Mike Boots: Modeling the Unknown

January 29, 2026

by Alexander Rony

Mike Boots is the chair of UC Berkeley’s Department of Integrative Biology. He focuses on the ecology and evolution of infectious diseases, but that can lead to a remarkably diverse range of research topics. His lab has published papers on poxvirus in squirrels, varroa mites in honeybees, tuberculosis in badgers, and malaria in birds.

Boots has a background in entomology and mathematical biology, which informs his disease modeling efforts for mosquitos and honeybees. Of course, each of these studies have ramifications for human health in addition to species conservation.

Boots spoke with UC Berkeley writer Alexander Rony about current threats and opportunities for zoonotic research, which investigates diseases that can spread from animals to humans.

Can you describe your research?

Mike Boots: I ask “why” questions: Why are some infectious diseases more virulent than others? Why is it that some viruses kill people really quickly and some are very mild? Why do some diseases emerge and others don't?

In the context of zoonosis, those questions become very important, but very difficult. We don't understand, in a basic way, what is likely to happen.

Much of evolutionary theory assumes that everything is in a steady state, but once a disease comes into a new population, it's changing continually and growing quickly. We need to develop different theories to understand that.

We're trying to understand better why diseases sometimes jump between species. Pollinator systems can help us do that. They share viruses. We can go out, measure them, see how they're jumping, and do that in a controlled way. We think about how different processes are likely to affect the spread of infectious disease then apply it to specific diseases, like dengue.

How do you tackle these “why” questions without knowing the mechanisms that the diseases rely on?

I'm a believer in models, even when we don't understand things, because the models allow you to think rigorously about the most important thing to find out. They guide us in terms of the data we need to collect, and they allow us to make broad predictions.

Take COVID. COVID taught us how little we understand about the evolution of infectious diseases as they emerge. Omicron happens. The way it behaves is completely different to what happened before. It's like a completely different virus, phenotypically. It's shocking to us because we don't understand these processes.

A man with crossed arms and a button-up shirt

PROFESSOR MIKE BOOTS

Even though we have lots of people who've modeled infectious disease over many years, there are still huge, basic questions that haven't been addressed. If you look at COVID, the reason it was such a difficult disease to control was because of the asymptomatic infection. Individuals were going around infecting others, but they didn't feel sick, so they wouldn't quarantine. There were a few fundamental papers on asymptomatic infection and what it does to infectious disease spread, but we didn't have a baseline understanding of what would happen. Everyone was suddenly modeling, trying to catch up in real time.

Long COVID is very interesting. While you're infected, you can infect other people, but there's still significant harm and potentially mortality after you've recovered that's caused by the fact you had the disease. Our models of disease spread don't include that. The typical model assumes that, if you're going to die of the disease, you die while you're infected, but that's not true of COVID and a lot of diseases. So we build a new model. It's that kind of work that we do, inspired by diseases and big, general questions.

Infectious diseases obviously threaten humans. What should people realize about the threats that infectious diseases pose to bees or plants?

THE BOOTS LAB LOGO

These sorts of threats are not science fiction in any way. It's a frightening thought…

Mike Boots

What's a world without bees? Economically, how are you going to pollinate almonds? Have you ever been to the Central Valley when the almond blooms are? There's nothing alive to pollinate them. We have to bring honeybees there to pollinate them. A world without bees is a disaster.

You look at all these other agricultural diseases and see the potential for complete catastrophe: Dutch elm disease, citrus greening. Diseases destroyed the American chestnut tree.

People's food security is fundamentally at risk from infectious diseases. How many things do we eat? When you think about it, it's not that many.

We need people studying the fundamentals of infectious disease evolution for these bigger, existential disease threats. Look at Interstellar. The whole world's gone because this fungal disease has taken out all the crops. That could happen. These sorts of threats are not science fiction in any way. It's a frightening thought...

What could we learn from plant research to better deal with human diseases?

Typically, what we think about how you deal with a pathogen is you stop yourself getting infected or you fight it. Another way you can defend yourself is just to mitigate the harm that it causes you. You develop mechanisms that deal with the damage the pathogens cause. We call that tolerance. In the plant literature, people talk about this all the time. In agriculture, cultivars are planted that have defense against a common disease. They still get infected, but the yield is still high. For the immunologists, it's all, “turn on these mechanisms, fight the bacteria.”

Have you been impacted by any changes to federal programs in the past year?

The National Science Foundation ran the Ecology and Evolution of Infectious Disease program for a couple of decades. It's co-funded by the National Institutes of Health and the USDA. This is where people are asking those fundamental questions of how a disease might emerge or how it might spread through a population, as opposed to the molecular mechanisms, which are also important. NSF archived that entire community that has been built up.

It's very hard to imagine where you would fund this work. I worry that the importance of fundamental research on understanding infectious disease is not understood. These long-term studies are absolutely vital. Even if it's just a temporary hit, we're going to lose that time series. How we are going to adjust to keep this research going is what worries me. The sort of stuff we do is relatively low cost, but once we don't collect for a few years, it can kill.

That's the sort of long-term research that government agencies can do. What worries me is that the appropriations for NSF out of the Senate are flat. They didn't cut NSF, but NSF could say they're not spending anything on biology, ecology, climate change, evolution, or infectious disease and spend it all on nanocomputing and AI. The priorities within the agency are what's worrying.

Typically, agricultural research has been seen as safe and bipartisan. What might the concerns have been from the federal side?

We had the greatest ever loss of bees, greater than colony collapse disorder. What worries me is I have no sense of what's happening at that agency, whether they have funding, and whether people have lost their jobs. It's not very transparent. We're sitting here going, “What's actually happening?” We need to know if it's a virus. Somebody should care about that.

I don't think there's been an active sense that we don't need research in agriculture, but if they're shrinking all these agencies across the board, then that's the knock-on effect.

People in America are not immune to the threats of these infectious diseases. That's obvious from 2020, and it's going to come again.

Mike Boots

Some officials have dismissed global health research as charity. How do you make the case for U.S. funding for diseases like dengue and malaria that are more common in the Global South?

People in America are not immune to the threats of these infectious diseases. That's obvious from 2020, and it's going to come again. We're going to have another pandemic.

We need to understand infectious disease at some fundamental level. You develop this scientific knowledge by studying infectious diseases wherever they're found.