Tuesday, February 24, 2009

Final Thoughts


Many of you have worked hard this semester and have learned a great deal of biology. You should be congratulated for that. You still have a long way to go, so I encourage you to keep working hard. If you are frustrated by your performance in the course thus far don't be disappointed. You have two more midterms, lab, and the final exam to raise your grade so keep at it.

Thanks for making this a great semester. I have enjoyed getting to know some of you a little bit this semester and I look forward to getting to know more of you in the future. I would like to say that I will miss you all, but I am ready for a break! Have a great semester and keep in touch.

See you at the final,

Mark McG

Answer Key for Second Midterm

The BAC will meet Wednesday at noon in room 204 in McClellan Hall. Please attend if you can, but don't miss a class to come to the BAC meeting.

Multiple Choice Answers

Form 1 and Form 2

1. a
2. b
3. b
4. a or e
5. d
6. c
7. d
8. b
9. a
10. b
11. d
12. a
13. d
14. b
15. b
16. c
17. d
18. a
19. b
20. e
21. b
22. c
23. a
24. d
25. d
26. a
27. d
28. c
29. b
30. a

Essay Questions

Photosynthesis Question

The rate of photosynthesis can be limited directly, or indirectly, by a variety of environmental factors. Agriculture provides us food and fiber and is a major component of the economy in many parts of the world. Farmers attempt to increase the production of their crops by fertilizing and irrigating.
Discuss how fertilization and irrigation can increase agricultural production by increasing rates of photosynthesis. An excellent answer will indicate how these activities affect the physiology of plants in a way that increases the rate of photosynthesis.

The rate of photosynthesis can be limited by a variety of environmental factors including temperature, light level, carbon dioxide, soil fertility, and water availability. Some of these factors (e.g., soil fertility and soil moisture level) can be manipulated by farmers in a way that can increase photosynthetic rates production whereas other factors (e.g., temperature and atmospheric carbon dioxide concentration) are harder to manipulate on a large scale. Thus, most large scale agriculture involves increasing soil nutrients by adding fertilizers and increasing soil moisture availability by irrigation.

Water can indirectly regulate the rate of photosynthesis. Irrigating crops increases the soil moisture content. When plants are water stressed they respond by closing their stomata which blocks carbon dioxide from entering the leaf by diffusion. Carbon dioxide is required in the light independent reactions of photosynthesis. The ultimate purpose of the light independent reactions is to use energy from ATP and NADPH to convert carbon dioxide to glucose which contains chemical energy stored in its chemical bonds. Specifically, carbon dioxide is involved in the following reaction-
CO2 + RuBP  PGA
Irrigating crops increases the soil moisture content which allows plants to keep their stomata open longer which allows them to take up carbon dioxide for a longer period of time which allows photosynthesis to occur longer.

Fertilizing can add a number of potentially limiting resources to the soil. An important nutrient in all fertilizers is nitrogen. Because nitrogen is an important element in amino acids, increasing soil nitrogen content can increase the rate of nitrogen uptake which allows plants to make more proteins. By far the most protein in plants is RuBP carboxylase, the enzyme that catalyzes the reaction between carbon dioxide and RuBP. Fertilizing with nitrogen increases the amount of RuBP carboxylase in the plant which speeds up carbon fixation and allows more carbon to be produced in the Calvin Cycle.

Life Cycle Question

Diagram the life cycle of a fern. Discuss the characteristics of ferns that makes them advanced relative to the mosses and primitive relative to the gymnosperms. Be sure to discuss the evolutionary advantage of the advanced traits relative to the primitive traits.
(I am sorry that this doesn't look right when it is posted)

zygote (2N) ==> sporophyte (2N) ==> sporangia (2n)
fertilization
meiosis
archegonia => (egg N) <== gametophyte <== spores
angtheridia=> (sperm N) mitosis


Ferns appeared at an intermediate step of the evolution of plants. Thus, they are advanced relative to the bryophytes but primitive relative to the gymnosperms. Ferns are considered to be advanced relative to the bryophytes because they are diploid dominant and have a vascular system and they are considered to be primitive to the gymnosperms because they are homosporous rather than heterosporous and they reproduce by spores rather than seeds.

Diploid dominance is advantageous relative to haploid dominance because individuals are not as adversely affected by lethal alleles. If an organism is haploid then they will die if they get a lethal mutation. However, if that lethal mutation is recessive, then that allele can be masked in the heterozygote state in a diploid organisms. Thus, dipoloid dominant species should have higher survival levels than homozygous dominant species.

The evolution of the vascular system (xylem, phloem, roots, stems, leaves) which occurred for the first time in ferns is a major adaptation for terrestrial plants. Plants with a vascular system produce true roots that can take up water and nutrients from the soil. They have xylem, the tissues that carry water and nutrients from the roots to the leaves, and phloem that carries sugar around the plant. Having a vascular system is a huge advantage because it allows plants to achieve a much larger size and allows them to inhabit more arid regions.

Heterospory, the production of two types of spores to produce two types of gametophytes, is an advantage over homospory, the production of one type of spore to produce one type of gametophyte because heterosporous plants no longer have to rely on swimming sperm. Thus, heterosporous plants have the potential to live in environments that are arid year around.

Reproducing by seeds is a major advantage relative to reproducing by spores because an individual seed has a much larger probability of survival. Seeds contain an embryo, seed coat and nutritive tissues. The resources held in the seed are used to nourish the germinating seedling until it is has established its roots and leaves well enough to collect its own food.

Thursday, February 19, 2009

Plant Diversity- The Gymnosperms and Angiosperms


Gymosperms and angiosperms are the "seed plants".

Gymnosperms

Expected Learning Outcomes


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

- defne and contrast homospory and heterospory
- discuss the evolutionary advantage of heterosporty over homospory
- identify the parts of a seed and discuss why reproducing by seeds is an advantaged compared to reproducing by spores
- discuss the life cycle of a pine
- discuss the characteristics of pines that are advanced relative to the ferns and those that are primitive relative to the angiosperms


Angiosperms

Expected Learning Outcomes


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

- discuss the parts of a flower
- discuss the evolutionary advantage of reproducing by flowers rather than by cones
- discuss the life cycle of an angiosperm
- discuss the characteristics of angiosperms that are advanced relative to the pines and those that are primitive relative to the angiosperms
- discuss why angiosperms are the most successful of all plant groups

Plant Diversity- Ferns


Ferns are examples of the first vascular plants.

Expected Learning Outcomes

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

- discuss the components of the vascular system
- discuss the advantage of a having a vascular system
- diagram the life cycle of a fern
- discuss the morphological and physiological characteristics of ferns
- discuss the characteristics of ferns that makes them considered to be advanced relative to mosses but primitive relative to the gumnosperms
- discuss how the morphological and life history characteristics limits their size and geographic distrubution

Wednesday, February 18, 2009

Plant Diversity- Algae to Mosses


As I mentioned in class, plants are interesting to me because the are so different than we are. At first these differences will cause unfamiliarity but eventually you will not be so bogged down by learning new vocabulary and you will hopefully come to realize that plants are more interesting than you might have thought (and besides, no plants means no dorritos, french fries, or beer?).

Further Viewing

1) Here is the slideshow that I will use in class for the final three lectures.

http://www.slideshare.net/secret/DBv71wnKTH1YBN

2) Here is a powerpoint presentation from a group called "world of teaching" that covers plant diversity? There are many "quiz questions" that should be helpful to look at.

http://www.worldofteaching.com/powerpoints/biology/Plant%20Divisions.ppt

Primitive Plants

Expected Learning Outcomes

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

- functionally define a plant
- discuss the characteristics of a primitive plant such as Chlamydomonas
- diagram a life cycle of a human
- diagram the life cycle of Chlamydomonas
- distinguish between oogamy and isogamy
- discuss the evolutionary advantage of multicellularity, diploid dominance, and oogamy

Transition to Land

Expected Learning Outcomes


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

- discuss the problems plants face when moving to the land
- discuss the characteristics of the ancestor of land plants
- diagram the life cycle of a moss
- discuss the morphological and physiological characteristics of mosses
- discuss the characteristics of mosses that makes them considered to be advanced relative to primitive plants but primitive relative to the ferns
- discuss how the morphological and life history characteristics of mosses limits their growth and geographic distribution

Tuesday, February 17, 2009

Cellular Respiration


Cellular respiration converts chemical energy in glucos to chemical energy in ATP which is the ultimate source of energy used to do "biological work".

Glycolysis

1) Glycolysis animation

http://www.youtube.com/watch?v=7hiwSCUoSZY

2) Another Glycolysis animation- this one goes into a little more chemical detail so it might be useful if you are intersted in knowing more about the chemistry

http://www.youtube.com/watch?v=x-stLxqPt6E


Anaerobic Respiration

Alcohol Fermentation and Lactic Acid Fermentation

Further Reading

Alcohol Fermentation- http://www.tempeh.info/fermentation/alcohol-fermentation.php

Lactic Acid Fermentation- http://www.tempeh.info/fermentation/lactic-acid-fermentation.php

Further Viewing

http://www.youtube.com/watch?v=y_k8xLrBUfg


Aerobic Respiration

1) Aerobic Respiration

http://www.youtube.com/watch?v=iXmw3fR8fh0

2) Krebs Cycle

http://www.youtube.com/watch?v=aCypoN3X7KQ&feature=related

3) Electron Transfer Chain

http://www.teachertube.com/view_video.php?viewkey=a67b8fcdafb25c122359

Expected Learning Outcomes

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

- discus glycolysis, anaerobic respiration, alcohol fermentation, lactic acid fermentation, aerobic respiration, the Kreb's Cycle, and electron transport
- compare and contrast aerobic respiration with anaerobic respiration
- discus why the breakdown of glucose to produce ATP is so much more efficient when oxygen is present
- describe where in the cell the different parts of cellular respiration take place

Factors That Limit the Rate of Photosynthesis


The rate of photosynthesis can be limited by a variety of environmental factors including

1) light
2) concentration of carbon dioxide
3) water
4) soil nutrients

Which factor most limits photosynthesis varies between environments.

Light- Can directly limit the rate of photosythesis by limiting the rate at which ATP and NADPH are produced

Carbon dioxide- can directly limit the rate of photosynthesis by limiting the rate at which the Calvin Cyle takes place

Water- can indirectly limit the rate of photosynthesis. When plants are water stressed they close their stomata (long before the concentration of water in the cell becomes too low for water to supply electrons to P680). Thus, the rate of photosynthesis is water stressed plants is directly limited by the amount of carbon dioxide in the leaf.

Soil Nutrients- Sometimes the rate limiting step in photosynthesis is the rate at which carbon dioxide + RuBP ==> PGA. This reaction is catalyzed by the enzyme RuBP carboxylase. Increasing the amount of RuBP carboxlyase in the cell can increase the rate at which this reaction occurs. Fertilizing plants with nitrogen will increase the amount of RuBP Carboxylase produced by the plant.

Expected Learning Outcomes

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

- discuss the factors that can directly or indirectly limit the rates of photosynthesis
- discuss how the most limiting factors should vary between environments
- discuss how the activities of farmers such as irrigation and fertilization can increase photosynthetic rates
- interpret the graph at the top of the post (irradiance measures light intensity and the three lines represent different concentrations of carbon dioxide)
- explain what why the graph shows that shape

Why Are Plants Green? or Why Aren't Plant Black?


If I was hired as an engineer to design a machine whose job was to convert light energy into chemical energy I probably would not choose to use a green pigment. Instead, I would choose to use a black pigment because black pigments would absorb more energy because they would absorb all wavelengths of light. If you look at a field of plants you will notice that they are green (OK this doesn't work too well around Lubbock in the winter)and we have learned that chlorophyll, a green pigment, is the dominant photosynthetic pigment. What is going on?

Here is one theory about why chlorophyll is the dominant photosynthetic pigment in plants today. Early on there were photosynthetic bacteria with purple pigments (purple is a combination of red and violet). These aquatic bacteria had a very simple sort of cyclic electron flow that was able to convert light energy into energy in ATP (they didn't have non-cyclic flow or the Calvin Cycle).

Origin of chlorophyll- The purple pigment absorbed all wavelengths of light except for the reds and violets. Thus, any bacteria using purple pigments that lived deeper in the water than the purple bacteria on the surface would have no light to use because it had all been absorbed by the surface bacteris (exploitative competition). Because red and violet wavelengths pass through to deeper water, bacteria that contained a pigment that was able to absorb these wavelengths would be able to coexist with the purple bacteria. This was the origin of chlorophyll.

Competition purple and green photosynthetic pigments. Over time there was competition between organisms with purple photosynthetic pigments and green photosynthetic pigments. Obviously, the green photosynthetic pigments won this competition because chlorophyll is the dominant photosynthetic pigment today (there are still examples of photosynthetic bacteria with purple pigments, but they are limited to very harsh environments). Interestingly, chlorophyll came to dominate, not because it was a better at absorbing light energy, but rather because the cyclic flow machinery associated with chlorophyll was more efficient at producing ATP than the machinery associated with the purple pigment was. Thus, it is an evolutionary accident that modern plants are green.

Black Plants

It would be possible for modern plants to be black if they had enough accessory pigments to allow them to absorb all wavelengths of light. In fact, some red algae that live deep below the surface where light levels are low are basically black. Because the amount of light is not the factor that limits the rate of photosynthesis in most terrestrial plants, it is not worth the cost of producing extra accessory pigments. However, deep in the ocean where light levels are low, plants benefit from being able to absorb all wavelengths of light so deep marine algae have invested in extra accessory pigments.

Expected Learning Outcomes

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

- discuss why terrestrial plants to not invest in the accessory pigments required to make them black

Carbon Fixation




Technically, arbon fixation is defined as the first chemical reaction that incorporates carbon dioxide into an organic molecule (a molecule with more than one carbon atom).

In C3 photosynthesis the following step is considered to be carbon fixation-

carbon dioxide + RuBP ==> PGA

In CAM photosynthesis the following is considered to be carbon fixation-

carbon dioxide ===> malate

Note: CAM plants also have the reaction- carbon dioxide + RuBP ===> PGA, but in this case this step is not considered to be carbon fixation.

Sometimes people will loosely use the term carbon fixation to mean the production of glucose by photosynthesis. Be sure that you are aware of how different authors are using the term and you should attempt to use the term as precisely as possible in your own work.

Expected Learning Outcomes

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

- define carbon fixation
- identify carbon fixation in C3 and CAM photosynthesis

CAM Photosynthesis


CAM photosynthesis is an alternative mode of photosynthesis found in some plants adapted to living in desert environments. CAM plants are able to separate the timing of carbon uptake from the timing of the use of carbon dioxide in the Calvin Cycle which reduces the water loss of these plants.

Critical Point- All of the nuts and bolts of photosynthesis (e.g., photosystems, light dependent reactions, and Calvin Cycle) take place the same in C3 and CAM plants.

Epected Learning Outcomes

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

- discus the timing of carbon uptake and glucose production in CAM plants
- discuss the advantages and disadvantages of CAM photosynthesis
- explain why CAM photosynthesis is limited to plants growing in arid environments
- compare and contrast photosynthesis if C3 and CAM plants

Leaf Structure


In most plants, leaves are the major sites of photosynthesis. Thus, we can think of leaves as "photosynthesis machines" and use our knowledge of natural selection to try to understand aspects of leaf structure.

Further Reading

http://micro.magnet.fsu.edu/cells/leaftissue/leaftissue.html

Expected Learning Outcomes

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

- discuss important differences between animals and plants in gas uptake
- diagram the cross section of a leaf
- explain the adaptive basis of leaf structure

Sunday, February 15, 2009

Global Carbon Cycle Revisited


Here is some more information that I would like you to know about the global carbon cycle

Mauna Loa Curve

The best data that we have examining is from Mauana Loa in Hawaii (see Mauna Loa Curve- http://www.eoearth.org/article/Mauna_Loa_curve). This curve shows two things. First, that the concentration of carbon dioxide in the atmosphere has indeed increased over time. Second, that there is seasonal variation in the concentration of carbon dioxide in the environment. Carbon dioxide is most abundant in the atmosphere in the North American winter and lowest in the North American summer. This pattern is caused by seasonal variation in the amount of photosynthesis. In the summer, when photosynthetic rates are the highest, carbon dioxide is removed from the atmosphere at a high rate which reduces the amount of carbon in the atmosphere. Because there is more land mass in the Northern Hemispere and most photosynthesis happens on land, the global pattern is determined by seasons in the Northern Hemispere (this is truly a global cycle, carbon dioxide move so quickly though the environment that the conentration is virtually the same all over the world)

Expected Learning Outcomes

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

- diagram how carbon dioxide concentration in the atmosphere varies seasonall.
- discuss the causes of this pattern

What is Happening to the Rate Carbon Dioxide is Being Added to the Atmosphere?

Here is an article from the Associated Press entitled- Climate Warming Gasses Rising Faster than Expected that was published yesterday. Chris Field, one of the scientists quoted in this article, was one of my professors at University of Utah.

CHICAGO (AP) -- Despite widespread concern over global warming, humans are adding carbon to the atmosphere even faster than in the 1990s, researchers warned Saturday. Carbon dioxide and other gases added to the air by industrial and other activities have been blamed for rising temperatures, increasing worries about possible major changes in weather and climate.

Carbon emissions have been growing at 3.5 percent per year since 2000, up sharply from the 0.9 percent per year in the 1990s, Christopher Field of the Carnegie Institution for Science told the annual meeting of the American Association for the Advancement of Science.

''It is now outside the entire envelope of possibilities'' considered in the 2007 report of the International Panel on Climate Change, he said. The IPCC and former vice president Al Gore received the Nobel Prize for drawing attention to the dangers of climate change.

The largest factor in this increase is the widespread adoption of coal as an energy source, Field said, ''and without aggressive attention societies will continue to focus on the energy sources that are cheapest, and that means coal.''

Past projections for declines in the emissions of greenhouse gases were too optimistic, he added. No part of the world had a decline in emissions from 2000 to 2008.

Anny Cazenave of France's National Center for Space Studies told the meeting that improved satellite measurements show that sea levels are rising faster than had been expected. Rising oceans can pose a threat to low level areas such as South Florida, New York and other coastal areas as the ocean warms and expands and as water is added from melting ice sheets.

And the rise is uneven, with the fastest rising areas at about 1 centimeter -- 0.39 inch -- per year in parts of the North Atlantic, western Pacific and the Southern Ocean surrounding Antarctica, she said.

Also, highly promoted efforts to curb carbon emissions through the use of biofuels may even backfire, other researchers said. Demand for biologically based fuels has led to the growing of more corn in the United States, but that means fields were switched from soybeans to corn, explained Michael Coe of the Woods Hole Research Center. But there was no decline in the demand for soy, he said, meaning other countries, such as Brazil, increased their soy crops to make up for the deficit.
In turn, Brazil created more soy fields by destroying tropical forests, which tend to soak up carbon dioxide. Instead the forests were burned, releasing the gasses into the air. The increased emissions from Brazil swamp any declines recorded by the United States, he said.

Holly Gibbs of Stanford University said that if crops like sugar and oil palm are planted after tropical forests are burned, the extra carbon released may be balanced by lower emissions from biofuel in 40 to 120 years, but for crops such as corn and cassava it can take hundreds of years to break equal.

''If we run our cars on biofuels produced in the tropics, chances will be good that we are effectively burning rainforests in our gas tanks,'' she said.

However, there could be benefits from planting crops for biofuels on degraded land, such as fields that are not offering low productivity due to salinity, soil erosion or nutrient leaching.

''In a sense that would be restoring land to a higher potential,'' she said. But there would be costs in fertilizer and improved farming practices.

In some cases simply allowing the degraded land to return to forest might be the best answer, she said.

Friday, February 13, 2009

BAC Results Retest

The answer key for the retest has been corrected.

Here are the results of the meeting with the BAC on Wednesday. The committee brought me four questions to look at.

Question 12.

The correct answer for this question is (b). A mutualism is an interaction between two species in which both species gain a benefit. This is true when there is reciprocal altruism between different species of birds.

Correct answer (b)

Question 27.

The correct answer is (c). Some peopole argued that a similar question was on a past test that showed answer (a) as correct. The purpose of showing you old exams is to give you some idea of the form that the questions will take. This question was not on any information that I supplied you this year.

Correct answer (c)


Question 29.

The correct answer is (b). Some people tried to argue that (a) is also correct so ansswer (d) should be a suitable answer. However, by definition dN/dt = rN any time that r is not equal to zero, dN/dt must depend on population size.

Correct answer (b)

Question 30.

I wrote this question thinking that males fertilizing a female in pines was an example of exploitative competition (when an egg is fertilized it is effectively "consumed" because so other male can fertilize it). However, the way I wrote the question the same logic could be used to choose (b) as a correct answer. this confusion caused several students to choose answer (e). Thus, there is no best answer. I will throw out this question and everyone will receive credit for it.

Thursday, February 12, 2009

Photosynthesis- Summary




One you understand the light dependent reactions, the light independent reactions, and how these two sets of interactions are linked together then you understand the basics of photosynthesis. The pattern of photosythesis that we have discussed so far is known as "C3 photosynthesis" (it is named this becasue the first stable product of the Calvin Cycle is a molecule that contains three carbon atoms). C3 photosynthesis is considered to be the basic mechanism of photosynthesis.

As I have mentioned in class the best way to assure that you understand what is going on is that you should be able to describe photosynthesis at different levels of detail.

1) the one sentence answer
2) the one paragraph answer
3) the full detail answer

In my experience, students quickly get lost by worrying about the details. Thus, I suggest that you start at the one sentence answer, then move to the one paragraph answer, and finally finish up with the full detail answer. You will find that by thinking about the one sentence and the one paragraph answers you will have already figured out how to organize your full detail answer.

I suggest that you try writing out the answers to these questions at the three levels.

1) What is photosynthesis?
2) What are the light dependent reactions of photosynthesis?
3) What are the light independent reactions of photosynthesis?
4) What is a photosystem?

I encourage you to post your answers here and then to provide critical feedback to your classmates about their answers.

Photosynthesis- Light Independent Reactions- Calvin Cycle


In the light independent reactions the energy stored in ATP and NADPH is converted to energy stored in glucose. This invovles a chemical cycle known as the Calvin Cycle.

Expected Learning Outcomes

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

- discuss what links the light dependent and light independent reactions of photosynthesis
- describe the initial step of the Calvin Cycle
- describe the chemical reaction catalyzed by the enzyme RuBP carboxylase
- discuss some interesting characteristics of RuBP carboxylase
- define "carbon fixation" and identify the carbon fixation step in the different modes of photosynthesis
- diagram the Calvin Cycle (at the level of detail that I talked about in class)
- discuss where and why ATP and NADPH are required in the Calvin Cycle
- disucus where in the cell that the Calvin Cycle takes place

Further Viewing

1) This is an excellent animation (narrated by a man with a perfect "announcer's voice"). This animation goes into the amount of detail you are required to know for this class. It even has its own quiz, so see how you do.

http://highered.mcgraw-hill.com/sites/0070960526/student_view0/chapter5/animation_quiz_1.html

2) I didn't know that photosynthesis was such a popular subject for musicians (I can't belive I gave up what would surely have been a lucrative career as a rock star to become a biologist- who knew I could have combined the two). The guy in the video is kind of a dufus, but the song is pretty cool, and I learned something from watchig it.

http://www.youtube.com/watch?v=OYSD1jOD1dQ

3)This is quite a good video (sorry, no song involved). Note, this video concludes that glyceraldehyde phosphate is the result of the Calvin Cycle. For our purposes in this class we are going to conclude that glucose is the end result of this cycle.

http://www.youtube.com/watch?v=mHU27qYJNU0

4) Maybe you will find this animation to be helpful

http://www.science.smith.edu/departments/Biology/Bio231/calvin.html

Photosynthesis- The Light Dependent Reactions



Photosythesis takes place in two steps. In the first step, known as the light dependent reactions, light energy is converted into chemical energy held in the bonds of ATP and NADPH.

Expected Learning Outcomes

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

- list the parts of a photosystem
- discuss the function of a photosystem
- describe where the light dependent reactions of photosythesis occur and discuss why these reactions occur in this location
- describe cyclc electron flow, be able to explain both the energetic result and what chemcical changes occur
- describe non-cyclic electron flow, be able to explain both the energetic result and what chemical changes occur
- describe the cause and the result of chemiosmosis
- answer the question- "why doesn't photosynthesis stop after the production of ATP and NADPH in the light dependent reactions

Further Reading

Here is a link to some fairly detailed info about photosynthesis (it contains some very good diagrams).

http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookPS.html



Further Viewing

These videos contain animations that might help you to understand what is happening in the light dependent reactions. I encourage you to watch each of these videos.

1) This video has some great animations of what is going on in the light dependent reactions.

http://www.youtube.com/watch?v=hj_WKgnL6MI

2) This short video is a good review of the light dependent reactions.

http://www.youtube.com/watch?v=eY1ReqiYwYs&feature=related

3) This is a video of a woman with a very southern accent talking about photosyntheis with some decent animations.

http://www.youtube.com/watch?v=RFl25vSElaE&feature=related

4) This one comes complete with a "Photosyntheis Song." I guarantee that you will be humming this as you walk around campus!

http://www.teachertube.com/view_video.php?viewkey=dc9810ac32b3c413fb29

Intro to Energetics


Energy is required to do work. In order to understand the two important energetic processes taking place in living organims (photosynthesis and cellular respiration) it is useful to understand some basics of energetics.

Expected Learning Outcomes

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

- give examples of biological work
- list different forms of energy, give examples of the different forms, and give examples of energy conversions
- define the First and Second Laws of Thermodynamics and discuss why these laws are important for biologists
- discuss electromagnetic energy, including the wavelengths associated with different forms of electromagnetic energy and the relationship between wavelength and energy
- define a photon
- discuss the three things that can happen when a photon of light hits a molecule
- define a pigment
- draw and interpret an absorption spectrum

Further Reading

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

Wednesday, February 11, 2009

Retest BAC and 1st Midterm Essay Regrades

Retest BAC

If you have comments to submit to the BAC you may either put them in the box on the ledge outside of Dr. Dini's office (there must be received by 3:30) or email them to me (these must be received by 1:45)

Essay Regrades

If you feel that there has been a significant mistake in how your essays fromthe first midterm were graded then you need to type out a description of why you feel that your answer was not fairly graded. Please make sure that you have read the answer key that I posted on the web! There is nothing more frustrating to me than reading a comment from a student that says "I put down everything in the answer key!". The order of words does matter!!!

Please turn these in the box outside my office (r00m 215) in McClellan Hall by 12:00 (noon) on Friday Feb 14th.

MC answers for Retest

1. d
2. b
3. b
4. c
5. a
6. a
7. c
8. d
9. a
10. d
11. c
12. b
13. c
14. e
15. a
16. b
17. e
18. b
19. e
20. a
21. e
22. d
23. c
24. a
25. c
26. a
27. c
28. e
29. b
30. omitted from exam

Monday, February 9, 2009

Essay Questions Answer Key

Graph Question

the graphs have been a pain to post so I will show them in class.

b) Over time, the population size increases until the population size reaches the carrying capacity (100 ind) where it remains.

Initially the population growth rate is at its maximum. Over the time the population growth rate decreases until the population growth rate equals zero where it remains.

c)



d) Over time the population size decreases until the population size reaches its carrying capacity where it remains.

Initially, the population growth rate is very negative. Over time the growth rate becomes less negative until the population growth rate reaches zero where it remains.











If you answered the questions about lyrebirds


Male lyrebirds have two distinctive characteristics. First, they produce an elaborate lyre-shaped tailed that they use in mating displays. Second, male lyrebirds are uncanny mimics. In addition, to being able to mimic the sounds of other birds living in the forest, they are also able to mimic human-produced sounds that they hear. It is possible that female lyrebirds examine both the tail and mimicking ability when choosing the mate.

Many females choose to mate with males with extreme traits. Thus, female lyrebirds might be selected to mate with the male with the longest tail. There are two hypotheses that explain why females should choose to mate with males with extreme traits- (1) the handicap principle and (2) the sexy sons hypothesis.

According to the handicap principle, the long tail of the lyrebird makes it more difficult for the males to move about the forest and increases their likelihood of dieing. Thus, a male with an extremely long tail is carrying a large handicap. A male with a long tail who has been able to survive in spite of that handicap must have genes that code for particularly vigorous survival skills. Thus, by choosing to mate with a male with the longest tail the female ensures that she is mating with a male with good survival skills and hopefully those survival skills get passed on to both her sons and her daughters who in turn should have higher survival.

According to the sexy sons hypothesis, if females prefer to mate with males with extreme traits, then any female who mates with a male with less extreme traits will produce sons with less extreme traits so her son will not be attractive to other females. Thus, female lyrebirds may choose to mate with males with the longest tails because in doing so they will produce sons with long tails who will thus be more effective at mating with females.

Females often prefer to mate with older males because older males have proven that they are good at surviving. If male lyrebirds learn to copy sounds over time, then it is possible that older birds are able to mimic more sounds than younger birds. Thus, females who chose to mate with males who mimicked more sounds might benefit because they pass on good genes for survival to both their sons and their daughters who should therefore have higher survival ability.

It is likely that female lyrebirds would use both tail length and number of songs sung as a way of choosing mates. Two signals of males genetic quality would allow females to make more effective choices than if they relied on only one trait.


If you answered the question in general

Females use a variety of means to determine who is the “best male”. What it means for a male to be “best” depends upon whether or not males provide resources to the female before mating or help the female to care for the baby after it is born. In these cases, the best male is the male that provides the most resources because the female can use these resources to make more or stronger babies. For example, in scorpionflies females prefer to mate with the male who provides them the largest food gift at the time of mating. Studies have shown that females that eat a larger food gift are able to produce more eggs. Similarly, this might explain why human females are attracted to wealthier men (e.g., Anna Nicole and the billionaire).

In most cases, the only thing that a male provides to the female is DNA, so the best male is the male that has the “best genes”. Good genes are those that code for traits that make males good at surviving or reproducing. Thus, if a female mates with males with good genes, the desireable traits should end up in her offspring. Experiments, for example in mice, have shown that females are able to choose to mate with the male with the best genes.

The cues that females use to identify the male with the best genes vary across species. Females would like to mate with a male that is good at survival (the result of finding food, resisting predators and disease). The best way for a male to show he is good at survival is for them to have lived for a long time so females of different species use a variety of cues to determine which males is oldest (e.g., deep croak in frogs, song repertoire in mockingbirds). Females would also like to be able to determine if males are generally good at foraging (e.g., female guppies choosing males with more red spots). Females would like to be able to choose males that are healthy. One indication of general health is symmetry so females prefer to mate with symmetric males. Another indication of health is skin coloration in some species of birds and mammals that use patches of skin in mating displays. Skin coloration is influenced by the health of the male; diseased males have duller skin than healthy males so females should choose to mate with males with brighter skin. A male might also show that he is healthy by carrying around some sort of an extreme trait that acts as a handicap to his survival. Thus, by choosing to mate with this male the female is passing on good survival genes to her sons and daughters (handicap principle).

Thursday, February 5, 2009

Global Carbon Cycle and Global Warming


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).

Unfortunately, there is a lot of misinformation about this topic. For example, on Thursday February 5th there was a letter to the Lubbock Avalanche Journal about global warming that clearyly contained some misstatements of fact. 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


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

Saturday Update

The Saturday(February 7, 2009) issue of the Lubbock Avalance Journal contains another letter to the editor talking about global warming. The letter right refers reader to a site, www.petitionproject.org, where they claim that over 30,000 scientists (9000 of them have Ph. D.s) have signed a petition "firmly disagreeing with global warming theory". I would be interested in what you guys thought about the information available on this site relative to the info on the posts I have listed above.

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://www.biology.usu.edu/labsites/ernestlab/portal/index.html

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 influence my facvorite phrase "the world is complicated"

Wednesday, February 4, 2009

BAC Results

The BAC met at 4:00 PM on Wednesday afternoon to review concerns that people had about the test.

The committee reviewed all of the comments that people turned into me on paper and via email. After meeting the committee brought three questions to me for consideration.

Question #8 (green test-2) #12 (blue test-1)

This question is not clearly worded. Several people asked me questions about this question during the exam and I told them to answer the question one way. When I rereade the question after the exam I saw that there was a justifiable different way to interpret the question.

Thus, for this question both answers a and d will receive credit

Question # 23 (green test-2) #26 (blue test-1)

Cryptic coloration is an adaptation to either capturing prey, catching prey or both. I don't think that cryptic coloration has anything to do with attracting mates (how could being hard to see be a good tactic for attracting a mate?). Thus, I clearly think that answer d is the best answer. However, when I cut and pasted the question from form 1 to form 2 answer e was deleted from form 2. Thus, students taking the blue test had the option to pick a wrong answer that was not available to the students who took the blue test which is unfair.

Thus, for this question I will award credit for both answers d and e

Question #12 (green tetst-2) #8 (blue test-1)
The key phrase in the paragraph associated with this question is " scientists have documented that healthier males are able to produce longer eyestalks than those produced by less healthy males". This sentence tells me that large eyestalks are a signal of health. Thus, females who choose to mate with males with large eyestalks should pass on those genes for "good health" to their offspring (both sons and daughters). Thus, I consider answer d to be the best answer.

Many students thought that females should benefit from producing sons that were better at mating. It is possible that if her sons remained healthy for their whole life that they would produce traits that would make them popular with females. However, this is not as likely as producing healthy sons and daughters.

The key in answering this question is to choose the best answer. If the female is mating with a male with "healthy" genes then these genes should be expressed in both sons and daughters. Thus, I might have awarded credit for an answer that said a, b, and c were true, but because that was not an option.

Thus, only answer d will receive credit.

I would like to thank all members of the BAC for taking an hour out of their day to try to make sure that the testing process is as fair as possible.

Interesting Video from Kruger Park in South Africa


One of your fellow students just sent me a link to this video. It seems like almost everything that we have talked about so far in BIOL 1404 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. Enjoy!

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

First Midterm - Answer Key and BAC Info

Here are the answers for both forms of the multiple choice portion of the test.

BAC

The Biology Advisory Committee will meet with me this afternoon at 4:00 to discuss test questions. If you thought that there was a problem with one of the test questions here is what you need to do.

1. Write a thoughtful statement explaining to me how a student with a strong understanding of biology could have chosen a different answer.

2. You may turn these into me either on paper or via email.

Paper- I will place a box on the ledge outside of Dr. Dini's office. Comments submitted via paper must be in that box by 3:30 on Wednesday

Email- you may send me your comments via email. These comments must be received before 1:45 PM on Wednesday.

Answers Midterm #1


Form 1

1. b
2. a
3. c
4. b
5. c
6. c
7. c
8. d
9. b
10. d
11. c
12. d or a
13. a
14. d
15. b
16. c
17. d
18. b
19. a
20. b
21.c
22. c
23. d
24. b
25. e
26. d or e
27. e
28. c
29. b
30. a

Form 2

1. b
2. a
3. c
4. b
5. c
6. d
7. c
8. a or d
9. a
10. c
11. c
12. d
13. b
14. c
15. d
16. b
17. d
18. b
19. c
20. d
21. b
22. e
23. d or e
24. e
25. c
26. b
27. a
28. a
29. b
30. c

Tuesday, February 3, 2009

HHMI Undergraduate Research Fellowships

As I mentioned in class, the HHMI Undergraduate Research Fellowships are one of the great opportunities that we are able to offer students at Tech. If you are interested in gaining some research experience I urge you to check this program out.

The application deadline is February 25th, so it is time to get started!!!

For more info check out the website-

http://www.ciser.ttu.edu/hhmi/default.aspx

The people working with HHMI are all very nice and will help you with any questions or problems that you have. Tell them that I sent you and they will treat you especially well!