Tuesday, September 25, 2012

Guest Post: Anna Tomasulo On HealthMap

This week I am happy to be hosting a post on Science Decoded by guest blogger Anna Tomasulo, project coordinator for Healthmap and Editor-in-Chief of The Disease Daily. Please note that I am not personally promoting Healthmap as a service, I just think it is an interesting case-study of the way the internet can be harnessed to gather data in real-time so I asked Anna to give us some background.

I never focused too long on the myriad of ways that the Internet has changed our lives, until recently. This past February, The Atlantic published excerpts of Polish pundit Piotr Czerski’s “manifesto” titled, “We, the Web Kids.” The essay put my relationship to the Internet into a new light- particularly when compared to how my parents, for example, interact with the Web. “The Internet to us is not something external to reality but a part of it: an invisible yet constantly present layer intertwined with the physical environment. We do not use the Internet, we live on the Internet and along it,” writes Czerski. The Web kids rely on this shared memory drive; we extract information, contribute to it, and re-post it at our leisure. We learn about new scientific research at home and participate virtually in uprisings across the ocean. Geographic barriers dissolve. And we expect to do this all instantaneously; we want it “here and now, without waiting for the file to download.”

This essay also put my first post-graduate school job into a new light. Admittedly, I am not very tech savvy; I’ve always thought of myself more as a qualitative, literature-oriented person. But my international experience, French language skills, and recently acquired MPH landed me at HealthMap, a research group, co-founded by a software developer and an epidemiologist, that uses online media to track infectious diseases worldwide. And it does this in real time, in an almost completely automated manner.

The healthmap homepage

HealthMap was founded in 2006 by John Brownstein, PhD and Clark Freifeld, MS. Back then, Brownstein and Freifeld understood that there was a large gap between the beginning of an infectious disease outbreak and the public becoming aware of and responding to that outbreak. They attributed this lag to traditional public health reporting, which is often troubled by structural hierarchies and geographic and political barriers. For example, a typical public health worker in a small, remote village may take note of a strange syndrome that is surfacing in a handful of young kids. He or she might provide that information to medical professionals who will want to take samples for analysis. Well, the samples will need to be sent to laboratories miles away and it’s rainy season so the roads are washed out. Let’s say the samples did get to the lab. Once an infectious disease agent is confirmed, the report will then move on to district, national and then international officials. This whole process could take weeks. And during those weeks, infectious diseases can spread.

Brownstein and Freifeld recognized that there was a wealth of information available through the Internet that would fundamentally change the picture of global health. So, they created a freely available online platform that gave people access to this information.

Essentially, the system mines the Web for formal and informal sources of infectious disease news. Data is collected by carefully developed language specific search strings (HealthMap has news feeds in over a dozen languages) that sift through various news aggregators (Google News, Baidu, allAfrica), RSS feeds, mailing lists and chat rooms. The collected data is then automatically assigned a pathogen and location of the outbreak, based on information in the article (or chat room, mailing list, etc.). Then, the system determines the relevancy of each alert and filters it into one of six categories: Breaking, Context, Warning, Old News, Non-Disease Related, or International Significance. Any duplicate data is clustered together. The end product, http://healthmap.org, is a highly organized data set that allows public health officials, international travelers, government agencies and interested community members to access a real-time view of infectious disease outbreaks around the globe.

The HealthMap platform has been used to track public health threats in many contexts. Every year before the Hajj, we begin heightened disease surveillance on the countries that send the most pilgrims, and post all infectious disease news from these countries to a map created especially for Hajj. Similarly, we mine formal and informal sources for information regarding the wildlife trade because of its role in spreading zoonotic diseases.

The Internet has radically changed our way of life. It is no longer a tool that we use to perform a specific task or a tool that requires special training to use; it is an interactive system where people can deposit and build upon collected intelligence- an idea that Czerski hints at and with which Mike Kuniavsky, an entrepeneur who studies people’s relationships to digital technology, agrees. In 2008, Kuniavsky explained that all real world objects have “information shadows,” or digital representations, that exist on the Internet. These information shadows can be built upon and interacted with by other users. As a result, the Internet grows exponentially.

Arguably, HealthMap takes information shadows of disease outbreaks (local news reports, tweets, chat room questions, status updates, etc.) and augments official public health reports with real time information. But what makes HealthMap truly unique, is that it takes the informal information, or information shadows, and automatically makes it immediately useful to those who can act upon it.

Czerski differentiated our generation from others by pointing out that we are the first generation that exists not on paper, but on and through the Web. HealthMap is exemplary of the Web kid generation, as it has transported information disease tracking to the Web, and made it an immediate and global process. Not only is outbreak information available online and in real time, but it is also freely available. Czerski finishes the manifesto with: “What we value the most is freedom: freedom of speech, freedom of access to information and to culture. We feel that it is thanks to freedom that the Web is what it is.” As a freely available site, HealthMap provides international users with knowledge to make informed health-related decisions. A true product of the Web kids, HealthMap has leveraged the power of the Web, and our existence on it, to improve disease surveillance and timely responses.

Wednesday, September 19, 2012

Book Review: The Emperor of all Maladies

Due to my new job as a writer at the Dana-Farber Cancer Institute I now find myself writing on a cancer biology beat. I feel like there are two ways to cultivate a beat, either you can grow into a beat by developing the background knowledge and sources over time, or you can be tossed into a beat and have to do your homework very quickly to get up to speed. Obviously, taking a job at DFCI forced me to take my basic knowledge of cancer research to a higher level very quickly.

I still have a long way to go before I'll feel comfortable with my cancer bio knowledge, but I've learned a lot from all of the great articles and books I've been reading over the last two months. One of the books I read on the recommendation of a colleague who said it really helped her when she started on this beat, was The Emperor of all Maladies: A Biography of Cancer by Siddhartha Mukherjee. A former DFCI fellow, Mukherjee is a physician, scientist, and writer. He wrote The Emperor of all Maladies in 2010, and it received a tremendous amount of acclaim including the Pulitzer Prize for General Nonfiction.

Very rarely in a book review do I say that I think everyone should read a book. More often I recommend books with caveats that if you aren't interested in the subject matter, don't like nonfiction, have trouble staying focused, etc perhaps you won't enjoy a book as much as I did. I am recommending The Emperor of all Maladies for everyone, regardless of what you normally read or are typically interested in. This book, and Mukherjee himself, deserve every ounce of praise that has been heaped upon them. There is a lot of information in The Emperor of all Maladies, and depending on how and where you read it might take you a long time to get through. It will be worth it.

I learned so much from this book, not just about cancer but about how to tell a long, complicated narrative in a way that is factual while still compelling. The patient narrative that the book starts and ends with brings a personal touch to the book, but the physicians, activists, and researchers interwoven into the story by Mukherjee also make this a deeply personal story. I think one of the biggest achievements of this book is being able to meld science and history to provide a foundation for the cast of characters that drive home the human impact of cancer.

The Emperor of all Maladies is masterful at doing something that so much science writing on the web and elsewhere fails to do - it provides background and context for all of the claims that it makes. Granted, developments that have advanced our knowledge of cancer biology aren't particularly controversial, but it is still necessary to illuminate the scientific process and make clear how these discoveries come to be. This book is just solid in so many ways. The structure is great, and very effectively drives the narrative forward. The personal stories add so much to the overall understanding of cancer and its impact. The science and medical information is clear and easy to understand.

There is just so much that you can learn from this book. I don't think I've come across another resource that was as interesting and entertaining while being as informative about all of the issues involved in cancer than this one. I recommend it to everyone because cancer is something that affects us all, if you don't have it yourself then you know someone who has had to face that diagnosis. The Emperor of all Maladies really is a biography of cancer, and the crash course that I think we all could stand to go through for a better understanding of this disease.

Monday, September 17, 2012

Science For Six-Year-Olds: Introducing The Scientist of the Month Segment

Science For Six-Year-Olds is a recurring segment on Science Decoded for Mrs. Podolak's first grade class at Lincoln-Hubbard elementary school. This year the posts are inspired by #iamscience (also a Tumblr) and #realwomenofscience two hashtags on twitter that drove home for me the importance of teaching people who scientists are and what they really do. 

Hello first graders, welcome to Science Decoded! I am so excited to be writing posts just for you this school year. We are going to have a lot of fun blogging together, because we are going to have a special year-long spotlight on who scientists are and what they do. We'll have our first Scientist of the Month in October, but before we do I first want to find out what you know about scientists. 

via Wikimedia Commons
What do you think a scientist looks like? Are they all wrapped up in a laboratory like this person on the right? How would you describe a scientist? Are they smart, funny, kind, brave, patient, or happy? Do scientists get to have fun? What do you think scientists do all day? How old do you have to be to be a scientist? Are scientists boys or girls or both? Do any of you know anybody who is a scientist? What are they like?

The reason I wanted to do this segment for you is because scientists aren't any one thing. Yes, they are all bound together by the fact that they very systematically analyze information to learn new things. But scientists are a very diverse group - they are lots of different people, with many different interests and backgrounds. Scientists also study all kinds of different things. A scientist can study plants, animals, cells, chemicals, energy, the way things move, medicine, space and how to build or put things together in addition to a lot of other stuff! 

Scientists are important to all of us, because they work hard to try to figure out things about the world that we don't know. There used to be a time when people didn't know that all living things are made of cells, but today we know so much more about them and have learned that understanding what goes on in cells is critically important. What are some of the things that you know about that scientists have discovered? Do you know the names of any scientists? 

I hope you have had a good time talking about who scientists are and what they do. I'm really looking forward to introducing you to some great scientists and helping you learn more about what it means to be a scientist. Our first scientist is a paleontologist and geochemist (don't worry, we'll learn what that means) but in the meantime if you have any questions for me, feel free to leave them in the comments. 

I'm not a scientist, I'm a science writer. I went to school to learn how to research, report on, and write stories about scientists and what they discover. But, even though I'm not a scientist, helping share scientists' ideas is my specialty. Hopefully, I'll be able to do that with these posts!

Sunday, September 9, 2012

The Question of Code

Earlier this week Bora Zivkovic (@boraz) blogs editor at Scientific American tossed out the following links on twitter, and asked for thoughts. Both links were to articles from the Nieman Journalism Lab, the first Want to produce hirable grads, journalism schools? Teach them to code and the second News orgs want journalists who are great a a few things, rather than good at many present two different ways of thinking about the skills journalists need to have. The links started a conversation on twitter (excerpted below) between Bora, Rose Eveleth (@roseveleth) Kathleen Raven (@sci2mrow) Lena Groeger (@lenagroeger) and myself (@erinpodolak) I felt like there was more to say on the topic, so I decided to take it to the blog so that I could respond to everyone's points without the confines of twitter brevity.

I definitely agree with this point from Rose, there are so many different skills you use as a journalist but a lot of what you need to know will vary based on your personal style and interests, what platform you write for, and what topics you are covering. I've found that I learned a lot more from going out and actually chasing down stories than I did sitting in classrooms. Of course, the guidance of journalism school makes learning by trial and error much less perilous than it can otherwise be, so classroom lessons have value too. 

I moaned an awful lot about how scary being turned loose into the unemployed masses at the end of grad school seemed. Journalism has adapted to changes in viewership, platform and the poor economy, and so too must journalists or we run the risk of ceasing to be relevant. Making yourself as employable as possible is a good thing, but only if you are going after jobs where you can really contribute. You'll only be able to contribute if either you know what you are doing or you have the desire and the drive to learn what to do. This thought brings me to the next point I made, not all the skills journalists use will appeal to all journalists. As a profession we can do a lot of different things, but that doesn't mean that everyone wants to do everything.

If you are looking for a job, you have to be honest with yourself and your resume. I think for young journalists there is a temptation to trumpet skills that we only sorta, kinda, maybe have from that two hour seminar we sat through that one time. You can fit what I know about code on the head of a pin, and I've sat through basic training courses multiple times. My resume says nothing about being able to code, because I honestly don't know how. It is always better to be honest about what you know. If you aren't an expert in something, don't claim to be. All you'll do is disappoint possible employers. I think you can go a lot farther being honest about where you are with your skills, if you don't know code but would like to then say so. If you've edited a video once or twice and would like to continue developing those skills then say so. Just don't make yourself into an expert in something when you aren't. 

I recently graduated from the professional track Master's program at the University of Wisconsin-Madison, a program that with only three core courses is left purposely open for students to do their own exploring. So what exploring did I do? I chose to spend my time taking science classes (mostly zoology) learning more about narrative writing and structure, and getting a better handle on social media, personal branding and marketing myself online. All good things to learn while at school, but I didn't learn code. I honestly have zero interest in code, it isn't something I've ever wanted to do, I don't have the patience for it and I feel like my brain just doesn't absorb even the basic information about code whenever it is presented to me. But that doesn't make me an inept science writer. Kathleen Raven  joined the conversation, and brought up the following reason why not knowing code can still be okay.

Part of the reason I think I haven't been particularly motivated to learn code is because I haven't needed it. I was able to set up this blog and my website (www.erinpodolak.com) on Wordpress using basic templates that suited my needs. I'm on Twitter, Facebook, LinkedIn and G+ but none of these online activities involve needing to write my own code. To do what I want to online I haven't run into the need to write code. Kathleen then made another point about a science journalism skill, the ability to do math, which can be overlooked but is important to a writer's skill set. 

Being able to do the math to fact check research reports and call bullshit when necessary is an important part of the reporting that science journalists do for their stories. If you know code but can't do math, you have a critical weakness in your skill set. In my opinion the same goes for being able to structure stories successfully, and handle difficult interviews well. If you don't have the basics, then the extras like code are just floating out there on your resume with no foundation. Being really good at the basics, and then selectively adding skills based on what you find that you need to know, and what you find you would like to know seems like a solid way to go about building your skill set. I think this gets us to the last points that Rose made:

You need to do something that you enjoy. If you don't enjoy code then in my opinion you shouldn't feel like it is an essential skill to have. You might want to be the kind of journalist that can do it all, kudos to you for that. But, I don't think there is anything wrong with wanting to have a few select skills and being really good at them. If you are honest with yourself and honest with employers I think you can definitely learn an array of skills that suit you and your job. We have options, and that is a great thing. Happy times, indeed. 

Note: This is only a brief excerpt from the first few days of this conversation. Much more was said, including more back and forth between Lena, Rose and myself about skills and how to present yourself to employers and from Bora, Lena, Rose and Dan Fagin (@danfagin) about the structure of jschool programs and the balance needed to meet students needs. Still plenty more to say about these topics!

This conversation took place before we started the hashtag #sci4hels to mark all of the tweets. Be sure to monitor the hashtag in the future to see more of the on going discussion between Kathleen, Lena, Rose, Bora, myself and others!