Archive for the ‘Health’ Category

Exploring Citizen Science

By August 1st, 2014 at 5:24 pm | Comment

This post, written by Christine Nieves, originally appeared on the Robert Wood Johnson Foundation Pioneering Ideas blog.  Check out the citizen science projects mentioned in the post, such as: FoldItSound Around You, and FightMalaria@Home.

Christine Nieves / RWJF

Christine Nieves / RWJF

I remember the distinct feeling of learning about Foldit. It was a mixture of awe and hope for the potential breakthrough contributions a citizen can make towards science (without needing a PhD!). Foldit is an online puzzle video game about protein folding. In 2011, Foldit users decoded an AIDS protein that had been a mystery to researchers for 15 years. The gamers accomplished it in 3 weeks. When I learned this, it suddenly hit me; if we, society, systematically harness the curiosity of citizens, we could do so much!

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Coop’s Citizen Sci Scoop: Patients Who Were Research Subjects and the Doctors Who Listened – the Citizen Science of HIV/AIDS Research

By July 20th, 2014 at 10:21 pm | Comment 1

Editor’s Note: Flight MH17 was a horrible tragedy, with many lives lost, including HIV/AIDS researchers en route to a conference.   In Caren Cooper’s latest Coop’s Citizen Sci Scoop, she explains how citizen science assisted with AIDS research, and how AIDS activists were able to become participatory members of the medical and scientific process.  Here, in full, is Caren’s post.

Many prominent people involved in HIV/AIDS research lost their lives when Malaysian plane MH17 was shot down over Eastern Ukraine. HIV/AIDS researchers exemplify how scientists serve the public good. A key to HIV/AIDS research has involved embracing a certain type of citizen science.

The rapid advances in HIV/AIDS treatment in the late 1980s and early 1990s occurred because of major changes in medical research brought about by the lay public. In part, AIDS activists were eager to reform clinical trials in the United States. But equally important, the biomedical research community was (ultimately) receptive to this change.

The term citizen science in this blog is used to describe projects where the public engages in scientific research. It is usually through collecting and sharing observations or by coding data online. Citizen science can also be used more broadly to describe ways that the lay public participates in and influences the practice of science. (Indeed, the term “citizen science” was initially coined by Alan Irwin in 1995 to mean just that).

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Oraquick HIV test, photo by Marcello Casal Jr

A colleague recently sent me a 1995 journal article by Steven Epstein. Now a prominent sociologist, his article is a condensed version of Epstein’s dissertation research about the social movement of AIDS activists. (For further reading, see his book).

I summarize Epstein’s research in this post. He examined how AIDS activists became seen as credible agents of the scientific community and developed into important partners to AIDS researchers and government officials in the United States.

In 1981, AIDS was recognized as an epidemic. In 1985, the HIV antibody test became available to the public. People, mostly in their twenties and thirties, were learning that they were infected long before they showed any symptoms. But this was long before any effective treatments were discovered. A positive test result was a like a death prophecy. Some accepted their fate; many others became activists searching for a cure.

In the United States, the group primarily seen as affected by the disease were already seasoned activists in making the public aware of gay identity. The homophile movement of the 1950s was followed by the gay liberation movement of the 1970s. The gay and lesbian community had already “demedicalized” gayness. They had redefined their social status, becoming a legitimate “interest group” in the pursuit of civil rights. They had resources, people of influence, funding, a strong public relations arm, lobby groups, and community-based organizations.

This group understood that the future of their health required a close working relationship with scientists. Anything less would be group suicide. AIDS research involved all types of scientists who had strong credentials, such as immunologists, virologists, molecular biologists, epidemiologists, and physicians. How could the lay public improve their research?

The answer was speed. Initially, AIDS activism focused on the FDA and the desire for more rapid approval of experimental drugs and the ability to obtain unproven treatments from other countries. When none of the existing drugs were working, activists focused on the NIH, seeking more drugs to test. It was in this way that treatment activists influenced not only the design, conduct, and interpretation of clinical trials, but also the speed in which they were carried out. The timeframe for testing the safety and efficacy of AIDS drugs was reduced, counted in months, rather than years. 

Treatment delayed was treatment denied. By 1987, more than 46,000 Americans were infected with HIV and over 13,000 had died from AIDS.

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Storm the NIH “die-in” in 1990, National Institutes of Health Library, Branson Collection

To take one example, Mark Harrington, a script writer with no scientific background, epitomizes the involvement of AIDS activists in science. Like other activists, Harrington helped ACT UP to organize demonstrations. In 1988, it was “Seize Control of the FDA.” On May 21, 1990, it was “Storm the NIH.” These protests drew attention, but a more nuanced discussion of scientific practices was needed. Activists did not want to be victims, or be powerless or oppressed. They wanted to help discover treatments, even if that meant trying lots of drugs that did not work. Harrington responded by learning the technical details of AIDS, until he could participate knowledgeably in scientific discussions. By 1992, Mark delivered his first plenary at the Eight International AIDS conference.  He began co-authoring peer-reviewed papers, and continued to publish for years (including, for example, a 2006 paper in PLOS Medicine).

How did Harrington go from street demonstrator to scientific collaborator? AIDS activists like Harrington took a four-pronged strategy to gain credibility and authority.

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Activists learned medical language: Abacavir, now used to treat HIV and AIDS, is a nucleoside analog reverse transcriptase inhibitor; photo by Bastique

First, influencing drug testing required a working knowledge of pharmaceutical companies and government. To be successful, the activists had to learn to speak the language of the researchers and learn the culture of medical science. Activists learning about biomedical research found it similar to learning a foreign language and entering another country. Immersion was best. This meant attending scientific conferences, critiquing research projects, even being tutored by scientists. They would read a protocol, learn as much as possible about how the drug is known to work, learn about virology, immune systems, statistics, as well become familiar with the regulations just like an informed patient. Harrington prepared a 50-page dictionary of the vocabulary. Soon activists could talk about viral assays, reverse transcription, cytokine regulation, epitope mapping. Once activists spoke the language, scientists were receptive to discussions.

Second, activists presented themselves as informed, knowledgeable representatives – voices of people who were suffering with AIDS/HIV. Researchers wanted to work with activists too because then they could better ensure that enough people would enroll in their treatment trials and comply with protocols. Activists brokered the relationship between researchers and patients.

Third, activists linked arguments about scientific methodological to moral arguments. For example, early trials were of middle-class white men, but affected populations included injection drug users, people with hemophilia, women, minorities, and heterosexuals. Activists conceived of experimental treatments as a social good to which everyone should have equal access. The history of clinical trials in the United States is full of stories of abuse, lack of informed consent, and people unknowingly exposed to risk and harm. Activists shifted discourse to emphasize the right of human subjects to assume the risks of experimental therapies and to be informed partners in scientific methods. They wanted policy that was credible both morally and scientifically.

Fourth, and perhaps most important, activists were taking sides in debates about clinical trials. Before activists took sides, most researchers performed only randomized, controlled, clinical trials with particular methods that did not allow research subjects to have access to potentially helpful treatment.

People who already tried one treatment would be excluded from tests of a new treatment in the name of “clean data.” But not all researchers believed in clean data. The world, after all, is messy and many researchers thought drugs should be tested in real-world situations.  Activists favored the pragmatic “messy” practice. They feared the “fastidious” practice of clean data from homogenous groups because it prevented terminally-ill patients from trying new treatments.  Activists argued that the only way to obtain clean data in a messy world was to unfairly manipulate and control people. But you could, they and scientist-allies argued, get reliable answers quickly in the real-world if there was a change in clinical trials.

Underlying the four-prong strategy is the basic premise that AIDS clinical trials function simultaneously as research and medical care.

After constant efforts, AIDS activists gained authority, which usually only comes from academic degrees and institutional affiliations. They went from diseased victims to activist-experts. They became citizen scientists.

Today such activists are voting members of NIH committees that oversee drug development.

They are representatives at FDA advisory committee meetings where drugs are considered for approval.

They serve on institutional review boards of hospitals and research centers.

And, like many of the passengers on Malaysian Airlines flight 17, they fly to global conventions on AIDS research.

Exploring a Culture of Health: How Can We Visualize Health Data for Better Communication?

By July 16th, 2014 at 4:53 pm | Comment

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This post is part of Exploring a Culture of Health, a citizen science series brought to you by Discover Magazine, SciStarter and the Robert Wood Johnson Foundation, serving as an ally to help Americans work together to build a national Culture of Health that enables everyone to lead healthier lives now and for generations to come.

There is a seemingly endless stream of health data. Visit the doctor and you get a report listing various bits of data such as your weight, blood pressure, cholesterol and blood sugar. Listen to the news and you hear statistics on risk factors, medication side effects or mortality rates. All potentially useful information, but without background or context, the numbers are likely confusing, meaningless and eventually forgotten. “For health data to be meaningful, the person needs to see themselves in that data. To make this happen, we need to understand how to present data so that it conveys a complete message, not just a number,” says Andrea Ducas, program officer at the Robert Wood Johnson Foundation (RWJF).

A team of scientists from the University of Michigan team set out to solve this problem, creating Visualizing Health, with support from RWJF, to explore ways to visualize health data. When designed well, visuals can be powerful tools for conveying information. “What we lack is data on how best to present data,” says Thomas Goetz, former RWJF Entrepreneur-in-Residence and collaborator on Visualizing Health.

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Me, Myself, and My Microbes

By March 19th, 2014 at 5:34 pm | Comment

Participate in American Gut to find out what bacteria live in your body and help scientists gather data on the diversity of microorganisms that affect our health.

Explore the microbiome around and inside you with these citizen science projects!

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Bacteria usually get a pretty bad rap. Perpetrators of strep throat, food poisoning, hospital infections, the list goes on. But not all bacteria are insidious in their intentions–in fact, many are harmless and even friendly, including the trillions that tag along in and on our bodies on a daily basis. In return for providing these microorganisms with a comfortable and long-lasting residence, they perform a number of chores for us and proactively help maintain our health.

Notably, they extract energy out of the food we eat, aid in the development of our immune system, and fend off intruding pathogens. Bacteria live in multiple areas on the human body, but bacteria in the gut have received the bulk of scientists’ attention so far. And not without good reason–these bugs amount to a whole kilogram in an average individual’s gastrointestinal tract, meaning that on a yearly basis a human adult will excrete their own weight in fecal bacteria. Recent work has shown that bacteria in the gut environment play a causative role in weight gain, obesity, and malnutrition, and that sustained changes in diet can have substantial effects on the composition of these bacterial populations. So not only do the bugs in our gut affect our health and well-being, but our diet and lifestyle modulate what bacteria live there, giving the phrase “you are what you eat” a whole new meaning.

Thus far, most scientific studies on gut-residing bacteria have focused on specific cohorts of carefully selected individuals. As a result, these studies reflect our diversity “to about the same extent that Congress does,” as a team of researchers at the University of Colorado, Boulder puts it. This team, led by microbial ecologists Rob Knight and Jeff Leach, wants to remedy current limitations by obtaining a larger set of bacterial data from a much more diverse population- basically people like you and me, or even literally you and me.

In a citizen science project called American Gut, Knight, Leach, and collaborators offer anyone living in the U.S. the opportunity to submit a biosample (from your skin, mouth, or fecal matter), and for a $99 donation they will process and analyze your sample and give you a detailed description of the microorganisms on your body, in your mouth, or in your gut (depending on the source of your sample). Additionally, the analysis offers you a relative comparison of your bacterial community to the thousands of other people who have participated in the project.

So what’s happening with all the data that’s being collected? American Gut asks participants to take a lifestyle survey and a detailed week-long dietary inventory to accompany their biosample. American Gut researchers and collaborators seek to associate different factors like smoking, veganism, or gluten intolerance to different microbial communities. ”We’re interested in whether we can pick up diet, geographical or seasonal associations. There are also some more specific projects being run through American Gut on inflammatory bowel disease, autism, and several other diseases” said Knight. Overall, scientists studying the human microbiome (or the collective genome of host-associated bacteria) want to know which of these factors make a difference in shaping our microbial populations and what that means for our health. By crowd-sourcing data from all walks of life, American Gut is amassing what’s arguably the largest and most diverse set of information on host-associated communities to start discerning this information. “It will substantially expand our knowledge of the kinds of microbiomes that are out there, will give us a better understanding of what matters and what doesn’t (in terms of factors and controls), and will perhaps allow us to start seeing similarities among different disease states (depending on how many people who are willing to share de-identified medical information sign up).”

Using a citizen science approach offers the benefit of having a large pool of data to work with, but there are some downsides. “The main challenge is cleaning up errors in the data, for example, we don’t really think we have participants who were born in 1060 or in the future (and we don’t know how they managed to bypass the web form validation either),” said Knight. In line with its citizen science goals, Knight and Leach have prioritized making the project open source and open access. The data, in the form of sequences of bacterial DNA (with no personal information), will be publically available for anyone to obtain and analyze. Most academic labs don’t have the funding to generate this type of data, so American Gut enables researchers to independently pursue their own hypotheses about the microbiome and its complex interplay with the environment and human health.

Interested in knowing what bugs are in and on your body? Perhaps you want to know how your bacteria change over time or what bacteria you share with a family member or significant other? Check out different options for your donation to American Gut. Even biosamples from dogs are welcome!

Image: Courtesy of Rob Knight at American Gut

More reading on the microbiome:

1. http://www.nytimes.com/2013/05/19/magazine/say-hello-to-the-100-trillion-bacteria-that-make-up-your-microbiome.html

2. http://www.scientificamerican.com/article/microbiome-graphic-explore-human-microbiome/


Sheetal R. Modi is a postdoctoral fellow at the Wyss Institute for Biologically Inspired Engineering at Harvard University where she studies how bacteria develop and spread antibiotic resistance. She has a PhD in Biomedical Engineering, and when she’s not growing her bacterial cultures (and repeatedly killing them), she enjoys science communication and being outside.

 

Meet Your Invisible Neighbors: Microbes in SPAAACE (and at home)!

By March 12th, 2014 at 11:20 am | Comment

They’re all around us–microbes, that is! Think of them as the neighbors you’ll never really meet. Here are some projects to help you explore the microbiome on earth, in space, and inside our own bodies.

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Project MERCCURI

It’s time! Microbes collected by citizen scientists are heading to the International Space Station this weekend! This project from UC Davis, SciStarter, Science Cheerleader, Space Florida and Nanoracks still needs your help collecting microbes from shoes and cellphone. Find out why, here. Get started!

 

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American Gut

Compare the microbes in your gut to those in the guts of thousands of other people in the US and elsewhere and help researchers learn more about the influence of microbes. American Gut is a project built on open-source, open-access principles. Get started!

 

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uBiome

uBiome is the world’s first effort to map the human microbiome through citizen science. The microbiome are the bacteria that live on and within us. Take a look at yours! Get started!

 

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GoViral

Think you have the flu? Join GoViral participants who report symptoms weekly using a website or mobile app and help researchers in the process. Get a Do-It-Yourself flu test kit, too. Get started!

 

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Clumpy

Help classify plant cell images by their “clumpiness” and give insights into the progression of bacterial infection in plant cells. Get started!

 


Want to bring citizen science into the classroom? Check out our Educators Page to learn more about how to integrate projects into your curriculum.

SciStarter and Azavea (with support from Sloan Foundation) spent the last year investigating developments in software, hardware, and data processing capability for citizen science. Here’s what we found.

Calling hackers and developers! SciStarter is organizing pop-up hackathons to develop open APIs and other tools to help citizen scientists. Contact the SciStarter Team if you’d like to join us in Boston, Philly, NYC, or Washington, DC in April! Email info@scistarter.com

Want your project featured in our newsletter? Contact jenna@scistarter.com