Lecture week 1 (8-22) - Notes unifying themes and hierarchy

Biol 114 Fall 2023

Week 1: 8/22

Unifying themes of Biology and the Biological Hierarchy,

1. Science

Science is the process of identifying patterns and asking questions that help us to best understand those patterns. More specifically, science is the process of disproving hypotheses (specific, testable, rejectable statements) in an effort to focus in on the true answer to a question. When several related phenomena are identified a much larger concept is described to explain them. This umbrella-like concept is what we call a theory. NOTE: in non-scientific terms, a theory is a statement that attempts to explain an event, and does not have much, or any, evidence to support it yet (sort of like a hypothesis). In science, a theory has a tremendous amount of evidence supporting the concept and patterns it describes. Theories are a way of bringing together multiple related, demonstrated hypotheses. Since scientific advancement is based on the assumptions of previous scientific discoveries, wide realms of scientific thought may be discarded by disproving a single hypothesis that supported one of the initial scientific assumptions.

No amount of experimentation can ever prove me right; a single experiment can prove me wrong.

– Albert Einstein

Such is the risk of scientific endeavors. However, because of this process, any hypothesis that has stood the test of time is likely one we can trust.

Theories (and most scientific concepts) generally consist of 2 parts: Pattern and Process. Pattern refers to the general observations of repetition one sees within a system (This is akin to the observation phase of the scientific method). Process, on the other hand, is the mechanism, or way in which the pattern occurs. Frequently, there may be several processes involved in an identified pattern. This may depend on how specifically the pattern is considered. Additionally, processes may be divided into proximate vs. ultimate processes or reasons. Proximate refers to that which occurs in the short-term (usually measured in fractions of lifetimes), where ultimate refers to a longer timeframe (e.g., most of a lifetime or more).

Example:

While walking through the woods, you notice that under- and mid-story trees (those with leaves below the uppermost canopy), tend to have larger leaves than upper-story trees do. You also notice that this sometimes occurs within a single tree. That is, lower leaves tend to be larger than leaves higher up. This is your pattern. What is the process? This question can be answered at many levels. You can think about it in terms of the physiology of the plant: what is the physiological mechanism involved in creating larger vs. smaller leaves (proximate)? Or you can ask it in a more ecological way: what environmental conditions exist that cause the tree to perform this pattern (proximate or ultimate, depending on timescale involved)? Also, underlying the whole system is an evolutionary question: what selective forces have caused this pattern and does this pattern increase the fitness (see below for definition) of the tree (ultimate)?

1. Unifying themes of Biology

There are two unifying (or underlying) themes in biology:

1. Cell Theory: All organisms are made of cells (a naturally occurring compartment bound by a thin, flexible plasma membrane, and contains chemicals in an aqueous solution that perform life functions), and all cells come from pre-existing cells. Implicit in this theory are two main ideas:
   1. Since many of the limitations that exist among cells exist among all cells, studying cell biology is roughly the same as studying life (Which is Biology!). Therefore, in many ways, understanding how an organism works is a function of understanding the structure and function of its cells. Obviously, this is an over-exaggeration (if it were literal, the only branch of Biology would be Cell Biology!). It is not the whole story (see Emergent Properties below.).
   2. Life is continuous. The 60 trillion cells that make up your body came from a single-celled, fertilized egg. That zygote came from the fusion of your parents’ gametes (sperm and egg), each of which came from a single-celled, fertilized egg, which came from their parents’ gametes, and so on.

One conclusion that can be drawn from Cell Theory, is that if you trace a cell’s lineage back far enough, you will conclude that all cells are descended from a common ancestral cell. Prior to the original description of Cell Theory, it was assumed that cells spontaneously generated. That is, cells come to being from certain conditions on their own.

1. Evolutionary Theory: All life, as we know it, is the product of evolutionary processes. Evolution is the heritable (i.e. genetic) change in a population over time. If certain heritable traits help individuals produce more offspring, then those traits become more common in the population over time. The primary mechanism of evolution is Natural Selection (which we will cover later).

Individuals live, give birth, and die, but their evolutionary success can only be seen over a time longer than their lifespan and by comparing their success with that of other members of the population.  Living a year and giving birth to three offspring is relatively successful if the average life span is 10 months with two offspring but relatively unsuccessful if the average is two years with six offspring.  In the first case, the individual is favored by evolution, but the same individual is not favored in the second scenario.  Evolution is a property of populations.

There are two general ideas within evolutionary theory:

1. Evolution explains variation, how that variation came about, and what can happen if environmental conditions change.
2. All species are related to each other through common ancestry. Natural Selection acts on individuals, but evolutionary change affects only populations.
3. The Biological Hierarchy

The biological hierarchy is a framework of organization regarding all life around us. It provides us with a simple way of guaranteeing we are talking about the same terms as we consider life across varying scales. This hierarchy may seem simplistic and out of place in a college Biology course. However, it has been my experience that when talking to students about biological concepts, the students frequently jump between levels of the hierarchy without meaning to and, as a result, speak incorrectly about their topic. For example, I frequently hear students referring to the “evolution of an individual”, when this is incorrect. Evolution is a process that happens at the population level, not at the individual or organismal level.

The Biological Hierarchy levels consist of: atoms, molecules, organelles, cells, tissues, organs and organ systems, organisms, populations, communities, ecosystems, and the biosphere. We will not be covering much information on the atoms, molecules, organelles, cells, tissues, and organ systems. These are more the realm of Biol 113. We will, however, cover the remaining levels throughout the course (with occasional dips into the former levels).

1. Organisms: Our course is primarily concerned with this level of the hierarchy on up.
   1. Organisms are individuals. They are typically a collection of organ systems. However, remember that organisms can be single-celled.
   2. Individuals are acted on by nat. sel.
   3. The organismal approach to studying biology is primarily concerned with how the organism behaves, its place in its population, community, etc and how it survives as a result of its behaviors and physiology.
2. Populations are collections of individuals of the same species. Typically interbreeding.
   1. Evolutionary change affects the population.
   2. Population biologists are concerned with population growth and evolutionary processes and other changes through time.
3. Communities are a collection of populations of different species living together in the same area.
   1. Boundaries may be set up by natural structure (eg mountains, islands, etc) or arbitrarily determined by us.
   2. Community biologists are concerned with diversity of species and relationships each species has with other species.
4. Ecosystems are communities plus their abiotic factors (water, temperature, geology, sunlight, etc.).
   1. Although ecosystems are communities plus abiotic factors, we frequently refer to ecosystems as much larger agents than communities (e.g., the Sonoran Desert ecosystem). Additionally, for many people, ecosystems are the same as biomes. However, generally, biome refers to a collection of very similar ecosystems, largely bounded by global influences like weather and climate (e.g., Tropical Rainforest Biome). So be careful that you know to which scale you are referring when talking about such things.
   2. Ecosystem biologists are concerned with, among other things, energy flow and matter cycling
5. The Biosphere is all the ecosystems (biomes) put together.
   1. All that gets in is sunlight. All that leaves is heat energy. Everything else stays here - for good or bad.
   2. Biosphere scientists are concerned with climate and climate change and other global issues.

Notes About the hierarchy:

• There is similarity between individuals within each level, with respect to structural and functional complexity (even if they have different functions).
• Units of each level define the next level. Typically the units of one level come together to create the next level (eg. Several organ systems come together to make an organism several organisms come together to make a population, etc.).
• A good question to ask at this point is: why organize the field of Biology in such a manner? Why not just study how individual plants and animals react to different factors and add up these responses in some fashion to predict what to expect from nature? The answer lies in the concept of emergent properties. Emergent property: The collection of the units at one level takes on a trait that is greater than the sum of the parts. This property is defined as (or helps to define) the next higher level in the hierarchy. Emergent properties are what provided the next higher level in the hierarchy an evolutionary advantage. We’ll see this again later when we cover general evolutionary trends.

To understand this, you have to have a clear idea of what the hierarchy is. The hierarchy is a means of grouping units of something (individual animals, say) into nested levels of groups. Thus, in an organism, atoms are grouped into kinds of molecules, which are grouped into different kinds of organelles, which are grouped into different kinds of cells, which are grouped into different kinds of tissues, etc. This grouping is not just for convenience but is a real grouping (i.e. it exists in nature). The biological hierarchy is real also, and we study it as such because some phenomena are only observable by studying a whole level of organization in the hierarchy.  The set of phenomena that can be explained only by looking at an entire hierarchical level are the emergent properties of that level.  We study populations, because one may not be able to understand why a species is rare just by looking at how many offspring an organisms can produce. The same reasoning leads us to consider community ecology as a separate subdiscipline, as it may be impossible to understand the change in one population without understanding its interactions with other species.

So, we have a hierarchy of biological subdisciplines because nature is hierarchical and there are phenomena that are understood only when one studies the appropriate level within the hierarchy.

Finally, having argued for separate subdisciplines, I want to caution you about considering them as independent of one another. All belong to the same hierarchy. As a result, changes in one of the levels, frequently brings about a change in the other levels as well.

• More examples of emergent properties: Organ systems by themselves cannot reproduce themselves (not even a reproductive system), but an organism can. Therefore, you would describe reproduction as an emergent property of the organismal level. (You might be able to argue that it’s really an emergent property of the population level for sexually reproducing species. Can you explain why?) Individuals do not have the emergent benefits of a social group (e.g. Safety in numbers, food sharing, etc.), but they do when you put them in a group. Evolution is the big emergent property of populations. Individuals do not evolve. Populations do. But natural selection acts on the individual.