Inspired by my friends Cindy and Eric, I’m learning to create art. The last time I put pen to paper for artistic study was in high school (hi sophomore art class). This is probably my fourth or fifth attempt to do learn how to make art in the last decade through lesson plans or tutorials, with ended in failure. My last visit to an art supply store was an avalanche of colored pencils and paper types and paints and tempera and markers–so many tools that I don’t know how to use, all of them daunting. I have no idea how to art, so how do I start learning what I don’t know?
I started with what I know. And if you want to learn to make art but are also feeling uncertain, overwhelmed, or terrified by the thought of creating art, starting with what you know (instead of a specific book or tutorial) might be the right path for you too.
While I haven’t created art of any kind in years, I have been making creative decisions my whole life. You have too. An artistic decision is everything from choosing the color of our clothes to picking what music to listen to after a rough day at work to simply choosing to touch the bark of a tree. You’re making a decision to experience a feeling in that moment. That is a creative act in your life, even if it doesn’t make art that others can enjoy. So we are all creative.
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Some of my most recent creative decisions have been in figure-making for academic journals, which might sounds boring (but stick with me). During my PhD I published two research articles that required not just figures showing data, but also schematics of what was going on at the molecular level. Creating these schematics isn’t entirely standardized, leaving room for artistic leeway. I ended up spending a lot of hours in Illustrator and Powerpoint building these schematics, not just for my research articles but also for presentations I gave on my work. This mostly consisted of arranging shapes and colors in a way that conveyed information but wasn’t painful to look at (seriously, lemon yellow will never look good on a projector). These each creative decisions, though I didn’t think of it at the time.
So for my first artistic endeavor, I started with something I know: my thesis work. Below is an artistic interpretation of what I discovered with my thesis work.
There are things I would change (and certainly a few things that are ‘scientifically inaccurate’) but overall I’m pretty happy with it. Here are some close-ups:
One of the biggest challenges (besides having to give up some scientific accuracy to artistic license) was figuring out what colors to use on the sketch. My previous experiences with color in this world have primarily come from 1) clothing choice, 2) creating Powerpoint documents and scientific figures, and 3) identifying plants and mushrooms. None of those translate super-well to watercolor pencils, so I took one of the sheets in my notebook and broke it into boxes to test color patterns for each part of the sketch. I then tested the final color palette on the other side:
Though it takes an extra piece of paper, this method was invaluable for seeing what colors look like next to each other (which does change) and I can keep it for subsequent projects, so I’ll count that as a technique learned!
Coming in for landing, probably free of biosecurity threats.
THREE hundred and seventy-eight days after my departure on trip around the world, I entered immigration carrying a backpack with some food: a jar of Buglarian pepper spread, a jar of store-bought Italian truffle butter, and a mix of store-bought chocolates and candy from across Asia and Europe. To my knowledge, everything conformed to U.S. Customs and Border Patrol (CBP) regulations, but I had checked the relevant boxes declaring that I was carrying plant and animal products, just to be safe. When the immigration agent glanced at my customs form and asked what I was carrying, I answered and he dismissed me with, “You’re free to go.” When I asked him whether I needed to visit customs, his reply was “No.” Thirty minutes later, I was at customs with agents rummaging through my bags, courtesy of a chance encounter with a cheerful sniffer beagle and his CBP agent near the exit. One of the agents dropped the accusatory line “You should have checked yes to these things on your customs form.” “I did, both on paper and at the kiosk,” I told him, “I even told the immigrations agent what I had.” He was surprised. Everything I had ended up clearing customs, but what if I had been carrying something more dangerous or I had lied? A little dog was the country’s last line of defense, and he was successful only by chance.
To CBP’s credit, biosecurity is hard. I’m not an expert, but to me biosecurity is the defense of the country’s borders against threats to human health, agriculture, or environment, meaning the CPB’s job is to ensure that everyone and everything coming into the United States is “safe”. It requires constant vigilance, like that of a shepherd guarding his flock from wolves or a firewall protecting your computer from attacks. It’s one of those problems where you can succeed a thousand times, but one failure is all it takes to lose. And the price of loss can be huge, whether it’s economic damage or loss of human lives.
I wrote this essay to organize my thoughts on biosecurity at our country’s border, specifically what it looks like now and how it might look in the future. Biosecurity can be broken up into three steps: prevention, quarantine, and mitigation. Prevention deals in minimizing the number of threats that get to our border and includes informing people what can and can’t be shipped. Quarantine is the second step, and should prevention fail, a biosecurity threat should be caught at this stage—this is essentially biosecurity at our border. This is the customs check at airports and shipping hubs, and is the last chance to catch something before it enters the country. After that, the threat is in the country and we’ve got to tackle it with the last step: mitigation, or more simply, ‘dealing with it.’ This includes tracking the threat to understand it, trying to contain it within specific counties or states, and running costly cleanups of areas to try and eradicate it. This is the most expensive and worst step to get to, so efforts to control entry of threats during prevention and quarantine. Prevention often relies on good faith in those importing, because eradication of a pest worldwide is difficult. All this leaves is quarantine, the biosecurity at the border.
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People wait after clearing immigration and customs in Taipei’s international airport. This is the biosecurity border for people and the goods they’re carrying.
WHAT biosecurity at the border looks like today depends on what threat you’re looking for and where you’re looking for it, but it broadly breaks down into searching for threats to agriculture and the environment, or threats to human health. In the first category are a panoply of pests ranging from microscopic bacteria to whole plants and animals, and they can be accidentally transported in everything from soil to fresh vegetables to wood carvings, making detection hard. The second category, threats to human health, is the transmission of anything that might cause disease in people. These threats are most often transmitted by people themselves or through human tissue, although the rising threat of bioterrorism has forced us to consider potential transport outside of the human body, like in glass tubes or sealed envelopes. While the threat of bioterrorism is what garners the most media attention (such as the 2001 anthrax attacks), accidental and intentional introduction of pests are far more costly, to the tune of $100 billion annually. So in thinking of biosecurity, it’s helpful to think beyond the potential for bioterrorism attacks to all forms of potential threats, both present and potential.
But while new biosecurity threats have emerged, the technology we have used to enforce biosecurity at the borders has changed little. The primary way to detect potential biosecurity threats is still sniffer dogs, animals trained to detect and alert CBP agents to the presence of a wide variety of smells. Though sometimes trained to directly smell a biosecurity threat, most dogs are instead trained to detect products that might harbor the potential threat, which then must be verified by hand and in lab. And while effective, these dogs are both expensive and time-consuming* to train and care for. The quality of your biosecurity is then limited by how many dogs you can have and how many hours they can work.
Potential biosecurity threats are also becoming more complex and difficult to detect. As the technology sequence and synthesize DNA continues to fall in price and DIY biology increases in popularity, more potential biosecurity threats will arrive in the country in the form of nonliving DNA, the material that encodes the instructions for all living things on earth. DNA that poses a biosecurity hazard is nearly impossible to detect because it is present on nearly every surface of the Earth and is indistinguishable unless sequenced; under chemical analysis, the DNA for poliovirus would look nearly identical to DNA from humans or hamsters. As our technological progress continues, it becomes easier to simply encode weapons of biological warfare into an inert, white powder indistinguishable without complex analysis. But while it’s easy to respond to this potential threat by banning DNA transport or synthesis outright, doing so would wither our efforts to make new cures for diseases or develop helpful biological technologies. We need to balance our freedom to make and move DNA with its potential risks.
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A crane moves shipping containers at the port in Keelung, Taiwan. With increasing movement of people and goods, how do we effectively detect biosecurity threats?
GIVEN the changing landscape of biosecurity threats and our current reliance on older or limited technologies to detect them, what does the future of biosecurity at our borders look like? While I can’t claim to be a biosecurity expert, I can imagine that in the shape of tomorrow we’re going to need biological technologies that both detect specific threats and detect threats whenever anything out of the ordinary appears. We’re now looking to detect three kinds of threats: live things, such as animals, fungi, bacteria, or viruses; dangerous or toxic biological products and toxins, and inert DNA that may encode a potential threat. The best technologies will help us detect both specific threats we know of and help us flag strange things that might represent new potential threats.
There are several new technologies that might help us detect specific threats, including handheld machinery and paper-based diagnostics. When it comes to biosecurity, prevention remains the best option, and potential biosecurity threats are held at secure labs with restricted access, while DNA synthesis companies screen customer orders to determine whether it might encode a potential threat. But this doesn’t protect against individuals or small groups with expertise synthesizing genes/DNA abroad and attempting to bring them into the U.S. Nor does it detect signals that a person may be harboring a dangerous pathogen in their body, either intentionally and unintentionally. A test that rapidly checks DNA sequences for whether they are potential threats, as well as machinery to detect protein or compound-based signs of biosecurity threats would be helpful. In the long run, the shrinking cost and footprint of sequencing means that we may one day have a handheld machine that searches for a panel of sequences that may pose a threat is ideal. In the interim, paper-based diagnostics that detect specific DNA sequences, such as those that can identify different strains of Ebola or detect Zika, appear promising. We could create paper-based diagnostics that bind and signal presence of specific DNA sequences, as well as potentially toxic compounds or proteins.
But perhaps the most exciting advances are in the chance to detect threats without knowing they yet exist. We are increasingly able to sequence microbiomes from a variety of sources, and with some modifications we could extend these technologies to sequence the microbiomes of everything from imported mangoes to dried wood, establishing patterns of ‘baseline’ microbiomes that are present in all safe samples. We could then take samples the microbial populations on all imports coming into the U.S. to screen and match to these baseline microbiome populations, flagging those which show results out of the ordinary for follow-up and barring those that show signs of potential biosecurity threats. This gives us the first chance to detect or identify anything that is “unusual” instead of looking for known abnormal things. While the same thing could be done with people, some serious ethical questions would arise as to who has access to the data, what it reveals about an individual, and what we’re comfortable with as a society. Given these questions, predictive microbiome sequencing is best left as a tool goods imported or carried by people, rather than the people themselves.
When nutria were introduced for fur trapping or Asian carp introduced for aquaculture, nobody guessed that these animals cause millions of dollars in economic and environmental damage. Nobody predicted the SARS outbreak of 2002 or the 2014 Ebola epidemic. We still have difficulty with guessing what new threats lurk beyond our horizon of knowledge, but we’re getting better at predicting which threats on the horizon will be most damaging. By pursuing technology to detect both conventional pests and DNA-based potential threats, to both check for known potential threats and flag unusual changes from the norm, the biosecurity at the border will protect us better.
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*Note: this link estimates the cost of training a dog to detect explosives, not biosecurity hazards per se. I couldn’t find data on the latter, but training a dog to detect biosecurity hazards should be more expensive, because of the wide variety of things they must be trained to detect.
On the way home from mushroom hunting, someone in the foraging group asks what I do for a living. That’s a tricky question. I could respond with the research I did for my PhD, which would be something like “biology” or “bioengineering” or “synthetic biology”, but none of these answers hold much meaning for people. So I go for the simplest answer that’s interesting. I tell them, “I built life.”
Some of the living things I’ve built.
I’m not exaggerating. My PhD was five and a half years working on engineering organisms that would improve human lives while using less of Earth’s resources. That goal is hundreds of separate projects in several lifetimes of work, so I focused on the part that serves as a lynchpin to them all: if we create a living thing with a function, how do we ensure it works as intended in complex environments? Like the plastic insulation protecting electrical wires, engineered life needs an isolating barrier protecting it from the surrounding natural life that could cause a short-circuit and stop working. Physical isolation tools exist, but they need to be maintained and have limited use. So for my PhD I engineered genetic isolation directly into cells, an insulation that they always carry with them. This genetic insulation protects the engineered cells from nature and vice-versa. And it means that we can one day use these engineered cells to create medicines, renewable energy sources, and environmental protection and repair systems.
A forest in Australia. It’s one of the many ecosystems I hope to preserve by creating living tools that help people live with more while taking from the environment less.
Back in the car, the response I get from the group is a mix of awe and horror, which is normal. Because I’m with a group of foragers, I can accurately predict the next step in the conversation. “It is just my opinion, but I don’t think we should be changing life, messing with it,” says the man beside me. I nod politely. Though the old knowledge of traditional cultures and new knowledge of academic research are entirely compatible and built on the same scientific methods, a mutual distain keeps the practitioners of these two camps aligned against each other. As scientist of academic research, I’ve lived this conversation a thousand times already. But it’s an important one, and it’s not about me convincing this guy that his opinion is wrong. It’s about understanding why.
By and large, people are uncomfortable with engineering life because they consider it special. We divide the world into living and non-living, and then spend much of our memorable lives interacting with the living: family, friends, pets, nature, food. We consider there to be some mysterious spark to life that we haven’t figured out, both philosophically and scientifically. To say you’re changing living things naturally raises hackles; the assumption is that in order to do that, you must have sacrificed your belief in the sanctity of life. That you don’t care about the consequences. Or, as quoted from Jurassic Park: “so preoccupied with whether or not [you] could, [you] didn’t stop to think if [you] should.”
Life is pernicious and controlling it can be hard: here, algae grows on the inside of a plastic cup on the beach.
But the truth is that we scientists think constantly about “whether you should.” It is the undocumented part of our lives, the part spent away from the laboratory equipment that everyone associates with us. In this time, four sources prompt us to consider the meaning and significance of our work. The first is from ourselves; as we’re naturally inclined to think (and overthink), we find ourselves imagining scenarios in which our research could be misused or go awry. The second is our peers and colleagues, who carry a mandate to question our work and ensure it is safe. The third is in grant proposals, where we meet the scrutiny of scientists and policy-makers who fund our work. And the fourth is in scenarios like the one occurring right now in the car, questions from our communities. Every one of these sources drives us to think about the impacts of our research and what could go wrong.
Yes, the conversations I have with people about my work “building life” can be uncomfortable. It’s not fun when someone tells you that your life’s work is objectionable, distasteful, an affront to society, or a one-way ticket to hell. But these conversations are important. They tell me what people are worried about, and by extension, what I should worry about in my work. These conversations are also a brief chance for me to explain how much we scientists care about the impact of our work, contrary to scientist stereotypes. It’s not easy, but somebody’s gotta do it.
My research on creating genetic insulation for engineered organisms. If you leave here with one thing, know that we scientists hear and share your fears. It’s why we do research.
[This is a cross-post from my current main blog, Neverending Everywhere, where I document travelling around the world.]
The endless sea of ideas beyond the bramble of writers’ block
Hey reader!
It’s been a while since a post, hasn’t it? I’ve learned a few things in starting this blog that I want to share with you below because I’d wager a lot of people face similar problems. If you’ve been stalled on your blogging/writing, I give you 100% permission to borrow this post, blame it on one the problems below, and start anew:
Writing what you know well isn’t always the easiest. You get bogged down in the details and you want it to be perfect. This is compounded in academia because you worry about the balance between reaching people outside of academia and those who might read it in the academic circle. To make blogging easier, begin with subjects you know some about and you won’t be dragged down into the deep details. Yes, sometimes you’ll write things that won’t make sense later or might be wrong, but that’s FINE. We learn nothing by venturing nothing.
Don’t feel beholden to a post you said you’d do, and you can always postpone a post to later. This is a hard one for me because I feel strongly about commitments and following through. It’s the same feeling that gives us anxiety when we leave an email unanswered for what we think is ‘too long’ or haven’t posted on a blog in a while. You feel like you’re letting your audience down, whether it’s one person or a million people. But you don’t owe the internet anything—you’re a free person.
This is an extension of 3, but it’s important to say on its own:write what you want. The easiest way to kill a blog is by having writing ideas but putting them aside because you “said you’d do” a specific post next. Likewise if you’re writing just for likes/favorites/exposure. It’s going to feel like an awful chore if you don’t write about what you want, so write about what you’re interested in, what you want to learn about, what won’t leave your mind. Get your thoughts out into the world.
So I’m holding off on writing in-depth about my PhD work for now. But I also didn’t want to be beholden to #1, so I wrote you a six-sentence summary of what I did in my PhD. Is it perfect? No. But it is:
As I described in the previous post, if we want to use living systems (organisms, cells) as technology, we want them to work as expected because we can’t rely on them if they don’t. One of the biggest problems is that most of life uses the same genetic code, so engineered cells can pick up genetic information from the environment that messes with their intended function. It’s as if we were all running the same version of Windows; you could install a program on any of our systems and it would run–including viruses and malicious code. To solve this problem, my PhD showed that changing the genetic code of an engineered cell makes it harder for genetic information in the environment to mess with the cell’s function, making it more stable. It was like we modified the “operating system” in our engineered cells, making it harder for malicious pieces of genetic information such as viruses to infect. In the future, we can change the genetic code in living systems to ensure they work as expected, bringing applications of biotechnology and synthetic biology closer to realization.
What will I write about next? We’ll see what I feel like, although posts will probably remain infrequent while we travel around the world (more on that here). One of the big projects I want to do over the next year is learn the physics of aerodynamics and orbital mechanics, partly because both of these are really important for space travel and partly to dispel the persistent myth that you can’t transition from “softer sciences” to “harder sciences” later in life. Anyone should be able to learn anything regardless of their background.
What I wrote below highlights some of the risks of engineering living things, the goal of a field called “synthetic biology” . Is anything unclear? Email me! Ask questions! Your advice will make these posts better.
Microbes growing in lab
We’re at an amazing point in scientific history where we know enough about how living things work to begin tinkering with them. There have been thousands of studies in the last century looking at modifications of living things. At first, the tools we had were crude and the questions we asked were “what happens if make a bunch of mutations in a living thing? What kinds of properties does the living thing show? And what changed in the a living thing’s genes, in its DNA, that caused this change?” As our tools became more precise, so too did our questions. We began to ask what happened when we took out one gene, or added another. “What properties appear when we do this?” we asked. These two ages of research brought is much of what we know about how a genome, a collection of a living thing’s genes (stored in the DNA), work together to create life.
Now, we’re taking this knowledge and beginning to modify genomes with the goal of creating living things that exhibit specific traits, in a field dubbed “synthetic biology”. Want an apple that doesn’t brown when sliced? We’ve got you covered. How about a microbe that produces an extremely expensive anti-malaria drug, making it more accessible? Yep, we have that too. These advances are the products of the last three decades, where concerted effort and millions of dollars bore fruit to create life with an engineered function. But with the ability to do create living things with desired properties, a new problem arose: how do we ensure a living thing we create works the way we intended?
Sea life grows in a plastic cup washed up during a storm; we may one day engineer life to break down plastic in the oceans
To understand this problem, we have to look at the biological purpose of life. Every living creature has a sole directive: to make more of itself, as many copies of itself as possible. From single-celled bacteria to the complex mass of tissues and organs we call animals, all living things strive to give rise to more of themselves. This directive manifests everywhere around us: the battle for self-preservation, consumption and conflict over resources, the care shown to offspring. It also leads to extreme scenarios, such as when a male spider accepts his death for a chance to mate with a female; in this case, the chance to create more life overrides even the powerful instinct of survival. At every level, in every living thing, this rule acts to reward those that succeed at making more of themselves, as these offspring give rise to more offspring. The winners that are better at following the directive keep winning. The losers disappear from the menagerie of life.
This is where our aspirations of engineering functions into life meets reality. Living things aren’t interested in what we want them to do and our engineered functions are forever secondary to the sole directive of life. Even worse, the changes we make to create these engineered functions are often contrary to this sole directive: they make the living thing less capable of making more of itself. The result is that once we’ve created a living thing with a specific function, such as production of biofuels, it begins trying to undo what we’ve done. The offspring of our living things should have the same engineered functions, but those that manage to undo what we’ve done are better at making more of themselves. In as little as one generation, the function we engineered can disappear. The system is never stable.
A tree overgrows a wall in Hong Kong. Life has a tendency to escape any bounds put on it.
This is a serious problem because if we engineer a living thing and it doesn’t work as expected, what will it do? In the best case scenario, the living thing loses its function and we’ve got to find a way to get it working again. There are some straightforward ways to do this that I won’t cover here, but basically this scenario just costs some time and money. More worrying is a worse case scenario: where the function we engineered into a living thing to exist within certain limits or parameters, but it breaks free. This is the “Jurassic Park” scenario, where something meant to be contained and safe gets loose and wreaks havoc. And because the function of limiting a living thing to certain parameters is both incredibly useful and directly contrary to life’s sole directive, it’s less a matter of if and more a matter of when this happens. As Jeff Goldblum’s character Ian Malcom says, “life finds a way.”
