Difference between revisions of "Week 2"

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(→‎References: paste in Academic Honesty section and shared journal)
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'''This journal entry is due on Thursday, September 12, at 12:01am Pacific time.'''
 
'''This journal entry is due on Thursday, September 12, at 12:01am Pacific time.'''
  
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The purpose of this assignment is:
 
The purpose of this assignment is:
 
# To understand the nature of models and modeling and connect this with the process of science.
 
# To understand the nature of models and modeling and connect this with the process of science.
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# To review key concepts in the central dogma of  molecular biology and evolution.
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# To review key concepts in genetics, biochemistry, evolution, and the central ''model'' of  molecular biology.
 
# To learn the skills needed to create and maintain a high quality electronic laboratory notebook.
 
# To learn the skills needed to create and maintain a high quality electronic laboratory notebook.
  
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=== Homework Partners ===
 
=== Homework Partners ===
  
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You will work in groups of two or three for this week's assignment.  Please sit next to your partner in class.  You will be expected to consult with your partner, in order to complete the assignment.  However, unless otherwise stated, each partner must submit his or her own work as the individual journal entry (direct copies of each other's work is not allowed).  Homework partners for this week are:
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You will work in groups of two for this week's assignment.  Please sit next to your partner in class.  You will be expected to consult with your partner, in order to complete the assignment.  However, unless otherwise stated, each partner must submit his or her own work as the individual journal entry (direct copies of each other's work is not allowed).  Homework partners for this week are:
  
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* (Genetics)
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* Marcus & Emma (Genetics)
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* (Biochemistry)
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* Michael & Kaitlyn (Biochemistry)
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* (Molecular Biology)
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* Jonar & Aby (Molecular Biology)
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* (Evolution)
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* Iliana & Naomi (Evolution)
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* Christina & DeLisa (Genetics)
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* Ivy & David (Biochemistry)
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* John & Mihir (Molecular Biology)
  
 
=== Background ===
 
=== Background ===
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* References to data and files should be made within the methods and results section of your notebook, listed above.
 
* References to data and files should be made within the methods and results section of your notebook, listed above.
 
* In addition to these inline links, create a "Data and Files" section of your notebook to make a list of the files generated in this exercise.
 
* In addition to these inline links, create a "Data and Files" section of your notebook to make a list of the files generated in this exercise.
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==== Acknowledgments ====
 
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In this section, you need to acknowledge anyone who assisted you with your assignment, either in person, electronically, or even anonymously without their knowledge (see below). 
 
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# You '''''must''''' acknowledge your homework partner or team members with whom you worked, giving details of the nature of the collaboration.  An appropriate statement could be (but is not limited to) the following:
 
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#* I worked with my homework partner (give name and link name to their user page) in class.  We met face-to-face one time outside of class.  We texted/e-mailed/chatted online three times.  We worked on the <details> portion of the assignment together.
 
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#** Sign this statement with your wiki signature.
 
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# Acknowledge anyone else you worked with who was not your assigned partner.  This could be Dr. Dahlquist (for example, via office hours), the TA, other students in the class, or even other students or faculty outside of the class.
 
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# If you copied <code>wiki syntax</code> or a particular ''style'' from another wiki page, acknowledge that here.  Provide the user name of the original page, if possible, and provide a link to the page from which you copied the syntax or style.  If you need to reference '''''content''''', use your References section (see below).
 
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# You '''must''' also include this statement unless otherwise noted:  "While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source."
 
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==== References ====
 
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*In this section, you need to provide properly formatted citations to any '''''content''''' that was not entirely of your own devising.  This includes, but is not limited to:
 
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** data
 
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** facts
 
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** images
 
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** documents, including the scientific literature
 
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* The references in this section should be accompanied by ''in text citations'' on your page that refer to these references.
 
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* The references should be formatted according to the [http://libguides.lmu.edu/c.php?g=324079&p=2174128 APA guidelines].
 
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* For more detailed guidelines, please see the document [[Media:BIOL368_Fall2016_GuidelinesforLiteratureCitations.pdf | Guidelines for Literature Citations in a Scientific Paper]] that you were given on the first day of class.
 
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=== Academic Honesty ===
 
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As discussed in class, each weekly individual journal assignment needs to conclude with an '''Acknowledgments''' and '''References''' section.
 
  
 
==== Acknowledgments ====
 
==== Acknowledgments ====
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* The references should be formatted according to the [https://owl.purdue.edu/owl/research_and_citation/using_research/documents/20180719CitationChart.pdf APA guidelines].
 
* The references should be formatted according to the [https://owl.purdue.edu/owl/research_and_citation/using_research/documents/20180719CitationChart.pdf APA guidelines].
 
* For more detailed guidelines, please see the document [[Media:BIOL367_Fall2019_GuidelinesforLiteratureCitations.pdf | Guidelines for Literature Citations in a Scientific Paper]] that you were given on the first day of class.
 
* For more detailed guidelines, please see the document [[Media:BIOL367_Fall2019_GuidelinesforLiteratureCitations.pdf | Guidelines for Literature Citations in a Scientific Paper]] that you were given on the first day of class.
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* Cite the appropriate weekly Assignment page.  For example, the citation for the [[Week 1]] Assignment page is: LMU BioDB 2019. (2019). Week 1. Retrieved August 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_1
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* Cite the appropriate weekly Assignment page.  For example, the citation for the [[Week 1]] Assignment page is: LMU BioDB 2019. (2019). Week 1. Retrieved August 27, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_1
 
* Even if you have nothing else to cite, the References section must be present and include the citation to the appropriate weekly assignment page.
 
* Even if you have nothing else to cite, the References section must be present and include the citation to the appropriate weekly assignment page.
  
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* Add the "Journal Entry" and "Shared" categories to the end of the wiki page (if someone has not already done so).
 
* Add the "Journal Entry" and "Shared" categories to the end of the wiki page (if someone has not already done so).
  
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=== Read and Reflect ===
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=== Read ===
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* [http://www.ncbi.nlm.nih.gov/books/NBK21121/#A5818 Brown, T.A. (2002) ''Genomes 2'', Ch. 3.3.2: The link between the transcriptome and the proteome] (freely available on NCBI Bookshelf)
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* [https://www.sciencedirect.com/science/article/pii/S0968000403003025 Nirenberg, M. (2004) Deciphering the Genetic Code&mdash;a Personal Account. ''Trends in Biochemical Sciences'' 29:  46-54. DOI: 10.1016/j.tibs.2003.11.009] (also on [https://brightspace.lmu.edu Brightspace])
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* [https://www.cell.com/trends/biochemical-sciences/fulltext/S0968-0004(04)00083-0 Kaji, A., Kaji, H. (2004) The history of deciphering the genetic code: setting the record straight. ''Trends in Biochemical Sciences''  29:  293. DOI: 10.1016/j.tibs.2004.04.005] (also on [https://brightspace.lmu.edu Brightspace])
 +
* Moody, G. (2004) ''Digital Code of Life'', Chapter 1, Hoboken, New Jersey:  John Wiley & Sons, pp. 1-9. (on [https://brightspace.lmu.edu Brightspace])
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* Hayes, B. (2004) Ode to the Code, ''American Scientist'' 92: 494-498. (on [https://brightspace.lmu.edu Brightspace])
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=== Reflect ===
 +
 
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# What is the biggest discovery that I made from these readings?
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# What part of the readings did I understand the least?
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# What is the relationship between the genetic code and a computer code?
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[[Category:Assignment]]

Latest revision as of 10:16, 5 September 2019

This journal entry is due on Thursday, September 12, at 12:01am Pacific time.

Overview

The purpose of this assignment is:

  1. To understand the nature of models and modeling and connect this with the process of science.
  2. To review key concepts in genetics, biochemistry, evolution, and the central model of molecular biology.
  3. To learn the skills needed to create and maintain a high quality electronic laboratory notebook.

Individual Journal Assignment

  • Store this journal entry as "username Week 2" (i.e., this is the text to place between the square brackets when you link to this page).
  • Create the following set of links. (HINT: These links should all be in your personal template that you created for the Week 1 Assignment; you should then simply invoke your template on each new journal entry.)
    • Link to your journal entry from your user page.
    • Link back from your journal entry to your user page.
    • Link to this assignment from your journal entry.
    • Don't forget to add the "Journal Entry" category to the end of your wiki page.

Homework Partners

You will work in groups of two for this week's assignment. Please sit next to your partner in class. You will be expected to consult with your partner, in order to complete the assignment. However, unless otherwise stated, each partner must submit his or her own work as the individual journal entry (direct copies of each other's work is not allowed). Homework partners for this week are:

  • Marcus & Emma (Genetics)
  • Michael & Kaitlyn (Biochemistry)
  • Jonar & Aby (Molecular Biology)
  • Iliana & Naomi (Evolution)
  • Christina & DeLisa (Genetics)
  • Ivy & David (Biochemistry)
  • John & Mihir (Molecular Biology)

Background

Protocols

Assignments to sections are listed under the Homework Partners section above.

  • Part I: Genetics
    • Complete the "Specific Tasks to do with this tool" beginning on page 8.
    • Complete the tables and questions on pages 9-12.
    • When the protocol says "Data Blog", this means your wiki journal for this week (electronic lab notebook).
  • Part II: Biochemistry
    • Complete the "Specific Tasks for this section" beginning on page 11.
    • Complete the tables and questions on pages 11 to 14.
    • When the protocol says "Blog", this means your wiki journal for this week (electronic lab notebook).
  • Part III: Molecular Biology
    • Complete the "Specific Tasks for this section" beginning on page 7.
    • Complete the tables and questions on pages 7 and 8.
  • Part IV: Evolution
    • Complete "A", "B", and "C" questions on pages 5 to 9.

Electronic Lab Notebook

Complete your electronic notebook for your assigned part of the Molecular Genetics Explorer project on your individual journal page. Your notebook entry should contain:

  • The purpose: what was the purpose of your investigations?
  • Your methods: what did you actually do? Give a step by step account.
    • There should be enough detail provided so that you or another person could re-do it based solely on your notebook.
    • You may copy protocol instructions on your page and modify them as to what you actually did, as long as you provide appropriate attribution.
    • Take advantage of the electronic nature of the notebook by providing screenshots, links to web pages, links to data, etc.
  • Your results: the answers to the questions in the protocol, plus any other results you gathered.
    • Usually it makes sense to embed your answers to the questions/results in the "methods" in the order in which you obtained them.
  • A scientific conclusion: what was your main finding for today's project? Did you fulfill the purpose? Why or why not?

Data and Files

  • Files left on the Desktop or My Documents or Downloads folders on the Seaver 120 computers will be deleted upon restart of the computers. Files stored on the T: drive will be saved. However, it is not a good idea to trust that they will be there when you next use the computer.
  • Thus, it is a critical skill for data and computer literacy to back-up your data and files in at least two ways:
  • References to data and files should be made within the methods and results section of your notebook, listed above.
  • In addition to these inline links, create a "Data and Files" section of your notebook to make a list of the files generated in this exercise.

Acknowledgments

In this section, you need to acknowledge anyone who assisted you with your assignment, either in person, electronically, or even anonymously without their knowledge.

  1. You must acknowledge your homework partner or team members with whom you worked, giving details of the nature of the collaboration. You should include when and how you met and what content you worked on together. An appropriate statement could be (but is not limited to) the following:
    • I worked with my homework partner (give name and link name to their user page) in class. We met face-to-face one time outside of class. We texted/e-mailed/chatted online three times. We worked on the <details> portion of the assignment together.
  2. Acknowledge anyone else you worked with who was not your assigned partner. This could be Dr. Dahlquist (for example, via office hours), the TA, other students in the class, or even other students or faculty outside of the class.
  3. If you copied wiki syntax or a particular style from another wiki page, acknowledge that here. Provide the user name of the original page, if possible, and provide a link to the page from which you copied the syntax or style.
  4. If you need to reference content (such as the methods of a protocol), that belongs in the References section where you will give a include a formal APA-formatted citation (see below).
  5. You must also include this statement unless otherwise noted:
    • "Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
  6. Sign your Acknowledgments section with your wiki signature.

References

  • In this section, you need to provide properly formatted citations to any content that was not entirely of your own devising. This includes, but is not limited to:
    • methods
    • data
    • facts
    • images
    • documents, including the scientific literature
  • Do not include extraneous references that you do not cite or use on your page.
  • The references in this section should be accompanied by in text citations on your page that refer to these references.
  • The references should be formatted according to the APA guidelines.
  • For more detailed guidelines, please see the document Guidelines for Literature Citations in a Scientific Paper that you were given on the first day of class.
  • Cite the appropriate weekly Assignment page. For example, the citation for the Week 1 Assignment page is: LMU BioDB 2019. (2019). Week 1. Retrieved August 27, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_1
  • Even if you have nothing else to cite, the References section must be present and include the citation to the appropriate weekly assignment page.

Shared Journal Assignment

  • Store your journal entry in the shared Class Journal Week 2 page. If this page does not exist yet, go ahead and create it (congratulations on getting in first :) )
  • Link to your journal entry from your user page.
  • Link back from the journal entry to your user page.
    • NOTE: you can easily fulfill the links part of these instructions by adding them to your template and using the template on your user page.
  • Sign your portion of the journal with the standard wiki signature shortcut (~~~~).
  • Add the "Journal Entry" and "Shared" categories to the end of the wiki page (if someone has not already done so).

Read

Reflect

  1. What is the biggest discovery that I made from these readings?
  2. What part of the readings did I understand the least?
  3. What is the relationship between the genetic code and a computer code?
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