Citizen Science – 2014 – Citizen Syllabus
Citizen Section 10 – Citizen Daniel
[Newsome] Presiding
Email for Citizen Daniel: dlnuzum@mifami.org
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.
Citizen Blog [off line for the
moment]
REFRESH THIS
PAGE EVERY TIME YOU OPEN IT
If the
"Updated" time (below) is more than a few hours old, REFRESH –
REFRESH – REFRESH ! ! !
Remember, the
Chrome browser might not work for the PDFs. Try another if you have a problem.
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. Éthen lunchÉ ThenÉ 1:30 –
2:30 for CE Training in Olin LC 118É Éand 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. 1st -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. ItÕs very
important that you be on time. 2nd – 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. 3rd – From 12:00 to 1:30 we
can eat a leisurely lunch. 4th – 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. 5th – 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 3rd 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 canÕt 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 DawkinsÕ
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. IÕll 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 DawkinsÕ
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 DawkinsÕ
The Blind Watchmaker [2.2 MB].
[ca. 30pp] - Read the following: DiamondÕs
ÒWorst MistakeÓ essay and this excerpt from Hesiod on PandoraÕs
Box. And then read Genesis
punishments, Chapter 3, pp. 24-28. -Optional interest: Della PortaÕs Natural
Magick (from 16th/17th century) recipes for stuff similar
to ElephantÕs 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 Òweapon
salve.Ó Notes to myself: -NovaÕs ÒDogs DecodedÓ (excerpts). Discussed evolution and genetic
traits. |
Thursday, 1/9/14 PBL |
10:00 – 12:00 and 1:30 – 3:30 Heg. rm. 102 and ÒmandatoryÓ academic orientation in Heg. 102 from 3:30-4:45. |
- Read Chapter 4 from DawkinsÕ
The Blind Watchmaker [2.2 MB].
[ca. ??pp] - Read these three things: ÒThe
Story behind the ScienceÓ – on A. R. Wallace [2.5 MB] WallaceÕs
essay, ÒHow to Civilize Savages.
[ this is a .doc and itÕs 26.5 KB] Darwin excerpt from
the ÒThe Descent of ManÉÓ [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 GouldÕs 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 LevyÕs ÒThe Challenge of antibiotic
resistanceÓ [in antibiotic resistance section of anthology that you have in
3-ring binder.] Also here Levy-SciAm-AntibioticRes.pdf -Read PollanÕs
ÒPower Steer.Ó [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. IÕll post
this stuff over the weekend.
WeÕll 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, 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
ÒInheritanceÓ 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 SpectorÕs ÒGerms Are Us.Ó [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
weÕd 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 ÒphagesÓ].
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 therapeuticallyÉ 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 doesnÕt 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 FridayÉ 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.
DonÕt 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 peopleÕs worth of work.] Choice
2: Write and/or record theme
music for our radio show. Listen
to some ÒRadioLabÓ episodes and any other audio productions of a similar
nature like ÒThis American LifeÓ to get some idea on how music and/or
non-verbal sound might work. [The
RadioLab on ÒSpeedÓ and ÒPatient ZeroÓ 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 outÉ that
would be great. Off hand, I can
imagine a sort of ÒPeter and the WolfÓ [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 IÕd 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 ÒDarwinian EvolutionÓ and/or Òrandom
mutationÓ 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
Òphages.Ó 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:
ÒOutsmarting a SuperbugÓ 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). WeÕll 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
StoneÕs 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-
ÒHow HIV Defeats the Immune SystemÓ -Optional: Here is a research paper on
FMT: ÒFecal
microbiota transplantation in relapsing Clostridium difficile infection-2012Ó Optional: If anyone is interested, here is an
abstract to a paper fro 2013: ÒFecal microbiota
transplantation: past, present, and future.Ó 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 QuammenÕs
chapter on mathematical modeling and malaria. WeÕll 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 QuammenÕs
chapter on mathematical modeling and malaria. RememberÉ 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. IÕd 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
takenÉetc. 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 funÉ. the arty and musicy stuffÉ. |
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. IÕll
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 recordedÉ. -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 donÕt
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 IÕd like you to fill out
in pairs: population
graph questions.pdf -Start graphing, statistics, and
probabilities on paper. -My Excel simple population model. -JoeyÕs 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 binderÉ. 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 |
102 |
hecto |
h |
10-3 |
milli |
m |
103 |
kilo |
k |
10-6 |
micro |
µ |
106 |
mega |
M |
10-9 |
nano |
n |
109 |
giga |
G |
10-12 |
pico |
p |
1012 |
tera |
T |
10-15 |
femto |
f |
1015 |
peta |
P |
10-18 |
atto |
a |
1018 |
exa |
E |
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