Modern Genetics

An understanding of the molecular basis of how genotype influences phenotype can be useful in a variety of areas including attempting to cure genetic diseases, producing genetically modified organisms, and using genetic techniques to identify individuals.

DNA Fingerprinting

http://protist.biology.washington.edu/fingerprint/dnaintro.html

http://www.wisegeek.com/what-is-dna-fingerprinting.htm

http://blogs.scientificamerican.com/guest-blog/2011/05/02/how-do-you-id-a-dead-osama/

Geneticall Modified Organisms

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

Expected Learning Outcomes

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

1) briefly discuss how cells that contain the same genetic information can have different phenotypes,

2) briefly and generally discuss how mutations could lead to diseases,

3) breifly discuss the production of geneticall modified organisms,

4) describe the use of DNA fingerprinting to identify individuals

Genotype to Phenotype

We know that our genotype helps to determine our phenotype. I think that it makes sense to originally think about things backwards.

phenotype <= chemical reactions in cell <= enzymes in the cell <= order of amino acids in proteins <= order of nucleotides in DNA.

Genetic information in DNA is converted to information in mRNA by the process of transcription and information in mRNA is used to determine the order of amino acids in a protein.

Website

I encourage you all to spend some time looking at the LearnGenetics website created by the University of Utah. Consider this website to be your interactive textbook for this portion of the class.

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

I suggest you examine the following sections in detail.

Tour of the Basics
DNA to Protein

The other sections are cool as well and they will help you to understand how our knowledge about genes to phenotype can be applied.

Video

This video does a pretty good job of discussing the processes of transcription and translation (but goes into just a bit more detail than required in this class).

 http://www.youtube.com/watch?v=Ynmxwqiv7j8&feature=related

Expected Learning Outcomes

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

1) discuss the structure of the three important macromolecules (DNA, RNA, and proteins) and identify their subunits.

2)  briefly discuss the process of genetic replication

3) briefly discuss the process of translation and transcription

4) if provided with the DNA sequence of a gene determine (a) the order of bases in the complementary strand of DNA, (b) the order of bases in the complementary strand of mRNA, and (c) determine the order of bases in the anticodon in the complementary tRNA and which amino acid should be attached to that tRNA.

Global Carbon Cycle and Climate Change

Human activity, including burning fossil fuels, deforestation, and buring trees, has altered the global carbon cycle. This alternation of the global carbon cycle is the proposed cause of global climate change (global warming).

Obviously, global climate change is a very imporant issue facing us today. If you are alive and paying any attention, then you probably know that there is some disgreement out there about (1) whether global warming is occuring, (2) if it is occuring is it a natural occurence or is it caused by humans, and (3)what should we as individuals and a society do about these issues. As I mentioned in class, it is very important that you understand what components of the debate are facts and what components of the debate are based on mathematical models or other forms of argument. I think that it is important that you should be able to explain to other people why scientists will never be able to conduct the experiment that will nail down whether or not humans are causing global warming (we have only one earth).

I think that it is important for you to have access to good information. Here are some links to what I consider to be some of the best and most reliable sources of information about this topic. Although some of these articles go into much more detail than are required for this class you should know where to find reliable information about this topic.

Further Reading

Carbon cycle- http://www.eoearth.org/article/Carbon_cycle

Global warming- http://www.eoearth.org/article/Global_warming

Global warming Frequenty Asked Questions- http://www.eoearth.org/article/Global_warming_frequently_asked_questions

Climate change FAQ- http://www.eoearth.org/article/Climate_change_FAQs

Intergovenmental Panel on Climate Change- http://www.eoearth.org/article/Intergovernmental_Panel_on_Climate_Change_%28IPCC%29

IPCC Assessment for Policymakers- http://www.eoearth.org/article/IPCC_Fourth_Assessment_Report%2C_Working_Group_I%3A_Summary_for_Policymakers

If you would like additional information about global climate change then you can take a look at a presentation I developed for another class.

Global Carbon Cycle and Global Climate Change
http://www.slideshare.net/secret/C6iDTujQlIh73C

Expected Learning Outcomes

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

- diagram the global carbon cycle
- discuss how humans have altered the global carbon cycle
- discuss how the atmospheric concentration of carbon dioxide varies annually
- discuss the proposed relationship between human caused changes in the global carbon cycle and global warming
- discuss alternative causes of global warming
- discuss the experiment that would be required to determine whether or not human activity is the cause of global warming
- articulate and defend their own personal view of how they intend to deal with the global warming issue

Ecosystem Ecology

Ecosystem ecologists focus on the flow of enery and the cycling of nutrients through the ecosystem.

Further Readings

Ecosystems- http://www.eoearth.org/article/Ecosystem

Ecological energetics- http://www.eoearth.org/article/Ecological_energetics

Nitrogen cycle- http://www.eoearth.org/article/Nitrogen_cycle

Expected Learning Outcomes

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

- diagram and discuss the flow of energy through an ecosystem
- diagram, discuss the causes of, and discuss some of the implications of the enegy pyramid
- diagram nitrogen cycle within an ecosystem
- discuss the factors that influence the rate of flow from dead bodies to the soil and discuss the implications of differences in this rate

Community Ecology: The Portal Experiment

Here are some photos from the research site in Portal, Arizona. For more information about the research project at Portal you can look at their website at
http://portal.weecology.org/

Expected Learning Outcomes

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

- distinguish between direct and indirect, positive and negative effects
- describe the experiemental design that Dr. Brown and his colleagues used to study exploitative competition between desert rats and rodents
- discuss the "search the the missing indirect positive effect of rodents on ants" and how that dilema was solved
-discuss why and how the outcome of studies of interactions betwen organisms can vary over time
- discuss the way that the ecological community responded when they learned the importance of long term studies
- discuss how indirect interactions lead to one of my favorite phrases "the world is complicated"

Best Community Ecology Video Ever!?!?!?

A past biology student sent me a link to this video. It seems like almost everything that we have talked about so far in Honors Integrated Science is going on in this video. The highlight of my biology life was visiting Kruger Park when I was about 13 (how sad to peak so young). I saw lots of amazing animals, but I didn't see anything like this. This video keeps getting better so watch it all the way to the end. Enjoy!!

http://www.youtube.com/watch?v=LU8DDYz68kM

Community Ecology

Community Ecology will be the final topic covered on the First Midterm.

Required Readings

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

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

Interspecific Competition- http://www.eoearth.org/article/Interspecific_competition

Exploitative Competition- http://www.eoearth.org/article/Exploitative_competition

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

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

Expected Learning Outcomes

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

- define competition, exploitative competition and interference competition

- identify and explain examples of exploitative and interference competition from a variety of environments

- define predation (narrow and broad sense), herbivory, and parasitms

- identify and explain examples of predation, herbivory, and parasitism from a variety of environments

- identify examples of morphological and behavioral adaptations that animals have to help capture their food

- identify examples of morphological, biochemical, or behavioral adaptations that animals have to protect them from predators

- identify and explain examples of mutualisms from a variety of habitats

Recent Article on the Effects of Human Population Growth on the Environment

I found this article on CNN's website on Sunday.

Please watch the video and read the article.

Th Earth is Full- http://www.cnn.com/2012/04/08/opinion/gilding-earth-limits/index.html?hpt=op_bn2

Remember- One of the common questions that I ask on exams is "Do you think that human population growth is a "problem"? If you were Queen/King of the World, then what would you do about this issue?

Human Population Growth

I have spent a lot of time telling you that exponential growth is an unrealistic model of population growth. Interestingly, human populations have experienced exponential-like growth. How can this be?

What makes humans different from other species?

In other species per capita birth rates and per capita deaths rates are density dependent. However, as human populations have increased there has been no corresponding decline in per capita birth rates or increase in per capita death rates. What makes humans different from other species?

Humans have the ability to alter their environment so that they can avoid the density dependent effects on birth and death rates. 1) Humans have increased food production by improvements in agriculture (e.g., irrigation, fertilization, mechanized farming, genetically improved crops). 2) Humans have been able to decrease death rates by improvements in medicine and public health (things as simple as not pooping in the water you drink helps a lot!). 3) Humans have elimnated most human predators (ocassionally, someone gets killed by a shark or a mountain lion).

Where is human population growth occuring?

The rates of human population growth are not the same in all regions. Today, human populations are increasing in size much faster in developing countries (e.g., Mexico, other countries in Central America, Africa, and Southeast Asia) than they are in developed countries (e.g, USA, Canda, Western Europe). The figure at the top of this post shows the patterns of population growth in developed and developing nations.

Thus we see that populations are increasing most rapidly in the countries that are least able to deal with a rapidly increasing population. See "Population Challenges-The Basics" that can be downloaded from the Population Institute's website.
http://www.populationinstitute.org/population-issues/index.php

Human Population Growth Problem?

There is a great deal of debate about whether increasing human populations are a problem or not, and if they are what should be done about it. Unfortunately, we don't have time to discuss this issue in very much detail in class. My personal opinion is that we have too many people consuming too many resources and the last thing that we need are billions more people living on the planet. This is an issue that I am always intersted in talking more about if you would like to chat.

Further Reading

Here is a link to the article "Human Population Explostion" from the EoE.
http://www.eoearth.org/article/Human_population_explosion

7th Billion Person- http://www.thehindu.com/sci-tech/science/article2412108.ece

Really Cool Videos

Here is a link to a YouTube video on "World Population" The first minute and a half or so is a little boring, so you can skip over it if you wish. However, I think the animation showing when and where human population growth has been occuring is really cool.
http://www.youtube.com/watch?v=4BbkQiQyaYc

This video uses a cool, dynamic graphical approach to examine changes in income, health, and population size in 200 countries over the past 200 years. I bet you never thought that graphs could be so fun!!
http://talkingpointsmemo.com/archives/2010/12/200_years_in_4_minutes.php

This link contains lots of interesting data- take a look
http://www.worldometers.info/

Expected Learning Outcomes

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

- describe patterns of human population growth in developed and developing nations

- discuss some reasons why the pattern of population growth in humans is so different from that in other species

- describe the demographic transition

- discuss their own personal view of human population growth.

Update for th Rest of the Semester

Now that it is finally dawned on me that it is April, I have realized that classes end next month. Thus, I think that it is wise for us to revisit what you will be doing to earn grades during my portion of the class.

First Midterm- Thursday April 19th (NOTE: this exam is scheduled for Thursday April 16th in the syllabus- don't know what calendar I was looking at when I made those plans)

Term Paper- Due May 8th (I will provide more details about the paper next week in class)

Second Midterm - 1:30 - 4:00PM, Monday May 14th

Population Ecology

Here is a brief introduction to some of the important parameters that we will need to understand to be able to study population ecology. For each of the parameters it is important that you know (1) the name of the parameter, (2) the algebraic symbol used to represent the parameter, (3) the units of measurement for the parameter, (4) how to calculate the parameter, and (5) how to describe (in words) what a particular value of that parameter means.

It is probably easiest for me to introduce these concepts using an example.
Imagine that in a population of 100 elephants that in one year 10 elephants are born and 5 elephants die.

1) Population Size (N) units- individuals. Measures the number of individuals in a population.

N = 100 individuals

In this population, there are 100 elephants.

2) Population Birth Rate (B) units- number of births per time. Measures the number of births per time that occur in a population.

B = 10 births/year

In this population, each year there are 10 births.

3) Population Death Rate (D) units- number of deaths per time. Measures the number of deaths per time that occur in a population.

D = 5 deaths/year

In this population, each year there are 5 deaths.

4) Population Growth Rate (dN/dt) units- number of idividuals per time. Measures the rate of change of the population size.

dN/dt = B - D

dN/dt = 10 births/year - 5 deaths/year = 5 individuals/year

In this population, the population size increases by 5 individuals each year.

5) Per Capita Birth Rate (b) units- births per time per individual. Measures the number of births per time averaged across all members of the population.

b = B/N

b = (10 births/year)/100 individuals = 0.10 births/year/individual

In this population, each year 0.10 babies are born for each individual in the population.

6) Per Capita Death Rate (d) units - deaths per time per individual. Measures the number of deaths per time averaged across all members of the population.

d = D/N

d = (5 deaths/year)/100 individuals = 0.05 deaths/year/individual

In this population, each year 0.005 individuals die for each individual in the population.

7) Per Capita Growth Rate (r) units = individuals/time/individual. Measure the rate of change in population size averaged across all individuals. The per capita growth rate can be calcuated two ways.

a) r = b - d

r = 0.10 births/year/individual - 0.05 deaths/year/individual = 0.05 ind/year/ind

b) r = (dN/dt)/N

r = (5 individuals/year)/100 individuals = 0.05 individuals/year/individual

In this population, each year 0.05 individuals are added for each individual in the population.

Practice Problem

In a population of 50 tigers, in one year 10 tigers are born and 20 tigers die. What is B, D, dN/dt, b, d, r?

Readings


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

Population ecology- http://www.eoearth.org/article/Population_ecology

Population growth rate- http://www.eoearth.org/article/Population_growth_rate

Exponential growth- http://www.eoearth.org/article/Exponential_growth

Logistic growth- http://www.eoearth.org/article/Logistic_growth

Carrying capacity- http://www.eoearth.org/article/Carrying_capacity


Expected Learning Outomes

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

- define and calculate the value of basic population ecology parameters

- draw and interpret the following graphs

a) how population size changes over time in exponential growth

b) how population size changes over time in logistic growth

- explain why exponential growth is an unrealistic pattern of growth for most species

- define and explain the carrying capacity

- discuss the factors that regulate population size, be able to distinguish between density dependent and density independent factors that regulate population growth and give examples

Cultural Selection

In humans there are examples of alturistic behaviors that appear to be difficult to explain by kin selection of reciprocal altruism (e.g. soldiers sacrificing their lives in battle, police or firefighters risking their lives, catholic priests remaining celibate).

Genes are self replicating molecules. Genes produce our bodies which in turn produce more copies of their genes. Richard Dawkins has suggested that we think about genes as being "replicators" and our bodies as being "vehicles" whose job it is to make more copies of the replicators. If we can not explain altruistic behaviors as strategy for increasing the transmission of genes into the next generation them maybe we need to search for another kind of "replicator". Dawkins has suggested that "ideas" (he calls them "memes") are also capable of self replication. Because ideas differ in how long they survive and how well they are passed on it should be possible to have selection for ideas (cultural selection).

Expected Learning Outcomes

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

- identify examples of altruistic behavior that might be explained by cultural selection
- be able to compare and contrast "natural selection" with "cultural selection"

Further Readings

Cultural evolution http://plato.stanford.edu/entries/evolution-cultural/

One of my favorite books of all time is "The Selfish Gene" by Richard Dawkings. He discusses some of his ideas about cultural selection in the final chapter of this book. Here is a link to that chapter in case you are interested
http://www.rubinghscience.org/memetics/dawkinsmemes.html

I think this chapter is a must read for any educated person, I hope you enjoy.

Reciprocal Altruism and Evolutionary Psychology

Drawing of a hungry vampire bat (right) solicits food from a potential donor, first by grooming around the stomach area (c) and then licking the donor's face (d). The donor bat then responds by regurgitating blood (e) if receptive. (Wilkinson 1990)

Altruistic acts among non relatives can be understood by reciprocal altruism. As we discussed in class we would expect reciprocal altruism to be limited to species that show long term associations and are "smart" emough to be able to recognize individuals and remember who owes them and who does not.

Further Readings

Reciprocal Altruism http://www.bbc.co.uk/nature/animals/mammals/explore/altruism.shtml

Reciprocal Altruism in Vampire Bats http://www.bio.davidson.edu/people/vecase/behavior/Spring2002/Perry/altruism.html

The Evolution of Reciprocal Altruism. Robert Trivers. 1971
http://www.nbb.cornell.edu/wkoenig/wicker/NB4340/Trivers%201971.pdf

If you are interested in learning more about Evolutionary Psychology here is a link to a bunch of Frequently asked questions. Some of this goes into way more detail than we need to be worried about for this class.
FAQ Evolutionary Psychology http://www.anth.ucsb.edu/projects/human/evpsychfaq.html

Video

Stone Age Minds: A conversation with evolutionary psychologists Leda Cosmides and John Tooby
http://www.youtube.com/watch?v=nNW_B8EwgH4

David Buss and Richard Dawkins on Evolutionary Psychology
http://www.youtube.com/watch?v=QZw3lxyuhEU

Expected Learning Outcomes

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

- define reciprocal altruism
- discuss the conditions under which altruistic acts can be explained by reciprocal altruism
- examine an example of an altruistic behavior and determine whether reciprocal altruism is the best explanation
- explain how participants benefit by being involved in reciprodal altruism in real world examples (e.g, vampire bats)
- define a cheater in a reciprocal altruism system and discuss (a) why cheating is a problem in the system and (b) what organisms can do to reduce cheating
- discuss Trivers' ideas about how human psychology has been influenced by reciprocal altruism (be able to provide your opinion about Trivers' ideas and be able to back up your opinions)

Altruism Part 1

Photo: Belding's Ground Squirrels, the subject of research on altruism


From our discussion about natural selection you should have learned that organisms have the traits they do because traits that produce phenotypes that are more successful at transmitting genes to the next generation (surviving and reproducing) become more common in a population over time. Thus, we expect organisms to have traits that maximize their individual survival and reproduction (we call these selfish traits).

Examples of Altruistic Behaviors

1. Broken wing display by kildeer
kildeer live around here so you should be able to see this behavior later on this spring (that will require going outside!)

http://www.youtube.com/watch?v=TNG7y0caqj0

2. Group defense in musk oxen
you can't see this around here even if you go outside.

http://www.youtube.com/watch?v=pb6Rke7jiTc

3. Food sharing in African Wild Dogs

http://www.sandiegozoo.org/animalbytes/t-wild_dog.html

4. Prairie dogs giving warning calls

http://www.youtube.com/watch?v=rXCPaNWcTFo

We should originally be a little bit confused when we learn about altruistic traits. How can genes that produce traits that decrease an organisms abilty to survive or reproduce become more common in a population?!? Luckily, we have learned that understanding what happens in natural selection requires us to focus on the transmission of genes. Apparently, organisms that behave altruistically are actually passing on more genes by behaving altruistically than they would by behaving selfishly. How can this be? (this problem perplexed Darwin).

Fortunately, a lot of really smart scientists have thought about altruism and have recognized that their are a variety of different ways that organisms behaving altruistically could pass on more genes than organisms acting selfishly. There are at least 4 different hypotheses that can explain the evolution of altruistic behaviors (one of these will probably only help to explain altruism in humans).

The first explanation for why organisms were altruistic was the idea of group selection. Group selection is the idea that organisms have traits becasue those traits "assure the survival of the species". At first glance this seems like a pretty useful idea, but it actually does not work and it has been a very difficult idea to remove from the minds of the general public even though scientists have know that it is wrong and unecessary (there are much better theories about the causes of altruism) for over forty years. It would take a while for me to explain why group selection doesn't work so I won't spend any more time talking about it either in class or here on the blog. However, if you are interested in learning more about this I would be happy to chat with you.

It is important for this class that you are able to understand under which conditions the other hypotheses could explain the presence of altruistic behaviors.

Hamilton's Rule

Hamilton's Rule is a mathematical equation that helps scientists understand under which conditions organisms should behave altruistically and when they should behave selfishly. It is important that you understand (1) how sceintists use mathematical models to help us understand the world and (2) what Hamilton's Rule tells us about when organisms should behave altruistically.

Suggested Readings

Biological Altruism- http://plato.stanford.edu/entries/altruism-biological/


Expected Learming Outcomes

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

1) define altruistic traits and provide several examples

2) compare and contrast selfish traits and altruistic traits

3) explain why altruistic traits at first glance appear to be difficult to understand based on what we know about the process of natural selection

4) discuss at least four possible hypotheses that explain the presence of altruistic traits and explain under which circumstances these theories are expected to apply

5) use “Hamilton’s Rule” as an example to illustrate how biologists use mathematical models to help them understand biology

6) discuss how Sherman’s work with Belding’s Ground Squirrels provided support for Hamilton’s Rule

7) be able to determine which hypothesis best helps you understand any examples of altruistic traits that I give you and be able to justify that answer

The Influence of the Abiotic Environment on the Dominant Plant Types

Here is a link to a slideshow I prepared exploring the physical environment (primarily precipitation and temperature) affect the dominant plant types. This seems like a great place for us to start out exploration.

Deserts, prairies, and forests http://www.slideshare.net/secret/aVrFdv9S7038HJ

The Physical Environment- Global Patterns

Introduction

The physical environment can have a profound influence on ecology at a variety of levels. For example, the physical environment can act as a strong selective presssure to produce adaptations or can influence the rates of nutrient cycling through an ecosystem. For our simple purposes here, the two most important components of the physical environment are temperature and precipitation. I suggest that we can predict a lot about what is going on ecologically in an environment if we know something about temperature and precipitation patterns.

From watching the nightly news we all know how difficult it is for the local weatherperson to accurately predict what the weather is going to be like tomorrow. Fortunately, it is much easier to understand broad patterns of variation in temperature and precipitation.

The following information should be a review of what you have already learned from Dr. Lee.

Temperature



The dominant global temperature pattern is that it tends to get cooler as you move away from the poles. The cause of this is relatively simple. Because the earth is so far from the sun, the light rays hitting the earth are basically paralell to each other. Because of the curvature of the earth, sunlight hitting the earth near the equator falls over a smaller area than sunlight hitting near the poles. Because the same amount of light energy is hitting a smaller area near the equator, the concentration of energy/area is greater near the equator than the pole thus resulting in higher temperatures.

Elevation is another factor that influences global temperatures. Because there is less insulating atmosphere above areas of high elevation temperatures tend to decrease as you go up in elevation.

Large bodies of water can mediate temperature variations. For example, seasonal and daily variation in temperatures are much lower in areas near the ocean (maritime climates) than they are in areas far from the ocean (continental climates).

Global temperature patterns can also be affected by patterns of ocean circulation. For example, the west coast of continents are often cooled by cool water flowing from the poles to the tropics while the east coasts of continents can be warmed by warmer water from the tropics to the poles (e.g., the Gulf Stream). If you have ever been to the beach in southern California you surely noticed how cold the water was; east coast beaches at similar latitudes have much warmer water.

Precipitation

In order to understand global precipitation patterns you need to understand global patterns of atmospheric circulation. Hopefully, after studying the article on atmospheric circulation you will be able to explain-

1. why there tends to be high precipitation in tropical regions and

2. why precipitation tends to be low at 30 degrees North and South of the equator.

Patterns of precipitation can also be influenced by the presence of mountains. As air masses containing moisture hit a mountain they are forced upward. Because rising air cools and cool air







holds less moisture, precipitation occurs on the windward side of mountains. Once the air mass has passed over the mountain in falls to lower elevations and gets warmer. Because most of the moisture has been lost as precipitation on the windward side of the mountain and the warmer air holds more moisture there is very little precipitation on the leward side of the mountain resulting in a "rainshadow desert".

Let's think about Lubbock!

Let's see if we can use our newfound understanding of some of the factors influencing temperature and precipitation to make predictions about what the climate should be like in Lubbock. What information do we need about the geographic location of Lubbock to help us understand the climate? First, we need to know the latitude; Lubbock is located approximately 33 degrees north. Second we need to know something about the proximity to the ocean. As an old beach boy, I can guarantee you that we are a long, long way from the ocean in Lubbock. Third, where is Lubbock in relation to mountains? Lubbock is located to the east of the southern extension of the Rockies.

Why is all of this important?

1. What can we learn from the latitude of 33 degrees North? This latitude is still close enough to the equator to be warm so we expect relatively high temperatures. Because Lubbock lies near the 30 degree zone of low precipitation we would predict relatively low precipitation. At 30 degrees North we would predict that Lubbock would receive predominately winds from the west.

2. From the continental location of Lubbock we would predict fairly extreme daily and seasonal fluctuations of temperatures.

3. Because Lubbock lies in the Westerlies most of the precipitation that is arriving in Lubbock comes from the Pacific Ocean. Because these winds have passed over the Rockies we would predict that Lubbock would lie in a rainshadow, again causing low precipitation.

How did we do. If anyone has ever been in Lubbock (especially in the spring time) you would know that the wind almost always blows in from the west. Temperatures are relatively warm but there is fairly large seasonal and daily variations in temperature. Lubbock has a semi-arid climate and receives on average about 18 inches of precipitation per year. Thus, with just a little bit of knowlege about the factors that influence global patterns of temperature and precipitation we were able to fairly accurately the climate in Lubbock. Thus, I would expect that organisms native to Lubbock should be well adapted to the low precipitation, continental climate of the region (the short grass prairie was the dominant vegetation type presettlement).

See use these patterns to understand climate in your town (note climate patterns in Texas are complicated in central and eastern Texas becasue of the influence of air masses coming up from the Gulf). Compare the temperature and precipitation of your town with that if very divergent locations around the globe.


Further Reading

If you would like some more detailed information about factors affecting climate and the atmosphere you can check out the Atmosphere Chapter in Michael Pidwirny's online Physical Geography textbook http://www.physicalgeography.net/fundamentals/contents.html.

Powerpoint Presentation

Click here to see the powerpoint presentation "Factors Influencing the Physical Environment".
http://www.slideshare.net/secret/EaVq4nm5KuSsBI

Expected Learning Outcomes

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

- describe global patterns of variation in temperature and precipitation and be able to explain the causes of these patterns

- for any location in the world, use your knowledge of the factors that affect global patterns to preict the local climate

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

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


Readings

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

Here is a link to a website from UC Berkeley that might be useful to take a look at-

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

Honors IS Lab- the t-test

Today in lab I introduced you to the t-test, showed you how to conduct a t-test on Excel to compute the p-value, and finally how to use the p-value to help you correctly evaluate your hypotheses. Although I think that people were getting a hang of what was going on by the end of lab, my experience tells me that unless you sit down and think deeply about the material before next week that you will be unlikely to master the material. As I mentioned today, there will be a midterm testing your knowledge of the statistical tests. I think it would be helpful for you to get some practice answering the types of questions that you will be required to answer on the exam.

1. When do you use a t-test to help test your hypotheses?

2. Why do you use a t-test to help test your hypotheses?

3. Give an example of a question that needs to be answered using a two-tailed, paired t- test. (be sure to state the Ha and Ho and how you will collect the data)

4. Give an example of a question that needs to be answered using a one-tailed, unpaired t-test. (be sure to state the Ha and Ho and how you will collect the data)

5. Scientists is interested in knowing whether adding insecticides to a cotton field increases cotton yield. In several fields they spray insecticide on the fields and in several fields they do not add insecticides (the control plots).

Q. What statistical test should the scientists do to help answer their question?

6. Scientists are interested in knowing whether there is a difference in the male and the female students with the top GPAs in a univesity. They collected their data by examining the GPAs of the top male and female students at Texas Tech, Texas A&M, UT, and 12 other universities in Texas.

Q. What statistical test should the scientists do to help answer their question?

7. John, a new third grade teacher, noticed that his male students seemed to need to leave the class the restroom more often than did his female students. He decided to see if male students in his class peed on average more often each week than female students. For four weeks he counted the number of time that each student was excused from class to go the the restroom. What statistical test should John use to analyze his data?

(a) one-tailed, paired t-test
(b) one-tailed, unpaired t-test
(c) two-tailed, paired t-test
(d) two-tailed, paired t-test
(e) John does not need to use statistics to answer his question.

8. A scientist was interested in testing whether the grapefruit diet (eating only grapefruits for three months) or the doughnut diet (eating only doughnuts for three months( resulted in greater weight loss. Researchers located 30 volunteers and randomly assigned half of them to each diet. After three months the researchers determined the amount of weight lost by each participant. Here is the data-

weight loss (lbs)

Grapefruit Diet

5
4
3
5
2
1
3
0
5
7
5
3
9
2
4

Doughnut Diet

1
2
2
3
1
4
2
5
1
2
3
1
3
2
1

Follow all of the steps of the hypothesis testing protocol to determine which diet was most effective (make sure you write down all of the steps of the hypothesis testing protocol).

Something Silly from "The Onion"

Kansas Outlaws Practice of Evolution

http://www.theonion.com/articles/kansas-outlaws-practice-of-evolution,2098/

Oklahoma Doesn't Want to Be Left Out

Oklahoma is also considering new legislation.

JANUARY 23, 2012, 11:38 AM- The Wall Street Journal

A ‘Critique’ of Evolution Proposed in Oklahoma

If it seems like we keep hearing about the fight over teaching evolution in schools and teaching creationism, we do. It comes up like clockwork, despite the Scopes Monkey Trial of 1925.

Oklahoma is the latest state to breach the subject, but the language of the proposed law is different, even if, as critics suspect, the goal is the same. According to the National Center for Science Education, Oklahoma Senate Bill 1742 is the sixth anti-evolution bill introduced in 2012, following bills in New Hampshire, Missouri and Indiana.

The bill purports to recognize “the importance of critical thinking, logical analysis and objective discussion,” and directs schools to include “a scientific critique of the theory of evolution,” but maintains that its purpose is not to teach creationism or intelligent design, and not to promote any religious doctrine or set of religious beliefs.

The model for the bill, which is stated explicitly in it, is the Louisiana Science Education Act, which was passed in 2008, and is part of so-called “academic freedom” laws. Louisiana’s bill was opposed by every scientific society that took a position on it.

Oklahoma’s bill would cover discussion of evolution, the origin of life, global warming, and human cloning. It states that teachers would use standard scientific text books, and supplement lessons with additional texts and “instructional materials.” Section 5 of the bill declares that an “emergency” exists, and for the “preservation of public peace, health and safety,” the provisions of the bill would go into effect immediately upon passage and approval. The bill can be read in full on the NCSE website.

A study published last year found that only 28% of biology teachers follow the National Research Council’s recommendations to describe evolution in a straightforward manner and explain the ways in which it is a unifying part of all biology, the New York Times reported.

The study, which was called “Defeating Creationism In The Courtroom, But Not In The Classroom,” found that 13% explicitly advocate creationism, despite federal courts consistently holding such practice unconstitutional. The rest — “the cautious 60%,” as the study calls them — avoid controversy by not endorsing evolution or intelligent design.

And in New Hampshire as Well

I am putting links to these articles because they have been in the news recently. I look forward to hearing your comments on this.

New Hampshire’s 2012 anti-evolution legislation (and the shocking thing a sponsor said).

The link from this article in the Washington Post wasn't working so I will post the entire article.


New Hampshire’s 2012 anti-evolution legislation (and the shocking thing a sponsor said)
By Valerie Strauss
You can’t make up this stuff: The chief sponsor of a new anti-evolution piece of legislation in New Hampshire said that Darwin’s theory is “godless” and that such thinking is linked to Nazi atrocities, the 1999 Columbine shootings and more.

That analysis came from Republican Rep. Jerry Bergevin, who introduced one of two new anti-evolution bills (see below for full text of bills) in the Granite State’s legislature.

His House Bill 1148 would require that evolution is “taught in the public schools of this state as a theory, including the theorists’ political and ideological viewpoints and their position on the concept of atheism.”

Why?

Bergevin was quoted as saying this in the Concord Monitor:

“I want the full portrait of evolution and the people who came up with the ideas to be presented. It’s a worldview and it’s godless. Atheism has been tried in various societies, and they’ve been pretty criminal domestically and internationally. The Soviet Union, Cuba, the Nazis, China today: they don’t respect human rights.”

And this: “As a general court we should be concerned with criminal ideas like this and how we are teaching it. . . . Columbine, remember that? They were believers in evolution. That’s evidence right there.”

Leaves you speechless, doesn’t it?

The second piece of New Hampshire legislation, House Bill 1457, would require science teachers “to instruct pupils that proper scientific inquire [sic] results from not committing to any one theory or hypothesis, no matter how firmly it appears to be established, and that scientific and technological innovations based on new evidence can challenge accepted scientific theories or modes.”

In other words, the sponsors, Republican Reps. Gary Hopper and John Burt, want creationism taught in public schools right along with evolution.

That thinking ignores the overwhelming scientific consensus on the validity of evolution and tries to equate biology’s animating principle with creationist theory, which the science establishment rejects. (But why let science get in the way?)

Hearings on both bills are scheduled to be held in February.

The New Hampshire legislation are the first new anti-evolution bills introduced in any state in 2012 so far, according to the National Center for Science Education, a non-profit membership organization that defends the teaching of evolution in public schools.

Last year there were at least nine anti-evolution bills in seven states but none became law; at least one was postponed for considering this year. Many of those bills cited “academic freedom,” the idea that teachers should have the freedom to teach creationism and evolution equally.

The issue is important, especially at a time when most high school biology teachers are reluctant to endorse evolution in class, according to a 2011 poll conducted by Penn State political science professors Michael Berkman and Eric Plutzer and published in Science magazine:

*About 28 percent consistently implement National Research Council recommendations calling for introduction of evidence that evolution occurred, and craft lesson plans with evolution as a unifying theme linking disparate topics in biology.

* About 13 percent of biology teachers “explicitly advocate creationism or intelligent design by spending at least one hour of class time presenting it in a positive light.”

* The rest, about 60 percent, “fail to explain the nature of scientific inquiry, undermine the authority of established experts, and legitimize creationist arguments.”


Here are the two new New Hampshire bills:

HOUSE BILL 1148

AN ACT requiring the teaching of evolution as a theory in public schools.

SPONSORS: Rep. Bergevin, Hills 17

COMMITTEE: Education


ANALYSIS

This bill requires evolution to be taught as a theory in public schools.


STATE OF NEW HAMPSHIRE

In the Year of Our Lord Two Thousand Twelve

AN ACT requiring the teaching of evolution as a theory in public schools.

Be it Enacted by the Senate and House of Representatives in General Court convened:

1 New Paragraph; Duties of the State Board of Education. Amend RSA 186:11 by inserting after paragraph XXXVI the following new paragraph:

XXXVII. Theory of Evolution. Require evolution to be taught in the public schools of this state as a theory, including the theorists’ political and ideological viewpoints and their position on the concept of atheism.

2 Effective Date. This act shall take effect 60 days after its passage.

--

And here is the text of HOUSE BILL 1457

HOUSE BILL 1457

AN ACT relative to scientific inquiry in the public schools.

SPONSORS: Rep. G. Hopper, Hills 7; Rep. Burt, Hills 7

COMMITTEE: Education


ANALYSIS

This bill requires instruction in the proper methods of scientific inquiry.

STATE OF NEW HAMPSHIRE

In the Year of Our Lord Two Thousand Twelve

AN ACT relative to scientific inquiry in the public schools.

Be it Enacted by the Senate and House of Representatives in General Court convened:

1 New Paragraph; Duties of the State Board of Education. Amend RSA 186:11 by inserting after paragraph XXXVI the following new paragraph:

XXXVII. Scientific Inquiry. Require science teachers to instruct pupils that proper scientific inquire results from not committing to any one theory or hypothesis, no matter how firmly it appears to be established, and that scientific and technological innovations based on new evidence can challenge accepted scientific theories or modes.

2 Effective Date. This act shall take effect 60 days after its passage.

-0-

By Valerie Strauss | 04:00 AM ET, 01/06/2012

Indiana Passes Law Allowing Teaching of Creationism in Science Classes

Indiana Creationism Bill Passes the Senate

http://ncse.com/news/2012/01/indiana-creationism-bill-passes-senate-007182

Tech Professor Receives Hate Mail From Climate Change Deniers

Hello Everyone,

Here is a link to a couple of articles about Tech Political Science Professor Katharine Hayhoe. Dr. Hayhoe is a climate scientist whose research supports the conclusion that human activity have helped to cause global climate change. Dr. Hayhoe is perhaps unique in the debate about climate change because she is an evangelical Christian and she and her husband, a pastor, have written a book about climate change from an evangelical perspective.

http://www.katharinehayhoe.com/

I was quite disturbed to learn that her views have led to her receiving death threats!! If you would like to know more about this then please take a look at the following articles. I think these articles show how misunderstood the process of science is by many Americans!

Texas Tech scientist sees intimidation effort behind barrage of hate mail. http://texasclimatenews.org/wp/?p=4153

Newt Dumps Christian Climate Scientist
http://motherjones.com/environment/2012/01/newt-dumps-leading-climate-scientist

Politicians and Science

As we enter an election year I hope that you are all paying attention to the scientific views of the candidates. I thought that these articles were both interesting.

Scientists and politicians – the same but different?
http://theconversation.edu.au/scientists-and-politicians-the-same-but-different-4051

Why Scientists Are Smarter Than Politicans
http://www.time.com/time/health/article/0,8599,2095264,00.html

Celebrities and Science

Here are links to a couple of recent articles about misguided statements about science made by some popular celebrities.

2011 Celebrities and Science- http://www.senseaboutscience.org/resources.php/82/2011-celebrities-and-science

Simon Cowell, Gwyneth Paltrow and Nicole Polizzi make celebrity 'bad science' list
http://www.telegraph.co.uk/health/healthnews/8980192/Simon-Cowell-Gwyneth-Paltrow-and-Nicole-Polizzi-make-celebrity-bad-science-list.html

Maybe we shouldn't be looking to Snookie as the source of scientific wisdom!!

Course Syllabus- HONS 2406-H01

Honors Integrated Sciences - Spring 2012
HON 2406-H01 TR 9:30-10:50
Instructors

Dr. Jeff Lee Dr. Mark McGinley
Holden Hall 209a McClellan Hall 215
Mail Box: Holden Hall 248 mark.mcginley@ttu.edu
E-mail: jeff.lee@ttu.edu. OH: MWF- 11 – 12 or by apt.
Office hours: M 9-9:50 or by appointment.

Textbook
Lee, J. A., 2000, The Scientific Endeavor, Benjamin Cummings.

Course Web Page
Course materials are available on the class web page, found at www.blackboard.ttu.edu These include study guides, and the lecture notes. Login with your eraider name. If you have problems, see the Blackboard home page or call the Texas Tech IT Help Desk at 742-HELP.

Course Blog for Dr. McGinley’s Section (both lecture and lab)
http://honorsintegratedsciencettu2012.blogspot.com/


Grading
Your grade for HON 2406 will be made up of three parts
Biology Lecture Section (Dr. McGinley) 37.5%
Earth Science Lecture Section (Dr. Lee) 37.5%
Lab (Dr. McGinley) 25.0%

Dr. Lee’s Portion of Lecture Grade:
Your grade in this portion of the class will be based on your scores on two exams and weekly assignments. The exams will be essay and the written assignments will be given during the semester.

You will read the assigned chapters in Scientific Endeavor each week and answer the questions at the end of each chapter. Each week you also will have one or more readings, each with questions to answer. On Thursdays, you will turn in your written answers (chapters and other readings) and we will discuss them in class.

The grade you earn in this part of HONS 2406 will be based on a total of 200 points. There will be two exams worth 67 points each. The other 66 points is divided between book questions (8 points per week, total 48 points), article questions (3 points per week, total 18 points).

Dr. McGinley’s Portion of the Lecture Grade:
Your grade in my portion of the lecture course (200 points) will be based on your performance in two exams (worth 75 points each) and one paper (worth 50 points). More details coming about the paper.

Schedule
Week of
19 January Introduction
23 October Systems; Origins
Thursday: Ch. 1, 2; Galileo
30 January Plate Tectonics
Thursday: Ch. 3; Wegener; Hutton
6 February Hydrology & Streams
Thursday: Ch. 4,5; Powell; Marsh
13 February Exam 1: Tuesday, Solar Energy
Thursday: Ch. 6, Milankovitch
27 February McGinley
5 March Solar Energy & Seasons, Energy in the Atmosphere
Thursday: Ch. 7; Darwin; Huxley; Wallace
12 March Spring Break
19 March McGinley
26 March Winds & Precipitation
Thursday: Ch. 8, 9; Global Warming
2 April Global Climate Change
Exam 2 Thursday
9 April McGinley
16 April McGinley- Exam 1 (Thursday)
23 April McGinley-
30 April McGinley
7 May McGinley (Final Paper Due)

Second McG Exam scheduled during the Final Exam Period

Thursday readings for Dr. Lee’s portion are in Scientific Endeavor (“Chapters”) and Encyclopedia of Earth (www.eoearth.org).

Any student who, because of a disabling condition, may require some special arrangement to meet course requirements should contact the instructors as soon as possible to make the necessary accommodations. Students should present appropriate verification from Disabled Student Services, Dean of Student’s Office. No requirement exists that accommodation be made prior to this approved University process.

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 has notified the instructor of each scheduled class that the student would be absent for a religious holy day.

Honors Integrate Science Lab

Required Book
The Process of Science. By Mark McGinley (get them from me, not the bookstore)

Grading
Chapter Reviews, Participation, Assignments 30%
Statistics Exam 20%
Research Project/Presentation (more details coming) 50%

Expected Learning Outcomes

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

1. Define science and describe the process of science. Assessed by performance in quizzes and class discussion.

2. Discuss how scientists generate hypotheses. Assessed by performance on quizzes and class discussion.

3. Discuss when and why scientists need to use statistics and apply the appropriate statistical tests. Assessed by performance on quizzes and research project.

4. Develop a testable hypothesis and collect data to tests these hypotheses. Assessed by performance on research project.

5. Analyze the data and draw appropriate conclusions. Assessed by performance on research project.

6. Report your findings to a wider audience. Assessed by performance on research project final report


Course Schedule
January 24- Introduction
January 31- Chapters 1 and 2
February 7- Chapters 3 and 4, Appendix 1 (t-test)
February 14- Chapter 4 revisited and Chapters 5
February 21- Chapter 6 and 7
February 28- exam on statistics
March 6- Begin projects
March 13- Spring Break
March 20- work on projects- first project report
March 27- work on projects,
April 3- work on projects- second project report
April 10- work on projects
April 17- finish projects
April 24- prepare project reports
May 1- Student Presentations
May 8- Student Presentations