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Lecture 02: The Scientific Method, Design Challenge and The Basic Unit of Life: The Cell - Biology

Lecture 02:    The Scientific Method, Design Challenge and The Basic Unit of Life:  The Cell - Biology


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The Scientific Method and the Design Challenge

The scientific method overview

An example of oversimplification that confounds many students of biology (particularly early in their studies) is the use of language that hides the experimental process used to build knowledge. However, while we often write and speak about topics in biology with a conviction that gives the appearance of "factual" knowledge, reality is often more nuanced and filled with significant uncertainties. The "factual" presentation of material (usually lacking discussion of evidence or confidence in the evidence) plays to our natural tendency to feel good about "knowing" things, but it tends to create a false sense of security in the state of knowledge and does little to encourage the use of imagination or the development of critical thinking.

A better way to describe our knowledge about the natural world would be to explicitly qualify that the knowledge presented represents our current best understanding that has not yet been refuted by experiment. Unfortunately, repeated qualification becomes rather cumbersome. The important thing to remember is that while we may not say so explicitly, all of the knowledge we discuss in class represents only the best of our current understanding. Some ideas have withstood repeated and varied experimentation while other topics have yet to be tested as thoroughly. So if we're not as certain about things as we'd like to believe sometimes, how do we know what to put confidence in and what to be skeptical of? The complete answer is non-trivial but it begins with developing an understanding of the process we use in science to build new knowledge. The scientific method is the process by which new knowledge is developed. While the process can be described with long lists of "steps" (often seen in textbooks), its core elements can be described more succinctly.

Succinct description of scientific method (adapted from Feynman)

  1. Make an observation about the world.
  2. Propose a possible explanation for the observation.
  3. Test the explanation by experiment.
  4. If the explanation disagrees with experiment, the explanation is wrong.

At its core, that's it! In science there may be multiple, simultaneously proposed explanations or ideas that are tested by experiment. The ideas that fail experimentation are left behind. The ideas that survive experimentation move forward and are often retested by alternative experiments until they too either fail or continue to be retained.

Making an observation and asking a question

The ability to make useful observations and/or ask meaningful questions requires curiosity, creativity, and imagination—this cannot be overstated. Indeed, historically, it is first and foremost the application of these skills, perhaps more than technical ability, which has led to big advances in science. Many people think that making meaningful observations and asking useful questions is the easiest part of the scientific method. This is not always the case. Why? Seeing what others have not yet asked and creativity takes work and thoughtful reflection! In addition, our senses of observation are often biased by life experience, prior knowledge, or even our own biology. These underlying biases influence how we see the world, how we interpret what we see, and what we are ultimately curious about. This means that when we look at the world, we can miss a lot of things that are actually right under our noses. Douglas Adams, who is best known for his book entitled The Hitchhiker’s Guide to the Galaxy, once expanded on this point by writing:

“The most misleading assumptions are the ones you don't even know you're making.”

Scientists, therefore, need to be aware of any underlying biases and any assumptions that may influence how they internalize and interpret observations. This includes approaching our bias that the variety of places we get our knowledge (i.e., textbooks, instructors, the Internet) are representing the absolute truth with a healthy dose of skepticism. We need to learn to examine the evidence underling the “facts” we supposedly know and make critical judgments about how much we trust that knowledge. More generally, taking the time to make careful observations and to uncover any assumptions and biases that could influence how they are interpreted is, therefore, time well spent. This skill, like all others, needs to be developed and takes practice and we’ll try to start you on this in BIS2A.

For fun, and to test your observation skills, Google “observation tests”. Many of the search results will take you to interesting psychological tests and/or videos that illustrate how difficult accurate observation can be.

Generating a testable hypothesis

The "possible explanation" referred to in step three above has a formal name; it is called a hypothesis. A hypothesis is not a random guess. A hypothesis is an educated (based on prior knowledge or a new viewpoint) explanation for an event or observation. It is typically most useful if a scientific hypothesis can be tested. This requires that the tools to make informative measurements on the system exist and that the experimenter has sufficient control over the system in question to make the necessary observations.

Most of the time, behaviors of the system that the experimenter wants to test can be influenced by many factors. We call the behaviors and factors dependent and independent variables, respectively. The dependent variable is the behavior that needs explaining while the independent variables are all of the other things that can change and influence the behavior of the dependent variable. For example, an experimenter that has developed a new drug to control blood pressure may want to test whether her new drug actually influences blood pressure. In this example, the system is the human body, the dependent variable might be blood pressure, and the independent variables might be other factors that change and influence blood pressure like age, sex, and levels of various soluble factors in the blood stream.

Note

In BIS2A, and beyond, we prefer to avoid using language like “the experiment proved her hypothesis” when referring to a case like the blood pressure example above. Rather we would say, “the experiment is consistent with her hypothesis.” Note that for convenience (one of the language shortcuts we discussed earlier), we referred to the alternative hypothesis simply as “her hypothesis”! It would be more correct to state, “the experiment falsified her null hypothesis and is consistent with her alternative hypothesis.” Why take this shortcut since doing so adds confusion when a student is trying to learn? In this case, it was done to illustrate the point above about language shortcuts and hence the lengthy explanation. However, be aware of this commonly used shortcut and learn to make sure you can read in the correct meaning yourself.

Note: possible discussion

What does the statement about falsifying hypotheses mean in your own words? Why is falsification critical to the scientific method?

Controls

In an ideal case, an experiment will include control groups. Control groups are experimental conditions in which the values of the independent variables (there may be more than one) are maintained as close to those in the experimental group with the exception of the independent variable being tested. In the blood pressure example, an ideal scenario would be to have one identical group of people taking the drug and another group of people identical to those in the experimental group taking a pill containing something known to not influence blood pressure. In this oversimplified example, all independent variables are identical in the control and experimental groups with the exception of the presence or absence of the new drug. Under these circumstances, if the value of the dependent variable (blood pressure) of the experimental group differs from that of the control group, one can reasonably conclude that the difference must be due to the difference in independent variable (the presence/absence of the drug). This is, of course, the ideal. In real life it is impossible to conduct the proposed drug dosage experiment; the sheer number of possible independent variables in a group of potential patients would be high. Fortunately, while statisticians have come to the rescue in real life, you won’t need to understand the nuances of these statistical issues in BIS2A.

Accuracy in measurement, uncertainty, and replication

Finally, we mention the intuitive notion that the tools used to make the measurements in an experiment must be reasonably accurate. How accurate? They must be accurate enough to make measurements with sufficient certainty to draw conclusions about whether changes in independent variables actually influence the value of a dependent variable. If we take, yet again, the blood pressure example above. In that experiment, we made the important assumption that the experimenter had tools that allowed her to make accurate measurements of the changes in blood pressure associated with the effects of the drug. For instance if the changes associated with the drug ranged between 0 and 3 mmHg and her meter capably measured changes in blood pressure with a certainty of +/- 5 mmHg, she could not have made the necessary measurements to test her hypothesis or would have missed seeing the effect of the drug. For the sake of the example, we assume that she had a better instrument and that she could be confident that any changes she measured were indeed differences due to the drug treatment and that they were not due to measurement error, sample-to-sample variability, or other sources of variation that lower the confidence of the conclusions that are drawn from the experiment.

The topic of measurement error leads us to mention that there are numerous other possible sources of uncertainty in experimental data that you as students will ultimately need to learn about. These sources of error have a lot to do with determining how certain we are that experiments have disproven hypothesis, how much we should trust the interpretation of the experimental results and, by extension, our current state of knowledge. Even at this stage, you will recognize some experimental strategies used to deal with these sources of uncertainty (i.e., making measurements on multiple samples, creating replicate experiments). You will learn more about this in your statistics courses later on.

For now, you should, however, be aware that experiments carry a certain degree of confidence in the results and that the degree of confidence in the results can be influenced by many factors. Developing healthy skepticism involves, among other things, learning to assess the quality of an experiment and the interpretation of the findings and learning to ask questions about things like this.

Note: possible discussion

After moving to California to attend UC Davis, you have fallen in love with fresh tomatoes. You decide that the tomatoes in the stores just don’t taste right and resolve to grow your own.

You plant tomato plants all over your back yard; every free space now has a freshly planted tomato seedling of the same variety. You have planted tomatoes in the ground in full sunlight and next to your house in full shade.

Observation: After the first year of harvest, you make the observation that the plants growing in full shade almost always seem shorter than those in the full sun. You think that you have a reasonable explanation (hypothesis) for this observation.

Based on the information above, you create the following hypothesis to explain the differences in height you noticed in your tomatoes:

Hypothesis: The height that my tomato plants reach is positively correlated to the amount of sunlight they are exposed to (e.g., the more sun the plant gets, the taller it will be).

This hypothesis is testable and falsifiable. So, the next summer you decide to test your hypothesis.

This hypothesis also allows you to make a prediction. In this case you might predict that IF you were to shade a set of tomatoes in the sunny part of the yard, THEN those plants would be shorter than their full-sun neighbors.

You design an experiment to test your hypothesis by buying the same variety of tomato that you planted the previous year and plant your whole yard again. This year, however, you decide to do two different things:

  1. You create a shade structure that you place over a small subset of plants in the sunny part of your yard.
  2. You build a contraption with mirrors that redirects some sunlight onto a small subset of plants that are in the shady part of the yard.

Question 1: We used a shortcut above. Can you create statements for both the null and alternative hypothesis? Work with your classmates to do this.

Question 2: Why do you create a shade structure? What is this testing? Based on your hypothesis what do you predict will happen to the plants under the shade structure?

Question 3: Why do you create the mirror contraption? Why do you potentially need this contraption if you already have the shade structure?

New data: At the end of the summer you measure the height of your tomato plants and you find, once again, that the plants in the sunny part of the yard are indeed taller than those in the shady part of the yard. However, you notice that there is no difference in height between the plants under your shade structure and those right next to the structure in full sun. In addition, you notice that the plants in the shady part of the yard are all about the same height, including those that had extra light shined on them via your mirror contraption.

Question 4: What does this experiment lead you to conclude? What would you try to do next?

Question 5: Imagine an alternative scenario in which you discovered, as before, that the plants in the sunny part of the yard were all the same height (even those under your shade structure) but that the plants in the shady part of the yard that got “extra” light from your mirror contraption grew taller than their immediate neighbors. What would this say about your alternate hypothesis? Null hypothesis? What would you do next?

Question 6: What assumptions are you making about the ability to make measurements in this experiment? What influence might these assumptions have on your interpretation of the results?

In this class, you will occasionally be asked to create a hypotheses, to interpret data, and to design experiments with proper controls. All of these skills take practice to master—we can start to practice them in BIS2A. Again, while we don’t expect you to be masters after reading this text, we will assume that you have read this text during the first week and that the associated concepts are not completely new to you. You can always return to this text as a resource to refresh yourself.

Disclaimer

While the preceding treatment of the experimental method is very basic—you will undoubtedly add numerous layer of sophistication to these basic ideas as you continue in your studies—it should serve as a sufficient introduction to the topic for BIS2A. The most important point to remember from this section is that the knowledge represented in this course, while sometimes inadvertently represented as irrefutable fact, is really just the most current hypothesis about how certain things happen in biology that has yet to be falsified via experiment.

The Design Challenge

Your BIS2A instructors have devised something that we call “The Design Challenge” to help us approach the topics we cover in the course from a problem solving and/or design perspective. This pedagogical tool helps us:

(a) develop a frame of mind or way of approaching the material and
(b) design a set of sequential steps that help structure thinking about course topics in a problem-solving context.

How is it intended to work? Briefly, when we encounter a topic in class, “The Design Challenge” encourages us to think about it in the following problem-solving centric way:

  1. Identify the problem(s) - this may include identifying "big" problems and also decomposing them into "smaller" nested sub-problems
  2. Determine criteria for successful solutions
  3. Identify and/or imagine possible solutions
  4. Evaluate the proposed solutions against the criteria for success
  5. Choose a solution

By using the structure of the design challenge, topics that are typically presented as lists of facts and stories are transformed into puzzles or problems that need solving. For instance the discussion about the topic of cell division is motivated by a problem. The problem statement can be: "The cell needs to divide." Some of the criteria for success can include needing to have a near identical copy of DNA in each daughter cell, distributing organelles between the daughter cells so that each remains viable etc. These would be considered sub-problems to the larger “the cell needs to divide” problem. One can then go on to explore what the challenges are and try to use their existing knowledge and imagination to propose some solutions for each of those problems. Different solutions can be evaluated and then compared to what Nature seems to have done (at least in the cases that are well studied).

This exercise requires us to use imagination and critical thinking. It also encourages the student and instructor to think critically about WHY the particular topic is important to study. The design challenge approach to teaching biology attempts to MAKE the student and instructor focus on the important core questions that drove the development of the knowledge in the first place! It also encourages students to dream up new ideas and to interact with the material in a manner that is question/problem-centered rather than “fact”-centered. The question/problem-centered approach is different from what most people are used to, but it is ultimately more useful for developing skills, mental frameworks and knowledge that will transfer to other problems that they will encounter during their studies and beyond.

The guiding problem in BIS2A is to understand “How to Build a Cell.” This rather complex problem will be broken down into several smaller sub-problems that include:

  • acquiring the building blocks to construct cellular parts from the environment
  • acquiring the energy to build cellular parts from the environment
  • transforming the building blocks of the cell between different forms
  • transferring energy between different storage forms
  • creating a new cell from an old cell
  • problems we identify in class

As we explore these sub-problems, we will at times explore some of the different ways in which biology has addressed each issue. As we get into details, let us however make sure to stay focused on and not forget the importance of always staying linked to the questions/problems that motivated us to talk about the specifics in the first place.

Scientific Method vs. The Design Challenge

At this point you might be thinking: "What is the difference between the scientific method and the design challenge rubric and why do I need both?" It's not an uncommon question so let's see if we can clarify this now.

The design challenge and the scientific method are both processes that share similar qualities. The critical distinguishing feature, however, is the purpose behind each of the processes. The scientific method is a process used for eliminating possible answers to questions. A typical scenario where one might use the scientific method would involve someone making an observation, proposing multiple explanations, designing an experiment that might help eliminate one or more of the explanation and reflecting on the result. By contrast the design process is used for creating solutions to problems. A typical scenario for the design challenge would start with a problem that needs solving, defining criteria for a successful resolution, devising multiple possible solutions that would meet the success criteria and either selecting a solution or reflecting on changes that might be made to the designs to meet success criteria. A key operational difference is that the design challenge requires that criteria for success be defined while the scientific method does not.

While both are similar the differences are still real and we need to practice both processes. We'll assert that we use both of these processes in "real life" all of the time. A physician, for instance, will use both of these processes interactively as she forms hypotheses that try to determine what might be causing her patient's ailments. She will turn around and use the design process to build a course of treatment that meets certain success criteria. A scientist may be deep into hypothesis generation but he will eventually need to use a design process for building an experiment that will, within certain definable success criteria, help him answer a question.

Both of these processes, while similar, are important to use in different situations and we want to begin getting better at both.

The Basic Unit of Life: The Cell

Cellular structure of Bacteria and Archaea

In this section, we will discuss the basic structural features of both bacteria and archaea. There are many structural, morphological, and physiological similarities between bacteria and archaea. As discussed in the previous section, these microbes inhabit many ecological niches and carry out a great diversity of biochemical and metabolic processes. Both bacteria and archaea lack a membrane-bound nucleus and membrane-bound organelles, which are hallmarks of eukaryotes.

While Bacteria and Archaea are separate domains, morphologically they share a number of structural features. As a result, they face similar problems, such as the transport of nutrients into the cell, the removal of waste material from the cell, and the need to respond to rapid local environmental changes. In this section, we will focus on how their common cell structure allows them to thrive in various environments and simultaneously puts constraints on them. One of the biggest constraints is related to cell size.

Although bacteria and archaea come in a variety of shapes, the most common three shapes are as follows: cocci (spherical), bacilli (rod-shaped), and spirilli (spiral-shaped) (figure below). Both bacteria and archaea are generally small compared to typical eukaryotes. For example, most bacteria tend to be on the order of 0.2 to 1.0 µm (micrometers) in diameter and 1-10 µm in length. However, there are exceptions. Epulopiscium fishelsoni is a bacillus-shaped bacterium that is typically 80 µm in diameter and 200-600 µm long. Thiomargarita namibiensis is a spherical bacterium between 100 and 750 µm in diameter and is visible to the naked eye. For comparison, a typical human neutrophil is approximately 50 µm in diameter.

Figure 1. This figure shows the three most common shapes of bacteria and archaea: (a) cocci (spherical), (b) bacilli (rod-shaped), and (c) spirilli (spiral-shaped).

A thought question:

One question that comes to mind is why are bacteria and archaea typically so small? What are the constraints that keep them microscopic? How could bacteria such as Epulopiscium fishelsoni and Thiomargarita namibiensis overcome these constraints? Think of possible explanations or hypotheses that might answer these questions. We'll explore and develop an understanding of these questions in more detail below and in class.

The bacterial and archaeal cell: common structures

Introduction to the basic cell structure

Bacteria and archaea are unicellular organisms, which lack internal membrane-bound structures that are disconnected from the plasma membrane, a phospholipid membrane that defines the boundary between the inside and outside of the cell. In bacteria and archaea, the cytoplasmic membrane also contains all membrane-bound reactions, including those related to the electron transport chain, ATP synthase, and photosynthesis. By definition, these cells lack a nucleus. Instead, their genetic material is located in a self-defined area of the cell called the nucleoid. The bacterial and archaeal chromosome is often a single covalently closed circular double-stranded DNA molecule. However, some bacteria have linear chromosomes, and some bacteria and archaea have more than one chromosome or small non-essential circular replicating elements of DNA called plasmids. Besides the nucleoid, the next common feature is the cytoplasm (or cytosol), the "aqueous," jelly-like region encompassing the internal portion of the cell. The cytoplasm is where the soluble (non-membrane-associated) reactions occur and contains the ribosomes, the protein-RNA complex where proteins are synthesized. Finally, many bacteria and archaea also have cell walls, the rigid structural feature surrounding the plasma membrane that helps provide protection and constrain the cell shape. You should learn to create a simple sketch of a general bacterial or archaeal cell from memory.

Figure 2. The features of a typical prokaryotic cell are shown.

Constraints on the bacterial and archaeal cell

One common, almost universal, feature of bacteria and archaea is that they are small, microscopic to be exact. Even the two examples given as exceptions, Epulopiscium fishelsoni and Thiomargarita namibiensis, still face the basic constraints all bacteria and archaea face; they simply found unique strategies around the problem. So what is the largest constraint when it comes to dealing with the size of bacteria and archaea? Think about what the cell must do to survive.

Some basic requirements

So what do cells have to do to survive? They need to transform energy into a usable form. This involves making ATP, maintaining an energized membrane, and maintaining productive NAD+/NADH2 ratios. Cells also need to be able to synthesize the appropriate macromolecules (proteins, lipids, polysaccharides, etc.) and other cellular structural components. To do this, they need to be able to either make the core, key precursors for more complex molecules or get them from the environment.

Diffusion and its importance to bacteria and archaea

Movement by diffusion is passive and proceeds down the concentration gradient. For compounds to move from the outside to the inside of the cell, the compound must be able to cross the phospholipid bilayer. If the concentration of a substance is lower inside the cell than outside and it has chemical properties that allow it to move across the cell membrane, that compound will energetically tend to move into the cell. While the "real" story is a bit more complex and will be discussed in more detail later, diffusion is one of the mechanisms bacteria and archaea use to aid in the transport of metabolites.

Diffusion can also be used to get rid of some waste materials. As waste products accumulate inside the cell, their concentration rises compared to that of the outside environment, and the waste product can leave the cell. Movement within the cell works the same way: compounds will move down their concentration gradient, away from where they are synthesized to places where their concentration is low and therefore may be needed. Diffusion is a random process—the ability of two different compounds or reactants for chemical reactions to interact becomes a meeting of chance. Therefore, in small, confined spaces, random interactions or collisions can occur more frequently than they can in large spaces.

The ability of a compound to diffuse depends on the viscosity of the solvent. For example, it is a lot easier for you to move around in air than in water (think about moving around underwater in a pool). Likewise, it is easier for you to swim in a pool of water than in a pool filled with peanut butter. If you put a drop of food coloring into a glass of water, it quickly diffuses until the entire glass has changed color. Now what do you think would happen if you put that same drop of food coloring into a glass of corn syrup (very viscous and sticky)? It will take a lot longer for the glass of corn syrup to change color.

The relevance of these examples is to note that the cytoplasm tends to be very viscous. It contains many proteins, metabolites, small molecules, etc. and has a viscosity more like corn syrup than water. So, diffusion in cells is slower and more limited than you might have originally expected. Therefore, if cells rely solely on diffusion to move compounds around, what do you think happens to the efficiency of these processes as cells increase in size and their internal volumes get bigger? Is there a potential problem to getting big that is related to the process of diffusion?

So how do cells get bigger?

As you've likely concluded from the discussion above, with cells that rely on diffusion to move things around the cell—like bacteria and archaea—size does matter. So how do you suppose Epulopiscium fishelsoni and Thiomargarita namibiensis got so big? Take a look at these links, and see what these bacteria look like morphologically and structurally: Epulopiscium fishelsoni and Thiomargarita namibiensis.

Based on what we have just discussed, in order for cells to get bigger, that is, for their volume to increase, intracellular transport must somehow become independent of diffusion. One of the great evolutionary leaps was the ability of cells (eukaryotic cells) to transport compounds and materials intracellularly, independent of diffusion. Compartmentalization also provided a way to localize processes to smaller organelles, which overcame another problem caused by the large size. Compartmentalization and the complex intracellular transport systems have allowed eukaryotic cells to become very large in comparison to the diffusion-limited bacterial and archaeal cells. We'll discuss specific solutions to these challenges in the following sections.

Eukaryotic Cell: Structure and Function

Introduction to eukaryotic cells

By definition, eukaryotic cells are cells that contain a membrane-bound nucleus, a structural feature that is not present in bacterial or archaeal cells. In addition to the nucleus, eukaryotic cells are characterized by numerous membrane-bound organelles such as the endoplasmic reticulum, Golgi apparatus, chloroplasts, mitochondria, and others.

In previous sections, we began to consider the Design Challenge of making cells larger than a small bacterium—more precisely, growing cells to sizes at which, in the eyes of natural selection, relying on diffusion of substances for transport through a highly viscous cytosol comes with inherent functional trade-offs that offset most selective benefits of getting larger. In the lectures and readings on bacterial cell structure, we discovered some morphological features of large bacteria that allow them to effectively overcome diffusion-limited size barriers (e.g., filling the cytoplasm with a large storage vacuole maintains a small volume for metabolic activity that remains compatible with diffusion-driven transport).

As we transition our focus to eukaryotic cells, we want you to approach the study by constantly returning to the Design Challenge. We will cover a large number of subcellular structures that are unique to eukaryotes, and you will certainly be expected to know the names of these structures or organelles, to associate them with one or more "functions", and to identify them on a canonical cartoon representation of a eukaryotic cell. This memorization exercise is necessary but not sufficient. We will also ask you to start thinking a bit deeper about some of the functional and evolutionary costs and benefits (trade-offs) of both evolving eukaryotic cells and various eukaryotic organelles, as well as how a eukaryotic cell might coordinate the functions of different organelles.

Your instructors will, of course, propose some functional hypotheses for you to consider that address these broader points. Our hypotheses may sometimes come in the form of statements like, "Thing A exists

because

of rationale B." To be completely honest, however, in many cases, we don't actually know all of the selective pressures that led to the creation or maintenance of certain cellular structures, and the likelihood that one explanation will fit all cases is slim in biology. The causal linkage/relationship implied by the use of terms like "

because

" should be treated as good hypotheses rather than objective, concrete, undisputed, factual knowledge. We want you to understand these hypotheses and to be able to discuss the ideas presented in class, but we also want you to indulge your own curiosity and to begin thinking critically about these ideas yourself. Try using the Design Challenge rubric to explore some of your ideas. In the following, we will try to seed questions to encourage this activity.

Figure 1. These figures show the major organelles and other cell components of (a) a typical animal cell and (b) a typical eukaryotic plant cell. The plant cell has a cell wall, chloroplasts, plastids, and a central vacuole—structures not found in animal cells. Plant cells do not have lysosomes or centrosomes.

The plasma membrane

Like bacteria and archaea, eukaryotic cells have a plasma membrane, a phospholipid bilayer with embedded proteins that separates the internal contents of the cell from its surrounding environment. The plasma membrane controls the passage of organic molecules, ions, water, and oxygen into and out of the cell. Wastes (such as carbon dioxide and ammonia) also leave the cell by passing through the plasma membrane, usually with some help of protein transporters.

Figure 2. The eukaryotic plasma membrane is a phospholipid bilayer with proteins and cholesterol embedded in it.

As discussed in the context of bacterial cell membranes, the plasma membranes of eukaryotic cells may also adopt unique conformations. For instance, the plasma membrane of cells that, in multicellular organisms, specialize in absorption are often folded into fingerlike projections called microvilli (singular = microvillus); (see figure below). The "folding" of the membrane into microvilli effectively increases the surface area for absorption while minimally impacting the cytosolic volume. Such cells can be found lining the small intestine, the organ that absorbs nutrients from digested food.

An aside: People with celiac disease have an immune response to gluten, a protein found in wheat, barley, and rye. The immune response damages microvilli. As a consequence, afflicted individuals have an impaired ability to absorb nutrients. This can lead to malnutrition, cramping, and diarrhea.

Figure 3. Microvilli, shown here as they appear on cells lining the small intestine, increase the surface area available for absorption. These microvilli are only found on the area of the plasma membrane that faces the cavity from which substances will be absorbed. Credit: "micrograph", modification of work by Louisa Howard

The cytoplasm

The cytoplasm refers to the entire region of a cell between the plasma membrane and the nuclear envelope. It is composed of organelles suspended in the gel-like cytosol, the cytoskeleton, and various chemicals (see figure below). Even though the cytoplasm consists of 70 to 80 percent water, it nevertheless has a semisolid consistency. It is crowded in there. Proteins, simple sugars, polysaccharides, amino acids, nucleic acids, fatty acids, ions and many other water-soluble molecules are all competing for space and water.

The nucleus

Typically, the nucleus is the most prominent organelle in a cell (see figure below) when viewed through a microscope. The nucleus (plural = nuclei) houses the cell’s DNA. Let’s look at it in more detail.

Figure 4. The nucleus stores chromatin (DNA plus proteins) in a gel-like substance called the nucleoplasm. The nucleolus is a condensed region of chromatin where ribosome synthesis occurs. The boundary of the nucleus is called the nuclear envelope. It consists of two phospholipid bilayers: an outer membrane and an inner membrane. The nuclear membrane is continuous with the endoplasmic reticulum. Nuclear pores allow substances to enter and exit the nucleus.

The nuclear envelope

The nuclear envelope, a structure that constitutes the outermost boundary of the nucleus, is a double-membrane—both the inner and outer membranes of the nuclear envelope are phospholipid bilayers. The nuclear envelope is also punctuated with protein-based pores that control the passage of ions, molecules, and RNA between the nucleoplasm and cytoplasm. The nucleoplasm is the semisolid fluid inside the nucleus where we find the chromatin and the nucleolus, a condensed region of chromatin where ribosome synthesis occurs.

Chromatin and chromosomes

To understand chromatin, it is helpful to first consider chromosomes. Chromosomes are structures within the nucleus that are made up of DNA, the hereditary material. You may remember that in bacteria and archaea, DNA is typically organized into one or more circular chromosome(s). In eukaryotes, chromosomes are linear structures. Every eukaryotic species has a specific number of chromosomes in the nuclei of its cells. In humans, for example, the chromosome number is 23, while in fruit flies, it is 4.

Chromosomes are only clearly visible and distinguishable from one another by visible optical microscopy when the cell is preparing to divide and the DNA is tightly packed by proteins into easily distinguishable shapes. When the cell is in the growth and maintenance phases of its life cycle, numerous proteins are still associated with the nucleic acids, but the DNA strands more closely resemble an unwound, jumbled bunch of threads. The term chromatin is used to describe chromosomes (the protein-DNA complexes) when they are both condensed and decondensed.

Figure 5. (a) This image shows various levels of the organization of chromatin (DNA and protein). (b) This image shows paired chromosomes. Credit (b): modification of work by NIH; scale-bar data from Matt Russell

The nucleolus

Some chromosomes have sections of DNA that encode ribosomal RNA. A darkly staining area within the nucleus called the nucleolus (plural = nucleoli) aggregates the ribosomal RNA with associated proteins to assemble the ribosomal subunits that are then transported out to the cytoplasm through the pores in the nuclear envelope.

Note: possible discussion

Discuss amongst yourselves. Use the Design Challenge rubric to consider the nucleus in more detail. What "problems" does an organelle like the nucleus solve? What are some of the qualities of a nucleus that may be responsible for ensuring its evolutionary success? What are some of the trade-offs of evolving and maintaining a nucleus? (Every benefit has some cost; can you list both?) Remember, there may be some well-established hypotheses (and it is good to mention these), but the point of the exercise here is for you to think critically and to critically discuss these ideas using your collective "smarts".

Ribosomes

Ribosomes are the cellular structures responsible for protein synthesis. When viewed through an electron microscope, ribosomes appear either as clusters (polyribosomes) or single, tiny dots that float freely in the cytoplasm. They may be attached to the cytoplasmic side of the plasma membrane or the cytoplasmic side of the endoplasmic reticulum and the outer membrane of the nuclear envelope (cartoon of cell above).

Electron microscopy has shown us that ribosomes, which are large complexes of protein and RNA, consist of two subunits, aptly called large and small (figure below). Ribosomes receive their "instructions" for protein synthesis from the nucleus, where the DNA is transcribed into messenger RNA (mRNA). The mRNA travels to the ribosomes, which translate the code provided by the sequence of the nitrogenous bases in the mRNA into a specific order of amino acids in a protein. This is covered in greater detail in the section covering the process of translation.

Figure 6. Ribosomes are made up of a large subunit (top) and a small subunit (bottom). During protein synthesis, ribosomes assemble amino acids into proteins.

Mitochondria

Mitochondria (singular = mitochondrion) are often called the “powerhouses” or “energy factories” of a cell because they are the primary site of metabolic respiration in eukaryotes. Depending on the species and the type of mitochondria found in those cells, the respiratory pathways may be anaerobic or aerobic. By definition, when respiration is aerobic, the terminal electron is oxygen; when respiration is anaerobic, a compound other than oxygen functions as the terminal electron acceptor. In either case, the result of these respiratory processes is the production of ATP via oxidative phosphorylation, hence the use of terms "powerhouse" and/or "energy factory" to describe this organelle. Nearly all mitochondria also possess a small genome that encodes genes whose functions are typically restricted to the mitochondrion.

In some cases, the number of mitochondria per cell is tunable, depending, typically, on energy demand. It is for instance possible muscle cells that are used—that by extension have a higher demand for ATP—may often be found to have a significantly higher number of mitochondria than cells that do not have a high energy load.

The structure of the mitochondria can vary significantly depending on the organism and the state of the cell cycle which one is observing. The typical textbook image, however, depicts mitochondria as oval-shaped organelles with a double inner and outer membrane (see figure below); learn to recognize this generic representation. Both the inner and outer membranes are phospholipid bilayers embedded with proteins that mediate transport across them and catalyze various other biochemical reactions. The inner membrane layer has folds called cristae that increase the surface area into which respiratory chain proteins can be embedded. The region within the cristae is called the mitochondrial matrix and contains—among other things—enzymes of the TCA cycle. During respiration, protons are pumped by respiratory chain complexes from the matrix into a region known as the intermembrane space (between the inner and outer membranes).

Figure 7. This electron micrograph shows a mitochondrion as viewed with a transmission electron microscope. This organelle has an outer membrane and an inner membrane. The inner membrane contains folds, called cristae, which increase its surface area. The space between the two membranes is called the intermembrane space, and the space inside the inner membrane is called the mitochondrial matrix. ATP synthesis takes place on the inner membrane. Credit: modification of work by Matthew Britton; scale-bar data from Matt Russell

Note: possible discussion

Discuss: Processes like glycolysis, lipid biosynthesis, and nucleotide biosynthesis all have compounds that feed into the TCA cycle—some of which occurs in the mitochondria. What are some of the functional challenges associated with coordinating processes that have a common set of molecules if the enzymes are sequestered into different cellular compartments?

Peroxisomes

Peroxisomes are small, round organelles enclosed by single membranes. These organelles carry out redox reactions that oxidize and break down fatty acids and amino acids. They also help to detoxify many toxins that may enter the body. Many of these redox reactions release hydrogen peroxide, H2O2, which would be damaging to cells; however, when these reactions are confined to peroxisomes, enzymes safely break down the H2O2 into oxygen and water. For example, alcohol is detoxified by peroxisomes in liver cells. Glyoxysomes, which are specialized peroxisomes in plants, are responsible for converting stored fats into sugars.

Vesicles and vacuoles

Vesicles and vacuoles are membrane-bound sacs that function in storage and transport. Other than the fact that vacuoles are somewhat larger than vesicles, there is a very subtle distinction between them: the membranes of vesicles can fuse with either the plasma membrane or other membrane systems within the cell. Additionally, some agents such as enzymes within plant vacuoles break down macromolecules. The membrane of a vacuole does not fuse with the membranes of other cellular components.

Animal cells versus plant cells

At this point, you know that each eukaryotic cell has a plasma membrane, cytoplasm, a nucleus, ribosomes, mitochondria, peroxisomes, and in some, vacuoles. There are some striking differences between animal and plant cells worth noting. Here is a brief list of differences that we want you to be familiar with and a slightly expanded description below:

1. While all eukaryotic cells use microtubule and motor protein the based mechanisms to segregate chromosomes during cell division, the structures used to organize these microtubules differ in plants versus animal and yeast cells. Animal and yeast cells organize and anchor their microtubules into structures called microtubule organizing centers (MTOCs). These structures are composed of structures called centrioles that are composed largely of α-tubulin, β-tubulin, and other proteins. Two centrioles organize into a structure called a centrosome. By contrast, in plants, while microtubules also organize into discrete bundles, there are no conspicuous structures similar to the MTOCs seen in animal and yeast cells. Rather, depending on the organism, it appears that there can be several places where these bundles of microtubules can nucleate from places called acentriolar (without centriole) microtubule organizing centers. A third type of tubulin, γ-tubulin, appears to be implicated, but our knowledge of the precise mechanisms used by plants to organize microtubule spindles is still spotty.

2. Animal cells typically have organelles called lysosomes responsible for degradation of biomolecules. Some plant cells contain functionally similar degradative organelles, but there is a debate as to how they should be named. Some plant biologists call these organelles lysosomes while others lump them into the general category of plastids and do not give them a specific name.

3. Plant cells have a cell wall, chloroplasts and other specialized plastids, and a large central vacuole, whereas animal cells do not.

The centrosome

The centrosome is a microtubule-organizing center found near the nuclei of animal cells. It contains a pair of centrioles, two structures that lie perpendicular to eachother (see figure below). Each centriole is a cylinder of nine triplets of microtubules.

Figure 8. The centrosome consists of two centrioles that lie at right angles to each other. Each centriole is a cylinder made up of nine triplets of microtubules. Nontubulin proteins (indicated by the green lines) hold the microtubule triplets together.

The centrosome (the organelle where all microtubules originate in animal and yeast) replicates itself before a cell divides, and the centrioles appear to have some role in pulling the duplicated chromosomes to opposite ends of the dividing cell. However, the exact function of the centrioles in cell division remains unclear, as cells that have had their centrosome removed can still divide, and plant cells, which lack centrosomes, are capable of cell division.

Lysosomes

Animal cells have another set of organelles not found in plant cells: lysosomes. Colloquially, the lysosomes are sometimes called the cell’s “garbage disposal”. Enzymes within the lysosomes aid the breakdown of proteins, polysaccharides, lipids, nucleic acids, and even "worn-out" organelles. These enzymes are active at a much lower pH than that of the cytoplasm. Therefore, the pH within lysosomes is more acidic than the pH of the cytoplasm. In plant cells, many of the same digestive processes take place in vacuoles.

The cell wall

If you examine the diagram above depicting plant and animal cells, you will see in the diagram of a plant cell a structure external to the plasma membrane called the cell wall. The cell wall is a rigid covering that protects the cell, provides structural support, and gives shape to the cell. Fungal and protistan cells also have cell walls. While the chief component of bacterial cell walls is peptidoglycan, the major organic molecule in the plant cell wall is cellulose (see structure below), a polysaccharide made up of glucose subunits.

Figure 9. Cellulose is a long chain of β-glucose molecules connected by a 1-4 linkage. The dashed lines at each end of the figure indicate a series of many more glucose units. The size of the page makes it impossible to portray an entire cellulose molecule.

Chloroplasts

Chloroplasts are plant cell organelles that carry out photosynthesis. Like the mitochondria, chloroplasts have their own DNA and ribosomes, but chloroplasts have an entirely different function.

Like mitochondria, chloroplasts have outer and inner membranes, but within the space enclosed by a chloroplast’s inner membrane is a set of interconnected and stacked fluid-filled membrane sacs called thylakoids (figure below). Each stack of thylakoids is called a granum (plural = grana). The fluid enclosed by the inner membrane that surrounds the grana is called the stroma.

Figure 10. The chloroplast has an outer membrane, an inner membrane, and membrane structures called thylakoids that are stacked into grana. The space inside the thylakoid membranes is called the thylakoid space. The light harvesting reactions take place in the thylakoid membranes, and the synthesis of sugar takes place in the fluid inside the inner membrane, which is called the stroma. Chloroplasts also have their own genome, which is contained on a single circular chromosome.

The chloroplasts contain a green pigment called chlorophyll, which captures the light energy that drives the reactions of photosynthesis. Like plant cells, photosynthetic protists also have chloroplasts. Some bacteria perform photosynthesis, but their chlorophyll is not relegated to an organelle.

Evolution connection

Endosymbiosis

We have mentioned that both mitochondria and chloroplasts contain DNA and ribosomes. Have you wondered why? Strong evidence points to endosymbiosis as the explanation.

Symbiosis is a relationship in which organisms from two separate species depend on each other for their survival. Endosymbiosis (endo- = “within”) is a mutually beneficial relationship in which one organism lives inside the other. Endosymbiotic relationships abound in nature. For instance, some microbes that live in our digestive tracks produce vitamin K. The relationship between these microbes and us (their hosts) is said to be mutually beneficial or symbiotic. The relationship is beneficial for us because we are unable to synthesize vitamin K; the microbes do it for us instead. The relationship is also beneficial for the microbes because they receive abundant food from the environment of the large intestine, and they are protected both from other organisms and from drying out.

Scientists have long noticed that bacteria, mitochondria, and chloroplasts are similar in size. We also know that bacteria have DNA and ribosomes, just as mitochondria and chloroplasts do. Scientists believe that host cells and bacteria formed an endosymbiotic relationship when the host cells ingested both aerobic and autotrophic bacteria (cyanobacteria) but did not destroy them. Through many millions of years of evolution, these ingested bacteria became more specialized in their functions, with the aerobic bacteria becoming mitochondria and the autotrophic bacteria becoming chloroplasts. There will be more on this later in the reading.

The central vacuole

Previously, we mentioned vacuoles as essential components of plant cells. If you look at the cartoon figure of the plant cell, you will see that it depicts a large central vacuole that occupies most of the area of the cell. The central vacuole plays a key role in regulating the cell’s concentration of water in changing environmental conditions.

Silly vacuole factoid: Have you ever noticed that if you forget to water a plant for a few days, it wilts? That’s because as the water concentration in the soil becomes lower than the water concentration in the plant, water moves out of the central vacuoles and cytoplasm. As the central vacuole shrinks, it leaves the cell wall unsupported. This loss of support to the cell walls of plant cells results in the wilted appearance of the plant.

The central vacuole also supports the expansion of the cell. When the central vacuole holds more water, the cell gets larger without having to invest a lot of energy in synthesizing new cytoplasm.


Context for Use

At the beginning of the scientific method unit I use the lab to introduce and cover the process. instead of using lecture.
Scientific Method Lab

1. The purpose of this lab is to use the Scientific Method to solve a problem.
A) Observe and ask questions that lead to a problem

C) Test the hypothesis with a controlled experiment my making observations and gathering data.

E) Reject or Accept your hypothesis

2. Materials
2 small pieces of wax paper
1 meter long piece of string
1 meter stick
2 different pieces of bubble gun labeled A and B

3. READ directions carefully before starting the lab. Each group will need one piece of gum labeled A and one labeled B. Make 3 observations about each brand of gum.


Problem: Which piece of bubble gum blows the biggest bubble?

Hypothesis: Predict which piece of gum will blow the biggest bubble and why.


Procedure:
1. The person with brand A will chew their piece of gum for 3 minutes. The person with brand B does not begin chewing until all the tests on brand A are
completed.

3. Using a string, your partner will measure the diameter (distance across) the bubble. Put the string on the meter stick to measure the distance in centimeters (cm).

4. Record the measurement in a data table. Repeat the process for trials 2 and 3.

5. Find the average bubble size for brand A (add all the distances up and divide by 3) and put in the data chart.

6. Repeat steps 1-5 with brand B gum.

Data Table: Design a data collection table to fit the data you will be investigating

Conclusion: Forming a theory
What brand of gum is the best at blowing bubbles and why? Support your answer with observations and your data.
______________________________________________________________________________
PART 2

Combine with another group to complete this part of the lab.

Problem: How does gum strechability relate to bubble size?

Hypothesis: Make an educated guess that would answer the above question.

Procedure:
1. The person with brand A will roll their gum into a ball.

2. Hold the gum (brand A) by using the piece of wax paper. Another person in the group would hold the same piece of gum with another piece of wax paper. Hold the gum near your chest, begin to walk slowly backwards.

3. The third person in the group should hold the meter stick and measure the distance in centimeters the gum stretched before breaking.

4. Record the measurement in the data chart. ONLY DO ONE TRIAL

5. Repeat #1-4 for brand B gum.

Data Table: Create a data table to fit the data you will be gathering


Conclusion:
COMPARE DATA FROM BOTH GROUPS IN PART 1 AND PART 2


How does gum stretchability relate to bubble size?


With your lab partner, list 5 variables that may affect the outcome of this experiment.

Explain how the data you collected can be described as both qualitative and quantitative
____________________________________________________________________________________________________________________________________________________________

Were SI units used in this lab? Explain. _________________________________
____________________________________________________________________

List any questions you still have about the scientific method.
__________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ Complete lab (Rich Text File 6kB Aug11 09)


NOTES

1. See, for example, Kuyper (1991).

2. See, for example, the proposal by Pigman and Carmichael (1950).

3. See, for example, Holton (1988) and Ravetz (1971).

4. Several excellent books on experimental design and statistical methods are available. See, for example, Wilson (1952) and Beveridge (1957).

5. For a somewhat dated review of codes of ethics adopted by the scientific and engineering societies, see Chalk et al. (1981).

6. The discussion in this section is derived from Mark Frankel's background paper, &ldquoProfessional Societies and Responsible Research Conduct,&rdquo included in Volume II of this report.

7. For a broader discussion on this point, see Zuckerman (1977).

8. For a full discussion of the roles of scientific societies in fostering responsible research practices, see the background paper prepared by Mark Frankel, &ldquoProfessional Societies and Responsible Research Conduct,&rdquo in Volume II of this report.

9. Selected examples of academic research conduct policies and guidelines are included in Volume II of this report.

10. See, for example, Holton's response to the criticisms of Millikan in Chapter 12 of Thematic Origins of Scientific Thought (Holton, 1988). See also Holton (1978).

11. See, for example, responses to the Proceedings of the National Academy of Sciences action against Friedman: Hamilton (1990) and Abelson et al. (1990). See also the discussion in Bailar et al. (1990).

12. Much of the discussion in this section is derived from a background paper, &ldquoReflections on the Current State of Data and Reagent Exchange Among Biomedical Researchers,&rdquo prepared by Robert Weinberg and included in Volume II of this report.

13. See, for example, Culliton (1990) and Bradshaw et al. (1990). For the impact of the inability to provide corroborating data or witnesses, also see Ross et al. (1989).

14. See, for example, Rennie (1989) and Cassidy and Shamoo (1989).

15. See, for example, the discussion on random data audits in Institute of Medicine (1989a), pp. 26-27.

16. For a full discussion of the practices and policies that govern authorship in the biological sciences, see Bailar et al. (1990).

17. Note that these general guidelines exclude the provision of reagents or facilities or the supervision of research as a criteria of authorship.

18. A full discussion of problematic practices in authorship is included in Bailar et al. (1990). A controversial review of the responsibilities of co-authors is presented by Stewart and Feder (1987).

19. In the past, scientific papers often included a special note by a named researcher, not a co-author of the paper, who described, for example, a particular substance or procedure in a footnote or appendix. This practice seems to.have been abandoned for reasons that are not well understood.

20. Martin et al. (1969), as cited in Sigma Xi (1986), p. 41.

21. Huth (1988) suggests a &ldquonotice of fraud or notice of suspected fraud&rdquo issued by the journal editor to call attention to the controversy (p. 38). Angell (1983) advocates closer coordination between institutions and editors when institutions have ascertained misconduct.

22. Such facilities include Cambridge Crystallographic Data Base, GenBank at Los Alamos National Laboratory, the American Type Culture Collection, and the Protein Data Bank at Brookhaven National Laboratory. Deposition is important for data that cannot be directly printed because of large volume.

23. For more complete discussions of peer review in the wider context, see, for example, Cole et al. (1977) and Chubin and Hackett (1990).

24. The strength of theories as sources of the formulation of scientific laws and predictive power varies among different fields of science. For example, theories derived from observations in the field of evolutionary biology lack a great deal of predictive power. The role of chance in mutation and natural selection is great, and the future directions that evolution may take are essentially impossible to predict. Theory has enormous power for clarifying understanding of how evolution has occurred and for making sense of detailed data, but its predictive power in this field is very limited. See, for example, Mayr (1982, 1988).

25. Much of the discussion on mentorship is derived from a background paper prepared for the panel by David Guston. A copy of the full paper, &ldquoMentorship and the Research Training Experience,&rdquo is included in Volume II of this report.

26. Although the time to the doctorate is increasing, there is some evidence that the magnitude of the increase may be affected by the organization of the cohort chosen for study. In the humanities, the increased time to the doctorate is not as large if one chooses as an organizational base the year in which the baccalaureate was received by Ph.D. recipients, rather than the year in which the Ph.D. was completed see Bowen et al. (1991).

27. Some universities have written guidelines for the supervision or mentorship of trainees as part of their institutional research policy guidelines (see, for example, the guidelines adopted by Harvard University and the University of Michigan that are included in Volume II of this report). Other groups or institutions have written &ldquoguidelines &rdquo (IOM, 1989a NIH, 1990), &ldquochecklists&rdquo (CGS, 1990a), and statements of &ldquoareas of concern&rdquo and suggested &ldquodevices&rdquo (CGS, 1990c).

The guidelines often affirm the need for regular, personal interaction between the mentor and the trainee. They indicate that mentors may need to limit the size of their laboratories so that they are able to interact directly and frequently with all of their trainees. Although there are many ways to ensure responsible mentorship, methods that provide continuous feedback, whether through formal or informal mechanisms, are apt to be the most successful (CGS, 1990a). Departmental mentorship awards (comparable to teaching or research prizes) can recognize, encourage, and enhance the


Assessment of the Scientific Information for the Radiation Exposure Screening and Education Program (2005)

The scientific issues related to radiation and associated health effects are complex and may be confusing for persons not professionally involved with them. The topics are even more complicated in the context of the Radiation Exposure Compensation Act (RECA) and the Radiation Exposure Screening and Education Program (RESEP). This chapter will give concerned readers an opportunity to become familiar with the terminology and concepts used in the radiological sciences. It is limited to scientific topics directly related to the basic charge presented to the committee. The chapter is divided into three sections. The first presents the principles of physics related to ionizing radiation. The second presents the biology necessary for understanding how radiation affects cells and the mechanisms of radiation injury and repair. The third section describes the methods used to identify and measure the risks to persons who are exposed to radiation.

RADIATION PHYSICS

Definition of Radiation

Observable matter is made up of discrete components known as atoms and molecules. Atoms are divisible into particles, such as electrons, protons, and neutrons. Other elementary particles are part of the fabric of nature, but they are more elusive and do not directly form stable atoms or molecules. When a particle or group of particles is accelerated, it can reach high energies and travel a large distance in a very short time. Radiation can be defined as any collection of

elementary particles that have sufficient energy to interact with and transfer some of their energy to objects or materials that intercept their path.

Ionizing Radiation

Many different types of interactions can take place when radiation strikes an object. For instance, atoms in an irradiated object are neutral they each consist of a positively charged nucleus (made up of protons and neutrons) surrounded by negatively charged electrons. The process of removing an orbital electron from an atom is called ionization.

Some types of radiation can transfer energy in a manner that creates ionization in the object. X rays and gamma rays are particles called photons that can create ionization. Microwaves, ultraviolet radiation, visible light, and infrared are also photons, but they do not result in ionization and are referred to as nonionizing radiation.

Ionization created by radiation in living systems can have unique biologic consequences that are different from those caused by nonionizing radiation. RECA is related specifically to diseases found to have an association with exposure to ionizing radiation.

The process that accelerates particles to form radiation can occur naturally. For example, the sun continuously emits particles that reach the atmosphere and result in a continuous shower of elementary particles on the surface of the earth. Some sources of radiation are man-made, such as x-ray machines, particle accelerators used for cancer therapy, and nuclear power reactors used to generate electricity.

Radioactivity

Radioactivity is another important source of ionizing radiation. Every element such as hydrogen, oxygen, or iron are defined by the number of protons in the nucleus. However, atoms of the same element can have a different number of neutrons in the nucleus. These are called isotopes. Isotopes are identified by the name of the element and the total number of protons and neutrons in the nucleus. For example, the element hydrogen has one proton, 1 H. There is another isotope of hydrogen with one proton and one neutron, 2 H, called deuterium and also one proton and two neutrons, 3 H, called tritium. Some nuclei are unstable, and these can transform (decay) into more stable nuclei by emitting particles&mdasha process called radioactive decay. The emitted particles are a form of radiation originating from radioactivity.

Every element in the periodic chart has at least one isotope that is radioactive. For instance, sodium-23 ( 23 Na) is stable, but sodium-22 ( 22 Na) and sodium-24 ( 24 Na) are radioactive similarly, iodine-127 ( 127 I) is stable, and iodine-131 ( 131 I) is radioactive. A salt containing natural potassium will always contain some radioactive potassium-40 ( 40 K). Potassium is an essential mineral in our

diet. Some of the ingested potassium is absorbed in tissue. That process is not limited to potassium, but can occur with iodine, sodium, radium, and so on. Therefore, all persons contain some radioactivity.

Each radioactive isotope has unique properties. One property is the type of particles emitted, and another is the energy of the particles emitted. No two radioactive isotopes emit the same combination of particles and energies. Therefore, one can identify the presence of a specific isotope at a given location by measuring the types and energies of the emitted particles.

Radioactive decay is a random process: it is impossible to determine when a given nucleus will decay. However, it is possible to estimate how many nuclei in a group will decay during a given period. The half-life of an isotope is the time it takes for half the nuclei in a group or sample to decay. Thus, isotopes with short half-lives decay rapidly and those with long half-lives decay more slowly. No two isotopes have the same half-life. For example, the half-life of nitrogen-16 ( 16 N) is 7.3 seconds that of radon 222 ( 222 Rn), 3.8 days that of 131 I, 8 days and that of uranium-238 ( 238 U), 4.5 billion years.

Radioactivity specifically refers to the rate at which decays occur. The amount of radioactivity present depends on the number of radioactive atoms and their corresponding half-life. The rate at which atoms are decaying is proportional to the number of atoms divided by the half-life. This decay rate is described in units of either Becquerels (Bq) in the International System, SI, of units or Curies (Ci) in the traditional system of units used in the United States 1 Bq is equal to 1 decay per second, and 1 Ci is equal to 37 billion decays per second. The amount of radioactivity is often stated in terms of a millicurie (mCi), which is one thousand times smaller than a Curie. One microcurie (µCi) is one million times smaller than a Curie and one picocurie is one trillion times smaller than a Curie. The amount of radioactivity at any time is reduced by one-half in a period of time equal to one half-life.

Radioactivity generates radiation by emitting particles. Radioactive materials outside the body are called external emitters, and radioactive materials located within the body are called internal emitters.

Types of Ionizing Radiations

Radioactive nuclei can emit several kinds of particles, but there are three primary types: alpha particles (&alpha), beta particles (&beta), and photons that are either x rays or gamma rays (&gamma). Several properties distinguish those particles from one another. One is electric charge alpha particles are emitted with a positive charge of 2, beta particles are emitted with either 1 negative charge (electron) or 1 positive charge (positron), and x rays and gamma rays have no charge and are thus neutral.

Another important property is penetration of the particles through matter. Alpha particles lose energy rapidly and stop in a very short distance. Most travel

no more than 3-5 centimeters in air and only about 30-50 microns in water or tissue. They cannot penetrate clothes or skin. Alpha particles must be emitted very close to biologic targets to produce an effect. External alpha emitters therefore are generally not considered to pose a health hazard. However, radioactive materials can enter the body through inhalation, ingestion, or transfer through cuts and wounds. Some of this radioactive material passes through the body and is eliminated, and some remains in tissues that might contain radiosensitive cells. The distribution of the radioactive material in the body depends on the chemistry of the radioactive element. For example, radium has chemical properties similar to those of calcium, and the alpha-particle emitter radium-226 ( 226 Ra) will accumulate with calcium in bone.

Beta particles are electrons that lose energy rather slowly when passing through materials. A high-energy beta particle can travel several centimeters through water and tissue. Lower-energy beta particles travel some fraction of that distance. External emission of low-energy beta particles, as in the decay of tritium, which is an isotope of hydrogen ( 3 H), or carbon-14 ( 14 C) is not considered a health hazard, whereas external emission of high-energy beta particles from strontium-90 ( 90 Sr) reach some regions of the body that are sensitive to radiation. As in the case of alpha-emitters, the distribution of internal beta-emitters depends on the chemistry of the radioactive element. Strontium has chemistry similar to that of calcium, and 90 Sr will accumulate in bone. Most of the iodine in the body that is not excreted will accumulate in the thyroid. Beta particles from 131 I can originate in the thyroid and deposit most of their energy there.

Photons can be very penetrating. High-energy x rays and gamma rays travel many meters in air and through many centimeters of concrete, iron, and tissue. Thus, external gamma rays can penetrate and deposit energy throughout the body. The distribution of internal gamma-emitters depends on the chemistry of the radioactive element. Internally emitted gamma rays can deposit energy in the tissue of residence or neighboring tissues. For example, cesium-137 ( 137 Cs) deposited in soft tissues, and the entire body is exposed uniformly to gamma rays.

Radiation Measurements and Units

Radiation can be described and measured in many ways. For purposes of radiobiology and radiation protection, the concept of absorbed dose, D, is most commonly used. It does not measure each particle but describes the energy deposited in a specified region. Absorbed dose is the energy absorbed in a volume of material divided by the mass of the material. It is the result of the physical interactions of the ionizing radiation within the volume of material. An absorbed dose can be delivered by any type or combination of types of radiation in any type of material.

The units of absorbed dose are the gray (Gy) in the SI and the rad in the traditional system often still used in the United States 1 Gy is equivalent to 100

rad. The centigray (cGy) is a unit of convenience often used in cancer therapy that is equivalent to 1 rad.

Dose rate refers to the distribution of dose as a function of time. It can be expressed as Gy per second (Gy s &minus1 ), per minute (Gy min &minus1 ), per hour (Gy h &minus1 ), and per year (Gy y &minus1 ). A protracted dose is one received over a long period of time. A given dose delivered within 1 h often will have different consequences than the same total dose delivered over a period of one year. In some cases, if the dose rate is constant for long periods, it is referred to as continuous exposure to radiation. A dose rate can change with time radiation could occur in the form of random pulses or vary periodically.

Dose fractionation describes the case in which a dose is delivered in segments or fractions over a specified period. For example, in radiation therapy for cancer, a total dose of 50 Gy might be delivered at a high dose rate of 2 Gy min &minus1 for only 1 minute per day over a period of 25 days (5 weeks, excluding weekends).

Equivalent Dose

The concept of absorbed dose, D, was created to estimate biologic effects of ionizing radiation. Scientists hoped that absorbed dose could serve as a universal predictor of biologic effects and corresponding risks to humans from exposure to ionizing radiation. However, it was soon discovered that similar doses of radiation from different particles produced different amounts of biologic damage. In some cases, up to 1 Gy of gamma rays is needed to produce the same effect as 0.1 Gy of alpha particles. That was observed for many biologic systems and was ultimately referred to as relative biological effectiveness (RBE).

RBE is related to the density or rate of ionization produced by a particle as it passes through matter. Linear energy transfer, LET, is a measure of the rate of energy loss and therefore ionization along the track of a particle. Alpha particles have short tracks, but create large amounts of ionization along the track and are referred to as high LET radiation. Electrons and beta particles are sparsely ionizing and are referred to as low LET radiation. X rays and gamma rays create electrons when they interact in materials and are also considered to be low LET radiation. To a first approximation, RBE increases with LET.

Rules for and regulation of radiation protection of humans must be related to the risks associated with exposure to ionizing radiation. RBE makes it impossible to base a system of regulations on absorbed dose alone. It was necessary to include the type of radiation in a consistent manner that reflected changes in the biology as well as the physics. For this reason, the concept of equivalent dose was established for purposes of radiation protection. Equivalent dose (HT) in a tissue or organ, T, is the product of absorbed dose averaged within a tissue (DT) and a radiation weighting factor (wR), and thus HT = DT × wR.

The radiation weighting factor is used to adjust the absorbed dose to reflect the RBE for radiation of type R. It is thus related to LET. Alpha particles have

a wR of 20. Beta particles, x rays and gamma rays have a wR of 1.0. Equivalent dose is described in sievert (Sv) or rem.

Effective Dose

Some tissues and organs are more sensitive to radiation than others. When the entire body is irradiated uniformly, all organs receive a dose and contribute to the total risk of a health effect, such as cancer. In some cases, particularly with internal emitters, only one or two organs receive a dose, and the other organs are not at risk. When one needs to know the combined risk for such a case, it is necessary to include a factor that is related to the risk to each of the exposed organs. The equivalent dose, HT, in each tissue, T, is multiplied by a tissue-weighting factor, wT. The effective dose, E, is then the sum of HTwT for all exposed tissues. Effective dose is a risk averaged dose that serves as a measure of risk including adjustments for both the type of radiation, wR, and the tissues exposed, wT. Effective dose is expressed in sievert (Sv) when the absorbed dose is measured in Gy, or in rem when the dose is measured in rads 1 Sv = 100 rem.

The International Commission on Radiological Protection (ICRP, 1991) has made recommendations for values of wT on the basis of the occurrence of cancer and hereditary effects observed in exposed populations. The currently accepted values are shown in Table 3.1.

One way to interpret Table 3.1 is for a large population of persons irradiated uniformly. Some people might develop cancer as a result of the absorbed dose received. The types of cancer associated with radiation would be distributed according to the fraction represented by wT in Table 3.1. ICRP makes recom-

TABLE 3.1 Currently Recommended Tissue Weighting Factors, wT a

a wT for the remainder is divided equally between adrenals, brain, upper large intestine, small intestine, kidney, muscle, pancreas, spleen, thymus, and uterus.

mendations for revising the values as new evidence on cancer incidence and tissue sensitivity becomes available.

Natural Background Radiation

All persons are exposed to ionizing radiation from natural sources. Sources of background radiation can be outside the body (external radiation) or inside the body (internal radiation). The primary contributions to external radiation from natural background are cosmic rays and penetrating gamma rays emitted by radioactive materials in rocks and soil, in particular 40 K, 232 Th and 238 U. The primary contributions to internal radiation from natural background are radioactive materials that enter the body through the diet&mdash 40 K, carbon-14 ( 14 C), 226 Ra&mdashand inhaled radioactivity originating from 222 Rn.

Natural background radiation can have large variations. Exposure rates around the world depend on geography, geology, and housing environments. Table 3.2 shows a summary of the average annual effective dose received from natural background radiation by persons in the United States and the average received by persons residing near the mountains in the western part of the country (NCRP, 1987).

There are other exposures to ionizing radiation. The most common sources are medical examinations that prescribe diagnostic x rays and computed tomography (CT) scans. Table 3.3 shows the effective dose received from several types of diagnostic examinations (NCRP, 1987).

In addition to medical examinations, the general population may be exposed to radiation from industrial applications and consumer products. Figure 3.1 shows the relative contribution to effective dose for an average person in the United States from natural background and man-made sources (NCRP, 1987).

In Figure 3.1, cosmic refers to the contribution from external radiation from penetrating particles originating in the atmosphere. Terrestrial refers to the contribution from external gamma rays originating in radioactivity in soil, rocks, and building materials. Internal radiation refers to the contribution from radioactivity deposited throughout the body from diet and inhalation. Radon represents

TABLE 3.2 Average Annual Effective Dose Received by People in the United States from Natural Background Radiation

TABLE 3.3 Effective Dose Received from Diagnostic Examinations of Specific Organs and Tissues

Upper gastrointestinal tract

the contribution from inhalation and deposition of radioactivity in the lung that originates from radon gas. Medical represents the contribution from diagnostic medical examinations. Other represents the contribution from man-made sources of ionizing radiation, such as the nuclear-power industry and consumer products (for example, smoke detectors, CRT monitors, porcelain, and tobacco).

Uranium

The original nuclear-weapons program depended on exploration, mining, and milling of natural uranium. At that time, most of the known uranium deposits were deep underground and required extensive mining operations that were labor-intensive. As mentioned earlier, uranium is radioactive and has a very long half-life. When uranium decays, it emits an alpha particle. The remaining nucleus, thorium, is also radioactive. It promptly decays by emitting a beta particle. That radioactive sequence continues for 13 decays until a stable isotope of lead is

FIGURE 3.1 Relative contribution to average effective dose received by persons living in the United States. The striped sections are from man-made sources of ionizing radiation. The other sections are from natural background radiation.

formed. Thus, alpha (&alpha), beta (&beta), and gamma (&gamma) radiations are present in underground mines. Their presence can result in external exposure to gamma rays and internal exposure to alpha, beta, and gamma radiations from inhalation and unintentional ingestion of ore dust.

Risk to Miners

In general, the most hazardous exposure pathway for underground miners is not related to the ore dust itself or external gamma rays. About halfway through the uranium decay process, 226 Ra decays into 222 Rn. Radon is an inert gas that escapes from the rocks and begins to accumulate in the mine. It ultimately decays. This initiates a prompt series of decays that occur within a matter of minutes:

Those four short-lived radioactive descendants or decay products of radon have historically been called radon daughters. They can become suspended in air and are respirable. Inhaled radon is rapidly exhaled whereas radon decay products can deposit in the airways. Alpha particles emitted by 218 Po and 214 Po can deliver a large amount of energy and result in a large dose to cells in the airways. Those processes have been directly associated with the development of lung cancer in uranium miners. They are also the reasons for concern in family dwellings that have high concentrations of indoor radon from natural background.

The concentration of the short-lived decay products of radon is measured in working level (WL). A person&rsquos exposure at a given location is based on the concentration of decay products and the amount of time the person spends at the location. That exposure is expressed in working level month (WLM). For the purposes of this definition, 1 month is considered to be 170 h. Thus, 1 WLM is equivalent to 1 WL for 170 h, 2 WL for 85 h, 5 WL for 34 h, and so on. The risk of radiation-induced lung cancer is related to the exposure in WLM. For comparison purposes, 1 WLM delivers an effective dose of about 10 mSv (1 rem) to the trachea bronchial region of the respiratory tract.

Risk to Ore Transporters and Millers

After uranium ore is extracted from the mine, it is shipped to a mill, where it is crushed into fine sand and subjected to a chemical process to remove uranium selectively from the ore. The final product, uranium oxide (U3O8), often called yellowcake, is used for the production of weapons or as fuel for nuclear reactors. The remaining sands, called uranium mill tailings, are placed into a tailings pile close to the mill.

Yellowcake has a much higher concentration of uranium than the original ore removed from the mine. However, because uranium has an extremely long half-life, the radioactivity is not the principal hazard. The most serious hazard is heavy-metal chemical toxicity because of ingestion or inhalation.

Risk from Mill Tailings

The fine silt and sands in mill tailings contain all the other radioactive isotopes in the ore except the uranium. In effect, that represents all the radioactivity in the uranium decay series, including radon. Because radon is a noble gas, it can escape from the sands and is a potential route of exposure of persons residing near the mill or of exposure later when the tailings are used for construction or landfill around homes. Exposure to external radiation and radon decreases rapidly with distance from the tailings.

Nuclear Weapons and Fallout

Yellowcake is an oxide of natural uranium. Natural uranium consists of the isotopes 238 U (99.3%), 235 U (0.7%), and 234 U (trace). 235 U is necessary for a nuclear weapon. Thus, the yellowcake must undergo another process to increase the proportion of 235 U. That is called enrichment, and the desired product is enriched uranium. The remaining byproduct is called depleted uranium and is almost exclusively 238 U.

When a nuclear weapon is detonated, energy is released through a process called fission. Fission occurs when a heavy nucleus absorbs an additional neutron and then violently splits into two pieces and a few extra neutrons. If neutrons survive to produce another fission, the process can sustain itself. Weapons are designed to generate enough fissions to initiate an explosion in a fraction of a second following detonation. The first nuclear weapons released energy equivalent to 15,000 tons (15 kiloton) of TNT. Later versions used either 235 U or plutonium-239 ( 239 Pu) to produce fission yields over 1,000 kilotons.

The two nuclear fragments that remain after fission are called fission products. Many possible combinations of fragments can occur. One or both of the fission products can be radioactive. Some have very short half-lives and so decay within seconds or minutes. Others have half-lives of days (for example, 131 I) or years (for example, 90 Sr, and 137 Cs).

Fission products are propelled into the atmosphere by the force of the explosion. They can remain suspended and transported by winds. Eventually, the radioactive fission products settle back toward the surface of the earth and are called fallout. Fallout can be increased locally by precipitation wash-out (Beck, 2002 Bennett, 2002). Fallout can be responsible for both external and internal exposures of people in the vicinity. More than 150 fission products have half-

lives greater than 1 h. Some of the important radioactive fission products in fallout and their principal exposure pathway are listed in Table 3.4.

Dosimetry

Dosimetry is the process of determining the effective dose received by persons exposed to ionizing radiation. The most accurate way to determine dose to an individual is to make measurements with a dosimeter assigned to each person. That is required today for radiation workers that might be exposed during routine occupational activities. Area monitors measure external radiation or radioactivity suspended in the air at specific locations. No dosimeter can directly measure the dose to the lung from the inhalation of radioactive materials, so area monitors are the principal instruments used for measuring and controlling internal exposure in underground mines.

Personal dosimeters were not available for all persons who might have been affected by fallout from atmospheric weapons testing. The US Atomic Energy Commission collected fallout on gummed film at more than 100 locations in the United States and its territories. The film was collected regularly and analyzed to estimate radioactivity deposited on the ground (Beck et al., 1990). The resulting data and weather patterns were used to create maps of fallout across the country.

Dose reconstruction is a computational process for estimating the dose to persons in situations when direct measurements are incomplete or unavailable. The National Cancer Institute has developed maps that show concentrations of radioactivity deposited in the United States from fallout during the period of atmospheric

TABLE 3.4 Some Important Fission Products in Fallout and Their Exposure Pathways. They are Ordered with Increasing Atomic Mass

weapons testing. These data can be used to estimate the dose from internal and external radiation to persons living downwind of a test site. A more extensive description of these maps and dose calculators is presented in Chapter 4.

RADIATION BIOLOGY

When people are exposed to ionizing radiation from sources outside or inside the body, the radiation may interact with molecules in cells in their path. As described earlier in this chapter, some ionizing radiation can travel through a few or several layers of cells (beta-particle radiation) or through many cell layers into and through tissues deep within the body (x and gamma radiation), whereas alpha-particle radiation has short paths or tracks. The rate at which radiation loses energy along its tracks is referred to as linear energy transfer (LET) and depends on its track length. Thus, beta-particle radiation and the electrons associated with x and gamma rays, which are sparsely ionizing, are described as low-LET radiation, and alpha-particle radiation, which is densely ionizing, as high-LET radiation.

Biologic Actions of Ionizing Radiations

The main target of importance with respect to radiation damage is the deoxyribonucleic acid (DNA) in the cell&rsquos nucleus. The interactions between ionizing radiation and DNA can be direct or indirect.

Direct interactions occur when the radiation is deposited or transfers its energy directly to DNA. However, the probability of direct interactions is low because the volume of DNA is small relative to the total volume of the cell. Direct interactions occur more commonly when the radiation is of the densely ionizing type, such as alpha- or beta-particle radiation, than when it is less densely ionizing, such as gamma and x radiation.

Radiation interacts indirectly with DNA by first interacting with water molecules in the vicinity of the DNA, causing ionizations that result in the formation of free hydroxyl radicals. The free radicals can then diffuse to the vicinity of the DNA and can cause alterations in it. About 60% of the DNA damage caused by radiation is the result of indirect interactions. However, few of the many interactions that occur result in DNA damage, because most of the free radicals disperse and deposit their energy without interacting with DNA.

Biologic Sensitivity to Ionizing Radiations

An important concept in radiation biology is that the most rapidly dividing cells are the least well differentiated and are the most sensitive to radiation and thus are the most vulnerable to radiation-induced death and injury. The concept of radiosensitivity was formulated by Bergonie and Triboneau (1906). Some

proliferative cells in the testis, red bone marrow, and intestinal mucosa, are among the most radiosensitive. Cells that divide more slowly, if at all, and cells that are highly differentiated, such as mature red blood cells and muscle and nerve cells, typically are relatively insensitive to radiation. Large lymphocytes (a type of white blood cell) divide more frequently than do small lymphocytes, but they are both highly sensitive to radiation. One of the earliest clinical effects of an acute whole-body dose of radiation&mdashover about 250 mSv (25 rem)&mdashin humans is a rapid fall in the number of large lymphocytes, beginning within 24 h. Because small lymphocytes divide infrequently radiation-induced changes in their DNA are more persistent, so aberrations in them can persist for many years after a large radiation dose (Goans et al., 2001).

A radiation dose delivered all at once or within a short period has a greater biologic effect than the same total dose delivered in small amounts over a period of weeks (fractionation) or in very small amounts continuously over a long period (protraction). In the latter cases, fewer cells are likely to be killed or lethally damaged at one time. DNA repair can proceed in the intervals between the successive exposures of a single cell from a fractionated exposure, or may be sufficient to counteract damage occurring during a protracted exposure, so that low dose rates allow for cell recovery or replacement.

Radiation-Induced Biological Damage

External exposure of the whole body or a substantial part of the body to penetrating radiation, such as gamma and x rays, can damage DNA in the cells of tissues deep within the body. External radiation dose is deposited independent of differential uptake in cells and sub-cellular regions due to ongoing local metabolic processes. Inhomogeneous dose distribution is more characteristic of internal emitters than external radiation sources. When an exposed person leaves the vicinity of an external source of radiation, no further dose is received from that source.

High-energy alpha- or beta-particles deposited on or close to the skin can penetrate the outer layers of dead and aging skin cells to reach the deeper or germinal layer in which cells are actively dividing. Radioactive particles that enter the body are distributed through many organs according to the nature of the metabolism of the particles, and the functions of the different organs. Only rarely are they distributed uniformly throughout the body most are deposited in target tissues or organs for example, 131 I, like stable iodine, targets the thyroid gland. The dose deposited in different organs is the best measure of radiation to use in correlations of internal dose with observed and expected effects. Doses to different organs from radioactive particles in the body are likely to be quite heterogeneous large differences between organs are based on metabolic factors. Radioactivity taken into the body persists until it decays away or the radioactive element is eliminated from the body.

Repair of Radiation-Induced Damage

Repair of DNA damage caused by radiation from sources outside or inside the body is an effective, normal biologic process. This highly efficient repair process, which has evolved over many millennia, enables organisms, including humans, to survive and thrive despite constant exposure to background levels of radiation in the environment that in earlier millennia were much higher than they are now. However, ionizing radiation is more likely to damage both strands of DNA simultaneously than are normal metabolic processes. That is because ionizations may occur close together along the tracks of charged particles (electrons, protons, and alpha particles), thereby damaging both DNA strands and producing DNA double-strand breaks or other damage affecting both DNA strands in close proximity.

Repair of radiation-induced damage is usually complete and accurate, restoring damaged DNA to its full function. But if the damage is irreparable and the cells die immediately or are unable to divide to produce new cells of the same type, cell systems become depleted and if the rate of depletion exceeds the rate at which the body can replace the lost cells, the underlying radiation-induced biologic damage is likely to become clinically evident in the form of adverse health effects. Radiation biologists describe such effects as deterministic effects because their type and severity are determined by the nature and magnitude of the radiation dose received. DNA repair also can be incomplete or inaccurate, in which case cells survive and divide but with some probability of changes, or mutations, in some of their genes. In time, such mutations may result in other adverse health effects, primarily cancer. Radiation biologists describe these late or delayed-onset effects as stochastic effects because their occurrence follows some random probability distribution or pattern that is, they are effects that occur at random with some degree of probability that is related to a person&rsquos radiation dose.

Human Health Effects of Radiation-Induced Biologic Damage

The onset of deterministic health effects may be acute or delayed, depending on the type.

Acute or Early Deterministic Effects

Acute or early deterministic effects become clinically evident within minutes up to about 2 months after an acute radiation exposure of the whole body or partial body of sufficient magnitude to cause a critical number of cells in individual tissue systems, such as the blood-forming tissues, to die prematurely or to lose their ability to divide. The higher the acute radiation dose, the earlier the deterministic effects occur after the exposure and the more severe they are. Clini-

TABLE 3.5 Estimated Threshold Absorbed Doses for Selected Deterministic Effects of Acute Exposure to low LET Radiation a

Depression of blood cell formation process

a SOURCE: Adapted from IOM, 1999.

cal, epidemiologic, and animal studies have shown that threshold doses of radiation are required to cause specific deterministic effects, that is, dose thresholds below which specific types of deterministic effects are not seen (Mettler and Upton, 1995). The minimum or threshold doses necessary to cause specific deterministic effects depend on the radiation sensitivities of the exposed cell systems. Estimated threshold absorbed doses for selected deterministic effects of acute exposure to low-LET radiation are shown in Table 3.5.

The spectrum of early signs and symptoms observed after a whole- or partial-body dose of 0.5-1.0 Gy or more is known as the acute radiation syndrome (ARS). The clinical features of the ARS have been described in detail by Young (1987). On the basis of the committee&rsquos review of information about reconstructed radiation dose estimates of downwinders and onsite participants, it is considered highly unlikely that people in the RECA populations received acute whole- or partial-body doses of gamma radiation of sufficient magnitude to cause deterministic effects, including the ARS (Lloyd et al., 1990 Henderson and Smale, 1990 Till et al., 1995 Caldwell et al., 1983).

Exposure to ionizing radiation at natural background levels normally present in the environment does not result in discernible deterministic health effects in humans.

Late Deterministic Effects

Some types of deterministic effects may appear many months or years after an exposure to a relatively high dose of radiation these effects result from cell death or injury that occurred at the time of the exposure but which do not become clinically evident until a long period has passed. This category includes radiation-induced cataract, fibrosis, fibrovascular atrophy, thyroid dysfunction, and effects in an exposed embryo or fetus.

Cataract is one of the few health effects of radiation exposure that essentially is pathologically characteristic, at least in its early stages, of radiation injury.

Cataracts of the posterior subcapsular type have been described as being clinically detectable and distinguishable from cataracts due to other causes after doses to the lens of about 2 Gy of low LET radiation and a minimum latent period of about 10-12 months.

The threshold doses of radiation to localized areas of the body sufficient to result in radiation-induced fibrosis, fibrovascular atrophy, and thyroid dysfunction are considerably higher than the threshold dose for cataract induction.

Exposure of a pregnant woman to radiation may cause nonspecific deterministic effects in the embryo or fetus. Such in utero effects may be expressed clinically in the embryo or fetus or after the child&rsquos birth. The nature of these effects and their severity are related to the radiation dose to the embryo or fetus and the period of the pregnancy (gestation) in which the exposure occurred (Brent, 1999) (see Chapter 7).

Stochastic Effects

Radiation-induced damage that is incompletely or incorrectly repaired increases the probability of genetic mutations in affected cells. If the affected cells are of the somatic type, that is, the type of cell that is not handed on to a person&rsquos offspring, the probability is increased for stochastic (late) effects such as cancer, appearing in irradiated people years or even decades after exposure. If the affected cells are of the reproductive type&mdashthat is, they are transmitted to the next generation&mdashthere also is a small probability of radiation-induced heritable genetic effects in the progeny of those exposed. Such effects, which are not peculiar to radiation, occur randomly with frequencies and probabilities that increase with increasing dose. Their severity is unrelated to dose. In the absence of definitive biologic or epidemiologic data to the contrary, it is assumed that there is no dose threshold below which the risk of stochastic effects is zero.

Cancer and the Carcinogenic Effect of Radiation Cancer is a collective term used to describe many types of malignant diseases. Their induction and development follow a multistage process that is not yet fully understood but is known to be influenced by many factors inside and outside the body. Cancer occurs mainly in older people. The American Cancer Society estimates that 40-45% of the US population develop some form of cancer during their lifetime and that cancer accounts for about 25% of deaths in the United States (Jemal et al., 2004). Exposure to radiation has been shown to increase the cancer risk in the exposed population by some amount that is often related to the dose and to the normal or background risk in the nonexposed population.

After exposure to radiation, mutations induced in somatic cells (cells whose genes are not passed on to the next generation) of an exposed person may alter cell proliferation and result in benign or noncancerous tumors. Additional mutations may then cause malignant changes whereby a benign tumor becomes malig-

nant. Theoretically, radiation-induced mutations in a single somatic cell can eventually result in the cell and its progeny becoming malignant or cancerous this progression is complex and depends on a variety of factors, only some of which have been characterized. On the basis of animal and epidemiologic studies, factors known to influence radiation induction of tumors include age at the time of exposure, sex, genetic background, and immune status these host factors and other known factors are discussed in more detail in Chapters 4 and 7.

In the absence of definitive data, scientists generally assume that all types of cancers are susceptible to induction by ionizing radiation. However, animal and epidemiologic studies have shown some cancers to be more likely to have been caused by radiation than others. Various types of cancer grouped by the strength of their statistical association with radiation and available risk estimates obtained in analyses of data from epidemiologic studies of populations at risk of exposure are shown in Table 3.6.

The time between the induction of any disease and its clinical detection or diagnosis is known epidemiologically as the latent period. Because we do not know precisely when a tumor is induced after a radiation exposure, the latent period of a radiation-induced tumor in an exposed person generally is taken to be the time between exposure and detection or diagnosis of the tumor. On the basis of epidemiologic data, the minimum latent periods for radiation-induced leukemia and most solid cancers usually are taken to be about 2 years and 10 years, respectively. For thyroid and bone cancers, the minimum latent periods are estimated to be about 5 years. Age-at-exposure and the magnitude of the radiation dose have been shown in epidemiologic studies to influence the latent periods of some specific tumor types that have been causally associated with radiation exposure.

The relative risk (RR) of developing leukemia (all types except CLL) after radiation exposure appears to rise to a plateau about 15 years after exposure and then about 25 years after exposure to begin a gradual decline toward the risk in the general, or nonexposed, population. The RRs for solid cancers appear to increase to a plateau at about 25 years after exposure and to remain at that level for an extended period&mdashpossibly for life, depending on the type of cancer.

Radiogenic cancers, cancers that can be attributed to radiation exposure, are histopathologically and clinically indistinguishable from spontaneous, or naturally occurring, cancers in nonexposed populations. As is discussed later in this chapter, attribution of cancer in general or of specific cancer types to radiation therefore must depend on the observation of statistical differences between their frequencies in populations exposed and those not exposed to radiation (other than background exposures).

When a specific type of cancer is described as radiogenic it does not mean that every cancer of that type was caused by radiation rather, it means that it is a type of cancer that has been statistically associated with radiation exposure in studies of exposed populations. Similar findings for a specific cancer type in


Biology

The purpose of science education is to develop scientific literacy, helping learners: to be interested in, and understand, the world around them to engage in discourse about the scientific and technological aspects underlying global and local issues to understand the testable and contestable nature of science, and question the claims made by others about scientific matters to be able to identify questions, draw evidence-based conclusions and discuss their validity and to form opinions, that are reasoned and informed, about the environment, about their own health and well-being, and about the role and impact of science on society. Biology is the study of the fascinating diversity of life as it has evolved and as it interacts and functions. Investigation of biological systems and their interactions, from the molecular level to cellular processes to ecosystem dynamics, has led to biological knowledge and understanding that enable us to explore and explain everyday observations, find solutions to biological issues, and understand the processes of biological continuity and change over time.

Rationale

Knowledge and understanding of science, scientific literacy and scientific methods are necessary for learners to develop the skills to resolve questions about their natural and constructed world.

The purpose of science education is to develop scientific literacy, helping learners: to be interested in, and understand, the world around them to engage in discourse about the scientific and technological aspects underlying global and local issues to understand the testable and contestable nature of science, and question the claims made by others about scientific matters to be able to identify questions, draw evidence-based conclusions and discuss their validity and to form opinions, that are reasoned and informed, about the environment, about their own health and well-being, and about the role and impact of science on society.

Biology is the study of the fascinating diversity of life as it has evolved and as it interacts and functions. Investigation of biological systems and their interactions, from the molecular level to cellular processes to ecosystem dynamics, has led to biological knowledge and understanding that enable us to explore and explain everyday observations, find solutions to biological issues, and understand the processes of biological continuity and change over time.

Biology aims to develop learners&rsquo:

  • sense of wonder and curiosity about life and respect for all living things and the environment
  • understanding of how biological systems interact and are interrelated the flow of matter and energy through and between these systems and the processes by which they persist and change
  • understanding of major biological concepts, theories and models related to biological systems at all scales, from subcellular processes to ecosystem dynamics
  • appreciation of how scientists use biology in a wide range of applications, and how biological knowledge influences society in local, regional and global contexts
  • ability to plan and carry out fieldwork, laboratory and other research investigations including the collection and analysis of qualitative and quantitative data and the interpretation of evidence
  • ability to use sound, evidence-based arguments creatively and analytically when evaluating claims and applying biological knowledge
  • ability to communicate biological understanding, findings, arguments and conclusions using appropriate representations, modes and genres.

Learning Outcomes

On successful completion of this course, learners will be able to:

  • plan activities and monitor and evaluate progress be organised to complete activities and meet deadlines contribute to completion of group activities in the context of biology
  • apply scientific techniques and practical skills using equipment safely and competently to collect data related to biology
  • use scientific inquiry to develop, conduct, interpret and evaluate experiments related to biology
  • collect and record primary and secondary data from a variety of relevant sources
  • apply discriminating research skills and adhere to the principles of academic integrity
  • communicate, predict and explain biological phenomena, using qualitative and quantitative representations in appropriate modes and genres, and following accepted conventions and terminology
  • make connections between knowledge of biology and ethical, political, cultural, social, economic and scientific considerations in differing contexts
  • apply biological concepts to describe processes at all levels of biological organisation: the chemical basis of life cells organisms and continuity of organisms and survival of changes
  • interpret information and apply biological concepts and processes to discuss problems and make plausible predictions
  • interpret data to draw valid conclusions.

Access

Pathways

This course is designed for learners who are interested in, and curious about, the science of the living world. The successful completion of Life Sciences Level 2 would provide useful preparation for the study of Biology .

The study of Biology will provide a foundation for learners to critically consider and to make informed decisions about contemporary biological issues in their everyday lives.

It may be studied as part of a pathway to tertiary study and careers in areas such as agriculture, botany, zoology, marine science, biotechnology, health science, pharmacy, medicine, nursing or veterinary science. It is also suitable for learners wishing to study a science as part of a general education.

Resource Requirements

Course Size And Complexity

This course has a complexity level of 3.

At Level 3, the learner is expected to acquire a combination of theoretical and/or technical and factual knowledge and skills and use judgement when varying procedures to deal with unusual or unexpected aspects that may arise. Some skills in organising self and others are expected. Level 3 is a standard suitable to prepare learners for further study at tertiary level. VET competencies at this level are often those characteristic of an AQF Certificate III.

This course has a size value of 15.

Course Requirements

All content areas of Biology are compulsory, however, the order of delivery is not prescribed.

This course has a design time of 150 hours. A minimum of 45 hours is to be spent on practical activities, which are an integral part of the course, and are to be used as a means of teaching and consolidating the course content as well as a means of assessment.

Case studies may be used to engage learners and integrate content from different parts of the course.

Course Content

For the content areas of Biology , the three (3) interrelated strands &ndash Science Inquiry Skills Science as a Human Endeavour and Science Understanding &ndash build on students&rsquo learning in F-10 Australian Curriculum: Science. In the practice of science, the three strands are closely integrated: the work of scientists reflects the nature and development of science it is built around scientific inquiry and it seeks to respond to and influence society. These three strands will be integrated into all areas of study in this course.

Learners will develop an understanding of scientific method and also biology as a human endeavour, throughout the course.

Science understanding will be developed through the study of four (4) sections:

  • The chemical basis of life (Criterion 5)
  • Cells (Criterion 6)
  • Organisms (Criterion 7)
  • Continuity of organisms and survival of changes (Criterion 8).

Each section will be studied with reference to relevant underlying concepts and processes from the following:

  • structure reflecting function
  • materials input/output
  • energy input/output
  • maintaining equilibrium
  • DNA: the code of life
  • managing challenges.

All sections of the course will be assessed against Criteria 1, 2, 3 and 4.

The course content structure is summarised in the table below:

Overarching Strands

Science Inquiry Skills, Science as a Human Endeavour, Science Understanding

  • Identify, research and construct questions for investigation propose hypotheses and predict possible outcomes
  • Design experiments, including the procedure(s) to be followed, the materials required, and the type and amount of primary and/or secondary data to be collected observe risk assessments and consider research ethics, including animal ethics
  • Safely, competently and methodically collect valid and reliable data from practical investigations
  • Represent data in meaningful and useful ways organise and analyse data to identify trends, patterns and relationships qualitatively describe sources of measurement error, and uncertainty and limitations in data and select, synthesise and use evidence to make and justify conclusions
  • Select, construct and use appropriate representations to communicate conceptual understanding, solve problems and make predictions
  • Interpret a range of scientific resources, for example, research and media reports, and evaluate processes, claims and conclusions by considering the quality of available evidence and use reasoning to construct scientific arguments
  • Communicate to specific audiences for specific purposes using appropriate language, nomenclature, genres and modes, including scientific reports.

SCIENCE AS A HUMAN ENDEAVOUR

  • Scientific knowledge can enable scientists to offer valid explanations and make reliable predictions
  • ICT and other technologies have dramatically increased the size, accuracy and geographic and temporal scope of data sets with which scientists work
  • Models and theories are contested and refined or replaced when new evidence challenges them, or when a new model or theory has greater explanatory power
  • The acceptance of scientific knowledge can be influenced by the social, economic and cultural context in which it is considered
  • People can use scientific knowledge to inform the monitoring, assessment and evaluation of risk
  • The use of scientific knowledge may have beneficial and/or harmful and/or unintended consequences
  • Science can be limited in its ability to provide definitive answers to public debate there may be insufficient reliable data available, or interpretation of the data may be open to question
  • Scientific knowledge can be used to develop and evaluate projected economic, social and environmental impacts and to design action for sustainability.

Experimental Design (Criterion 2)

  • Propose a testable hypothesis that identifies clearly the independent and dependent variable
  • Design a controlled experiment:
    • Explain the requirements for only one independent variable and the importance of controlling all other variables (fixed variables)
    • Explain the need for a control treatment for comparison
    • Explain the need for an appropriate sample size and replications and the limitations where this is not possible
    • Explain the economic, ethical and environmental constraints on the design.
    • Select appropriate analysis and data representations (graphs/tables)
    • Describe patterns/trends in results
    • Provide a reasonable interpretation/explanation of the results
    • Provide a summary conclusion as to whether results support or negate the hypothesis
    • Identify the strengths and weaknesses of an experimental design
    • Identify the limitations and sources of possible errors in the study
    • Suggest possible improvements to the method
    • Suggest further/alternative experiments.

    Application and impact of biological science in society (Criterion 4)

    • Biological knowledge can enable scientists to offer valid explanations and make reliable predictions. This knowledge, and understanding by society, is relevant to biological issues and informs decision making
    • People&rsquos values (ethical, political, cultural, social, economic, scientific) are important in decision making
    • Pressure groups/stakeholders influence decision making on biological issues
    • The use of scientific knowledge may have beneficial and/or harmful and/or unintended consequences
    • Current issues demonstrate the complexity and tensions (ethical, political, cultural, social, economic, scientific) surrounding decision making on biological issues.

    The chemical basis of life (Criterion 5)

    Cells carry out a variety of functions which require nutrients to be able to manufacture material for growth, maintenance and repair. Respiration and photosynthesis are essential for the production of energy of animals and plants. Cells require inputs of suitable forms of energy, including light energy or chemical energy in complex molecules, and matter, including gases, simple nutrients, ions, and removal of wastes, to survive. The activities of cells require a variety of biological molecules for metabolic activities. Enzymes are a catalyst that assist in many reactions.

    STRUCTURE REFLECTS FUNCTION

    Enzymes have specific structure and functions which can be affected by various factors.

    • Structure and function of enzymes
    • Role and characteristics of enzymes
    • Factors affecting rate of enzyme action
      • temperature
      • pH
      • concentration of substrate
      • concentration of enzyme
      • induced fit model
      • competitive and non-competitive inhibitors.

      Organisms need raw materials in the form organic and inorganic nutrients. All organisms need carbohydrates, proteins, lipids and nucleic acids.

      • Basic properties and functions of biological compounds
      • Differences between organic and inorganic compounds
      • Carbohydrates: monosaccharides, disaccharides and polysaccharides
      • Lipids: triglycerides only
      • Proteins: polymers of amino acids
      • Vitamins
      • Minerals and water.

      (Details of chemical structure not required.)

      Energy is used by all cells to carry out &ldquowork&rdquo. All activities of organisms are the result of their metabolism. Energy is used to build new molecules and break up old molecules and as a result all activities of cells use chemical energy.

      • Capture release and transfer of energy
      • Photosynthesis is a biochemical process that occurs in the chloroplasts of plant cells using light energy to synthesise organic compounds the overall process can be represented by a balanced chemical reaction:
        • initial reactants and final products (individual biochemical reactions not required)
        • factors affecting the rate of photosynthesis including: temperature, concentration of carbon dioxide, light intensity and light quality
        • initial reactants and final products including energy release for aerobic respiration and anaerobic respiration
        • anaerobic respiration in bacteria, yeast and plants (producing alcohol)
        • anaerobic respiration in animals (producing lactic acid)
        • sites of anaerobic and aerobic respiration
        • ATP as energy currency
        • carbohydrates and lipids as energy storage molecules.

        (Individual biochemical reactions not required.)

        All living organisms contain the genetic material deoxyribonucleic acid (DNA).

        • The structure and role of DNA
        • Structure and replication of DNA (details of enzymes not required)
        • Protein synthesis: a basic understanding of transcription and translation (details of enzymes involved not required)
        • Gene (or point) mutations as the source of genetic variation.

        Cells (Criterion 6)

        Cells are the basic functional unit of all living organisms, their structure varies according to their function. They contain DNA which is a helical double-stranded molecule that occurs bound to proteins in chromosomes in the nucleus, and as unbound circular DNA in the cytosol of prokaryotes and in the mitochondria and chloroplasts of eukaryotic cells.

        STRUCTURE REFLECTS FUNCTION

        • Structure reflects function in cells and cell organelles
        • Differences between plant and animal cells
        • In eukaryotic cells, specialised organelles facilitate biochemical processes of photosynthesis, cellular respiration, the synthesis of complex molecules, and the removal of cellular products and wastes
        • Identification and function of organelles:
          • nucleus, nucleolus, nuclear membrane
          • mitochondrion
          • chloroplast
          • Golgi apparatus
          • ribosome
          • endoplasmic reticulum (rough and smooth)
          • vacuole, lysosome, vesicle
          • centrioles
          • cell membrane, cell wall, including the fluid mosaic model
          • contractile vacuole
          • cilium, flagellum.

          Movement of materials across membranes occurs via diffusion, osmosis, active transport and/or endocytosis.

          • Cells need materials and remove waste
          • Passive processes: diffusion, facilitated diffusion and osmosis
          • Active processes: active transport, exocytosis and endocytosis
          • Significance of surface area to volume ratio.
          • Maintaining equilibrium in cells
          • Substances are kept in balance in cells &ndash salts, water
          • The mechanism of the contractile vacuole as an example of maintaining equilibrium in some single-celled organisms.
          • Cell division
          • Significance of mitosis and meiosis in asexual and sexual reproduction as a source of genetic variation (details of processes not required).

          Organisms (Criterion 7)

          STRUCTURE REFLECTS FUNCTION AND MATERIALS INPUT / OUTPUT

          • Structure reflect function in organisms &ndash examples to be studied in the context of input, breakdown, transfer and output of material in selected organisms
          • The principles involved in the following processes in vertebrates and plants (dicots only), with reference to the relationship between structure and function:
            • Digestion and absorption
              • the need for digestion in herbivores, carnivores and omnivores
              • physical and chemical digestion (including a variety of diets)
              • characteristics of efficient gas exchange (surfaces in animals and plants)
              • blood as a transport medium
              • the heart as a pump (not including foetal circulation)
              • arteries, veins and capillary structures
              • transport of water and food in plants (dicots only)
              • transpiration (including mechanisms) and translocation (not the mechanism)
              • nitrogenous wastes as products produced in the liver from excess amino acids (ammonia, urea and uric acid)
              • ultrafiltration and reabsorption in the kidney.
              • Adaptations of plants and animals (including structural, physiological and behavioural) to environmental variations in:
                • temperature
                • water availability (osmoregulation).

                Homeostasis involves a stimulus-response model in which change in external or internal environmental conditions is detected and appropriate responses occur via negative feedback in vertebrates, receptors and effectors are linked via a control centre by nervous and/or hormonal pathways.

                • Basic feedback mechanisms in vertebrates (homeostasis)
                • The concept of negative feedback mechanisms in the regulation of:
                  • temperature
                  • blood glucose
                  • water balance.

                  Continuity of organisms and survival of changes (Criterion 8)

                  • Asexual and sexual reproduction: genetics
                  • Significances of sexual and asexual reproduction
                  • Variations in the genotype of offspring arise as a result of the processes of meiosis and fertilisation, as well as a result of mutations. Monohybrid crosses, including incomplete dominance and co-dominance, multiple alleles (only for ABO bloods).
                  • Frequencies of genotypes and phenotypes of offspring can be predicted using probability models, including Punnett squares, and by taking into consideration patterns of inheritance, including the effects of dominant, autosomal and sex-linked alleles and multiple alleles (only for ABO bloods)
                  • Sex linkage
                  • Pedigrees.
                  • The species concept and the binomial system of nomenclature
                  • Speciation including isolating mechanisms
                  • Darwin&rsquos theory of evolution by natural selection
                  • The concepts of a gene pool, genetic drift, gene flow and changes in gene/allele frequency.
                  • Functions in relation to defence against disease
                  • Lymph nodes, lymph vessels, lymph, spleen, thymus, appendix and tonsils.

                  Organisms that cause disease

                  • Difference between infectious and non-infectious diseases: Infectious disease differs from other disease (for example, genetic and lifestyle diseases) in that it is caused by invasion by a pathogen and can be transmitted from one host to another
                  • Conditions under which an organism is described as a pathogen
                  • Difference between the following pathogens prions, viruses, bacteria, fungi, protists and parasites
                  • Transmission of diseases: Pathogens have adaptations that facilitate their entry into cells and tissues and their transmission between hosts transmission occurs by various. mechanisms including through direct contact, contact with body fluids, and via contaminated food, water or disease-specific vectors.

                  Lines of defence inside the body

                  Immunity is the human body&rsquos ability to resist almost all types of organisms and toxins that tend to damage the tissues or organs.

                  Non-specific (innate) immune responses

                  • Barriers to prevent entry of pathogens to humans:
                    • Structural
                      • skin, mucous membranes, cilia
                      • pH
                      • Competition from non-pathogenic organisms.
                      • Body&rsquos defence mechanisms: When a pathogen enters a host, it causes physical or chemical changes (for example, the introduction of foreign chemicals via the surface of the pathogen, or the production of toxins) in the cells or tissues these changes stimulate the host immune responses.
                      • 2 nd Line of defence mechanisms:
                        • Inflammatory &ndash histamine release, increased blood flow and permeability of blood vessels
                        • Phagocytic &ndash phagocytic cells and NK cells
                        • Physiological &ndash fever
                        • Chemical &ndash cytokines, complement proteins.

                        Specific (adaptive) immune responses

                        In humans, adaptive responses to specific antigens include the production of humoral immunity through the production of antibodies by B lymphocytes, and the provision of cell-mediated immunity by T lymphocytes in both cases memory cells are produced that confirm long-term immunity to the specific antigen.

                        • Humoral response:
                          • Production and function of antibodies
                          • Complement proteins.
                          • Cytotoxic T cells, helper T cells, suppressor T cells
                          • Activated phagocytes
                          • Antigen presenting cells &ndash macrophages, dendritic cells, B cells
                          • Graft rejection.

                          Passive or active immunity

                          In humans, immunity may be passive (for example, antibodies gained via the placenta or via antibody or T lymphocyte serum injection) or active (for example, acquired through actions of the immune system as a result of natural exposure to a pathogen or through the use of vaccines).

                          • Difference between passive and active immunity
                          • Immunisation
                          • Primary and secondary response to antigen.

                          Assessment

                          Criterion-based assessment is a form of outcomes assessment that identifies the extent of learner achievement at an appropriate end-point of study. Although assessment &ndash as part of the learning program &ndash is continuous, much of it is formative, and is done to help learners identify what they need to do to attain the maximum benefit from their study of the course. Therefore, assessment for summative reporting to TASC will focus on what both teacher and learner understand to reflect end-point achievement.

                          The standard of achievement each learner attains on each criterion is recorded as a rating &lsquoA&rsquo, &lsquoB&rsquo, or &lsquoC&rsquo, according to the outcomes specified in the standards section of the course.

                          A &lsquot&rsquo notation must be used where a learner demonstrates any achievement against a criterion less than the standard specified for the &lsquoC&rsquo rating.

                          A &lsquoz&rsquo notation is to be used where a learner provides no evidence of achievement at all.

                          Providers offering this course must participate in quality assurance processes specified by TASC to ensure provider validity and comparability of standards across all awards.To learn more, see TASC's quality assurance processes and assessment information.

                          Internal assessment of all criteria will be made by the provider. Providers will report the learner&rsquos rating for each criterion to TASC.

                          TASC will supervise the external assessment of designated criteria which will be indicated by an asterisk (*). The ratings obtained from the external assessment will be used in addition to internal ratings from the provider to determine the final award.

                          Quality Assurance Process

                          The following processes will be facilitated by TASC to ensure there is:

                          • a match between the standards of achievement specified in the course and the skills and knowledge demonstrated by learners
                          • community confidence in the integrity and meaning of the qualification.

                          Process &ndash TASC gives course providers feedback about any systematic differences in the relationship of their internal and external assessments and, where appropriate, seeks further evidence through audit and requires corrective action in the future.

                          External Assessment Requirements

                          The external assessment for this course will comprise:

                          For further information see the current external assessment specifications and guidelines for this course available in the Supporting Documents below.

                          Criteria

                          The assessment for Biology Level 3 will be based on the degree to which the learner can:

                          1. apply personal skills to plan, organise and complete activities
                          2. develop, interpret and evaluate biological experiments*
                          3. collect, record, process and communicate information
                          4. discuss the application and impact of biology in society
                          5. describe and apply concepts and processes of the chemical basis of life*
                          6. describe and apply concepts and processes involving cells*
                          7. describe and apply concepts and processes within organisms*
                          8. describe and apply concepts and processes related to continuity of organisms and survival of changes*

                          * = denotes criteria that are both internally and externally assessed

                          Standards

                          Criterion 1: apply personal skills to plan, organise and complete activities

                          Rating A Rating B Rating C
                          selects and uses techniques and equipment safely, competently and methodically, applying them to unfamiliar contexts selects and uses techniques and equipment safely, competently and methodically uses familiar techniques and equipment safely and competently
                          follows instructions accurately and methodically, adapting to new circumstances follows instructions accurately and methodically to complete activities follows instructions accurately to complete activities
                          monitors and critically evaluates progress towards meeting goals and timelines, and plans realistic future actions monitors and evaluates progress towards meeting goals and timelines, and plans/negotiates realistic future actions monitors progress towards meeting goals and timelines and plans/negotiates future actions
                          meets planned timelines and addresses all aspects of the activity with a high degree of accuracy meets planned timelines and addresses all aspects of the activity meets planned timelines and addresses most aspects of the activity
                          performs and monitors own contribution, and guides others in their contribution to successful completion of group activities. performs tasks and monitors own contribution to successful completion of group activities. performs tasks to contribute to successful completion of group activities.

                          Criterion 2: develop, interpret and evaluate biological experiments

                          This criterion is both internally and externally assessed.

                          Rating A Rating B Rating C
                          expresses a hypothesis to explain observations, as a precise and testable statement that can be supported or refuted by an experiment expresses a hypothesis to explain observations, as a precise and testable statement expresses a hypothesis to explain observations, meeting most of the criteria of a testable hypothesis
                          designs a controlled, safe and ethical experiment, identifying all variables and including all accepted elements of experimental design, to efficiently collect valid, reliable data designs a controlled, safe and ethical experiment, identifying the main variables, to collect valid, reliable data designs a controlled experiment, identifying the main variables and considering safety and ethics, to collect valid data
                          critically analyses, interprets and explains data to draw a valid conclusion that relates to a hypothesis analyses, interprets and explains data to draw a valid conclusion that relates to a hypothesis based on data, provides some explanation and draws a conclusion that relates to a hypothesis that has some validity
                          discusses significant limitations and sources of error in experimental design, with reference to evidence identifies significant limitations and sources of error in experimental design identifies some limitations and sources of error in experimental design
                          critically analyses an experimental design and provides an evidence-based critique and discussion on valid improvements and alternatives. evaluates an experimental design and describes a number of possible valid improvements. identifies a valid improvement in an experimental design.

                          Criterion 3: collect, record, process and communicate information

                          Rating A Rating B Rating C
                          uses a variety of relevant sources to collect information and critically evaluates their reliability uses a variety of relevant sources to collect information and evaluates their reliability uses differing relevant sources to collect information
                          collects a wide range of relevant and accurate qualitative and quantitative experimental data, and records it methodically in a format that allows analysis collects relevant and accurate qualitative and quantitative experimental data and records it in a format that allows analysis collects and records relevant qualitative and quantitative experimental data, with some degree of accuracy
                          accurately follows accepted complex conventions and terminology in written responses accurately follows accepted conventions and terminology in written responses follows accepted conventions and terminology to achieve clarity in written responses
                          clearly identifies the information, images, ideas and words of others used in the learner&rsquos work clearly identifies the information, images, ideas and words of others used in the learner&rsquos work differentiates the information, images, ideas and words of others from the learner&rsquos own
                          clearly identifies sources of the information, images, ideas and words that are not the learner&rsquos own. Referencing conventions and methodologies are followed with a high degree of accuracy. clearly identifies sources of the information, images, ideas and words that are not the learner&rsquos own. Referencing conventions and methodologies are followed correctly. identifies the sources of information, images, ideas and words that are not the learner&rsquos own. Referencing conventions and methodologies are generally followed correctly.
                          creates appropriate, well-structured reference lists/bibliographies creates appropriate, structured reference lists/bibliographies creates appropriate reference lists/bibliographies
                          selects and uses appropriate scientific formats for effective and accurate communication of information for specific audiences and purposes. uses an appropriate scientific format for clear and accurate communication of information for specific audiences and purposes. uses an appropriate scientific format for communication of information.

                          Criterion 4: discuss the application and impact of biology in society

                          Rating A Rating B Rating C
                          explains relevance of identified science background to an issue describes relevant science background to an issue identifies relevant science background to an issue
                          evaluates aspects and explains significant components of an issue to present a detailed and balanced discussion with reference to evidence evaluates aspects and describes components of an issue to present a balanced discussion identifies key components of an issue and presents a discussion
                          critically evaluates the tensions and connections between all significant relevant influences (ethical, political, cultural, social, economic, scientific) in a range of contexts discusses the connections between an issue and most of the relevant influences (ethical, political, cultural, social, economic, scientific) in a range of contexts outlines connections between an issue and some of the relevant influences (ethical, political, cultural, social, economic, scientific) in more than one context
                          analyses and evaluates to present a complex argument related to benefits of the use of scientific knowledge, and any harmful or unintended consequences discusses benefits of the use of scientific knowledge, and any harmful or unintended consequences describes benefits of the use of scientific knowledge, and any harmful or unintended consequences
                          argues a reasoned conclusion, linking it to relevant evidence, and assesses the relative impact of influences on their decision making. argues a reasoned conclusion, linking it to relevant evidence. presents a reasoned conclusion, using some relevant evidence.

                          Criterion 5: describe and apply concepts and processes of the chemical basis of life

                          This criterion is both internally and externally assessed.

                          Related to the study of the chemical basis of life, the learner:

                          Rating A Rating B Rating C
                          correctly explains concepts and processes correctly describes concepts and processes correctly identifies fundamental concepts and processes
                          applies concepts and processes to explain the chemical basis of life, analyses and interprets complex problems, and makes reasoned, plausible predictions in familiar and unfamiliar contexts applies concepts and processes to explain the chemical basis of life, analyse and interpret problems, and makes plausible predictions in familiar and some unfamiliar contexts applies fundamental concepts and processes to describe the chemical basis of life, interprets problems, and makes plausible predictions in familiar contexts
                          justifies the selection of data as evidence, critically analyses and interprets evidence with reference to concepts, and draws evidence-based conclusions that identify any limitations. selects appropriate data as evidence, analyses and interprets evidence with reference to concepts, and draws valid conclusions based on data. uses data to demonstrate links to fundamental concepts, and presents simple valid conclusions based on data.

                          Criterion 6: describe and apply concepts and processes involving cells

                          This criterion is both internally and externally assessed.

                          Related to the study of cells, the learner:

                          Rating A Rating B Rating C
                          correctly explains concepts and processes correctly describes concepts and processes correctly identifies fundamental concepts and processes
                          applies concepts and processes to explain cells, analyses and interprets complex problems, and makes reasoned, plausible predictions in familiar and unfamiliar contexts applies concepts and processes to explain cells, analyses and interprets problems, and makes plausible predictions in familiar and some unfamiliar contexts applies fundamental concepts and processes to describe cells, interprets problems, and makes plausible predictions in familiar contexts
                          justifies the selection of data as evidence, critically analyses and interprets evidence with reference to concepts, and draws evidence-based conclusions that identify any limitations. selects appropriate data as evidence, analyses and interprets evidence with reference to concepts, and draws valid conclusions based on data. uses data to demonstrate links to fundamental concepts, and presents simple valid conclusions based on data.

                          Criterion 7: describe and apply concepts and processes within organisms

                          This criterion is both internally and externally assessed.

                          Related to the study of organisms, the learner:

                          Rating A Rating B Rating C
                          correctly explains concepts and processes correctly describes concepts and processes correctly identifies fundamental concepts and processes
                          applies concepts and processes to explain organisms, analyses and interprets complex problems, and makes reasoned, plausible predictions in familiar and unfamiliar contexts applies concepts and processes to explain organisms, analyses and interprets problems, and makes plausible predictions in familiar and some unfamiliar contexts applies fundamental concepts to describe organisms, interprets problems, and makes plausible predictions in familiar contexts
                          justifies the selection of data as evidence, critically analyses and interprets evidence with reference to concepts, and draws evidence-based conclusions that identify any limitations. selects appropriate data as evidence, analyses and interprets evidence with reference to concepts, and draws valid conclusions based on data. uses data to demonstrate links to fundamental concepts, and presents simple valid conclusions based on data.

                          Criterion 8: describe and apply concepts and processes related to continuity of organisms and survival of changes

                          This criterion is both internally and externally assessed.

                          Related to the study of continuity of organisms and survival of changes, the learner:


                          Integrative Biology (INTEGBI)

                          Terms offered: Fall 2021, Fall 2020
                          An introduction to the biomes, plants, and animals of California. The lectures will introduce natural history as the foundation of the sciences, with an overview of geology, paleontology, historical biology, botany, zoology, ecosystem ecology, and conservation biology. The field labs will include activities on the UC Berkeley campus and around the Bay Area. Course is open to all students without prerequisite and will provide a foundation for advanced study in biology and field biology.
                          California Natural History: Read More [+]

                          Objectives & Outcomes

                          Course Objectives: Create detailed natural history observations with georeferenced photos and videos
                          Enjoy local ecosystems and museum collections as sources of study and inspiration
                          Identify the common organisms in your community with colloquial and scientific names
                          Produce sophisticated observations of organismal behavior and ecosystem processes
                          Synthesize your observations into comprehensive species lists for specific geographic areas
                          Understand the relationship between history, climate, and species composition in California

                          Rules & Requirements

                          Credit Restrictions: Students will receive no credit for INTEGBI㺋 after completing INTEGBI W11. A deficient grade in INTEGBI㺋 may be removed by taking INTEGBI W11.

                          Hours & Format

                          Fall and/or spring: 15 weeks - 2 hours of lecture and 1 hour of discussion per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Letter grade. Final exam required.

                          INTEGBI W11 California Natural History 4 Units

                          Terms offered: Prior to 2007
                          An introduction to the biomes, plants, and animals of California. Course is open to all students without prerequisite and will provide a foundation for advanced study in biology and field biology. Students will have the flexibility to choose their own adventure within the fields of geology, botany, and zoology, with possible emphases in paleontology, historical ecology, morphology, animal behavior, ecosystem ecology, or conservation biology. Fieldwork is a requirement and may be conducted remotely. There will be special field and lab opportunities available in the Bay Area and on the UC Berkeley campus for students who can attend.
                          California Natural History: Read More [+]

                          Hours & Format

                          Summer: 8 weeks - 6 hours of web-based lecture, 4 hours of fieldwork, and 2 hours of web-based discussion per week

                          Online: This is an online course.

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Letter grade. Alternative to final exam.

                          INTEGBI C13 Origins: from the Big Bang to the Emergence of Humans 4 Units

                          Terms offered: Fall 2018, Fall 2016, Fall 2014
                          This course will cover our modern scientific understanding of origins, from the Big Bang to the formation of planets like Earth, evolution by natural selection, the genetic basis of evolution, and the emergence of humans. These ideas are of great intrinsic scientific importance and also have far reaching implications for other aspects of people's lives (e.g., philosophical, religious, and political). A major theme will be the scientific method and how we know what we know.
                          Origins: from the Big Bang to the Emergence of Humans: Read More [+]

                          Hours & Format

                          Fall and/or spring: 15 weeks - 3 hours of lecture and 2 hours of discussion per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Letter grade. Final exam required.

                          Instructors: Marshall, Quataert

                          Also listed as: ASTRON C13

                          INTEGBI㺘 Freshman Seminars 1 Unit

                          Terms offered: Fall 2021, Spring 2021, Fall 2020
                          The Berkeley Seminar Program has been designed to provide new students with the opportunity to explore an intellectual topic with a faculty member in a small-seminar setting. Berkeley Seminars are offered in all campus departments, and topics vary from department to department and semester to semester.
                          Freshman Seminars: Read More [+]

                          Rules & Requirements

                          Repeat rules: Course may be repeated for credit when topic changes.

                          Hours & Format

                          Fall and/or spring: 15 weeks - 1 hour of seminar per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: The grading option will be decided by the instructor when the class is offered. Final Exam To be decided by the instructor when the class is offered.

                          INTEGBI㺟 The Ecology and Evolution of Animal Behavior 3 Units

                          Terms offered: Summer 2021 8 Week Session, Summer 2020 8 Week Session, Summer 2019 8 Week Session
                          Principles of evolution biology as they relate to animal behavior and behavioral ecology with broad coverage of animal groups. Special attention will be paid to the emerging discipline of behavioral ecology.
                          The Ecology and Evolution of Animal Behavior: Read More [+]

                          Rules & Requirements

                          Prerequisites: Open to all students designed for those not specializing in biology

                          Credit Restrictions: Students will receive no credit for Integrative Biology 31 after taking Integrative Biology 144, C144 or Psychology C115B.

                          Hours & Format

                          Fall and/or spring: 15 weeks - 2 hours of lecture, 1 hour of demonstration, and 1 hour of discussion per week

                          Summer:
                          6 weeks - 5 hours of lecture, 5 hours of demonstration, and 5 hours of discussion per week
                          8 weeks - 4 hours of lecture, 2 hours of demonstration, and 2 hours of discussion per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Letter grade. Final exam required.

                          INTEGBI C32 Bioinspired Design 3 Units

                          Terms offered: Spring 2021, Spring 2020, Spring 2019
                          Bioinspired design views the process of how we learn from Nature as an innovation strategy translating principles of function, performance and aesthetics from biology to human technology. The creative design process is driven by interdisciplinary exchange among engineering, biology, art, architecture and business. Diverse teams of students will collaborate on, create, and present original bioinspired design projects. Lectures discuss biomimicry , challenges of extracting principles from Nature, scaling, robustness, and entrepreneurship through case studies highlighting robots that run, fly, and swim, materials like gecko-inspired adhesives, artificial muscles, medical prosthetic devices, and translation to start-ups.
                          Bioinspired Design: Read More [+]

                          Rules & Requirements

                          Prerequisites: Open to all students

                          Hours & Format

                          Fall and/or spring: 15 weeks - 2 hours of lecture and 1 hour of discussion per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Letter grade. Alternative to final exam.

                          Instructor: Full

                          Formerly known as: Integrative Biology 32

                          Also listed as: L & S C30Z

                          INTEGBI㺡 Topics in Paleontology: The Age of Dinosaurs 3 Units

                          Terms offered: Fall 2013, Fall 2012, Fall 2010
                          Open without prerequisite to all students and designed for those not specializing in paleontology. Evolution, history, and ecology of the dinosaurs and their world, including the earliest mammals and birds.
                          Topics in Paleontology: The Age of Dinosaurs: Read More [+]

                          Hours & Format

                          Fall and/or spring: 15 weeks - 3 hours of lecture per week

                          Summer:
                          6 weeks - 8 hours of lecture per week
                          8 weeks - 6 hours of lecture per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Letter grade. Final exam required.

                          INTEGBI N33 Topics in Paleontology: The Age of Dinosaurs 2 Units

                          Terms offered: Summer 1996 10 Week Session
                          Open without prerequisite to all students and designed for those not specializing in paleontology. Evolution history, and ecology of the dinosaurs and their world, including the earliest mammals and birds.
                          Topics in Paleontology: The Age of Dinosaurs: Read More [+]

                          Rules & Requirements

                          Repeat rules: Course may be repeated for credit with instructor consent.

                          Hours & Format

                          Summer: 8 weeks - 4 hours of lecture per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Letter grade. Final exam required.

                          INTEGBI㺣AC Human Biological Variation 4 Units

                          Terms offered: Fall 2020, Fall 2019, Summer 2019 8 Week Session
                          This course addresses modern human biological variation from historical, comparative, evolutionary, biomedical, and cultural perspectives. It is designed to introduce students to the fundamentals of comparative biology, evolutionary theory, and genetics.
                          Human Biological Variation: Read More [+]

                          Hours & Format

                          Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

                          Summer: 8 weeks - 6 hours of lecture and 2 hours of discussion per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Letter grade. Alternative to final exam.

                          Instructor: Hlusko

                          INTEGBI㺥 Topics in Paleontology: The Antecedents of Man 3 Units

                          Terms offered: Prior to 2007
                          . Open without prerequisite toall students and designed for those not specializing in paleontology. Survey the evolution, ecology, and history of the primate order. Special emphasis will be given to primate origins, geographic distribution, and the evolution of the human lineage.
                          Topics in Paleontology: The Antecedents of Man: Read More [+]

                          Hours & Format

                          Summer: 8 weeks - 3 hours of lecture and 2 hours of laboratory per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Letter grade. Final exam not required.

                          INTEGBI㺧C Topics in Integrative Biology 2 Units

                          Terms offered: Spring 2013, Spring 2012, Spring 2011
                          Reading and discussion of the literature on particular topics in the field of integrative biology. Term paper and oral presentation. Section topics will vary from semester to semester. Students should check with department secretary for each semester's offerings.
                          Topics in Integrative Biology: Read More [+]

                          Rules & Requirements

                          Prerequisites: Preferentially open to freshmen consent of instructor

                          Hours & Format

                          Fall and/or spring: 15 weeks - 2 hours of discussion per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Offered for pass/not pass grade only. Final exam required.

                          INTEGBI㺩 Marine Mammals 2 Units

                          Terms offered: Fall 2021, Summer 2021 8 Week Session, Summer 2020 8 Week Session
                          A survey of marine mammal evolution, biology, behavior, ecology, and politics with a concentration on those species found in the North Pacific. Coverage would include: origin and evolution of cetaceans, pinnipeds, sirenians, and sea otters basic biology and anatomy of marine mammal groups, and North Pacific species in particular ecological interactions and role in nearshore and pelagic marine communities and interactions between humans and marine mammals.
                          Marine Mammals: Read More [+]

                          Rules & Requirements

                          Prerequisites: Designed for those not specializing in Integrative Biology

                          Hours & Format

                          Fall and/or spring: 15 weeks - 2 hours of lecture per week

                          Summer:
                          6 weeks - 5 hours of lecture per week
                          8 weeks - 4 hours of lecture per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Letter grade. Final exam required.

                          INTEGBI㺪 Primate Biology 3 Units

                          Terms offered: Summer 1996 10 Week Session
                          An introduction to the order of mammals of which we are members. The niches of primates in modern ecosystems, their anatomical and behavorial specialization, and their role as indicator species in conservation. The mechanisms and variety of primate social organization compared with that of other animals.
                          Primate Biology: Read More [+]

                          Rules & Requirements

                          Credit Restrictions: Open to all students but designed for those not specializing in biology.

                          Hours & Format

                          Summer: 8 weeks - 6 hours of lecture per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Letter grade. Final exam required.

                          INTEGBI㺫 What Lives Inside Us? Microbiomes and Symbiosis 4 Units

                          Terms offered: Not yet offered
                          We live in a microbial world, and the evolution of multicellular organisms has been intimately affected by microbes. Their influences range from mutualistic benefits to disease and represent a fundamental force that shapes plant and animal phenotypes and evolutionary trajectories. Recent advances in genomic methodologies have further increased our appreciation of the role of microbes in host health and fitness by unraveling the commonness of microbial communities in all organisms and their complex interactions with their hosts. This course will consider the broad range of host-microbe interactions and underlying mechanisms – from mutualism to pathogenesis, and from binary host-microbe interactions, to the microbiome.
                          What Lives Inside Us? Microbiomes and Symbiosis: Read More [+]

                          Rules & Requirements

                          Credit Restrictions: Students will receive no credit for INTEGBI㺫 after completing INTEGBI𧅶.

                          Hours & Format

                          Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Letter grade. Final exam required.

                          Instructor: Shapira

                          INTEGBI㺳 Origins and Evolution of Food Plants 3 Units

                          Terms offered: Not yet offered
                          The course will review major groups of food plants from an evolutionary and historical perspective, by examining the origins from wild relatives to current distribution and varieties today. Examples will be reviewed from a diversity of crops from around the world, such as grains, pulses, vegetables, fruits, nuts and others (e.g., caffeine-producing plants). General concepts covered will include plant morphology, evolutionary processes (domestication, hybridization , polyploidy, diversification) and relevant ecology (e.g., pollination biology, pest and pest control). Focus will include California agriculture and crops as illustrated through field trips.
                          Origins and Evolution of Food Plants: Read More [+]

                          Hours & Format

                          Summer: 8 weeks - 4 hours of lecture per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Letter grade. Final exam required.

                          Instructor: Harris

                          INTEGBI㻍A Integrative Human Biology 1 Unit

                          Terms offered: Fall 2021, Fall 2020, Fall 2019
                          Each week a different Integrative Biology faculty member will give a one hour lecture on how their research field contributes to our understanding of human biology. The integration of the disciplines of evolution, ecology, paleontology, comparative physiology, and comparative anatomy in the study of how humans function in ecosystems illuminates our understanding of human biology. During each presentation, the faculty member will also inform students about IB courses they teach, research in their lab, and which Berkeley Natural History Museum they may be affiliated with. This course gives undergraduates an opportunity to learn about the spectrum of research and courses offered by the different IB faculty.
                          Integrative Human Biology: Read More [+]

                          Rules & Requirements

                          Credit Restrictions: 77A and 77B may each be taken once for credit. Majors are required to take at least one semester of 77A OR 77B.

                          Hours & Format

                          Fall and/or spring: 15 weeks - 1 hour of seminar per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Offered for pass/not pass grade only. Final exam required.

                          Instructor: Carlson

                          INTEGBI㻍B Integrative Human Biology 1 Unit

                          Terms offered: Spring 2021, Spring 2020, Spring 2019
                          Each week a different Integrative Biology faculty member will give a one hour lecture on how their research field contributes to our understanding of human biology. The integration of the disciplines of evolution, ecology, paleontology, comparative physiology, and comparative anatomy in the study of how humans function in ecosystems illuminates our understanding of human biology. During each presentation, the faculty member will also inform students about IB courses they teach, research in their lab, and which Berkeley Natural History Museum they may be affiliated with. This course gives undergraduates an opportunity to learn about the spectrum of research and courses offered by the different IB faculty.
                          Integrative Human Biology: Read More [+]

                          Rules & Requirements

                          Credit Restrictions: 77A and 77B may each be taken once for credit. Majors are required to take at least one.

                          Hours & Format

                          Fall and/or spring: 15 weeks - 1 hour of seminar per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Offered for pass/not pass grade only. Final exam required.

                          Instructor: Carlson

                          INTEGBI㻔 Sophomore Seminar 1 or 2 Units

                          Terms offered: Fall 2021, Spring 2021, Fall 2020
                          Sophomore seminars are small interactive courses offered by faculty members in departments all across the campus. Sophomore seminars offer opportunity for close, regular intellectual contact between faculty members and students in the crucial second year. The topics vary from department to department and semester to semester. Enrollment limited to 15 sophomores.
                          Sophomore Seminar: Read More [+]

                          Rules & Requirements

                          Prerequisites: At discretion of instructor

                          Repeat rules: Course may be repeated for credit when topic changes.

                          Hours & Format

                          Fall and/or spring:
                          5 weeks - 3-6 hours of seminar per week
                          10 weeks - 1.5-3 hours of seminar per week
                          15 weeks - 1-2 hours of seminar per week

                          Summer:
                          6 weeks - 2.5-5 hours of seminar per week
                          8 weeks - 1.5-3.5 hours of seminar and 2-4 hours of seminar per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: The grading option will be decided by the instructor when the class is offered. Final Exam To be decided by the instructor when the class is offered.

                          INTEGBI㻗 Introduction to Research Methods in Biology 2 Units

                          Terms offered: Summer 2014 8 Week Session, Summer 2013 8 Week Session, Summer 2012 8 Week Session
                          This course provides a functional understanding of hypothesis/data driven research and exposure to current approaches and methods in biological science. The lectures address foundational concepts of the scientific method, research ethics, scientific communication, and how to understand scientific literature. The labs provide exposure to faculty research and experimental methods. The course is geared to incoming freshmen, sophomores, and transfer students interested in learning more about research.
                          Introduction to Research Methods in Biology: Read More [+]

                          Rules & Requirements

                          Prerequisites: Consent of instructor

                          Hours & Format

                          Summer: 8 weeks - 1 hour of lecture, 1 hour of discussion, and 3 hours of laboratory per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Letter grade. Final exam not required.

                          Instructor: Matsui

                          INTEGBI㻘 Leadership Communications for Biology Scholars 1 Unit

                          Terms offered: Fall 2009, Fall 2008, Fall 2007
                          Leadership skills and abilities such as communication, collaboration, critical thinking, and resourcefulness are critical to academic, professional, and personal success. The need for enlightened leaders is evident in every aspect of health and science such as designing innovative health programs, obtaining funding, conducting cutting-edge research, developing and gaining support to implement policy solutions. This course provides an understanding of the principles of leadership and communications for students in the Biology Scholars Program. Students will nurture those traits in themselves and apply those principles in situations specifically related to the health and science sectors.
                          Leadership Communications for Biology Scholars: Read More [+]

                          Rules & Requirements

                          Prerequisites: Acceptance into Biology Scholars Program

                          Hours & Format

                          Fall and/or spring: 15 weeks - 2 hours of lecture per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Letter grade. Final exam required.

                          Instructors: Hayes, Kim, Myrick

                          INTEGBI㻟 Special Research Project in Biology 1B 2 Units

                          Terms offered: Spring 2017, Fall 2016, Spring 2016
                          Students enrolled in Biology 1B can participate in special field research in addition to attending regular laboratory sections. Students work independently with minimal supervision. Students will learn how to develop a project, collect and record data, conduct and analyze experiments, write a report, and make an oral presentation. Project may require traveling to off-campus sites, and may include night or weekend work.
                          Special Research Project in Biology 1B: Read More [+]

                          Rules & Requirements

                          Prerequisites: Consent of instructor selected by interview

                          Hours & Format

                          Fall and/or spring: 15 weeks - 4 hours of fieldwork and 2 hours of discussion per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Offered for pass/not pass grade only. Final exam not required.

                          INTEGBI㻟B Lawrence Hall of Science Teaching Assistant 1 - 2 Units

                          Terms offered: Prior to 2007
                          Enrollment into this course is for students interested in teaching science to children under the guidance of the Lawrence Hall of Science Instructors and Staff. As a LHS Teaching Assistant (TA), you will have the opportunity to assist with workshops serving grade school-aged children and to lead small discussion groups. The workshops consist of organismal biology related materials. You will undergo training in the Hall’s Animal Discovery Room to ensure that you are prepared to support school and public programs scheduled in that space. There will also be opportunities to travel to nearby school districts to give presentations on the materials you work with.
                          Lawrence Hall of Science Teaching Assistant: Read More [+]

                          Rules & Requirements

                          Prerequisites: Students must be concurrently enrolled or have completed Biology 1B

                          Repeat rules: Course may be repeated for credit without restriction.

                          Hours & Format

                          Fall and/or spring: 15 weeks - 3-6 hours of fieldwork per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Offered for pass/not pass grade only. Final exam not required.

                          INTEGBI C96 Studying the Biological Sciences 1 Unit

                          Terms offered: Fall 2021, Fall 2020, Fall 2019
                          Students will be introduced to the "culture" of the biological sciences, along with an in-depth orientation to the academic life and the culture of the university as they relate to majoring in biology. Students will learn concepts, skills, and information that they can use in their major courses, and as future science professionals.
                          Studying the Biological Sciences: Read More [+]

                          Rules & Requirements

                          Prerequisites: Consent of instructor

                          Hours & Format

                          Fall and/or spring: 15 weeks - 2 hours of lecture per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Offered for pass/not pass grade only. Final exam required.

                          Instructor: Matsui

                          Also listed as: MCELLBI C96/PLANTBI C96

                          INTEGBI㻢 Directed Group Study 1 - 4 Units

                          Terms offered: Fall 2021, Spring 2021, Fall 2020
                          Lectures and small group discussions focusing on topics of interest, varying from semester to semester.
                          Directed Group Study: Read More [+]

                          Rules & Requirements

                          Prerequisites: Freshmen and sophomores only

                          Repeat rules: Course may be repeated for credit without restriction.

                          Hours & Format

                          Fall and/or spring: 15 weeks - 1-4 hours of directed group study per week

                          Summer:
                          6 weeks - 2.5-10 hours of directed group study per week
                          8 weeks - 1.5-7.5 hours of directed group study per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Offered for pass/not pass grade only. Final exam not required.

                          INTEGBI㻢BC Berkeley Connect 1 Unit

                          Terms offered: Fall 2021, Spring 2021
                          Berkeley Connect is a mentoring program, offered through various academic departments, that helps students build intellectual community. Over the course of a semester, enrolled students participate in regular small-group discussions facilitated by a graduate student mentor (following a faculty-directed curriculum), meet with their graduate student mentor for one-on-one academic advising, attend lectures and panel discussions featuring department faculty and alumni, and go on field trips to campus resources. Students are not required to be declared majors in order to participate.
                          Berkeley Connect: Read More [+]

                          Rules & Requirements

                          Repeat rules: Course may be repeated for credit without restriction.

                          Hours & Format

                          Fall and/or spring: 15 weeks - 1 hour of lecture per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Offered for pass/not pass grade only. Final exam not required.

                          INTEGBI㻣 Supervised Independent Study and Research 1 - 3 Units

                          Terms offered: Spring 2015, Spring 2014, Fall 2013
                          Lower division independent study and research intended for the academically superior student. Enrollment only with prior approval of faculty adviser directing the research.
                          Supervised Independent Study and Research: Read More [+]

                          Rules & Requirements

                          Prerequisites: GPA of 3.4 or greater

                          Repeat rules: Course may be repeated for credit without restriction.

                          Hours & Format

                          Fall and/or spring: 15 weeks - 0 hours of independent study per week

                          Summer:
                          6 weeks - 1-3 hours of independent study per week
                          8 weeks - 1-3 hours of independent study per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Offered for pass/not pass grade only. Final exam not required.

                          Formerly known as: Botany 99, Physiology 99, Anatomy 99

                          INTEGBI𧅤B Principles of Biodiversity 3 Units

                          Terms offered: Fall 2012, Spring 2002, Spring 2001
                          Biogeographic, temporal, and historical patterns of change in biological diversity phylogenetics and systematics processes involved in origin and extinction of taxa and floras/faunas population structure and demography (including human populations) community processes and maintenance of diversity ecosystem function global change human uses of and effects on biodiversity conservation biology.
                          Principles of Biodiversity: Read More [+]

                          Rules & Requirements

                          Prerequisites: Biology 1B

                          Hours & Format

                          Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Letter grade. Final exam required.

                          INTEGBI C100 Communicating Ocean Science 4 Units

                          Terms offered: Spring 2020, Spring 2018, Spring 2016, Spring 2015
                          For undergraduates interested in improving their ability to communicate their scientific knowledge by teaching ocean science in elementary schools or science centers/aquariums. The course will combine instruction in inquiry-based teaching methods and learning pedagogy with six weeks of supervised teaching experience in a local school classroom or the Lawrence Hall of Science with a partner. Thus, students will practice communicating scientific knowledge and receive mentoring on how to improve their presentations.
                          Communicating Ocean Science: Read More [+]

                          Rules & Requirements

                          Prerequisites: One course in introductory biology, geology, chemistry, physics, or marine science required and interest in ocean science junior, senior, or graduate standing consent of instructor required for sophomores

                          Hours & Format

                          Fall and/or spring: 15 weeks - 3 hours of lecture and 2 hours of fieldwork per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Letter grade. Final exam required.

                          Instructor: Rhew

                          Formerly known as: Earth and Planetary Science C100/Geography C146/Integrative Biology C100

                          Also listed as: EPS C100/GEOG C146

                          INTEGBI𧅥 Introduction to Scientific Writing 4 Units

                          Terms offered: Spring 2020, Spring 2019, Spring 2018
                          This course will introduce students to concepts and techniques for effective communication of scientific findings, both within the scientific community and to the general public. Students will be exposed to a variety of formats, including systematic observations in field journals, proposals, conference presentations, seminars, journal articles, popular science writing, and interviews. Students can expect to gain a sense of confidence in writing and public speaking about research. Direct language is valued in scientific writing, but creative approaches to style and structure will be emphasized.
                          Introduction to Scientific Writing: Read More [+]

                          Hours & Format

                          Fall and/or spring: 15 weeks - 4 hours of seminar per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Letter grade. Alternative to final exam.

                          Instructor: Fine

                          INTEGBI𧅦LF Introduction to California Plant Life with Laboratory 4 Units

                          Terms offered: Spring 2020, Spring 2018, Spring 2015
                          The relationship of the main plant groups and the plant communities of California to climate, soils, vegetation, geological and recent history, and conservation. Laboratory will also include at least two Saturday field trips and focus on main plant groups and major plant families in California, and use of keys to identify introduced and especially native pteridophytes, conifers, and flowering plants of the state.
                          Introduction to California Plant Life with Laboratory: Read More [+]

                          Rules & Requirements

                          Prerequisites: Biology 1B or consent of instructor

                          Credit Restrictions: Student will receive partial credit for 102LF after taking 102.

                          Hours & Format

                          Fall and/or spring: 15 weeks - 2 hours of lecture and 6 hours of laboratory per week

                          Summer: 8 weeks - 4 hours of lecture and 12 hours of laboratory per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Letter grade. Final exam required.

                          Formerly known as: 102L

                          INTEGBI𧅧LF Invertebrate Zoology with Laboratory 5 Units

                          Terms offered: Fall 2019, Spring 2018, Spring 2016
                          Introductory survey of the biology of invertebrates, stressing comparative functional morphology, phylogeny, natural history, and aspects of physiology and development. Laboratory study of invertebrate diversity and functional morphology, and field study of the natural history of local marine invertebrates.
                          Invertebrate Zoology with Laboratory: Read More [+]

                          Rules & Requirements

                          Prerequisites: Biology 1A-1B

                          Credit Restrictions: Students will receive partial credit for 103LF after taking 103.

                          Hours & Format

                          Fall and/or spring: 15 weeks - 3 hours of lecture and 6 hours of laboratory per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Letter grade. Final exam required.

                          INTEGBI𧅨LF Natural History of the Vertebrates with Laboratory 5 Units

                          Terms offered: Spring 2021, Spring 2020, Spring 2019
                          Biology of the vertebrates, exclusive of fish. Laboratory and field study of local vertebrates exclusive of fish.
                          Natural History of the Vertebrates with Laboratory: Read More [+]

                          Rules & Requirements

                          Prerequisites: Biology 1A-1B

                          Credit Restrictions: Students will receive partial credit for 104LF after taking 104.

                          Hours & Format

                          Fall and/or spring: 15 weeks - 3 hours of lecture, 4 hours of fieldwork, and 3 hours of laboratory per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Letter grade. Final exam required.

                          Instructors: McGuire, Bowie, Shabel

                          INTEGBI C105 Natural History Museums and Biodiversity Science 3 Units

                          Terms offered: Fall 2021, Fall 2020, Fall 2019
                          (1) survey of museum resources, including strategies for accession, conservation, collecting and acquiring material, administration, and policies (2) strategies for making collections digitally available (digitization, databasing, georeferencing, mapping) (3) tools and approaches for examining historical specimens (genomics, isotopes, ecology, morphology, etc) and (4) data integration and inference. The final third of the course will involve individual projects within a given museum.
                          Natural History Museums and Biodiversity Science: Read More [+]

                          Hours & Format

                          Fall and/or spring: 15 weeks - 2 hours of lecture and 3 hours of laboratory per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Letter grade. Alternative to final exam.

                          Instructors: Gillespie, Mishler, Will, Marshall, McGuire

                          Also listed as: ESPM C105

                          INTEGBI𧅪A Physical and Chemical Environment of the Ocean 4 Units

                          Terms offered: Spring 2012, Spring 2010, Spring 2008
                          The biological implications of marine physics and chemistry. History and properties of seawater. Geophysical fluids. Currents and circulations. Deep sea. Waves, tides, and bottom boundary layers. The coastal ocean estuaries. Air/sea interaction. Mixing. Formation of water masses. Modeling biological and geochemical processes. Ocean and climate change.
                          Physical and Chemical Environment of the Ocean: Read More [+]

                          Rules & Requirements

                          Prerequisites: Biology 1B Chemistry 1A or 4A Mathematics 1A or 16A Physics 7A or 8A. Recommended: Integrative Biology 82

                          Hours & Format

                          Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Letter grade. Final exam required.

                          INTEGBI C107L Principles of Plant Morphology with Laboratory 4 Units

                          Terms offered: Spring 2019, Fall 2017, Fall 2016
                          An analysis of the structural diversity of land plants plants with emphasis on the developmental mechanisms responsible for this variation in morphology and the significance of this diversity in relation to adaptation and evolution.
                          Principles of Plant Morphology with Laboratory: Read More [+]

                          Rules & Requirements

                          Prerequisites: Biology 1A-1B

                          Hours & Format

                          Fall and/or spring: 15 weeks - 1 hour of lecture, 1 hour of discussion, and 4 hours of laboratory per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Letter grade. Final exam required.

                          Instructor: Specht

                          Also listed as: PLANTBI C107L

                          INTEGBI𧅬 Marine Biology 4 Units

                          Terms offered: Summer 2021 8 Week Session, Summer 2020 8 Week Session, Summer 2019 8 Week Session
                          This course will focus on the interactions among marine organisms and on their relationship to the environment. Topics will include an overview of marine organisms, functioning of marine ecosystems, anthropogenic impacts, and conservation. Lectures will consist of discussions of primary literature, videos, and student presentations and discussion sections will review and expand on topics covered on lecture. By the end of the course, you should be able to compare marine ecosystems, identify the major marine organisms and explain their role within a community, explain the main abiotic factors affecting the distribution of marine organisms, and discuss the impacts that humans are imposing on the marine environment.
                          Marine Biology: Read More [+]

                          Rules & Requirements

                          Prerequisites: Biology 1B

                          Hours & Format

                          Fall and/or spring: 15 weeks - 4 hours of lecture and 1 hour of discussion per week

                          Summer: 8 weeks - 8 hours of lecture and 2 hours of discussion per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Letter grade. Final exam required.

                          INTEGBI C109 Evolution and Ecology of Development 3 Units

                          Terms offered: Fall 2019, Fall 2018, Fall 2016
                          From the seahorse’s body to the venus flytrap’s jaws to the human brain, nature abounds with amazing adaptations. This interdisciplinary course explores how and why such biodiversity evolves as well as what limits diversity. Lectures and case studies will focus on core concepts, recent advances, and integrative approaches, placing special emphasis on the interplay between gene regulatory networks, the environment, and population genetics.
                          Evolution and Ecology of Development: Read More [+]

                          Objectives & Outcomes

                          Student Learning Outcomes: • Explain how an interdisciplinary approach involving genetics, development, evolutionary
                          biology, and ecology can be used to understand the processes that generate patterns of
                          biodiversity.
                          • List and describe major questions, findings, and experimental approaches in the field of
                          ecological and evolutionary developmental biology.
                          • Discuss biological research using specialized terminology and defend your opinions.
                          • Critically evaluate and interpret the primary scientific literature.
                          • Combine factual material with deductive reasoning to propose hypotheses and future
                          research directions

                          Rules & Requirements

                          Prerequisites: BIOLOGYفA and 1B

                          Hours & Format

                          Fall and/or spring: 15 weeks - 3 hours of lecture per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Letter grade. Alternative to final exam.

                          Instructor: Blackman

                          Also listed as: PLANTBI C109

                          INTEGBI C110L Biology of Fungi with Laboratory 4 Units

                          Terms offered: Fall 2021, Fall 2020, Fall 2016
                          Selected aspects of fungi: their structure, reproduction, physiology, ecology, genetics and evolution their role in plant disease, human welfare, and industry. Offered even fall semesters.
                          Biology of Fungi with Laboratory: Read More [+]

                          Rules & Requirements

                          Prerequisites: Biology 1B

                          Hours & Format

                          Fall and/or spring: 15 weeks - 2 hours of lecture and 6 hours of laboratory per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Letter grade. Final exam required.

                          Instructors: Bruns, Taylor

                          Also listed as: PLANTBI C110L

                          INTEGBI𧅰 Horticultural Methods in the Botanical Garden 1 Unit

                          Terms offered: Fall 2021, Spring 2020, Fall 2019
                          An introduction to horticultural techniques utilizing the diverse collections of the University Botanical Garden.
                          Horticultural Methods in the Botanical Garden: Read More [+]

                          Rules & Requirements

                          Prerequisites: Consent of instructor

                          Hours & Format

                          Fall and/or spring: 15 weeks - 3 hours of fieldwork per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Offered for pass/not pass grade only. Final exam not required.

                          Instructor: Licht

                          Formerly known as: 112L

                          INTEGBI𧅱L Paleobiological Perspectives on Ecology and Evolution 4 Units

                          Terms offered: Spring 2021, Spring 2020, Spring 2019
                          This course will center around answering the following questions: What do the fossil and geologic records have to tell us about the nature of ecological and evolutionary processes? What do they teach us that cannot be learned from the living world alone? In answering these questions, the course will provide an introduction to the analysis of key problems in paleobiology, with an emphasis on how evolutionary and ecological processes operate on geologic timescales.
                          Paleobiological Perspectives on Ecology and Evolution: Read More [+]

                          Rules & Requirements

                          Prerequisites: Prior biology experience, or consent of instructor. No paleontological or geological background required

                          Hours & Format

                          Fall and/or spring: 15 weeks - 3 hours of lecture and 3 hours of laboratory per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Letter grade. Final exam required.

                          Instructor: Marshall

                          Formerly known as: 108

                          INTEGBI𧅲 Infectious Disease Dynamics 4 Units

                          Terms offered: Summer 2021 8 Week Session, Spring 2021, Summer 2020 8 Week Session
                          Many of the challenges of managing infectious disease are essentially ecological and evolutionary problems. Disease follows the rules of species interactions as it spreads through host populations while resistance to antibiotics occurs through the rules of evolutionary biology. The key aim of the module is to teach ecological and evolutionary principles in the light of infectious diseases affecting human populations and societies as well as agriculture and wildlife. This is applied ecology and applied evolution writ large.
                          Infectious Disease Dynamics: Read More [+]

                          Objectives & Outcomes

                          Student Learning Outcomes: - Understanding the role of infectious disease in natural populations and communities
                          - Understand the role of disease in shaping human agriculture and societies
                          - Describe how infectious disease may be important in conservation
                          - Discuss when parasite virulence makes sense in the light of evolution
                          - Explain how to apply ecological and evolutionary principles to the treatment and control of infectious
                          - Present a scientific poster on the evidence for coevolution between a pair of species.

                          Rules & Requirements

                          Prerequisites: Bio 1A and Bio 1B or equivalent required, Ecology or Evolution course suggested

                          Hours & Format

                          Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

                          Summer: 8 weeks - 5 hours of lecture and 2 hours of discussion per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Letter grade. Final exam required.

                          Instructor: Boots

                          INTEGBI𧅳 Introduction to Systems in Biology and Medicine 4 Units

                          Terms offered: Spring 2015, Spring 2014, Fall 2013
                          This course is aimed at students wishing to understand the general principles of how biological systems operate. Topics include feedback regulation competition and cooperation genetic switches and circuits random processes chaos mechanisms for error correction and the properties of networks. Examples are selected from many fields including medicine, physiology, ecology, biochemistry, cell biology, and genetics. Students will learn to conceptualize and quantify interactions within biological systems using simple mathematical models and computer programs. No previous experience in programming is required.
                          Introduction to Systems in Biology and Medicine: Read More [+]

                          Rules & Requirements

                          Prerequisites: Biology 1A, Mathematics 1A or 16B

                          Hours & Format

                          Fall and/or spring: 15 weeks - 2 hours of lecture and 2 hours of laboratory per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Letter grade. Final exam required.

                          Instructor: Lim

                          INTEGBI𧅴L Medical Parasitology 4 Units

                          Terms offered: Summer 2021 First 6 Week Session, Summer 2020 First 6 Week Session, Summer 2019 First 6 Week Session
                          This course includes the biology, epidemiology, pathogenesis, treatment, and prevention of various medically important parasitic infections. Life cycles of parasitic helminths and protozoa, the biological aspects of the host-parasite relationship, the epidemiology of the infection, and the interplay of social, economical, and ecological factors which contribute to the disease will be covered in both lectures and videos.
                          Medical Parasitology: Read More [+]

                          Rules & Requirements

                          Prerequisites: 1A, 1B, or equivalent

                          Hours & Format

                          Summer: 6 weeks - 6 hours of lecture and 6 hours of laboratory per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Letter grade. Final exam required.

                          Instructor: Sakanari

                          Formerly known as: 116

                          INTEGBI𧅵 Medical Ethnobotany 2 Units

                          Terms offered: Fall 2021, Fall 2020, Fall 2019
                          Biological diversity and ethno-linguistic diversity sustain traditional botanical medicine systems of the world. Major topics covered in this course include cultural origins of medicinal plant knowledge on plant-derived pharmaceuticals and phytomedicines field research methods in ethnobotany and ethnopharmacology examples of how traditional botanical medicines provide safe, effective, affordable, and sustainable primary health care to tropical countries human physiology, human diseases, and mechanisms of action of plant-derived drugs.
                          Medical Ethnobotany: Read More [+]

                          Rules & Requirements

                          Prerequisites: Bio 1A

                          Hours & Format

                          Fall and/or spring: 15 weeks - 2 hours of lecture per week

                          Summer: 6 weeks - 5 hours of lecture per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Letter grade. Final exam required.

                          Instructor: Carlson

                          INTEGBI𧅵LF Medical Ethnobotany Laboratory 2 Units

                          Terms offered: Fall 2021, Fall 2020, Fall 2019
                          Laboratory will focus on studying medicinal plants from the major ecosystems and geographical regions of the world. Students will learn common names, scientific names, plant families, field identification, habitats, and ethnomedical uses of medicinal plants. How the medicinal plant is prepared, administered, and used as a phytomedicine will also be discussed. There will be reference to the phylogenetic relationships between the plant families and genera represented by the medicinal plants.
                          Medical Ethnobotany Laboratory: Read More [+]

                          Rules & Requirements

                          Prerequisites: Bio 1B

                          Hours & Format

                          Fall and/or spring: 15 weeks - 6 hours of laboratory per week

                          Summer: 6 weeks - 8 hours of laboratory per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Letter grade. Final exam required.

                          Instructor: Carlson

                          INTEGBI𧅶 Organismal Microbiomes and Host-Pathogen Interactions 4 Units

                          Terms offered: Fall 2021, Fall 2020, Fall 2019
                          We live in a microbial world, and microbes have shaped (and continue to shape) plant and animal physiology and evolution through a myriad of contributions – from mutualistic benefits to disease. Recent advances in genomic methodologies have further increased our appreciation of such contributions by highlighting the prevalence of organismal microbial communities and their complex interactions with their hosts. Through lectures and discussions, IB 118 will consider the broad range of host-microbe interactions – from mutualism to pathogenesis, and from pairwise interactions to the microbiome - learning the principles that shape these interactions, the technologies used to interrogate them and the molecular mechanisms underlying them.
                          Organismal Microbiomes and Host-Pathogen Interactions: Read More [+]

                          Rules & Requirements

                          Prerequisites: Biology 1A-1B

                          Hours & Format

                          Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Letter grade. Final exam required.

                          Instructor: Shapira

                          INTEGBI𧅷 Evaluating Scientific Evidence in Medicine 3 Units

                          Terms offered: Spring 2015, Fall 2014, Spring 2013
                          A course in critical analysis of medical reports and studies using recent controversial topics in medicine. Course will focus on information gathering, hypothesis testing, evaluating study design, methodological problems, mechanisms of bias, interpretation of results, statistics, and attribution of causation. Students participate in a mock trial as a way to demonstrate their abilities to gather, critically analyze, and present scientific and medical evidence.
                          Evaluating Scientific Evidence in Medicine: Read More [+]

                          Rules & Requirements

                          Prerequisites: Biology 1A-1B

                          Hours & Format

                          Fall and/or spring: 15 weeks - 2 hours of lecture, 1 hour of discussion, and 1 hour of laboratory per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Letter grade. Final exam required.

                          Instructor: G. Caldwell

                          INTEGBI𧅸 Introduction to Quantitative Methods In Biology 4 Units

                          Terms offered: Spring 2021, Spring 2020
                          This course provides a fast-paced introduction to a variety of quantitative methods used in biology and their mathematical underpinnings. While no topic will be covered in depth, the course will provide an overview of several different topics commonly encountered in modern biological research including differential equations and systems of differential equations, a review of basic concepts in linear algebra, an introduction to probability theory, Markov chains, maximum likelihood and Bayesian estimation, measures of statistical confidence, hypothesis testing and model choice, permutation and simulation, and several topics in statistics and machine learning including regression analyses, clustering, and principal component analyses.
                          Introduction to Quantitative Methods In Biology: Read More [+]

                          Objectives & Outcomes

                          Student Learning Outcomes: Ability to calculate means and variances for a sample and relate it to expectations and variances of a random variable.
                          Ability to calculate probabilities of discrete events using simple counting techniques, addition of probabilities of mutually exclusive events, multiplication of probabilities of independent events, the definition of conditional probability, the law of total probability, and Bayes’ formula, and familiarity with the use of such calculations to understand biological relationships.
                          Ability to carry out various procedures for data visualization in R.
                          Ability to classify states in discrete time Markov chains, and to calculate transition probabilities and stationary distributions for simple discrete time, finite state-space Markov chains, and an understanding of the modeling of evolutionary processes as Markov chains.
                          Ability to define likelihood functions for simple examples based on standard random variables.
                          Ability to implement simple statistical models in R and to use simple permutation procedures to quantify uncertainty.
                          Ability to implement standard and logistic regression models with multiple covariates in R.
                          Ability to manipulate matrices using multiplication and addition.
                          Ability to model simple relationships between biological variables using differential equations.
                          Ability to work in a Unix environment and manipulating files in Unix.
                          An understanding of basic probability theory including some of the standard univariate random variables, such as the binomial, geometric, exponential, and normal distribution, and how these variables can be used to model biological systems.
                          An understanding of powers of matrices and the inverse of a matrix.
                          An understanding of sampling and sampling variance.
                          An understanding of the principles used for point estimation, hypothesis testing, and the formation of confidence intervals and credible intervals.
                          Familiarity with ANOVA and ability to implementation it in R.
                          Familiarity with PCA, other methods of clustering, and their implementation in R.
                          Familiarity with basic differential equations and their solutions.
                          Familiarity with covariance, correlation, ordinary least squares, and interpretations of slopes and intercepts of a regression line.
                          Familiarity with functional programming in R and/or Python and ability to define new functions.
                          Familiarity with one or more methods used in machine learning/statistics such as hidden Markov models, CART, neural networks, and/or graphical models.
                          Familiarity with python allowing students to understand simple python scripts.
                          Familiarity with random effects models and ability to implement them in R.
                          Familiarity with the assumptions of regression and methods for investigating the assumptions using R.
                          Familiarity with the use of matrices to model transitions in a biological system with discrete categories.

                          Rules & Requirements

                          Prerequisites: Biology 1A, Biology 1B, a course in statistics such as Data 8, Stat 2 or Stat 20, and two semesters of college level math including calculus such as Math 10A and Math 10B. Undergraduate students engaged in honors research, or other supervised research, are preferred. Previous knowledge of R is not necessary

                          Credit Restrictions: A deficient grade in INTEGBI𧅸 may be removed by taking INTEGBI 201.

                          Hours & Format

                          Fall and/or spring: 15 weeks - 3 hours of lecture and 3 hours of laboratory per week

                          Additional Details

                          Subject/Course Level: Integrative Biology/Undergraduate

                          Grading/Final exam status: Letter grade. Final exam required.


                          Effective Use of Lesson Plans

                          Lesson plans can be a helpful guide for delivering engaging and thought-provoking lessons that help students understand the material and take an interest in the subject matter. A well thought out lesson plan also has the ability to serve as a reference to make sure a lecture stays on track and within a preset time limit.

                          Using a lesson plan template effectively can be a bit more of a challenge since it is likely that you’ll be working with formatting done by another person who may think differently about how to put together an engaging lesson for students.

                          However, there are many benefits to using a lesson plan template, including:

                          There’s no shame in managing your own time by using a lesson template, and frequently it can help you assess how reliable or efficient different templates can be in a real-world scenario. Lesson plans also can limit the amount of multi-tasking that you’ll be doing while trying to teach students which can simplify and space out learning opportunities.

                          Clear lesson plans also include enough time for questions, reflection, and opportunities to encourage in-depth student thinking to enhance learning. Assignments can then be coordinated to be purposeful instead of becoming just busy work that doesn't reinforce the essentials discussed in class.


                          Though the scientific theory of management provided tools for workers to enhance their output and efficiency, employees did only menial work and hence the theory criticism of the classical theory of management faced critics for developing an assembly-line atmosphere. With this as a reason, the theory falls out of favor by various companies but still consider as a valuable tool in many companies for its principles.

                          A good example where techniques of classical and scientific management theory can apply is in factories where repetitive tasks achieved. The importance of scientific management theory and principles are,

                          • Employees must be selected based on their skills and abilities related to the job.
                          • Incentives and wages provide to employees should base on encouraging them and enhancing their output.
                          • The leadership within the organization should be one that develops a standard method for doing a certain job with the assistance of scientific management theory.
                          • There should be attention to eradicating interruptions while planning work.
                          • Rule of thumb work methods replaced with other methods which are based on the scientific study of tasks.

                          Minor in Chemistry

                          Courses required for a minor must be taken for a letter grade and all courses below are required:

                          Course List
                          Units
                          CHEM 33Structure and Reactivity of Organic Molecules5
                          CHEM 121Understanding the Natural and Unnatural World through Chemistry5
                          CHEM 123Organic Polyfunctional Compounds3
                          CHEM 124Organic Chemistry Laboratory3
                          CHEM 131Instrumental Analysis Principles and Practice5
                          CHEM 151Inorganic Chemistry I4
                          CHEM 171Foundations of Physical Chemistry4
                          Total Units29


                          FINAL NOTE

                          Problem-based learning is alive and flourishing in the medical and professional school setting that gave rise to the method (Samford University, PBL Initiative) and has numerous proponents and practitioners in the K–12 education community (Torp and Sage, 1998). With apologies to the many dedicated PBL instructors in these settings (and to the many practitioners worldwide), the focus of this column has been on PBL implementation in the undergraduate setting in the United States—simply because this is the context with which the corresponding author is most familiar. We hope that the references and resources provided can further inform the reader about these other important settings.


                          Watch the video: Intro to Human Biology and the scientific method p 1 (January 2023).