Adults get whooping cough, too

I’ve had a cough for a couple of weeks now. It comes and goes during the day, and makes it harder to get to sleep. It’s mainly been annoying. But recently it’s been getting worse and waking me (and my partner) up several times at night. So my partner finally persuaded me to go to Urgent Care.

It’s not the first time I’ve had a cough like this – I had bronchitis several times in my teens and early twenties, and it produced the exact same cough. But I was surprised and dismayed to learn that there is a significant chance that this time I actually have pertussis (whooping cough).

I’ve always associated pertussis with young children – it’s firmly in the “childhood disease for which there is a vaccine” category in my head. In very young children – particularly infants who have not been vaccinated – pertussis infection is frighteningly likely to lead to hospitalization, severe complications or (rarely) death.

What I didn’t know is that pertussis is increasingly more common in adults and teens – particularly in a hotbed of vaccine exemption like Boulder, CO, where I live now. The local vaccination rate dropped below herd immunity levels years ago, and Boulder County (along with many other U.S. cities) experienced an epidemic-level outbreak of pertussis back in 2012 and 2013.

Pertussis cases in Colorado since 2011. from CO Dept of Public Health and the Environment
Pertussis cases in Colorado since 2011, via CO Dept of Public Health and the Environment. You can check CDC reports to see if your state has had a lot of cases of pertussis recently. If you live in Colorado, you can find the latest data on reported cases at the the state Department of Public Health and the Environment website. You can find out about the latest outbreaks in your city or county by doing an Internet search for the name of your city + “pertussis” or “whooping cough”.

It turns out that pertussis is still in Boulder. And adults are getting it. It’s not likely to kill me or put me in the hospital, but it is extremely unpleasant. And other adults like me who don’t realize what they have until they’ve already been contagious for weeks, are major sources of infection for more vulnerable populations.

Here is what I have learned about pertussis in the past 24 hours:

1) Pertussis is often missed in adults. A case of pertussis starts out looking exactly like the common cold, and is particularly difficult to distinguish symptomatically from other common respiratory infections. It can take a few weeks for the infection to progress from coldlike symptoms to severe cough. Many adults who contract pertussis never exhibit a “whooping” cough or experience any severe symptoms at all – so the true number of cases of pertussis may be somewhat higher than what’s reported to state and national public health agencies.

2) Adults are major spreaders of pertussis, in particular because they are harder to diagnose, and because we are often well through the most contagious period of the disease (the first two-three weeks) before we seek medical help and obtain a diagnosis – if we ever do at all. Finally, adults are less likely than children to have been recently vaccinated (see #7).

By the way, pertussis is *extremely* contagious. In a household where no one has current immunity, everyone will get it.

3) The coughing from pertussis can last three *months*. At its mildest, it’s ‘just a cough’. At its worst, the coughing can be so severe that it makes you vomit and/or experience sleep loss, cracked ribs, severe headaches and exhaustion. It sucks. It sucks a whole lot. You can get prescription drugs to treat it, but they make you drowsy; so during the day you have only cough drops and humidifiers and hot tea with honey to help.

4) You may never know with any certainty whether you actually had pertussis or not. No diagnostic test is 100% accurate. Pertussis testing is quite expensive, and kids always get priority over adults. Currently, your chance of getting a false negative result on a pertussis culture or PCR test increases over the course of the infection, because there are fewer and fewer bacteria in your mucus to detect1. Tests are also done by humans and subject to human error (contamination, etc.). So the benefit of testing may not outweigh the cost. Healthcare providers will probably assume you have pertussis AND other common respiratory bugs and treat you for all of them at once.

5) The best way to protect the most vulnerable populations isn’t early treatment or better diagnosis. It’s just not feasible to forcibly test everyone with cold symptoms early in their disease, nor is it in our best interest to blanket everyone with cold symptoms with the antibiotics we use to treat pertussis. We’d end up giving a lot of people antibiotics they don’t need, and accelerating the evolution of antibiotic resistant bacteria that will only come back to hurt us more.

So we will inevitably miss a lot of cases of pertussis in adults. The best way to protect ourselves and our loved ones from suffering from pertussis is prevention, through vaccination.

6) OTC cough meds are no more effective than placebo at reducing the duration of a cough.2,3

7) The immunity you acquire from pertussis vaccination or from contracting pertussis infection wanes over time. You need a booster every couple of years to maintain significant immunity to pertussis. If you spend a lot of time around young children or around adults susceptible to respiratory infection, you definitely need a regular booster.

8) Immunity isn’t the only benefit from vaccination. Vaccinated people not only less likely to get infected with pertussis, they’re likely to experience less severe symptoms than the unvaccinated.

9) If you get the right antibiotics within the first two or three weeks of illness, you stand a chance at reducing the duration of symptoms. After that, antibiotics will reduce your contagiousness, but may have no effect on the duration of your cough.


More information:

Featured image: The Flatirons in winter, Boulder, CO. CC BY-SA 2.5 Wikimedia Commons

The science of science communication, summarized

No, do not do a Google image search for "scientist" if you do not want to be depressed and outraged.
Is this what scientists think of “the public”? Stock Photo from Getty via jacks of science.
I’ve identified as a scientist for most of my life, despite leaving at the end of my master’s to pursue a career in science communication. The biggest challenge for me in that career shift – next to learning to meet a zillion little deadlines every day in lieu of huge ones once every few years – was learning to be present and relatable.

By default I am the classic cerebral, shy, white-coat nerd type. I’m still constantly fighting my own tendencies to live inside my own head and spew evidence faster than others can process it – tendencies that the culture of academic science enhanced in me, even socialized into me and my former science colleagues. I think I’ve finally managed to internalize the notion that I’m not just trying to reach “the public” with science; in fact I am part of “the public.”

The point is, sometimes scientists need to be reminded of their own humanity. And who better to do that than humanities scholars?

There’s a whole issue of PNAS out dedicated to the science of science communication, based on a meeting of the same name that I at one point was dying to attend. It turns out many of the sessions were recorded and you can still view them online at the meeting website. Or you can go to the 2013 meeting!

I doubt I will make it to the 2013 meeting. But I have the videos and the special issue of PNAS to relish. One piece from the special issue, Communicating science in social settings, includes a summary and discussion of assumptions scientists often make about “the public” and “the media” that, based on lots of social science studies and extensive survey data, deserve further scrutiny. Here are my takeaways from that section:

  • 1. More information is not better.
    Resist the urge to summarize your entire body of scientific knowledge in one conversation. Make one point. Make it quickly and make it well.
  • 2. The public still trusts scientific institutions.
    There goes that excuse.
  • 3. Stories are much more powerful than lectures.
    How well do you remember the last three movies you saw? How well do you remember the last three two-hour lectures you saw?
  • 4. No one totally ignores his own worldview when interpreting scientific information.
    That includes scientists.
  • #ESA2013 Ignite: Open Science

    I had sooooo much fun organizing my first Ignite talk session. I would do it again in a heartbeat. I met several excellent people and learned a lot about data, R and collaboration tools. I am also super proud of how awesome my speakers and moderator are, and how thoughtful and stimulating the discussion was.

    So I’m sharing it all like a proud session mama. Here are the session details from the program and, when available, the talks themselves:

    Sharing Makes Science Better

    Organizer: @sandramchung | Moderator: @jacquelyngill

    Scientists too often labor alone. The need to closely guard ideas during the race to immortalize them in professional publications can make the practice of science crushingly lonely and ill-informed by tools and knowledge that could make science easier and better. Occasional scientific meetings are often the only opportunities to share ongoing work and connect with colleagues outside of one’s immediate working environment. But there’s a fertile online science ecosystem of innovation, collaboration and mutual support that carries on all year round, and its lifeblood is a network of scientists and science lovers who openly share tools, data, knowledge and ideas that help all researchers to do stronger, better, faster science. The rapidly growing open source and online science communities suggest a new model of doing science in which we build our work on tools, data, knowledge and ideas that are freely offered and contribute our own in return. This session features several free and open-source tools that ecologists have created specifically to help fellow researchers do the work of ecological science, as well some other tools we didn’t create but have tried and found enormously useful. We encourage our colleagues to try them, improve upon them, and perhaps most importantly, share what they’ve learned so that others can benefit as they have.

    IGN 2-1

    Big Data in Ecology

    | @ethanwhite, Biology, Utah State University, Logan, UT

  • Slides and text
  • Increasingly large amounts of ecological and environmental data are available for analysis. Using existing data can save time and money, allow us to address otherwise intractable problems, and provide general answers to ecological questions. I will discuss why we should be actively using this data in ecology, how to get started, and give examples of what can be accomplished if we embrace an era of big data in ecology.

    IGN 2-2

    EcoData Retriever – automates the tasks of fetching, cleaning up, and storing available data sets

    | @bendmorris, University of North Carolina, Chapel Hill, NC

    Ecology often relies on data that has already been collected, and an ever-increasing amount of biological and environmental data is now available online. However, it can be difficult and time consuming to compile synthetic datasets from data files stored in various online repositories or research web sites. The EcoData Retriever is a community-centered tool that automates discovering, cleaning up, and organizing ecological data into the format of your choice. I’ll speak about problems solved by the Retriever and touch on future directions aimed at further utilizing community effort and the web to automate ecological data access.

    IGN 2-6

    R-based tools for open and collaborative science

    | @recology_ (Scott A. Chamberlain), Department of Ecology and Evolutionary Biology MS 170, Rice University, Houston, TX

    Open science is the practice of making the elements of scientific research – methods, data, code, software, results, and publications – readily accessible to anyone. While this has great potential for advancing research, the absence of an open science toolkit prevents open science from being more widespread. We are building bridges between data (e.g, Dryad) and literature (e.g., PLoS journals) repositories and the open source R software, a programming environment already familiar to many ecologists. These bridges facilitate open science by bringing together data acquisition, manipulation, analysis, visualization, and communication into one open source, open science toolkit.

    IGN 2-7

    Social media for scientific collaboration

    | @sandramchung, NEON Inc.

    Sharing Makes Science Better: Social Media for Ecologists from Sandra M Chung on Vimeo.

    Scientific research is about the nurturing of knowledge and ideas. And to knowledge- and idea-lovers, the Internet is a door to an infinite candy store. Social media provide a means to quickly access exactly the online knowledge you want – by filtering the grand store of information through interaction with the people, topics and communities that matter to you. I wouldn’t stop at just knowledge consumption, however. Sharing your science online can connect you with mentors and collaborators, sharpen and deepen your science, hone your communication and teaching skills, and even earn you funding.

    IGN 2-9

    The power of preprints: the open publication project for ecologists

    | @cjlortie, Biology, York University, Toronto, Canada

    Ideas are free but not cheap. Peer-reviewed publications are still the major form of accepted dissemination of ecological ideas. Even with open access however, this communication modality is outdated. Discussion, feedback, transparent review, versioning, ranking, and articulation of both idea development and peer-review are needed to accelerate scientific discovery. A new communication venue is proposed herein: archival of open access pre-prints similar to arXiv but with annotation, review, and discussion. Think stackoverflow + arXiv for ecologists; not a final step in the evolution of scientific communication but an affordable idea we need to explore.

    Add your Twitter username to your conference badge


    A Twitter sticker in action
    A Twitter sticker in action

    I designed these Twitter stickers in July 2012 to hand out at the ESA meeting in Portland during and after the social media workshop I ran with Jacquelyn Gill. They’re getting more and more popular (as of ESA 2013, I’ve handed out nearly all of the original 300 I printed) so I thought I’d share the artwork and information on how to order them.

    I used Sticker Mule to order custom 3.5″x.75″ rounded corner stickers that fit nicely below your name on your scientific conference badge (right).

    ADDENDUM 2013.08.12
    Feel free to re-use, modify and share the design. But please do not sell the stickers. They are for only personal and academic use.

    Thank you, Canada, for Chris Hadfield

    We’ve sent hundreds of people into space already, but only one of them is Chris Hadfield:

    The best of Chris Hadfield on social media (This is from the Vancouver Sun)

    Commander Hadfield returns to Earth tonight. Hadfield, I’m sure your loved ones are happier when you’re safe and sound on Earth, but many of us wish you’d stayed out in space longer so we could keep learning and sharing your joy up there.

    This is what outreach can be. More and more I’ve come to think that the best and coolest science gigs are just too precious to waste on people who aren’t outright ambassadors for the greatest things science has to offer: a sense of wonder and joy in the universe, and the beauty of curiosity and knowledge.

    How to make non-scientists hate scientists and ignore science

    Inspired by Brendan Leonard’s “How to Get Your New Boyfriend/Girlfriend to Hate Your Sport”.

    1. Place all the blame for everyone else’s inability to understand or appreciate your work on inadequate science education. You shouldn’t have to change the way you communicate with people of different academic background from you. No one is going to understand or appreciate what you do until they know as much about it as you do, and people who don’t know as much about your science as you do should go back to school and learn it.

    2. If you are forced to explain your science to a non-scientist, explain it in the most condescending tone possible to make sure the person understands that a) s/he is stupid and b) s/he is wasting your time. People who want to ask you questions about your work should read every paper you’ve ever written before they talk to you so they can ask you more intelligent questions.

    3. Socialize only with other scientists. If you somehow find yourself at a mixed party, ignore the non-scientists and talk with only the scientists. Remember, any social situation where you’re not talking about research with another researcher is a waste of your time and intellect.

    4. You know the business staff, office managers, administrative assistants, project managers, IT? All those people who do all the trivial tasks that are a waste of your time and scientific talent? Don’t talk to them except to complain about something that’s pissing you off. Always demand that they drop everything else and fix it right away so you can get back to your science without delay. Your science is more important than anything else they could possibly be doing.

    5. All those people who aren’t doing what the (your) studies recommend? Point out that their belief and values systems are total bullshit and that they should stop being stupid and get with the objective evidence. Science is truth*.

    6. Dismiss any sort of story or presentation about science that is not as dense, dry and technical as a graduate school seminar as “dumbed down”. Because you know, only dumb people like that simplistic popular science crap.

    * Except when it’s tainted by faulty methodology, unconscious bias and deliberate data manipulation.

    We are the seeders of collaboration clouds

    This is a ScienceOnline-inspired ditty, written with the other sciosatellite leaders and Bora, Karyn and Anton in mind:

    We nudge the primordial specks of the universe,
    Atoms upon atoms
    Closer, closer
    Till gravity seizes them, draws them into intimate quarters,
    And together, they birth bright stars and galaxies.

    We fine-tune the sequence of amino acids and the acidity and hyrophilicity of their environment
    Till the first protein self-assembles, a thing of great beauty and complexity.

    We share the code.

    Open-source life evolves and grows far beyond even what we imagined,
    Staring at atoms and molecules
    Dreaming of great things they might do together.

    We induce microbes to express a glue that binds them together,
    To form hardy biofilms where they help each other thrive.

    We tinker, hypothesize, develop models for conditions that cause
    Different species to assemble and thrive and endure together in a
    Grand ecosystem.

    We are the seeders of collaboration clouds.
    We are the engineers and the ecologists
    Of community.

    #Altecology, a call to unconference action

    The rise of the unconference | Ecology is changing | What are you proposing? | How do I make my voice heard? | Get in touch

    Wordle: #esa2012 wednesday
    A Wordle of all the tweets to the hashtag #esa2012 on Wednesday of the 2012 ESA Annual Meeting. Word size corresponds to the frequency with which it appeared in the tweets.

    Note: This post is cross-posted on Scott Chamberlain’s blog here.

    The rise of the unconference

    The Ecological Society of America meeting is holding its 98th annual meeting next year in Minneapolis, MN. Several thousand students and professionals in ecological science and education will gather to hear and read the latest work and ideas in ecology in the familiar poster and lecture formats that are the core of every major scientific conference. But a subset of these people will get a taste of something a little bit different: an unconference within the conference.

    The most important difference between traditional science conferences and the unconference format is that it prioritizes human interaction. Often the best and most important parts of science meetings are the interactions between talks, next to posters, and at the end of the day over drinks. These connections pave the way for collaborations and friendships that nourish our professional and personal lives with shared opportunities, camaraderie and support.

    In recognition of the increasing relative importance of the “meeting” part of a science meeting, the unconference format emphasizes interaction over presentation. It attempts to engage participants to the maximum extent reasonable in discussion and doing. Science Online is a good example of this unconference format, in which the session topics are typically decided on democratically by the conference attendees (partly before arrival, partly on arrival), and you vote with your feet by going to and leaving sessions as you desire.

    Ecology is changing

    Ecology is now adopting some of the same online and social tools that are already accelerating innovation in computing and other science disciplines. Ecologists, ecology students and educators are asking many of the same basic questions they have always asked: What should we be doing? How do we do it better and faster? Social media, open source software, open science, altmetrics, crowdsourcing, crowdfunding, data visualization, data sharing, alternative peer review, and an increasing emphasis on more and better communication and collaboration are just some of the newer tools being put forth to help address those questions in the 21st century.

    Social media is rapidly becoming more common in ecologists’ toolkits to disseminate news of their new papers, communicate about research and research tools, and even filter the deluge of publications. Tools like blogs, Twitter and Facebook are filling the communication gaps between annual meetings and adding a new layer of conversation and connection to conferences and classrooms.

    Social media, in turn, is connecting scientists directly to people besides their immediate colleagues who appreciate the impact of their work and want it to continue. The crowdfunding movement – exemplified by Kickstarter – has spurred similar alternative science funding projects such as SciFund. #SciFund project has shown that social media engagement increases donations to crowdfunded research (interview with Jarrett Byrnes).

    In addition, we are in the era of big data, and this includes ecology. To deal with this “data deluge”, ecologists increasingly want to learn how to manage, share, retrieve, use, and visualize data. There are new tools for all of these tasks – we need to aid each other in learning them. Online and offline communities are coalescing around the development and dissemination of these tools for the benefit of ecological science, and they are meeting face-to-face at our ecological unconference.

    Science in general is becoming increasingly complex and calling for larger and larger collaborations. This growth in turn is spurring a drive toward more openness and transparency within the culture of science. The more collaborative and complex scientific study becomes, the more scientists depend upon each other to do good work that we can all build upon with confidence. The often unstated assumption about ecology, and all of science, is that research findings are reproducible; but that assumption is quite shaky given the increasing number of retractions (see the Retraction Watch blog) and findings that much research is not reproducible (see media coverage here and here).

    A recent initiative seeks to facilitate attempts to reproduce research: The Reproducibility Initiative. Jarrett Byrnes spoke at #ESA2012 of how transparent, online discourse enhances our ability to discuss and improve our work and the work of our peers, both before and after publication. One way we as ecologists can quickly make our research more reproducible is the way we write. By simply using tools that make reproducing what we have done easy to do, we can avoid retracted papers, failed drugs, and ruined careers.

    Much of the ecological science community shares one or both of these goals: to do the best possible science, and to do it in a way that is most useful and accessible to colleagues and to society at large. The goal of this year’s ecological unconference is to introduce as many people as possible to resources – both tools and people – that can help all of us achieve those goals, on our own, or together.

    What are you proposing?

    We originally thought about a separate event from ESA itself, modeled after Science Online, incorporating a variety of topics. However, we thought testing the waters for this sort of non-traditional unconference format would be better in 2013. We are gathering ideas from the community (see “How do I make my voice heard?” below). The ideas on the wiki that get the most traction, and have 1-2 champions that are willing to see the idea through and lead the workshop at ESA will be turned in to proposals for ESA workshops. In addition, we will be submitting a proposal for an Ignite session at ESA. To summarise, we will be running:

    • A few workshops (at lunch hours, and half-day). Topics may include:
      • Data sharing
      • Data visualization
      • Data management
      • Alternatives to academia
      • Blogging
      • Social media
      • Reproducible science writing
    • One Ignite session on “Tools for better/faster science”. See more about Ignite sessions here.
    • A “tweetup” event to socialize in a more relaxed atmosphere

    These will all be loosely aggregated under the #AltEcology hashtag.

    How do I make my voice heard?

    We have set up a wiki in which anyone can contribute. Please share your ideas and voice your support for existing ones at the wiki here. You can just throw ideas out there, or even propose new workshops and nominate people to lead them. We’re currently moving to transform existing ideas into ESA workshop and Ignite proposals to meet the November 29 deadline, but we’ll be incorporating input from the wiki right up to the meeting itself in August 2013.

    Get in touch

    If you have any questions/comments, let us know in the comments section below, tweet us (Sandra: @sandramchung, Scott: @recology_), or email (Sandra, Scott).