The Evolution of Antibiotic Resistance

I think that the evolution of antibiotic resistance is an interesting and important issue. Below I has listed the expected learning outcomes for this topic in BIOL 1404. Because this topic has widespread medical relevance I have included a lot of additional readings and a powerpoint presentation that I developed for another class last semester. This info is not required, but is only intended to provide more info to interested students.

Expected Learning Outcomes

By the end of the course a fully engaged students should be able to

- discuss the causes of the development of antibiotic resistance

- discuss what we have learned from ecology and evolutionary biology about potentila problems associated with antibiotic use

- discuss what we have learned from evolutionary biology that should help us fight microbial diseases more effectively

Past Exam Questions (answers at the bottom of the post)

In the 1950s, Japanese physicians began to notice that some hospital patients suffering from bacterial dysentery, which produces severe diarrhea, did not respond to antibiotics that had generally been effective in the past.

1. In order for the result described above to have occurred, which of the following must have been true in the population of dysentery-causing bacteria?
(a) there was variation in the susceptibility of the bacteria to antibiotics
(b) antibiotic resistance was heritable
(c) bacteria that were more resistant to antibiotics had higher survival rates than less resistant bacteria
(d) a, b, and c
(e) neither a, b, or c was true


2. What can be done in future to limit the problem of antibiotic resistance in disease-causing microorganisms?
(a) Doctors should only describe antibiotics when appropriate
(b) Doctors should prescribe larger doses of antibiotics
(c) patients should make sure to take all of the pills when antibiotics are prescribed
(d) a and c
(d) a, b, and c

Answers 1. d 2. d

Further Reading

Evolution of Antibiotic Resistance-
http://www.pbs.org/wgbh/evolution/library/10/4/l_104_03.html

Antibiotic resistance: Questions and Answers- CDC
http://www.cdc.gov/getsmart/antibiotic-use/anitbiotic-resistance-faqs.html

Antibiotic resistance- delaying the inevitable (parts 1 and 2) UC Berkeley
http://evolution.berkeley.edu/evosite/relevance/IA1antibiotics2.shtml

HIV the ultimate evolver (parts 1-3) UC Berkeley
http://evolution.berkeley.edu/evosite/relevance/IA2HIV.shtml

When Penicillin Pays: Why China Loves Antibiotics a Little Too Much http://www.time.com/time/world/article/0,8599,2103733,00.html

The Super-Resistant Bacteria That Has India 'Hell Scared' http://www.theatlantic.com/international/archive/2012/01/the-super-resistant-bacteria-that-has-india-hell-scared/251731/

Antibiotic-Resistant Bacteria Found in 37 U.S. States
http://news.yahoo.com/antibiotic-resistant-bacteria-found-37-u-states-204438989.html

Superbugs: A Ticking Time Bonb
http://www.cbsnews.com/8301-3445_162-57566049/superbugs-a-ticking-time-bomb/

Powerpoint Presentation

Here is a link the the powerpoint presentation I used in another class.

http://www.slideshare.net/secret/rPekyBdLalUvFY

Natural Selection

An understanding of the process of natural selection helps us to understand the amazing diversity of life on the earth.

Expected Learning Outcomes

By the end of the course a fully engaged students should be able to

1) define the process of natural selection

2) distinguish between the patterns of stabilizing, disruptive, and directional selection and provide examples of each pattern

3) describe how the process of natural selection has produced a trait that is an adaptation to a particular environmental condition.

4) explain why organisms are not expected to be perfectly adapted to their environments

5) discuss the conditions that would cause natural selection to stop

6) explain why natural selection is expected to produce selfish traits

Readings

Natural selection http://www.eoearth.org/article/Natural_selection


Here is a link to a website from UC Berkeley-

http://evolution.berkeley.edu/evolibrary/article/evo_25

Here is a copy of the "famous" frequency distribution of heights that I was looking for.  Thanks Alex!!

The Hierarchical Nature of Ecology

In order to understand the science behind environmental issues it will be necessary to have a basic knowledge of the science of ecology.

Ecology has been defined in many ways. The definition that I prefer is that "ecology is the scientific study of the interactions between organism and their environment." Organisms interact with two distincly different parts of the environment. The "abiotic (non-living) environment" includes all of the non-living attributes of the environment including water, soil characteristics, temperature, etc. The "biotic environment" includes all of the living organisms and involves interactions such as competition, predation, mutualism, etc.

Hierarchical Organization of Ecology

Ecology can be studied at different hierarchical levels.

1. Individuals have phenotypic characteristics such as morphology (e.g., eye color, height, etc.), physiology (blood type, photosynthetic ability, etc.), and behavior (food preferences, response to stimuli, etc.). We can understand the characteristics of organisms by studying how natural selection has affected those traits.

2. A population is a group of individuals of the same species that live in the same area. Individuals in the same population interact via competition and sometimes predation (e.g., canibalism).

Some species live in very large populations whereas others live in very small populations. Ecologists are interested in understanding the factors that influence population size (this is important because when population size equals zero individuals then a population has gone extinct.)

3. A community is a group of different species living together in the same environment. Interspecific interactions including competition, predation, and mutualisms are some of the most interesting, and most important, aspects of ecology.

4. An ecosystem involves all of the biotic components in a community as well as the abiotic components. Unlike the lower levels of the ecological hierarchy where the focus is on living organisms, ecosystem ecologists are interested in understanding theh flow of energy and nutrients through the ecosystem. Some of the most important environmental issues facing us today are caused by human alteration of these cycles.

Expected Learning Outcomes

By the end of this course a fully engaged student should be able to

- define ecology

- define individual, population, community, and ecosystem

- diagram and discuss the hierarchical organization of ecology

- discuss examples of how one level of ecology can bge affected by the level above or below it

Reading

Ecology- http://www.eoearth.org/article/Ecology

Organization of Life: Species, Populations, Communities, and Ecosystems in PhysicalGeography.net by Michael Pidwirny
http://www.physicalgeography.net/fundamentals/9d.html

What is Science?

“The whole of science is nothing more than a refinement of everyday thinking.” Albert Einstein

What is Science?

Science is a way of learning about the world. Other ways of learning about the world include philosophy and religion.

Science is differentiated from alternative ways of learning about the world by
1) what it studies
2) how it studies it

(a) Science deals with the natural world and assumes that the world is governed by “natural laws” (I don’t spend too much time worrying about where these laws came from, I just accept that they exist)and (b) science only studies things that can be observed

Religion, on the other hand, deals with the supernatural, so science simply can’t study it.

Scientists learn about the world using the scientific method. Scientists use observations and experiments to test predictions of hypotheses. Thus, data determines “truth” in science. Religious truth often relies on “revelations” not data.

Thus, science and religion differ on what they can study and how they study it. Here is the critical question- which way of learning about the world is best? Any particular method is not the best, they are complementary ways of learning about the world and each works best within its intended boundaries. For example, science has nothing to say about religion, faith, or God.

My suggestion is that if you want to study observable phenomena that take place in the natural world then science is the best approach. We spend our lives surrounded by the applied knowledge that comes from using the process of science.

Think about a couple of examples

1) you come out in the morning and you can’t start your car.

Possible hypotheses
- you left your lights on and the battery has gone dead
- something is wrong with the starter

Where do these hypotheses come from? The knowledge that engines run according the laws of physics and chemistry helps us to understand how they work.

Alternative hypotheses
- you ran over a fairy on the way home last night and they are punishing you
- your neighbor is a witch and has put a hex on your car because your dog barks too much

We are likely to laugh at these alternative hypotheses because we understand the mechanical basis of car problems. Who do you take your car to for repairs- (i) Gus the mechanic (who whether he knows it or not uses his knowledge of physics and chemistry to diagnose what is wrong and repair your car) or (ii) Princess Fatima the Gypsy around the corner? Obviously, we choose Gus.

2) What do you do if you get sick?

The most obvious answer is that you go to the Doctor and do what they tell you. Certainly you might ask people to pray for you or pray for yourself. Some religions (e.g., Christian Scientists) rely on spiritual healing alone and will not take their children to the doctor when they are sick. I doubt that most people around here would support that position.

Readings

What is science? from Understanding Science: How Science Really Works. UC Berkeley
http://undsci.berkeley.edu/article/whatisscience_01

For an interesting discussion of the difference between "belief knowledge" and "research knowledge" check out "What is science?" by Bruce Tiffney from the University of California Museum of Paleontology
http://www.ucmp.berkeley.edu/education/events/tiffney3a.html

Expected Learning Outcomes

By the end of this course a fully engaged student should be able to

- define science

- distinguish science from other ways of learning about the world

- articulate their personal view of how science relates to their everyday life

The Mark McGinley Story

Here is the perfect cure for insomnia!

The Formative Years
I was born in Corpus Christi, TX and after a couple of moves we ended up in Rosenberg, (near Houston) where I attended grade school. I was interested in biology from an early age; I watched Marlin Perkins and Jacque Cousteau (your parents should know who they are) and I spent a lot of time outdoors on family camping and fishing trips. Even though I grew up near Houston during the Apollo years, I always thought that it would be much cooler to be a biologist than an astronaut.

When I was in the sixth grade my family moved to Australia for four years. This was an amazing life change for a kid who thought that the annual trip to my grandparents’ house in Oklahoma was a big deal. I had the incomparable experience of living in another country and experiencing a whole new way of life. Probably the biggest difference between Australia and the U.S. was the schools. I went to an all-boys English-style, private school where we had to wear uniforms (suits and ties) and straw boater hats to class everyday (this probably explains my preferred style of dress today).

The move also provided me with the opportunity to travel the world. During trips through Europe and Asia we saw many places of historical and cultural interest. Among my favorites were the Coliseum in Rome, the Tower of London, and Mt. Fuji in Japan. More importantly, my travels exposed me to many new biological experiences including seeing hippos, gazelles, elephants, and a cheetah in South Africa, snorkeling and beachcombing in Hawaii, Tahiti, Fiji, and the Great Barrier Reef, chasing emus through the Australian outback, watching a male lyrebird do his mating dance, watching fairy penguins come ashore for the night off of the coast of southern Australia, and many sightings of other Australian wildlife including kangaroos and koalas (how many people do you know that have ever seen a koala running along the ground?).

During the summer before my sophomore year in high school we moved to Thousand Oaks, CA (old-timers will remember TO as the former summer home of the Dallas Cowboys before they were ruined by Jerry Jones) where I graduated from high school. During my senior year I spent a week studying ecology and philosophy in Yosemite National Park and this trip confirmed by desire to be a biologist.

Education

I enrolled at the University of California, Santa Barbara to study biology. UCSB is an incredible place to go to school (I could see the ocean from my bedroom window three out of the four years that I was there) and it also happened to have one of the best ecology programs in the world. Joe Connell (one of the most influential ecologist of our era) taught the ecology section of my intro biology course and also taught my first ecology course, so it is probably his fault that I am here today because after finishing his course I knew that I wanted to be an ecologist. Later, after taking courses from Steve Rothstein and Bob Warner, I became interested in behavioral and evolutionary ecology and I decided to go to grad school to study behavioral ecology. I went to Kansas State University in Manhattan, KS which was a pretty big change from UCSB. I enjoyed K-State (I learned to bleed purple for Wildcat basketball) and I was lucky to be able to spend summers working for my advisor Chris Smith at the Mountain Research Station in Colorado studying pollination in lodgepole pine. My Masters Thesis extended optimal foraging models to examine woodrats foraging for non-food items (sticks that they use to build their houses). I also did a theoretical study examining how food stress should affect sex ratios. I earned a Ph. D. at the University in Salt Lake City. For my Ph. D. thesis with Jon Seger, I developed models and conducted experiments to understand the causes of seed size variation in plants. During my little free time, I played volleyball with the U of U Volleyball Club team and I was probably the only person in the whole city who did not ski (I still don’t see the point of intentionally getting cold). I spent two years working as a post-doctoral researcher with Dave Tilman at the University of Minnesota. Our research focused on succession in old fields at Cedar Creek Natural History Area just north of Minneapolis.

Life at Texas Tech
I started as an Assistant Professor in the Department of Biological Sciences at Texas Tech University in 1991. I am currently an Associate Professor with a joint position in the Honors College and the Department of Biological Sciences. In the Honors College I work closely with the Environment and the Humanities degree. (http://www.depts.ttu.edu/honors/evhm/)

Teaching

I teach a wide variety of classes at Tech. Two of my favorite courses are Tropical Marine Biology (taught in Jamaica and Belize) and the Rio Grande Class (we take a week-long canoe trip through Big Bend over Spring Break). For the past 6 summers I have worked as a scuba instructor and marine biologist with Odyssey Expeditions leading sailing and scuba trips through the Caribbean (British Virgin Islands, Martinique, St. Lucia, and St. Vincent & the Grenadines).

Scholarship
For several years I conducted ecological research in the sand shinnery oak community in West Texas. My current interests are in science curriculum development, environmental education, and informatl science education. I serve as a member of the Stewardship Committee of the Environmental Information Coalition and as an Associate Editor for the Encyclopedia of the Earth (http://www.eoearth.org/). In the Malaysian Bat Education Adventure we are using the ecology of Malaysian Bats as the focus of an integrated science curriculum for students in Kindergarten through 8th grade.

Fulbright in Malaysia

I spent the 2010-2011 academic year as a Fulbright Visiting Scholar at the University of Malaya in Kuala Lumpur, Malaysia. In addition to teaching a class at the UM, I was able to travel throughout the Malaysia and other parts of SE Asia (Thailand and Cambodia). In enjoyed exploring the rainforests and islands of Malaysia.  Some of the coolest things I saw were a sea turtle laying eggs, Orangutans, and a Borneo Pygmy Elephant. To learn more about my adventures in Malaysia you can check out my blog. http://markinmalaysia.blogspot.com/

Traveling

I enjoy traveling and I have been able to explore my passion for scuba diving on dive trips in Texas (San Solomon Springs in Balmorhea and the Flower Garden Banks) throughout the Caribbean as well as Yap, Palau, Solomon Islands, Fiji, Malaysia, Indonesia, and Galapagos Islands. My favorite marine critters include hammerhead sharks, pygmy sea horses, and “the pea”. On Friday I returned from a trip to Malaysia where I went scuba diving in Redang and Perhentian Islands and visited the capital city, Kuala Lumpur.

Course Syllabus

Ecology: The Science Behind Environmental Issues, Fall 2013

EVHM 3305-H01 MWF 11 - 11:50 English 301

Instructor

Dr. Mark McGinley

Room 215 McClelland Hall

mark.mcginley@ttu.edu

Office Hours:

T-Th- 10-11 or by appointment

I encourage you to make an appointment to meet with me if you need to see me. The easiest ways to do this are (1) to talk to me either before or after class or (2) to send me an email listing times when you are available to meet with me and then I will let you know which works best for me.

Course Outline

Climate change, extinction, the ozone hole, deforestation, pollution, invasive species, wind or nuclear power, and water supply are all environmental issues facing us today and in the future. If we are going to make wise decisions about these and other issues related to the environment then it will be necessary for us to have a strong understanding of the science behind the issues. This course will provide the background in ecology necessary to understand environmental issues and then examine important environmental issues affecting us at a local, state, national, and global scale.

THIS COURSE FULFILLS 3 HOURS OF THE HONORS SEMINAR REQUIREMENT AND UPPER DIVISION BIOLOGY CREDIT.

Student Absence for Observation of Religious Holy Days

A student who is absent from classes for the observation of a religious holy day shall be allowed to take an examination or complete an assignment scheduled for that day within a reasonable time after the absence if, not later than the fifteenth day after the first day of the semester, the student had notified the instructor of each scheduled class that the student would be absent for a religious holy day.

Academic Integrity.

Texas Tech University faculty strive to foster a spirit of complete honesty and high standards of integrity. Any attempt by students to present as their own work any work not honestly performed is regarded by faculty and administration as a most serious offence and renders offenders liable to serious consequences, possibly suspension from the university. “Scholastic dishonesty” includes, but is not limited to, cheating, plagiarism, collusion, falsifying academic records, misrepresenting facts, and any act designed to give an unfair academic advantage to a student. A detailed list of offenses is available in the Code of Student Conduct, found in Part IX, pp. 20-21 in the current Student Handbook, available on line at:

http://www.studentaffairs.ttu.edu?publications/SA_handbook_2005-2006.pdf.

Any student who, because of a disability, may require special arrangements in order to meet the course requirements should contact the instructor as soon as possible to make any necessary arrangements. Students should present appropriate verification from Student Disability Services during the instructor’s office hours. Please note instructors are not allowed to provide classroom accommodations to a student until

appropriate verification from Student Disability Services has been provided. For additional information, you may contact the Student Disability Services office at 335 West Hall or 806-742-2405.

Expected Learning Outcomes

Upon completion of this course, a fully-engaged student will be able to:

1. Discuss basic concepts in population, community, and ecosystem ecology. Assessed by performance in class discussions, exams, written papers, and class presentation.

2. Discuss the ecological concepts that underlie environmental issues such as eutrophication, effects of invasive species, etc. Assessed by performance on in class discussions, exams, written papers, and class discussion.

3. Lead and participate in group discussions about ecology and environmental issues. Assess by performance on class discussion and presentation.

4. Write about environmental issues. Assessed performance on written papers.

5. Present information about ecology and environmental issues to a “non expert” group. Assessed by performance on class presentation.

6. Become more aware of current environmental issues. Assessed by performance in class discussions, exams, written papers, and class presentation

Grading

Midterm exam 20%

Final exam 10%

Participation in workshops, online, and discussion 10%

Writing assignments 30%

Presentation 30%

It is extremely important that all assignments be turned in on time!!!

Midterm and Final Exam

The written midterm and final exams will cover material discussed in lectures, class readings, and discussions. 

Writing Assignments

2 papers. These papers will be three pages maximum double spaced (more details to follow).

Class Presentation

Each student will give a 40 minute presentation on an environmental topic of their choice (more details to follow).

Course Blog

I have created a blog for this course. This blog will be an important means of communication between us so I encourage you to check the blog early and often. The blog is located at http://ecology2012.blogspot.com/. Hopefully, most of your questions about the details of the class will be answered somewhere on the blog. In addition, I will list specific “expected learning outcomes” for each lesson to help you focus your study efforts.

Required Reading

There is no required textbook for this course. I will assign readings throughout the semester on the course blog http:/evhm/ecology2013.blogspot.com/

Books About Writing

Writing well is important for effective communication. Thus, improving your writing skills is an important component of this course. Here are a couple of references that would be useful for you to have on your shelf (and use) throughout your college career. (these books are not required).

The Elements of Style by William Strunk Jr. and E.B. White.

Eats, Shoots & Leaves. The Zero Tolerance Approach to Punctuation. By Lynne Truss.

Tentative Course Schedule

Week 1. (August 26 - 30)

Introduction  

Critical Thinking

Week 2. (September 4 - 6)

Monday Sept. 3rd- Holiday

Ecology in Brief

Environmental Issues in Brief

Week 3. (September 9 - 13)

Biosphere Level

- Climate Change

 - Week 4. (September 16 - 20)

Ecosystem Level

- Ecosystem Services

- Draft writing assignment #1 due September 20st

Week 5. (September 23 - 27)

Ecosystem Level

- Nitrogen cycle, eutrophication, dead zones

- Final draft assignment #1 due September 27

Week 6. (September 30 - October 4)

Community Level

- Importance of Indirect Effects

- Invasive species

Week 7. (October 7 - 11)

Community Level

- Habitat Destruction

Week 8. (October 14 - 18)

Community Level

- Conservation Biology
- Rough draft writing assignment #2 due October 14th (workshop papers on Oct. 13)

 

Week 9. (October 21 - 25)

Population Level

- Extinction
- Final draft writing assignment #2 due October 21st

- Midterm Exam- October 23rd

Week 10. (October 28 - November 1)

Population Level

- Human Population Growth

Week 11. (November 4 - 8)

Student presentations

Week 12. (November 11 - 15)

Student presentations

Week 13. (November 18 - 22)

Student presentations

Week 14. (November 25)

Student presentations

Week 15.  (December 2 - 4)

Student presentations

Final Exam- 

Friday December 6th, 7:30 - 10:00 AM