Branching it out

If you’re puzzled about phylogenetic trees, this paper is for you! It may help with your analysis for your blog post!




Baseball in the time of Cholera

Please watch this tonight. Tomorrow we’re going to learn about Cholera and the recent controversial involvement of the UN in initiating the outbreak.

<p><a href=”″>Baseball in the Time of Cholera</a> from <a href=””>RYOT</a&gt; on <a href=””>Vimeo</a&gt;.</p>



Night time work!

Thank you for your wonderful participation in reading and performing today. You guys are a riot. I especially appreciated the contributions during the vaccination discussion.

Thank you Sophie for the podcast suggestion. Here is the link if anyone would like to listen to the whole thing!

Tomorrow we are in the lab in the afternoon. Please read the lab handout about environmental isolates, transformation and the Keyboard Proposal. There will be a quiz in the morning about the lab and what we learnt today about vaccination. I will email out the  Keyboard Proposal and transformation lab info.

Writing assignment due Monday morning at 9am. Please write a blog post between 500-700 words. It can be a story, a news report or an opinion piece etc. I would like you to write about one of the papers that we have covered in the class (Paul Turner phage therapy, Patient zero HIV genotyping, your assigned journal club paper or vaccination using the documents I handed out today and a paper I will put in the email tonight). I want you to include a Figure from the paper and to talk about it (what are the variables, what kind of figure is it, what did you learn from the figure). I’d also like you to include at least one piece of creativity/media (link to a podcast, illustration, photo, video, poem) and to include it in your story/news report etc. explaining how it is relevant to your story. Please submit a draft by email to me by tomorrow at 5pm. The draft should tell me what you plan to write and include a short paragraph of one of the ideas you are going to expand on.

Finish Part III and IV for the Tragic Choices case study. Please write at least 200 words for your response. You have all the info you need from the handouts you received today. This is due by tomorrow morning.

The weekend will be lighter for homework. Please push yourselves, we are finished Rotation 2 today and starting Rotation 3 tomorrow! Remember we are in a new room in RKC.

Have a great night!


Wednesday Work!

Thank you for all your presentations today. You have come up with some fun and interesting experiments to do in the lab!

Contagion screening

7pm at RKC 103. Please write about at least 3 concepts you see in the movie that we have discussed in class and write 1 question you have about the science in the movie. Enjoy the movie, see you there!

Journal Club

Tomorrow you will be presenting your assigned genome sequencing paper (Influenza, TB, Hemp, Economics) tomorrow in groups. Be prepared to teach your paper to your classmates.

Proposal Review

You will be assigned 3 proposals to read and review. I will send you an email with a table that shows which proposals you have to review and whether you are Primary (1), Secondary (2) or Tertiary (3) reviewer for that proposal.

As the “Primary” reviewer for the paper, please write a paragraph (200 words at least) giving a summary and your review of the proposal. Please provide positive and constructive feedback about the proposal. Support and defend your statements. Also provide a score for each category and the final score (average of the score you gave for each category). As the “Secondary” reviewer write a sentence and give a score. As “Tertiary” reviewer just give a score.

When you score- give a score under each category and then take the average of all your scores excluding the final score (to get the average, add up the score from each category and divide by the number of categories). This number (your final score) should fall under the score possibilities for the Final Score. Make it clear what your individual category scores and final scores are.


Final score:

Outstanding                                       3.5- 5.0

Acceptable, but low priority         2.5- 3.5

Rejected                                              0.0- 2.5



Outstanding                                       3.5- 5.0

Acceptable, but low priority         2.5- 3.5

Rejected                                             0.0- 2.5



Outstanding                                       3.5- 5.0

Acceptable, but low priority             2.5- 3.5

Rejected                                             0.0- 2.5



Outstanding                                       3.5- 5.0

Acceptable, but low priority             2.5- 3.5

Rejected                                             0.0- 2.5



Outstanding                                       3.5- 5.0

Acceptable, but low priority             2.5- 3.5

Rejected                                             0.0- 2.5


Credibility (references):

Outstanding                                       3.5- 5.0

Acceptable, but low priority             2.5- 3.5

Rejected                                             0.0- 2.5


Final Score

(add all scores and divide by 5)



Homework tonight!

Remember to be on time to CE tomorrow morning and have fun! It is a much better experience for the 8th graders if you have fun and are enthusiastic.

For homework:

Become an expert (to the best of your ability) in the paper that you have been assigned. I want to see your concept map… here is an example of one:



In addition to the concept map, take notes and/or draw cartoon for the methods. Pick a Figure and look at the Figure description/Results section/Methods section that refers to the Figure. I don’t expect you to explain all the details, but I’d like you to try and write what you do understand and don’t understand. I want to see that you tried and battled through the technical terms to find the meaning. Tomorrow you will present the paper and what you understand about the paper.

For your research proposals, I’d like you to make sure that everyone’s role is equal and indicated on the proposal. I want you to think about variables and controls, how will the other tests such as the Kirby- Bauer and motility tests characterize your isolate? Do you anticipate your isolates to be Gram negative or positive- how will you test for that? I want you to comment on how the number of samples you use in your experiment will affect/support/or reject your hypothesis. You will present your proposals tomorrow afternoon. Be ready to talk about the part that you contributed. We will give the proposals to Dr. Will’s class at the end of the day.

If you’d like to watch the videos from today here they are:

Thank you for your participation (and bearing with the pseudo structured) Jeopardy game today. If there are concepts that we reviewed that you are still a bit weary about, please email me. I am happy to explain, provide a video or podcast etc. to help you learn.

Good night!

Sample proposal

Happy Saturday!

I hope all of you are enjoying your weekend, getting some sleep and tackling the homework! Here is an example of a research proposal. Please remember to put a space between your sections or mark them as bold with a header. I would prefer them not to be in this example’s condensed format. As for the content- look at the type of language used and try to incorporate that style in your writing.


TGIF… but homeworks for the weekend!

Thank you for all your participation today! I really appreciate the feedback and reflections from the week. I will try my best to incorporate all of your suggestions. If you haven’t received feedback from at least one homework assignment, not to worry, I have been reading them and will provide feedback soon. I will be sending out midterm feedback this weekend by email. I believe all of you can achieve a Satisfactory pass of citizen science and I will provide some feedback on how to continue or make changes to get on the Satisfactory path.

For homework this weekend:

Read the Nature paper I will send by email. Be an active reader and take notes on what you don’t understand (terminology, techniques, concepts). Write an abstract that summarizes background, hypothesis, methods, results and major outcomes of the study. Be prepared to explain one of the Figures with phylogenetic trees. I will also be emailing a phylogenetic tree activity that will help you understand how the trees in the Nature paper were built and  I have included a Review paper that explains some of the major concepts in the Nature paper.

I’d like you to write 3 sentences at least on quarantine. What is it? Is it regulated or voluntary? Are there differences in quarantine procedures across  the US or is there a federal plan? How do you think a deadly or unknown disease carrier should be treated? What would your steps be to protect the person and the public?

I will include in the email a paper about variables and elements of experimental procedures by Fisher. I would like you to write out at least 3 important elements of the experimental method that are discussed in the reading.  Explain how they can influence the outcome of an experiment.

All of the readings and writings are due Tuesday by 10 am.

Please bring them to class or email them.

Remember that a written copy your Group Research Proposal is due Tuesday 10am. I would like the 2-3 pages length with all of the categories listed on the assignment sheet (excluding in the length) including the list of sources. Make sure you divide and conquer and everyone in the group has equal amounts of work.

You have 3 days to work on all of this so I am expecting substantial and rich content in your writing. I know you are all great writers and I would like to be pleasantly surprised by the efforts you put into your Research Proposals and your other writing assignments.

Remember you have the option for a final project. This is your moment to get creative with science. The sky is the limit in the format (write a blog post, make a video, record a podcast, write a song, perform a play, draw something, paint something, dance). The content should relate to a concept in infectious diseases that we do in the course and I would like you to explain how it relates to the course in a sentence or two.

Have a lovely weekend! Monday afternoon we are in Faculty Talks in Olin Hall. Check your schedule for the time. I will be there taking attendance 15 min before.


HIV life cycle videos


We have done a lot of talking, auditory clips and a few videos about the human immunodeficiency virus (HIV). We talked about anti-retroviral drugs like protease inhibitors that are used against HIV. For further specific information about HIV life cycle, reverse transcriptase and how the drug AZT targets reverse transcriptase, I have posted three short video animations.