One of the things that Kristin and I are both really fascinated by is the things that people are not seeing. Kristin and I had a great conversation about all the data that can be collected from the world around us and all the life forms we can’t see. I’m a microbiologist by training, so I’m constantly worried about things just outside of the scale of our perception, but our conversation concerned more the movements, the comings and going, and the migrations of organisms we can perceive, but simply are like two ships in the night. We don’t see because they are just out of eyesight, or that we miss seeing by only a few minutes, or that we just didn’t know how to look for. Every year thousands of birds fly from their winters in the Caribbean or elsewhere in the tropics fly north along the Mississippi and pass through Chicago on their way further north, towards the conifer forests of the Upper Midwest, Great Lakes, and Canada. I know during the spring and the fall that these birds are flying by my apartment; I pay attention online for sightings of palm warblers and chestnut-sided warblers, and while I don’t see them every year, I know they’re less than a mile from me a few weeks of the year.
This got me thinking of a research paper I absolutely love. The paper asks the question: what’s living in the subways of New York City? The answer: A lot! And what was there was fascinating. Researchers swabbed and collected genetic information from every subway stop in New York City, as well as collecting data from a few other select sites like the Gowanus Canal. What they found was fascinating. First, there’s a lot of bacterial species around you at all times in the subways, a huge fraction of which we have no idea what they are. It’s strange to think about all the things we interact with on an everyday basis that we don’t know that we’re interacting with, but adding on that we don’t know what they are adds another level. Even the things we do know, like DNA found that closely resembled the Mountain Pine Beetle, just tells us about how much we still don’t know (The Mountain Pine Beetle was listed in genomic data bases at the time, but related species, cockroaches, were not).
What further fascinates me about this paper is what people were unaware of that were potentially dangerous. When grown in a lab on plates full of antibiotics, many bacteria continued to grow. Many sites had bacteria resistant to drugs used to fight infections and diseases, and they were on the surfaces all around busy MTA riders.
There are two more things that are worth pointing out. One is one of the many authors of this paper. Ellen Jorgensen is a respected molecular biologist with a number of impressive roles, but in this paper her affiliation is listed as Genspace. Genspace is a community biology lab in New York City that I mentioned in an earlier post. While Dr. Jorgensen is a trained scientist, citizen science played a key role in this paper.
The other thing that is worth stressing that brings me back to my conversation with Kristin is the vast amount of data in this paper. Each of the six figures in this paper (And the twelve supplemental figures and seven supplemental tables) are jam packed with data. Data on sequences. Data on growth of bacteria in the presence of antibiotics. Data on methodology. There’s enough to look at here to keep you busy for a couple of days. And this is a snapshot for a few specific sites in New York City, not through investigations of the entire ecosystem or even every part of the subway system. My students often ask if we could collect this data on the L here in Chicago, and yeah, we could. We’d have to collect a few partners from a few labs with better equipment than I have access to, but we could definitely get these data. The data are out there waiting for us to collect them. And that data can be absolutely fascinating.
In fields of science and art, what’s exciting is to discover what you are not looking for! Hold space for this thought. For now, it’s our north star.
Andy and I have a mutual fascination with the complexity of ecosystems and a shared concern about how ecosystems are shifting as a result of climate change.
Icon, a Megellanic penguin I sponsor near the Strait of Magellan, has been rearing chicks. Warming waters and rising temperatures have pushed species out of range and Icon must travel farther than ever to find a food source. At the nesting site, scientists are documenting a loss of body mass among breeding Magellanic penguins.
Reports of declining bird populations make frontpage news these days but impacts on critical life forms that we cannot see, such as bacteria and fungi, are under documented and under reported. To understand impacts on and relationships within an ecosystem, you need data over time, so today Andy and I began exploring publicly available biodiversity datasets. These datasets are impressive yet they can be overwhelming in amount. We have arrived at an idea to explore and over the next two weeks we will play around with what that might look like.
Here is a sketch of a related project that I plan to launch in spring of 2021. It’s a project that I began working on almost a year ago and that has been on pause for the past six months due to the pandemic. It has been generative for framing questions, concerns and pitfalls about working on a hybrid project that falls somewhere between art and science.