Please Take This Survey

One of my colleagues is working on a Ph.D. dissertation and she is interested in knowing how people perceive encyclopedia articles. She has sent me a survey that she would like to use as part of her research. She said that is should take about ten minutes to complete.

Thanks for participating in this survey. Please email me after finishing the survey to let me know you have done it.

http://www.uvm.edu/~ikubisze/experiment/

Slime Molds

Readings

Introduction to the Slime Molds- UC Berkeley Museum
http://www.ucmp.berkeley.edu/protista/slimemolds.html

Slime Mold Factsheet- Cornell University
http://plantclinic.cornell.edu/FactSheets/slimemold/slimemold.htm

http://www.discoverlife.org/20/q?search=Eumycetozoa

Powerpoint Presentation

http://www.slideshare.net/secret/g0zJfjt4xfG5ca

Expected Learning Outcomes

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

- distinguish between plasmodial and cellular slime molds

- discuss the life cycle of plasmodial and cellular slime molds

- discuss altruism, cheating, and kin recognition in the life cycle of cellular slime molds

Plant-mycorrhizal fungi interactions

Readings

Symbiosis Mycorrhiza and Lichens
http://www.botany.hawaii.edu/faculty/wong/BOT135/Lect26.htm

Powerpoint Presentation

http://www.slideshare.net/secret/1jjuM1QpoCit0i


Expected Learning Outcomes

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

- list important plant macronutrients

- disucss nutrient uptake in plants

- discuss the basic characteristics of fungi

- discuss why fungi are unusual and important

- distinguish between sexes and mating types

- distinguish between ectomycorhhiza and endomycorrhiza

Rhizobia-Legume Interactions

Readings

General

Rhizobia-http://en.wikipedia.org/wiki/Rhizobia

Scientific Literature

Here are some papers from the scientific literature examining this system. We don't expect you to understand everything in these papers, but we would like you to see the diversity of approaches that moderm scientists are using to study this system.

Lifestyle alternatives for rhizobia: mutualism, parasitism,
and forgoing- symbiosis
http://people.umass.edu/lsadler/adlersite/kiers/Alternativelifestyles1.pdf

Host sanctions and the legume–rhizobium mutualism-
http://www.nature.com/nature/journal/v425/n6953/abs/nature01931.html (then click on "full text"

A mechanistic molecular test of the plant-sanction hypothesis in legume–rhizobia mutualism
http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VR3-4WPS9PP-1&_user=2605799&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_searchStrId=1100808123&_rerunOrigin=google&_acct=C000055350&_version=1&_urlVersion=0&_userid=2605799&md5=491bf0585068046d9ae2f49e3bb7a905

Powerpoint Presentation

Plant-Microbe Interactions: Rhizobia/Legumes
http://www.slideshare.net/secret/AZNj5BIH5bqGC8

Expected Learning Outcomes

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

- discuss how and why participants in an apparently mutualistic relationship should be "selfish"

- describe the pattern of nodule formation

- discuss the importance of nitrogenase and leghaemogolbin for nitrogen fixation

- discuss circumstances under which plants would like to limit nodulation or nitrogen fixation by rhizobia

- discuss "partner choice" and "santioning" in this system

- intepret data and draw conclusions in experiments examining rhizobia-legume interactions

Writing Assignment # 4

Reading

A Mutual Affair- http://judson.blogs.nytimes.com/2008/04/08/a-mutual-affair/

Assignment

This article by Olivia Judson from the New York Times discusses a number of interesting issues in mutualisms. In this class we have discussed the roles that microbes play as parasites, predators, competitors, and mutualists.

Using the knowledge you have gained during this course, and from reading the assignmed article, discuss the variety of ecological roles through which microbes affect humans. For each of the ecological roles that you discuss in your paper, we would like you to mention at least one interesting or "cool" thing that you have learned about the behavior of microbes in those interactions.

Your essay should be a minimum of two pages and a maximum of three pages in length.

Important Dates

Tuesday November 24th- Rough draft due

Thursday November 26th- Eat excessive amounts of turkey (or tofurkey)

Thusday December 3rd- Workshop papers (and remind Dr. McG that it is his Mom's birthday)

Tuesday December 9th- Final draft due

Microbial Diseases

Readings

Understanding Microbes in Sickness or Health- National Institute of Allergy and Infectious Disease

http://www3.niaid.nih.gov/topics/microbes/PDF/microbesbook.pdf

Websites

Nanobugs- http://www.nanobugs.com/
This website, designed for kids, is cool/cute/creepy but it might give you some basic background on important microbial diseases.

Expected Learning Outcomes

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

- discuss reservoirs for diseases
- discuss how microbes can enter their hosts
- discuss strategies microbes use to adhere, colonize, and invade their hosts
- discuss ways that microbes evade host defenses
- discuss the production of virulence factors
- discuss the endysymbiotic origin in mitochondria
- define pathogenicity islands
- define PROMISCUOUS and use it in a sentence

Global Climate Change Webinar

Here is the link to the Climate change webinar that Dr. San Francisco talked about.

http://learningcenter.nsta.org/products/symposia_seminars/fall09/NOAA/webseminar1.aspx

Microbes and Coral Reefs

Readings

Coral reefs- http://www.eoearth.org/article/Coral_reef

Threats to Coral Reefs-
http://www.eoearth.org/article/Threats_to_coral_reefs

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

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

Global warming takes a toll on coral reefs
http://www.eoearth.org/article/Global_warming_takes_a_toll_on_coral_reefs

Patterns of CAribbean coral loss
http://www.eoearth.org/article/Patterns_of_Caribbean_coral_loss

Coral disease-
http://www.reef.crc.org.au/discover/coralreefs/Coraldisease.htm

Coral stress and disease
http://www.reefrelief.org/Image_archive/diseases/index.shtml

Powerpoint Presentation

http://www.slideshare.net/secret/MXAjnaF502X8PL

Expected Learning Outcomes

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

- discuss the characteristics or the cnidarian polyps and zooxanthellae that make up a corals

- discuss the "dilema of the inverteed trophic pyramid" and the role that the discovery of zooxanthellae played in solving that mystery

- discuss the mutualism between cnidarian polyps and zooxanthellae

- discuss some of the threats facing coral reefs

- discuss coral bleaching and some of the proposed mechanisms of bleaching

- discuss the characteristics of some of the important coral diseases

Atmosphere, Solar Radiation, Microbes, and You

Reading

Electromagnetic Radiation- http://www.eoearth.org/article/Electromagnetic_radiation

Atmospheric Composition- http://www.eoearth.org/article/Atmospheric_composition

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

Expected Learning Outcomes

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

- Discuss electromagnetic energy and identify the portion of the electromagnetic spectrum that is used for photosynthesis

- discuss the composition of the atmosphere

- identify organisms capapble of photosynthesis

- define carbon fixation

- briefly discuss what happens in the light dependent reactions of photosynthesis

- briefly discuss what happens in the light independent reactions of photosynthesis

- discuss the processes involved in cycling organic carbon to carbon dioxide and back in aerobic and anaerobic environments.

- define the photo zone

- discuss conditions at the bottom of the ocean

-

Writing Assignment #2

Here are some recent news articles that address some of the issues that we have covered in class.

Nobel prize for chemistry: antibiotics scientists share 2009 award
http://www.telegraph.co.uk/science/science-news/6268585/Nobel-prize-for-chemistry-antibiotics-scientists-share-2009-award.html

Dangerous liaisons: Bacterial 'sex' causes antibiotic resistance
http://esciencenews.com/articles/2009/06/11/dangerous.liaisons.bacterial.sex.causes.antibiotic.resistance
TIMELY ASSIGNMENT NOTE- The play "Dangerous Liaisons" is being performed on campus this weekend.

Obama, Farm Industry Clash Over Antibiotics
http://www.wired.com/wiredscience/2009/07/farmantibiotic/

Assignment

Write a 1-2 page organized paper dealing with 1 or more of these topics. Include in your paper:

An Introduction-Set up the problem at hand and its general importance

Body-discuss why this topic is important to medicine, human health and society at large; what are pros and cons of different perspectives on these issues

Coda-Your own thoughts about the future related to the topic

Important Dates

Rough Draft Due- Tuesday October 20

Workshop- Thursday October 22

Final Draft Due- Tuesday October 27

Literature cited-References

Targets of Antibiotics and Mechanisms of Antibiotic Resistance

Readings

Targets of Antibiotics (figure)
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mboc4.figgrp.4624

How antibiotics work: the mechanisms of action
http://www.tufts.edu/med/apua/Miscellaneous/mechanisms.html

Antibiotics that affect the cell envelope
http://pathmicro.med.sc.edu/fox/antibiotics1.htm

Mechanisms of Antibiotic Resistance in the Microbial World
http://www.moleculartb.org/gb/pdf/transcriptions/11_YZhang.pdf

Expected Learning Outcomes

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

- discuss the targets of antibiotics
- discuss the mechanisms of antibiotic resistance
- pronounce "efflux" correctly

Antibiotic Resistance

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

Resisting our drugs-
http://understandingevolution.com/evolibrary/article/0_0_0/bergstrom_03

Turbochared evolution-
http://understandingevolution.com/evolibrary/article/side_0_0/turboevolution_01

Relevance of evolution:medicine-
http://understandingevolution.com/evolibrary/article/0_0_0/medicine_01

Powerpoint Presentation

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

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

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 where antibiotics come from

- 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

Sex Lives of Bacteria

Reading

Genetic recombination in bacteria
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/A/Avery.html

Recombination in bacteria
http://www.emunix.emich.edu/~rwinning/genetics/bactrec.htm

Expected Learning Outcomes

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

- discuss how mutation, transformation, conjugation, and transduction adds to the genetic variation of bacteria.

Microbes and the Evolution of Sex

Based on our understanding of natural selection, at first glance sexual reproduction doesn't appear to be advantageous from the female perspective (due to the two-fold cost of sex). However, the fact that sexual reproduction is so common in all groups of organisms suggests that there must be some major benefits of sex that outweight the costs.

Reading

The Advantages of Sex- Matt Ridley
http://www.pbs.org/wgbh/evolution/sex/advantage/index.html

Expected Learning Outcomes

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

- explain "the two-fold costs of sex"
- discuss possible benefits of sexual reproduction including adaptation to environmental uncertainty and fighting disease
- be able to discuss the problem of the evolution of antiobiotic resistant microbes
- be able to discuss what the medical field may be able to learn from observing how nature fights disease.

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

Africa's Big Three

Tuberculosis

Readings

Tuberculosis Fact Sheet- Centers for Disease Control and Prevention
http://www.cdc.gov/tb/publications/factsheets/general/tb.htm

Pulmonary Tuberculosis- https://www.google.com/health/ref/Pulmonary+tuberculosis

Tackling Tuberculosis in Africa http://web.worldbank.org/WBSITE/EXTERNAL/COUNTRIES/AFRICAEXT/0,,contentMDK:21696343~pagePK:146736~piPK:226340~theSitePK:258644,00.html


Malaria

Readings

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

Malaria in Africa
http://www.rollbackmalaria.org/cmc_upload/0/000/015/370/RBMInfosheet_3.htm

Diseases and development challenges in Africa
http://www.eoearth.org/article/Diseases_and_development_challenges_in_Africa


HIV

Readings

HIV Basic Information - Centers for Disease Control and Prevention
http://www.cdc.gov/hiv/topics/basic/index.htm

HIV and AIDS in Africa
http://www.avert.org/aafrica.htm


Expected Learning Outcomes

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

- briefly discuss the biological characteristics of the causal agents for the Big Three diseases

- discuss the means of transmission of these diseases

- discuss the means of preventing the spread of these diseases

- discuss the impact that these diseases have had on people in Aftica

Articles about AIDS Vaccine

AIDS vaccine promising; experts urge caution- San Francisco Chronicle
http://www.sfgate.com/cgi-bin/article.cgi?f=/c/a/2009/09/24/BANM19S3NR.DTL

For the first time AIDS vaccine shows some success- New York Times
http://www.nytimes.com/2009/09/25/health/research/25aids.html?_r=2

Thanks to Mathew Sexton for forwarding this link to us.

H1N1 Flu

Readings

H1N1 Swine Flu- from Centes for Disease Control and Prevention/
http://www.cdc.gov/H1N1FLU/

H1N1- www.flu.gov

2009 Flu Pandemic- http://en.wikipedia.org/wiki/2009_flu_pandemic

Swine Flu 2009/2010
Honors College recommendations for students, faculty and staff

If you must miss work or class because you have symptoms of the flu described below, and must see a doctor, please do not forget to bring a note indicating that you have done so. Students, please be aware that while reasonable extensions will be permitted to make up work due to the flu will be granted, you are ultimately responsible for your work. Please also be sure to contact your professor as soon as possible if you are ill. Faculty, please make your students aware of how you will permit make-up work for short- and long-term absences because of the flu. Also provide the dean’s office with information of how you wish your class to be covered in case of an extended absence by you because of the flu. Staff, please notify your supervisor as soon as possible if you have to miss work.

Our recommendations are taken directly from the Centers for Disease Control.
http://www.cdc.gov/h1n1flu/qa.htm

What are the signs and symptoms of this virus in people?

The symptoms of 2009 H1N1 flu virus in people include fever, cough, sore throat, runny or stuffy nose, body aches, headache, chills and fatigue. A significant number of people who have been infected with this virus also have reported diarrhea and vomiting. Severe illnesses and death has occurred as a result of illness associated with this virus.

What can I do to protect myself from getting sick?

There is no vaccine available right now to protect against 2009 H1N1 virus. However, a 2009 H1N1 vaccine is currently in production and may be ready for the public in the fall. As always, a vaccine will be available to protect against seasonal influenza

Actions that can help prevent the spread of germs that cause respiratory illnesses like influenza are presented below.
Take these everyday steps to protect your health:
Cover your nose and mouth with a tissue when you cough or sneeze. Throw the tissue in the trash after you use it.
Wash your hands often with soap and water. If soap and water are not available, use an alcohol-based hand rub.*
Avoid touching your eyes, nose or mouth. Germs spread this way.
Try to avoid close contact with sick people.
If you are sick with flu-like illness, CDC recommends that you stay home for at least 24 hours after your fever is gone except to get medical care or for other necessities. (Your fever should be gone without the use of a fever-reducing medicine.) Keep away from others as much as possible to keep from making others sick.

Other important actions that you can take are:
Follow public health advice regarding school closures, avoiding crowds and other social distancing measures.
Be prepared in case you get sick and need to stay home for a week or so; a supply of over-the-counter medicines, alcohol-based hand rubs,* tissues and other related items might could be useful and help avoid the need to make trips out in public while you are sick and contagious

What is the best way to keep from spreading the virus through coughing or sneezing?

If you are sick with flu-like illness, CDC recommends that you stay home for at least 24 hours after your fever is gone except to get medical care or for other necessities. (Your fever should be gone without the use of a fever-reducing medicine.) Keep away from others as much as possible. Cover your mouth and nose with a tissue when coughing or sneezing. Put your used tissue in the waste basket. Then, clean your hands, and do so every time you cough or sneeze.

If I have a family member at home who is sick with 2009 H1N1 flu, should I go to work?
Employee
s who are well but who have an ill family member at home with 2009 H1N1 flu can go to work as usual. These employees should monitor their health every day, and take everyday precautions including washing their hands often with soap and water, especially after they cough or sneeze. Alcohol-based hand cleaners are also effective. If they become ill, they should notify their supervisor and stay home. Employees who have an underlying medical condition or who are pregnant should call their health care provider for advice, because they might need to receive influenza antiviral drugs to prevent illness. For more information please see General Business and Workplace Guidance for the Prevention of Novel Influenza A (H1N1) Flu in Workers.

What is the best technique for washing my hands to avoid getting the flu?

Washing your hands often will help protect you from germs. Wash with soap and water or clean with alcohol-based hand cleaner*. CDC recommends that when you wash your hands -- with soap and warm water -- that you wash for 15 to 20 seconds. When soap and water are not available, alcohol-based disposable hand wipes or gel sanitizers may be used. You can find them in most supermarkets and drugstores. If using gel, rub your hands until the gel is dry. The gel doesn't need water to work; the alcohol in it kills the germs on your hands.

What should I do if I get sick?

If you live in areas where people have been identified with 2009 H1N1 flu and become ill with influenza-like symptoms, including fever, body aches, runny or stuffy nose, sore throat, nausea, or vomiting or diarrhea, you should stay home and avoid contact with other people. CDC recommends that you stay home for at least 24 hours after your fever is gone except to get medical care or for other necessities. (Your fever should be gone without the use of a fever-reducing medicine.) Stay away from others as much as possible to keep from making others sick. Staying at home means that you should not leave your home except to seek medical care. This means avoiding normal activities, including work, school, travel, shopping, social events, and public gatherings.

If you have severe illness or you are at high risk for flu complications, contact your health care provider or seek medical care. Your health care provider will determine whether flu testing or treatment is needed.
If you become ill and experience any of the following warning signs, seek emergency medical care.

In adults, emergency warning signs that need urgent medical attention include:
Difficulty breathing or shortness of breath
Pain or pressure in the chest or abdomen
Sudden dizziness
Confusion
Severe or persistent vomiting
Flu-like symptoms improve but then return with fever and worse cough

What is the positive, definitive test for the swine flu?

The ONLY way a test can be confirmed positive is through PCR or culture methods!! Some doctors’ offices are reporting positive results for H1N1-swine-like from the “rapid flu tests”. These tests can indicate that you have the flu but not the SWINE FLU. If you want to read some more go to www.flu.gov for info. H1N1 can be seasonal or swine-like as well, a rapid can't determine the difference.

Gene Therapy

Readings

Gene Therapy- Human Genome Project Information

http://www.ornl.gov/sci/techresources/Human_Genome/medicine/genetherapy.shtml

Viruses

Readings

Introduction to the Viruses- http://www.ucmp.berkeley.edu/alllife/virus.html

Viruses, viruses, viruses by David Baltimore
http://eands.caltech.edu/articles/LXVII1/viruses.html


Expected Learning Outcomes

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

- discuss the characteristics of a virus
- discuss the basic shapes of viruses
- define "bacteriophage"
- compare and contrast the mechanism gene injection of viruses that infect bacteria and those that attack animal cells
- distinguish between the infection pathways of DNA viruses, simple RNA viruses, and retroviruses

Biofilms

Reading

What is biofilm?
http://www.erc.montana.edu/CBEssentials-SW/bf-basics-99/bbasics-01.htm

Biofilm
http://en.wikipedia.org/wiki/Biofilm

Expected Learning Outcomes

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

- define a biofilm

- compare and contract bacteria that live as individuals and those that live in biofilms

- discuss why biofilms cause such large medical problems

Brief History of Microbiology

Scientists have studied microbes for a much shorter period of time than they have learned about animals and plants. The above figure shows some of the important events during the history of microbiology.

Expected Learning Outcomes

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

- discuss the contributions of important Microbiologists such as Leeuwenhook, Redi, Jenner, and Flemming

- discuss the role that "serendipity" played in the discovery of penicillin

Pacific Yew- Taxus brevifolia

Last week Dr. San Franciso mentioned the Pacific Yew tree (Taxus brevifolia)as an example of a species that has been used to provide chemicals that are useful in medicine.

One of your classmates, Jeffrey Chen, did a little research about the Pacific Yew, so I thought that we would share it with you. Thanks to Jeffrey for organizing this material! You are all invited to send us any info that you think might be interesting to the class and we will post it to the site.

Pacific yew (found in Pacific Northwest: from southern Alaska, to central California, ot even Idaho)
Uses:
1) native inhabitants: used for its hardiness Ex: digging sticks, harpoons, war weapons
2) native inhabitants: medicinal uses:
a) rub branches of tree against body to enhance potency
b) compress fresh yew leaves and soak in water (used to bathe infants and elderly): helps rid them of physical defects
c)crush the yew leaves, soak in water, then boil the water before drinking the misture to help alleviate internal pains and wounds
d) chew up the yew leaves and then spatter them on the wounds

2) modern day uses for cancer treatment
-the drug paclitaxel (chemo drug) extracted from bark of pacific yew tree

-has been shown effective in

a) prostate cancer

b) ovarian cancer

c) breast cancer

- paclitaxel's complex structure is hard to synthesize, so since discovery of its anticancer properties, the pacific yew tree has been heavily harvested


Readings- If you want to learn some more check out-

http://www.herbs2000.com/herbs/herbs_pacific_yew.htm

http://toptenhealthproducts.com/yewimmune5-free-report.html

http://www.prostate-cancer.com/prostate-cancer-glossary/pacific-yew-tree.html

Thanks again to Jeffrey!!!

Human Microbiota

From: “Prescott’s Principles of Microbiology”, Willey, Sherwood, Woolverton; McGraw-Hill, 2009.

Readings

The Normal Flora of Humans

http://bioinfo.bact.wisc.edu/themicrobialworld/NormalFlora.html

Expected Learning Outcomes

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

- distinguish between psycrophilic, themophilic, mesophilic, and barophilic bacteria

- define "adaptation" in the non-evolutionary sense

- briefly discuss "gene expression"

- discuss generation times of bacteria under different conditions

- discuss areas of the human body where bacteria are and are not typically found

- distinguish between Gram positive and Gram negative bacteria

- discuss some bacteria found on your skin and how they may play a "positive" role in your life

Cells

Readings

Cellupedia- http://library.thinkquest.org/C004535/introduction.html

This website has a lot of information about cells. Have fun poking around in this site

Amazing Cells from Learn.Genetics. http://learn.genetics.utah.edu/content/begin/cells/

This site also has a lot of great information in it about cells.

Expected Learning Outcomes

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

- discuss the characteristics of prokaryotic cells

- discuss the characteritics of a eukaryotic cell

- identify the function of organelles/cellular structures such as nucleus, mitochondria, lysosomes, chloroplasts

- compare and contrast the characteristics of a prokaryotic and eukaryotic cell

- conpare and contrast chromosomes of prokaryotic and eukaryotic cells

Introduction to Some Biologically Important Molecules

It is difficult to talk about some parts of biology without understanding some basic biochemistry.

Readings

Learn.Genetics. http://learn.genetics.utah.edu/

This website, from the University of Utah, contains some great information. In particular, you should check out the sections on "Tour the Basics" and "Amazing Cells".

Expected Learning Outcomes

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

- define inportant chemical terms including, but not limited to, polymer, protein, amino acid, nucleic acids, nucleotides, purines, pyrimidines, fatty acids

- disucss the biologically important polymers and identify the sub-units of each of these polymers

Prebiotic Environment and the Origin of Life

Readings

Introduction to Exobiology- http://www.chem.duke.edu/~jds/cruise_chem/Exobiology/index.html

This website from Duke University has good information about the conditions of the prebiotic environment, the Miller Urey Experiment, and other issues.

Expected Learning Outcomes

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

- discuss the characteristics of the prebiotic environment

- discuss how the prebiotic environment differs from the environment we live in today

- discuss some reasons why the current environment differs from the prebiotic environment

- discuss the methodology and the results of the Miller-Urey experiment

- disuss the gaps in our knowledge and understanding of the origin of life

- state the year of Dr. San Francisco's birth

Timeline of the Universe and of the Earth

An understanding of the timeline of events in the history of the universe and in the history of the universe will be helpful for this course.

Timeline of History of the Universe



Timeline of History of the Earth



Expected Learning Outcomes

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

- state the approximate age of the universe

- state the approximate age of the earth

- state the age of life on earth

Writing Assignment #1

So far in this class we have had very general discussions about critical thinking, what is life, the prebiotic environment and the origin of life, and prokaryotic and eukaryotic cells. This essay provides you the opportunity to integrate what you have learned so far.

Assignment- Answer the question- are bacteria alive?

In order to provide a full and thoughtful answer to this question is is probably necessary to address at least some of the following issues.

- what do you think is the best definition of life?

- what are bacteria?

- what are the characteristics of an organism that we are used to thinking about (e.g., your goldfish, your puppy, or your little brother) that make you think that they are alive?

- which of these characteristics apply to bacteria?

Critical Thinking Rubric

This table lists characteristics of work done by individuals with different levels of critical thinking skills. Hopefully, this information will help you to (1) write your own papers and (2) critically analyze papers written by your fellow students.

Note: If you double click on the table it will get larger so it is easier to read.

Exobiology and Prebiotic Conditions

Readings

From Primordial Soup to the Prebiotic Beach: An interview with exobiology pioneer, Dr. Stanley L. Miller, University of California San Diego
http://www.accessexcellence.org/WN/NM/miller.php

Titan may host prebiotic brew: Evidence from flybys suggests the Saturnian moon’s environment is similar to that of the early Earth
http://www.sciencenews.org/view/generic/id/46172/title/Titan_may_host_prebiotic_brew

Critical Thinking Exercise

There are lots of controversial issues on campus, in Lubbock, in Texas, and in the USA that would allow us to practice our critical thinking skills. However, sometimes I think it is easier to think critically about issues that don't seem to immediately affect us. Thus, I would like us to explore an issue that has been in the news recently that is happening in Malaysia.

Malaysia is a very interesting county. If you would like to know more about Malaysia, their environment, and the people that live there you can check out this powerpoint presentation. This slideshow, which is think is pretty cool, was developed by one of my Natural History and Humanities classes to be used in a 5th grade classroom. Even though it was intended for kids, it still serves as a useful introduction to Malaysia.

http://www.slideshare.net/secret/3JwD4G3hq4RjhQ

Crticial Thinking Exercise

Here is a link to the slideshow that I used in class.

http://www.slideshare.net/secret/9SnjQ9zV1GFQMX

Further Viewing

Malaysian woman to be caned for drinking beer - 23 Aug 09
http://www.youtube.com/watch?v=xnOWgCz5fj4

Further Reading

If you want to learn more about this story then here are links to a couple of CNN and BBC articles. It seems to me that the outcome of this story is still uncertain, so it will be interesting to follow it to see what happens.

Malaysian model, mother to be caned for drinking beer in public
http://www.cnn.com/2009/WORLD/asiapcf/08/20/malaysia.caning/index.html?iref=newssearch

Malaysia postpones woman's caning
http://www.cnn.com/2009/WORLD/asiapcf/08/24/malaysia.model.caning/index.html?iref=newssearch

Malaysia delays caning beer woman
http://news.bbc.co.uk/2/hi/asia-pacific/8217440.stm

The political cost of caning Kartika
http://www.mysinchew.com/node/28703?tid=14

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

Critical Thinking

Further Reading

Critical Thinking: What is is and why does it count?
http://www.criticalthinking.org/aboutCT/define_critical_thinking.cfm

A Working Definition of critical thinking by Michael Scriven and Richard Paul
http://lonestar.texas.net/~mseifert/crit2.html

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 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 Natural History and Humanities degree (http://www.depts.ttu.edu/honors/nhh/)

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 and environmental education. I serve as a member of the Stewardship Committee of the Environmental Information Coalition and as an Author and Topic 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.

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, Indonesia, and Galapagos Islands. My favorite marine critters include hammerhead sharks, pygmy sea horses, and “the pea”.

Course Syllabus

Course Syllabus

So You Think You Are Alone? Fall 2009
HONS 1302-H02
T-Th 12:30 – 1:50 AD 243

Instructors
Dr. Mark McGinley Dr. Michael San Francisco
Room 215 McClellan Hall Room 210 McClellan Hall
mark.mcginley@ttu.edu michael.sanfrancisco@ttu.edu
Office Hours- MWF 11- 12 Office hours-Friday 9-11
or by appointment

We encourage you to make an appointment to meet with us if you need to see us. The easiest ways to do this are (1) to talk to us either before or after class or (2) to send an email listing times when you are available to meet.

Course Outline
Did you know ….. That there are more cells that do not belong to you on your body? There are more bacteria on the planet than all other organisms combined? That you cannot survive “normally” without microorganisms? This interactive course will focus on the interactions between microorganisms and the environment. Topics that will be covered include microbes on the human body; microbes in soils/oceans; microbes and medicine; microbes and agriculture; microbes and disease; microbes and climate. We will discuss these topics from microbial and ecological perspectives. This course is writing-intensive.

THIS COURSE FULFILLS THE CORE CURRICULUM TECHNOLOGY AND APPLIED SCIENCE REQUIREMENT.

Students graduating from Texas Tech University should be able to demonstrate understanding of how technology and applied science affect society and the environment and to demonstrate understanding of the relationship between ethics and technology.

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 IntegrityTexas 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. “Think critically” about scientific issues related to microbiology. assessed by performance in class discussions, midterm exam, and written papers

2. Define and apply basic concepts in microbiology, evolutionary biology, and ecology. assessed by performance on exams and written papers

3. Demonstrate understanding of how rapid pace of technology and applied science may have good and bad outcomes. assessed by performance on class discussion and written paper
4. Discuss the role of microbes in the ecosystem and organismal biology. assessed by performance exams and written papers
5. Write effectively about scientific issues related to microbiology. assessed by performance on exams and written papers





Grading
Midterm exam 10%
Final exam 15%
Meaningful participation in workshops, online, and discussion 15%
Writing assignments 60%
#1 = 10%, 2 & 3 = 15%, 4 = 20%

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 and discussions.

Writing Assignments
These papers will be three pages maximum double spaced.
You will turn in a draft of this paper that will be critiqued by your classmates and the instructors during a “Workshop” class period.
You can revise your paper and turn in a final copy of paper to be graded!

Course Blog
We 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://soyouthinkyouarealone.blogspot.com/. Hopefully, most of your questions about the details of the class will be answered somewhere on the blog.

Blog posts will include your reading assignments and occasionally practice questions to check your learning. In addition, we 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. We will assign readings throughout the semester on the course blog http://soyouthinkyouarealone.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.




Important Dates
Week 1. (August 27)

Week 2. (September 1 - 4)

Week 3. (September 8 - 10)
First Writing Assignment- Due September 10

Week 4. (September 15 - 17)
Tuesday- workshop papers
First Writing Assignment- Final Draft Due September 22

Week 5. (September 22 - 24)

Week 6. (September 29 - October 2)

Week 7. (October 6 - 8) Midterm Exam- Friday October 9th

Week 8. (October 13 - 15)
Second Writing Assignment- Due October 15

Week 9. (October 20 - 22)
Tuesday- workshop papers

Week 10. (October 27 - 30)
Second Writing Assignment- Final Draft Due October 27

Week 11. (November 3 - 5)
Third Writing Assignment- Due November 5

Week 12. (November 10 - 12)
Tuesday- Workshop Papers

Week 13. (November 17 - 19)
Third Writing Assignment- Final Draft Due November 17

Week 14. (November 24)
Fourth Writing Assignment- Due November 24

Week 15. (December 1 - 3)
Thursday- Workshop Papers

Week 16. (December 8)
Fourth Writing Assignment- Due December 8

Final Exam- Saturday December 12th- 1:30 to 4:00 PM.

What is Life?

Biology is defined as "the scientific study of life" so an obvious question is- "What is life?"

In most cases if we want to know the definition of a word we would turn to a dictionary. Unfortunately, the typical definition is not too helpful.

Life- The property or quality that distinguishes living organisms from dead organisms and inanimate matter.

It turns out that actually defining life is more difficult than you might have originally have thought, so it is a concept that definitely deserves a little more thought.

Reading

Origin and Definition of Life from PhysicalGeography.net by Michael Pidwirny
http://www.physicalgeography.net/fundamentals/9a.html

Expected Learning Outcomes

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

- discss the difficulties in easily defining life

- develop their own definition of life and be able to defend why they chose that definition.