SCI 115 Introduction to Biology Full Course STR

For your primary post, select ONE of the following discussion topics. Please select only one of the three topics listed. Using your own words, write a primary post of at least 125 words that follows the instructions. Be sure to address everything listed in the instructions. Each topic has two subtopics [a, b]; please address both of them.

Your primary post is worth up to 14 points. Also, make a substantive reply to a fellow classmate on any topic. Use your own words. You don’t need to use any sources other than the ones specified, but if you do use other sources, you must cite them.

Topic 1. Climate Change / Terrestrial Species. Watch the 7.5 minute video by Jim Cox (1)* about how climate change affects the “species range” of terrestrial species. This video can be found in the “Instructor Insights” of Week 1. Based on the video, address the following:

1. Describe three things you learned from the video.
2. Explain how the video relates to the field of biology.

Topic 2. Evo-devo. Watch the video (2)* featuring Sean Carroll discussing the science of evolution and the field of evolutionary-developmental biology (evo-devo).

1. Describe three things you learned from the video.
2. Tell me what these things teach us about biology.

Topic 3. The cusp of a revolution in medicine. In a recent op-ed, Craig Venter (3)* shares his opinion that we are “on the cusp of a revolution” in medicine. Venter also addresses the issue of human germline editing, which is something we discuss in a later part of this course. For now, let me just note that editing the human germline means making permanent changes to the DNA of eggs, sperm, or a fertilized ova. Such changes would be permanent and would be passed on to future generations.

1. Describe three things you learned from this opinion article.
2. Explain how this article relates to biology.

*References (in Strayer Writing Standards format).

1. James F. Cox, 2016, Climate change and species range (version 2), Found in course shell Week 1, Instructor Insights tab or via the following link: https://cdnapisec.kaltura.com/index.php/extwidget/preview/partner_id/956951/uiconf_id/38285871/entry_id/0_y2jwwltc/embed/dynamic
2. Erik Olsen, June 25, 2007, Sean Carroll on evolution and the science of evo-devo, https://www.nytimes.com/video/science/1194817104756/the-science-of-evolution.html
3. Craig Venter, December 13, 2017, Genetic sequencing is the future of medicine, https://www.washingtonpost.com/news/theworldpost/wp/2017/12/13/human-genome/

Biochemistry & Structure of Living Cells.

Select one of the following discussion topics for your primary post, which should address the discussion question in your own words. Your primary post should be at least 125 words. Also, please respond to a fellow student on any topic.

Topic 1: Internet Research on Carl Woese. Carl Woese (1928-2012) worked out a new method for classifying organisms. Research his activities on the internet, and then address issues (a), (b) and (c), that are given below, and cite your source(s).

• (a) Carl Woese used ribosomal RNA (rRNA) to look at relatedness between organisms. Describe the basic logic of this approach. How can you tell if two organisms are closely related or distantly related from their rRNA?
• (b) Name one of Woese’s most important findings.
• (c) Describe one way that this relates to this week’s lesson.
• Don’t forget to cite your source or sources.

Topic 2: Chemicals of Life Video. Watch Dr. Cox’s video on the “Chemicals of Life” (1)* in the “Instructor Insights” area of Week 2. Then, answer questions (a) and (b).

• (a) Describe three things you learned from this video.
• (b) Describe at least one way that this video relates to this week’s lesson.
• To get credit for this topic, your post must be based on the video. Answers based on other materials will receive a grade of zero.

Topic 3: Lokiarchaeum Article. Read about Lokiarcheum in the article by Yong (2)* and/or the article by Zimmer (3)*. Both articles describe recently discovered evidence about a previously unknown organism. Address issues (a), (b) and (c), that are given below, and cite your source(s)

• (a) Lokiarchaeum may be a “transitional form” between archaea and eukarya. What evidence suggests this?
• (b) Describe one way that this relates to this week’s lesson.
• Cite whichever article you use. If you use both, cite them both. There’s no particular reason why you should need any other source, but if you do use any other source, you must cite it, too.

*References:

1. James Cox, 2016, The chemicals of life – revised, see “Instructor Insights” (Week 2) or Media Gallery in this course shell.

2. Ed Yong, May 6, 2015. New Loki microbe is closest relative to all complex life, http://phenomena.nationalgeographic.com/2015/05/06/new-loki-microbe-is-closest-relative-to-all-complex-life/

3. Carl Zimmer, May 6, 2015, Under the sea, a missing link in the evolution of complex cells, http://www.nytimes.com/2015/05/07/science/under-the-sea-a-missing-link-in-the-evolution-of-complex-cells.html?_r=0

Energy for Life / Energy Reactions and Processes

In your primary post, please write a response of at least 125 words to one of the following three topics, using your own words. In addition, please make a substantive reply to a fellow student on any topic.

Topic 1. The phytoplankton that brought Earth to life. Review the video (1)* about the “phytoplankton that brought Earth to life” from the link given below, or from the link in the Instructor’s Insights area. In this clip, which is under 5 minutes in length, Penny Chisholm discusses a tiny phytoplankton called Prochlorococcus. Based on that video, please address the following:

• (a) What is the importance of Prochlorococcus for life on the planet Earth, both historically and in the present day?
• (b) Explain what the known geographic variations in Prochlorococcus tell us about relationships between organisms and their environments.

Topic 2. Characteristics of ATP. If you choose this topic for your primary post, you must base your post on the instructor’s video about ATP (2)*. The video can be found in the Instructor Insights area.

• (a) Describe at least three specific points that the video makes about ATP.
• (b) Explain how this fits with this week’s lessons.
• Please note that I am looking for specific points that are covered in the video, so material gleaned from Wikipedia or other sources may not meet the requirements.

Topic 3. Chemosynthesis in the Giant Tubeworm. The Giant Tubeworm (Riftia pachyptila) is an animal that lives on the floor of the ocean, near hydrothermal vents that release very hot, chemical-rich water. The adult form of the tubeworm is sessile, which means that it plants itself in one place, and doesn’t have any locomotion. Riftia pachyptila has a unique way of getting the energy that it needs to stay alive (3)* (4)* (5)*.

• (a) Describe how Riftia pachyptila gets its energy.
• (b) Discuss how this relates to this week’s lessons.

References*

1. PBS Newshour, March 5, 2014, The phytoplankton that brought Earth to life, https://youtu.be/m_43nR11PW8
2. James Cox, 2015, Four minutes about ATP, see Kaltura video via the “Instructor’s Insights” area for Week 3.
3. Deep Marine Scenes, 2013, Facts: Giant tube worms, https://www.youtube.com/watch?v=IddCPTnmj4Q
4. JKM12988, December 5, 2016, Giant tube worms and symbiotic bacteria, https://www.youtube.com/watch?v=dg6ZewBTRj8&t=6s
5. Kristen M. Kusek, January 12, 2007, Deep-sea tubeworms get versatile ‘inside’ help, http://www.whoi.edu/oceanus/feature/deep-sea-tubeworms-get-versatile-inside-help

Week 4 Discussion: Genome, Transcriptome and Proteome.

For your primary post, please respond to one of the following three with a post of at least 125 words addressing each point given in the instructions. Also, please reply to at least one fellow student on any topic.

• Topic 1. Omics video. Watch the instructor’s video about “-omics” (1)*, in the Instructor Insights section.

Note: If you choose this discussion topic, your answer must be based on the material specifically covered in the video, rather than generic information on –omics from the internet. If you would rather research information from the internet, then choose discussion Topic 3.

• • (a) Explain the concept of genome.
  • (b) Explain how the concept of transcriptome relates to messenger RNA (mRNA).
  • (c) Describe at least two additional things that you learned from the video.

• Topic 2. Synthetic genome video. Watch the instructor’s video about the synthetic genome “Syn 3.0” (2)* in the Instructor Insights section. Subsequently, answer the following:
  • (a) Explain how Syn 3.0 is different from naturally-occurring microorganisms.
  • (b) What do you think we’ve learned, if anything, from Syn 3.0? Explain.
  • (c) In your opinion, what are the inherent risks of this research to human health or to the environment, if any?

• Topic 3. Patent protection for BRCA genes. On the Internet, read one or more articles about how the Supreme Court of the United States (SCOTUS) ruled in the case of Association for Molecular Pathology versus Myriad Genetics. In your answer, give must credit your source(s). Your answer must address the following:
  • (a) Describe some of the major reasons why the plaintiffs objected to Myriad’s patent on the breast cancer-related genes, BRCA1 and BRCA2.
  • (b) Describe the SCOTUS ruling regarding naturally-occurring DNA sequences, as well as their ruling regarding DNA sequences that do not exist in Nature.

Note: the rulings of lower courts are NOT of interest for our purposes. Please concentrate only on SCOTUS’s ruling. The objective here is to emphasize the precedent-setting ruling of the highest court (SCOTUS), rather than to recount the litigation history.

• • (c) What is your view on the issue of whether we should allow human genes to be patented?
  • (d) Be absolutely sure that you cite your sources, and list your references.

*References (in Strayer Writing Standards format).

1. James Cox, January 21, 2018, Omics video [v2], Video can be found in the course shell (Week 4, Instructor Insights tab) or via the following link: https://cdnapisec.kaltura.com/index.php/extwidget/preview/partner_id/956951/uiconf_id/38285871/entry_id/0_1dbmbx95/embed/dynamic
2. James Cox, April 25, 2016, Synthetic genome Syn 3.0, Video can be found in the course shell (Week 4, Instructor Insights tab) or via the following link: https://cdnapisec.kaltura.com/index.php/extwidget/preview/partner_id/956951/uiconf_id/38285871/entry_id/0_rl8yrtfl/embed/dynamic

Choose one of the following three topics for your primary post. Your primary post should address everything that the instructions call for (for the topic you choose). Your post should also be at least 125 words in length. Additionally, please respond to at least one other discussant on any topic.

Topic 1. Sexual Reproduction in Unicellular Eukaryotes. Watch the instructor’s video about “Sexual Reproduction in Unicellular Eukaryotes” (1)* which can be found in the Instructor Insights section for this week. For a single-celled species to be capable of sexual reproduction, the species must have both haploid and diploid forms

• (a) Describe four things that you learned from the video.
• (b) Explain how this relates to this week’s lesson.

Topic 2. Apoptosis. Watch the Khan Academy video about apoptosis (2)*, then address the following issues in your own words:

• (a) What is the difference between apoptosis and necrosis?
• (b) What is the role of apoptosis in the normal, healthy development of animals?
• Reminder: you don’t need to cite the Khan Academy video for this topic, but if you use any other sources, you must cite them.

Topic 3. Tumor-suppressor genes versus Proto-oncogenes. This is a library-research topic in which you are required to provide your sources. Mutations in tumor suppressor genes can contribute to or cause cancer, just as mutations in proto-oncogenes can also contribute to or cause cancer. However, tumor suppressor genes are very different from proto-oncogenes.

• (a) What is the basic difference between a tumor suppressor gene and a proto-oncogene?
• (b) Explain why a gain-of-function mutation to a proto-oncogene (or its promoter) may be associated with increased risk of cancer.
• (c) Explain why a loss-of-function mutation to a tumor suppressor gene may be associated with increased risk of cancer.

References:

1. James Cox, April 15, 2018, Sexual reproduction in a unicellular eukaryote (version 2). See the video in the Week 5 Instructor Insights or the following link https://cdnapisec.kaltura.com/index.php/extwidget/preview/partner_id/956951/uiconf_id/38285871/entry_id/0_7ruy782g/embed/dynamic
2. Khan Academy, No date given, Apoptosis, https://www.khanacademy.org/science/biology/cellular-molecular-biology/stem-cells-and-cancer/v/apoptosis

Discussion

Topic 1. Pedigree for Trait 1. Suppose that we are certain that Trait 1 follows a Mendelian pattern of inheritance and that Trait 1 is an autosomal dominant trait. Suppose further that the dominant allele is designated as A and the recessive allele is a.

• (a) Determine the genotype of Alan Blue and explain how you determined it. Go through your logic and reasoning step by step.
• (b) If we were wagering on the genotype of Harlan Brown, what genotype would you put your money on? Explain.

Topic 2. Pedigrees for Trait 2. Suppose that we are certain that Trait 2 follows a Mendelian pattern of inheritance and that Trait 2 is an autosomal recessive trait. Suppose further that the the dominant allele is B and the recessive allele is b.

• (a) Determine the genotype of Alan Blue and explain how you determined it. Go through your logic and reasoning step by step.
• (b) Determine the genotype of Denise Hawk and explain how you determined it. Go through your logic and reasoning step by step.

Topic 3. Esvelt’s Regret. In the article by Zimmer (1), Kevin Esvelt says that he made a huge mistake by championing the application of a technology that he now says is far too dangerous to actually deploy. In a post of about 125 words, address the following:

• (a) What is the technology that Esvelt championed? What does this technology do? Why does he think it’s too risky to use outside the lab?
• (b) In your opinion, what sorts of laws and regulations, if any, should society put into place to regulate the technology that Esvelt regrets championing?

Topic 4. Societal Aspects of Human Gene Editing. Read the article by Neuhaus (2) and/or the article by Ossola, then address the following:

• (a) Where do you think our procedures, regulations and laws ought to come down regarding human genome editing, with CRISPR (or any other tool)? Take a clear position on this.
• (b) Explain your rationale.

References

1. Carl Zimmer, November 16, 2017, ‘Gene drives’ are too risky for field trials, scientists say, https://www.nytimes.com/2017/11/16/science/gene-drives-crispr.html?_r=0
2. Carolyn P. Neuhaus, March 16, 2017, Genome editing: bioethics shows the way. http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2001934
3. Alexandra Ossola, August 6, 2015, Should bioethicists “get out of the way” of CRISPR research?, https://www.popsci.com/should- bioethicists-get-out-way-crispr-research

Select one of the following three topics for your primary post. In a primary post of at least 125 words, address the issues listed in the instructions. Also, make a substantive reply to a fellow student on any subject.

Topic 1. Co-evolution of rattlesnakes and squirrels. Read at least one of the following articles (1)* and/or (2)*. Please address the following questions: (a) How do squirrels adapt to rattlesnake venom? (b) How do rattlesnakes adapt to squirrel’s defenses against rattlesnake venom? (c) What do the results of this research tell us about evolution?

Topic 2. Climate change and Bergmann’s rule. View Dr. Cox’s video (3)* on climate change and Bergman’s rule (10 minutes) in the Instructor Insights folder for Week 7. Then, address the following issues: (a) Describe three things you learned from the video. (b) Explain what type of evidence you would accept as evidence of genetic evolution in response to changing climate conditions.

Topic 3. Into Thin Air. Watch Dr. Cox’s video (4)* entitled “Into Thin Air” (5.5 minutes) in the Instructor Insights folder for Week 7. Address the discussion question he poses in the last minute of the video.

*References:

1. May 18, 2016, How is rattlesnake venom like fine wine? Both have regional varieties, https://news.osu.edu/how-is-rattlesnake-venom-like-fine-wine-both-have-regional-varieties/
2. Sarah Kaplan, May 20, 2016, Snake venom evolved to kill specific squirrels with shocking precision. The Washington Post. Retrieved from https://www.washingtonpost.com/news/speaking-of-science/wp/2016/05/20/snake-venom- evolved-to-kill-specific-squirrels-with-shocking-precision/
3. James Cox, June 5, 2016, Climate change and Bergmann’s rule. Found in the “Instructor Insights” folder for Week 7.
4. James Cox, November 13, 2017, Into thin air. Found in the “Instructor Insights” folder for Week 7.

Pick one of the following topics and write a primary post of at least 125 words addressing that topic. Also, please make a substantive reply to one of your fellow students.

Topic 1. The Hawaiian Bobtail Squid and its bacterial endosymbiont. In a 4 minute video clip (1), Bonnie Bassler explains the relationship between the Hawaiian Bobtail squid and it’s endosymbiont, the bacterium Vibrio fisheri. Answer the following two questions about this arrangement:

• (a) What are the main characteristics of the partnership between these two species?
• (b) How does each species benefit?

Topic 2. Virus Reassortment and the Alaska Connection Read the article from MIT News (2) about tracking the spread of bird flu. Address the following:

• (a) The article (2) describes genetic reassortment of influenza viruses. Explain how genetic reassortment works and what the significance of it is for humans and for domestic fowl.
• (b) The article (2) explains that one way that influenza strains enters North America is through Alaska. Explain how that works and what the significance of it is for humans and for domestic fowl.

Topic 3. Endophytes that benefit plants. Read reference (3) or reference (4) or another article of your choosing.

• (a) Describe what an endophyte is and give a specific example
• (b) Provide an example of at least one beneficial effect of certain endophytes on their plant hosts.

References:

1. iBioEducation, 2013, Quorum sensing in bacteria – Bonnie Bassler, https://www.youtube.com/watch?v=LebqwdQSFHE

2. Anne Trafton, March 17, 2017, Tracking the spread of bird flu, http://news.mit.edu/2017/tracking-spread-bird-flu-alaska-north-america-0317

3. Universidad Politecnica de Madrid, December 18, 2015, Endophytic fungi in elm trees help protect them from Dutch elm disease, https://www.sciencedaily.com/releases/2015/12/151218085929.htm

4. Claire O’Connell, April 7, 2016, Plants get by with a little help from their microbial friends. https://www.irishtimes.com/news/science/plants-get-by-with-a-little-help-from-their-microbial-friends-1.2593676

For your primary post, please respond to one of the following three topics with a post of at least 125 words that addresses each point given in the instructions. Also, please reply to at least one fellow student on any topic.

Topic 1

: Population Distribution of Termites in a Savanna. Watch the video (1) describing Corina Tarnita’s research on the spacing of termite mounds in savanna ecosystems, and then address the following:

• What were Tarnita’s findings about the spacing of termite mounds?
• (b) What does Tarnita think is the main factor that governs the spatial distribution of the termite mounds?
• (c) How do the termite mounds benefit other organisms on the savanna?

Topic 2

: Pacific Lampreys. Watch the video about Pacific Lampreys (2)*, then address the following:

• (a) Where do Pacific lampreys fall in the taxonomy of vertebrates?
• (b) What challenges do Pacific lamprey populations face?
• (c) Why are Native American tribes of the Northwest concerned about them? (Please note: take care not to confuse the Pacific lamprey (described in the video) with the Sea Lamprey, which is a completely different species that is considered an invasive species in the Great Lakes).

Topic 3 [article]: Supporting the Energy Needs of a Large Brain. As discussed in the article by Zimmer (3)*, brain tissue is energetically expensive. For a species to evolve a large brain, it may need to make certain adjustments to ensure that enough energy is available to support brain function. Zimmer discusses various hypotheses about such adjustments in the human line of descent. Explain one of these adjustments.

*References (in Strayer Writing Standards format).

1. HHMI Biointeractive (2015, November 11) Analyzing patterns in the savanna landscape. [Video]. Retrieved from https://youtu.be/nJGpABrEatc
2. U.S. Fish & Wildlife Service. (2012). Taking the initiative to conserve Pacific Lamprey. [Video]. Retrieved from https://www.youtube.com/watch?v=dkwfDVAoSXk
3. Carl Zimmer, July/August 2011, The brain Discover, 32 (6), 18-19. https://search.ebscohost.com/login.aspx?direct=true&db=a9h&AN=61992134&site=ehost-live&scope=site

Post your original “primary post” of at least 125 words for one of the following three bulleted items. Also, reply to a fellow student on any topic

Topic 1. Trophic Cascades in theSerengeti. Watch Dr. Cox’s video (1) on “What Rinderpest eradication taught us about the Serengeti”, which can be found in the Instructor Insights folder for this week. Then address the following questions: (a) How did eradication of Rinderpest from East Africa increase both the tree and giraffe populations in the Serengeti? (b) How did eradication of Rinderpest from East Africa increase the population of predator species in the Serengeti? (c) What does this tell us about ecosystems?

Topic 2. Shrinking Red Knots. Read two of three articls (2) (3) (4) about the effects of artic warming on a migratory bird known as the red knot. Then, address the following issues: (a) In your own words summarize the basic story that the articles have in common; (b) of the two articles you read, which of them do you prefer? Why?

Topic 3. Biomes. The term “biome” is described in the textbook. For this topic, describe the biome where you grew up (or where you currently live). Identify your location, the biome of the region, and describe the major characteristics of that biome. Add enough detail and commentary from your own experience, so that your answer is 125 words or more. If you’re really ambitious, you could consider looking up the “ecoregion”. The United States Environmental Protection Agency (EPA) maintains information about that.

References.

1. James Cox, August 31, 2017, What Rinderpest eradication taught us about the Serengeti. https://cdnapisec.kaltura.com/index.php/extwidget/preview/partner_id/956951/uiconf_id/38285871/entry_id/0_922iecgu/embed/dynamic
2. Helen Briggs, May 13, 2016, Shrinking bird pays the bill for Arctic warming, http://www.bbc.com/news/science-environment-36266692
3. Joseph Dussault, May 12, 2016, Climate change chould be shrinking these arctic birds, http://www.csmonitor.com/Science/2016/0512/Climate-change-could-be-shrinking-these-Arctic-birds
4. Carl Zimmer, May 12, 2016, Climate change and the case of the shrinking red knots, http://www.nytimes.com/2016/05/17/science/climate-change-bird-red-knots.html?_r=0