Citizen Science – 2014 – Citizen Syllabus

Citizen Section 10 – Citizen Daniel [Newsome] Presiding Email for Citizen Daniel: dlnuzum@mifami.org

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This cover to Nature-Medicine shows numerous HIV-1 particles infecting a

cultured HeLa cell, captured using a Hitachi SU6600 environmental scanning electron

microscope. [Artificially colored]

Image courtesy of T. Deerinck, K. Fitzpatrick, J. Guatelli and M. Ellisman, NMCIR, UCSD.

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Citizen Blog [off line for the moment]

Bard’s CitSci -14 Web Site

Citizen Class Policy

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Updated: 1/21/14 7:31 AM

This Syllabus is only accurate for about one day in advance. The rest is pure speculation.

Date	When & Where	to do list for the meeting
Monday, 1/6/14 PBL and Civic Engagement	9:15 – 10:00 meet at New Henderson 100. Then go to Heg. 102 from 10:00 – 12:00. …then lunch… Then… 1:30 – 2:30 for CE Training in Olin LC 118… …and then from 2:30 – 3:30 our regular class back in Heg. 102.	Monday is a complicated day. Our class will be in motion most of the time. 1^st -We are meeting at 9:15 sharp at New Henderson 100 for a special assessment test. I recommend you get there a few minutes early. I will take attendance at 9:15 sharp. It’s very important that you be on time. 2^nd – We will meet in our regular classroom in Heg. 102 starting at ca. 10:00. We will have a regular class at this point, which will probably get out a bit early because of our special early-start time. 3^rd – From 12:00 to 1:30 we can eat a leisurely lunch. 4^th – From 1:30 to 2:30 in Olin LC 118 we will be trained for our Civic Engagement activity, which we will perform on Tuesday. 5^th – From ca. 2:30 to 3:30 we will have our regular class back at Heg. 102. Attendance will be taken at every step except the 3^rd one. The basics: evolution and faith Read and do the following things for the dribs and drabs of class time will have on Monday. -Read Citizen Class Policy. -Read: Public Policy Polling- Conspiracy Theories - 2013. Read these over fully and then do some cross-referencing and test some of your interpretations. E.g. Are Republicans more likely to buy into certain conspiracies than Democrats? Then think up a couple of conspiracy theories that you know of that were not included in this poll and write up a short paragraph describing them and the evidence for or against them. -Read: Gutting: Did Zeus Exist? What beliefs do we (probably) all share that result from our culture? Can you identify something that you believe in that you know is culturally constructed, or that is just silly, but it appeals to you all the same? Just list a couple, or if you can’t think of any, list some that you observe in the culture around you. [Crazy shit I or other people believe.] [ca. 3pp] -Read: Sandy Hook Conspiracy. -Read Chapter 1 from Dawkins’ The Blind Watchmaker [2.2 MB]. [ca. 17pp] Purely optional Late additions of interest: Here is someone trying to put some numbers on randomly assembling a 747 from a pile of parts: http://www.godsci.com/gsi/jmt/747.html. From the looks of the website, the author is building an argument for intelligent design.
Tuesday, 1/7/14 Civic Engagement Activity and regular class	Civic Engagement at 6:45 am. and 1:30 – 3:30 for regular class in Heg. 102.	We are officially supposed to be performing our Civic Engagement tasks in the morning. If CE is cancelled, just meet at 10:00 am at Heg. 102. I’ll post something on this web site and send an email if it is cancelled. Check your computers some time around 6:15 am for information. -Read Gould: Sex, Drugs, Disasters, and the Extinction of the Dinosaurs [PDF - 2.2 MB]. [7pp] - Read Keeley's "Of conspiracy theories." [2 MB]. [ca. 15pp] -Write up a couple of paragraphs on truth in relation to the Gould and Keeley readings. - Read Chapter 2 from Dawkins’ The Blind Watchmaker [2.2 MB]. [ca. 20pp] -Read over all the Citizen Science Faculty Bios and think about a person you might like to interview.
Wednesday, 1/8/14 PBL	10:00 – 12:00 and 1:30 – 3:30 Heg. rm. 102	- Read Chapter 3 from Dawkins’ The Blind Watchmaker [2.2 MB]. [ca. 30pp] - Read the following: Diamond’s “Worst Mistake” essay and this excerpt from Hesiod on Pandora’s Box. And then read Genesis punishments, Chapter 3, pp. 24-28. -Optional interest: Della Porta’s Natural Magick (from 16^th/17^th century) recipes for stuff similar to Elephant’s Toothpaste and invisible ink and other sciency tricks. Some totally reasonable, others totally crazy. Here is an excerpt from the first English edition on the legendary “weapon salve.” Notes to myself: -Nova’s “Dogs Decoded” (excerpts). Discussed evolution and genetic traits.
Thursday, 1/9/14 PBL	10:00 – 12:00 and 1:30 – 3:30 Heg. rm. 102 and “mandatory” academic orientation in Heg. 102 from 3:30-4:45.	- Read Chapter 4 from Dawkins’ The Blind Watchmaker [2.2 MB]. [ca. ??pp] - Read these three things: “The Story behind the Science” – on A. R. Wallace [2.5 MB] Wallace’s essay, “How to Civilize Savages. [ this is a .doc and it’s 26.5 KB] Darwin excerpt from the “The Descent of Man…” [4.9 MB] – For the Darwin reading, just skim over the first part but pay special attention to the last 2 pages. -Listen and take notes on this podcast - Bragg, Melvyn. 2012. "The Cell," In Our Time, BBC. Audio. Feel free to listen in groups and notate in groups. BBC link and/or my link. [same thing] Melvyn Bragg and his guests discuss the cell, the fundamental building block of life. First observed by Robert Hooke in 1665, cells occur in nature in a bewildering variety of forms. Every organism alive today consists of one or more cells: a single human body contains up to a hundred trillion of them. The first life on Earth was a single-celled organism which is thought to have appeared around three and a half billion years ago. That simple cell resembled today's bacteria. But eventually these microscopic entities evolved into something far more complex, and single-celled life gave rise to much larger, complex multicellular organisms. But how did the first cell appear, and how did that prototype evolve into the sophisticated, highly specialized cells of the human body? Guests: Steve Jones, Professor of Genetics at University College London; Nick Lane, Senior Lecturer in the Department of Genetics, Evolution and Environment, University College London; Cathie Martin, Group Leader at the John Innes Centre and Professor in the School of Biological Sciences at the University of East Anglia. - Brief introduction to cell biology: bacteria, viruses, etc. - Class debate. Is science good? Discuss Gould’s Dinosaurs. Krulwich on virus attack animation: http://www.youtube.com/watch?v=Rpj0emEGShQ
Friday, 1/10/14 Morning Laboratory and Afternoon PBL	Morning Lab from 9:30 – 12:30 in RKC rm. 111 and Afternoon PBL from 2:00 – 3:30 in RKC rm. 100	-Read over these laboratory regulations so that you can safely operate in the lab. -Look over the labs we'll be doing today. Pipetting. Environmental Isolates. - Read this: AntibioticResistantDeaths-CDC_Report-2013.htm - Read Levy’s “The Challenge of antibiotic resistance” [in antibiotic resistance section of anthology that you have in 3-ring binder.] Also here Levy-SciAm-AntibioticRes.pdf -Read Pollan’s “Power Steer.” [Write a short, short story somehow associated with this article.] -Look over these diagrams. Cell diagrams and bacterial names. I am hoping to put up a selection of materials on antibiotic resistance and to selectively assign some things to some people/groups. I’ll post this stuff over the weekend. We’ll discuss it all in class today.
Weekend		This stuff is all optional, but entertaining none-the-less. This just in on cats: Wade-CatsDecoded-SortOf-Unravels Some Mysteries.pdf. This is a short book review and excerpt from the book itself. Audio: -RadioLab “Speed” RadioLab on Rabies -RadioLab, WNYC, Jad Abumrad, Robert Krulwich, and others. 2011 [S10.04]. "Patient Zero," Radio Lab, WNYC. Audio, http://www.radiolab.org/2011/nov/14/ and/or iTunes podcasts and/or http://www.mifami.org/eLibrary/RL-PatientZero.mp3 (accessed 11/15/11). - InOurTime on Origins of Infectious Diseases -RadioLab “Inheritance” RadioLab has a website with more links and information if you want more resources.
Date	When & Where	to do list for the meeting
Monday, 1/13/14 Morning Laboratory and Afternoon PBL	Morning Lab from 9:30 – 12:30 in RKC rm. 111 and Afternoon PBL from 2:00 – 3:30 in RKC rm. 100	-Read Spector’s “Germs Are Us.” [This one is loads of fun.] - Read Maura-Bacteriophages21stC_food_medicine.pdf - Read Bacterial Resistance to Antibiotics.pdf- a short and sweet discussion of how bacteria become resistant to antibiotics. -Those who have people to interview on the topic of antibiotic resistance, please contact them and let them know that we’d like to interview them some time this week. Choose one of the following assignments: In both choices you must do some research on how bacteria can become resistant to antibiotics. I want you to pay attention to three things in particular: mutation, plasmids, and bacteriophages [sometimes referred to as simply “phages”]. By mutation, I simply mean the sort of mutation that would provide resistance to antibiotics. And plasmids and bacteriophages are other ways that bacteria can gain resistance. I have provided a few links to various sources that might help you figure this stuff out, but feel free to use other sources that you have or are out there. Be aware that plasmids and bacteriophages are both ways that bacteria can get genetic information that might give them the superpower of resistance to an antibiotic or antibacterial agent, but they also are being used therapeutically… they are used to put beneficial bits of genetic code into a bacterium. Choice 1: Write a story or descriptive essay about how bacteria can acquire antibiotic resistance. You can choose to write about them as biology or as allegory or metaphor. E.g. You could write about them in terms of computers with hardware and software. Write about all three ways listed below [i. random mutation, ii. plasmid, iii. bacteriophage]. This doesn’t have to be a fully polished product, but sketch out the concepts in some detail. It can be edited and prettied up later. The point here is to figure out a way to explain these mechanisms to regular people, so that they can understand the problem of antibiotic resistance and perhaps make better decisions in their personal lives, their consumer lives, and their political lives. Also refer to the Levy article from last Friday… the last page of that essay lists things that people and health care professionals should do to discourage the selective breeding of antibiotic resistant superbugs. Don’t make these too long. I am hoping we can use one or two of these, or sections from several, for our final project, so think of interesting approaches that would translate to a radio-audio-podcast format. Also feel free to think of stories of cows or sick children or space aliens or similar that might allow you to tell the story of antibiotic resistance. If you are so inspired, feel free to illustrate or provide accompanying original drawings that will assist in your thoughts, or do this as a comic strip of some sort. These may also be used in our pod-cast web site or similar. This could be a page or 2 of thoughts/ideas/pictures. [If you want, you may work in pairs, just make sure to do two people’s worth of work.] Choice 2: Write and/or record theme music for our radio show. Listen to some “RadioLab” episodes and any other audio productions of a similar nature like “This American Life” to get some idea on how music and/or non-verbal sound might work. [The RadioLab on “Speed” and “Patient Zero” uses sound quite effectively.] I could imagine having several jingles and interesting sounds or sound effects interspersed throughout the show. Think about the mechanisms involved in the transfer or development of antibiotic resistance. I realize that this is a rather tall order in abstract musical thought, but if you can figure something out… that would be great. Off hand, I can imagine a sort of “Peter and the Wolf” [Prokofiev] approach where you write up some sounds or musical lines associated with particular players like DNA, Plasmids, Bacteriophages, Mutation, Natural or Unnatural Selection, etc. I imagine only a few of you will feel comfortable doing this one. Please, someone do this one, even if you only sketch out a few ideas. Here are the three things I’d like you to research and incorporate in your Choice. i. Random or induced mutation combined with natural or unnatural selection. Our readings and discussions up until now have discussed this quite a bit. If you want more information, maybe try searching on “Darwinian Evolution” and/or “random mutation” or look this stuff up in a biology textbook or similar resource. Here is a general discussion of antibiotic resistance: /Antibiotic_resistance. ii. Plasmid exchange [Brock-Martinko-BiologyMicro-Bacteria.pdf [9.8MB], With this text you need not read or even understand this entire section, but several paragraphs starting on p. 156, then again starting on p. 159 describe how plasmids function. Feel free to read more. And/or look at wiki/Horizontal_gene_transfer and wiki/Transformation_(genetics) and wiki/Bacterial_conjugation. These cover plasmid genetic transfer and might be a nice simple starting point. iii. Bacteriophage, often referred to as “phages.” These are viruses that hijack bacteria. [Bacteriophage on Wiki, animation 1, animation 2, wiki/Transduction_(genetics)] We may watch this in class -Hunting-the-nightmare-bacteria-Frontline- ca. 1 hr. We will do this in class today or tomorrow: “Outsmarting a Superbug” in-class exercise.
Tuesday, 1/14/14 Morning Laboratory and Afternoon PBL	Morning Lab from 9:30 – 12:30 in RKC rm. 111 and Afternoon PBL from 2:00 – 3:30 in RKC rm. 100	-Read: Why I Donated My Stool- Fecal Transplants- NY Times -Read: Quammen AIDS-HIV. Read Chapters 85-96 (inclusive). We’ll finish the chapter tomorrow. Here is a link to explain the concept of R0, which is mentioned in this chapter. -Look over (read some of the abstracts and conclusions and look at the graphs and charts) the following early reports of what would later be called AIDS as you read about them in the Quammen reading: 1981-6.5-MMWR.pdf Read this one. It is a very famous report. pp. 250-252. 1981-7.3-MMWR.pdf pp. 305-308. 1981-10.0-Friedman-Kein-DisseminatedKaposiSarcoma.pdf 1983-Retroviruses-Marx-T-CellLeuk-linked-to-AIDS.pdf 1984-Auerbach-1984-ClusterOfCasesAIDS-patient0.pdf- Pay special attention to the chart on the second page. This is a very famous chart. 1984-Retrovirus-Levy-Isolation_of_Lymphocytopathic_Retroviruses-AIDS.pdf. Start to brainstorm about how this radio program will fit together. Look this over: World_Life_Expectancy.pdf Optional: Read: Curtis-Origin of AIDS- 1992- Rolling Stone as html or here as a PDF: Curtis-OriginOfAIDS-RollingStone-1992.pdf. As you read this very influential article, jot down criticisms you might have of its arguments and presentation. The conspiracy theory that this engendered is still playing out. 14pp. Here is Rolling Stone’s apology. Who do you think wrote this?
Wednesday, 1/15/14 Morning Laboratory and Afternoon PBL	Morning Lab from 9:30 – 12:30 in RKC rm. 111 and Afternoon PBL from 2:00 – 3:30 in RKC rm. 100	Read: Quammen AIDS-HIV. Read the rest this pdf. Read -Nowak- “How HIV Defeats the Immune System” -Optional: Here is a research paper on FMT: “Fecal microbiota transplantation in relapsing Clostridium difficile infection-2012” Optional: If anyone is interested, here is an abstract to a paper fro 2013: “Fecal microbiota transplantation: past, present, and future.” I probably can find the whole paper if anybody is intereted. - 4:00, RKC in lab 112, for interview with Anna Selmecki.
Date	When & Where	to do list for the meeting
Thursday, 1/16/14 Computer Laboratory and PBL	10:00 – 12:00 and 1:30 – 3:30 Both sessions in Hend. rm. 101A	- Read sections 23-25 (inclusive) in Quammen’s chapter on mathematical modeling and malaria. We’ll read the rest for tomorrow. -Listen to RadioLab, WNYC, Jad Abumrad, Robert Krulwich, and others. 2011 [S10.04]. "Patient Zero," Radio Lab, WNYC. Audio, http://www.radiolab.org/2011/nov/14/ and/or iTunes podcasts and/or http://www.mifami.org/eLibrary/RL-PatientZero.mp3 (accessed 11/15/11). Along with the content, notice the production, the sounds, the way interviews are incorporated, the structure, etc. -Population graphing exercise on paper then on computer.
Friday, 1/17/14 Computer Laboratory and Faculty Lecture Series	10:00 – 12:00 in Hend. rm. 101A and 1:00 – 3:30 Faculty Lectures in Olin Auditorium [I am moderating]	- Read sections 26 to the end in Quammen’s chapter on mathematical modeling and malaria. Remember… class at 10:00 in Old Henderson 101A and after lunch starting at 1:00 lectures at Olin Auditorium. Both manditory. Send me your notes, illustrations, and whatever else you have for the radio show asap so that I can edit them and put something together for tomorrow morning that we can actually record. I’d like to record the first few minutes of the show as well as have those Skype interviews done if at all possible.
Weekend		Interesting sidenotes: Recall my mention of Subcomandante Marcos? This is a really interesting documentary: http://www.youtube.com/watch?v=4TffwElt_UU
Date	When & Where	to do list for the meeting
Monday, 1/20/14 Faculty Lecture Series M. L. King Jr. Day	Faculty Lecture Series 9:00 – 12:00 in Olin Auditorium	Morning: STARTING at 9:00 am sharp. Set multiple alarms! I speak in the morning session. You are required to attend this. Attendance taken…etc. Optional final-project-work in afternoon. Nothing is scheduled for you in the afternoon, but, working on some radioshow stuff might be a good idea and potentially fun…. the arty and musicy stuff….
Tuesday, 1/21/14 Computer Laboratory and PBL	10:00 – 12:00 and 1:30 – 3:30 Both sessions in Hend. rm. 101A	Be prepared to discuss the Quammen material on malaria that was assigned last week. Below is the main part of the assignment due on Tuesday. I suggest reading one of each of these each day over this long weekend. Check back and refresh your browsers to see if more is added. I’ll probably be emailing many of you with project mini-assignments too. Be ready to read up on a couple of topics and write up some short scripts to be recorded…. -Read Fullilove-Two Worlds of AIDS-AIDSi n Black America-FRONTLINE.pdf -Read: Smith-HIVdenialInternetEra-2007.pdf- good overview of history of denials. -Read Hayes, B. (1998). "The Invention of the Genetic Code." American Scientist 86:8-14. This article is a bit dense at first. It describes several attempts at figuring out the code arrangement of DNA. The first several described don’t fully work out, but it demonstrates nicely how this stuff is developed. It also shows how mathematics intersects biology. In class: Population data: PopulationGraph-DataSheet.doc or in PDF if the .doc is giving you problems: PopulationGraph-DataSheet.pdf Here is a worksheet I’d like you to fill out in pairs: population graph questions.pdf -Start graphing, statistics, and probabilities on paper. -My Excel simple population model. -Joey’s R demo. along side Excel SIR. -Henrietta Lacks video may be shown in class.
Wednesday, 1/22/14 Computer Laboratory and PBL	9:30 – 10:30 10:30 – 12:00 and 1:30 – 3:30 All sessions in Hend. rm. 101A	Like the first day of class, we are once again taking that assessment test thingy. This time we meet in our regular computer lab room, Henderson 101A at 9:30 sharp. We will have our regular class starting at 10:30. The final readings are about two very contraversial studies. Read - Thomas_and_Quinn_Tuskegee.pdf Read - McNeil-SyphilisExperimentRevealed-U.S. ApologytoGuatemala-2010.pdf Read - Cohen-Lynch-GuatemalansUsedinExperimentsDeserveCompensation.pdf Read - Zimbardo-1973-StudyPrisonersGuardsPrison.pdf Optional: The Henrietta Lacks reading in you 3-ring binder…. or just watch this interview with Rebecca Skloot, the author of the story of Henrietta Lacks: Skloot interview And this update on the He-La story: HeLa-update.pdf (summer 2013) In class we will listen and look at the final project, in whatever state it is in.
Date	When & Where	to do list for the meeting

Useful links: WHO, CDC, PubMed, eterna, PloS

Useful information:

Prefixes to the Names of Units

We only use the centi, milli, and micro in lab.

Multiplier	Prefix	Symbol	Multiplier	Prefix	Symbol
10^-1	deci	d	10	deca	da
10^-2	centi	c	10^2	hecto	h
10^-3	milli	m	10^3	kilo	k
10^-6	micro	µ	10^6	mega	M
10^-9	nano	n	10^9	giga	G
10^-12	pico	p	10^12	tera	T
10^-15	femto	f	10^15	peta	P
10^-18	atto	a	10^18	exa	E

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Full references to some of the readings.

Dawkins, Richard. The Blind Watchmaker. New York: Norton, 1987.

Gould, Stephen Jay. "Sex, Drugs, Disasters, and the Extinction of Dinosaurs." In The Flamingo's Smile: Reflections in Natural History, 7pp. New York: W. W. Norton, 1984.

Keeley, Brian L. "Of conspiracy theories." The Journal of Philosophy 96, no. 3 (1999): 109-126.

Maura, Damien, and Laurent Debarbieux. "Bacteriophages as twenty-first century [sic] antibacterial tools for food and medicine." Applied Microbiolgy and Biotechnology 90 (2011): 851-859.

Pollan, Michael. "This Steer's Life (Power Steer)." New York Times Magazine, March 31, 2002.

Specter, Michael. "Germs Are Us." The New Yorker Oct. 22, 2012, 32-39.

Email for Citizen Daniel: dlnuzum@mifami.org