Book Review – Spillover: Animal Infections and the Next Human Pandemic by David Quammen

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Scanning electron micrograph of Ebola virus budding from the surface of a Vero cell (African green monkey kidney epithelial cell line). Credit: NIAID

I’ll admit it. Most of my perceptions of the Ebola virus and its effect on people have been based on what I read in ‘The Hot Zone’ when I was in college.

I received the book as a gift and started to read it as I traveled home for Christmas break.  I say ‘started’ because I couldn’t get past Richard Preston’s opening description of an infected patient’s meltdown while traveling on a small plane. Did I mention that I was traveling on a 19-seater airplane? Those images, when combined with my own motion sickness, created a very memorable experience.

While these images might have been memorable, I’ve realized, after reading David Quammen’s Spillover: Animal Infections and the Next Human Pandemic, that they are not that accurate. Quammen’s book centers on spillover events, moments when a pathogen (virus, bacteria, fungus, protist, prion or worms) crosses from one host to another and thrives in the new host. In this book, he details the diseases caused by the Hendra, Ebola, HIV, and SARS-CoV viruses, Plasmodium sp. protists, and Coxiella burnetii and Borrelia burgdorferi bacteria. And, while the symptoms of Ebola viral infections are horrible, most patients do not bleed profusely or meltdown.

Borrelia burgdorferi, the pathogen responsible for causing Lyme disease (Darkfield microscopy magnified 400x). Credit: CDC - PHIL #6631

Borrelia burgdorferi, the pathogen responsible for causing Lyme disease (Darkfield microscopy magnified 400x). Credit: CDC – PHIL #6631

Quammen’s updated reporting on several zoonotic infections was one of my favorite parts of the book. It’s been several years since my virology class in college so I enjoyed getting caught up on the latest (as of the 2012 publication date) research and knowledge for several viruses. This was especially true for Quammen’s chapters on HIV. Quammen does an excellent job of summarizing HIV research and the AIDS pandemic – human clinical discoveries, SIV research, and the search for the spillover event that merges the human and non-human primate diseases. I had followed HIV research while in college but hadn’t kept up with the big picture of the how, where, and when of the HIV infection timeline.

HIV budding out of a human immune cell. Credit: NIH - PD-USGov-NIH

HIV budding out of a human immune cell. Credit: NIH – PD-USGov-NIH

Another part that I liked about this book was the fact that Quammen traveled to the sources of the spillover events. In the HIV chapters, Quammen follows a proposed route through Cameroon and the Congo that brought HIV into the human population. When discussing Ebola, Quammen opens by describing a previous trip to Gabon while chronicling Michael Fay’s Megatransect for National Geographic; two of Fay’s crewmen has been present during an Ebola outbreak in a Gabonese village in 1996. The level of detail from this on-the-ground approach helps the reader visualize how these spillover events can and do occur.

Quammen concludes ‘Spillover’ with a discussion on the big question, ‘What’s next?’ What will be the next big disease outbreak and when will it happen? Quammen’s response – it depends – is followed by a list of all the activities that humans currently engage in that can contribute to the next spillover event. “…We visit monkey temples in Asia, live markets in India, picturesque archeological sites in New Mexico…and then we jump on our planes and fly home.” However, Quammen counters that this book isn’t meant to be a harbinger of doom but is meant to educate us and make us smarter about the choices we are making. When it comes to infection rates, any choice that an individual makes can have an impact on the infection rates for a population. “An individual human may choose not to…have unprotected sex with the prostitute, not to share the needle in a shooting gallery…not to board a plane while feeling ill…” It is through education that individuals will have the information necessary to make the type of decisions that will reduce the infection rates for everyone.

Taking Ownership of Your Career: Developing an Individual Development Plan (IDP)


Further elaboration on the IDP from the NIH Office of Intramural Training and Education….

Originally posted on OITE Careers Blog:

Silhouetee of a person looking at arrows pointing in different directions Have you drafted a career plan? Do you know if you have the required skills for your dream job? Figuring out the next step in your career and how to prepare for it can be stressful. But developing a plan, early on in your career, will help guide you through this process of identifying and achieving your career goals.

This year, the OITE will be dedicating its blog to help you develop a Career Success Plan, focusing on a variety of core competencies that are critical for your career development, the first being career exploration and planning. This is where creating an individual development plan (IDP) comes into play. But, what is an IDP? And why it is so important?

An IDP is a personalized document developed to help you define your career goals and implement strategies to help you accomplish those goals. There are many ways to develop…

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You Can’t Patent Me: the Supreme Court Ruling on the Patentability of Genetic Material

ImageThe Supreme Court recently declared that naturally occurring human genes (ie genes isolated from you or me) can’t be patented but forms of DNA that have been manipulated in the lab in a way that alters their natural state can. The court’s ruling came in a challenge launched by medical researchers and other concerned parties to seven patents owned by or licensed to Salt Lake City, Utah-based biotechnology company, Myriad Genetics Inc. on two genes linked to breast and ovarian cancer (BRCA1 and BRCA2).

Myriad appears to be partly relieved with the compromise outcome, as the ruling will have less impact on Myriad than if the court had barred patents for all types of human genetic material. The ruling was also a partial victory for patients and the biotechnology industry, making it easier for people to get cheaper genetic tests for disease risk. The BRCA1/BRCA2 test at the center of this case was supposedly the same one that Angelina Jolie used to determine that she had the mutation (along with a family history) and an extremely high risk of developing breast cancer; she subsequently got a double mastectomy.

Even though this case will almost certainly be beneficial for patients and allow for better access to testing in the future, the implications for current patentable (if not already patented) therapeutic and diagnostics and future research is less clear.

First of all, the court did not provide guidance on the boundary between “natural-made” and “man-made”. Does changing one base pair constitute enough change? (Probably not, and I think most genetic mathematicians would argue that somewhere, in somebody, that mutation exists). What if you put the gene into a vector? That is probably patentable. For many protein therapeutics, the goal is to make them as much like they occur in nature as possible; are these (current therapies) still patentable? What about the upcoming area of stem cell therapies? Scientists are inducing stem cells to become other cells that naturally occur in our bodies. Perhaps more researchers and companies will look to file “method” and “use” claims to protect their technologies.

When I first heard about this case, I was interested, as Myriad Genetics is one of the only bioscience industries in my old stomping ground, Salt Lake City (and the professional home to many University of Utah alums). In the end, both companies and researchers need to make money so they can continue to invest in their R&D and continue to develop great new technologies, therapeutics, and diagnostics. However, there needs to be a balance that keeps the ultimate goal in mind: patient health. Had Myriad licensed out their test to other parties so that patients could get a 2nd opinion on a test, would the lawsuit have even occurred? Of note, Myriad’s patent on their cDNA expires in 2015, and I would like to know the math: licensing their technology (for a fee, of course) or paying for a lawsuit only to have partial success that might be financially irrelevant in 2 years [Note: Myriad stated the decision left intact 24 different patents that relate to the BRACAnalysis test*].

Finally, in this world of sequesters and bipartisanship, the fact that this was a unanimous rule by nine Supreme Court Justices in our government feels like a small victory in itself. It will be interesting to see how future rulings play out and what the long-term effects are on research and drug development.

* Reference:

Another interesting ruling was Mayo v. Prometheus (2012):

Book Review – Outliers: The Story of Success by Malcolm Gladwell

When we look at successful people, there is a tendency to attribute their success to natural talent.  With Outliers, Malcolm Gladwell illustrates that success stories are seldom that simple. Success (as defined by being the best at something) is achieved through a series of seemingly random events combined with thousands of hours of hard work. In his book, Gladwell guides the reader through all of the twists and turns of each ‘success story’ and presents the reader with the opportunity to look at the data from a different angle. Nowhere in the book was this more evident for me than in Rice Paddies and Math Tests, a chapter that examines the successful performance of Asian students in math.

Working in the rice paddies in May in Sawara, ...

Working in the rice paddies in May in Sawara, Chiba, Japan. (Photo credit: Wikipedia)

The Trends in International Mathematics and Science Study (TIMMS) test is given to 4th and 8th grade students every four years to assess education standards on a global scale.  Historically, students from East Asian countries (Singapore, Korea, Hong Kong, Chinese Taipei, Japan) have outperformed the rest of the world’s students. This track record has led to a general assumption that students from these countries have an innate ability that makes them better at math.  But, to Gladwell, being good at math may just be an issue of culture. Besides having students that are good at math, Asian countries also have common ground in rice cultivation.  And cultivating rice is not an easy pursuit.  Growing rice is a labor-intensive, tedious task; all of the growing conditions, from the water level to the spacing between seedlings, have to be perfect.  And perfection takes time. But it’s this level of perfection that leads to a crop that can sustain a family for another year.

This is the root of Gladwell’s argument; cultural expectations in Asian countries are based on the lessons learned from cultivating rice. If you don’t put in the time (hours of practice), you’re never going to be successful.  So, if being successful at math is directly proportional to the amount of time spent doing math, there should be obvious differences in class time allotments between Asian countries and the other countries on the TIMMS list.  And, for Gladwell, there were.

Sannensei: Third Graders

Sannensei: Third Graders (Photo credit: danaspencer)

One of the readouts that Gladwell focused on was the length of the school year.  In South Korea and Japan the school year is 220 and 243 days long, respectively, while, in the United States, the school year is 180 days long.  Students from Asian countries are in school for 40-60 days more than students in the U.S.

For me, this realization was the most enjoyable part of reading Outliers.  As I mentioned earlier, Gladwell gives you a chance to see the data from a different view.  Recently, I was working on a project that was based on using informal science education opportunities to increase student science literacy.  For background research, I read through the results from the TIMMS test and other aptitude tests.  I found it very depressing.  This knowledge made it difficult for me to propose a solution for increasing science literacy when there were so many factors involved and none that I could directly change.  But, seeing the test results through Gladwell’s eyes, was liberating.  If poor math performance is only based on hours of practice, then it isn’t the fault of one teacher or one school or one parent.  If math performance is truly cumulative, then we can all be doing our part to make sure each students gets as much exposure to math as possible.

Speaking of outliers, there are some schools in the US that perform better on the TIMMS test than the US as a whole.  For instance, in 2011, the average US TIMMS test score for 8th graders was 509; in Massachusetts, the average score was 561.  Maybe Gladwell can uncover that success story in his next book.

Want to know how well you would do on the TIMMS test?  Try out Dare to Compare.

The United States’ Leaky STEM Pipeline

Erin recently authored a blog post, Investing In Women In STEM: Because Girls Grow Up, with Janet Koster, C.E.O. and Executive Director of the Association for Women in Science (AWIS).  They discuss the disconnect that exists with encouraging more women to pursue STEM careers; why continue to recruit if today’s work environment isn’t supportive of employing women in STEM fields?

Your Brain on Chocolate

As if I need another reason to enjoy cocoa-rich morsels, I came across an article in the New England Journal of Medicine that concludes chocolate consumption enhances cognitive function and may help you become a Nobel laureate.

Studies have suggested that dietary flavanoids may improve cognitive function. A subclass of flavonoids, called flavanols, which are widely present in cocoa, green tea, red wine, and some fruits, seem to be effective in slowing down or even reversing the reductions in cognitive performance that occur with aging. In this analysis, Dr. Franz H. Messerli reported on the correlation between a country’s level of chocolate consumption and its population’s cognitive function. Although Dr. Messerli identifies several study limitations, including unknown specific chocolate intake of each Nobel laureate and unknown cumulative dose of chocolate that is required to increase the odds of getting that phone call from Sweden, he still found a significant linear correlation (r2=0.791, P < .0001) between chocolate consumption per capita and the number of Nobel laureates per 10 million persons in a total of 23 countries.

“It remains to be determined whether the consumption of chocolate is the underlying mechanism for the observed association with improved cognitive function.”…If anyone out there would like to further investigate this mechanism, I would volunteer as a study participant…as long as I wasn’t in the placebo group.

Reference: F.H. Messerli, N Eng J Med (2012).

Helping early career scientists answer the question, “What do I do with my life?”

FBI Laboratory scientist.Studying to become a scientist is a relatively straightforward process. But finding a career as a scientist can be a little more problematic. The standard academic positions are difficult to secure due to market saturation. Choosing a career outside academia, although becoming more common, can be intimidating due to a lack of mentoring advice or knowledge of alternative scientific careers options.

Enter myIDP,  a tool designed to help early career scientists discover which career options are right for them. Developed by the AAAS IT Department, Science Careers and several partner organizations, this web application assists in the creation of an Individual Development Plan (IDP) to help scientists define and pursue their career goals. The biggest selling point for myIDP is the fact that it was designed by people with an intimate knowledge of scientific careers and the scientific career market.

For more information, check out these sources.

Podcast interview about myIDP with Jim Austin, editor of Science Careers

Science Careers articles on using myIDP

Shark Watch:There’s an App for That!

Marine biologists at Stanford now monitor sharks and other wildlife via mobile robotic receivers and are beginning to create a “wired ocean”. Backed by the Blue Serengeti Initiative, the wired ocean project projects real-time information of marine predators like tuna, white sharks, sea turtles, seals, and albatross right into your living room. The Shark Net iPhone/ iPad app (free on iTunes) allows users to follow the lives of about 20 sharks. Users can support, email, and even tweet their favorite shark.  Read the full story at:

‘Flipping the Classroom’ – Integrating Education with Technology

I just watched a segment on “60 Minutes” about the Khan Academy.  Apparently, I missed it the first time around…it was originally broadcast in March. For those of you, like me, who are uninformed, the Khan Academy is a not-for-profit organization whose goal is to provide a ‘free world-class education for anyone anywhere’ in the form of 10 minute videos.  Created by Salman Khan, these videos cover topics from K-12 math to biology and physics and are totally free of charge.

English: Salman Khan, famous for the Khan Acad...

Salman Khan, famous for the Khan Academy, speaking at TED 2011. (Photo credit: Wikipedia)

There were a few things that jumped out at me from the television segment. Originally, the videos were constructed by Khan himself, working out math problems with a microphone and a digital blackboard. As Khan stated in the 60 Minutes segment, “I’m 95 percent of the time working through that problem real-time. Or I’m thinking it through myself if I’m explaining something. And to see that it is actually sometimes a messy process. That, you know, it isn’t always this clean process where you just know the answer.” I really liked that quote.  Learning is messy.  It’s full of scribbles and crossed-out answers and do-overs. It’s a process.  And I think that children need to know that it’s okay to make mistakes. We need to emphasize that perfection, or getting the right answer, isn’t often achieved the first time.

Another portion of the segment that got my attention was the actual application of the Khan concept to an education environment. This model is based on having the students watch the videos outside of school hours and then working through the related problem sets during school.  This is where the idea of ‘flipping the classroom’ comes from.  Basically, ‘school work’ or lecture time occurs after school while ‘homework’ or the application of knowledge to problems occurs during school.  This means that the teacher spends his/her time helping the students with the problems, not using the time for lectures.  This idea makes perfect sense.

However, like the doubting scientist that I am, I’d like to see the data behind the model. How does applying the Khan concept to standard education practices affect student learning?  As of the original broadcast of the segment, most of the schools involved in a pilot study were in California, not selected randomly from across the country.  Also, to fully incorporate this model, students must have access to computers.  California schools in the pilot program removed the issue of a lack of personal computers at home by staying open longer.  Yet, this solution, which requires an extreme time commitment from teachers and an extension of resources to keep the school open, might not be an option for schools around the country.

Despite my questions, I still find Khan’s commitment to learning and education to be very impressive.  He has changed many lives by doing something as simple as narrating 10 minute videos about things he was interested in or curious about.  Plus, he also has a video that has a direct application to my own life.  After watching the television segment, I explored the Khan Academy website. And, lo and behold, there’s an immunology lesson about B cells/B lymphocytes.  So, for all of you who have asked me over the years what I study, watch and learn!  That includes you, Mother!

Khan Academy B Lymphocyte video

“What’s a hypothesis?”

Dinosaur Train Preview

Dinosaur Train Preview (Photo credit: tweenina)

Echoing one of the most quotable lines from my new favorite show, Dinosaur Train, a hypothesis is stated to be “an idea that you can test.”  Arguably, I do not fit the 3-6 year old demographic that the show is intended for. But who can’t help but love animated dinosaurs singing and dancing to inspire children to “get up, get outside and get into nature” (Watch the ‘Get Into Nature Song’ under Music videos).

However, what I’m really impressed with is the simplicity with which the show explains the process of scientific discovery.  Most of us were taught that proper research is only accomplished by following the scientific method. In fact, most children are still taught that today in their school science curriculum. The problem with this formal approach is that it is too formal.  As a science researcher, my experiments didn’t begin with a formal hypothesis.  They always began with my principal investigator asking me a question that I couldn’t answer.  To get the answer, I did the experiment. It was a direct cause and effect relationship, not a step-by-step process.

So, what can each of us learn from “Dinosaur Train”?  For children, it is teaching them that science doesn’t have to be a set of formal steps that you have to follow. It removes the intimidation factor and reinforces the fact that everyone can do, and is doing, scientific work. Science is just about asking questions and figuring out how to answer them.  Plus, if the Scientific Method is taught the same way as it was when I was in school, starting with a hypothesis means that you’re already predicting the outcome of the experiment.  In my education, the Hypothesis statement included the question and the answer.  This, I believe, leads to an inherent bias in the experiment. Although scientists are meant to be objective, any predictions as to the outcome of the experiment can influence the analysis stage of the experiment.  It can also influence the way in which the data are presented. Tis better to do the experiment and be pleasantly surprised by the outcome than to predict what you might see.

For scientists, “Dinosaur Train” takes us back to the basics. It reminds us of the time when science was fun. Now, it’s easy to get weighed down by the ‘publish or perish’ mentality or the demands of having to find grant funding. It also reminds us that science is about the question, whatever it may be. Children are the ultimate scientists. As much as parents might hate the never-ending ‘Why?’ question from their children, it is only through asking questions that children are able to gain knowledge.  The same applies to scientists.  If we focus on the question then it makes the act of performing the experiments so much more enjoyable. Answering the question is what got us involved in science in the first place.  We need to remember that.

For more information on childhood learning, see the NSF press release, ‘Babies are Born Scientists’ and the ‘What Do Babies Think?’ TED talk.