ASIC 200
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MAINPAGE (JAN – APR 2016)
terry home | course outline | Brave World Now
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WELCOME!
General details for ASIC200 such as office hours, philosophy, grading, due dates can be found in the course outline link.
This page aims to collect concurrent pertinent info regarding the weekly lectures. This includes the pre-reading assignments, copies of Dave and Allen’s lecture notes, further reading, interesting links, assignment/scheduling reminders. In other words, a good place to bookmark, and check back at least once a week.
Note that we will be using a twitter hashtag for community networking. “#ASIC200” We will ask that everyone participate in this activity, so do please sign up an account at twitter.com (You can even use an anonymous name if you prefer).
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COURSE TIMELINE/NOTES WILL BE PRESENTED AS WEEKS PROGRESS
(Details below pertain to pre-reading for each class unless otherwise noted)
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We meet in room 102 of the Michael Smith Building (next door to the UBC Bookstore),
from 6pm to 9pm, on thursday evenings. Doors to the building are unlocked from 5:30pm
to 6:05pm and 7:20pm to 7:40pm (for our mid class break).
Session 1: (Jan 7) Administration and Overview of Global Issues
• Introduction into course logistics.
• The “global” as a “scientific” concept (pdf of slides)
• Meet and Greet: Surviving the Zombie Apocalypse (BREAK in here)
• The “global” as a “social science, and humanities” concept.
Reading for after class:
– Sciencegeek Fundamentals No. 1 (link)
– Browse and familiarize yourself with the IPCC website located at: http://www.ipcc.ch/index.htm Read the AR5 “Summary for Policymakers” (pdf link) or click on the orange “Summary for Policymakers” button.
– Executive Summary, The Emissions Gap Report 2014. A UNEP Synthesis Report. The United Nations Environment Program, 2014. (pdf link)
Required viewing before January 14:
– One of the videos highlighting tabletop role playing games (link) – note full RPG details here.
– ASIC 200 Climate Change Science videos parts one | two | three | four
– Dave’s lecture notes for the 4 videos (pdf)
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Session 2: (Jan 14) Climate Change Science (IPCC summary) (+RPG stuff)
• Finish zombie exercise.
• Brief overview of some of things in the IPCC AR5 Policy Summary report (pdf of slides)
• Table Top RPG assignment overview – schedule link | overview link
• Solo assignment #1 is due on February 4th. Link to details.
• Set up for Copenhagen simulation – each student should have their secret document + general instruction sheet (pdf).
Required viewing before January 14:
– Climate Change Arts Videos (Parts one | two | three | four)
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Session 3: (Jan 21) Copenhagen Simulation
• Copenhagen Simulation (please check twitter feed for some photo highlights – great job everyone!)
• Just for your records, the final outcome as drawn out below:
Required viewing before January 28:
– Climate Change Arts Videos (Parts five | six | seven | eight | nine)
Assignment to hand in before class January 28:
– The reflection piece on the simulation that is due next week – instructions on the last page of the Copenhagen general instruction sheet (pdf). Please hand in a hardcopy of your reflection at the beginning of class.
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Session 4: (Jan 28) Climate Change lecture + RPG group setup
• Allen finishes his Climate Change lecture by talking about the Paris Agreement (COP21) – pdf of slidespdf of slides
• Groups for the RPG project were (more or less) worked out. If you were away for this, please email Dave at db@mail.ubc.ca
Assignment to hand in before class on February 4th:
– The first Earth 2116 RPG solo assignment is due next week – instructions for this can be found here. Please bring two copies to the class (one to hand in, and the other for you to use when you discuss as a group).
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Session 5: (Feb 4) RPG Group meeting #1
• Individuals in each group will briefly introduce themselves, and then share their SOLO assignment work. Then, they will work together to world build their game setting according to the same categories as outlined in the SOLO 1 assignment. Finally, groups will start thinking about potential backstory (i.e. brainstorm some bullet point ideas for the narrative of the game).
Required reading before February 11:
“A Monk’s Flourishing Garden: The Basics of Molecular Biology Explained” The Science Creative Quarterly (link).
“Breakfast of Champions does Replication” The Science Creative Quarterly (link).
Required viewing before February 11:
– ASIC 200 Personal Genomics Science videos parts one | two | three | four
– Dave’s lecture notes for the 4 videos (pdf)
Hand in before February 11:
An electronic copy of your group’s 1st world building exercise (to asic200@gmail.com or via google docs). Note, we won’t be marking it, we just want to make sure that it’s been done.
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Session 6: (Feb 11) Science Lecture on Personal Genomics | In Search of Tiger Joe.
• Dave will give an in class lecture continuing on from his video series. This will cover new developments in whole genome sequencing, SNPs (microarrays), as well as a brief mention of CRISPR/Cas genome editing technologies. (Slides | pdf of Dave’s notes).
• The class will be guided through an RPG session (In Search of Tiger Joe – back story here). We will likely continue this, for the first 30 to 40 minutes of the next class.
Required reading before February 25 (note that there is no class on Feb 18 due to reading break):
Reading One: Diane B. Paul: “What Was Wrong with Eugenics? Conflicting Narratives and Disputed Interpretations,” Science and Education, Vol. 23 (February 2014), 259 – 271. Available at: http://link.springer.com/article/10.1007/s11191-012-9556-3/fulltext.html
Reading Two: Bernard E. Rollin, “The Perfect Storm – Genetic Engineering, Science, and Ethics,” Science and Education, Vol. 23 (February 2014), 509 – 517. Available at: http://link.springer.com/article/10.1007/s11191-012-9511-3/fulltext.html
Reading Three: Yann Joly and Patricia N. Tonin, “Social, ethical and legal considerations raised by the discovery and patenting of the BRCA1 and BRCA2 Genes,” New Genetics and Society, Vol. 33 (May 2014), 167-180. Available at: http://www.tandfonline.com/doi/full/10.1080/14636778.2014.914849
Reading Four: Maui Hudson, et. al., “The art of dialogue with indigenous communities in the new biotechnology world.” New Genetics and Society, Vol. 31 (March 2012), 11-24. Available at: http://www.tandfonline.com/doi/full/10.1080/14636778.2011.597979
Required viewing before February 25:
– ASIC 200 Personal Genomics Social Science and Humanities videos:
Parts one | two | three | four | five | six | seven
Don’t forget that you can start on your SOLO assignment #2 (due before March 3rd class), but also remember that it’s also dependent on you having finished picking a group locale and generally having a good sense of the place’s parameters as defined in SOLO assignment #1.
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Session 7: (Feb 25) Social Science Lecture on Personal Genomics | In Search of Tiger Joe (continue playing).
• Class continues playing the RPG session (In Search of Tiger Joe – back story here).
• Allen gives his social science lecture on personal genomics. (pdf of slides)
Assignment to hand in before class on March 3rd:
– The second Earth 2116 RPG solo assignment is due next week – instructions for this can be found here. Please bring two copies to the class (one to hand in, and the other for you to use when you discuss as a group).
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Session 8: (Mar 3) RPG Group meeting #2
• Individuals in each group will briefly share their SOLO 2 assignment work. Then, they will work together to world build their game setting according to the same categories as outlined in the SOLO 2 assignment.
Hand in before March 10th:
An electronic copy of your group’s 1st world building exercise (to asic200@gmail.com or via google docs). Note, we won’t be marking it, we just want to make sure that it’s been done.
Required reading before March 10th:
– If you have been flagged to do the DNA lab next week, then please revisit the material on replication (either via the video link or via this reading). No need to memorize or study – just familiarize yourself with the material.
– If you have not been flagged to do the lab next week, then please look over the group assignment section at the Brave World Now website (link). Here, you will get a sense of what is upcoming, and you can prep accordingly. For your first class working on this, note the following:
“For the first class devoted to designing this game (March 10 or March 17 depending on your time of lab), the group will need to flesh out/finalize their backstories, work out (at least) a skeleton of the adventure scenario (i.e. their story elements/scenes, drafts of maps), as well as discuss what everyone’s player characters can be (i.e. so we avoid situations where everyone is the same). Homework for the second class (March 24th) will entail each student fleshing out their player character contribution (in principle, each group will therefore have a set of pre-generated characters for people to choose from and use when the games are played on the last day). Homework may also entail delegating folks to finalize backstory and map tasks, as well as brainstorm for possible details associated with each element/scene.”
You can also check out the adventure module (In Search of Tiger Joe pdf) for the game that we played in previous weeks, to see how sections and characters can be written up.
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Session 9 and 10: (Mar 10 and 17) PCR DNA Lab OR Start Group Game Design Project
• Folks from the following groups – southwestern BC, Vancouver (w/Emilia), Scotland, and Vancouver (w/Shannah) avoided fruit and went to the lab on March 10th. The other groups will attend on March 17th (slides – materials will not be required for exam)
Regarding the lab, here is your reflection question.
THE PCR LAB was intended to show you how molecular biology is, at its heart, fairly straightforward to do, whilst being capable of generating some very weighty data. For this lab commentary, I’d like you to comment on the two queries presented below. You can write informally if you’d prefer, but we are looking for a relatively well thought out response (somewhere in the 500 word range altogether). Ideas are strongly encouraged. Please send your answer to ASIC200@gmail.com (please use “PCR” as the subject heading). We’ll do our best to reply to confirm receiving your email, but you may actually just receive your mark a week or so after you submit. Note that this assignment is due by midnight on the thursday after your lab (note that one need not fully understand the mechanics of PCR to do this assignment).
1. It was important to stress that the experiment we did in the genetics lab aimed at looking for a genetic element with no real consequence. However, the methodology (PCR) can very easily be adapted to look at something of significant consequence – i.e. a diagnosis of a genetic disorder like Huntingtons (a fatal and nasty neurodegenerative disease). What type of ethical situations come to mind when an individual is put in the position of getting one of these genetic tests done.
2. If the opportunity presented itself, would you get one of these tests done? Why or why not?
• Groups not at the lab will use the class session to work on their group game design assignment. Here are the general guidelines of what you can try to get done in this 3 hour block.
Familiarize yourself with the “Group” section at the braveworldnow.wordpress.com site (link). Get into your groups and see if you can finish the following tasks:
– At least a skeletal narrative of the scenes (2 or max 3) in your adventure module. Rough maps for each of these scenes.
– Good edit of backstory for players
– Good edit of backstory for GM
– Discussion over the types of player characters you want to include in your adventure module (this way, each student can properly generate their character sheet before the next group meeting on March 24th)
Note that there will be copies of the “In Search of Tiger Joe” module floating around if you want to take a look (also available as a pdf at the Brave World Now site).
PCR data!
Recap information on the below data and what PCR is, can be found here.
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Session 11 and 12: (Mar 24 and 31) Continue with game design group project.
The next two weeks, you have class time to devote to working on your group project (see this link)
Note that it’s probably best to see if you can meet the following benchmarks:
(For end of March 24th)
– Make sure everyone looks like they’re on track with their character generation task.
– Assign GM roles (to one or two team members).
– Use the 3 hour block to essentially work on your elements/scenes so that they are starting to be in good (penultimate) shape.
– Delegate tasks to each team member, so that you’re group project is more or less finished before the next class meeting. i.e. backstories, maps, characters, scenes/elements.
(For March 31st)
– Ideally, if you follow the above, then this class session can be used for final edits, so that the project is basically finished and ready to hand in. If you have time left over, you can even “walk through” the game to see if it more or less works.
Information on the final exam, and some sample questions:
So, the final exam has been designed to take approximately 2 hours (1 hour for each the science and humanities). In brief, Allen’s section will ask you to write two essays, and Dave’s section will be composed of 6 short answer questions. Details for each section (with sample questions) below:
Part 1. Humanities:
Basically, you’ll be given a choice of two essay prompts for climate change, and two essay prompts for personal genomics. In each case, you’ll have to choose one to compose and write your essay on (i.e. two essays in total to work on in about an hour – each one about 3 pages double spaced). Below are a few examples of the sorts of essay prompts to expect.
Climate Change Essay Question
1. Can the UNFCCC process respond adequately to the global challenge of climate change? Discuss the basic provisions of the UNFCCC and the Kyoto Protocol, as well as subsequent efforts to establish a new treaty. What are the challenges that need to be overcome if a new treaty replacing Kyoto is to be signed and implemented? In your answer, include concepts and content from class, the instructional videos, the Copenhagen conference simulation, and at least two of the following readings (then, there would be a small list of the readings that is composed from those assigned in class).
Personal Genomics Essay Question
1. How might the sequencing of the human genome impact the relationship between medical services and patients? In what ways will medical decisions be impacted? What larger political and social concerns are raised by these changes? In your answer include concepts and content from class, the instructional videos, as well as those from at least two of the following readings (then, there would be a small list of the readings that is composed from those assigned in class).
Part 2. Science:
Essentially, the science section will be 6 short answer questions (1/2 page each, point form o.k) done within a timeframe of about 1 hour. Both topics (climate change and personal genomics will be on the agenda) The basic premise is that the first will be pretty easy, with the second getting a little tougher and so on. As well, it is my intention that if you study the notes well, 4 out of the 6 questions will be relatively straightforward – in fact like a lot of science final exams, if you really know your stuff, it would actually take you far less time than the one hour to complete (This is why at your usual 3 hour chemistry, physics or biology exams, you alway see a few students handing in their papers after an hour).
The last two science questions, I’m actually going to try and design it so that the answer is not immediately obvious. i.e. you’ll have to look at things a little more conceptually to get at the answer. Anyway, below are four examples of the kind of questions you can expect, the last one here being more in the conceptual vein.
1. Can you define “climate” and explain how the term is different from “weather.”
2. DNA polymerase plays a key role in replication. In terms of their function, they adhere to two steadfast biochemical rules. What are these two rules?
3. You’ll note that by looking at this graph of temperature change according to layer of atmosphere, the stratosphere goes from hot to cold as you lose altitude. Can you explain why?
4. I’m not sure if it was mentioned in the lecture (video or class) but the human genome has upwards of 97% of its code being non-functional or junk DNA. Bacteria on the other hand tends to not have any non-functional or junk DNA. Can you hypothesize why we (as humans) would have so much filler or useless DNA?
ANSWERS?
Well, the first three should be pretty straightforward if you peruse through the lecture notes. The last, however, takes a bit more thought, because the answer doesn’t technically exist (and certainly isn’t something I specifically went over in class). However, I’d be looking here for a good hypothesis that could explain why so much of “your” DNA appears to have no function (as compared to the e.coli example).
Answers could range from:
“Maybe we just think it’s non-functional, and haven’t discovered what it’s doing yet.” Not a great answer, because it would imply that there must be a hugely fundamental difference between bacteria and us – so fundamentally different that we can’t decipher at all what it is doing. i.e. whilst a possible hypothesis, there really isn’t a good argument for it (other than we’re still ignorant), although depending on the strength of your rebuttal of why we could be easily ignorant about such things you could still score on this question.
“We’re high maintenance, as compared to e.coli. We exist due to many cell divisions that act in a nuanced convoluted way. For crying out loud, it takes 9 months for us to even get out into the world. This means we want to protect ourselves from errors in the code as much as possible. One mechanism to do this is to dilute our genome with a high amount of places where errors are inconsequential. E.coli don’t have that because it’s no big deal if one of them messes up – these suckers duplicate themselves every 20 minutes. Mutations in the grand scheme of things is o.k. with e.coli. For us, mutations could be catastrophic for something so high maintenance and constantly in progress.”
“Maybe the 97% has something to do with how the good stuff is physically organized. i.e. Not all genes are used by each and every cell, so there needs to be a mechanism to allow certain genes to be accessible, whilst others are hidden or not allowed to be used. Maybe this 97% has something to do with this – it’s a question of controlling the architecture of that big old piece of DNA.” In other words, the 97% may be non-functional from a coding context, but happen to play a different role.”