Tiny invisible bosses

“We are bulky ornaments on life’s skin,

riding the surface, only dimly aware

of the microscopic multitudes

that make up the rest of the body,”

From the book, The Forest Unseen, by David Haskell.

Sometimes the scale of things makes all the difference. My microbes are invisible to my eyes, but increasingly important to how I “see” my own health and our collective public health.

My gradual change in thinking began a few years ago when I donated information from my home and my own body to two different research projects. One was the Ubiome project, which is mapping the microbes in thousands of human guts. The other was the Wild Life of our Homes project, which is mapping the microbes of homes in all 50 states in the United States.

For the Wild Life project, I used a swab that looked like an overgrown Q-tip to take samples from doorways and my kitchen counters and my pillow. I mailed that swab in a vial to the researchers. For the Ubiome project, I took a sample of feces from my toilet paper and sent that. In each case, the samples eventually were sequenced. A lab checked a portion of the RNA sequences in the samples to identify the microbes.

Do the microbes in my own gut make me healthy? Is the ecosystem of my gut different than my husband’s? Each project is asking a question about the vast largely uncharted multitudes of microbes that live in and on our bodies, and in our homes. I wrote in  earlier blog post about these projects.

Donating these microbes made me curious. Learning more about my own skin – literally what lives on my skin – made me wonder more and more. Living in Seattle, I am surrounded by science that probes what is known as “big data.” Our town is especially full of scientists who specialize in mind-bogglingly  large sets of data, including terabytes of information from the genetic sequences of thousands of bacteria living in the human gut, to name one example. These data scientists have to invent their own education, because typical classes don’t serve them. I met some of them when writing a story for Seattle Business magazine.

Many microbiologists will tell you – the microbes don’t just outnumber us on Earth, they add up to more biomass than all the terrestrial mammals of earth added together.  While the comparison may seem unfair, the point is that we should not overlook the microscopic world of our planet.  Our indifference to these creatures because of their scale is exactly what author David Haskell in the quote above eloquently points out is blindness.

During a recent conference of citizen scientists, I had reason to think about this blindness. Our session explained how people donate microbes  for a variety of research projects. The participation itself, I would argue, changes the way you look at the microbes. But it also changes the way you think about scale. You appreciate that the collective action of millions of small creatures may influence bulky organisms like ourselves. In a similar way, going to a conference can make one appreciate the collective ecosystem of thousands of citizens. Might we make big changes happen?

During the conference, many of us talked about whether people who volunteer to collect data for science emerge from the experience with new outlooks. There are more and more people involved in citizen science, so it is worth wondering whether they will vote or spend money differently because of it.

What may seem like an abstract discussion could save the life of someone you love, if they spend time in a hospital and come home with an infection from an organism known as clostridium difficile. These organisms can make people terribly sick and transplants of gut bacteria (in fecal matter) from healthy people have cured some of those patients. Recently, the Centers for Disease Control released new statistics suggesting that nearly half-a-million Americans are  infected per year.

Thinking differently about scale is one reason that pioneers thought of the fecal transplants to treat patients with C. diff infections. While we don’t understand enough to define a “healthy” microbiome, the change in thinking is mammoth. Most people share some similarities within their families of their gut microbiome and there’s some evidence we acquire our microbiome from our Mom.  Many questions spin out from this change in thinking.

One day when washing some carrots from a local farm, I wondered if the microbes in the dirt I was washing away might actually hold more benefit for me than the carrots themselves. At my local gym, I wondered if the reason people who exercise in groups seem to live longer could be related to to the microbe sharing that happens when we share mats and weights. I’m not suggesting either of these ideas is true but just pointing out that once you view the microbes as potential actors in your health, it makes you see differently.

Scientists around the world are now asking questions about microbial life in relation to human health, as well as the ecological health of our built environment and our wild places. They are demonstrating a new way to “see” questions about health. There is research on the relation of gut health to autism, obesity, diabetes and depression, just to give some examples.

As our knowledge about microbes increases, we may see our world very differently. We may be minor players in a game driven partly by these microscopic actors. Stay tuned for more posts on this topic. I welcome your questions.

Let me leave you with a wonderful 25-minute video by  microbiome reseacher,  Jonathan Eisen, who presented in March at a meeting called the Future of Genomic Medicine.  Sorry that the video begins with a short advertisement.

Image above used with permission of the Pacific Northwest National Labs. Taken by Janine Hutchison. Green is lactobacillus reuteri, purple is collagen microsphere, and brown is intestinal cell.

Shallow dive in Seattle big data projects

Seattle has a rich resource of both data-driven research projects and scientists who enjoy designing tools that mine data.

I was asked to talk about that big data heritage here in Seattle as part of a meeting of the Northwest Science Writers Association.

Consider this blog post a cheat sheet for those of you who did not take notes during my presentation or didn’t attend.

1. Big Data is defined as having volume, velocity and variety. If you put sensors on the ocean floor, as researchers are doing at the University of Washington, you will bring back real-time data by the server loads on temperature, salinity, and even on genetic sequences of the microorganisms there. The data will stream at high volume and velocity and with amazing variety. But finding insights from that fire hose of data is not so easy. There is a shortage of the data scientists who know the best way to parse the flood, according to Professor Ed Lazowska, who commented for my recent story.

Lazowska and a team have pioneered the eScience Institute on campus to nurture data science and provide a meeting place, a sort of water cooler, for the best conversations and exchanges among disciplines.

2. Most of us already understand the retail use of big data, because predictive models of our own buying behavior surround us. Apps that help you choose restaurants, airlines, music and other commodities are using models built on the buying habits of thousands of other consumers. The same desire for prediction is driving medical research now. Researchers in Seattle at the Institute for Systems Biology and Fred Hutchinson Cancer Research Center and Allen Institute for Brain Science are all using algorithms to try to understand vast amounts of data about human disease. One wonderful overview of this new way of seeing human disease was just published in Cell by Eric Topol in April.

Among the things Topol envisions in the very near future: “With the power of sequencing, it is anticipated that the molecular basis for most of the 7,000 known Mendelian diseases will be unraveled in the next few years.”

Many human diseases are a complicated mixture of vulnerabilities combined with environment and behavior. Knowing their molecular basis does not mean curing them is easy. But this level of understanding will create new opportunities.

One of the foremost Seattle scientists in genomics is Jay Shendure. You can read why NIH Director Francis Collins praises his newest ambition.

3. For my last comment on this quick overview about Seattle, I want to change the focus of the big data from sensors and molecules to the “big” pool of people that are increasingly seen as a resource for research itself. Patients are key players in new efforts to accelerate medical research by drawing in volunteer patients who free data about themselves. One of the pioneers of this approach is Sage Bionetworks, lead by Stephen Friend and John Wilbanks.  I wrote an earlier post about Friend, when the White House gave him an award. Recently, Forbes wrote about the way drawing on the public may bring faster cures.

Seattle sits at the center of many different strengths in using big data. We have leaders in a variety of sciences, including oceanography and proteomics, but we also have leaders in the creative destruction of the old models for disease discovery. As science journalists, I think you can mine many data projects for stories.

 Photo above is of poster session at the eScience Institute at the University of Washington.




Learning to share big data

A UW effort aims to help scientists make better use of the vast amounts of information being collected.

The full story was published in Seattle Business Magazine. read it here.

The University of Washington has launched a new project that could dramatically increase the power of academic research by giving a broad universe of scientists — including astronomers, physicists, chemists and biologists — faster and smarter ways of extracting information and meaning from the increasingly large amounts of data they have available to them.