When Agencies Collaborate: What EEID Teaches Us About Pandemic Preparedness

The research team moved carefully through the forest canopy platform at dusk, nets ready. In Gabon and the Republic of Congo during the mid-2000s, international ecologists were hunting for the reservoir host of Ebola virus. They targeted fruit bat colonies—hammer-headed bats, Franquet’s epauletted bats, little collared fruit bats—collecting blood samples and oral swabs.

By December 2005, they had their answer, published in Nature. They’d found Ebola RNA and antibodies in three species of fruit bats across Central Africa. For years, scientists had known Ebola emerged periodically, but couldn’t identify where the virus persisted between human epidemics. This research provided the answer: fruit bats, widely distributed and increasingly in contact with humans as deforestation pushed people deeper into forests.

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That discovery triggered a wave of follow-up research, much of it funded through the Ecology and Evolution of Infectious Diseases program—EEID—a joint NSF-NIH-USDA initiative I would later help oversee. EEID-funded teams documented how human activities created spillover opportunities: bushmeat hunting, agricultural expansion into bat habitat, mining operations bringing workers into forests. They identified cultural practices that facilitated transmission: burial traditions, preparation of bushmeat, children playing with dead animals. They built mathematical models of how Ebola moved from bats to humans and then through human populations. The science showed where Ebola lived, how it spilled over, and which human behaviors created risk.

Yet nine years after that initial Nature paper—after years of EEID-funded research mapping Ebola ecology—the virus emerged in Guinea in late 2013 and was identified in March 2014. A two-year-old boy, likely exposed through contact with bats, became patient zero. Within months, the outbreak had spread to Liberia and Sierra Leone. By 2016, more than 28,000 people were infected and 11,000 died. The economic impact exceeded $2.8 billion.

I was leading NSF’s Biological Sciences Directorate at the time, overseeing NSF’s role in EEID. We had funded years of follow-up research. We knew fruit bats harbored Ebola. We had models for predicting transmission. We had mapped high-risk regions. And yet 11,000 people died anyway. All of this was foreshadowing what would happen with SARS-CoV-2 later and on a much larger scale.

Here is the uncomfortable question I’ve been wrestling with ever since: If we funded the right science and had years of warning, why were we not better prepared?

What EEID Was Supposed to Do

EEID launched in 2000 because infectious disease ecology fell between agency missions. NSF supported ecology but wasn’t focused on disease. NIH funded disease research but wasn’t equipped for field ecology. USDA cared about agricultural diseases but not the broader ecological context. The program brought all three together: NSF’s ecological expertise, NIH’s disease knowledge, and USDA’s understanding of agricultural-wildlife interfaces.

The administrative structure was elegant on paper. All proposals submitted through NSF underwent joint review by all three agencies, and then any agency could fund meritorious proposals based on mission fit. For Ebola research, this meant NSF might fund the bat ecology, NIH’s Fogarty International Center might support the human health surveillance component, and USDA might fund work on bushmeat practices—different pieces of the same puzzle, coordinated through a single program.

The program typically made 6-10 awards per year, totaling $15-25 million across agencies. Not huge money, but enough to support interdisciplinary teams working across continents. And it worked—EEID funded excellent science at the intersection of ecology and disease that no single agency could have supported alone.

Why Interagency Collaboration Is Genuinely Hard

When I arrived at NSF in 2014 with the outbreak at its peak, I inherited EEID oversight and quickly discovered that elegant-on-paper doesn’t mean easy-in-practice. The deepest challenges weren’t administrative—they were cultural.

NSF and NIH approach science from fundamentally different starting points. NSF’s mission is discovery-driven basic research. When NSF reviewers evaluate proposals, they ask: Is this important science? Will it advance the field? NIH’s mission is health-focused and translational. NIH reviewers want to know: Will this help prevent or treat disease? What’s the public health significance?

I saw this play out in a particularly contentious panel meeting around 2016. Our panelists were reviewing a proposal on rodent-borne hantaviruses in the southwestern U.S.—excellent ecology, good epidemiology, solid modeling. The NSF reviewers loved it: beautiful natural history, important insights about how environmental variability affects transmission. The NIH reviewers were skeptical: where was the preliminary data on human infection? How would this lead to intervention?

An hour passed debating what constituted “good preliminary data.” For NSF reviewers, the PI’s previous work establishing field sites was sufficient—it showed feasibility. NIH reviewers wanted preliminary data on the virus itself, on infection rates. They weren’t being unreasonable—they were applying NIH’s standards. But we were talking past each other.

That debate crystallized the challenge. Two agencies with different cultures had to agree on the same proposals. Sometimes it created productive tension. Sometimes it just meant frustration.

The administrative burden on investigators was worse than we acknowledged. When NIH selected a proposal for funding instead of NSF, the PI had to completely reformat everything for NIH’s system—different page limits, different budget structures, different reporting requirements. This could add 3-6 months to award start dates. Try explaining to a collaborator in Guinea why you don’t know which U.S. agency will fund your project or when you’ll actually get money.

For program officers, EEID meant constant coordination overhead—meetings to discuss priorities, coordinating review panel schedules across agencies, negotiating which agency would fund which proposals. This work wasn’t counted in official program costs, but it was real. Hours we could have spent on other portfolio management.

Despite all this friction, EEID succeeded at its core mission. It funded research that advanced both fundamental science and disease understanding. When the 2014 Ebola outbreak hit, epidemiologists reached for transmission models developed through EEID grants. The program had trained a generation of researchers in genuinely interdisciplinary work.

What the 2014 Outbreak Exposed

But here’s what haunts me: we funded the science but not the systems. By 2014, nearly a decade of research had confirmed fruit bats as Ebola reservoirs, mapped their distribution across Africa, and identified high-risk human-bat contact zones. Papers were published in top journals. And then… nothing. No one built surveillance systems in West African villages where contact with bats was common. No one established early warning networks. No one created mechanisms to translate “we found Ebola in these bats” into “we’re monitoring for spillover in Guinea.”

EEID funded research, not surveillance. That’s appropriate—it’s a research program, not an operational public health system. But there was no mechanism to bridge the gap. When EEID-funded scientists discovered important findings, those findings stayed in academic papers. They didn’t flow to CDC, didn’t trigger surveillance efforts, didn’t inform preparedness planning.

During our quarterly coordination calls with NIH and USDA program officers, the question would occasionally arise: Who’s responsible for acting on what we’re learning? If EEID research identifies high-risk pathogen reservoirs, whose job is it to establish surveillance? The answer was usually silence, then acknowledgment that it wasn’t our job—we fund research—but uncertainty about whose job it was.

The missing infrastructure was organizational, not intellectual. We knew enough to be better prepared. The problem was lack of systems to act on knowledge. No agency was responsible for translating academic research into surveillance systems. CDC focuses on domestic diseases. NIH funds research but doesn’t run operations overseas. USAID’s PREDICT program did fund surveillance but didn’t have coverage in Guinea. We had pieces of the puzzle but no mechanism to assemble them.

I remember discussions about whether EEID should become more operational—perhaps requiring funded projects to include surveillance components. The response was always that this would fundamentally change the program’s character. NSF resists mission-directed research. My former agency’s strength is supporting investigator-driven discovery. Making EEID operational would require multiple agencies and authorities, and, most importantly, substantially more funding. A research program can’t solve an operational preparedness gap.

The scale problem was obvious. At $15- $ 25 million per year, EEID could support excellent science but not comprehensive surveillance. Think about what that would require: ongoing monitoring in multiple countries, relationships with local health systems, rapid response capacity, and laboratory infrastructure. This requires hundreds of millions annually, not tens of millions.

The timeline mismatch was equally frustrating. Research operates on slow timescales—EEID grants ran five years, and from proposal to publication might take 6-7 years. The initial bat reservoir discovery was published in 2005. If that had immediately triggered surveillance in West Africa, we’d have had nearly nine years before the 2014 outbreak. But triggering surveillance takes decisions, funding, international coordination—processes that themselves take years. By the time anyone might have acted, attention had moved elsewhere.

What This Means for Pandemic Preparedness

The most troubling insight: we knew enough to be better prepared for Ebola, and later for COVID-19, but knowledge alone wasn’t enough. EEID succeeds at advancing knowledge but can’t create surveillance systems, can’t fund operational preparedness, can’t bridge the gap between discovering threats and preventing epidemics. That gap is organizational and political, not scientific.

Should we expand EEID? More funding would support more projects, but it wouldn’t solve the fundamental problem. You could triple EEID’s budget and still have the research-to-surveillance gap. More papers about bat reservoirs don’t automatically create early warning systems. The limitation isn’t insufficient research funding—it’s absence of operational systems to act on research findings.

We need something structurally different. Here’s what I’d do:

First, create a rapid-response funding mechanism within EEID. When Ebola emerged in 2014, imagine if researchers could have gotten funding within weeks to investigate transmission dynamics and surveillance in surrounding regions, rather than waiting for the next annual competition. Model this on NSF’s RAPID program—streamlined review, modest awards ($100-200K for one year), quick deployment—but create an entirely different pocket of money for it from all the participating funders.

Second, establish formal connections between EEID and operational agencies. This is the biggest gap. Require EEID-funded researchers to submit one-page “surveillance implications” memos with final reports, which program officers share with CDC, USAID, and WHO. Better yet, have CDC or BARDA co-fund some EEID proposals with clear surveillance applications. Create visiting scholar programs where CDC epidemiologists spend time with EEID research teams and vice versa.

Third, strengthen international partnerships with genuine co-leadership. The 2014 outbreak showed the cost of inadequate surveillance infrastructure in West Africa. Expand EEID to include more disease hotspot regions—India, Brazil, Indonesia, DRC, West African nations—where foreign investigators can be lead PIs, foreign institutions receive and administer funds, and research priorities reflect host country needs. This isn’t altruism—it’s pragmatic self-interest.

The Larger Lesson

Interagency collaboration is genuinely hard—the friction I described isn’t fixable through better management. It’s inherent when bringing together organizations with different missions and cultures. EEID proves such collaboration can work and produce excellent science. But it requires sustained effort, goodwill, and tolerance for complexity.

The alternative—each agency in its silo—is worse. Infectious disease ecology requires expertise no single agency possesses. Complex problems require complex solutions. EEID demonstrated this is possible. The challenge is making it sufficient.

What haunts me is that we’re probably going to repeat the pattern. Right now, post-COVID, pandemic preparedness has political salience. But history suggests this won’t last. After the 2014-2016 Ebola outbreak, there was similar urgency. Within a few years, budgets declined and attention shifted. USAID’s PREDICT program was terminated in 2019—just months before COVID—due to budget constraints. We cut surveillance funding during a quiet period, then paid an enormous price when the next pandemic hit.

Prevention is invisible. We never know which pandemics we successfully prevented. There’s no constituency defending preparedness funding when cuts loom. That’s the structural problem we haven’t solved.

What Needs to Happen

Will we learn from EEID’s experience and build the infrastructure we need? Or will we fund the right research but lack systems to act on it—again?

The answer depends on recognizing that pandemic preparedness isn’t primarily a scientific challenge—we know enough—but an organizational and political one. Can we create structures spanning research and operations? Can we sustain funding between crises? Can we build systems robust enough to survive political leadership changes?

EEID succeeded at what a research program can do: funding excellent science that advanced understanding. The larger failure—inadequate pandemic preparedness—requires solutions at different organizational levels. But EEID’s experience provides a foundation: proof that interagency collaboration can work, that we can identify threats before they become catastrophes.

The team in Central African forests collecting bat samples did their job. They found the virus, mapped the threat, advanced our understanding. The question for the rest of us—program officers, policymakers, public health officials, citizens who fund this through taxes—is whether we’ll do our job: building systems that turn knowledge into prevention.

Science can identify threats. But preventing pandemics requires more than science. It requires sustained organizational commitment, interagency coordination, international cooperation, and political will—especially during quiet periods when threats seem distant. EEID demonstrated the scientific component is feasible.

The rest is up to us. And based on what I’ve seen, I’m not optimistic we’ll get it right before the next one hits.

Why I’m Taking Science Policy Insider International

A View from Abroad

Mid-competition week for a panel reviewing proposals on genes and cells: the fifteen-minute clock starts, and the five of us assigned to this proposal dive in. We consider factors such as whether the proposer is early in their career and how the COVID pandemic might have affected their laboratory’s productivity. We carefully assess their plan for mentoring trainees, including their previous track record and plans. The excellence of the proposer is evaluated, not by raw bibliometric measures such as H-index, but by substantive contributions to the field. And we take a very close look at the proposal itself—not only in terms of intellectual merit, but also to make sure that it is distinct from the investigator’s other supported science. Is this an NIH study section? Nope. Is this an NSF panel? Again, no. This is a peer review for another G7 nation, to be unnamed in this post.

What struck me wasn’t that this country did peer review differently than NSF or NIH. What struck me was how similar it was. Same careful attention to mentoring. Same suspicion of bibliometrics. Same concern about overlaps with existing funding. I could have been in any panel room I’d sat in over three decades in Washington. And that’s when it hit me: among the wealthy nations that fund science, we’re all running variations on the same basic system. We argue about details – overhead rates, review criteria, funding durations – but we share fundamental assumptions about how science should work.

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Or so I thought. Until I stepped outside the world of science funding and began looking at how other countries organize technical knowledge. My second book project examines how Boeing, Airbus, and Embraer design commercial aircraft – and that research has revealed something I’d missed in all my years in government and academia.

Civic Epistemologies

The scholar Sheila Jasanoff has a concept called ‘civic epistemologies’ – the idea that different societies have fundamentally different ways of producing and validating knowledge. It’s not about organizational charts or funding mechanisms. It’s deeper than that. It’s about cultural assumptions: What questions are worth asking? What counts as evidence? Who gets to decide? How do we measure success?

When Americans design an airplane, we assume that technical decisions should be made by engineers based on data, with regulators checking compliance after the fact. Europeans embed social and labor concerns directly into the design process – workers’ councils have a say in production methods, and safety regulators are involved earlier. Brazilians organize around different assumptions entirely, shaped by their position as a developing economy entering a market dominated by established players.

Same engineering principles. Same physics. The same goal of building a safe, efficient aircraft. But fundamentally different answers to the question: Who should decide how this gets done?

I saw the same pattern as a working neuroscientist. American neuroscience tends to bet on fundamental discovery—map the circuits, understand the mechanisms, and applications would follow. Recording sea slug neurons during my training embodied this approach: study simpler systems, find conserved principles, apply them to humans. Europeans start closer to the clinic, organizing major research programs around disease categories and patient needs. Japanese neuroscience builds unusually tight links between academic labs and industry—electronics and engineering companies actively embedded in research networks, with clear paths toward commercialization: same neurons, same biology—different assumptions about how knowledge should flow from laboratory to society.

My new book project

So, where is this taking me? The short answer is I’m working on a new book about how American, European, and Brazilian cultures (think Boeing, Airbus, and Embraer) shape commercial aviation technology. Why planes? In my lifetime, I experienced firsthand the jet revolution: I started on the Comet, went on to the Pan Am 707s, and these days still enjoy the grandeur of the big twin aisle giants that connect us across oceans.

In the new book, I’m interested in comparing technical cultures through the lens of those jets (as technical artifacts). But beyond my lifetime fascination with aviation, the same questions apply to science policy itself: why do different countries organize technological knowledge differently? What can we learn from how other G7 nations fund science? And what cultural assumptions shape what gets built (airplanes OR research programs)?

Science Policy Insider Expands Its Scope

This brings me back to Science Policy Insider and where we’re headed. We are broadening our remit. In the future, we’ll expand to include a comparative analysis of research funding systems—both public agencies and private industry—drawing on insights from my aviation research. We’ll examine how different countries handle current challenges: AI governance, climate research, and research security.

On the practical side, we’ll provide insights for American researchers who work internationally or plan to—from navigating different grant systems to understanding why collaborations succeed or fail across cultural boundaries. And above all, we’ll consider what viewing American science policy from the outside reveals about our own system.

We’ll maintain our bi-weekly publishing schedule.

Science Policy Insider started with my promise to explain how American science policy really works from someone who was inside the system. Now we’re also going to explore what it looks like from the outside and what that perspective reveals about our own system.

I continue to invite readers’ questions, now not only about how things work in our own American discovery machine, but also about international science policy.

Bold Ventures in Science: NSF’s NEON and NIH’s BRAIN Initiative

My favorite projects…

As loyal readers know, these are my two favorite science initiatives. They stand out as beacons of progress: the National Science Foundation’s National Ecological Observatory Network (NEON) and the National Institutes of Health’s Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative. These groundbreaking endeavors showcase the commitment of U.S. science agencies to tackling complex, large-scale challenges that could revolutionize our understanding of the world around us and within us.

NSF’s NEON: A Continental-Scale View of Ecology

Imagine having a window into the ecological processes of an entire continent. That’s precisely what NEON aims to provide. Initiated in 2011, this audacious project is creating a network of ecological observatories spanning the United States, including Alaska, Hawaii, and Puerto Rico.

Yes, NEON has faced its share of challenges. The project’s timeline and budget have been adjusted since its inception, growing from an initial estimate of $434 million to around $469 million, with completion delayed from 2016 to 2019. But let’s be honest: when did you last try to build a comprehensive ecological monitoring system covering an entire continent? These adjustments reflected the project’s complexity and the learning curve in such a pioneering endeavor.

The payoff? NEON is now collecting standardized ecological data across 81 field sites from Hawaii to Puerto Rico and in between. This massive time series in some 200 dimensions will allow scientists to analyze and forecast ecological changes over decades. From tracking the impacts of climate change to understanding biodiversity shifts, NEON provides invaluable insights that could shape environmental policy and conservation efforts for future generations.

NIH’s BRAIN Initiative: Decoding Our Most Complex Organ

Meanwhile, the NIH’s BRAIN Initiative is taking on an equally monumental task: mapping the human brain. Launched in 2013, this project is aptly named, as it requires a lot of brains to understand… well, brains.

With annual funding that has grown from an initial $100 million to over $500 million, the BRAIN Initiative is a testament to the NIH’s commitment to unraveling the mysteries of neuroscience. Mapping all 86 billion neurons in the human brain by 2026 might seem a tad optimistic. But I’m increasingly impressed with our progress, and I am hopeful we’ll be able to get some meaningful statistics about variability across individuals.

The initiative has already led to the development of new technologies for studying brain activity, potential treatments for conditions like Parkinson’s disease, and insights into how our brains process information. It’s like a real-life adventure into the final frontier, except instead of outer space, we’re exploring the inner space of our skulls.

The Challenges: More Feature Than Bug

Both NEON and the BRAIN Initiative have faced obstacles, from budget adjustments to timeline extensions. But in the world of cutting-edge science, these challenges are often where the real learning happens. They’ve pushed scientists to innovate, collaborate, and think outside the box (or skull, in the case of BRAIN).

These projects have also created unique opportunities for researchers to develop new skills. Grant writing for these initiatives isn’t just an administrative hurdle; it’s a chance to think big and connect individual research to grand, overarching goals. It’s turning scientists into visionaries, and isn’t that worth a few late nights and extra cups of coffee?

Conclusion: Big Science, Bigger Possibilities

NEON and the BRAIN Initiative represent more than just large-scale scientific projects. They’re bold statements about the value of basic research and the importance of tackling complex, long-term challenges. They remind us that some questions are too big for any single lab or institution to answer alone.

As these projects evolve and produce data, they’re not just advancing our understanding of ecology and neuroscience. They’re also creating models for conducting science at a grand scale, paving the way for future ambitious endeavors.

So here’s to the scientists, administrators, and visionaries behind NEON and the BRAIN Initiative. They’re showing us that with enough creativity, persistence, and, yes, funding, we can tackle some of the biggest questions in science. And who knows? The next breakthrough in saving our planet or understanding consciousness could be hidden in the data they’re collecting right now.

How to reform NIH…

Recently, I’ve mostly written in this respect about the NSF, but I also spent six years at the NIH, as a staff fellow in the intramural program (the biomedical medical center in Bethesda Maryland). When most folks think about the NIH, they are not really focussing on the intramural program. Rather, it’s the extramural program that gives out grant awards to biomedical researchers at US Colleges and Medical Centers that gets the attention. And I guess that’s fine because the extramural program represents about 90% of the NIH budget.

But, if I were going to magically reform the agency, I would focus on the intramural program. That’s because it has so much potential. With an annual budget north of $4B/year, America’s largest research medical center and thousands of young researchers from all over the world, it has so much potential. If Woods Hole is a summer nexus for life sciences during the summer, the NIH Bethesda campus is that thing on steroids year round.

The special sauce for the intramural program is that ideas can become experiments and then discoveries without the usual intermediate step of writing a proposal and waiting to see if it was funded. When I was at NIH, I could literally conceive of a new experiment, order the equipment and reagents and publish the results several months later. Hence, the intramural program has the structure in place to be a major science accelerator.

But, for some reason, when we think of such science accelerators, we generally consider private institutions like HHMI, the Allen Institutes and perhaps the Institute for Advanced Study in Princeton. What about NIH? On the criteria of critical mass, it dwarfs those places.

To my mind the problem lies in NIH’s ‘articles of confederation’ nature: it’s really 27 (or so) different Institutes and other units that are largely quite independent (especially the NCI), with a relatively weak central leadership. And this weak confederation organization plays out, not only on the Hill or in the awarding of extramural awards, but crucially also on the Bethesda campus, where intramural institute program directors rule fiefdoms that are more insular than academic units on a college campus. And this weak organizational architecture acts in the opposite direction of the science accelerator advantage that I wrote about above.

So here’s a big idea: let’s make the intramural program it’s own effective NIH institute. And have Congress authorize it and fund it separately, as a high risk, high payoff biomedical research program for the country. Does that sound like ARPA-H? Ooops. Well, then maybe we should just give the Bethesda campus to ARPA-H.