Lab: Stickleback Evolution

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Complete all the activities in this lab instruction packet: Lab 4: Stickleback Evolution, Part 2.  Work through the instruction packet step by step. Record your results in the worksheet as you progress through this instruction packet.

For any sections that request that you “take notes”, the notes should be in your own words summarizing information learned. You should not copy and paste information from the Internet including media and resources accessed in this lab. Directly copying and pasting information is considered plagiarism in this course.

Lab 4: Stickleback Evolution, Part 2

 

General Instructions

 

Be sure to read the general instructions from the Lessons portion of the class prior to completing this packet.

 

Remember, you are to upload this packet with your quiz for the week!

 

Background

In this experiment, you will analyze the pelvic structures of stickleback fish collected from two lakes around Cook Inlet, Alaska, to determine whether there are significant differences between the two populations. You will then use your data and information about the lakes to draw conclusions about the possible environmental factors affecting the evolution of pelvis morphology.

 

 

Specific Lab Instructions

 

Name:

Date:

 

Return to: The Virtual Stickleback Evolution Lab

Link: https://media.hhmi.org/biointeractive/vlabs/stickleback2/index.html?_ga=2.222191320.1578381481.1524156496-368479012.1521089692

 

You are going to perform Experiment 2 for the Stickleback lab this week.

 

Begin with Tutorial 2. When you are comfortable scoring a pelvis in fossil fish, you may move on (Note: it is a little more difficult in fossils than live fish, so you may want to spend a little time here).

 

1. What score would you assign to a fossil specimen that has only one pelvic spine visible?

2. A stickleback fossil may show no signs of pelvic structures. What are possible sources of error associated with scoring the pelvis of such a fossil as “absent”?

 

When you feel you have mastered scoring fossils, you may move on to Experiment 2.

1. In your own words describe the overall objective of Experiment 2 and explain what the data you collect will allow you to estimate.

 

2. What is one type of information that researchers can gain from studying fossils that they cannot obtain from living populations?

 

Lab 4: Stickleback Evolution, Part 2

 

Page 1 of 9

Begin the experiment in the window on the left. Complete Part 1: Preparing Fossils (click on the bench to get started).

 

3. You will collect data on pelvic structures using fossils from rock layers 2 and 5. Approximately how many years of deposition separate these two layers?

 

4. Which layer is older, 2 or 5? Explain your answer.

 

 

 

Complete Part 2 of the lab in the window on the left.

Score Your Fossils

 

 

5. Based on the pelvic phenotypes you measured, do the fossils in layer 2 differ from those in layer 5? Explain how.

 

6. After your collect data for the pelvic phenotype in layers 2 and 5, add your totals, and submit. As in lab 3, you may use the graph feature in the program as it works fine, or you can create your own Excel graph. Insert a screenshot here.

7. How do your data compare to those collected by Dr. Bell and colleagues?

 

8. Take the quiz. What can be inferred about the presence or absence of predatory fish when the Truckee Formation was a lake? Describe the evidence.

 

9. After completing the quiz, click on Experiment 2 Analysis.

10.

11. Complete the tables below as you perform the rate calculations. (The link to the instructions is very helpful.)

Sample Layer Number of Fish with a Complete Pelvis Total Number of Fish Sampled Relative Frequency of Complete Pelvis Trait in Population Sampled
1

2

3

4

5

6

 

Time Decrease in Percentage of Complete Pelvis Trait per Thousand Years (Rate of Change)
First 3,000 years (Layer 1 to Layer 2)

Next 3,000 years (Layer 2 to Layer 3)

Next 3,000 years (Layer 3 to Layer 4)

Next 3,000 years (Layer 4 to Layer 5)

Next 3,000 years (Layer 5 to Layer 6)

Total 15,000 years (Layer 1 to Layer 6)

 

 

1. What does it mean when the rate of change is a negative number?

 

2. Complete the Analysis Quiz.

3. Describe the trend in the data over time.

 

4. Why is it important to calculate the rate of change over time?

 

5.

6. In what way is the change in the complete pelvis phenotype in the fossils from the Nevada lakebed similar to what might have occurred in Bear Paw Lake from Experiment 1?

 

 

 

 

Adapted from: Brokaw, A. (2013). Stickleback Evolution Virtual Lab. HHMI Biointeractive Teaching Materials.

 
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Biology Experiement Homework2

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Transcription and Translation – Introduction

Be sure that you have read over our online lecture this unit on DNA and read pp 177 to 181 in your book before starting. DNA can be a complex concept to grasp, and there is a lot of terminology to keep straight. These first two exercises will focus on transcription and translation, the two processes responsible for taking the information embedded in our DNA and using it to create a protein.

There are segments in our DNA called genes that code for the proteins needed to carry out cellular functions. These genes are a sequence of nucleotides; adenine (A), thymine (T), cytosine (C) and guanine (G) and the specific sequence of these nucleotides is what conveys the information needed to produce a given protein. In humans, the smallest gene is 252 nucleotides long, whereas the largest is more than 2 million nucleotides long! The genetic code is used to decipher the sequence of nucleotides into a sequence of amino acids. The code uses a series of three-nucleotide sequences called codons. Each different codon codes for an amino acid and it is this specific sequence of amino acids that determines what protein is formed.

DNA is found in our nucleus, yet our proteins are synthesized in the cytoplasm. A gene must first be transcribed into a form that can leave the nucleus. Transcription is the process in which a sequence of DNA used to synthesize a complementary strand of messenger RNA (mRNA). This mRNA acts a template and is used to translate the original DNA sequence into a protein, based on the information in its codons and the Genetic Code.

For example, the DNA sequence ATG-CGT-TAG-CGT-ATTC would be transcribed into the mRNA sequence UAC-GCA-AUC-GCA-UAA. Then, using Fig 10.11 on p 180 in your book, you can determine that this mRNA would be translated into the amino acid sequence Tyrosine-Alanine-Isoleucine-Alanine-Stop.

In Exercise 1, you will have the opportunity to demonstrate your understanding of transcription and translation. You will be using the following website; be sure that you are able to access and use the site:

University of Utah. No date. Transcription and Translation

http://learn.genetics.utah.edu/content/molecules/transcribe/ (Links to an external site.)

In Exercise 2, you will apply what you learned in Exercise 1 and evaluate the effect that different types of mutations have on the outcome of transcription and translation. You’ll want to review these mutations on pp 186-187 of your book and in our online lecture on DNA before starting. You will be using the following website; be sure that you are able to access and use the site:

McGraw Hill. No date. Virtual Lab: DNA and Genes

http://www.glencoe.com/sites/common_assets/advanced_placement/mader10e/virtual_labs_2K8/labs/BL_04/index.html  (Links to an external site.)

Finally, in Exercise 3, you will complete a series of calculations to determine the probability of a mutation occurring within a gene that results in a change in protein structure.

UNIT 5 EXPERIMENT ANSWER SHEET Please submit to the UNIT 5 Experiment SUBMISSION LINK no later than Sunday midnight.

SUMMARY OF ACTIVITIES FOR UNIT 1 EXPERIMENT ASSIGNMENT

· Experiment 5 Exercise 1 – Transcription and Translation

· Experiment 5 Exercise 2 – Translation and Mutations

· Experiment 5 Exercise 3 – Mutation Rates

 

Experiment 5 Exercise 1: Transcription and Translation

This exercise will ensure that you have a good understanding of the processes of transcription and translation. To get started, go to the following website:

University of Utah. No date. Transcription and Translation

http://learn.genetics.utah.edu/content/molecules/transcribe/

 

Procedure

A. Read over the information on the first screen and click on the click here to begin to proceed.

B. On the next screen transcribe the give DNA strand.

Table 1. Transcription of the DNA sequence (1.5 pts).

RNA                                            

 

C. Once you have finished transcribing the DNA, you will then translate the RNA sequence. Follow the instructions on the screen.

Table 2. Translation (1.5 pts)

  Codon Amino Acid
Codon 1    
Codon 2    
Codon 3    
Codon 4    
Codon 5    
Codon 6    

 

 

Experiment 5 Exercise 2: Translation and Mutations

Now that you know how to transcribe DNA and translate the mRNA message, let’s take a look at the different types of mutations that might disrupt this process. Review pp 186-187 in your book before beginning. In this exercise you will need to use the following website:

McGraw Hill. No date. Virtual Lab: DNA and Genes http://www.glencoe.com/sites/common_assets/advanced_placement/mader10e/virtual_labs_2K8/labs/BL_04/index.html

Read over the information in the Mutation Guide and close it when you are done. Note that there are several pages; you will need to click on Next to proceed through the Guide. If you want to review this material, you can click on the Mutation Guide button. You are going to run a series of simulations in which an mRNA sequence and its corresponding amino acid sequence is provided. You will be told what type of mutation you will you apply (= Mutation Rule) and you will have to determine the new, mutated mRNA and the resulting protein sequence.

Procedure

A. Click on the Mutate button to get started.

B. Find the Mutation Rule (lower left corner) and enter it into Table 3 below (see the Example provided).

C. Drag the appropriate nucleotides to build the new, Mutated mRNA sequence. If you make a mistake building the new mRNA sequence, drag the correct nucleotide and place it on top of the incorrect one (you cannot actually remove a nucleotide).

D. Once you have generated your Mutated mRNA sequence, you now need to build your Mutated amino acid sequence by matching the appropriate amino acid with each codon. Click on Genetic Code Chart to see the code or you can use Figure 10.11 on p 160 in your book.

NOTE: If you add a STOP codon, do NOT add any more amino acids after it!

 

E. Once you have finished, click on the Check button. If you are correct, then continue with Step F. If you had errors, you will have to Reset the simulation and start over with Step A. Here is what the results look like for the example provided:

F. When you have been successful, enter the Original mRNA sequence and the Original amino acid sequence in the Table below. Then enter the Mutated mRNA and Mutated protein sequence.

G. Click on Reset and repeat Steps A through F four more times so that you end up with FIVE replicates. Do not reuse the same Mutation Rule and do not use the rule used in the example (“the 4th A becomes a C”). If you get the same Mutation rule twice, Reset the simulation and run again.

Do NOT use the same Mutation rule as shown in the example and do NOT use the same Mutation Rule twice!

Table 3. Mutation rules, mRNA sequences and amino acid sequences (10 pts).

Rep Mutation Rule and Sequences
E

X

A

M

P

L

E

 Mutation rule: The 4th A becomes a C
  Original mRNA sequence AUG CAC ACG GUG CGA GGG AGU CUG
  Original amino acid sequence Met (Start) – His – Thr – Val – Arg – Gly – Ser – Leu
  Mutated mRNA sequence AUG CAC ACG GUG CGC GGG AGU CUG
  Mutated amino acid sequence Met (Start) – His – Thr – Val – Arg – Gly – Ser – Leu
  Consequence Substitution appears to have had no effect; Arg Arg
1 Mutation rule:
  Original mRNA sequence  
  Original amino acid sequence  
  Mutated mRNA sequence  
  Mutated amino acid sequence  
  Consequence  
2 Mutation rule:
  Original mRNA sequence  
  Original amino acid sequence  
  Mutated mRNA sequence  
  Mutated amino acid sequence  
  Consequence  
3 Mutation rule:
  Original mRNA sequence  
  Original amino acid sequence  
  Mutated mRNA sequence  
  Mutated amino acid sequence  
  Consequence  
4 Mutation rule:
  Original mRNA sequence  
  Original amino acid sequence  
  Mutated mRNA sequence  
  Mutated amino acid sequence  
  Consequence  
5 Mutation rule:
  Original mRNA sequence  
  Original amino acid sequence  
  Mutated mRNA sequence  
  Mutated amino acid sequence  
  Consequence  

 

Questions

1. What is a silent mutation? Did you see any examples of this in your mutations above? If so, which mutation rule(s) generated it? Cite your sources (2 pts).

 

2. What is a missense mutation and how does it differ from a nonsense mutation? Did you see examples of either of these types of mutation and if so, which mutation rule(s) generated it? Cite your sources (2 pts).

3. What is a frame-shift mutation and why are they so damaging? Did you see any examples of this in your mutations above? If so, which mutation rule(s) generated it? Cite your sources (2 pts).

 

4. Find a genetic disorder that develops as a result of one of the types of genetic mutations we have examined in this exercise. Identify the disorder and briefly describe the mutation responsible. Cite your sources (3 pts).

 

 

Experiment 5 Exercise 3: Mutation Rates

We learned in our second exercise that not all mutations have an observable effect. Yet the risk of a mutation being damaging is fairly significant, so it is important to understand the probability of them occurring. In this exercise, we are going to calculate the probability of a mutational event within a gene. You are given the necessary information below to complete the calculations. Do not let them overwhelm you; this is simple math, so think things through.

Assume that:

· there are approximately 3,000,000,000 base pairs in the mammalian genome (genes constitute only a small portion of this total)

· there are approximately 10,000 genes in the mammalian genome

· a single gene averages about 10,000 base pairs in size

 

Questions

1. Based on the assumptions above, in the mammalian genome, how many total base pairs are in all the mammalian genes? Show your math (2 pts).

2. What percentage (%) of the total genome does this represent? Show your math (2 pts).

 

3. What is the chance (%) that a random mutation will occur in any given gene? Show your math (2 pts).

 

4. Only 1 out of 3 mutations that occur in a gene result in a change to the protein structure. What is the probability that a random mutation will change the structure of a protein? Show your math (2 pts).

 

UNIT 1 Experiment Grading Rubric

Component Expectation Points
Experiment 5 Exercise 1 Demonstrates an understanding of the process of transcription and translation (Table 1 and 2). 3 pts
Experiment 5 Exercise 2 Correctly implements the proper mutation and transcribes the mRNA correctly (Table 3). 10 pts
  Demonstrates an understanding of the different types of mutations and their consequences (Questions 1-4). 9 pts
Experiment 5 Exercise 3 Correctly calculates the necessary information (Questions 1-4). 8 pts
TOTAL   30 pts

 

 

 

1. Explain the four roles that DNA plays in cells? How are these roles influenced by DNA’s structure? Be sure you demonstrate your understanding of DNA’s structure in your answer.

 

Citation(s):

 

2. Match the terms with the most suitable description.     _____ genetic code             a.  Examples of RNA processing     _____ promoter                   b. Sequence of three nucleotides that code for an amino acid.     _____ exon                          c. Location on DNA where RNA polymerase attaches.     _____ intron                        d. Sequence of three nucleotides that is complementary to a codon triplet.     _____ anticodon                  e. Portion of a gene that is excised from the RNA transcript.      _____ codon                        f.  Rules that convert a nucleotide sequence into a protein.     _____ cap and tail               g. Parts of a gene that are expressed.

3. Briefly explain the differences among messenger RNA, transfer RNA and ribosomal RNA in terms of the roles they play in transcription and translation and where they are found in the cell.

 

Citation(s):

 

4. Using the genetic code table (Fig 10.11 on p 180), take the following DNA sequence and complete the following. Note that the mRNA is generated from the complementary DNA strand.                                           T A C C C C A T G T A A C A T A C C A C T

Complementary DNA strand _______________________________________________

mRNA strand ___________________________________________________________

Amino acid sequence _____________________________________________________

 

5. Part of the coding sequence of a gene produces an mRNA sequence of  A U G A A G G C U C C U C C A A G C G G C

What is the DNA sequence __________________________________________________

What is the amino acid sequence _____________________________________________

6. Review pp 178-185 in your book and view the following animation. Then complete the following table. You may need to watch it the video more than once to catch the details.

Genome British Columbia. Gene Expression. 2007. Web. 25 July 2016. https://www.youtube.com/watch?v=OEWOZS_JTgk (Links to an external site.) undefined

Question Transcription Translation
What is it, in brief?    
Where does it occur in the cell?    
What is the product?    
Describe how the product is modified to reach its final form.    

Citation(s):

 

Updated April 2015

 
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Case 6-1: An Adolescent Couple with HIV

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Discussion Post

—Word Count Is Your Discretion for All Questions Except Question 6 750 Words Minimum!!!

—MLA Format

— Cite All Sources

— Due 2pm American/ New York Time

— 2/14/18

**Read Case Study 1 Attached & Answer Question 1**

Case 6-1: An Adolescent Couple with HIV

Question 1: “You are the nurse in the clinic on the day Alexa finds out she has HIV. She remains in the clinic for more than an hour with you while you try to support and console her. You have had formal HIV counseling training, so you apply your skills as you communicate with her. Several weeks later, after Alexia is more composed and has had time to think more about her situation, she drops by the clinic and wants to talk with you on a more personal basis. She needs comforting. What approaches will you use with Alexa? Please explore how to use and apply the nursing ethical competencies to help Alexa. Be specific with your approaches and rationales. You can approach this issue keeping in mind the three key ethical principles of autonomy, beneficience and nonmaleficense as they relate to your nursing interventions.

** Read Case Study 2 Attached & Answer Question 2 **

Question 2: CBRT Case Study Attached. Use article to answer questions below

1. Phosgene exposure causes inflammation and pulmonary edema that is deleterious to the function of the lungs. (a) What are the three physical factors that influence pulmonary ventilation? How would each of these factors be affected by inflammation and edema?

2. After exposure to phosgene gas, the partial pressures of both O2 and CO2 would be altered in the blood and tissues, because the mechanism for moving these gases in and out of the body has been compromised. After severe exposure to phosgene, what would you expect to find if you measured the partial pressure of oxygen (PO2) and carbon dioxide (PCO2) in the alveoli, the blood plasma, and the cells of the tissues?

3. The transport of oxygen and carbon dioxide in the blood is critical for survival. The victims with the most severe symptoms would need mechanical ventilation to overcome the inability of their respiratory systems to maintain normal blood levels of oxygen and carbon dioxide. Phosgene gas would reduce the amount of oxygen available for transport to the tissues. In addition, the metabolic waste product carbon dioxide is transported by three mechanisms back to the alveoli in the blood. Here carbon dioxide crosses the respiratory membrane, driven by a pressure gradient that favors its exit via the lungs during exhalation. By knowing which mechanism transports the most CO2, predict what would happen to the blood pH if the CO2 level dramatically increased?

** Read Below & Answer Question 3**

Question 3: Give a brief description of Botox & briefly describes how it affects the nervous system and action potential conduction. You should have a minimum of 2 academically appropriate resources.

** Read Below & Answer Question 4 I Attached Chapters**

Question 4: Please read Controversy 13 in your text, about Childhood Obesity and Early Chronic Diseases. As with many public health concerns, there is a controversy around personal responsibility and environmental influence. This conflict is further complicated when it involves children. Discuss what individuals, groups, or agencies you think are responsible for addressing childhood obesity? Please propose two to three solutions to address this concern and provide evidence to support your ideas.

** Read Below & Answer Question 5**

Question 5: Please read the following scenario and submit a report with a response to each of the associated questions. Cite sources in APA style.

Mini Case Study of Betsy’s Bones

Betsy is a 72-year-old retired teacher who lives alone. She used to love gardening, but since moving to a condo, doesn’t get much time outside, and spends most of her days reading or talking on the phone. She presents to her doctor complaining of right leg pain and muscle weakness. Her laboratory results showed deficient vitamin D and reduced bone density, and a diet recall included:

• Breakfast: two hard-boiled eggs, 1 whole grapefruit with 1 tsp sugar, 12 oz. black coffee

• Lunch: cucumber sandwich (made with a ½ cup of sliced cucumber, 2 slices white bread, and 1 T mayonnaise), 1 oz. potato chips, 16 oz. unsweetened iced tea

• Dinner: pasta (1 c.) with meatless marinara sauce (1/2 c.), small white roll, 1 glass red wine, fun-size Milky Way.

Betsy is 5’4” and weighs 126# (57kg). She says she loves to cook, but since it’s just her, she usually just prepares something quick and easy. Every Sunday she goes to church and to the grocery store, but otherwise, she doesn’t leave the house much.

1. Estimate how much protein Betsy is getting. How much does she need? Is her intake adequate? What recommendations do you have regarding Betsy’s protein intake?

2. What about Betsy’ fluid intake? Is she getting enough water? What are potential consequences of not taking in enough fluid?

3. Her doctor recommended a vitamin D supplement. What other ways can Betsy improve her vitamin D status? List some foods that are good sources of vitamin D.

4. Betsy’s mom had osteoporosis and she’s concerned about developing it too. What steps can Betsy take to maintain her bone health? Are there specific nutrients other than vitamin D and calcium that are important to bone health?

5. Why is vitamin D deficiency more common in the elderly?

** Read Below & Answer Question 6**

Question 1: You are required to post 750-word summary of a personal response to a attached article (MATERNAL-FETAL CONFLICT). The summary should reflect self-awareness and critical thinking regarding why you chose both the article and the subject matter. Validate your opinion with references to the code of ethics. Articles and references used in researching the topic summary must be cited using proper APA format.

* Provide some background describing it and why it is timely and worth consideration.

* What are the pro and con arguments about the problem? Refer to ethical concepts, theories and principles in your book.

* What is your position on this problem and why? How do you think it could be resolved?

.

** View the Video Below & Answer Question 7**

https://www.youtube.com/watch?v=gE4ef0yQZRU&feature=youtu.be

Question 7: Reflection: After viewing the “Unusual Support Group” material, why is it that infection rates went up AFTER better sanitation? If Polio had infected the human population for centuries and only a small percentage has long-lasting damage, why were we so determined to “fight” this infection and eradicate it?

 
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Lab 12 Model Ecosystems Lab Activity

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Lab 12 Model Ecosystems Lab Activity

 

Complete your answers in the spaces provided. USE YOUR OWN WORDS – Yes even for definitions! Remember to add your last name and first initial to the file name prior to saving and submitting your completed assignment through Canvas.

 

The lab website has post lab questions – these are not necessary – you only have to complete the questions in this lab assignment document.

 

Use your textbook, notes and this website to answer the pre lab questions. http://www.vtaide.com/png/foodchains.htm http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/F/FoodChains.html http://www.mbgnet.net/

 

 

 

Pre Lab Questions:

 

1. What is the ultimate source of energy for all organisms on this planet?

 

 

 

 

2. List the biomes of the Earth.

 

 

 

 

 

 

 

 

 

 

 

3. What biome do we live in here in Philadelphia?

 

 

 

 

4. What attributes define a biome?

 

 

 

 

Click on the link below to access the online lab. http://www.mhhe.com/biosci/genbio/virtual_labs_2K8/pages/ModelEcosystems.html

 

Download and print the instructions for reference as you work through the lab. As you work through the lab fill in the table below. Use this information to answer the questions that follow contained in this document.

 

5. Complete all five ecosystems and record your data in Table 1. The different ecosystems are listed across the top. Fill in the data for each trophic level for each ecosystem. For the numbers click on the [Pyramid of Numbers] button. Next click on the [Pyramid of Energy] button. Calculate the Energy Conversion Efficiency Ratio (ECE) by dividing the higher trophic level energy by the energy one trophic level down.

 

List the organisms by name. Provide the number of organisms present. Provide the amount of energy present. Calculate the ECE value. This value will be a decimal value. There is no ECE calculation for producers as you would have to divide the producer energy by the amount of energy provided by the sun. We don’t have that value. I have done the first column for you. :)

 

If you have any organisms out of place in the pyramid you will not be able to get the numbers you need to complete the calculations. You need to move the various organisms to their correct positions in order to continue.

 

Table 1

  Deciduous

Forest

 Hot Desert Grassland Antarctic

Ocean Shore

 Freshwater

Lake
Producers

Organisms

Present

 Deciduous

trees ferns wildflowers berry bushes Grasses

        
Energy: 6011        
Numbers: 7996        
           
First Order

Heterotrophs Organisms Present

 Chipmunks

Chikadees Insects Rabbits Deer

        
Energy: 623        
Numbers: 4559        
E.C.E.*: .103 (A)        
           
Second Order

Heterotrophs Organisms Present

 Snakes

Woodpeckers

Opossum

Fox Owls Toads Frogs

        
Energy: 61        
Numbers: 1418        

 

 

E.C.E.*: .097 (B)        
           
Third Order

Heterotrophs Organisms Present

 Wolves

Hawks

        
Energy: 6        
Numbers: 50        
E.C.E.*: .098 (C)        

 

Just so you know exactly how to calculate the ECE

A = 623/6011 = .103

B = 61/623 = .097

C = 6/61 = .098

 

Post Lab Questions

 

6. What is the relationship of numbers to energy as you go up the trophic levels?

 

 

 

 

 

 

7. From the ecosystems you studied in this lab, which one is the most efficient? Explain how you determined your answer.

 

 

 

 

 

 

 

 

 

 

 

8. What would happen to an ecosystem without decomposers?

 

 

 

 

 

 

 

9. From the ecosystems you studied in this lab, which one is the most productive? (This cannot be the same as question 7) Explain how you determined your answer.

 
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