Ebola – How many will be infected?

Credit: CDC/ Sally Ezra

Credit: CDC/ Sally Ezra

There is lots of discussion both in the popular and scientific media about how many people will be infected, and how many more will die. As both the discussion, fear, and grim resolve to do something increase, it is important to understand what uncertainties are in the predictions.

Science Insider has a brief write-up here of the Gomes et al paper in PLoS Currents. The paper is a good read, and pay particular attention to the disease model section to get a nice write-up of the inner workings of their estimates.

The paper does a nice job of breaking down R0, or R nought, the basic reproduction rate. If the paper is to much, run on over to Wikipedia here for a quick brush-up on what R0 is and how it is used.

Christian Althaus’s paper, also in PLoS Currents contains one more piece of the puzzle:

Two key parameters describing the spread of an infection are the basic and the effective reproduction numbers, Ro and Re, which are defined as the number of secondary infections generated by an infected index case in the absence and presence of control interventions. If Re drops below unity, the epidemic eventually stops.

Re is an interesting variable, and this is really the variable that news organizations are struggling to define. Re address the question of what happens to the infection rate if the proper health care steps, “control interventions” are put in place. This gets to the point of the question, how many will continue to be infected?

Short Guide To Presenting Scientific Material – Part 3 – Presentation

I had a public speaking teacher in college who used to sit in the back of the classroom and start to moan when the presentations got to boring. If the presentation didn’t improve she would crumple some paper and start to throw it at us, we all knew she was a total nut-job, but the cool thing was that she was always right. When she started to complain, it was only mirroring what the class was already thinking. When she was completely fed-up, we were completely bored. If the internet and the laptop had been invented yet, we would have all wandered away, instead we just stared blankly, hoping it would be over soon.

There are a bunch of things that you can do to engage your audience. Try all of these things, remember, SCIENCE IS TOUGH, GIVE THE AUDIENCE A BREAK!

  • Start off the right way. Introducing yourselves is always smart, even if everyone knows you. A presentation is just like welcoming someone into your house, greet those who are in the audience as you would a guest.
  • Try not to refer to other speakers with pronouns. Use names, it puts your audience at ease. Each time you introduce someone, say “[Name] will tell you more about [topic]. It let’s the audience know what is going to happen next, and who will tell them about it.
  • Talk to the audience. It is good to have reference cards or screen notes, but you must engage the audience. This can be very hard and it takes practice, as you often want to have reference cards to keep yourself on task. Practice reading a sentence or two and then looking up to make sure that your audience is with you.
  • Don’t read directly from the slides. It turns your back to the audience and worse often seems like you have never seen the material on the slides before.
  • Speakers should come out from behind the podium. The podium and all that stuff on it often acts a crutch, it lets the speaker hide behind a protective wall of wood, glass, metal, and technology. Don’t use it this way. Move around, use your body language to make points and engage the audience. Look at them, use their faces to gauge wether or not they understand (or care) about your topic.
  • If you are not presenting. Have a seat, you don’t have to stand there and feel funny. It looks odd to the audience.
    • If you cannot sit, them move off to the side and look interested in what the presenter is saying. Do not engage in side conversations or distract the audience in any way.
  • Watch out for “you knows”, “ahs”, “likes” and “ums”.
    • These are unavoidable when you first begin speaking in front of audiences, it will pass. Just be aware of it, and each time you speak it will become less frequent.
    • If you get nervous or confused about what you want to say next, take a break and have a sip of water. Ask if the audience has any questions while you think and get back on track.
  • If you want to take a quick audience survey, use a show of hands. An audience will often raise their hands before they speak.
    • Don’t throw questions out there and then wait for someone to answer as this gets awkward quickly. Have a backup plan, “let’s see a show of hands…”, often works.
  • Practice the entire presentation with all of the presenters there. Look for redundancy and remove it from the overall presentation.
  • If you are nervous when giving a presentation be sure to separate nervous laughter from actual laughter. The audience does not see the difference, so if you talk about robberies where people are killed, and you laugh, even if it is just nervous laughter, it will be misinterpreted.
  • Never guess at answers to questions you don’t know. Just admit you don’t know and you will look it up and get back to them. There is no way that you can know all the answers, the audience will understand.
    • If you feel it is something that you absolutely think you know, but are a little unsure, tell the audience that you are speculating, and you and they will have to check your answer.
  • Restate questions; it give you time to think and also let’s the questioner know that you understand what they are asking. This way the  the whole audience understands both the question and your response.

Exercise, Vitamins, and Health

ImageReading through the New York Times I came across a cool article describing an unusual relationship between antioxidant type vitamins and health. The NYT article point to the Journal of Physiology article which contains a number of very cool insights. You can take a look at that article here.

 The coolest part about all this is how much it makes sense, though at this point, be forewarned, all of this is speculation. During exercise the body needs lots of oxygen, and that is just what the individuals in this study did. Now these individuals were divided into two groups, one taking antioxidant vitamins C and E, the second placebo.

Both groups went through training and both groups showed improvement in running performance. Yet the antioxidant group lacked an increase in “mitochondrial COX4 protein content”. “Big deal”, you say but here is the kicker, and the reason for my little mitochondria picture. COX4 protein content is a proxy for measuring how many new mitochondria are being added to cells. The exercise that the participants are doing should do a number of things to their muscles. Satellite cells should start dividing, muscle mass may increase; skeletal muscles will adapt to the new stresses being placed on them. One of those adaptions are increases in the number of mitochondria within muscle cells.

The authors have a hypothesis that this disruption of mitochondrial biogenesis is intimately tied to the redox state of the cell. If the cells don’t built up enough free radicals, the mitochondrion producing machinery doesn’t get turned on. In the literature this is refered to as the connection between mitochondrial biogenesis and the cellular redox state. That assertion is well supported in the literature; for a quick review of this, have a look here. What is cool about this study is the connection between reasonable oral does of antioxidant vitamins (maybe not reasonable, but have a look here) and endurance training. We will have to see what happens next.

Short Guide To Presenting Scientific Material – Part 2 – Content

This is part 2 of a three part series.

Content is king. Nothing puts an audience off more quickly than if they think (rightly or wrongly) that they have been had. Content goes back to when you accepted the offer to speak, make sure that you have something important to say, and that you say it clearly, informatively, and with an eye to keeping your audience interested. Science is hard and it is harder to try to explain science, you are always on the edge of simplifying without watering down the complexities of what you are presenting. If you do this right, you start with a story that leads to larger concepts, which in turn, lead to some synthesis of those ideas. The coolest part of this is when this last step of synthesis happens in the minds of your audience.

Prepare yourself, be the expert, make it clear, know your material!

General Points

  • Stay on topic; remember it is a scientific presentation. This is true for any presentation that you do. Once you have assembled all of your material, ask yourself if each of the slides belongs. If the slide is not DIRECTLY related to what you are presenting move it to the end of the presentation. This way you have it if someone asks, but you don’t present it during the normal presentation.
  • Avoid “public service announcement” type language. We all know that some of these things are bad for us. This is a healthcare presentation. Stick to the facts that are relevant for that audience.
  • This point is really related to the larger concept of knowing your audience. Don’t waste time on material that your audience already knows. There is to little time in life to have to listen to material that you have heard before. You know what you and your peers have already heard. Tell them a complete story, but don’t spend to much time on review.


  • I think the video is always tough choice. It can go either way, and I am often interested to see what the class’ response to the video might be.
  • The rule of thumb for video use? Only if it is directly applicable to the topic.
  • If you decide to use one, have it queued-up and ready to go. Check before your presentation that everything works (audio and video).
  • Don’t use videos to take up presentation time. This is always painfully obvious.


  • Use standard capitalization and punctuation.
  • Instead of acronyms I would prefer that you use the full names of things with their acronyms in parentheses. Take the time to write acronyms out, that way we can all relearn them. When speaking, feel free to use the acronym.

You Are The Expert

  • When giving a presentation, you are the expert, Do not:
  • present a hypothesis as fact
  • present opinion as fact
  • You can present a hypothesis and you can state your opinion, but you MUST be very clear that you are now covering the hypothetical and opinion. People will believe what you say. You have the honor and the responsibility of being an expert.
  • Whenever you refer to s study, let us know:
  • Who did the study.
  • Where was it done.
  • Where was it published
  • Has it been repeated?

Study Types

Classification of different study types (Röhrig et al, 2009) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689572/

Classification of different study types (Röhrig et al, 2009) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689572/

•When describing complex names such as compounds, diseases, people, and places they should be practiced  known. You are teaching us, it is your responsibility to practice beforehand and teach us the most common pronunciation.

•If you are going to project a figure, you should check to make sure that the audience can read the material. Go to the room where you are presenting beforehand if possible and check. Use the best resolution figure possible.

Finally feel free to be a bit redundant (but only a bit) when closing your talk. COme back to your central thesis.

Prepare yourself, be the expert, make it clear, know your material!

Short Guide To Presenting Scientific Material – Part 1 – Organization

Presentations are hard work and in allot of ways you are out there alone in front of a group, opening up in ways that can be difficult for you and the audience. The challenges and mistakes that I see are pretty common and I have identified some of those. With a little preparation and review you can avoid most of these issues, and present difficult material in a way that engages your audience. Most of the items below really boil down to the trust between you and your audience. A presentation is an agreement between you and them. You promise that you understand and have researched what you are presenting and they give you their time and attention.

It is a great opportunity for you and them. Don’t waste it.


  • Use standard referencing. Each slide’s contents must have a small, but identifiable reference on it. At the end your last slide should be the list of all of the references used throughout the presentation. This way you only need author year, on the individual slides.
    • Use this site as a guide for how references should be formatted: http://jama.jamanetwork.com/public/InstructionsForAuthors.aspx#References
    • Break up complex items into smaller diagrams, tables or slides. You are asking the audience to digest lots of information at a time. Break complex ideas down into understandable parts.
    • Avoid spelling errors in slides. It just puts the viewer off; they immediately distrust you if there is sloppy unchecked work in the presentation.
    • Any visual, chart or graphic must have the reference directly on the slide. If you took the material from somewhere else, then be sure to give them credit. This way you do not get into trouble.

“And That Concludes Our Presentation”…


Graduates From j.o.h.n. walker’s Flickr photostream

When we ask students what drives them crazy, they sometimes respond that they wish we had given them a packet describing everything they would have to do to graduate.

There is, and we do tell them. The thing here is continuity of service. They start getting these packets from day 1, before they even sign on to the college. Some things are verbal, some things are written. All get repeated.

The problem with being a student is the continuity. Most students don’t realize that the program that they are in is fluid, so students admitted the year before and students admitted the year after may well have a different curriculum and requirements.

This shocks students. It is their education, it seems to the students that it is a giant monolithic event, one unchanged path towards a degree. Yet for faculty and administrators the curriculum and requirements are a fluid space, different for almost every year.

So back to continuity, how do we take the two perspectives and bring them into one place, where students are satisfied and faculty understand. Students should allows have access to a forward and backward look across their own curriculum and requirements, but currently that takes some work to figure out.

Yes, I can hear you thinking, as a school we already have allot of this functionality, but we don’t use it.

The Rx system we use here, or really, any portfolio system could be used this way, students get a pre-formatted space when they arrive. Pre-formatted in the sense that their handbook goes from a dead pdf online to a more interactive space that they (the student) fill with their grades and accomplishments, as it fills, they can check items off and see how close (or far) they are from reaching their goals, that year, that rotation, ultimately graduation.

Tough request, but there are places were we could do a better job. Since students get packaged by “year of entry” we could probably use the same system as is in place now, but we would improve the continuity for the student by moving it to a live space online where they could look at it when they are ready.

We tell them everything they will have to do in the beginning of their first year, but all they hear is “and that concludes our presentation”. Towards the end they ask us what is it that they have to do and are they almost done, but all we hear is our own perspective whispering, “they didn’t listen”.

That is the divide that we have to cross.