Biology Question

Part A: Kinematics

Task 1: Calculate functional hip joint centre using optimisation method. Use the optimal hip centre location

algorithm of Gamage and Lasenby (2002) (use Jupyter notebook from Tutorial 1) to calculate a functional hip

joint centre for the left and right hip joint using the C3D trials provided (jw_hip_lstar1.c3d and

jw_hip_rstar1.c3d)

. You will need to export the marker trajectories as a .trc file using Mokka (double check to

make sure the marker labels match what is in your python script…they are case sensitive!)

. Filter your marker

data using a low

pass Butterworth filter with a cut

off frequency that you think is reasonable. Determine the x,

y, z locations of the left and right hip joint centre in the pelvis coordinate system (refer to the

ISB standard hip

CS.

pdf

document)

.

Task 2: Calculate hip joint centre using regression equations. Tylkowski et al. (1982) published a paper with an

updated set of parameters of a linear regression to estimate the hip joint centre, based upon the distance (d)

between the left and right superior iliac spines (LASIS and RASIS, respectively)

. The parameters describe the

position of the hip joint centre relative to the ASIS marker, as shown in Figure 1 below. Use the static standing

trial (jw_staticfor.c3d) to obtain the anatomical landmarks. Determine the x, y, z locations of the left and right

hip joint centre in the pelvis coordinate system.

Reference: Tylkowski, C. M.

, Simon, S. R.

, & Mansour, J. M. (1982)

. The Frank Stinchfield Award Paper. Internal rotation gait in spastic

cerebral palsy

. The Hip, 89

125.

Figure 1. Tylkowski et al. (1982) regression parameters to predict the hip joint centre of an adult pelvis, given the

distance, d, between the anterior superior iliac spine landmarks. The blue points indicate the predicted hip joint

centre and red points are the actual hip centre from a segmented CT scan.

Task 3: Scale the generic OpenSim gait model to match the experimental markers. Open the

gait2354_simbody

.osim model file and attach the markers from the Grand Knee Challenge marker set

(GrandKneeMarkerSet.xml) (ignore the upper limb markers)

. Use the experimental markers from the static trial

(jw_staticfor.c3d) to scale the pelvis, thigh, shank, and foot segments of the OpenSim model. Save the scaled

.osim file and then search in the model file for the x, y, z location of the left and right hip joint centres. Record

these values with respect to the pelvis coordinate system.

Task 4: Add two more dofs to the knee model. The default knee in this model has only one degree of freedom

(flexion

extension)

. If we want to calculate the net joint moment about other axes (abduction

adduction or

internal

external rotation) we will have to include these DOFs in the model. Modify the scaled model from Task

3 using Notepad++ to include knee internal

external rotation and adduction

abduction (as shown during Tutorial

4)

. Place appropriate constraints on these new DOFs.

Task 5: Perform inverse kinematics (IK)

. Perform IK on the normal over ground walking trial (jw_ngait_og1.c3d)

using the scaled model from Task 3. You will need to ensure that the y

axis is vertical, so after you export the .trc

file from Mokka, use the python script provided from Tutorial 3 to rotate the marker data. You can use equal

weighting for all markers when you generate the IK solution. Save the resulting .mot file, as you will need to

generate some graphs from these generalized coordinates.

ax

= 0.22

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Biology Question

In this assessment, you will categorize a group of animals by two forms of classification: phylogeny (cladistics) and Linnaean taxonomy. For phylogeny, you will create a cladogram for your groups of animals. For Linnaean classification, you will create a taxonomy chart or concept map that categorizes your species by taxa. Select one of the two groups of animals listed below for your project.

  • Bird Group: Blue Jay, robin, cardinal, canary, and pelican
  • Insect Group: African honeybee, grasshopper, black widow spider, mosquito, and yellow jacket

Make sure the following items are included in your classification project:

Part A: Taxonomy Chart

  • Organize your five animals by kingdom, phylum, class, order, family, genus, and species within your chart. This information can be accessed in a Web search of your animal.
  • You may choose any format you wish for the taxonomy chart. It can follow the student example provided but does not have to replicate it exactly. Concept maps or circle diagrams are also appropriate for organizing your animals.

Part B: The Cladogram

  • Organize your five animals by their evolutionary relationships with one another. This information can be accessed in a web search about your animal. (Hint: Review evolutionary relationships, ancestral traits, and derived traits from the lesson.)
  • There is no wrong way to make a cladogram. As long as you can justify species location on the cladogram, your chart will be correct. Your cladogram does not have to match the student example.
  • Remember, no matter what the relationship is between the groups depicted in a cladogram, there will always be one less clade than the number of groups.

Part C: Summary Questions
Answer the questions below.

  • Describe the physical traits your animals had in common with one another in your taxonomy chart. Break down your descriptions by taxa. (Example: All animals in the class Reptilia breathe air, lay shelled eggs, and have skin covered in scales.)
  • Explain the positions of each species in your cladogram. Why did you place each of your animals in those positions?
  • Which was more difficult to make, the Linnaean taxonomy chart or the cladogram? Explain your answer.

You can create your diagram and chart in any of the following ways:

  • Use any word processor program
  • Use any drawing or presentation program.

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Biology Question

Reading Homework 1: The Biosphere & Population EcologY

  1. Summarize the account of the 1950s debate about DDT in the environment.

  2. Explain how organisms adapt to abiotic and biotic factors.

  3. Describe the effect of our local mountains on precipitation. What is meant by the phrase “rain shadow?”

  4. What do the variables referred to as density and dispersion patters attempt to quantify?

  5. How do limiting factors relate to the logistic population growth model?

Reading Homework 2:

Community Ecology

  1. Name five types of interspecific interactions, note the effect (+/-) on each species involved, and provide an example for each type of interaction.
  2. Describe coevolution using an example.
  3. Explain the ecological process yielding the pattern shown in Figure 36.6.
  4. What do food webs and food chains have to do with each other?
  5. List and describe three terrestrial biomes and three aquatic biomes.

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Review Homework 1: Biosphere & Population Ecology

  1. Draw a diagram that depicts some effects of intense solar radiation near the equator on global patterns of rainfall and winds. Upload your drawing to canvas for this portion of the assignment.
  2. How do ocean currents affect the climate? Provide an example.
  3. Draw and label a graph that depicts the boom and bust cycle that often happens as a result of predator and prey interactions. Provide a caption to your diagram that explains what it is showing. Upload your drawing to canvas for this portion of the assignment.
  4. Draw and label a diagram for both exponential and logistic growth. Provide a caption explaining the circumstances depicted in each of these growth

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Review Homework 2: Community Ecology

  1. 1Read section 37.1 in your text, watch the Yellowstone wolves video, and read the briefing about the effect of the wolves on the Yellowstone ecosystem. Write your own paragraph (5-6 sentences at least) describing the Yellowstone ecological community before and after the wolves were introduced.

  2. Read section 37.3 in your text again. Identify and describe one example of interspecific competition, and explain how it affects the Yellowstone community.

  3. Read section 37.4 in your text again. Identify and describe one example of mutualism, and explain how it affects the Yellowstone community.

  4. Read section 37.5 in your text again. Identify and describe one example of predation, and explain how it affects the Yellowstone community.

  5. Read section 37.6 in your text again. Identify and describe one example of herbivory, and explain how it affects the Yellowstone ecosystem.

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Review Homework 10: Evolution

  1. What is the biological species concept?
  2. List and explain some examples of prezygotic and postzygotic species barriers.
  3. What is allopatric speciation?
  4. Why are islands considered showcases of speciation?
  5. What is meant by the term punctuated equilibrium?

Reading Homework 10: Evolution

  1. Explain the significance of fossils as evidence for evolution. What is the relevance of transitional forms?
  2. What are homologies? Why are they significant evidence for evolution?
  3. Why did Darwin breed fancy pigeons?
  4. Why do we say that evolution occurs within populations?
  5. Describe the constraints of natural selection.

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Biology Question

When you are ready to make a behavior change, set a goal to improve your likelihood of success! SMART goals include five important characteristics:

  • Specific: Rather than trying to completely overhaul your lifestyle, focus on just one behavior at a time.
  • Measurable: Include a definite way to track your progress.
  • Achievable: To avoid discouragement, make sure the goal is realistic for you.
  • Relevant: Choose a goal that is worthwhile and in alignment with what is going on in your life right now.
  • Timed: Set a due date.

As a guide for format, here is a SMART goal related to energy balance:

By March 1st, I will increase my physical activity to at least 30 minutes per day, 5 days per week. I will do this by meeting with a friend to walk around campus before dinner. I will track my progress using a FitBit.

You can see that this goal is specific (focuses on one behavior change), measurable (minutes of physical activity per day), achievable (it would be feasible to walk for 30 minutes on most days of the week), relevant (it would help with weight management, reduce stress, and improve my metabolic health), and is timed (due date is March 1st).

After you have analyzed your dietary data, identify an area related to energy balance that could use some improvement. For example, many students experience some weight gain during their college years. Write a SMART goal for yourself that would modify your energy intake, energy expenditure, or both. Make it relevant for you.

1. SPECIFIC: What is one specific behavior that you would like to change related to energy balance (i.e., calories in versus calories out)?

2. MEASURABLE: How could you measure this behavior?

3. ACHIEVABLE: What are some practical strategies you will use to achieve your goal?

4. RELEVANT: Describe how this behavior change goal is worthwhile and in alignment with what is going on in your life right now.

5. TIMED: By what date would you like to achieve your behavior change?

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Biology Question

Look carefully at the following 6 “make-believe organisms”. Try to classify them into four different groups.

What one simple observational criterion could you use?

Question 1. Write one obvious characteristic of body form which you could use to “slot” the six different animals above into 4 groups. (The characteristic should have 4 types or variations.)

Question 2. Give a descriptive name to each of your four groups. List the different “animals” above (A-F) which would fall into each of your four groups:

Descriptive Name of Group

Animals in Group

Question 3. Give three examples of organisms that exhibit bilateral symmetry.

  1. _____________________________________________________
  2. _____________________________________________________
  3. _____________________________________________________

Question 4. Give 4 examples of organisms with radial symmetry.

  1. _____________________________________________________
  2. _____________________________________________________
  3. _____________________________________________________
  4. _____________________________________________________

Which echinoderm is it most difficult to identify radial symmetry?

_____________________________________________________

Question 5. Observe the sponges and draw two examples below.

Question 6. How are the segments in the crayfish modified?

Question 7. Give one example of an organism with an exoskeleton.

Question 8. Give one example of an organism with an endoskeleton.

Question 9. Give one example of an organism with a hydrostatic skeleton.

Question 10. Give two examples of animals with 2 pairs of locomotive appendages.

Question 11. Give two examples of animals with 3 pairs of locomotive appendages.

Question 12. Give two examples of animals with 4 pairs of locomotive appendages.

Question 13. What organism is shown with a complete digestive tract?

Question 14. What type of digestive tract do humans have?

Question 15. Draw a simple grasshopper, and draw and label its spiracles.

Your 5 assigned unknown information below

Phylum Subphylum Superclass Class Order Common example

___ .

___ .

___ .

___.

___ .

TABLE 2

Ecological Classification Compared with Evolutionary Classification:

Ten Common Chaparral Animals

Procedure:

On the table marked “Chaparral Animals” you will find ten numbered animal specimens. Identify each animal to Phylum and Class (if applicable) and record your findings in the table below. Next, read the natural history card that goes with each animal and complete the table using your knowledge about ecological classification which you learned on the previous page.

specimen

number

Phylum and other

classification if

applicable

common

name

Habitat

requirements:

where does it live?

What does this

animal eat?

Ecological

Classification

1

Fence Lizard

2

Ground Squirrel

3

Darkling

Beetle

4

Scrub

Jay

5

Earthworm

6

Termite

7

Slug or

Snail

8

Bat

9

Gopher

Snake

10

Tick

  1. Review Exercise

Learn to recognize the names of animal taxonomic groups and also their common names. The following exercises will help you:

  1. List the names of the 9 animal phyla you have observed today, along with common names of animals you observed:

Phylum Name: Common Name:

  1. You were asked to learn 5 major groups (Classes) in the Phylum Arthropoda. List these 5 groups and describe the unique characteristics of each.

Your instructor may ask you to identify these groups on a quiz, so you must be able to distinguish one group from another.

Class Name: Identifying characteristics:

1)

2)

3)

4)

5)

  1. You were asked to learn 7 major groups (6 Classes and 1 Superclass) in the Phylum Chordata.

List these 7 groups below and describe the unique characteristics of each.

Your instructor may ask you to identify these groups on a quiz so you must be able to distinguish one group from another.

Class Name: Identifying characteristics:

1) Superclass:

2) Class

3) Class

4) Class

5) Class

6) Class

7) Class

  1. The various limb forms of the Superclass Tetrapoda are a good example of adaptive radiation.
  2. Define adaptive radiation:
  1. List 4 examples of tetrapods with different limb shapes and decide whether these limbs are homologous or analogous. Explain why.
  1. Assuming that adaptive radiation is the result of natural selection, suggest a selective agent which may have been responsible for the different limb shapes.
  1. Complete the following “Evolutionary tree” (cladogram) for the 9 most common animal phyla you were asked to learn. Be able to place the phyla names in their proper locations.

Figure 3. A practice version of Figure 1: Evolutionary Tree Diagram with the names of the phyla removed.

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Biology Question

A- Review your dietary intake (i.e., the foods and beverages in your Spreadsheet Report). What were two leading sources of saturated fat in your dietary pattern?

B- When you are ready to make a behavior change, set a goal to improve your likelihood of success! SMART goals include five important characteristics:

  • Specific: Rather than trying to completely overhaul your lifestyle, focus on just one behavior at a time.
  • Measurable: Include a definite way to track your progress.
  • Achievable: To avoid discouragement, make sure the goal is realistic for you.
  • Relevant: Choose a goal that is worthwhile and in alignment with what is going on in your life right now.
  • Timed: Set a due date.

As a guide for format, here is a SMART goal related to saturated fat intake:

By November 15th, I will decrease my usual saturated fat intake to less than 10% of my total calories. I will do this by using oil and vinegar to top my salads instead of bleu cheese salad dressing and by limiting myself to 1 ounce of cheese per day. I will track my progress using NutritionCalc Plus.

You can see that this goal is specific (focuses on one behavior change), measurable (percent of calories from saturated fat), achievable (it would be simple to switch salad dressings and reduce portions of cheese), relevant (it would improve my blood lipid levels), and is timed (due date is November 15th).

After you have analyzed your dietary data, identify an area related to lipids that could use some improvement. For example, many college students discover that their intake of saturated fat is higher than recommended. Think of a SMART goal for yourself that would improve your intake of lipids. Make it relevant for you.

1. SPECIFIC: What is one specific behavior that you could change to improve your intake of lipids?

2. MEASURABLE: How could you measure this behavior?

3. ACHIEVABLE: What practical strategies will you use to achieve this goal?

4. RELEVANT: Describe how this behavior change goal is worthwhile and in alignment with what is going on in your life right now.

5. TIMED: By what date would you like to achieve your behavior change?

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Biology Question

Earlier this semester, we learned about the biodiversity of the Los Angeles River and you collected data on trash in your neighborhood to help the Council for Watershed Health better understand the threats that our waterways face from trash. Now, you will be revisiting the same location to collect a second trash assessment. These data are important in helping CWH understand how the quantity and types of trash changes over time – critical information for designing effective trash mitigation programs.

Assignment Requirements

Step 1: Complete your trash survey

Your second trash survey must be completed in the same location as your first trash survey. Please locate the same storm drain and gutter and complete your trash survey there. If you are unable to complete your trash survey in the same location, please send me a Canvas message and we’ll come up with an alternative plan.

Use the ArcGIS123 survey (Links to an external site.) to complete your second trash survey. You can use either a web browser or the ArcGIS Survey123 field app to enter your data. As you are completing your survey, you will need to take a picture of at least two pieces of trash that you see. Please wear a mask and adhere to social distancing guidelines while completing your trash survey.

Remember that honestly and accurately inputting your data is crucial to the work of the Council for Watershed Health. If you are unsure about any part of the data collection process, please revisit the All Drains Lead to the Ocean – Tutorial. If you can’t find the answer to your question there, please send me a Canvas message.

Step 2: Write a blog post

You will be writing a short blog post (minimum 300 words) that reflects on your experience doing the trash assessments in your neighborhood and explains the importance of monitoring and reducing trash in the environment. This blog post is targeted at a general audience, so you should make it both interesting and informative.

In your blog post, you should include the following:

  • A headline that will catch the reader’s attention and explain the topic of your blog post clearly
  • An engaging introduction that will draw the reader in and make them want to read more
  • One or two paragraphs that discuss your experience doing trash assessments and the ways in which your contribution to this CWH trash monitoring project could help the environment
  • A conclusion with at least one action that the reader can take
  • The pictures of the two pieces of trash from your assessment
    • While not required, you are welcome to include additional pictures of your neighborhood or of you completing your trash assessment!

Here are some tips for writing an effective blog post:

  • Write in first person. While formal science writing typically avoids the use of “I”, you are writing about your experience here and this blog is all about your perspective!
  • Make it personal. Share your thoughts, feelings, and personal experience to help the reader connect to your writing.
  • Keep it interesting. You can include humor, anecdotes, or fun facts so long as they are relevant to your post.
  • Make it straightforward. Keep your sentences and paragraphs short. Your writing style should be conversational and focused – don’t include a lot of extraneous information. If you are writing about a complex topic or idea, it is important to write clear explanations and avoid use of too much technical terminology.

Make sure to cite any and all sources of information that you use!

Here are some examples of good blog posts:

Submission Guidelines

Submit your blog post by uploading a single file (Word doc or pdf) to this assignment.

Note: I will receive separate confirmation from Council for Watershed that you completed your ArcGIS123 survey.

Grading

To see how this assignment will be graded, scroll down to view the grading rubric. If no rubric is visible, click on the three dots in the upper right corner of this page, then click “Show Rubric”. If you’re reviewing this assignment using the Canvas mobile app, the rubric is included in the Grade tab.

Helpful Resources

Rubric

Trash Assessment Blog post

Trash Assessment Blog post

Criteria Ratings Pts

This criterion is linked to a Learning OutcomeArcGIS123 survey

5 pts

Full Marks

ArcGIS123 survey is completed and includes complete and accurate data for the site and trash assessment. Data quality assurance questions are answered and any uncertainties are described.

0 pts

No submission

ArcGIS123 survey was not completed

5 pts

This criterion is linked to a Learning OutcomeBlog post

10 to >8.0 pts

Excellent

Blog post meets content, formatting and length guidelines and is engaging and informative. Includes photos of at least two pieces of trash and cites sources appropriately.

8 to >6.0 pts

Good

Blog post meets most requirements for content, formatting and length, but needs further detail or is missing a minor element

6 to >0.0 pts

Developing

Blog post is missing multiple elements or is too brief.

0 pts

No submission

10 pts

Total Points: 15

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Biology Question

Final project Assignment

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The final project for the lab will consist of a literature research paper. The topic of your research will be on the natural history and biology of any organism of your choice. I prefer that you narrow your research to an organism that occurs locally (native or introduced, NOT just at the zoo).

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Potential sources of ideas for organisms to present can be found by searching the web for Southern California native plants or endemic species or marine organisms, or any combination that leads you in the direction you want to go. If you want to talk about an organism that has been introduced, you can search SoCal invasive plants, insects, birds, mammals, etc.

Guidelines:

  • Length must be no less than 5 pages double spaced.
  • Include a picture of your organism at the end of your report. Note this should be an additional page ( 6th page)
  • Full Linnaean classification (taxonomy – K P C O F G s)
  • Where it is placed in the phylogenetic tree
  • Description
  • Life history
  • Where it is found
  • What it eats
  • Life cycle stages, breeding habits, etc
  • You must include at least three academic (preferably more) source of information (i.e. from the library). Academic means a scientific article or book written by a scientist and that was reviewed by other scientists (peer-reviewed), not from a popular magazine such as National Geographic or Discovery.Make sure you cite your sources where you. Remember in Biology we always use the CSE format when citing references. Websites for your information sources will not do, unless it is for an online peer-reviewed journal.
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    ➢ Format for reference section:

    – Journal article:

    o Author last name, first initial (for each author).Year.Article title.Journal title.vol#(issue#):page#s.

    – Book:

    o Author last name, first initial (for each author).Year.Chapter title in Book title.Publisher name, place.Page#.

    – Format for citation on slide: 1 author – (Smith 1984);

    2 authors – (Smith & Jones 1984);

    + 2 authors – (Smith et al. 1984)

  • Cite your sources for your images on or under the image (small font is ok).You can say ©John Smith, or something like that, rather than the whole Wikipedia link, if that is where you get them from. EvaluationThepoints for your research paper will be equally divided among the followingfactors: ·
  • factual accuracy · apparent depth of research · sources beyond the internet · CSE format
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