1.1: How to succeed in BIS2A- online - Biology

1.1: How to succeed in BIS2A- online - Biology

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BIS2A is a 5-unit course with online learning resources (readings and videos), which can be accessed at any time, plus a 2-hour zoom-based Discussion, which can only be accessed at your scheduled Discussion time, each week. Live zoom office hours and study halls are also available on a drop-in basis- see your "General Information" module for times.

BIS2A is one of three courses in the lower division core sequence in the biological sciences. BIS2A provides a foundation in key biological concepts that are of use across a broad spectrum of majors. Students are introduced to the fundamental chemical, molecular, genetic, and cellular building blocks of life, biological mechanisms for the recruitment and transfer of matter and energy, basic principles of biological information flow and cellular decision making, and core concepts underlying the relationships between genetic information and phenotype.

It is important to realize that BIS2A is not a survey course in biology. Biology is an exciting, broad, and dynamic field. It is critical for students in biology or related fields to develop a strong conceptual foundation and to demonstrate their ability to use it in contexts that may be novel to them. Students in Bis2A will be asked to begin developing the ability to identify and articulate the key scientific and biological questions that are at the core of the course content. Students will be expected to learn and use correct technical vocabulary in their discussions of course content. Students will be expected to begin conceptualizing course content from a question-driven and problem-solving perspective.

Yes, BIS2A will require you to work hard, but we also hope that you will have fun discovering new aspects of biology and exploring the many unanswered questions concerning what it means to be alive.

The main course learning objectives include:

  • Apply principles of chemistry and bioenergetics in the context of biological systems to describe how cells acquire and transform matter and energy to build and fuel various life sustaining processes, including chemical transformations of elemental compounds, cellular replication, and cellular information processing.
  • Explain the relationship between genotype and key genetic processes that create phenotypic diversity.
  • Describe the processes regulating the management of cellular information; how information is stored, read, rearranged, replicated; how cells interact with their environment and how these processes can control cellular physiology.

Who should I ask when I have questions about the course?

  1. General information about the logistics of the course: You'll find this in the "General Information" module of our Canvas site. For the quickest answers to many of your questions, we highly recommend looking at the course schedule and the HELP document before contacting one of the staff.
  2. General information about course material in BIS2A: Any BIS2A instructor or TA having office hours should be able to answer general questions about the videos, readings, and Discussion material. However, they cannot help you answer material on quizzes until after the due date. If they can’t answer your questions, they will be happy to refer you to someone who can. You are not obliged to see just your own Discussion TA- all TAs can help. See the HELP sheet and Canvas home page for office hour/study hall schedules. You can also email your instructors and TAs (via Canvas) with questions, but it is very time consuming (and error prone) to write answers to science question- please don't expect this. Instead, make use of office hours/study halls. You can also start a Chat with your fellow students about any topic, and we are organizing all students into 4-5 student study groups, based on their shared Discussion section. Of course you can also organize your own study groups too.
  3. Technical issues with grades: Your Lecture TA (Christine Tabouloc, [email protected]) is a great source of information about the lecture material, but also supervises the loading of scores into your grade book (available on Canvas).
  4. Discussion material: Your discussion TA is the best source of information about the discussion material present in your specific discussion section, but here again, all the TAs should be able to help you.
  5. All course content related material: Your instructor is a great resource for questions about course related material. Please make use of office hours/study halls! We are also introducing a google doc in which you are welcome to list your questions; popular questions will be addressed in study hall, and perhaps in the creation of an additional video addressing the "Murkiest Concept of the Week". Do not send email inquiries about course content, except for yes or no questions.
  6. Vocabulary issues: We have been told that the scientific glossaries that also translate scientific terms into foreign languages are not always accurate. The two most common languages spoken at home by non-native English speaking families of our students are Spanish and Mandarin. We are putting together a glossary of scientific terms defined in these languages, and would love to have you help in this project! IF you are a native speaker of Spanish or Mandarin please assist us by submitting candidates for this glossary to our google doc. If you are interested in participating in this project i other ways let your instructor know.

Some of your responsibilities

BIS2A is a team effort. Several professors are involved in developing the course content and assessment materials. There are also teaching assistants, who not only run the discussion sections, but also provide insights into which concepts students find the most difficult.

Please keep up with your responsibilities as a student. Do the assigned reading, watch the videos, and master new vocabulary. We suggest you do the reading first, making note of any confusing issues. Formulating questions is work, but it's the best way to learn because its an active, rather than passive, experience. Then watch the videos and see if your questions are answered (and if more questions are raised). I suggest downloading the slides (available on Canvas) for the instructor videos, and taking notes on them. If you're still confused, take your questions to your TA or instructor in office hours/study hall. Seek out assistance immediately when you need it- there are office hours available throughout the day. Please also do us a favor by making note of your issue in the Murkiest Issue google doc! Remember, if you fall behind, things will become more difficult- the effect will snowball. If you keep up, everything will make more sense and therefore make learning easier and more interesting. If everyone in the class can conscientiously do these things, we’ll all have fun this quarter (even while working hard) and be a happy and smarter bunch at the end of the term!

Strategies for Success

Research shows that the most successful students are those who take charge of their own learning and follow a simple but disciplined strategy.

  • Identify the important vocabulary words and key concepts presented in lecture. Be able to recall this information and find opportunities to use it outside class: limiting your studying to reading a text book does not constitute effective studying in this class. To be successful, you need to be able to use the information. Therefore, we have designed question-driven lectures that will ask you to practice using your knowledge in both the readings/videos and your discussion sections.
  • Recall information from your memory regularly: effective studying cannot be done the day before the exam. If you want to master a concept, you need to work on problems that ask you to apply that concept (and practice your vocabulary) at regular intervals throughout each week. Learning is a biologically-based process- approaching a concept on a regular basis, from different angles, will build resilient new neural connections.
  • Apply your knowledge to different problem types and new situations: we will give you the chance to do this with pre-class questions embedded in the readings and videos, but coming up with your own questions is ideal. Obviously, forming a study group will give you a lot of opportunities to do this. Your questions and curiosity will give other members of your group an opportunity to think, explain, and learn. If you have a lot of questions, you'll be helping your study group practice their knowledge.

Investment of Time

To be successful in BIS2A, you need to make sure that you have sufficient time each week to devote to the class. Units at UC Davis are assigned based on time spent in class and time requirements associated with out-of-class work. For one lecture unit, you are expected to attend one hour of lecture per week and to spend about two hours per week out-of-class studying the material associated with this lecture. BIS2A has three hours of "lecture" per week, and normally you would be expected to spend at least six additional hours per week studying. Now there's no time spent in "lecture", but about the same amount of time will be spent working with the videos. BIS2A also has two hours of discussion per week. For the two discussion units, you are expected to attend one two-hour discussion section per week and to spend about four hours per week out-of-class studying the material associated with this discussion. So in total, you are expected to be spending about 15 hours/week on BIS2A!

What is the most productive way to use this -15 hours/week? Material in BIS2A is cumulative and getting behind can have a major negative impact on your grade. Therefore, the key to being successful in BIS2A is to study the material every day. “Studying” includes any time spent learning the vocabulary, doing the reading, watching/answer questions in the videos, preparing for class by identifying problem topics, reviewing the slides and your notes after class, and completing the quizzes..

How to Prepare for Class

We have prepared/identified a variety of readings/activities designed to help you get the most out of the videos.

Read the whole document and comment (to yourself, or a friend) on all parts - particularly the suggested discussion items. Study groups are a great way to encourage mastery of the material through conversation. They provide an opportunity to learn from and with your classmates and to use information you've learned from earlier modules. Raise questions on material you don't understand- and see if these items are clarified in the videos. If not, consider asking about them in office hours/study hall and listing these in "Murkiest concepts".

We have attempted to boldface any vocabulary words. Again, ask for help if definitions remain unclear after your best efforts (it is better for you to try first on your own than for you to immediately ask someone for help- you'll remember better this way). You may encounter words that you don't understand but are not in boldface- regard these as words you need to learn also! You can bet that if your instructor uses these terms, you may face them later on a test. Keep a list of unfamiliar words for review prior to tests.

Lecture slides will be posted.

I strongly suggest printing out the lecture slides and taking notes on them. If any video slide or other resources are missing, send a reminder note to me (your instructor, Dr. Britt, [email protected])- I may be unaware of this.

Please note that an early slide for each of Dr. Britt's videos include a list of learning goals. You should take these very seriously; this list is what she will be reviewing when she makes up the exams!

What happens in lecture

Class time will be spent discussing course topics. Your instructor will expect that you have completed the assigned reading before you come to class and that you have attempted to answer the questions in the libretext readings.

What to do after watching and reading

You have access to the lecture slides. The slides will allow you to review the videos (and of course, you can always re-watch) and to confirm the accuracy of your lecture notes. if you were unable to answer some of the questions in the readings before class, go back to them now. If you generated pre-video questions of your own- were they answered?

Previous exam questions

Dr. Britt will post last year's exam and midterms about a week prior to each test. You should attempt to answer all the questions, and keep notes on topics that were difficult for you. Go for help only after doing your best. Exams do not necessarily cover every topic every year to the same degree, so please do not let one year's exam over-influence your selection of study topics. Again, learning goals are listed in the lecture slides. Practice midterm keys will be posted a day or two before the Review sessions.

We have found that many students don't use these questions as effectively as they could. These are NOT meant to be exercises in memorization! Your instructor will not, in all likelihood, ask you the exact same question. Many students fall into a trap of using these questions as a last-second study guide, cross-referencing with a key and mentally checking off that they understand a topic, because the answer choice "makes sense". Beware! If you are falling into this trap, you likely have a false sense of the depth of your real understanding.

How to use previous exam questions effectively

  • Ask yourself if there are any vocabulary terms that appear multiple times in the exam or any vocabulary words that you don't understand. Sometimes, just knowing the precise meaning of a term is enough to answer the question.
  • Ask yourself WHAT learning goal(s) are associated with each question and what skills do you need to have mastered in order to able to answer the question. Remember, some questions may require you to integrate learning goals.
  • Ask yourself HOW the instructor is testing whether or not you have mastered the learning goals you identified above. Figure out what you needed to know to be able to answer the question and how the instructor asked you to demonstrate this.
  • Ask yourself how you might RECAST the question (changing some details or specifics) in a way that still tested whether or not a student had mastered the associated learning goals and not just memorized the answers to the old exam questions. We as instructors do this all the time.
  • Asking yourself how you might CREATE a new question that an instructor could use to test the same learning goals. We as instructors do this all the time too.

Concept maps

Draw pictures or flowcharts to illustrate concepts stressed in class. Do this first without any online or textbook resources. This can be a great way to identify holes in your knowledge.

Review Sessions...

... will be based entirely on questions from the audience, so bring questions. Students usually find that review sessions really help them see the "big picture".

The cumulative nature of BIS2A

By its very nature, the material in BIS2A is cumulative and it is very easy to get behind. Try to study the material in a lecture both the night before (based on the readings) and the night after the lecture (based on the slides and perhaps podcast, plus your own reading). It has been demonstrated that the brain actively builds new connections based on what we have experienced during the day, and it does this especially well with material we have experienced immediately before going to sleep.

Habits associated with highly successful BIS2A students

Over the years, your instructors have talked with many, many students to try and understand why some students are more successful than others. The picture is, as you might expect, complicated. However, there seem to be at least two habits that we can consistently associate with highly successful students and that we find are practiced much less frequently by students who struggle. These are:

  • Reviewing and studying material associated with a module. This includes reviewing the video and reading notes, vocabulary, and doing associated exercises. This ALSO includes making lists of concepts that still aren't clear and trying to have those questions cleared up before moving on to the next module.
  • Constant self-testing. That is, most successful students have developed methods (there are many) for assessing their comfort level with their understanding of the course material and spending more time on areas they find MOST challenging.

The first point is relatively easy to understand. Don't procrastinate. Material builds up quickly, concepts are often layered and exams sneak up on you very fast in the quarter system. It is difficult to identify the holes in your understanding of a topic and fill them appropriately two days before the exam.

The second point about self-testing is more subtle. Basically, students that are good at this skill have ways of asking themselves "do I really understand the point of this question and the reason for the answer?" This can happen in a number of ways. We suggested one above. Try to invent new exam style questions for a concept or skill. Another good way to test yourself is to work in groups and explain a topic or question to another student, as if you were the instructor. This is often more difficult than it seems. While this exercise can be hard - particularly if you are not used to flexing these mental muscles - this type of introspection is important to develop for both your short and long term success and we encourage you to look inward and test yourself and your understanding often when you are studying.

Questions during Study Hall

You are always welcome to ask questions! I love questions, that's why I'm a professor I know it is hard to ask questions if you're worried that everyone else knows the answer. If you're confused, it's a good guess that a significant number of other students are confused too, so please ask. You are welcome to come to Study Hall and just listen in, but you'll increase your value per unit time if you have questions ready to go.

In every lecture, I will ask you to answer questions, usually with anonymous clickers, and sometimes from volunteers. I will not "cold-call". These questions serve several purposes:

Questions in videos

  • It can be very hard to focus on a video; I know when I'm watching an instruction video I sometimes don't even realize that I've started thinking about other things. To some extent, we're adding simple questions to videos just to refocus your attention
  • However, questions also help you consolidate your knowledge by asking you to review what you just heard. This moves material from short-term to longer-term memory.
  • Questions act as mini "self-tests" for students. If you are uncertain about what question is being asked or how to answer it, this is a good time to review this material, perhaps using other resources. If the instructor took the time to ask you the question, this is a big clue that he/she thinks that both the question and the answer are important.
  • Some in-video questions will ask students to formulate questions themselves! This is typically an exercise that is designed to force the student to reflect on and try to articulate the point of the lesson. These are critical exercises that force you to think more deeply about a topic and to place it in the broader context of the course.

Group questions are designed to stimulate thought and discussion rather than to elicit a discrete answer. In this case, you should not feel compelled to have one "right" answer!! Understanding this is very important. While it is okay to not know "the answer", it is nevertheless important for you to attempt to answer. .

Your job

We cannot emphasize too strongly that YOU have the primary responsibility for learning the material in this (or any other) course. Although we are invested in your success, your instructors and TAs cannot magically implant knowledge. Like any other discipline that requires mastery (e.g. sports, music, dance, etc.), we can help guide you and critique your performance, but we can not replace the hours of practice necessary to become good at something. You would never expect to become a proficient pianist by going to lessons once or twice a week and never practicing. To most of us, it seems self-evident that you need practice to become good at something like music, art, or sports. It should not be surprising that the same rule applies with learning Biology or any other academic subject.

We see ourselves as your coaches for this class; we want all of you to succeed. However, for this to happen, you have to take your practice seriously. This means studying the material covered in class as soon as possible, not falling behind, identifying where you are uncertain and getting help to clarify those topics as soon as possible, and trying to make thoughtful contributions to online discussions.

Bottom line: You need to be active participants in your learning.

Knowledge and Learning

Teaching and Learning Science

Teaching and learning science are both challenging endeavors. As instructors, we need to communicate complex, highly interconnected concepts that will serve as a foundation for all your future studies. We also want our students to demonstrate mastery of these ideas at a high level. As students, you need to learn a large new vocabulary, create mental models on which you can "hang" the new conceptual knowledge, and demonstrate that you can actually use this new knowledge. The process challenges both the instructor and the student. Although the process involves hard work, it can also be incredibly rewarding. There is nothing more satisfying for an instructor than those “Aha!” moments when a student suddenly understands an important concept.

In BIS2A we face some interesting teaching and learning challenges. One key challenge is that we discuss physical things and ideas that exist or happen on time and/or size scales that are not familiar to most students. What does this mean? Consider the following example:

Example: Some challenges associated with creating mental models

An instructor teaching wildlife biology may want to talk about concepts in evolution by using bird beaks as a starting point for discussion. In this case, the instructor does not need to spend time creating mental pictures of different shaped bird beaks (or at the very least only needs to show one image); most students will readily draw on their past knowledge and everyday lives to create mental pictures of duck, eagle, or woodpecker beaks and infer the different functional reasons why Nature might have selected different shapes. As a consequence, the students will not need to expend any mental effort imagining what the beaks look like and can instead focus all of their energies on the core evolutionary lesson.

More colloquially: If you are asked to think about something new that is closely related to something you already know well, it is not too difficult to focus on the new material.

By contrast, in BIS2A we ask students to think about and discuss things that happen on the atomic, molecular and cellular scales and at rates that span microseconds to millennia. Most students, we will guess, have not lived life on the micro to nanometer scale. Yet, this length scale is where most of the events common to all biological systems takes place. Beginning students, who have not thought much about how things happen at the molecular scale, lack of mental models upon which to add new information. This starting point places a burden on both the student and the instructors to create and reinforce NEW mental models for many of the things we talk about in class. For instance, to really talk about how proteins function, we first need to develop a common set of models and vocabulary for representing molecules at the atomic and molecular levels. Not only do these models need to find ways of representing the molecule’s structure, but the models must also contain abstract ideas about the chemical properties of molecules and how these molecules interact. Therefore, students in BIS2A need to put some effort into constructing mental models of what proteins "look" like and how they behave at the molecular scale. Since the entire course centers around biomolecules and processes that happen at a microscopic scale, a similar argument can be made for nearly every topic in the class.

Note: Possible Discussion

How do you interpret the term "mental model" and why do you think that it is important for learning?

Some of the readings' exercises and clicker questions are designed to help with meet this challenge; most students have found them very useful. However, some students are more accustomed to studying for exams by memorizing information rather than understanding it. (It's not their fault; that's what they were asked to do in the past). As a result, if the problems are approached with the "memorize-at-all-costs" attitude


of the BIS2A exercises may initially seem pointless. For instance, why are your instructors asking you to repeatedly draw some of the concepts described in class? What multiple-choice question could that exercise possibly prepare you for? While it is true that some of your instructors won't ask you to draw complicated figures on an exam, these drawing exercises are not trying to prepare students for one specific question. Rather the instructor is trying to encourage you to begin creating a mental model for yourself and to practice using it. The act of drawing can also serves as a "self test." When you force yourself to write something down or to create a picture describing a process on paper, you will be able to independently assess how strong your conceptual grasp of a topic really is by seeing how easy or hard it was to put your mental image of something onto paper. If it is hard for you to draw a core concept or process from class WITHOUT EXTERNAL ASSISTANCE, it is likely that you need more practice. If it is easy, you are ready to add new information to your model. Throughout the course, you will continue to add new information to your mental model or to use the concept represented in your mental model in a new context. Keep your drawings - or other self-testing mechanisms - current. Don't fall behind.

Incidentally, the presentation of a course concept on an exam in a context that the student has never seen before is NOT an evil plot by the instructor. Rather it is a way for the instructor and student to assess whether the concept has been learned and whether that knowledge can be used/transferred by the student outside of the specific example given in class or in the reading. Asking the student to repeat the latter would represent an exercise in memorization and would not be an assessment of valuable learning and independent thinking or a representation of what happens in real life.

IMPORTANT: The idea that students in BIS2A will be tested on their ability to USE concepts in specific contexts that they haven't seen before is critical to understand! Take special heed of this knowledge. Developing usable conceptual knowledge takes more discipline and work than memorizing. The quarter also moves VERY fast and concepts are layered one on top of the other. If you get too far behind, it is very, very difficult to make up for lost time two or three days before an exam. Be as disciplined as you can and keep up with course materials.

So, some concepts are hard to teach and to understand. What are we to do? Something instructors and students both do is to use various communication tricks to simplify or make abstract ideas more relatable. We use tools like analogies or simplified models (more on the importance of these shortly) to describe complex ideas. Making things more relatable can take various forms. Instructors might try to use various similies or metaphors to take advantage of mental pictures or conceptual models that students already have (drawn from everyday life) to explain something new. For instance, the thing X that you don't understand works a little like thing Y that you do understand. Sometimes, this helps ground a discussion. Another thing you might catch an instructor or student doing is anthropomorphizing the behaviors of physical things that are unfamiliar. For example we might say molecule A “wants" to interact with molecule B to simplify the more correct but more complex description of the chemical energetics involved in the interaction between molecules A and B. Anthropomorphisms can be useful because, like similes and metaphors, they attempt to link the creation of new ideas and mental models to concepts that already exist in the student's brain.

While these tools can be great and effective they nevertheless need to be used carefully - by both the instructor and the student. The main risk associated with these simplifying tools is that they can create conceptual connections that shouldn't exist, that lead to unintended misconceptions, or that makes it more difficult to connect a new concept. So while these tools are valid, we - students and instructors - also need to be vigilant about understanding the limits these tools have in our ability to learn new ideas. If these pedagogical tools are useful but their use also carries risk, how do we proceed?

The remedy has two parts:

  1. Recognize when one of these "simplifying" tools is being used and
  2. Try to determine where the specific analogy, metaphor etc. works and where it fails conceptually.

The second instruction is the most difficult and may prove challenging for learners, particularly when they are first exposed to a new concept. However, the act of simply thinking about the potential problems associated with an analogy or model is an important metacognitive exercise that will help students learn. In BIS2A your instructors will occasionally expect you to explicitly recognize the use of these pedagogical tools and to explain the trade-offs associated with their use. Your instructors will also help you with this by explicitly pointing out examples or prodding you to recognize a potential issue.

Note: Possible Discussion

Can you give an example from your previous classes where an instructor has used an anthropomorphism to describe a nonhuman thing? What were/are the trade-offs of the description (i.e. why did the description work and what were its limitations)?

Using vocabulary

It is also worth noting another problematic issue that can needlessly confound students just starting out in a discipline - the use of vocabulary terms that potentially have multiple definitions and/or the incorrect use of vocabulary terms that have strict definitions. While this is not a problem unique to biology, it is nevertheless important to recognize that it occurs. We can draw from real-life examples to get a better sense of this issue. For instance, when we say something like "I drove to the store", a couple of things are reasonably expected to be immediately understood. We don't need to say "I sat in and controlled a four-wheeled, enclosed platform, that is powered by the combustion of fossil fuel to a building that collects goods I want to obtain and can do so by exchanging currency for said goods" to convey the core of our message. The downside to using the terms "drove" and "store" is that we have potentially lost important details about what really happened. Perhaps the car is battery powered and that is important to understanding some detail of the story that follows (particularly if that part of the story involves calling a tow truck driver to rescue you up after the car has run out of power- they never seem to bring enough electrons). Perhaps knowing the specific store is important for understanding context. Sometimes those details don't matter, but sometimes if they aren’t known it can lead to confusion. Using vocabulary correctly and being careful about word choice is important. Knowing when to simplify and when to give extra detail is also key.


In the laboratory, undergraduate students in biology will often report back to their mentors that "my experiment worked" without sharing important details of what it means to have "worked", what the evidence is, how strong the evidence is, or what the basis is for their judgment - all details that are critical to understanding exactly what happened. If and/or when you start working in a research lab do yourself and your advisor the favor of describing IN DETAIL what you were trying to accomplish (don't assume they'll remember the details), how you decided to accomplish your goal (experimental design), what the exact results were (showing properly labeled data is advised), and providing your interpretation. If you want to end your description by saying "therefore, it worked!" that's also great.

Note: Possible Discussion

Can you think of an example where the imprecise or incorrect use of vocabulary caused needless confusion in real life? Describe the example and discuss how the confusion could have been avoided.

Problem Solving

Educators and employers alike have all argued strongly in recent years that the ability to solve problems is one of the most important skills that should be taught to and nurtured in university students. Problem solving ability consistently ranks as one of the most sought after traits employers want from their hires. Medical, professional, and graduate schools alike look for students with demonstrated ability to solve problems; the MCAT has even recently changed its format to more specifically assess student’s ability to solve problems. Life is full of problems to solve, irrespective of the profession one chooses. This is important!

Despite a clear demand for this skill set it is surprisingly rare to find problem solving taught explicitly in formal educational settings, particularly in core science courses where the transmission of “facts” usually takes precedence. In BIS2A we aim to start changing this. After all, nobody really cares if you’ve memorized the name or catalytic rate of the third enzyme in the citric acid cycle (not even standardized tests), but a lot of people care if you can use information about that enzyme and the context it functions in to help develop a new drug, design a metabolic pathway for making a new fuel, or to help understand its importance in the evolution of biological energy transformations.

Your instructors believe that the ability to solve problems is a skill like any other. It is NOT an innate – you’ve either got it or you don’t – aptitude. Problem solving can be broken down into a set of skills that can be taught and practiced to mastery. So, even if you do not consider yourself a good problem solver today, there is no reason why you can’t become a better problem solver with some guidance and practice. If you think that you are already a good problem solver, you can still get better.

Cognitive scientists have thought about problem solving a lot. Some of this thinking has focused on trying to classify problems into different types. While problems come in many different flavors (and we’ll see some different types throughout the course) most problems can be classified along a continuum of how well structured they are. At one end of the continuum are well-structured problems. These are the types of problems that you usually encounter in school. They usually have all of the information required to solve the problem, ask you to apply some known rules or formulae, and have a pre-prescribed answer. On the other end of the continuum are ill-structured problems. These are the types of problems you will usually face in real life or at work. Ill-structured problems may start poorly defined, usually do not present themselves with all of the information required to solve them, there may be different ways of solving them, and many possible “correct” outcomes/answers.

Note: Possible Discussion

Well-structured problems (like the story-problems you might often encounter in text books) are often set in an artificial context while the ill-structured problems one faces in every day life are often set in a very specific context (your life). Is it possible for multiple people to observe the same situation and perceive

different problems

associated with it? How does context and perception influence how one might identify a problem, its solution, or its importance?

To have a fruitful/enriching discussion it pays to start by presenting an example AND some direct reasoning. Replies that acknowledge the initial comment and either provide an extension of the original argument (by way of a new perspective or example) or provide a reasoned counter-argument the are most valuable follow-ups.

Problems can also be “simple” or “complex” depending on how many different variables need to be considered to find a solution or be considered “dynamic” if they change over time. Other problem classification schemes include story problems, rule-based problems, decision-making problems, troubleshooting problems, policy problems, design problems, and dilemmas. As you can see, problem solving is a complicated and deep topic and a proper discussion about it could fill multiple courses.

While the topic of problem solving is fascinating, in BIS2A

we aren’t interested in teaching the theories of problem solving per se

. However, we ARE interested in teaching students skills that are applicable to solving most types of problems, giving students an opportunity to practice these skills, and assessing whether or not they are improving their problem solving abilities. Note: Since we are asking you to think explicitly about problem-solving it is fair to expect that your ability to do so will be evaluated on exams. Do not be surprised by this.

We are going to incorporate problem solving into the class a number of different ways.

  1. We will have some questions in the readings and lectures that encourage problem solving.
  2. We will make use of the pedagogical tool we call the “Design Challenge” to help structure our discussion of the topics we cover in class.

When we are using the Design Challenge in class we are working on problem solving. Within the context of the Design Challenge your instructor may also present other specific concepts related to problem solving – like decision-making. Slides will be marked explicitly to engage you to think about problem solving. Your instructor will also remind you verbally.

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If learning requires that students construct ideas for themselves, then demanding the active participation of every single student in a class is essential to learning. Currently, though, many undergraduate students in biology classrooms can navigate an entire term without speaking aloud in a course. They sit in the back of our large classrooms, and they attempt to appear to be busily writing when a question is asked in a small class. Being called upon to answer a question or share an idea can be deeply uncomfortable to many students, and we as instructors may not be doing enough to build students’ confidence to share. While few instructors would find this lack of active, verbal participation in science acceptable for emerging scientists such as graduate students or practicing scientists themselves, we somehow allow this for undergraduate students. The participation of a only few students in our classrooms on a regular basis, often from the front rows, distracts us from the fact that usually the vast majority of students are not participating in the conversation of biology. To encourage, and in fact demand, the participation of all students in a biology classroom, you can use the following six strategies with little to no preparation or use of class time.

5. Hand Raising

Actively enforcing the use of hand raising and turn taking in a classroom is likely to provide greater access to more students than an open, unregulated discussion. Novice instructors, sometimes awash in silence and desperate for any student participation, can allow the classroom to become an open forum. Some would say this is much like the culture of science in settings such as lab meetings and seminars. However, the undergraduates in our courses are novices, not only to the concepts we are sharing but also to the culture of science itself. As such, providing structure through something as simple as hand raising can establish a culture that the instructor expects all students to be participating. With hand raising, the instructor can also be explicit about asking for “hands from those of us who haven't had a chance yet to share” and strive to cultivate a classroom conversation that goes beyond a few students in the front row.

6. Multiple Hands, Multiple Voices

After asking a question, some instructors call on just a single student to answer. However, this is problematic in many ways. The same students can often end up sharing repeatedly during a class, as well as from class session to class session. In addition, if the goal is to better understand how students are thinking, having a single student share gives a very narrow and highly skewed picture of what a classroom full of students may be thinking. One simple strategy for broadening participation and increasing the breadth of ideas flowing from students to instructors is to generally ask for multiple hands and multiple voices to respond to any question posed during class time (Allen and Tanner, 2002). Instructors can set the stage for this by asserting, “I’m going to pose a question, and I’d like to see at least three hands of colleagues here who would share their ideas. I won't hear from anyone until I’ve got those three volunteers.” Additionally, this particular use of hand raising allows instructors to selectively call on those students who may generally participate less frequently or who may have never previously shared aloud in class. Importantly, instructors really must always wait for the number of hands that they have called for to share. Hearing from fewer than the number of volunteers called for can entrain students in a classroom to know that they simply have to outwait the instructor. Finally, if the number of requested hands have not been volunteered, the instructor can charge students to talk in pairs to rehearse what they could share if called upon to do so.

7. Random Calling Using Popsicle Sticks/Index Cards

Raising hands allows for the instructor to structure and choose which students are participating verbally in a class, but what if no one is raising a hand or the same students continually raise their hands? Establishing the culture in a classroom that any student can be called on at any time is another option for promoting student engagement and participation. How this is done can be critical. If the spirit of calling on students feels like a penalty, it may do more harm than good. However, if the instructor is explicit that all students in the course have great ideas and perspectives to share, then random calling on students in courses that range in size from 10 to 700 can be a useful strategy for broadening student participation. Practically, there are a variety of ways to call randomly on students. In smaller-sized courses, having a cup with popsicle sticks, each with the name of a student on it, can make the process transparent for students, as the instructor can clearly hold up the cup, draw three names, read the names, and begin the sharing. This can minimize suspicions that the instructor is preferentially calling on certain students. For larger course class sizes, instructors can collect an index card with personal information from each student on the first day. The cards serve two purposes: 1) to enable instructors to get to know students and to assist with learning students’ names, and 2) to provide a card set that can be used each class and cycled through over the semester to randomly call on different students to share (Tanner, 2011).

8. Assign Reporters for Small Groups

Promoting student engagement and classroom equity involves making opportunities for students to speak who might not naturally do so on their own. If the decision about who is to share aloud in a class discussion is left entirely to student negotiation, it is no surprise that likely the most extroverted and gregarious students will repeatedly and naturally jump at all opportunities to share. However, this sets up an inequitable classroom environment in which students who are unlikely to volunteer have no opportunities to practice sharing their scientific ideas aloud. Assigning a “reporter”—an individual who will report back on their small-group discussion—is a simple strategy to provide access to verbal participation for students who would not otherwise volunteer. The assignment of reporters need not be complex. It can be random and publicly verifiable, such as assigning that the reporter will be the person wearing the darkest shirt. In smaller classes, one can use simple tools to assign a reporter, such as colored clips on individual student name tents or colored index cards handed to students as they enter the class. It can also be nonrandom and intended to draw out a particular population. For example, assigning the group reporter to be the person with the longest hair will often, not always, result in a female being the reporter for a group. Or instructors can choose to hand out the colored clips/cards specifically to students who are less likely to share their ideas in class. Early on, it may be useful to assign based on a visible characteristic, so the instructor can verify that those students reporting are indeed those who were assigned to report. After the culture of assigned reporters is established, and everyone is following the rules, assignments can become less verifiable and prompt more personal sharing, such as the reporter is the person whose birthday is closest. Whatever the method, assigning reporters is a simple strategy for promoting classroom fairness and access to sharing ideas for more than just the most extroverted students.

9. Whip (Around)

Actively managing the participation of all students in smaller courses is sometimes well supported by the occasional use of what is termed a “whip around” or more simply just a “whip.” In using a whip, the instructor conveys that hearing an idea from every student in the classroom is an important part of the learning process. Whips can be especially useful toward the beginning of a course term as a mechanism for giving each student practice in exercising his or her voice among the entire group, which for many students is not a familiar experience. The mechanics of the whip are that the instructor poses a question to which each individual student will respond, with each response usually being <30 s in length. On the first day of class, this could be something as simple as asking students what their favorite memory of learning biology has been. As the course progresses, the question that is the focus of the whip can become more conceptual, but always needs to be such that there are a variety of possible responses. Whips can be follow-ups to homework assignments wherein students share a way in which they have identified a personal connection to course material, a confusion they have identified, or an example of how the material under study has recently appeared in the popular press. During a whip, students who may wish to share an idea similar to a colleague who has previously shared are actively encouraged to share that same idea, but in their own words, which may be helpful to the understanding of fellow students or reveal that the ideas are not actually that similar after all. Importantly, the whip is a teaching strategy that is not feasible in large class sizes, as the premise of the strategy is that every student in the class will respond. As such, this strategy is unwieldy in class sizes greater than ∼30, unless there is a subgroup structure at play in the classroom with students already functioning regularly in smaller groups. Possible ways to implement a whip in a large classroom could be to call on all students in a particular row or in a particular subgroup structure particular to the course.

10. Monitor Student Participation

Many instructors are familiar with collecting classroom evidence to monitor students’ thinking, using clicker questions, minute papers, and a variety of other assessment strategies. Less discussed is the importance of monitoring students’ participation in a classroom on a regular basis. It is not unusual to have a subset of students who are enthusiastic in their participation, sometimes to the point that the classroom dialogue becomes dominated by a few students in a room filled with 20, 40, 80, 160, or upward of 300 students. To structure the classroom dialogue in such a way as to encourage, demand, and actively manage the participation of all students, instructors can do a variety of things. During each class session, instructors can keep a running list—in smaller classes mentally and in larger classes on a piece of paper—of those students who have contributed to the discussion that day, such as by answering or asking a question. When the same students attempt to volunteer for the second, third, or subsequent times, instructors can explicitly invite participation from other students, using language such as “I know that there are lots of good ideas on this in here, and I’d like to hear from some members of our community who I haven't heard from yet today.” At this juncture, wait time is key, as it will likely take time for those students who have not yet participated to gather the courage to join the conversation. If there are still no volunteers after the instructor practices wait time, it may be time to insert a pair discussion, using language such as “We cannot go on until we hear ideas from more members of our scientific community. So, take one minute to check in with a neighbor and gather your thoughts about what you would say to a scientific colleague who had asked you the same question that I’m asking in class right now.” At this point it is essential not to resort to the usual student volunteers and not to simply go on with class, because students will learn from that behavior by the instructor that participation of all students will not be demanded.

Overcoming Density-Dependent Regulation

Humans have exceeded density-dependent limits on population by enacting various environmental changes to accommodate our needs for hygiene, shelter, and food.

Learning Objectives

Describe ways in which humans overcome density-dependent regulation of population size

Key Takeaways

Key Points

  • Humans’ ability to alter their environment is an underlying reason for human population growth, enabling people to overcome density-dependent limits on growth, in contrast with all other organisms.
  • Abilities, such as construction of shelter, food cultivation, and the sharing of technology, have helped humans overcome factors that would have otherwise limited their population growth.
  • Originating from Africa, human migration to nearly every inhabitable area of the globe has enabled colonization of areas where people were previously absent.
  • Advances in medicine, notably vaccines and antibiotics, as well as improvements in nutrition and vector control, have significantly curbed mortality from disease.

Key Terms

  • density-dependent: Processes that occur when population growth rates are regulated by the size of a population in a given amount of resources such as food or habitat area.
  • vaccine: A substance given to stimulate the body’s production of antibodies and provide immunity against a disease, prepared from the agent that causes the disease, or a synthetic substitute.
  • infectious disease: Illness caused by introduction of a pathogen or parasite into the body via contact with a transmitting agent such as vector organism or an infected person.

Humans are uniquely able to consciously alter their environment to increase its carrying capacity. This capability is an underlying reason for human population growth as humans are able to overcome density-dependent limits on population growth, in contrast with all other organisms.

Human intelligence, society, and communication have enabled this capacity. For instance, people can construct shelters to protect them from the elements food supply has increased because of agriculture and domestication of animals and humans use language to pass on technology to new generations, allowing continual improvement upon previous accomplishments. Migration has also contributed to human population growth. Originating from Africa, humans have migrated to nearly every inhabitable area on the planet.

Public health, sanitation, and the use of antibiotics and vaccines have lessened the impact of infectious disease on human populations. In the fourteenth century, the bubonic plague killed as many as 100 million people: between 30 to 60 percent of Europe’s population. Today, however, the plague and other infectious diseases have much less of an impact. Through vaccination programs, better nutrition, and vector control (carriers of disease), international agencies have significantly reduced the global infectious disease burden. For example, reported cases of measles in the United States dropped from around 700,000 a year in the 1950s to practically zero by the late 1990s. Globally, measles fell 60 percent from an estimated 873,000 deaths in 1999 to 164,000 in 2008. This advance is attributed entirely to a comprehensive vaccination program.

Measles cases reported in the United States, 1944-2007: Measles cases reported in the United States, represented as thousands of cases per year, declined sharply after the measles vaccine was introduced, in 1964.

Developing countries have also made advances in curbing mortality from infectious disease. For example, deaths from infectious and parasitic diseases in Brazil fell from second place as the most important causes of death in 1977 to fifth place in 1984. The improvement is attributed in part to increased access to essential goods and services, reflecting the country’s rising prosperity. Through changes in economic status, as in Brazil, as well as global disease control efforts, human population growth today is less limited by infectious disease than has been the case historically.

Countries by Fertility Rate Comparison: The advent of modern medicine is very closely tied to childhood mortality, as well as the number of children per mother (Fertility Rate). As modern medicine decrease child mortality, the birth rate decreases.

How Nurses Use Microbiology on the Job

Nurses must have a deep understanding of microbiology in their daily nursing practice. The knowledge that nursing students gain in Microbiology courseshelps them to interact with patients in a variety of settings. Although nurses are responsible for caring for their patient, it is not possible to do so without putting health and safety first. Nurses use concepts of microbiology to maintain environments that are free of contamination and infection.

Nurses use microbiology on the job in many ways. When nurses administer smears for the gram positive and negative testing, they use microbiology to analyze the smears for bacterial contamination. Nurses must also use microbiology when it comes to the disposal of biomedical waste of all types. They must determine the proper procedure to handle the waste so that it does not cause infection. The concepts of microbiology help nurses to see beyond what their eyes are able to see.


Raw RNA-seq retrieval and processing

We downloaded raw RNA-sequencing reads from the dbGAP GTEx [46] project version 7 (phs000424.v7.p2). We included 36 tissues with a total of 7584 samples (Additional file 4: Table S2) after applying all filters in the mutation calling pipeline (see below). We also processed DNA exome sequencing reads from 105 whole-blood samples that had a matched RNA-seq sample.

Reads were mapped to the human genome Hg19 (NCBI build GRCh37.p13) using STAR [47] with the following parameters: requiring uniquely mapping reads (--outFilterMultimapNmax 1), clipping 6 bases in the 5′ end of reads (--clip5pNbases 6), and keeping reads with 10 or fewer mismatches and less than 10% mismatches of the read length that effectively mapped to genome (--outFilterMismatchNmax 10, --outFilterMismatchNoverLmax 0.1). To avoid germline variant contamination during the somatic mutation calling phase, all SNPs from dbSNP [48] v142 were masked to Ns and ignored in downstream processing (

After mapping, we removed duplicate reads to avoid biases arising from PCR duplicates during library preparation using a custom python script.

DNA somatic mutation calling from RNA sequencing

Identifying DNA variants from RNA-seq requires filtering out many sources of false positives. These include sequencing errors, RNA editing events, mapping errors around splice junctions, germline variants, and other sequencing/mapping biases. To address these issues, we developed a custom mutation calling pipeline that borrows ideas from classical DNA-based variant calling coupled with extra filters to increase the fidelity of the mutation calls from RNA-seq.

After mapping the raw RNA-seq reads, the pipeline consists of three main parts: (1) identifying positions with two base calls, (2) removing germline variants, and (3) filtering out other potentially spurious variants.

Identifying positions with two base calls

After mapping, bam files were scanned to identify genomic positions that were covered by reads having exactly two different base calls. Given the intrinsic sequencing error rate, we only considered positions with high coverage and high sequencing quality for this step. Stringent cutoffs were set for coverage (c ≥ 40 reads) and sequencing quality (qs ≥ 30 in Phred scale) this is in comparison twice what some DNA-based calling algorithms have used [21]. Finally, only positions in which the minor allele was supported by at least 6 reads were considered (n ≥ 6). In combination, these parameters define a theoretical distribution of the probability of observing a mutation due to sequencing errors, which is small for a wide range of sequence coverage levels (Additional file 1: Figure S1a). In addition, we included a filter to only consider variants with a probability of sequencing error p < 0.0001 (see filters below). These strict cutoffs ensure a low probability of observing sequencing errors even in highly covered genes nonetheless, we still apply further filters to account for sequencing errors (see below).

Identifying and eliminating germline variants

Common and rare germline variants have to be excluded for the proper identification of somatic mutations. To eliminate common variants, a strict filter was applied by using a human genome masked with Ns for positions known to have common variants from dbSNP v142 (see above).

To eliminate all other germline variants, including rare ones, we utilized the low confidence germline variants called by GTEx. These calls were made by GTEx using GATK’s HaplotypeCaller v3.4 on whole-genome sequencing data at 30x coverage from whole-blood samples. We specifically used the vcf file GTEx_Analysis_2016-01-15_v7_WholeGenomeSeq_652Ind_GATK_HaplotypeCaller.vcf which contains all germline variants before filtering for MAF and low-quality variants. Our goal was to exclude as many germline variants as possible, so we reasoned that using all germline variants called by GTEx—including the low-quality ones—was the safest option to minimize germline mutation contamination in our somatic mutation calls. While these variants were called in whole-blood samples, germline variants should be present in all tissues of an individual and as such these variants were excluded in a per-individual basis across all tissues of that individual. Only sites that had heterozygous or homozygous variants for the alternate allele were excluded from the mutation calls of the given individual.

Filtering out artifacts

A total of 13 filters were applied to exclude a variety of artifacts:

Blacklisted regions. We excluded sex chromosomes, unfinished chromosomal scaffolds, the mitochondrial genome, and the HLA locus in chromosome 6 which is known to contain a high density of germline variants [49] making accurate mapping challenging and is hence a potential source of false-positive calls.

RNA edits. The most prevalent type of RNA editing in humans is Adenine-to-Inosine (A>I) which is observed as an A>G/T>C substitution in sequencing data. The Rigorously Annotated Database of A-to-I RNA editing (RADAR) [50] has extensively curated RNA-edit events including calls identified using the GTEx data [51]. We also obtained RNA-edit information from the Database of RNA editing (DARNED) that includes further edit types curated from published studies [52]. We excluded all positions described in RADAR v2 ( and in DARNED ( and observed an average decrease of 10% mutations per sample in our RNA-sequencing calls but not in our DNA-sequencing calls from GTEx (Additional file 1: Figure S2a), indicating that we are indeed eliminating real RNA-edit events that would otherwise be false-positive mutation calls.

Splice junction artifacts. Splice junctions are difficult to resolve during mapping because a gap has to be introduced in reads spanning a splice junction to map it to the corresponding exons in the genome. We observed that the mutation rate was higher close to annotated exon ends and it stabilized at

7 bp away from the exon end across all tissues (Genecode v19 genes v7 annotation file) (Additional file 1: Figure S1b). Most of these are likely mapping artifacts, and we therefore excluded all mutations located less than 7 bp away from an annotated exon end.

Sequencing errors. While sequencing errors are unlikely to be found given the parameters established in the first part of the mutation calling pipeline (see above), we additionally filtered out mutations that had a probability of being sequencing errors greater than 0.01%. This probability was calculated using the upper tail integral of the binomial distribution where the number of successes is the number of reads supporting the alternate allele, the number of events is the coverage in that position, and the probability of success is the conservative assumption of p = 0.001 which equals our cutoff of phred score 30 during the first part of the pipeline (see above). This is extremely conservative because it does not incorporate the probability of observing the exact same base call across all reads supporting the alternate allele.

Read position bias. To eliminate any systematic bias of a mutation being consistently called around the same position along reads supporting it versus the rest of the reads, we excluded mutations that had a p value less than 0.05 when applying a Mann-Whitney U test of the positions in the read supporting the alternate allele vs the positions supporting the reference allele. For these tests, we used BCFtools [53] mpileup.

Mapping quality bias. We excluded mutations that had a p value less than 0.05 when applying a Mann-Whitney U test comparing mapping quality scores of the base calls supporting the alternate allele vs the mapping quality scores of reads supporting the reference allele. For these tests, we used BCFtools [53] mpileup.

Sequence quality bias. We excluded mutations with a p value less than 0.05 when applying a Mann-Whitney U test comparing sequencing quality scores of base calls supporting the alternate allele vs the scores of base calls supporting the reference allele. For these tests, we used BCFtools [53] mpileup.

Strand bias. We excluded mutations with a p value less than 0.05 when applying a Mann-Whitney U test comparing strand bias of bases supporting the reference and alternate allele (i.e., cases where mutations were only observed on one strand were excluded this is not related to the strand asymmetry we observed for some mutation types). For these tests, we used the “Mann-Whitney U test of Mapping Quality vs Strand Bias” of BCFtools [53] mpileup.

Variant distance bias. We excluded variants that showed a high or low mean pairwise distance between the alternate allele positions in the reads supporting it. Similar to the read position bias filter, this ensures that we filter mutations that are consistently observed around the same region of all the reads that support it. We used a cutoff of p < 0.05 for a two-tail distribution of simulated mean pairwise distances from the BCFtools [53] implementation.

RNA-specific allele frequency bias. We observed an enrichment of variants having a variant allele frequency (VAF) greater than 0.9 only in mutation calls from RNA-sequencing but not from the matched DNA-sequencing samples. This RNA-specific bias could be due to several factors, including allele-specific expression leading to enrichment of the alternate allele, RNA editing, or systematic artifacts during RNA extraction, library construction, and sequencing. We took a conservative approach and excluded all mutations that had a VAF greater than 0.7.

Tissue-specific mutation effects. To eliminate false positives arising by systematic artifacts of unknown origin, we first looked for recurrent mutations observed in many samples of a given tissue. While these mutations could be real and have a biological impact, they may also reflect a shared systematic artifact that is producing the same exact mutation across several samples of the same tissue. We decided to take a conservative approach and eliminated all mutations that were called in at least 40% of the samples in one tissue. Even though we labeled these mutations on a per-tissue basis, once identified, we removed them from any sample in any tissue that had them.

Overall systematic mutation bias. We further eliminated mutations that were present in at least 4% of all samples. Similarly, as in the previous step, these mutations are more likely to have originated from a systematic artifact.

Hyper-mutated samples. We excluded samples that had an excess of mutations compared to what it was expected from sequencing depth and biological factors. To do so, we looked at the residuals after applying a linear regression on mutation numbers using as features sequencing depth, age, sex, and BMI. We observed 48 samples that had residual values greater than 1500 (i.e., they had > 1500 more mutations than expected by other factors) (Additional file 1: Figure S1 g) and excluded them from further analysis, leaving 7584 remaining. We did not observe any hypo-mutated samples having similar residual values in the opposite direction.

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