1. The order of exam takers will be group 6, 2, 4, 1, 3, 5. Please arrive on time. If you are not around when your group takes the exam, you will be given one more test that does not appear in the pointers. This extra question will have something to do with the algae experiment.
2. Each person will answer 1 out of the 7 test items given in the pointers. Persons will be randomly assigned to items before the exam. You have 15 minutes to answer the item assigned to you. Answers will be submitted on the exam sheets, except for those assigned computer problems; in their case, they will show their solutions on the computer.
3. Grading will be as follows. Each item is worth 100 points, distributed as follows: 0, 20, 40, 60, 80, 100, with no in-betweens. Your exam grade will be the average between your performance in the item and the group performance average. Thus, if you get a performance grade of 0, and your group as a whole got a performance grade of 60, your personal grade for the exam will be 30. If in the same group you got 100 for performance, your exam grade will be 80.
4. Bring your notebooks. I will check them during the exam.
5. You have had two weeks to prepare. I wish I could say "good luck", but 2 weeks was more than enough to bring you above luck. See you on Wednesday!
Sunday, October 5, 2008
Wednesday, September 24, 2008
BSIT pointers for final exams bio lab 081008
1. Computer work with given data (lettuce lengths)
a. generate the histogram
b. find the average
c. find the standard deviation
d. get the 95% confidence interval (2pts)
2. Computer work with given data (algal growth)
a. calculate theoretical population numbers from a sigmoid curve or carrying capacity model
b. calculate chi-squares between observed and theoretical models
c. determine the best-fitted rmax using chi-squares (3pts)
3. Draw correctly
a. insect versus arachnid: highlight the differences (2pts)
b. annelid versus millipede: highlight the differences (2pts)
c. hydra
4. Computer work with given data (lettuce and hydra growth)
a. Calculate the IC50 from lettuce data
b. Calculate the EC50 from hydra data (2pts)
c. Calculate the LD50 from hydra data (2pts)
5. Draw correctly and label parts
a. dissected cockroach gastrointestinal tract with malpighian tubules
b. paramecium
c. vorticella with its stalk
d. euglena
e. tardigrade
6. Various
a. diagram how to prepare a serial two-fold dilution
b. draw the lettuce complete set-up: 8 petri dishes and their contents (including volumes and concentrations)
c. draw the hydra complete set-up: two 12-well culture plates with their contents (including volumes and concentrations)
d. draw the two forms of abnormal hydra and a normal hydra
e. describe how to prepare a solution of a given ppm
7. Draw and label
a. Warburg apparatus and ant set-up
b. rotifer
c. planaria
d. coleoptera
e. lepidoptera
a. generate the histogram
b. find the average
c. find the standard deviation
d. get the 95% confidence interval (2pts)
2. Computer work with given data (algal growth)
a. calculate theoretical population numbers from a sigmoid curve or carrying capacity model
b. calculate chi-squares between observed and theoretical models
c. determine the best-fitted rmax using chi-squares (3pts)
3. Draw correctly
a. insect versus arachnid: highlight the differences (2pts)
b. annelid versus millipede: highlight the differences (2pts)
c. hydra
4. Computer work with given data (lettuce and hydra growth)
a. Calculate the IC50 from lettuce data
b. Calculate the EC50 from hydra data (2pts)
c. Calculate the LD50 from hydra data (2pts)
5. Draw correctly and label parts
a. dissected cockroach gastrointestinal tract with malpighian tubules
b. paramecium
c. vorticella with its stalk
d. euglena
e. tardigrade
6. Various
a. diagram how to prepare a serial two-fold dilution
b. draw the lettuce complete set-up: 8 petri dishes and their contents (including volumes and concentrations)
c. draw the hydra complete set-up: two 12-well culture plates with their contents (including volumes and concentrations)
d. draw the two forms of abnormal hydra and a normal hydra
e. describe how to prepare a solution of a given ppm
7. Draw and label
a. Warburg apparatus and ant set-up
b. rotifer
c. planaria
d. coleoptera
e. lepidoptera
Monday, July 21, 2008
BioIT S1 08-09: Assignment for 30 July 2008
The following groups will demonstrate the following projects on Aug 6, 2008.
All of them involve research, checking out Internet sites and biology books.
They also involve some trial and error, practice, and planning. You will be making mistakes. I therefore suggest you start immediately.
I am available the whole week to provide assistance.
I. Group 6
4 Gatorade bottles containing the following:
1. Fruitflies, all female.
2. Fruitflies, all male.
3. Fruitfly larvae only
4. Fruitfly pupae only
Discuss how you went about your project.
Describe the life cycle and anatomy of the fruitfly.
Briefly present a simple research article on fruitflies that demonstrates their usefulness to man.
Note: Your main problem is that it takes up to 10 days to get larvae and pupae; so start immediately.
II. Group 2
Construct an ant farm.
Describe how you went about your project.
Describe the life cycle, anatomy, and social structure and behavior of ants.
Briefly present a simple research article on ants that demonstrates their usefulness to man.
Note: the farm itself is easy to construct. The trick is finding the ants.
III. Group 3
Construct a Warburg apparatus and demonstrate that it works for insects.
Describe how you went about your project, from construction to calculation.
Briefly present a simple research article that used a Warburg apparatus or something similar.
Note: Any insect will do, but larger ones give better readings. The difficult part is the construction of the apparatus itself. Though most components are simple materials, the capillary tubes are very fragile, and it is a challenge to seal the connections without breaking them. The apparatus is also very sensitive--even the temperature from your fingers will cause you problems. You'll get the hang of it, though.
IV. Group 1
Determine the wavelengths of light to which Euglena are most phototaxically attracted.
Describe how you went about your project.
Describe Euglena and phototaxis in Euglena.
Briefly present a simple research article that involves Euglena and/or phototaxis.
Note: The challenge here is to construct two mini dark rooms that allows you to split light and expose parts of the culture to only one color of light. The first dark room will use multi-colored cellophane; a second darkroom will use a prism. Differences in results are expected.
V. Group 4
(Warning: Some amoeba are potentially deadly, and their cysts or eggs can remain undetected in the water sample. Thus, the project entails some risk, particulary when isolating pure amoeba. Do not touch any part of your face when working with amoeba. Wear gloves and always wash your hands before and after working.)
Isolate amoeba using agar plates and pond water.
Describe amoeba and their anatomy.
Briefly present a simple research article on amoeba, demonstrating their importance to man.
Note: Although amoeba are very common in the wild, it is not guaranteed that you will be able to isolate them. Knowing where to look and how to collect ups your chances. And since they are transparent, they will not be easy to detect. That's what the agar is for: we will detect them because they eat the agar and will form visible canals.
VI. Group 5
Produce zebrafish embryos, and present a slide show of photographs you took in the course of observing their development.
Describe how you went about the project.
Describe zebrafish, their anatomy and life cycle, and their embryonic development.
Briefly present a simple research article on zebrafish, demonstrating their importance to man.
Note: The big challenge here is how to separate the females from the males. Getting the embryos is easy after that.
All of them involve research, checking out Internet sites and biology books.
They also involve some trial and error, practice, and planning. You will be making mistakes. I therefore suggest you start immediately.
I am available the whole week to provide assistance.
I. Group 6
4 Gatorade bottles containing the following:
1. Fruitflies, all female.
2. Fruitflies, all male.
3. Fruitfly larvae only
4. Fruitfly pupae only
Discuss how you went about your project.
Describe the life cycle and anatomy of the fruitfly.
Briefly present a simple research article on fruitflies that demonstrates their usefulness to man.
Note: Your main problem is that it takes up to 10 days to get larvae and pupae; so start immediately.
II. Group 2
Construct an ant farm.
Describe how you went about your project.
Describe the life cycle, anatomy, and social structure and behavior of ants.
Briefly present a simple research article on ants that demonstrates their usefulness to man.
Note: the farm itself is easy to construct. The trick is finding the ants.
III. Group 3
Construct a Warburg apparatus and demonstrate that it works for insects.
Describe how you went about your project, from construction to calculation.
Briefly present a simple research article that used a Warburg apparatus or something similar.
Note: Any insect will do, but larger ones give better readings. The difficult part is the construction of the apparatus itself. Though most components are simple materials, the capillary tubes are very fragile, and it is a challenge to seal the connections without breaking them. The apparatus is also very sensitive--even the temperature from your fingers will cause you problems. You'll get the hang of it, though.
IV. Group 1
Determine the wavelengths of light to which Euglena are most phototaxically attracted.
Describe how you went about your project.
Describe Euglena and phototaxis in Euglena.
Briefly present a simple research article that involves Euglena and/or phototaxis.
Note: The challenge here is to construct two mini dark rooms that allows you to split light and expose parts of the culture to only one color of light. The first dark room will use multi-colored cellophane; a second darkroom will use a prism. Differences in results are expected.
V. Group 4
(Warning: Some amoeba are potentially deadly, and their cysts or eggs can remain undetected in the water sample. Thus, the project entails some risk, particulary when isolating pure amoeba. Do not touch any part of your face when working with amoeba. Wear gloves and always wash your hands before and after working.)
Isolate amoeba using agar plates and pond water.
Describe amoeba and their anatomy.
Briefly present a simple research article on amoeba, demonstrating their importance to man.
Note: Although amoeba are very common in the wild, it is not guaranteed that you will be able to isolate them. Knowing where to look and how to collect ups your chances. And since they are transparent, they will not be easy to detect. That's what the agar is for: we will detect them because they eat the agar and will form visible canals.
VI. Group 5
Produce zebrafish embryos, and present a slide show of photographs you took in the course of observing their development.
Describe how you went about the project.
Describe zebrafish, their anatomy and life cycle, and their embryonic development.
Briefly present a simple research article on zebrafish, demonstrating their importance to man.
Note: The big challenge here is how to separate the females from the males. Getting the embryos is easy after that.
Tuesday, July 8, 2008
BioIT Sem 1 08-09: Protists
Microscopic animals and their parts
1. Paramecium
a. Cytoplasmic streaming: moving cytoplasm around the edges of the animal
b. Contractile vacuole: located centrally; circular; tends to shrink and expand; there may be two of them
c. Nucleus: dark-colored central body; usually circular
d. Peristome: median location; the funnel-shaped opening that leads to the esophagus
e. Esophagus: constriction that leads from the peristome to the food vacuole
f. Food vacuole: end of the esophagus; dark-colored if it contains food
2. Rotifer (multicellular)
a. Corona: the anterior ring lined with ciliated cells
b. Eyespot: small dark-colored spot located immediately posterior to the corona
c. Stomach: large, central, dark-colored chamber (if it contains food)
d. Vitellarium: the outer transparent skin
e. Foot: the long posterior organ that serves for attachment
f. Toe: the end of the foot
3. Planaria (multicellular)
a. Ocelli: the two eyespots
b. Mouth: the opening of the gastrointestinal tract, located ventral and medial
c. Pharynx: passage from the mouth to the two lateral branches of the gastrointestinal tract
4. Hydra (multicellular)
a. Mouth: located at the base of the tentacles
b. Tentacles: arms
c. Ectoderm: the outer layer of the skin
d. Gastroderm: the lining of the digestive cavity
e. Digestive cavity: hollow cavity where digestion takes place
f. Mesoglea: layer of cells between the ectoderm and the gastroderm
5. Euglena
a. Flagellum: whip-like motor organelle located posteriorly
b. Nucleus: large, round, central, dark-colored body; distinguished from the smaller eyespot
c. Eyespot: small, red-colored photoreceptor located anteriorly
d. Chloroplasts: green-colored organelles generally distributed throughout the body
2. Significance to humans. Summarize a recent research article to illustrate. For example: Upadhyaya A et al. Power limited contraction dynamics of Vorticella convallaria: an ultrafast biological spring. Biophys J. 2008, 94(1):265-272. “Vorticella convallaria is one of the fastest and most powerful cellular machines. The cell body is attached to a substrate by a slender stalk containing a polymeric structure---the spasmoneme. Helical coiling of the stalk results from rapid contraction of the spasmoneme, an event mediated by calcium binding to a negatively charged polymeric backbone. We use high-speed imaging to measure the contraction velocity as a function of the viscosity of the external environment and find that the maximum velocity scales inversely with the square root of the velocity. This can be explained if the rate of contraction is ultimately limited by the power delivered by the actively contracting spasmoneme…etc.”. Explain this to us in layman’s terms, especially the significance to humans. You may use illustrations and other strategies to make the presentation good. Suggested sources: PUBMED (a search engine that will give mostly summaries); Scientific American.
1. Paramecium
a. Cytoplasmic streaming: moving cytoplasm around the edges of the animal
b. Contractile vacuole: located centrally; circular; tends to shrink and expand; there may be two of them
c. Nucleus: dark-colored central body; usually circular
d. Peristome: median location; the funnel-shaped opening that leads to the esophagus
e. Esophagus: constriction that leads from the peristome to the food vacuole
f. Food vacuole: end of the esophagus; dark-colored if it contains food
2. Rotifer (multicellular)
a. Corona: the anterior ring lined with ciliated cells
b. Eyespot: small dark-colored spot located immediately posterior to the corona
c. Stomach: large, central, dark-colored chamber (if it contains food)
d. Vitellarium: the outer transparent skin
e. Foot: the long posterior organ that serves for attachment
f. Toe: the end of the foot
3. Planaria (multicellular)
a. Ocelli: the two eyespots
b. Mouth: the opening of the gastrointestinal tract, located ventral and medial
c. Pharynx: passage from the mouth to the two lateral branches of the gastrointestinal tract
4. Hydra (multicellular)
a. Mouth: located at the base of the tentacles
b. Tentacles: arms
c. Ectoderm: the outer layer of the skin
d. Gastroderm: the lining of the digestive cavity
e. Digestive cavity: hollow cavity where digestion takes place
f. Mesoglea: layer of cells between the ectoderm and the gastroderm
5. Euglena
a. Flagellum: whip-like motor organelle located posteriorly
b. Nucleus: large, round, central, dark-colored body; distinguished from the smaller eyespot
c. Eyespot: small, red-colored photoreceptor located anteriorly
d. Chloroplasts: green-colored organelles generally distributed throughout the body
6. Vorticella
a. Three rows of cilia: motile organelles located anteriorly forming three rows
b. Buccal funnel: or mouth; at the base of the rows of cilia
c. Superficial pellicle: the outer covering of the animal
d. Vacuole: contractile organelle located inside the animal
e. Macronucleus: central, dark body containing DNA; in the form of a horse-shoe
f. Peduncle: coiled spring-like appendage that attaches the animal to the substrate
REPORT ON
a. Three rows of cilia: motile organelles located anteriorly forming three rows
b. Buccal funnel: or mouth; at the base of the rows of cilia
c. Superficial pellicle: the outer covering of the animal
d. Vacuole: contractile organelle located inside the animal
e. Macronucleus: central, dark body containing DNA; in the form of a horse-shoe
f. Peduncle: coiled spring-like appendage that attaches the animal to the substrate
REPORT ON
1. Taxonomy, anatomy, habitat, and food requirements.
Wednesday, July 2, 2008
BioIT Sem 1 2008-2009: Assignment for the next 3 wks
We are going to have a free cut on the 16th of July as I will be out of town. To ensure you have a productive time, here is an assignment that I hope will challenge and entertain you.
It's called ARTIFICIAL LIFE.
Instructions (per group)
1. Search the Internet for simple simulation freeware. There are many; these include Framsticks, PhyloStrat, Simulistics, Boppers, Game of Life, etc. I recently found a good one (demonstrations.wolfram.com) which features thousands of simulations. For example, the Predator-Prey demo, a rather good model for rabbits and foxes, and viruses. You'll need to install the free Mathematica Player for this. These programs were designed as research tools to experiment on various aspects of life such as metabolism, ecological interaction, and evolution. SimCity and other such "games" are not allowed.
2. Study the documentation and examples. Play around a little. This playing part should take up more than half your time!
Then design and carry out an experiment in that virtual world.
a) What is/are the questions you would like to answer? Typical questions include "what if" (e.g. what would happen if I adjust the growth rates of predator and prey just so?); "what model explains" (e.g., the algae experiment); "compare and contrast" (e.g., which is better, grass tea or wheat tea for growing paramecium); and "classification and patterns" (e.g., how many kinds of general growth curves are there).
b) What is your tentative answer?
c) What experiment can you do to prove your answer is wrong? What data will prove you wrong?
d) In case your experiment proves your answer wrong, test other answers.
e) Right or wrong, prove everything with data.
3. Have me approve your problem first. Give me also a short description of the program and your approach. You may submit this as a comment on this blog.
3. Groups may use the same software, but they can not answer the same problems.
4. Each group will make a presentation on the 23rd July that will cover:
a) Introduction. Background and significance (yes, your problem should have significance) of the problem. Background of the software. Summary of the experiment and its results.
b) Methods and Materials
c) Data
d) Discussion. Includes possible weak points about your approach.
e) Conclusion and proposals for future work.
4. Not everyone has to speak; but everyone has to work.
It's called ARTIFICIAL LIFE.
Instructions (per group)
1. Search the Internet for simple simulation freeware. There are many; these include Framsticks, PhyloStrat, Simulistics, Boppers, Game of Life, etc. I recently found a good one (demonstrations.wolfram.com) which features thousands of simulations. For example, the Predator-Prey demo, a rather good model for rabbits and foxes, and viruses. You'll need to install the free Mathematica Player for this. These programs were designed as research tools to experiment on various aspects of life such as metabolism, ecological interaction, and evolution. SimCity and other such "games" are not allowed.
2. Study the documentation and examples. Play around a little. This playing part should take up more than half your time!
Then design and carry out an experiment in that virtual world.
a) What is/are the questions you would like to answer? Typical questions include "what if" (e.g. what would happen if I adjust the growth rates of predator and prey just so?); "what model explains" (e.g., the algae experiment); "compare and contrast" (e.g., which is better, grass tea or wheat tea for growing paramecium); and "classification and patterns" (e.g., how many kinds of general growth curves are there).
b) What is your tentative answer?
c) What experiment can you do to prove your answer is wrong? What data will prove you wrong?
d) In case your experiment proves your answer wrong, test other answers.
e) Right or wrong, prove everything with data.
3. Have me approve your problem first. Give me also a short description of the program and your approach. You may submit this as a comment on this blog.
3. Groups may use the same software, but they can not answer the same problems.
4. Each group will make a presentation on the 23rd July that will cover:
a) Introduction. Background and significance (yes, your problem should have significance) of the problem. Background of the software. Summary of the experiment and its results.
b) Methods and Materials
c) Data
d) Discussion. Includes possible weak points about your approach.
e) Conclusion and proposals for future work.
4. Not everyone has to speak; but everyone has to work.
Monday, June 23, 2008
EnvSci Sem 1 08-09: New reading
Xerox a copy of Broome, J. The ethics of climate change. Scientific American, June 2008, pp. 97-102. The issue is still on the display shelf in Lopez Library. This reading will be taken up on Aug 19. Note that this change is already reflected in the syllabus posted on this blog.
BioIT Sem 1 08-09. Counts for 23 June 2008
I counted these:
Group 4: 258/0.1
Grp 1: 55/0.4
Grp 2: 114 rods/0.1 (Ankistrodesmus is definitely a pretty thing!)
Grp 6: 166/0.1
Grp 3: 120/0.2
Grp 5 counted theirs. I think it's 176/0.1?
Scenedasmus and Ankistrodesmus are so unique that I think it will be a good idea to see the growth curves that result when we grow them in the same flask. Let's see if we have time.
I read an interesting article in the latest issue of Nature (vol. 453, no. 29, pp. 583-585) by N. Lane: "Origins of death". Apparently, certain unicellular organisms engage in apoptosis, i.e., programmed cell death. Also known as cell suicide, apoptosis is a regular feature of multicellular eukoryotes, that is, of plant and animal cells. It's what keeps your nose and other organs from growing too large; a defect in apoptosis is one feature of cancer. But it was unusual to find it in unicellular eukaryotes, because single celled organisms have usually been considered immortal: when they asexually multiply by splitting, the resulting daughter cells are considered "babies". They die only when there's a poison in the water, or it's too hot, etc. Now it seems some unicellular eukaryotes can initiate their own death under certain conditions, such as the presence of some virus in the culture. Mass suicide of a population containing infected algae might be a way of protecting neighboring populations from the virus.
Just in case your cultures suddenly crash, we will deep freeze them, then get in touch with some scientists who have the facilities to detect the tell-tale signals of apoptosis. A crashed culture will be a BIG thing; in fact, I'm almost hoping they do crash. This might get us published!
Group 4: 258/0.1
Grp 1: 55/0.4
Grp 2: 114 rods/0.1 (Ankistrodesmus is definitely a pretty thing!)
Grp 6: 166/0.1
Grp 3: 120/0.2
Grp 5 counted theirs. I think it's 176/0.1?
Scenedasmus and Ankistrodesmus are so unique that I think it will be a good idea to see the growth curves that result when we grow them in the same flask. Let's see if we have time.
I read an interesting article in the latest issue of Nature (vol. 453, no. 29, pp. 583-585) by N. Lane: "Origins of death". Apparently, certain unicellular organisms engage in apoptosis, i.e., programmed cell death. Also known as cell suicide, apoptosis is a regular feature of multicellular eukoryotes, that is, of plant and animal cells. It's what keeps your nose and other organs from growing too large; a defect in apoptosis is one feature of cancer. But it was unusual to find it in unicellular eukaryotes, because single celled organisms have usually been considered immortal: when they asexually multiply by splitting, the resulting daughter cells are considered "babies". They die only when there's a poison in the water, or it's too hot, etc. Now it seems some unicellular eukaryotes can initiate their own death under certain conditions, such as the presence of some virus in the culture. Mass suicide of a population containing infected algae might be a way of protecting neighboring populations from the virus.
Just in case your cultures suddenly crash, we will deep freeze them, then get in touch with some scientists who have the facilities to detect the tell-tale signals of apoptosis. A crashed culture will be a BIG thing; in fact, I'm almost hoping they do crash. This might get us published!
Wednesday, June 18, 2008
BioIT 08-09: Comparison of models
Here's a simpler comparison of three different growth models to describe algal growth.
1. Constant growth rate (A). The same number of algae are added to the population every time. That is, the rate at which N grows is the same at all times, or
dN/dt = rate
where "rate" is a constant.
2. Exponential growth (B). The rate at which N grows (dN/dt) is not constant, and depends at every time on the size of the population able to reproduce. The amount of new algae being added to the population represents, however, a constant proportion of the population. We call that constant proportion "rate", the equivalent of "interest rate" in banking.
That is,
dN/dt = N x rate 3. Sigmoid or density-dependent growth (C). As in the exponential model, the new population is a certain fraction of the old (dN/dt = N x rate). But now this proportion "rate" is not constant and depends on the N. That is, algae are reproducing maximally (rate = ratemax) when N is very low, and no longer reproducing (rate = 0) when the population reaches a certain size called the "carrying capacity", cc. (You might say the algae are "having the most fun when no one else is around" then become more and more "shy" as their neighbors increase. In reality, it has to do with less and less food and space as population grows: the culture has become too crowded for growth to be sustainable.) For simplicity, the relation between "rate" and N may be described by the linear curve in D.
Thus, as in the exponential
dN/dt = N x rate
but
rate = ratemax - (ratemax/cc) x N, the equation of the line in D.
Thus,
dN/dt = N x (ratemax - (ratemax/cc) x N), or factoring out
dN/dt = N x ratemax x (1 - N/cc)
What can make this confusing is the word "rate". In one context it refers to a proportion of the population (the variable "rate"), while in another context the same word refers to the number of new algae per unit time (dN/dt). Thus, if you are confused, change "rate" (proportion) into "interest" (as in banking), and use the word exclusively to refer to dN/dt.
Friday, June 13, 2008
Environmental Science Sem1 08-09 debates
Debate 1:
This house believes that order is not found in nature but is imposed on it by the human mind
Diaz-Hipolito-Asilo versus Sayo-Camello-Lim
Debate 2:
Earth's interconnectedness is evidence of intelligent design
Landong-Banalo-Aguila versus Siazon-Mindanao-Dona
Debate 3:
Man in his uncivilized state is inherently good
Verzosa-Abracosa versus Ortiz-Casilana
Debate 4:
To best protect its environment the Philippine government must impose socialist measures
Galang-Bendero versus Relucio-Laraya
Debate 5:
The state of knowledge today is sufficient to justify lifting all existing bans on the commercialization of genetically modified crops (or animals)
Valeroso-Gonzalez-Bato versus Perez-Toledo-Anastacio
Debate 6:
___ is the root of all environmental problems (Government defines ___)
Villafuerte-Benavidez-Calimlim versus Lee-Hiquiana-Marquez
FORMAT: Asian Parliamentary, modified to include audience participation
This house believes that order is not found in nature but is imposed on it by the human mind
Diaz-Hipolito-Asilo versus Sayo-Camello-Lim
Debate 2:
Earth's interconnectedness is evidence of intelligent design
Landong-Banalo-Aguila versus Siazon-Mindanao-Dona
Debate 3:
Man in his uncivilized state is inherently good
Verzosa-Abracosa versus Ortiz-Casilana
Debate 4:
To best protect its environment the Philippine government must impose socialist measures
Galang-Bendero versus Relucio-Laraya
Debate 5:
The state of knowledge today is sufficient to justify lifting all existing bans on the commercialization of genetically modified crops (or animals)
Valeroso-Gonzalez-Bato versus Perez-Toledo-Anastacio
Debate 6:
___ is the root of all environmental problems (Government defines ___)
Villafuerte-Benavidez-Calimlim versus Lee-Hiquiana-Marquez
FORMAT: Asian Parliamentary, modified to include audience participation
Thursday, June 12, 2008
Environmental Science 1st sem 2008-09 syllabus
Topics
1. Harvey, Introduction to the circulation (June 13)
2. Descartes, Rules for the direction of (June 17)
3. (June 20)
4. Thomas, World’s biggest membrane (June 24)
5. Tansley, The ecosystem (June 27)
6. Vernadsky, The biosphere (July 1)
7. Leopold, Odyssey (July 4)
8. Commoner, The closing circle (July 8)
9. Lovelock, The recognition of Gaia (July 11)
10. Free cut (July 14)
11. Free cut (July 18)
12. LONG EXAM 1 (July 22)
13. Miller, Dimensions of deformity (July 25)
14. (July 29)
15. Clemens, The climax concept (Aug 1)
16. Boulding, Economics of spaceship (Aug 5)
17. Dillard, Intricacy (Aug 8)
18. Hardin, The tragedy of the commons (Aug 12)
19. Leopold, The land ethic (Aug 15)
20. Broome, The ethics of climate change (Aug 19)
21. Marsh, Man and nature (Aug 22)
22. (Aug 26)
23. LONG EXAM 2 (Aug 29)
24. McKibben, The end of nature (Sep 2)
25. (Sep 5)
26. Grumbine, The politics of wilderness (Sep 9)
27. (Sep 12)
28. DEBATE 1 (Sep 16)
29. DEBATE 2 (Sep 19)
30. DEBATE 3 (Sep 23)
31. DEBATE 4 (Sep 26)
32. DEBATE 5 (Sep 30)
33. DEBATE 6 (Oct 3)
Reference: Selections from Keeping Things Whole: Readings in Environmental Science, 2003. The Great Books Foundation, Chicago, 298 pp.
1. Harvey, Introduction to the circulation (June 13)
2. Descartes, Rules for the direction of (June 17)
3. (June 20)
4. Thomas, World’s biggest membrane (June 24)
5. Tansley, The ecosystem (June 27)
6. Vernadsky, The biosphere (July 1)
7. Leopold, Odyssey (July 4)
8. Commoner, The closing circle (July 8)
9. Lovelock, The recognition of Gaia (July 11)
10. Free cut (July 14)
11. Free cut (July 18)
12. LONG EXAM 1 (July 22)
13. Miller, Dimensions of deformity (July 25)
14. (July 29)
15. Clemens, The climax concept (Aug 1)
16. Boulding, Economics of spaceship (Aug 5)
17. Dillard, Intricacy (Aug 8)
18. Hardin, The tragedy of the commons (Aug 12)
19. Leopold, The land ethic (Aug 15)
20. Broome, The ethics of climate change (Aug 19)
21. Marsh, Man and nature (Aug 22)
22. (Aug 26)
23. LONG EXAM 2 (Aug 29)
24. McKibben, The end of nature (Sep 2)
25. (Sep 5)
26. Grumbine, The politics of wilderness (Sep 9)
27. (Sep 12)
28. DEBATE 1 (Sep 16)
29. DEBATE 2 (Sep 19)
30. DEBATE 3 (Sep 23)
31. DEBATE 4 (Sep 26)
32. DEBATE 5 (Sep 30)
33. DEBATE 6 (Oct 3)
Reference: Selections from Keeping Things Whole: Readings in Environmental Science, 2003. The Great Books Foundation, Chicago, 298 pp.
Tuesday, May 27, 2008
Environmental Science, Summer 07-08
Dear students,
Please get your lab notebooks at the lab. Or else you'll have to claim it in Payatas.
Jay Lazaro
Please get your lab notebooks at the lab. Or else you'll have to claim it in Payatas.
Jay Lazaro
Thursday, May 15, 2008
UA&P EnvSci Summer 08-09 Lab Exam Pointers
The following are possible items for the lab practical exams
Each item should be completed within 10 min.
1. Calculate molarity, ppm, required grams, or required volumes.
2. Prepare, focus a slide to reveal gridlines, count cells. Count no less than 100 cells.
3. Create a carrying capacity model on Excel, with a given initial algae count, birthrate, deathrate, and carrying capacity. Time step = 0.1
4. Estimate birthrate of an actual culture by fitting the data to a (ready-made) carrying capacity model. Use the method of least squares to fit theoretical and actual counts.
5. Determine wind direction, temperature, relative humidity and CO2 concentration.
6. Plot (ready-made) lettuce and onion toxicity data, insert a regression line, and calculate the median inhibitory concentration from the equation of the line.
This is how the group will be graded.
1. Each member will draw an item at random and proceed to do the exercise within the allotted time.
2. For each item, you either get a perfect 1 or a 0. For person#1 the personal grade = p1.
3. Adding the items will give a group grade. Thus group grade, g = p1+p2+p3+p4+p5+p6
4. The INDIVIDUAL GRADE will be calculated as follows:
final personal grade of person#1= ((6*p1) + g)*100/12
If a group member is absent, his p1 = 0, and the group grade will include that number.
One group has only 5 members. The calculation is therefore,
final personal grade = ((5*p1) + g)*100/10
5. Notebooks will be collected just before you take the exam.
6. Group 1 will take the exam first, Group 6 last. While a group is taking an exam the others wait.
Arrange with me if you need to practice.
Good luck!
Each item should be completed within 10 min.
1. Calculate molarity, ppm, required grams, or required volumes.
2. Prepare, focus a slide to reveal gridlines, count cells. Count no less than 100 cells.
3. Create a carrying capacity model on Excel, with a given initial algae count, birthrate, deathrate, and carrying capacity. Time step = 0.1
4. Estimate birthrate of an actual culture by fitting the data to a (ready-made) carrying capacity model. Use the method of least squares to fit theoretical and actual counts.
5. Determine wind direction, temperature, relative humidity and CO2 concentration.
6. Plot (ready-made) lettuce and onion toxicity data, insert a regression line, and calculate the median inhibitory concentration from the equation of the line.
This is how the group will be graded.
1. Each member will draw an item at random and proceed to do the exercise within the allotted time.
2. For each item, you either get a perfect 1 or a 0. For person#1 the personal grade = p1.
3. Adding the items will give a group grade. Thus group grade, g = p1+p2+p3+p4+p5+p6
4. The INDIVIDUAL GRADE will be calculated as follows:
final personal grade of person#1= ((6*p1) + g)*100/12
If a group member is absent, his p1 = 0, and the group grade will include that number.
One group has only 5 members. The calculation is therefore,
final personal grade = ((5*p1) + g)*100/10
5. Notebooks will be collected just before you take the exam.
6. Group 1 will take the exam first, Group 6 last. While a group is taking an exam the others wait.
Arrange with me if you need to practice.
Good luck!
Sunday, May 11, 2008
UA&P EnviSci Summer 08-09 Water Toxicity Expt
Description of the Water Toxicity Experiment, 12 May 2008
The exercise is an example of the use of bioassays, i.e., tests that use live organisms.
The Payatas landfill in Quezon City is one of the Southeast Asia's biggest open landfill. It is 500 meters from the border of the La Mesa Watershed. Trash for the last 30 or so years have been dumped in this place to produce two mountains of trash covering 7 hectares and rising 7 or 8 stories above the level of the surrounding houses.
The trash produces a liquid called leachate. Leachate is a complex mixture of organic compounds and water, and possibly dissolved metals. It is toxic, and there is some danger that this liquid seeps into the groundwater. People who draw from contaminated deep wells might therefore be at risk for toxic effects.
We want to know two things. First, how do we measure the contamination? And second, knowing that, what are the risks to the populations surrounding the dump?
One way to measure contamination is to go to a chemical laboratory and have the components of the water analyzed. This gives exact amounts but has the disadvantage of being expensive and being selective only for the chemicals that are deliberately sought.
Another method is to use a bioassay. Although they have the disadvantage of not being able to identify the components of a sample, a toxic sample would cause a TOTAL toxic response on the test organism. It will simply reveal that a sample is toxic. But a bioassay is cheap, as it can make use of simple materials and test organisms that are readily sourced.
We used three test organisms: Lettuce (Lactuca sativa), Onion (Allium cepa) and a species of freshwater hydra (Hydra littoralis). Lettuce and onion were sourced from the supermarket, whereas Hydra was imported from the States and maintained at the laboratory.
To test for toxicity, we use a variation experiment; we use decreasing concentrations of the samples to check for a corresponding decrease in the toxic response. The toxic response we seek in the plants are inhibition of root growth; in hydra we look for death or abnormalities. Thus, at weaker and weaker concentrations of a toxic sample we should get longer and longer roots. The lengths should fall between the lengths obtained with clean water (negative control, or NC) and the lengths obtained with a maximal concentration of a positive control (copper for onion and zinc for lettuce).
What measure of toxicity is used and how is it obtained? Toxicity is measured by getting the average length of all roots per concentration of sample. Then all these averages are placed on a graph that shows average root length versus concentration. A line is then fit to these points using a mathematical procedure known as linear regression and the method of least sum of squares, which gives an equation for that best fit line. Then, using the equation of the line, we can compute for the concentration of sample that results in 50% inhibition of root growth, known as the median inhibitory concentration or IC50. Thus, if "clean water" gives a root length of 20 cm, and strong positive control gives 0 cm, then the IC50 of a sample would be the concentration required to give a root length of 10 cm. The IC50's can then be compared across all samples. Those with lower IC50's are the more toxic.
Now that we are able to measure toxicity, how are we going to measure risk? To be more specific, we are interested in knowing the direction in which the supposed leachate is flowing underground. Thus, we sample water from all directions around the dump (N, E, W, S) and then compare the IC50's of the samples. Given the terrain, we would expect to find more toxicity in the south wells, for example, but this will not always be the case.
Thus, this is what we must do:
1. Collect water samples from deep wells located north, east, west, and south of the Payatas dumpsite.
2. Dilute the samples and test them on lettuce, onion, and hydra.
3. After 3 days check for root growth inhibition in onion. After 4 days, check for death and abnormality in hydra. After 5 days, check for root growth inhibition in lettuce. Plot the data against concentration and determine IC50's by linear regression.
The exercise is an example of the use of bioassays, i.e., tests that use live organisms.
The Payatas landfill in Quezon City is one of the Southeast Asia's biggest open landfill. It is 500 meters from the border of the La Mesa Watershed. Trash for the last 30 or so years have been dumped in this place to produce two mountains of trash covering 7 hectares and rising 7 or 8 stories above the level of the surrounding houses.
The trash produces a liquid called leachate. Leachate is a complex mixture of organic compounds and water, and possibly dissolved metals. It is toxic, and there is some danger that this liquid seeps into the groundwater. People who draw from contaminated deep wells might therefore be at risk for toxic effects.
We want to know two things. First, how do we measure the contamination? And second, knowing that, what are the risks to the populations surrounding the dump?
One way to measure contamination is to go to a chemical laboratory and have the components of the water analyzed. This gives exact amounts but has the disadvantage of being expensive and being selective only for the chemicals that are deliberately sought.
Another method is to use a bioassay. Although they have the disadvantage of not being able to identify the components of a sample, a toxic sample would cause a TOTAL toxic response on the test organism. It will simply reveal that a sample is toxic. But a bioassay is cheap, as it can make use of simple materials and test organisms that are readily sourced.
We used three test organisms: Lettuce (Lactuca sativa), Onion (Allium cepa) and a species of freshwater hydra (Hydra littoralis). Lettuce and onion were sourced from the supermarket, whereas Hydra was imported from the States and maintained at the laboratory.
To test for toxicity, we use a variation experiment; we use decreasing concentrations of the samples to check for a corresponding decrease in the toxic response. The toxic response we seek in the plants are inhibition of root growth; in hydra we look for death or abnormalities. Thus, at weaker and weaker concentrations of a toxic sample we should get longer and longer roots. The lengths should fall between the lengths obtained with clean water (negative control, or NC) and the lengths obtained with a maximal concentration of a positive control (copper for onion and zinc for lettuce).
What measure of toxicity is used and how is it obtained? Toxicity is measured by getting the average length of all roots per concentration of sample. Then all these averages are placed on a graph that shows average root length versus concentration. A line is then fit to these points using a mathematical procedure known as linear regression and the method of least sum of squares, which gives an equation for that best fit line. Then, using the equation of the line, we can compute for the concentration of sample that results in 50% inhibition of root growth, known as the median inhibitory concentration or IC50. Thus, if "clean water" gives a root length of 20 cm, and strong positive control gives 0 cm, then the IC50 of a sample would be the concentration required to give a root length of 10 cm. The IC50's can then be compared across all samples. Those with lower IC50's are the more toxic.
Now that we are able to measure toxicity, how are we going to measure risk? To be more specific, we are interested in knowing the direction in which the supposed leachate is flowing underground. Thus, we sample water from all directions around the dump (N, E, W, S) and then compare the IC50's of the samples. Given the terrain, we would expect to find more toxicity in the south wells, for example, but this will not always be the case.
Thus, this is what we must do:
1. Collect water samples from deep wells located north, east, west, and south of the Payatas dumpsite.
2. Dilute the samples and test them on lettuce, onion, and hydra.
3. After 3 days check for root growth inhibition in onion. After 4 days, check for death and abnormality in hydra. After 5 days, check for root growth inhibition in lettuce. Plot the data against concentration and determine IC50's by linear regression.
Friday, May 9, 2008
UA&P EnSci Summer 07-08, Pointers for 2nd LE
Here are pointers for the second long exam.
Lab questions.
1. Calculate final ppm or molarity given a description of the preparation procedure.
2. (Just an example) Estimate the slope (m) of the line y=mx + 3 that best fits the three points (1,5), (2,15), and (3, 16). Slope m should be an integer.
3. Draw three growth curves with the same carrying capacity but having different growth rates: high, medium, and low.
4. Describe how to make a solution of X, 0.5X, 0.25X, and 0.125X of a given quantity.
5. Describe, step by step, how to transfer algae aseptically from an algal culture into a flask of clean, fresh, and sterile medium.
6. Draw a Hydra attached to the bottom surface of a culture well.
7. Draw an onion set-up in a shot glass for a toxicity experiment.
Lecture questions.
1. What kinds of problems generally do not have a technical solution and why?
2. The world's carrying capacity for humans probably exists, but it is very hard to estimate it in the long term. Explain why.
3. What basis is there in fact (true/false) for saying that man SHOULD (good/bad) care for the environment. Be very specific about those facts.
4. Leopold and Hardin would probably disagree on many points about how the population "problem" should be addressed.
5. When Miller talks about man being part of nature does he advocate a return to the Ancient's way of thinking? Explain.
6. McKibben probably disagrees that genetic modification will solve the food supply problem, while Tansley will probably say the opposite. Who will side with McKibben and who will side with Tansley--Hardin or Boulding--and why.
7. Convert the following NON-SCIENTIFIC statements into SCIENTIFIC statements and give one negating evidence for the SCIENTIFIC version of each question.
a. Detergents are bad for plant growth.
b. Children are God's gifts to their parents.
c. Thou shalt not covet thy neighbor's goods.
d. Thou shalt not kill.
e. You! Over there! Yes, you're cheating!
8. Ethics, a question of good, must ultimately be based not on what is good but on what is true. Explain.
9. The postmodern theory that "What is good is what is good for me" is illogical and absurd. Show where the logical error lies.
10. "We shouldn't cut too many trees because Aldo Leopold says so" is an example of a certain kind of argument that is valid and acceptable under certain conditions. Give two of those conditions.
Lab questions.
1. Calculate final ppm or molarity given a description of the preparation procedure.
2. (Just an example) Estimate the slope (m) of the line y=mx + 3 that best fits the three points (1,5), (2,15), and (3, 16). Slope m should be an integer.
3. Draw three growth curves with the same carrying capacity but having different growth rates: high, medium, and low.
4. Describe how to make a solution of X, 0.5X, 0.25X, and 0.125X of a given quantity.
5. Describe, step by step, how to transfer algae aseptically from an algal culture into a flask of clean, fresh, and sterile medium.
6. Draw a Hydra attached to the bottom surface of a culture well.
7. Draw an onion set-up in a shot glass for a toxicity experiment.
Lecture questions.
1. What kinds of problems generally do not have a technical solution and why?
2. The world's carrying capacity for humans probably exists, but it is very hard to estimate it in the long term. Explain why.
3. What basis is there in fact (true/false) for saying that man SHOULD (good/bad) care for the environment. Be very specific about those facts.
4. Leopold and Hardin would probably disagree on many points about how the population "problem" should be addressed.
5. When Miller talks about man being part of nature does he advocate a return to the Ancient's way of thinking? Explain.
6. McKibben probably disagrees that genetic modification will solve the food supply problem, while Tansley will probably say the opposite. Who will side with McKibben and who will side with Tansley--Hardin or Boulding--and why.
7. Convert the following NON-SCIENTIFIC statements into SCIENTIFIC statements and give one negating evidence for the SCIENTIFIC version of each question.
a. Detergents are bad for plant growth.
b. Children are God's gifts to their parents.
c. Thou shalt not covet thy neighbor's goods.
d. Thou shalt not kill.
e. You! Over there! Yes, you're cheating!
8. Ethics, a question of good, must ultimately be based not on what is good but on what is true. Explain.
9. The postmodern theory that "What is good is what is good for me" is illogical and absurd. Show where the logical error lies.
10. "We shouldn't cut too many trees because Aldo Leopold says so" is an example of a certain kind of argument that is valid and acceptable under certain conditions. Give two of those conditions.
UA&P EnSci Summer 07-08 Project One Summary
Let me describe the approach we took in the algae experiments.
1. We set out to ask two questions regarding an important environmental issue. The BIG question was: "Are detergents toxic to plants?" We made an assumption that toxicity may be measured by its effects on birthrate. The more specific question, then, was "Do detergents in the water decrease the growth rate of algae?" Given that question, the best general strategy was to do a variation-type of experiment where we manipulate the concentration of detergent in water and then check for a co-variation in growthrate.
2. But, how do we measure growth rate? And then, what growth rate are we talking about: the intrinsic growth rate or the actual growth rate? In principle, measuring the intrinsic growth rate should be easy: Count the algae at some posterior day (say day 2), get the difference between that count and the previous day's count (day 1), and divide that difference by the previous day's count. The value we get should be the same for whatever pair of days we choose, if the growth of algae is EXPONENTIAL.
But are the actual algae cultures growing exponentially? Exponential growth is obtained under the very best conditions, i.e., practically unlimited space and resources, and no competition. A flask of algae, however, is a small world; so small that we may reasonably expect that as algae become many, their growth rate would decrease because of competition and rapid depletion of resources. Therefore, the growth rate would change rather quickly with time; that is, it will not be constant. The exponential model would be imprecise; it would be difficult for us to choose an appropriate anterior and posterior date to make the calculation.
So, it would seem that a CARRYING CAPACITY model is more appropriate to describe the real situation in the flask. But the model, like all models, requires some assumptions before it can be precisely defined in a form that can be tested. One assumption is that the actual growth rate is inversely proportional to the current population count.
Now, an inverse proportion is a linear relation that is easy to describe, but is not necessarily true. We had to test if the model containing that assumption was realistic.
3. So, we set up a growth experiment. We put various algae in flasks and counted their growth everyday for up to 12 days and plotted the population as a function of time. We then compared the actual growth curve to a theoretical growth curve predicted by a carrying capacity model, defined below:
dQ/dt = Q0 x birthrate x (1 - Q/carrying capacity), where Q0 is the algal population count at time 0 (the initial count) and Q the population at any particular time.
The Q for various times was calculated using a numerical method implemented on Excel. Thus, there was a theoretical Q and its corresponding actual Q at every point in time measured.
4. How do we know the model works? Check how close the theoretical and actual Q values are. This was done by first fixing the carrying capacity as the estimated maximum value of Q (which can be seen by the plot of real Q's as they approach some kind of stable value), then trying different birthrates, then getting the sum of the squares of the difference between actual and theoretical Q's for all time points tested, then choosing the birthrate that gives the lowest sum of squares.
5. What happened was that in most cases--if not all--the selected birthrate gave theoretical values that very closely matched the actual values. Graphically, this means that the plot of the actual and theoretical growth curves coincided rather well. This result suggested that we may use the carrying capacity model to calculate intrinsic birthrate even when the actual birthrate changes with time.
6. Thus equipped with a reliable way to calculate birthrate, we proceeded by repeating the algal growth curve experiment with various concentrations of a detergent called sodium dodecyl sulfate, or SDS, added to the culture medium. Using the carrying capacity model, we were able to estimate birthrates for every flask in the experiment.
7. A look at the all these growth rates showed that when the SDS concentration was higher, the growth rates were lower. This result suggested that SDS concentration does bring down growth rate. We deduce from this that SDS is toxic to algae.
8. In short
a. We wanted to know if detergent lowers growth rate.
b. We needed a way to estimate growth rate given realistic conditions. That way was to use a model, the carrying capacity model, which included growth rate as a factor. We defined the model mathematically so that it could be tested in Excel. An experiment comparing actual population with theoretical population (the number predicted by the Excel model) showed that we can estimate growth rate rather nicely, as seen by the beautifully fitted curves.
c. Equipped with a reliable and realistic (and rather beautiful) model, we proceeded to estimate growth rate in cultures to which detergent was added. The results showed that growth rate does go down as detergent concentration goes up.
1. We set out to ask two questions regarding an important environmental issue. The BIG question was: "Are detergents toxic to plants?" We made an assumption that toxicity may be measured by its effects on birthrate. The more specific question, then, was "Do detergents in the water decrease the growth rate of algae?" Given that question, the best general strategy was to do a variation-type of experiment where we manipulate the concentration of detergent in water and then check for a co-variation in growthrate.
2. But, how do we measure growth rate? And then, what growth rate are we talking about: the intrinsic growth rate or the actual growth rate? In principle, measuring the intrinsic growth rate should be easy: Count the algae at some posterior day (say day 2), get the difference between that count and the previous day's count (day 1), and divide that difference by the previous day's count. The value we get should be the same for whatever pair of days we choose, if the growth of algae is EXPONENTIAL.
But are the actual algae cultures growing exponentially? Exponential growth is obtained under the very best conditions, i.e., practically unlimited space and resources, and no competition. A flask of algae, however, is a small world; so small that we may reasonably expect that as algae become many, their growth rate would decrease because of competition and rapid depletion of resources. Therefore, the growth rate would change rather quickly with time; that is, it will not be constant. The exponential model would be imprecise; it would be difficult for us to choose an appropriate anterior and posterior date to make the calculation.
So, it would seem that a CARRYING CAPACITY model is more appropriate to describe the real situation in the flask. But the model, like all models, requires some assumptions before it can be precisely defined in a form that can be tested. One assumption is that the actual growth rate is inversely proportional to the current population count.
Now, an inverse proportion is a linear relation that is easy to describe, but is not necessarily true. We had to test if the model containing that assumption was realistic.
3. So, we set up a growth experiment. We put various algae in flasks and counted their growth everyday for up to 12 days and plotted the population as a function of time. We then compared the actual growth curve to a theoretical growth curve predicted by a carrying capacity model, defined below:
dQ/dt = Q0 x birthrate x (1 - Q/carrying capacity), where Q0 is the algal population count at time 0 (the initial count) and Q the population at any particular time.
The Q for various times was calculated using a numerical method implemented on Excel. Thus, there was a theoretical Q and its corresponding actual Q at every point in time measured.
4. How do we know the model works? Check how close the theoretical and actual Q values are. This was done by first fixing the carrying capacity as the estimated maximum value of Q (which can be seen by the plot of real Q's as they approach some kind of stable value), then trying different birthrates, then getting the sum of the squares of the difference between actual and theoretical Q's for all time points tested, then choosing the birthrate that gives the lowest sum of squares.
5. What happened was that in most cases--if not all--the selected birthrate gave theoretical values that very closely matched the actual values. Graphically, this means that the plot of the actual and theoretical growth curves coincided rather well. This result suggested that we may use the carrying capacity model to calculate intrinsic birthrate even when the actual birthrate changes with time.
6. Thus equipped with a reliable way to calculate birthrate, we proceeded by repeating the algal growth curve experiment with various concentrations of a detergent called sodium dodecyl sulfate, or SDS, added to the culture medium. Using the carrying capacity model, we were able to estimate birthrates for every flask in the experiment.
7. A look at the all these growth rates showed that when the SDS concentration was higher, the growth rates were lower. This result suggested that SDS concentration does bring down growth rate. We deduce from this that SDS is toxic to algae.
8. In short
a. We wanted to know if detergent lowers growth rate.
b. We needed a way to estimate growth rate given realistic conditions. That way was to use a model, the carrying capacity model, which included growth rate as a factor. We defined the model mathematically so that it could be tested in Excel. An experiment comparing actual population with theoretical population (the number predicted by the Excel model) showed that we can estimate growth rate rather nicely, as seen by the beautifully fitted curves.
c. Equipped with a reliable and realistic (and rather beautiful) model, we proceeded to estimate growth rate in cultures to which detergent was added. The results showed that growth rate does go down as detergent concentration goes up.
Friday, April 25, 2008
EnviSci Class schedule summer 2007-2008
Boldfaced titles are laboratory sessions (8-10 am)
Non-boldfaced titles are lecture sessions (10-12 am)
Commoner 28-Apr
Growth curve model (exponential) 28-Apr
Lovelock 29-Apr
Growth curve model (w/ carrying capacity)29-Apr
Miller 30-Apr
Clemens 2-May
Analysis growth curv 2-May
Boulding 5-May
Set-up stress expt 5-May
Dillard 6-May
FIRST LONG EX 6-May
Hardin 7-May
Construction of mini earth 7-May
Leopold (Land Ethic) 8-May
Marsh 9-May
Analysis stress expt 9-May
McKibben 12-May
Set-up bioassay 12-May
Grumbine 13-May
SECOND LONG EX 13-May
Debate 1/Last day for submitting revisions 14-May
Spawning zebra fish/Construct filter 14-May
Debate 2 15-May
Collect eggs and grow 15-May
Debate 6 16-May
Analysis bioassay 16-May
Debate 3 19-May
Prove the filter works on the fish 19-May
Debate 4 20-May
Debate 5 21-May
Lab practical exam/Collect notebooks 21-May
Non-boldfaced titles are lecture sessions (10-12 am)
Commoner 28-Apr
Growth curve model (exponential) 28-Apr
Lovelock 29-Apr
Growth curve model (w/ carrying capacity)29-Apr
Miller 30-Apr
Clemens 2-May
Analysis growth curv 2-May
Boulding 5-May
Set-up stress expt 5-May
Dillard 6-May
FIRST LONG EX 6-May
Hardin 7-May
Construction of mini earth 7-May
Leopold (Land Ethic) 8-May
Marsh 9-May
Analysis stress expt 9-May
McKibben 12-May
Set-up bioassay 12-May
Grumbine 13-May
SECOND LONG EX 13-May
Debate 1/Last day for submitting revisions 14-May
Spawning zebra fish/Construct filter 14-May
Debate 2 15-May
Collect eggs and grow 15-May
Debate 6 16-May
Analysis bioassay 16-May
Debate 3 19-May
Prove the filter works on the fish 19-May
Debate 4 20-May
Debate 5 21-May
Lab practical exam/Collect notebooks 21-May
Wednesday, March 26, 2008
EnviSci summer 2008 announcement 27 March 08
I will go to UAP on the 18th of April. I'd like to tell you what to expect.
I will call 1-2 people at random (daily, henceforth) to make a report. Both on Descartes.
Reporter 1. Makes a critique of the chapter. The format is as follows:
I. Introduction (suggested topics)
1. What is the article about?
2. Why was it written?
3. What do we need to know to understand it? What is generally known about the subject? What special terms were used and what's their meaning?
4. Give a brif outline of what to expect.
II. Thesis. What is the author's thesis? Summarize his argument.
III. Proof. What proofs (data, evidence, examples) does the author present in support of his thesis?
IV. Objections and Response. Give at least one strong objection to the author and respond to it. Possible sources of objections include:
1. Author was misinformed about something.
2. Author did not include information that should have been used.
3. Author was illogical about something.
4. Author's treatment can be viewed in other ways
V. Conclusion. Summarize the author's point in the light of all preceding information.
Reporter 2. Should be prepared to moderate a discussion on any question from the end of the chapter.
PASSPORT: To qualify as a reporter, you must submit a written critique following the above format, 2 pages max, printed on bond paper, single side single space. If called and you are unable to present that paper, you can not report; you automatically get a ZERO, the equivalent of a long exam.
I shuffle the cards daily. This means you may be called several times or not at all during the term. I strongly advise you to write those papers everyday.
Thus, use your four-day cut between the 14th and 17th to do as much advanced work as you can.
Looking forward to meeting you all soon.
I will call 1-2 people at random (daily, henceforth) to make a report. Both on Descartes.
Reporter 1. Makes a critique of the chapter. The format is as follows:
I. Introduction (suggested topics)
1. What is the article about?
2. Why was it written?
3. What do we need to know to understand it? What is generally known about the subject? What special terms were used and what's their meaning?
4. Give a brif outline of what to expect.
II. Thesis. What is the author's thesis? Summarize his argument.
III. Proof. What proofs (data, evidence, examples) does the author present in support of his thesis?
IV. Objections and Response. Give at least one strong objection to the author and respond to it. Possible sources of objections include:
1. Author was misinformed about something.
2. Author did not include information that should have been used.
3. Author was illogical about something.
4. Author's treatment can be viewed in other ways
V. Conclusion. Summarize the author's point in the light of all preceding information.
Reporter 2. Should be prepared to moderate a discussion on any question from the end of the chapter.
PASSPORT: To qualify as a reporter, you must submit a written critique following the above format, 2 pages max, printed on bond paper, single side single space. If called and you are unable to present that paper, you can not report; you automatically get a ZERO, the equivalent of a long exam.
I shuffle the cards daily. This means you may be called several times or not at all during the term. I strongly advise you to write those papers everyday.
Thus, use your four-day cut between the 14th and 17th to do as much advanced work as you can.
Looking forward to meeting you all soon.
Monday, March 24, 2008
Environmental science readings for summer 2008
To my summer 2008 students.
These readings are available for photocopying. Make sure that at the start of the classes you all have these readings already. We will take them up in sequence, approximately two meetings per reading. I may add to them later on.
Thus, on the first day of our meeting, April 18, I expect an essay on Descartes and an intelligent discussion on him from the one who will be called (see my policies on essays). REMEMBER: this essay is long exam, and it is revisable. But failure to submit when called means an automatic zero from which there is no redemption! I will also give a quiz on Descartes.
Coordinate with Zoila Santos-Pilola, our secretary.
The debate sessions remain unmarked. So are the laboratory exercises.
Descartes, Rules for the direction of
Thomas, World’s biggest membrane
Tansley, The ecosystem
Vernadsky, The biosphere
Leopold, Odyssey
Commoner, The closing circle
Lovelock, The recognition of Gaia
Miller, Dimensions of deformity
Clemens, The climax concept
Boulding, Economics of spaceship
Dillard, Intricacy
Hardin, The tragedy of the commons
Leopold, The land ethic
Marsh, Man and nature
McKibben, The end of nature
Grumbine, The politics of wilderness
SciAm Oct 07, Conservation
These readings are available for photocopying. Make sure that at the start of the classes you all have these readings already. We will take them up in sequence, approximately two meetings per reading. I may add to them later on.
Thus, on the first day of our meeting, April 18, I expect an essay on Descartes and an intelligent discussion on him from the one who will be called (see my policies on essays). REMEMBER: this essay is long exam, and it is revisable. But failure to submit when called means an automatic zero from which there is no redemption! I will also give a quiz on Descartes.
Coordinate with Zoila Santos-Pilola, our secretary.
The debate sessions remain unmarked. So are the laboratory exercises.
Descartes, Rules for the direction of
Thomas, World’s biggest membrane
Tansley, The ecosystem
Vernadsky, The biosphere
Leopold, Odyssey
Commoner, The closing circle
Lovelock, The recognition of Gaia
Miller, Dimensions of deformity
Clemens, The climax concept
Boulding, Economics of spaceship
Dillard, Intricacy
Hardin, The tragedy of the commons
Leopold, The land ethic
Marsh, Man and nature
McKibben, The end of nature
Grumbine, The politics of wilderness
SciAm Oct 07, Conservation
Sunday, March 23, 2008
Policies, envisci and biology
Lecture policies
1) The grade in the course consists of 75% lecture and 25% lab grades.
2) The lecture grade is the average of 3 unit grades and the final exam.
a) The semester is divided into 3 units, each with a unit grade. The unit grade consists of the average of quizzes and at least one long exam or recitation/essay.
b) Quizzes, all objective tests such as crossword puzzles, are given everyday. The quizzes are the basis for attendance.
c) The long exam of each unit is a take-home essay test (objective test during summer term). Optional for those who were called for graded recitation or participated in a debate.
d) Graded recitation takes place almost everyday. The procedure is as follows:
i) The teacher will call 1-5 people AT RANDOM (except for debaters). When called, the student must submit an assigned essay (1 page 8.5x11” page single spaced 12-point font) of the correct format. This essay is revisable for as many times as time allows.
ii) An essay of the correct format has the following parts, clearly marked:
1. Introduction (I, 5 pts)
2. Thesis (II, 5 pts)
3. Proof (III, 5 pts)
4. Objection and Response (IV, 5 pts)
5. Conclusion (V, 5 pts)
iii) The person called will give a presentation on the assigned chapter or on the essay that he/she wrote.
iv) No essay, no recitation, zero. This has the weight of a long exam.
v) The only time you know in advance when you will speak is for debate.
vi) Bonus points are given to audience members who make an intervention, either by providing their own arguments or by asking questions.
vii) Since the cards are randomly shuffled everyday, it is possible for a student to be called for graded recitation several times per unit or not at all. One recitation exempts a student from taking the long exam for that unit; several recitations will be averaged with the quizzes. The final exam is a multiple-choice test covering all readings and discussions, with no preference for those taken up later compared to those taken up at the start of the semester.
1) The grade in the course consists of 75% lecture and 25% lab grades.
2) The lecture grade is the average of 3 unit grades and the final exam.
a) The semester is divided into 3 units, each with a unit grade. The unit grade consists of the average of quizzes and at least one long exam or recitation/essay.
b) Quizzes, all objective tests such as crossword puzzles, are given everyday. The quizzes are the basis for attendance.
c) The long exam of each unit is a take-home essay test (objective test during summer term). Optional for those who were called for graded recitation or participated in a debate.
d) Graded recitation takes place almost everyday. The procedure is as follows:
i) The teacher will call 1-5 people AT RANDOM (except for debaters). When called, the student must submit an assigned essay (1 page 8.5x11” page single spaced 12-point font) of the correct format. This essay is revisable for as many times as time allows.
ii) An essay of the correct format has the following parts, clearly marked:
1. Introduction (I, 5 pts)
2. Thesis (II, 5 pts)
3. Proof (III, 5 pts)
4. Objection and Response (IV, 5 pts)
5. Conclusion (V, 5 pts)
iii) The person called will give a presentation on the assigned chapter or on the essay that he/she wrote.
iv) No essay, no recitation, zero. This has the weight of a long exam.
v) The only time you know in advance when you will speak is for debate.
vi) Bonus points are given to audience members who make an intervention, either by providing their own arguments or by asking questions.
vii) Since the cards are randomly shuffled everyday, it is possible for a student to be called for graded recitation several times per unit or not at all. One recitation exempts a student from taking the long exam for that unit; several recitations will be averaged with the quizzes. The final exam is a multiple-choice test covering all readings and discussions, with no preference for those taken up later compared to those taken up at the start of the semester.
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