Elizabeth Hénaff

Elizabeth Hénaff

 

 

Elaine:

Elizabeth Henaff is a computational biologist. She is an artist designer and programmer who looks at multispecies interactions, particularly between plants, microbes, and people, as well as toxic infrastructures and ecologies such as New York city subways and Superfund sites. Her projects take the form of scientific articles and specialized journals, data visualizations, experimental software, sensors, art exhibitions, and interdisciplinary collaborations. Elizabeth teaches at the department of Integrated Digital Media (IDM) at NYU Tandon School of Engineering.

Elizabeth:

Plant biology and plant biology research was kind of my first exposure to the experimental sciences. At that time, I was interested in plant transposons, which even for most biologists is kind of a cryptic field, but I think it’s an interesting idiosyncrasy of genomes. All genomes that have been studied, including humans contain what are called jumping genes. And so these jumping genes encode the proteins that are able to recognize their own DNA sequence. So it’s an interesting kind of self-referencing system. It’s a DNA sequence that encodes a protein that has the physical confirmation necessary to recognize the physical shape of that same DNA sequence that was its originator and do something with it.

These transposons are mutagenic elements because when they insert a new copy of themselves in a new location in the genome that can potentially disrupt the coding sequence of a gene. As such, they can have deleterious effects or bad effects if they insert themselves into an important gene. Why would organisms encode these kinds of mutagenic elements? It turns out that on a short time scale, these mutations or these transposition events can often be deleterious, but on a long evolutionary timescale, these types of mutations can lead to big genomic innovations. If you think of evolution as being a system of trying out combinations of many different possibilities, being able to generate really drastic mutations allows you to kind of jump around the solution space in ways that point-mutations, so changing one letter at a time, wouldn’t allow you.

So interestingly, there’s really big genomic innovations that have been attributed to transposition. So I did my PhD work on that and developed a novel algorithm at the time to be able to recognize those transposition events in genomic data. And I used it to characterize evolutionary properties and responses in plants. I went from studying plants as organisms that you can look at under a microscope, to studying plants as organisms that you can study through DNA sequencing. Using this lens of DNA sequencing to study organisms, I got interested in studying organisms that you can’t see such as microorganisms.

The discipline of studying microorganisms through the lens of DNA sequencing is the discipline of metagenomics. So if genomics is the study of a genome of a single organism, then metagenomics is the study of a set of genomes together. And so metagenomics has been pretty transformative in the study of microorganisms. Obviously we’ve known about microorganisms for a very long time, not actually a very long time, but most of the insights that we have gained in relation to microorganisms and their life cycles and their characteristics has been through culturing them in the lab, in petrie dishes. So if you want to study the microbiome of this table right here or soil or a wound, you would take a sample, streak it out in a Petri dish, put it in an incubator and see what would grow. You would have colonies that form and by the shape of the colonies and maybe their color and their growth rate, you would be able to infer something about their characteristics. So that is very useful, in many ways, but there’s many types of microorganisms that do not like to grow in petrie dishes. And so we call these recalcitrant organisms and a lot of environmental microbes are recalcitrant to culture in the lab.

Using the process of DNA sequencing, we’re able to study microbes without going through a step of culture. You can take an environmental sample, you know, take a swab of this table, take a teaspoon of soil, extract the DNA, sequence it. And then using that data, ask the question of what types of microorganisms are there, what types of functions do they encode, without going through that step of culture. And so you have a less biased perspective on the populations of microorganisms that you have in your environment than if you were to culture them.

Elaine:

How do you identify a set of organisms that somehow make sense together?

Elizabeth:

So usually they’re co-localized in a particular environment. The metagenome would correspond to a set of organisms that you took in one single sample, but then the way you take that sample dictates the set of organisms that you’re studying. So if you swab a square inch versus a square foot, you’re going to get a different metagenome. I think the apparatus very much defines the organism as you’re studying it. And that can play out in many different ways. Just as in any other experiment, it’s very important to define your controls, to be able to reach any kind of meaningful conclusions. But just to give an example, the material of the swabs that you use will introduce a bias as to the microorganisms that you collect. So if you look for clinical sterile swabs, you can usually find nylon swabs or cotton swabs and cotton and nylon have different adhesive properties for different microorganisms.

Depending on the material of the swab that you’re using, you will tend to pick up certain microorganisms over another type. Depending on the DNA extraction method that you use and the types of, um, solvents that you use to break down the cellular membranes, you will break down more easily, some membranes over others, and that will also introduce bias into the data that you get. So it’s definitely not free of instrumentation bias. But coming back to the topic of metagenomics, what’s interesting about studying microorganisms through, through this lens is that we’re starting to understand that a lot of the phenotypes or characteristics of multicellular organisms are related to their interaction with microorganisms. So for example, flowering time in plants has been shown to be dependent on the types of microorganisms that are in the soil in which they’re growing. And so that’s kind of a big deal in the plant biology world because time was thought to be like the canonical genetically determined, well understood pathway. So that kind of created big waves in the plant biology world when it was shown, that that pathway can be modulated by the types of microorganisms with which the plant is interacting. That’s also the case for mammals, including humans. We’re starting to become aware of the importance of the gut microbiome and human health. Grave states of disease, such as irritable bowel syndrome, or Crohn’s disease have been associated with disruptions in the gut microbiome, but it’s also been shown that more subtle characteristics of human health and well-being can be related to our interactions with microorganisms. For example, a large part of the serotonin that we use in our brain, which is, serotonin being a neurotransmitter that we use for normal brain function and deficiencies of which have been associated to psychological conditions like schizophrenia or depression. It turns out that a large part of the serotonin that we use in our brain is actually produced by microorganisms in our gut. And it’s not us that synthesize it.

Our interaction with microorganisms is modulating our identity as humans. So if we look at all these different cases, you know, the plant world and the mammalian world of how phenotypes or physical characteristics of these multicellular organisms are due, not only to the genetics of that multicellular organism, but also due to the genetic makeup of the microorganisms with which they’re cohabitating and interacting. That kind of begs a redefinition of genetic identity to include also the genetic identity of the microorganisms with which we live in symbiosis. And so that particular broadening of the notion of identity and of the individual has been discussed at length by Lynn Margulis, who coined the term of “holobiont.” So the term holobiont encompasses both the notion of host and symbiont and combines those two concepts to redefine the notion of the individual.

Elaine:

If you were to reverse that and think of the microorganism as the host and the multicellular organism as the symbiont, does it change how you think about identity?

Elizabeth:

Yeah. And so that’s an excellent question actually, because we evolved in a microbial world, right? Unicellular organisms existed a long time before multicellular organisms evolved. And so it is I think a very human-centric perspective to define the multicellular organism as the host or the director of operations and the unicellular organisms as the symbionts or the passengers. And so, it’s entirely possible that we basically evolved to be carriers and provide environments for microorganisms. Absolutely.

Elaine:

So let’s jump, I guess, to a larger scale, which is the canal as a very different kind of carrier. What is the history of the canal?

Elizabeth:

So the Gowanus canal used to be a creek, the Gowaine Creek, and it was dredged in the mid 1850s to serve as a means of transportation to and from the factories that were in operation around that area. Not only did it serve as a means of transportation, but it also served as a de facto dumping site for the industrial waste that was being generated by those factories. And so over the last 170 years, the Gowanus canal has accumulated about 10 to 15 feet of contaminated sediment at the bottom of the canal. And that sediment is composed of mostly complex hydrocarbons that are the byproduct of the coal tar extraction industry that was there, but also industrial solvents, heavy metals and other toxic compounds that were the byproduct of the various factories that were in operation. So then the canal was pretty much left as is until very recently. It was declared to be a Superfund site by the environmental protection agency in 2010. So, the Superfund program is a program that is led by the EPA to designate certain sites as priority for remediation, mostly due to their threat to human health. And so in this particular case, the Gowanus Canal is a toxic environment and it’s also embedded in a very residential neighborhood. As such, it poses a threat to human health. The EPA has led a series of studies to kind of identify the characteristics of this particular site. The way that they’re going to proceed with remediation is through dredging and capping, which is kind of a standard mode of operation for this particular type of configuration. The plan is to dredge the sediment that can be dredged and treat it elsewhere, cap the canal with concrete, and then let the water flow again.

Elaine:

Just to be clear, dredging and capping means what exactly? Dredge is dredging the sediment then capping is laying concrete over it. And the EPA wants to do both of those things.

 

Elizabeth:

Yep. So dredge the sediment that can be removed from the site and then cap the rest with concrete. So this has been shown to be effective in some other situations, similar situations, but it is a very destructive intervention into this particular environment. Granted it’s maybe the most, un-environmental environment you can think of, but if somebody proposed to dredge and cap a river and a forest, then you would feel that that would be a very kind of disruptive intervention. This observation spawned a project in collaboration with two landscape architects Ian Quate and Matthew Seibert, who were both working for Nelson Byrd Woltz [Landscape Architects in New York] at the time. The question that they posed was: If this destructive intervention is going to happen in this environment, what is the environment that is being intervened in at the moment? And so there’s not much macroscopic or multicellular life going on in the canal. And so they specifically wanted to look at potential microorganisms that would be living in the canal. So they collaborated with Genspace, which is a community molecular biology lab here in Brooklyn. Ian was a member of Genspace at the time. And so they organized a first sampling trip to collect sediment from the canal and they were able to extract DNA, but didn’t have the facilities to sequence that DNA. And so that’s when they reached out to Chris Mason at Weill Cornell, where I was working as a postdoc at the time and asked if the lab would be willing to sequence that DNA and analyze it. And so that was the first contact that I had with Ian and Matthew. And that project quickly caught my attention and my interest. Ian, Matthew and I founded the BK bioreactor, which is a project that aims to study, characterize and catalog the microbiome of the Gowanus canal.

We’ve been taking samples seasonally. So four times a year for the last five years. The big news is that there were microorganisms, or there are microorganisms living in the canal. So that sludge is amenable to life. We identified microorganisms that were related to marine environments, which makes sense, because it is a tidal system. We identified microorganisms related to the human gut, which makes sense also because there’s combined sewage overflow. But the question that arose from that particular analysis was: what are these microorganisms doing and how is it that they’re able to survive in such a contaminated environment?

So the source of toxicity in the Gowanus canal is from the sediment that has accumulated at the bottom. So the sediment that is accumulated at the bottom is black, viscous, smells like gasoline, and we refer to it as sludge. And so the sludge, which was the material that we wanted to sample, is under about anywhere from five to 20 feet of water. It’s not easily accessible to sample. And so we devised this DIY sampling technique, which involved getting 15-foot long PVC tubes and fitting them with this slightly flexible tubing at the end. And then we would go out in canoes that we borrowed from the Gowanus Canal Dredgers, which are a community organization that go out on the Gowanus Canal for fun! And they lent us their canoes. And so we would, you know, get into our hazmat suits, wielding our 15 foot long PVC tubes, canoe out into the middle of the Gowanus canal, and then dig these tubes into the sediment and cap the top of the tube. So using the same principle that your bartender will sample your cocktail with a straw before giving it to you. So we would dig these tubes into the sediment, cap it, pull it out and be able to retrieve kind of cores of sediment with that method.

So, you know, you’re doing real science when you’re wearing a hazmat suit. And oddly also there’s a Whole Foods that’s right on the canal. And so we would go there on weekends. And so sometimes we’d be like paddling under a bridge in our like full blown hazmat suits with our test tubes and everything. And then there’d be, you know, a cute Brooklyn family. They would be walking down and walking across the bridge and be like, “look, mom, they’re scientists!”

Elaine:

So the water is polluted enough that you need to wear a hazmat suit.

Elizabeth:

Yes. Because there’s a certain amount of splashing involved in retrieving these samples. And so we wanted to protect ourselves. More so from the sewage overflow that’s in the canal, than the sediment itself. You don’t want longterm exposure to that sediment, but you know, being splashed by it is fine. There’s a high concentration of fecal material in the canal and that’s what’s gonna make you sick. I would advise to not be in contact with the water as much as possible. The sludge is pretty inaccessible because it’s underwater. And you can see, depending on the tides, you can see sometimes oil slicks that form on the surface of the water. And, um, that’s not going to make you ill in the short term. It will make you ill in the long term.

Elaine:

So, actually, there are long term impacts on old timers, people who have been residents of that area for a long time, as well as newcomers or condominiums that are going up. Are there ways of protecting these people as well as you know, other species who actually will be there over the long term?

Elizabeth:

So the Gowanus Canal, once it was declared as a Superfund site in 2010, since then property values have gone up a 100%  and White population has gone up 63%. It’s in the process of massive gentrification. The efforts of remediation are to provide a less toxic environment for the human inhabitants of the neighborhood. But that also means that the people and families who have been exposed to these contaminants over the long term are likely not the people who are going to benefit from the cleaned up or remediated environment.

Elaine:

What is the promise of a site being declared a Superfund site?

Elizabeth:

Well, the promise is of the remediation of that site being funded, most importantly.

The Superfund program also puts into place legal mechanisms for holding the responsible parties financially accountable for the contamination. Even though that contamination has happened over the course of the last hundred plus years. When companies acquire other companies, they acquire both their assets and their liability. And so you can trace the liability of that contamination through the chain of mergers and acquisitions, and identify present day companies that are now liable for that. And so in this particular case, Con Edison is the company that is liable for the major part of the remediation. I mean, it’s all energy, right? So the like coal tar extraction was energy. And then, that just went down the chain of acquisitions and different forms of energy production. In a certain sense, the present day 2019 microbiome of the Gowanus Canal maintains a molecular record of the history of human intervention at that site. And arguably, maybe that record is actually more accurate than the human-kept records because human-kept records are biased are written by the victors, have omissions. But the bacterially kept records are a direct function of their environment.

Elaine:

You write that the DNA data is a molecular echo of the effect of human intervention. Tell us a little bit about that echo and its implications. One of the implications is that it allows us to tell a very different kind of history. Does working with microbes, teach us something different about language, history, creativity, all of which are attributes of the human?

Elizabeth:

A particular environment can be perceived in very different ways depending on the perspective from which you’re observing. So from the human scale, this site is toxic and in need of remediation at any cost and even in a destructive manner. And from a microbial perspective, this environment is amenable to life and productive. Some of these microbes have evolved to use these complex hydrocarbons as their primary carbon source. And so they need this kind of environment. I see this environment as a very rich environment with a precious ecosystem that should be acknowledged as such and valued.  So this microbiome encodes bioremediation functions, left to its own devices would clean up the canal, albeit very, very slowly, especially for our impatient human timescale. But left to its own devices, it is remediating this environment.

Bioremediation is the process of degradation of toxic compounds by living organisms. The microbiome as such is something that would be impossible to engineer in the lab. We can genetically engineer a microorganism to perform a particular function. We can engineer a microorganism to perform a couple of functions and maybe co-habitate with another microorganism. But it’s impossible to engineer a population of diverse microorganisms that are able to cohabitate with each other and as a whole perform a complex set of bioremediation functions and not be affected by this cocktail of toxicity that they’re challenged with. This is a unique environment that is very well adapted to the toxicity conditions of the canal. And it’s an important biotechnological resource for remediation of recently contaminated sites.

You could use a sample from the Gowanus canal to seed a recently contaminated environment that has been contaminated with a similar set of compounds. And it would accelerate remediation because that particular microbiome has had 150 years of evolution to optimize their response to this particular challenge. And so I don’t see the Gowanus Canal as an all-bad environment, but I see it as a resource and as a unique environment that should be preserved and catalogued in some way. And it is also an important biotechnological resource when thinking about bioremediation in general.

I would like to see a goal for design being one of collaboration with these organisms that have already been living and adapting to this environment rather than supplanting them with a technological solution.

Elaine:

And you seem to have the data to support this initiative. I’m wondering, have you been in communication with the EPA? Where is the project now as far as dredging?

Elizabeth:

So the EPA has conducted a pilot study in one of the turning basins in the Gowanus Canal to test the system of, of dredging. One of our collaborators is in contact with the EPA. At the moment, I do not foresee any possibilities for changes in that plan. That plan was drafted a long time ago in 2013, before I even started studying this. But my hope is to be able to create a living library of these organisms to kind of maintain this information and hopefully be able to catalog them in this way and potentially use this particular microbiome as a starting point for bioremediation solutions there or elsewhere.

Elaine:

Some people might say, how do we then guard against some of the unintended effects of, you know, taking sludge from, Gowanus canal, bring it into other environments, because in a way it’s introducing a novel material into another ecosystem, for example. I’m sure you’ve considered this. What might you say to that?

Elizabeth:

So the fear would be that a Gowanus Canal microbe would take over a particular environment that these, you know, super resilient Gowanus Canal mutant microorganisms would invade the environment in which they’re in which they’re placed. So to answer that, I would say that the Gowanus Canal microbes are, are very good at living where they are and have evolved to respond to that particular set of toxic compounds, but they spend a lot of energy doing that. And so microbes that are adapted to the Gowanus Canal are likely not well adapted to a different kind of environment. And that their selective advantage is one that corresponds to a contaminated environment. If we were to displace them and put them in a completely pristine environment, they would not have a selective advantage. So I don’t see a danger of mutant Gowanus Canal microbes taking over the world.

A more contained version of that approach is using extracted DNA rather than the living microbes. And so microbes are able to absorb DNA from their environment and kind of hot swap it in and just start using it. So we use that fact when we do microbial transformation, so genetic engineering. So the way you genetically engineer a microorganism is you make the DNA that you want for it to have, and then mix it up with your culture of bacteria and then stress them somehow. So either with heat or with electrical shock, and that causes them to spontaneously absorb DNA from their environment. That happens with a certain probability and then they start using it. You could think of seeding environments with extracted DNA from the Gowanus Canal microbes, as opposed to live Gowanus Canal microbes. What you’re doing there is setting up a situation where the local microbiome would be able to absorb and use the genes from the Gowanus Canal microbiome, but you are not transplanting living organisms.

  

Elaine:

Are there things you can teach people to see in the field? How do you get people to care? Why should people care? You know, how do you take this in a way, very large, very abstract, very frightening thing called climate change and scale it down in a way, you know, make it something that a high school student might understand.

Elizabeth:

That’s, that’s a very good question. And I think that that’s something that I struggle with as a biologist, but also as an educator, to be able to talk about things that you can’t see and be able to speak about them in a way that feels intuitive and be able to communicate the understanding that I have constructed over many years of studying these phenomena. I think that the fact that these organisms exist at a scale that is very different than ours impedes our understanding, but also our empathy for them. And that’s been something that I’ve been thinking about a good bit. And I think that there’s different ways to develop that kind of relationship. One of them being through scientific study, but another one being through art installations. And so this was actually the topic of an installation at the Detroit Science Gallery that I worked on in collaboration with Heather parish, who is a professor at the university of Iowa and a printmaker and Luna Husaid, who is an acoustics engineer at ARUP in the city. And so we created a multi-sensory immersive installation that tried to communicate through several different means this kind of duality in our relationship to the environment of the Gowanus canal.

In this installation, we had one part that was these jars of sludge. So we collected 10 gallons of sludge and like drove it to Detroit and this Mad Max kind of road trip adventure. So we collected 10 gallons of sludge from the Gowanus canal and installed it in these closed jars in the gallery and exposed them to grow lights. And so over the course of installation, which was only a couple of weeks, we saw all sorts of interesting life forms grow. And through close observation, we were able to see that there was actually all sorts of stuff going on in the sludge. So we had algal growths, there were little shrimp creatures, a kind of millipede worm, the shrimp and the worm were at war. The worm was trying to eat the shrimp. And then, we had a set of prints that were attempting to convey the relationship between macroscopic environments and human scale and microscopic environments. And then finally, a spatialized sound installation with a generative soundscape that follows a similar type of algorithm that dictate growth and decay patterns of microorganisms.

I think that the human centric perspective is always the one that people care most about. Decentralizing the human is I think, a difficult but necessary thing to do. We often consider humans in the environment to be separate entities, but trying to convey the fact that we are part of our environment, that we influence our environment, but that our environment also influences us is important. And I think that this kind of continuum of the microbiome is a good thread to pull at to talk about the relatedness of humans and their environment. Because if human health is related to the human microbiome and the human microbiome is influenced by the environmental microbiome and our design decisions for the environment sculpt the environmental microbiome, then ultimately that’s all kind of connected. And if we can figure out each one of those pair-wise relationships, we should be able to think about our environmental interventions as also part of this feedback loop.

With younger folk like high school students, it’s nice to be able to give very specific examples because the notion of environment or climate change are all very large and abstract, but being able to give specific examples that resonate with people and being able to talk about this specific example, which is the very iconic Gowanus Canal that is known to be a toxic wasteland and has inherited all of these, you know, different names like Lavender Lake, which is tongue in cheek terminology for the fact that it actually smells very bad most of the time. And so being able to speak to these very concrete examples and give hard data that supports the fact that this environment is active and that nature is remediating itself and responding to our interventions in a way that is also meaningful to us.

I currently teach a class in bio-design, which I frame around studying and designing interfaces between macroscopic and microscopic organisms. My students are usually either design students or art students or bioengineering students. And the best is when I have a class with a little bit of everything. And so the course is structured kind of in two parts. The first part is a crash course in biology and microbiology and methods in microbiology. So we do some lab experiments. We do some microscopy experiments. We learn how to analyze DNA sequences. We learn how to source primary source information in scientific journals. So how to even read a scientific article and parse out the format and read the methods and methodologies. So that’s the first part of the course and then the second part of the course is more like a studio practice where the students work in groups to design an interface between macroscopic and microscopic organisms that depart from the clinical interfaces that we have with microorganisms already.

So the swabs that I referred to, that we used to take microbial samples, they look like very clinical devices, so they’re white and they have like a white clinical looking label. They definitely belong in a doctor’s office. And so when we were doing the subway study we actually had some really interesting interactions with, um, various riders in the subway who directly interpreted that tool that we were using as a clinical tool. And so we were asked whether we were studying an epidemic in the subway. We were accused of bioterrorism and of implanting HIV in the subway. And so it was really interesting to see how this tool that we were using dictated the relationship that people had immediately before even knowing anything about the thing that we were studying. Taking a sample with these clinical looking swabs is the same thing as grabbing a handful of dirt. But if you grab a handful of dirt, you have all these associations of groundedness and earthy and healthy. And, if you asked someone to take a sample with a swab or to grab a handful of dirt and ask someone what do you think you’re getting with that swab or in that handful of dirt, then you’re going to get in general very different responses. And so the class is organized  as a response to that observation of how our tool dictates the relationship to the thing that we’re studying and it invites students to design new tools and new interfaces that are going to initiate and propose different kinds of relationships.

Elaine:

Thank you so much.

Elizabeth:

Thank you for having me.

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