Hope: What is most fulfilling to you about being a member of open-access data studies?
Circles in Human Biology studies a “sensitive” topic: The human areola!
All mammals have nipples, but only humans have areolas. Areolas are the pigmented circular markings that surround our nipples. How did we get these markings? Why are some areolas large and others small? Can we find the genes that build these circles and discover why we have them?
Anyone – of any gender! – can join. The study is especially interested in participants who have had genetic sequencing.
Participation is easy:
- Sign up on Open Humans
- Complete an online survey
- Use simple measurement tools to share data about your own body
- Share photos of your areolas with the researchers (helpful but not required)
Almost 400 people have signed up and shared their data so far!
By analyzing participant-reported data, the ‘Circles’ team has already learned that areolas are much more diverse than previously thought. They’ve also discovered that the diameter of a person’s areolas is unrelated to the number of areolar glands they have. In fact, people can have anywhere from 0 to more than 30 of these little bumps. Scientists believe these bumps help protect nipples during nursing and provide an olfactory cue to help newborn infants nurse, but research has yet to confirm this.
Learning about diversity in areola morphology could not only help scientists understand breast health, it could teach us about human genetic diversity in general.
To read a New York Times article about this study, click here.
We vary in all kinds of traits, from physical traits like height and hair color to sensory traits like taste or odor perception. These differences impact our lives in big ways, from what foods we eat to what medicines work for us to how we feed our babies. We are just starting to understand how these traits are built genetically and why they vary. These discoveries are going to give us fascinating new insights into the way our genomes build our bodies and influence our lives.
– Abby Wark, Project Director of ‘Circles’
Open Humans enables participatory research. Blurring the line between scientist and research participant is part of our mission – because we know that data sharers can become data explorers and tool builders, too!
Our two new activities are prime examples:
- Open Humans HealthKit Integration
You can install this member-created app to add ‘Health’ data from your iPhone to Open Humans.
- Open Pokemon GO GO GO!
Whether or not you’ve played the game, you can share HealthKit or Fitbit data to create a shared data set that we can explore together!
Read on to learn more…
Open Humans HealthKit Integration
Did you know iPhones store health data? You might have data you didn’t know about! Since 2014, iPhones have been tracking your activity (e.g. steps) data through the ‘Health’ app. They can also log lots of health data – from blood glucose to weight!
This data is private on your iPhone, but you can decide to share it. James Turner, one of our most engaged and “connected” participants, has applied his iOS developer skills to create the Open Humans HealthKit Integration app to allow you to export HealthKit data to Open Humans!
In the past few months, Open Humans has expanded our features to allow projects to add data to member accounts. We hope researchers use this to return data, but we’re thrilled to see it used by a community member to create a new, valuable data source!
There’s a ton of health and fitness data being captured by iOS users now, and the HealthKit Export app is an attempt to make that data accessible to researchers in a standardized format.
Open Pokemon GO GO GO
This non-study project allows you to contribute to an open data set of physical activity levels for summer 2016. The inspiration for this project was the Pokemon GO craze, but anyone with an iPhone or Fitbit can participate.
This is mostly a personal project. Pokemon GO has been such a phenomenon, and I wanted to create something fun in response! Sharing data like this can create invaluable resources for students and citizen scientists to explore. I also wanted to provide an open source demo for how to make projects on Open Humans – it’s easier than you think! I’ll be writing up an explanation on how it was set it up, and open sourcing the code used.
Join studies, connect and share data today.
Check out the 23 activities listed on our new Homepage
We’ve made it easier for you to:
– Find data sources to add
– Find new ways to share
– See the activities you’ve already added
Are you a researcher? It’s easy to add a project! Read more about it here.
Thank you for your ongoing contributions to research and citizen science!
Interested in what researchers are learning about microbiomes? Embriette Hyde is the Project Manager of American Gut and one of Forbes’ “30 Under 30”. I interviewed her last week.
Hope: I read in your bio that you’ve done some forensics microbiome work. Can you talk a little about that?
Embriette: When I was a grad student, I did research at one of two body farms in Texas where people study human cadavers. I don’t want to get too graphic, but insect activity increases, and then decreases again, as bodies decompose. By analyzing the progression of the microbiome associated with bodies, we identified microbial signatures that seemed to be associated both with insect activity as well as decomposition stages in general. This ‘microbial clock’ enabled us to get a pretty accurate determination of the time of death.
Microbiomes can also be used as a sort of fingerprint. Rob Knight, American Gut’s PI (Principal Investigator), co-led a study in 2010 that showed people can be identified from the microbes they leave behind on surfaces. After this research came out, CSI:Miami did an episode based on it!
Right now, human DNA helps to solve crimes, but research like ours is showing that forensics may one day consider microbial DNA as well.
Hope: What are some of the common effects of closed-space lifestyles on the microbiome of humans and animals?
Embriette: In industrialized nations, we spend a majority of our time indoors and in very hygienic areas. This doesn’t seem like a bad thing at face value, but there’s been an increase in chronic conditions such as asthma and allergies in industrialized nations as compared to non-industrialized nations. As a result, a “hygiene hypothesis” has developed: We think that we’re helping ourselves, but we actually may be doing ourselves a disservice.
I did research in which I looked at the microbiomes of 1. humans and pets compared to their home environments, 2. captive Komodo dragons (the biggest living lizard in the world, found in the wild only in Indonesia) and their enclosures, and 3. wild amphibians and their ponds. Humans, pets, and captive Komodos all share many of their microbes with their environment; wild amphibians do not. We don’t have enough information to make any definitive pronouncements or recommendations for what people might want to do about this in their homes, but a first step might be to alter how we care for animals in captivity.
Embriette: A ‘microbiome’ is a community of organisms that live in an environment. These organisms are called microbes. I think most people associate microbes with bacteria, but they also include microscopic fungi, archaea, and viruses. Microbes interact with us in an intimate way, evolve alongside us, and do things for us – like break down nitrates in our oral cavity – that have a snowball effect on our health.
Right now, a lot of people are jaded about the use of synthetic drugs, and I believe microbiomes will soon help us to treat disease more successfully.
They could also alter how we approach diet and dietary interventions. A study of diabetics in Israel recently showed that microbiome analysis can help create an algorithm that determines a personalized diet for blood sugar stabilization. One patient in the study was even found to have a better response to ice cream than to tomatoes! This sounds dubious, but it suggests that microbiome analysis could have a potentially life-changing impact (and also likely explains why one diet works for some but yields no results – or negative results – in others!)
I really believe that, one day, microbiome sampling could be as routine as taking a blood test!
Right now, though, it’s still much easier to study animals than humans since we can control their environment and they tend to be genetically similar. This is why it’s so important for projects like American Gut to study big sample sizes. We need to be able to observe physiologically relevant patterns despite the variability brought to the table by studying the human organism.
I’d like to add that the National Microbiome Initiative has given microbiome research a huge boost in national recognition. This, in turn, is influencing the financial and moral support that we’re garnering. A few years ago, I went to a general microbiology conference – not a microbiome specific conference like I’d been used to – and was surprised at the pushback regarding whether microbiome research is coming to conclusions too quickly. I think the NMI will open the door for more scientists to jump on board and help us to realize the tremendous potential for microbiomes in the coming decade.
Hope: What do you do on a typical day at work?
Embriette: Now that I’m the Project Manager for American Gut, I spend a lot of my time communicating with participants and collaborators. The project is growing, and we have developers working to improve the site, researchers who need help with IRB (Institutional Review Board) documents and sample collection, and students who are doing data analysis. I don’t do as much direct data analysis as I did in the past, but I’m involved in a lot of it.
I also participate in local events that help publicize American Gut, like the recent Rock ‘n’ Roll Marathon Series here in San Diego. In general, people in this area tend to be familiar with the concept of the microbiome, so we’ve received a lot of enthusiasm for the project — both from participants and potential collaborators. We’ve even had doctors who’ve approached us because they believe their patients would be interested in joining. We’re so thankful for the positive word of mouth that we’ve received!
Hope: What changes, if any, did you make to your diet or lifestyle after getting the results of your American Gut kit? How did it feel to be a participant in your own study? Did the experience make you any more likely to join other participatory research or “citizen science” projects?
Embriette: I was already changing my diet – eating less meat, processed foods, and candy – before I participated, so I knew I was on the right track. I just wish I had “before and after” samples so I could compare my current microbiome to what it was like five years ago! I also did 23andMe before I did American Gut, so between that and my research, I didn’t sign up as a participant looking for answers to specific questions. I did it more for curiosity’s sake, and to connect to others and be able to say, “I’ve done this, too.”
I’m definitely more likely to join other projects. I know how important participants are to the success of a study. We need people to sign up or we’ll never find answers to our questions.
Unfortunately, people sometimes forget that “citizen science” projects like American Gut are research studies. We’re not a company providing a service. The funding we collect allows us to gather data. I think it can be hard for people to hear that it takes time for science like this to produce actionable results.
Hope: Have you had the opportunity to compare the microbial communities of different cultures?
Embriette: The name “American Gut” is slightly deceptive since we accept participants from anywhere in the world. To date, we have 9,000 samples representing 28 countries in the cohort — and the majority are from the US, UK, and Australia because of our collaborations with Tim Spector at King’s College London (British Gut) and Phil Hugenholtz at the University of Queensland. We’re currently in the process of setting up a third aggregation site in Singapore with Scott Savage.
Comparing just the US to UK samples, for example, we see greater microbiome diversity in those from the UK. I’m not positive why this is, but I have some hypotheses. I’m not sure about the UK, but in Spain, there is still a big culture where people shop for and prepare food on a daily basis rather than relying on on pre-cooked, instant meals. I don’t think anyone has studied whether that has an effect on the microbiome or not, but I wouldn’t be surprised if it did.
Perhaps another reason is the fact that some medications are often not given as readily in other countries as in the US. We know that antibiotics have a negative impact on microbiomes, yet in the US it’s not unusual to be prescribed one for what may be a viral infection, or when the cause of the presenting infection is undetermined. It’s hard to change healthcare practices, but we might benefit from approaches that allow the body to fight infection without such aggressive intervention. When I was in Spain and had a recurring sinus infection, the doctor recommended that I see if my body could fight it off without drugs (and refused to give me the antibiotics I asked for!). Not only was I able to fight the infection, I’ve never had another sinus infection! That experience had a big impact on how I view medical intervention.
In the US, we also continue to give antibiotics to animals intended for food, which can represent a large source for antibiotic resistant bacteria. Europe has already banned this. Agriculturally, I believe they’re ahead of us in this regard.
As for Eastern countries, people there tend to eat more fermented foods – think of soy sauce, miso soup, kimchi – than we do in the US. Preliminary research shows that these foods have a positive effect on microbiome diversity. I have sauerkraut fermenting on my kitchen counter right now for this very reason!
Hope: On the Research Page of your website, you mention that you’re beginning to explore how vaginal ring drug delivery systems impact the vaginal microbiome of women. Can you explain the potential health outcomes of this research?
Embriette: Our focus is on a ring delivery system for preventative HIV drugs. We know that we can deliver the drugs this way; a few groups have done it. What we’re specifically studying, though, is the impact on the microbiome of wearing a ring like this continually. As of now, we don’t yet have enough data to make a determination, but the study is ongoing.
From reading your bio, I was curious to learn that you enjoy studying the Hebrew roots of Christianity. Do you think your religious knowledge affects your approach to science?
I love science and the more I learn, the more convinced I am that there’s a Creator who has provided this world for us. I don’t think this should be viewed as some sort of disconnect. That being said, I’m able to compartmentalize. At work, my focus is scientific truth. But just as we don’t understand everything in science, we don’t understand everything beyond science. I can believe in evolution, but that doesn’t mean I have to believe it’s the origin of everything.
Hope: What health-tracking technology do you wish existed?
Embriette: Smart toilets and personalized sequencers that give feedback saying “here’s what you can do today to keep your microbiome happy.” Also, portable, real-time sequencers for use in the field because sample preservation is sometimes difficult. Finally, an app with a plug-in that can upload data from samples to the Cloud. I’d definitely use that!
Hope: Last question! This year, you received an incredible honor: You were one of Forbes’ “30 Under 30”. How did you celebrate? Did they give you a trophy, and, if so, do you keep it at work or at home?
Embriette: They didn’t give a trophy, but I had the option to buy a plaque for $100 — which I didn’t do (yet)! But I have a nametag from the Forbes retreat that I went to and keep it at work along with other conference nametags.
I found out about this while I was in Spain. I went out for a celebratory dinner with my fiancé, his sister, and her husband. It was shortly after my fiancé’s sister had designed my personal website specifically for my application to Forbes, so I was really excited to be able to celebrate with her in person! But the honor wasn’t really about me; it was about American Gut. I am so fortunate to be leading the project, but there are lots of people who have helped make American Gut a success, and I hope this recognition helps the project more than it helps me.
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This is the first of what we hope will become a series of profiles of Open Humans members who intrigue and inspire us. If you’d like to be interviewed, too, let us know!
I approached Joshua Berk because he currently has the most connected data of anyone in the Open Humans community. He turned out to be friendly, thoughtful, and a passionate advocate for open-access data.
Hope: Thanks for taking the time to speak with me today, Joshua. First off, can you tell me how you learned about Open Humans?
Joshua: Sure. I had been interviewing with biotech companies and heard about George Church. He was also mentioned in a genomics course I was taking at Stanford, as was the Personal Genome Project. Reading up on the PGP led me to Open Humans.
Hope: Wow, you were taking a genomics course. Nice! How come you decided to participate in Open Humans?
Joshua: Primarily to be a good Samaritan. To my knowledge, rarely if ever has all of this data been available in such a publicly-accessible, useful way. I believe the benefits to research from Open Humans – especially as the data set becomes even larger and more statistically significant – will be enormous. “The whole is greater than its parts,” as Aristotle said.
Additionally, getting this information ultimately could provide me with knowledge that will help extend my longevity or allow me to avoid a hidden catastrophe. Data gives us a more accurate idea of reality and helps us to make better decisions. Not knowing is disabling. I can actively help myself in response to knowledge.
I also think to not know is to live a less nourished, less fulfilling life. Participating in the Open Humans studies doesn’t take a lot of time, and there’s potentially a huge payoff. I work in technology and everything in the tech world has been touched by open source initiatives. We wouldn’t have an iPhone without open source software. I think this same analogy applies to science. One-hundred years from now, people will reflect back and wonder why we didn’t do this sooner.
Hope: If there were one thing that you could say to other Open Humans members, what would it be?
Joshua: I know as little as anyone else. I’m just a normal dude trying to learn some stuff. But there’s no question that the more we contribute, the more valuable the data becomes.
You know the saying ‘the rising tide lifts all boats’? I can guarantee that being a part of this community will become even more rewarding over time as additional people join. It’s like money in a savings account. Small contributions add up in the end. It’s not a matter of if, but when.
Also, just the info that you can learn today is worthwhile — and requires minimal effort. Everything on my profile took a total $100-200 and just a few hours. Contributing health data doesn’t have to be your life’s purpose. The point is that you can make an incredible contribution that pays dividends that we can’t even see yet. You will get knowledge that far exceeds the cost and time required, and that is massively useful to research in the future.
Finally, it’s very rewarding to serve as a point of social proof for others regarding the benefits of getting involved in science. It’s an opportunity to normalize something so it begins to seem less exceptional.
One more thing: I encourage people to check out http://learn.genetics.utah.edu/. I stumbled upon this site, and found it to be an incredible resource — like a distilled version of the genomics course I took. Plus, it’s totally free!
Hope: What health-tracking technology do you wish existed?
Joshua: So many things! Smart dinnerware and utensils, a toilet for measuring digestive health from stool and urinalysis… I have a long list! Generally, though, I want to understand what’s going on in my brain. I want to be able to approach how I feel in a more scientific and precise way.
I believe the amount of knowledge we don’t have eclipses what we do know, and that the more we know, the more empowered we are. More data begets more knowledge. So much of health has been reactive and restorative. In the future, I have no doubt that it’s going to be proactive and geared towards optimization. This data enables that future to happen and hopefully gets us there sooner.
Don’t be driven by fear! Be driven by hope and optimism!
Hope: What a great motto to live by. Thank you, Joshua!
We held our latest GET Conference on April 25-26 in Boston. We know most Open Humans members couldn’t attend; we hope you enjoy some of these videos and highlights!
Kathy Hudson’s keynote address on the Precision Medicine Initiative and the rest of the 2016 GET Conference lectures are now on this PersonalGenomes.org Youtube Playlist.
Subscribe to this channel to be notified when we upload new videos!
GETy Award winners
The first ever GETy Awards honored excellence in participant-centered research. Learn about the GETY Award winners by reading this press release.
The GETy Awards honorees ended their acceptance speeches with a “codonku”, a nerdy sort of haiku that we invented. Here’s one of our favorites:
Autocatalysis usually goes
until annihilation. Imagine
us annihilating autocatalysis.
– Sonia Vallabh & Eric Minikel,
Participant Pioneer honorees,
People’s Choice Award: American Gut
At the conference, attending Open Humans members voted on the GETy “People’s Choice Award”. The award was won by American Gut! You probably already know about this terrific study – but if you don’t, you can go to the Activities page on Open Humans to learn more about them and other connected projects.
We’ve added five new data sources for Open Humans members. We know you have some great stuff to share with science. Get your data in so researchers know it’s there!
Easy links below: you can jump right into adding each source…
- Connect Fitbit
Health and fitness devices, including activity trackers that record steps, heartrate, and sleep, as well as a scale.
- Add Illumina Understand Your Genome
Whole genome sequencing, generated as part of symposium teaching attendees about their genome data.
- Connect Moves
An always-on location logging app for iPhone or Android. It counts steps and classifies activities as walking, cycling, running, and transit.
- Add uBiome
Sampling kits for individuals to test gut, mouth, and other locations, performing microbiome sequencing & profiling.
- Connect Withings
Health & fitness devices, including a scale and a blood pressure monitor, as well as the Health Mate smartphone app.
These sources are all “in development”. We won’t be able to generate files right away, but we will soon! Add the source and we’ll build our data processing based on what we see.
Sharing is always optional. You choose when to share & who to share with. Data is private by default!
Other data sources…
In case you missed them, here’s all our other data sources (some studies, some commercial). Do any look familiar? Follow the link to add it to your account!
- American Gut
- Harvard Personal Genome Project
- Wild Life of Our Homes
You can also add data files from anywhere using our Data Selfie feature!
GET Labs & GET Conference
As a reminder, Open Humans members are invited to GET Labs & GET Conference in Boston this April 25th and 26th! It’s a unique participatory science event that’s been running since 2010. Registration is still open – read more about it on our previous blog post.
On April 25th and 26th, leading thinkers, scientists, and participatory researchers will gather in Boston at Harvard Medical School for two days of interactive science and amazing talks.
- Tickets for GET Labs exclusively available to ALL Open Humans members (and ONLY Open Humans members) for a nominal fee of $16! Becoming a member just takes a minute.
- Tickets for the GET Conference are typically $299, but attendance is FREE for qualifying Open Humans members!
GET Labs on April 25th
This is an exclusive event for members of the Open Humans community!
What is “GET Labs”? This event is all about advancing science through direct participation. We bring together participants and researchers for a day of interactive labs. If you’ve never been, it’s a unique experience! Our community has helped advance all kinds of research, everything from viral profiling, perfect pitch, ancestry, fitness sensors, user interface design for genome reports, and – probably most popular last year – face mites! (Yep, turns out we all have Demodex mites.)
Fifteen research studies are already planning to attend, and the list is sure to grow. As in years past, the Harvard PGP, GoViral, and American Gut team will attend – and they’re planning to share free microbiome kits with qualifying members!
It’s also a chance to meet other Open Humans members! GET Labs invitations are open to ALL Open Humans members – and ONLY Open Humans members! – for a nominal fee of $16.
The day will close with our first ever GETy Awards ceremony, honoring excellence in participant-centered research, followed by a reception.
GET Conference on April 26th
We’ve got amazing talks & discussions lined-up this year! Come learn from leading experts about:
- Integrated Omics Profiles
- Microbiomes, Health, and Built Environment
- AI & Medicine
- Networked Biology
Part of what makes the GET Conference amazing is how the audience truly bridges researchers and participants. Each year, we reserve around half of the seats for participants from our community, as a thank you for engaging with us and collaborating in the creation of culture of participatory research. For qualified members, registration is free: all we ask is for a donation in the amount you can afford. For everyone else, tickets are $299.
To learn more, click the button below and look at the “special opportunity for Open Humans” on the registration page for how to qualify for your FREE Ticket.
As you can see, this year’s events are not to be missed. We hope you can make it! Full agenda here.