First Quarterly Report: Three Months on the Watson

The Watson Foundation doesn't require much in the way of deliverables. The only products it requests are four quarterly reports in the form of "long letters home" and a short presentation at our final conference. Here's the first of those reports.

First Quarterly Report

Date: October 27, 2017

Countries you were in: Brazil, Madagascar

Countries for next quarter: Madagascar, Indonesia

Current location: Centre ValBio, Fianarantsoa Province, Madagascar

Dear Watson Foundation,

I’m writing from a slate-tiled balcony attached to Centre ValBio above a bamboo rainforest in eastern Madagascar. The research station is nestled into a cliff face. To exit on ground level, I can walk down three flights of stairs, or up one. Either way, I’ll be surrounded by tree ferns, rain that rises from the ground as mist, and the tinkling song of Souimanga sunbirds, an endemic species that fills the ecological role of hummingbirds. Right now I’m watching a Mascarene martin swoop insects at eye-level. The sun is casting a brilliant white light on Cumulus congestus clouds, a brewing thunderstorm. Today is my break between lemur-trapping sites, so I’ll be cozy and dry as I listen to raindrops strike the roof.

Looking down on Centre ValBio Research Station from Ranomafana National Park.

As you’ll probably hear from thirty-nine other Watson Fellows, my experiences over the first quarter of this year have been too expansive to summarize in a letter, but here goes! I spent my first two months in Mato Grosso do Sul, a Brazilian cattle-raising state that you can locate by pointing your finger smack-dab in the center of a map of South America. My initial plan was to study peccary leptospirosis and its impact on food security in Pantanal. That didn’t work out. The Wildlife Conservation Society unexpectedly closed its Pantanal program a few months before I arrived, so I was welcomed into the Watson by scientists at loose ends, without funding, unemployed. At least, I figured, my worries were minor compared to theirs.

Lygia led me up to the edge of a cliff in Cerrado with my eyes closed so she could surprise me with this panoramic view of Pantanal below us.

I feel extremely lucky to have found a homestay with two women who I’ll call friends for life, environmental journalist Lygia Freitas and Cerrado botanist Duca Andrade Santos. Duca spent the past decade as outreach director for the WCS, and she’s called “the Mayor of Taboco” because she’s the person everyone turns to for help. I lived at Quinta do Sol, the postage-stamp nature preserve Duca built from scratch. At first, I was disappointed to realize I would be living not in my dream ecosystem, the Pantanal wetland, but its arid neighbor, the Cerrado savannah. That disappointment turned to gratitude as I fell in love with Cerrado’s wacky fruits, endemic buriti-palm swamps called veredas, and semi-deciduous forests.

Alexine, me, and Duca looking out over an expanse of intact Cerrado ecosystem.

Duca and I crafted a low-cost research project: a survey of vaccination in domestic cats and dogs. The project is a step toward conservation of jaguars, pumas, ocelots, maned wolves and crab-eating foxes, all of which can contract canine distemper and other diseases from pets. It was also an ideal excuse to meet fifty of Duca’s neighbors and move quickly beyond small-talk into topics like zoonosis, human-wildlife conflict, and vaccination. If we stopped by a house between the hours of 12 and 2, we were nearly always invited to stay for amorço, a lavish meal for which “lunch” is a bland translation. One of my favorite menus was feijoão (soupy, salty brown beans), arroz (white rice), salada (raw cabbage or tomato with vinegar) and cebollada (sautéed chunks of zebu beef with onions).

One rancher told me about his practice of placing dead cows in termite nests as a form of pest control. A vegetable-farmer treats her ill chickens with injections of milk. A man from town shared his pathogen-specific protocols for eating beef, explaining in Portuguese, “To prevent rabies, foot-and-mouth disease, and carbuncle, you just have to cook it well, but brucellosis is hard to kill––you must cover it with salt and leave it in the freezer for at least one night before cooking.” I have no idea how these practices align with institutional scientific knowledge, but I’d be interested to test them on a sort of Microbial Mythbusters.

I taught ultimate frisbee for gym class at Taboco's public middle-school.

Beyond the anecdotes, I developed a deep map of Taboco through its culture surrounding animal disease. Nearly all residents vaccinate against rabies, which affects humans, but very few against other diseases that can cross into wildlife, like canine distemper and parvovirus. As a conservation tool, I’m proposing that the Brazilian Ministry of Environment, whose mission includes endangered-species health, and the Ministry of Health, which runs the annual rabies campaign, work together to offer vaccinations against critical wildlife zoonoses to Cerrado pets.

Need a rabies vaccine? Are you a dog or cat? You've come to the right place.

When I wasn’t discussing puppy diarrhea over lunch, I realized my dream of swimming with giant vitoria rede water lilies in Pantanal, completed my first freshwater scuba-dive in the nobody-knows-how-deep Lagoa Misteriosa, and showered in the wind-blown Rio Peixe waterfall. I waded up to my waist through a mossy slot canyon at Vale do Bugio until Lygia noticed an enormous rattlesnake, coiled on a chilly boulder and blocking the way forward. (On my way out, I counted the bodies of seven bloated bats floating around me, another good reason to leave.) I learned to vaccinate cats against rabies by first holding them up to a tree, which they conveniently latch onto with their razor claws, and then injecting the bubblegum pink serum under a tent of skin. I played ultimate frisbee with middle schoolers, surveyed a forest for peccary-edible fruits, drank guaraná soda and terere tea at barbeque dance parties, and sat in on a falconry class at the Federal University. For my last week in the country, I attended an infectious disease conference called DIERN and incubated a whole colony of thoughts on collaborative survival with microbes, the topic of my most recent blog post. The best moments surfaced when I stuck my neck out and struck up conversations with strangers.

The Lagoa Misteriosa sinkhole before my first freshwater scuba-dive.

On a personal note, I struggled in Brazil with the lack of structure. When I woke up without an agenda, I was pulled in two directions: inertia coaxed me to the computer screen, where I’d organize data or write a blog, while momentum urged me to hike through a vereda or plant seedlings in Duca’s agroforestry garden. Either way, I felt uncertain if I was doing the right thing. How late should I sleep? How often should I help wash dishes? I reflected on my anxious thoughts, which I like to call brain weasels, and realized how much I fear disappointing the people I look up to. Living, eating, and working in the same home as my mentors gave me little space in which I felt okay being imperfect. When I opened up about these insecurities in a blog post, Lygia and Duca responded with tears, hugs, and hours of advice about the struggle to balance life goals, avoid workaholism, and just be happy. They helped me relax. I started singing while I cooked, sleeping in a bit later, and saying no thanks to invitations when I felt overwhelmed. Duca and Lygia challenged me to love generously and live intentionally. I can’t thank them enough for helping me transition from the rigid scaffold of college into the open-ended uncertainty of a Watson year.

Facing my fear of heights by peering out over the cliff of the Rio Peixe waterfall.

My flight from São Paulo to Johannesburg was delayed by an hour-and-a-half, just long enough to strand me in South Africa for a night with no currency and no clue. I managed to arrange an afternoon tour to Lion Park, where I met the megafauna species I’d grown up watching on TV: white lions and sacred ibis, blesbok and giraffes. My taxi driver gave me a thorough, unsolicited, and hugely appreciated lesson on Apartheid and South African politics. The detour to continental Africa turned out to be a highlight of my Watson experience, perhaps because it was so unexpected.

Unusual white lions at the Lion Park outside Johannesburg.

The next day, I arrived in Madagascar’s capital, Antananarivo, or just Tana. In the customs line, I was handed a pocket-sized tourist pamphlet advertising the tropical beaches of Nosy Be and a public service announcement: Pour prévenir la maladie à virus Ebola, eviter de changer de siège assigné au cours du vol. English translation: “For prevention of Ebola virus disease, avoid changing seat assigned during the flight.” Intriguing, from a disease perspective, if a bit unnerving. In Tana, everything felt different than anything I’d felt before. Verdant green rice paddies filled roadside ditches. The smoke of burning garbage was heavy in my nostrils. Within 48 hours I was vomiting, and an outbreak of pneumonic plague had one out of every four pedestrians wearing facemasks. The streets felt hostile. After three frantic days of organizing research equipment, I was relieved (and more than a little nauseated) to leave the city behind on a nine-hour drive to Centre ValBio, my current home in the eastern highland rainforest.

A market in Antananarivo.

Plague surveillance in rural Madagascar: a military-medical checkpoint where cars are stopped and the passengers are asked if they feel sick.

My initial plan was to assist Dr. Sarah Zohdy with her lemur-disease project, but when Sarah decided against visiting Madagascar with her new baby, I found myself running Project Hydra. For every challenge I tackle, three more sprout in its place. There are the scientific tools, camping equipment, food, schedule, transportation. There are the traps. There are the Microcebus mouse lemurs, or tsitsidy in Malagasy, world’s smallest and cutest primate. There’s blood to draw, lice to collect, hairs to tweeze, feces to scoop. There is money to wire, cash to withdraw, receipts to submit. There was the government minister who suddenly announced he would be tagging along for a week in the backcountry, and the equally sudden cancellation of said visit. There was the evening a Malagasy graduate student knocked on my bedroom door to inform me he would be joining the project. Somehow, I turned out to be a grad student’s mentor. Rakotondrasoa Maminiaina Gaetan, the student, has turned out to be an integral part of Team Tsitsidy.

Our nocturnal, outdoor "lab" on a blue tarp.

An especially orange mouse lemur, Microcebus rufus. We will let her go back on the same tree where we caught her, once we've stolen her lice and taken a blood sample.

On expedition days, Team Tsitsidy swells to include fourteen porters, a local guide, American scientists, Malagasy researchers, and a cook. In interstitial moments, the team condenses to its nucleus: me, Gaetan, and our expert guides, Zakamanana François (Zaka) and Rabaovola Bernadette (Menja). We spend eight days at a stretch camping in the fragmented forests around rural villages, isolated from internet and electronics by a half-day hike. These days are precious. My mouth waters over unsalted white rice with round-beans. Uninterrupted, I sit cross-legged on a rice bag and read book after book. I press ferns in my journal. Some afternoons, I trade sketches for Malagasy words with girls who intrude shyly into our camp after school.

Our local cook, Velomanana Edmonde, serving bowls of white rice for Team Tsitsidy at our camp near the village of Ampitavanana.

Inside Centre ValBio, I’ve struggled with the sterility of life in a research dorm. I miss the fruit bats that roosted in my bathroom at Quinta do Sol, the tree frogs that lived in my toilet, and the jubilant smiles of Duca and Lygia at breakfast. Another regret is that, ironically, I’ve had little opportunity to explore the primary rainforest for which Ranomafana is famous. My focus on fragmentation and disease draw me to the seedy outskirts of ecosystems. I wade through vary, rice paddies of translucent orange water and shocking green leaf, and tavy, slash-and-burn agriculture whose smoke obscures all but the nearest mountains.

The vegetable market in Ranomafana Town, where Menja helped me purchase tomatoes, ground beef, and rolls so I could prepare American-style hamburgers for Team Tsitsidy.

Rice paddies are flooded because rice can grow dry or wet, and the water keeps pests at bay.

On the fifth of December, I’ll ship a box of dried blood, ear lice, and lemur hair off to the States and set out to explore more of Madagascar. I have my eye on the spiny dry forest, the boulevard of baobabs, the Ifaty coral reefs (which I’ve heard are thoroughly bleached, making for an interesting comparison to my next stop), the gorgeous mitso color of Phelsuma day geckos, and any bird-watching tour I can join for cheap. On Christmas, I’ll fly from Tana to Bali. I’ve heard the Indonesian island will be on collective holiday through the first half of January, so I’m looking forward to solitude, writing up my thoughts, and acquainting myself with the local curries and seafood and birdlife before diving (get it?) into a project with Reef Check Indonesia. I’ll be helping two coral conservationists, Derta and Jaya, evaluate how successful their reef restoration program has been so far. I can’t wait to move in with a homestay, survey diseased reefs by scuba, and improve my limited Bahasa Indonesia vocabulary from the few tantalizing lessons I took this summer in a Minneapolis Starbuck’s.

The surface is ringed in forest as I float in Lagoa Misteriosa. I'm excited to do saltwater diving in my next country, Indonesia.

The past seems like a lifetime ago, and the future is nearly unimaginable through the tangled underbrush of the present. Thank you, Watson Foundation, for trusting me with this enormous year. Until next quarter!

Yours truly in bamboo and bacteria, Microcebus and microbes, vary and viruses,
Nina

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Subvisible Thoughts: Rewriting the War on Microbes

The auditorium was dark and air-conditioned. As lectures on yeast, HIV, and tuberculosis floated over my head, I scribbled notes in three languages: original Portuguese, translated English, and vocabulary I made up to lasso my thoughts onto paper. Words like subvisible, macrobe, germophile, biofiction and endogarden squeezed in sideways next to sketches of virions and DNA on the pages of my Watson journal.

Do you have that one study trick when you want to get ideas flowing? Maybe you need perfect silence of the library quiet room, or Frank Ocean in your earbuds. Simón Bolívar claimed to do his best thinking at the center of a crowded ballroom. Turns out, the overly-chilled halls of an infectious disease conference were my ideal habitat for incubating ideas.

Idea #1: How Might Our Relationship to Microbes Be Different if We Weren’t So Dang Visual?

As a species, human beings are extremely visual. Our eyes let us see a rainbow of colors, pick out meaning from black squiggles on a screen, and react to danger (like that of a snake across our path) before our mind consciously registers the threat. As eyes evolved, our smell, taste, touch, and hearing dwindled to perfunctory senses. Compare our nose to a dog’s, our ears to a bat’s, our tongue to a snake’s, or our touch to that of a star-nosed mole.

Our sight makes us biased. We save colorful species from extinction, yet we wonder if little brown birds can be that important to an ecosystem. We photograph wildflowers and ignore bark, stems, and roots. We cuddle stuffed jaguars and lions, but when was the last time you snuggled a plush microbe? (They do exist!)

A fluffy Streptococcus pneumoniae so you can finally fulfill your desire to snuggle pneumonia.
Photo credit: Wikimedia Commons.

An embroidered syphilis sculpture available on the Forgottenland Etsy for $80.

These two months in Brazil, I have not seen a single microbe. Why? Simple. I don’t have a microscope. Sure, I’ve seen the effects of the single-celled ones: an oozing wound in the back of a dachshund, a syringe full of hot-pink rabies antigen, a can of beer.

An infected sore on the back of Seo Claudio's dachshund was evidence of bacteria, but I could hardly tell anything about the microbes from this observation.

But it’s not the same as seeing the organisms themselves. Would you go on a jaguar tour to look at the scratch marks left on a tree? (Ok, jaguar scratches are pretty awesome, but the real thing would be cooler!)

Scratch marks on the mossy bark of a tree in Bonito. I like to imagine they were left by a jaguar, but the organism itself would leave a much larger impression.

Our excellent eyesight is limited by scale. We can’t see anything narrower than 0.04 millimeters. At least, we can't distinguish an object smaller than 0.04 millimeters from its neighbor. When we see a conglomeration of tiny particles, like the atoms in a table or the mold cells in a colony, we see their cumulative mass, not their individual bodies. Our eyesight's resolution probably isn't going to get much better, because it's already approaching its quantum limit.

What about our other senses? The linings of our nostrils can differentiate molecular structures of odorants, and our tongues taste the contours of tiny particles, like salt and sugar, with impressive fidelity. But both senses require billions of particles to cross the detection threshold. According to these pretty cool calculations, human taste and smell are operating at 10 orders of magnitude above the quantum limit, meaning that if evolution had taken a different course, we might be a species intimately aware of our single-celled cousins.

Vanilin

Eugenol

The structure of vanilin varies only slightly from the structure of eugenol. The only difference is an aldehyde group (an oxygen) versus an allyl group (a couple extra carbons), but the two smell as different as vanilla and cloves. Imagine what our noses could tell us about tiny things if we smelled in higher resolution.
Photos from Wikimedia Commons.

What would our relationship to microbes be like if we were a primarily smelling or tasting organism? Might we know salmonella and leptospira like we do jaguars and lions? Might we develop compassion and curiosity for pathogens, despite their ability to harm us? After all, we find a place in our hearts for macrobes that threaten the same: wolves, pumas, bears, and on down the list of beloved predators.

And that brings me to my next idea.

Idea #2: Writing Microbes Sensually

Artists and writers bring to life what our limited senses cannot. Impressionists paint motion and light into landscape. Surrealists depict the unconscious world of dreams. Poets tempt the sixth mass extinction into tangible proximity. (Check out The After, a poem about Anthropocene extinction by Melinda Mueller, my high-school biology teacher.)

One of the first things I learned in my favorite college course, Don Snow's “The Nature Essay,” was to write sensually. Breathe in Ellen Meloy's juniper scent, feel Amy Irvine's canyon mud suck your feet down, taste durian through David Quammen's prose. These nature writers push beyond vision to awaken worlds for their readers.

Write me a story from the perspective of the brain fungus that caused this ant to freeze in its tracks.

Show me schistosomiasis, not just the symptoms of a human infection but the sensual details of what it's like to live within the body of a snail.

Could we write microbes sensually? The genre might be called “speculative biofiction.” I want someone to evoke the satin skin of a gram-negative bacterium, the rigid reluctance of a gram-positive. I want to imagine the sour tang of Yersinia or the sweet tickle of Plasmodium on the tongue. (No sampling pathogens, please!) I want to attend a party of Lactobacillus through scent, following their appetites as they converge on a silo of sprouted barley and nibble in into beer.

I want someone to turn this biochemical diagram of how Klebisella evolved antibiotic resistance into a narrative ode to bacterial genius. I want to sympathize with the wounded, watch survivors invent counter-weapons, and understand resistance not just as a public health crisis, but as a story of resilience during war.

I want someone to describe the barbed armor and biochemical antics of two Streptococcus colonies as they battle for control of a Petri dish, so I can root for my favorite without having to peer down the eyepiece of an elusive microscope. I want to swim through the bloodstream and slip into DNA with an HIV virion. Could we transition from a society of germaphobes to one of germophiles?

I want to read a poem about this decadent feast, a decomposing cow in a vereda, the endemic wetland of the Cerrado. Which microbes live only in veredas, hoping for cows to die?

I want to know the inner workings of a gall wasp larva. How does it trick this leaf to house its invader?

How do the algal cells treat their fungal symbionts? What's it like living in a matrix of your neighbor's body?

I don’t have a microscope, and neither does anyone else outside a handful of college students and microbiologists. Scopes give me a headache, anyway. Let’s write microbes sensually, so we can cultivate compassion and curiosity for these remarkable little ones.

By now you might be asking… why does it matter if we have compassion and curiosity for microbes?

Idea #3: We Are Ignorant of Microbes as Individuals, so We Fear Them

Perhaps obviously, infectious disease is defined as an illness arising from an infectious agent: a pathogen, a germ, a microbe. This week, as I sat through dozens of presentations on infectious disease, I expected to see quite a few microbes on the projector screen.

Total microbe count: one.

Chikungunya was paired with images of swollen ankles, tuberculosis with scatter plots, candida with symptom charts. I knew I wouldn’t get to smell, taste, or feel microbes at a professional conference, but damn, I barely got to see a picture!

I know the Chikungunya virion only through the unpleasant response it causes in humans.

The only microbe actually shown all day was this yellow fever virion. I was so excited, I sketched yellow fever for the next half hour and forgot to listen... whoops!

We don't know our microbes. That ignorance contributes to our fear. And, sometimes, that fear leads us to overreaching and violent reactions to microbes.

A perfect illustration of our one-dimensional relationship with microbes based on fear. This slide is from a DIERN presentation I watched on antibiotic resistance.

This campaign to eradicate leishmaniasis paints the bacterium's vector, the sand fly, like a dangerous and wanted criminal.

And I think our skewed perception, our tendency to ignore the subvisible, might be confounding our imagination when it comes to living well with microbes. I listened to researchers who seek “solutions” to the “problem” of disease. I also heard, over and over, our failure to find that solution.

“Aedes aegypti mosquito vector eradicated in Brazil! Accidentally reintroduced twice…”

“Antibiotic kills Mycobacterium tuberculosis! Now, multi-resistant Tb is more lethal than ever…”

“Yellow fever was conquered for good! Now it's reemerging as climate shifts the habitat of its wildlife host, Amazonian monkeys….”

The multiple "eliminations" followed by "reinfestations" of the Aedes aegypti mosquito make eradication seem like a less-than-permanent state.

This slide depicts four drivers of yellow fever re-emergence in Brazil. The "R" in DIERN stands for re-emerging diseases, a sign that annihilation of microbial enemies may be a dead-end tactic.

The story of disease I heard at the DIERN conference tells that humans are engaged in warfare with microbes. We grasp onto this narrative because it's familiar. We have been waging war on macro-predators for millennia, and we've been winning. Saber-toothed lions went extinct; gray wolves and Bengal tigers are confined, for the most park, to controlled populations in parks. Although predators still take lives (read about human-wildlife conflict in Nepal, California, or Brazil), their impact on the human species is a shadow of what it once was.

But I think this narrative of war makes less sense when we look at our relationship with microbes. Our campaigns against large predators worked because we share a scale. Our smaller foes, the microbes, will not be so easy to knock off. If we declare war, we may be setting ourselves up to lose.

Idea #4: We Are Not Going to Win This War

Microbes operate on their own scale. Bacteria are generally about one micron wide. That's a millionth of a meter, six orders of magnitude smaller than you or me. Protozoan parasites are slightly larger, hovering around 50 microns. Don't even get me started on viruses. Those tiny machines are measured in nanometers. That's one billionth of a meter, or nine orders of magnitude smaller than us! If we are engaged in a war, then scale is the microbes' deadliest weapon, because it gives them two superpowers: speed and stealth.

Speed, in terms of evolution. Microorganisms evolve faster than you can load a YouTube video on sketchy WiFi. The typical generation time of E. coli is 20 minutes. The average for a human is about 15,000,000 minutes. Shorter generations allow faster evolution. E. coli and their ilk have us beat with their hands (ahem, flagella) tied.

Stealth, in terms of hiding from us. Tiny things are not only hard to see with our eyes, they are also hard to detect and target with our weapons, like medicines and immune systems. They evade our weapons by evolving around them. In the last eight years, Enterobacteria have started producing an enzyme to digest the strongest antibiotic we have, carbapenem, into a harmless waste product. Bacillus anthracis hangs out in permafrost for decades, waiting for warm temperatures. When it's kicked out of human apes, yellow fever virus takes shelter in wild monkeys. Brucella slip inside our cells to avoid detection by antibodies, the seek-and-destroyers of our immune system. Retroviruses slide inside our goddamn genome to hide! Good luck eradicating that with a shotgun.

A playbook for the war against microbes, "Tackling Antimicrobial Resistance on Ten Fronts," published by the Review on Antimicrobial Resistance and featured in one of the presentation I watched.

As I learned about the speed and stealth of our greatest foe, I started to feel like Cersei Lannister facing Daenerys’s dragons. (Game of Thrones, anyone?) Cersei, binary queen that she is, put it like this: “We fight and die, or we submit and die. I know my choice.” Maybe that’s how infectious disease researchers have been looking at our war with microbes. Drug resistance, zoonoses, superbugs, spillovers… it’s a losing battle, but we’d rather die fighting than watching from the sidelines. But what if those aren’t the only two choices?

Idea #5: Curiosity and Compassion as a Foundation for Collaborative Survival with Microbes

I suggest that another choice exists, the same one I wrote about last week in Edge Effects: collaborative, multispecies survival, a concept from Anna Tsing.

But does that mean, exactly? I started a list of “solutions” to microbes in my notebook and tried to decide where each one falls on the Collaborative Survival Scale. On the less desirable end of this scale are annihilation of other life forms, human monoculture, and collapse. On the more desirable end are collaboration with other life forms, multispecies ecosystems, and survival.

Antibiotics

Simply put, antibiotics are medicines that kill bacteria. With a name that literally means "against life," these tend toward the annihilation side of the scale, but there are levels of death within antibiotics. I watched a DIERN presentation on veterinary antibiotic use, and learned that the four levels of antibiotic dosing are therapeutic, metaphylactic, prophylactic, and additive.

• Therapeutic antibiotics are given to a sick, diagnosed, individual animal at a high dose for a short duration of time. (This is probably how you have experienced antibiotics prescribed by your doctor.) This usage poses little risk of developing antibiotic resistance because all the bacteria are killed, and the exposure of microbes to the medicine is limited.

• Metaphylaxis is when antibiotics are given to a herd of animals, a few of which are showing clinical symptoms of disease.

• Prophylaxis is a preventative measure, when antibiotics are given to a group of animals that are not showing clinical symptoms, but may be at risk for disease.

• Additive antibiotics are those given indefinitely to all animals on a property, at low dosage, to promote faster growth and lower production costs. This usage poses a high risk of developing resistance, because only the weakest bacteria are killed, and there is prolonged selective pressure on microbes to evolve defenses to the medicine.

This slide from DIERN does a good job summing them up. The three arrows, from left to right, indicate "dose," "duration," and "discussion" (meaning controversy). Therapeutic antibiotics have the highest dose, shortest duration, and lowest controversy. Additives have the lowest dose, longest duration, and highest controversy.

A version of my Collaborative Survival Scale for veterinary antibiotics.

In conclusion, additive antibiotics are tools of unilateral collapse, whereas therapeutic antibiotics have an important, but limited, role to play in health. Overall, antibiotics are a weapon, better suited to wars than to collaborative survival.

I love this charcoal drawing, hung on the wall of veterinary epidemiologist Dr. Ju Galhardo. An antibiotic-resistant microbe downs pills while I nervous dog watches on. This painting depicts fear of microbes, but it also gives the bug personality and humor. The artist is Ju's former veterinary student, Daniela Krambek.

Vaccines

The municipal veterinarian of Corguinho, Dr. Edmaureen, and I prepare to vaccinate cats and dogs against rabies in the free, compulsory, annual vaccination campaign. The sign in the background says "raiva," which translates to both "rage" and "rabies."

Vaccines are medicines that boost our immune systems against specific microbes, such as viruses or bacteria. Instead of killing microbes directly, vaccines help our body's biological microbe-fighting systems (antibodies, T-lymphocytes, B-lymphocytes, macrophages, and others) prepare for war by introducing a small quantity of the pathogen (or, more likely, a dead bit of a pathogen) called an antigen. Our immune system recognizes that bit of the pathogen and produces weapons against it, so if the real pathogen arrives, it won't stand a chance.

Here, I'm vaccinating a cat in my host-town of Taboco. It's easy when you hold the cat against a tree or post, because it grabs on with its claws and holds still.

Vaccines are held up as one of the best alternatives to antibiotics because microbes can't evolve resistance to them directly. But I started to wonder: could microbes evolve resistance to our own immune system?

The answer is a definite yes. The evolutionary arms-race between pathogens and hosts has been going on since life itself began. HIV is a prime example: so far, the virus has evolved at least fourteen "escape mutations" to evade specific immunity molecules. This game of hide-and-seek has had enormous impacts on the evolutionary path of every host, including humans. It may even explain why we have sexual reproduction.

This dog was not pleased about his rabies vaccine, but his owner was happy. Brazil's health system relies on owners to bring their pets to a central location if they live in town. If they live on rural property, Dr. Edmaureen and her vaccination team will make a house-call.

As I thought about vaccines, I realized they post the same risk of resistance as antibiotics, albeit on a longer time-scale. By boosting the quantity of immune molecules to which pathogens are exposed, vaccines must be increasing the selective pressure on microbes to evade our immune system. I dread the day when a microbe develops resistance not only to our drugs, but to our bodies’ defense. Unlike antibiotic resistance, which can be addressed by the development of new drugs, immune-system resistance cannot be invented away. It would take hundreds of generations and much human suffering to evolve new immune defenses.

Dr. Edmaureen and two Health Vigilance Specialists hand-made this pink dog bed out of a tire in an effort to boost participation in the vaccination campaign. Every owner who brought a pet to our tent got to enter a raffle ticket. There was a smaller bed for cats.

The crucial difference between antibiotics and vaccines is that antibiotics are the weapons, while vaccination relies on our immune system to provide the weapons. Although neither is an ideal tool for collaborative survival, vaccines seem to be a solution that will last longer before the bugs outsmart us, if only because our immune systems are more complex and dynamic than the individual chemicals present in antibiotics.

Genetic Improvement

I bring up this solution in the context of livestock, not humans. I consider this tactic a version of "assisted evolution," in which humans amplify selective pressures from pathogens by allowing only disease-resistance individuals to breed. Joel Salatin has long argued for breeding hardy chickens, and programs to improve the genetics of cattle through breeding are widespread.

Ted Turner's Flying D Ranch in Montana uses American bison, Bison bison, to produce burgers from a native, disease-resistant species. Collaborative Survival Ranking: high.

Fazenda Colorado in Mato Grosso do Sul, an arid state of Brazil, raises zebu, Bos indicus, a heat-tolerant species of domestic cattle of Indian origin that has some resistance to ticks.
Collaborative Survival Ranking: moderate.

A feedlot in Walla Walla, Washington fattens angus, Bos taurus, a European species of beef cattle known for the marbling (fat distribution) of its meat, not its hardiness against disease.
Collaborative Survival Raking: low.

Evolution through selective pressure is a proven process for living well with microbes. It's the primary tool that host species have used to coexist with microbes for four billion years, and it's dynamic. Theoretically, microbes can't evolve resistance to genetic improvement, because the livestock genes can always keep changing. In this case, we are still engaged in a war with microbes, but we are using evolution to provide the weapons.

Probiotics

Now I am straying into the realm of my own solutions, because I didn't hear mention of this at DIERN. Probiotics come to mind as a way to fight microbes with microbes, to control life with other life. The idea is to consume beneficial bacteria on purpose, most often Lactobacillus and Bifidobacterium. But the current state of affairs is summed up by the National Institute of Health like this: "We still don’t know which probiotics are helpful and which are not." I'm putting probiotics high on the Collaborative Survival scale because they rely on another age-old principle of ecology, biotic competition.

Body-Wide Symbioses (a flourishing microbiome)

Our body is built of more bacterial cells than human ones. Microbes digest our food, eat dust off our eyelashes, and keep our vaginas free from invaders. The most obvious solution to infectious disease seems, to me, to be a cultivated garden of diverse microbes living within and with-on us.

Perhaps garden isn't the right word, because that refers to a group of plants. A zoo comes to mind, but that's for animals. Microzoo? Endo-garden? We call a group of bacteria a culture or a colony, but when we speak of a functional community of microbes living with a body, the term microbiome rings true.

Biome-Wide Symbioses (a flourishing ecosystem)

The more I learned about antibiotic resistance, the more I wondered how non-human organisms deal with pathogens, these apparently unstoppable enemies. Time and again, I ran into examples of symbioses with other species. Salmon rely on cleaner fishes to rid their lice. Cattle egrets and cattle tyrants are two birds who have earned their names from performing the same service for our ubiquitous companions, the cows. Four years ago, when I lived in the Galápagos, I studied a similar interaction between parasite-eating wrasse and green sea turtles.

A cattle tyrant surfs the head of a capybara, world's largest rodent and a host for disease-carrying Amblyomma ticks.

A green sea turtle is grazed by white salema (Xenichthys agassizii) off San Cristóbal, a Galápagos Island.

Now that I think about it, I did hear one example of this idea at DIERN. Brazilian epidemiologists are infecting Aedes aegypti mosquitoes -- the notorious vectors of zika, dengue, and other viruses -- with  a bacterium called Wolbachia pipientis. You know what they say: a pathogen of a pathogen is a friend!

Some people in the United States keep guinea fowl for their tick-hunting reputation, but everyone I spoke with in Brazil insisted the spherical hens were only around to look pretty.

To test this idea of biome-wide symbioses as a strategy to control disease, a mad scientist might propose an experiment in which she toppled an existing symbiotic system and then measured the change in health of its organisms. Unfortunately, while this experiment sounds destructive and unethical, it is already being carried out around the world as ecosystems are degraded.

Rolling cattle pasture in Brazil where Cerrado forest previously harbored a complex web of plants, animals, and microbes.

In Brazil, a 50% increase in malaria resulted from a 4% deforestation by area. Here in Madagascar, the September forest-burning season forces black rats to flee toward villages, where their fleas can pass bubonic plague to humans. Ecosystems in distress have the potential to lose the balance mechanisms between hosts and pathogens. As David Quammen puts it in Spillover, "Shake a tree, and things fall out." Perhaps the converse, then, is to cultivate a forest of trees where things stay put.

Red-and-green macaws preen each other, removing parasites in a conspecific act of collaborative survival. Evolved and cultural behaviors like preening and burying the dead are important strategies for living well with pathogens.

Idea #6: Placing Ourselves Into Ecosystems

I came to realize that collaborative survival requires placing our pathogens, and ourselves, back into functioning ecosystems.

Disease has become the major Anthropocene concern for humans and our domestic animals because we have removed ourselves from a functioning, multispecies web. We’ve exponentially increased the resources available to microbes -- cow and human bodies -- while simultaneously removing those resources from their context, the biological interactions that kept pathogens in check.

I hypothesize that humans will be more successful at flourishing on this planet if we reframe our war against pathogens as survival alongside microbes, some of which cause us harm under certain conditions. Sensing and appreciating microbes for themselves is a first step; understanding their ecology is a second; reestablishing functional ecosystems inclusive of us and our livestock is a third.

Cultivating curiosity and compassion for microscopic life sounds like a refreshing and even enjoyable path, far superior to fighting a losing battle just to say we went down fighting. (I'm looking at you, Cersei.)

(Psst! You forgot collaborative survival!)

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