understanding the biochemical principles that explain what happens to eggs as they cook can help us understand how similar physical processes may be central to the cellular stress response and associated diseases. Understanding of the genetic and biochemical mechanisms that link genetic information to physical traits can help explain your eye color.

Studying biology even helps us understand things that are “out of this world”. For instance, understanding the requirements for life can help us look for life on Mars or deep in Earth’s crust. When we understand how to “rewire” cellular decision-making networks, we may gain the ability to regenerate functional limbs or organs from someone’s own tissue, or reprogram diseased tissues back to health. All of these examples represent a small fraction of the multitude that exist in the natural world. There are many exciting opportunities to explore. Mastering a few basic principles helps you understand and think more deeply about an array of topics. Keep this notion in mind throughout the course.

Biology: an interdisciplinary science

Questions in biology span size scales over ten orders of magnitude, from the atomic makeup and chemical behavior of individual molecules to planetary-scale systems of interacting ecologies. Whatever the scale of interest, to develop a deep and functional understanding of biology, we must first appreciate biological concepts. This involves integrating important ideas and tools from across the spectrum of science, including chemistry, physics, and mathematics. Biology is truly an interdisciplinary science.

The potential impacts that can come from studying biology are broad

Some people may think studying biology is only about medicine—however, it can lead to or influence many careers. Biology has applications that are both vast and wide-ranging. Applications include treating (human or other animal) patients, improving agricultural practices, developing new building materials, writing new energy policies, remedying global climate change, creating new works of art—the list goes on and on. For the curious, biology has plenty of unexplored mysteries.

As you study biology, appreciate its exciting questions and topics and be open-minded. Even though course topics may not always seem related at first, they likely are, in the end. Being open-minded helps you discover and appreciate the connections between the course’s topics and your interests. Discovering how seemingly different topics interrelate can give you a deeper appreciation for the things you enjoy and maybe even spark a new passion.

General Biology—from molecules to cells

This course focuses on the cell, one of the most fundamental units of life. Cells can be as simple as the disease-causing bacterium Mycoplasma genitalium, whose genome encodes just 525 genes (only 382 of which are essential for life), or as complex as a cell belonging to the multicellular plant Oryza sativa (rice), whose genome likely encodes ~51,000 genes. However, despite this diversity, all cells share fundamental properties. We explore basic problems that all cells must deal with. We study the building blocks of cells, some of their key biochemical properties, the encoding and expression of biological information in genetic material, and how all this combines to make a living system. We will also discuss ways in which living systems exchange matter, energy, and information with their environment (including other living things). We focus primarily on core principles common to all life on Earth, and because of biology's massive breadth, we put these ideas into a variety of contexts throughout the quarter.

Evolution and Natural Selection

Brief overview

Evolution and natural selection are core concepts in biology that are typically invoked to help explain the diversity of and relationships between life on Earth, both extant(opens in new window) and extinct(opens in new window).

The first idea you need to grasp is that evolution can be simply defined as the development/change of something over time. In the automotive industry, the shapes and features of cars can be said to evolve (change in time). In fashion, it can be said that style evolves. In biology, life and, in particular, reproducing populations of organisms with different traits evolve.

The second thing to understand is that natural selection is a process by which nature filters organisms in a population. What is the filter? Here it becomes a little more complicated (but only a little). The simplest explanation is that the selective filter is just a combination of all living and nonliving factors in an environment, which influence how successfully an organism can reproduce. The factors that influence the ability of an organism to reproduce are known as selective pressures. A small but important complication is that these factors are not the same everywhere; they change in time and by location. Thus, the selective pressures that create the filter are constantly changing (sometimes rapidly, sometimes slowly), and organisms in the same reproducing population could experience different pressures at different times and in different locations.

The theory of evolution by natural selection puts these two ideas together; it stipulates that change in biology happens over time and that the variation in a population is constantly subjected to selection based on how differences in traits influence reproduction. But what are these characteristics or traits? What traits/features/functions can be subject to selection? The short answer is: just about anything associated with an organism for which variation exists in a population and for which this variation leads to a differential likelihood of generating offspring will probably be subject to filtering by natural selection. We also call these traits heritable phenotypes. Organisms in a population that have phenotypes, which enable them to pass the selective filter more efficiently than others, are said to have a selective advantage and/or greater fitness.

It is important to reiterate that while the phenotypes carried by individual organisms may be subject to selection, the process of evolution by natural selection both requires and acts on phenotypic variation within populations. If neither variation nor populations in which that variation can reside exist, there is no opportunity or need for selection. Everything is and stays the same.

Common misconceptions and a course specific note

Finally, we draw your attention to a critical point and common misconception among beginning students in biology. This misconception can arise when, for the sake of discussion, we decide to anthropomorphize nature by giving it an intellect. For example, we may try to build an example for evolution by natural selection by proposing that a surplus of a particular food exists in an environment and there is an organism close by that is starving. It would be correct to reason that if the organism could eat that food, that this might give it a selective advantage over other organisms that cannot. If later we find examples of organisms that can eat that surplus food, it might be tempting to say that nature evolved this new phenotype to "solve the problem of utilizing the surplus food". The process of evolution by natural selection, however, happens randomly and without direction. That is, nature does NOT identify “problems” that are limiting fitness. Nature does NOT identify features that would make an organism more successful and then start creating diverse solutions that meet this need. The generation of variation is not guided. Variation happens and natural selection filters what works best. The observation that an organism exists that can eat the surplus food is not a reflection of nature actively solving a problem, but rather, a reflection of whatever processes that led to phenotypic variation in an ancestral population that created—among many other variants—a phenotype that increased fitness (possibly because the ancestral organisms were able to eat the surplus food).

This point of the preceding paragraph is particularly important to understand in the context of general biology at UC Davis because of the way we will be utilizing the Design Challenge to understand biology (more on this later in the reading). While the Design Challenge is intended to help focus our attention on functions under selection and their relationship to determining fitness, it can be easy—if we aren’t attentive—to lapse into language that would suggest that nature purposefully designs solutions to solve specific problems. Always remember that we are looking retrospectively at what nature has selected and that we are attempting to understand why a specific phenotype may have been selected over many other possibilities. In doing so, we will be inferring or hypothesizing to the best of our ability (which is sometimes wrong) a sensible reason to explain why a phenotype might have provided a selective advantage. We are NOT saying that the phenotype evolved TO provide a specific selective advantage. The distinction between these two ideas may be subtle, but it is critical!

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Possible NB Discussion Point

Examine the following statement: "Natural selection acts for the good of the species." Discuss what you think about this statement - perhaps invoking some of the reading above.

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