But rearranging the deck chairs can work
The call came from Jo Handelsman.
She was the White House microbiome czar — formally, Associate Director for Science at the Office of Science and Technology Policy — and one of the most respected microbiologists in the country. That mattered to me. This wasn’t a communications staffer working a headline. It was a scientist, operating inside the executive branch machinery, doing what that machinery required of her.
I was the Assistant Director for Biological Sciences at NSF — the head of a directorate called BIO, which meant I was the person she needed to talk to. About a minute in, she let me know the President was looking for about $140 million from our directorate. I was already mentally recoding program money across four related BIO program areas to hit that target. They were seeking a similar amount from colleagues at the National Institutes of Health. I figured they were aiming for around $1 billion.
I was annoyed. Not at Jo — she was doing her job with characteristic seriousness. I was annoyed by the situation itself — by the structural position we both occupied and by what the exercise revealed about how presidential science policy functions.
The constitutional problem hiding in plain sight
Here’s what never appears in White House press releases about presidential science initiatives: only Congress has the power to appropriate taxpayer money. This isn’t a technicality — it’s the foundational architecture of federal spending. When NSF receives its annual budget, those funds have been appropriated by Congress for specific purposes under statutory authority. Program officers and directorate heads are stewards of a congressional trust, ultimately answerable to the legislative branch, not the executive.
And yet the White House’s actual influence over that budget is, in practice, more limited than it appears. There’s an old saying in Washington: the President proposes, the Congress disposes. The President’s budget request is largely a messaging document — Congress typically starts over, setting topline numbers and leaving agencies to determine specific research directions from there. The Obama White House, for all its scientific vision, understood this. The bully pulpit was the real instrument, not the budget pen.
Which makes Jo’s phone call more interesting, not less. She wasn’t calling to redirect taxpayer funds — Congress would have the final say on that. She was calling to build a message. What she wanted from me was not new money but a credible number: existing programs that could be rebranded under the new initiative’s banner and counted toward a headline figure. The $140 million from NSF BIO wasn’t $140 million in new microbiome research — it was $140 million in ongoing biological research that could be plausibly connected to the microbiome, renamed, reframed, and counted.
This is a meaningful distinction. The White House wasn’t telling me where to spend money. It was asking me to redescribe how I was already spending it. That’s a subtler thing to object to — and I want to be precise about my objection, because I’ve had the chance to think it through more carefully in the years since, including in conversation with Jo herself.
I could have said no. Francis Collins, then the NIH Director, did exactly that, and the request was accepted. These were genuinely requests, not commands. The annoyance I felt on that call was partly at the exercise — the gap between the headline and the reality — and partly at myself, for how quickly I complied when I could have pushed back.
The science, though
Here is where I must complicate my own annoyance. I believed in the Microbiome Initiative. I still do — and the decade since its announcement has only deepened that conviction.
The microbiome is not a niche subject. The human body contains roughly as many microbial cells as human cells, and the collective genome of those microorganisms dwarfs our own in complexity and metabolic diversity. We are, in a very real sense, superorganisms: our health, our immune function, our neurological development, even our susceptibility to depression and anxiety, are all shaped in ways we are only beginning to understand by the trillions of organisms living inside us. The gut-brain axis — the bidirectional signaling pathway between the enteric and central nervous systems, mediated in part by the microbiome — may ultimately transform how we think about psychiatric disease. The relationship between the microbiome and cancer immunotherapy is already reshaping oncology: the composition of a patient’s gut microbiome can predict whether they will respond to checkpoint inhibitors, one of the most significant advances in cancer treatment in a generation.
Agriculture stands to be transformed just as profoundly. The soil microbiome — the invisible ecosystem beneath every field and forest — drives nutrient cycling, carbon sequestration, and plant immunity. Manipulating soil microbial communities offers a plausible path to reducing synthetic fertilizer use, improving crop drought resilience, and sequestering atmospheric carbon at scale. These are not speculative futures. They are active research programs producing results.
In 2016, this frontier was real, large, and seriously underexplored. The research questions weren’t manufactured for a press release. This wasn’t a vanity project. The science was — and is — among the most consequential in biology.
And the presidential megaphone, despite its distortions, is a real instrument in ways that go beyond simple optics. Industry investment follows demonstrated government commitment — companies want to see federal support before putting their own dollars in. The Initiative generated buzz that translated into real new resources from non-federal sources. It also had a genuine scientific ambition at its core: to get researchers working across systems — comparing, for instance, the recovery of the Gulf microbiome after the Deepwater Horizon disaster with the recovery of the human gut microbiome after a course of antibiotics — to develop broad ecological principles that no single-system study could reveal. The goal was comparative microbiome science at scale. That was, and remains, a serious idea.
So, the question I kept returning to during that call and afterward wasn’t whether the Microbiome Initiative was good science policy. It was whether the way we announced and funded it was honest — and whether I had been honest with myself about my own role in it.
I don’t think I had been entirely. Jo has since reminded me that I had a choice. Collins made a different one. The pressure to participate is real, but it isn’t irresistible. The annoyance I felt on that call was legitimate — the gap between the headline figure and the new money was real, and the public deserved to understand that distinction. But the annoyance I should have felt, and didn’t quite feel until later, was at my own compliance.
And I was not alone in the complexity of that position. Jo was navigating her own version of it — a scientist of very high distinction, channeling her expertise into a process that was as much political theater as scientific strategy, trying to leverage the bully pulpit for science she genuinely believed in. We were both serving the machine. That’s what made the call feel the way it did.
A later chapter
I left government in 2018 and returned to George Mason, where I had been a professor for many years before my time at NSF. I came back to teaching and research with a different perspective — more impatient, perhaps, but also more aware of which scientific questions mattered to people outside the academy.
One of those questions turned out to involve the microbiome.
In 2020, I published a paper in PLOS ONE with Kyle Brumfield, Anwar Huq, Menu Leddy, and Rita Colwell—a comparative analysis of whole-genome shotgun and 16S amplicon sequencing methods using publicly available data from the National Ecological Observatory Network. Rita Colwell is one of the foundational figures in environmental microbiology and a former Director of NSF. The fact that I ended up doing microbiome science alongside her is the kind of irony the federal science system occasionally produces and almost never acknowledges.
The NEON connection deserves a moment. Readers of this newsletter may recall an earlier piece — “Nothing But Tundra” — about how I flew to Alaska during my NSF tenure to inspect a NEON construction site that the paperwork said was progressing on schedule and found nothing but primeval tundra stretching to the horizon. What followed was one of the hardest decisions of my time in government: firing the managing organization and bringing in Battelle to rescue the project. NEON eventually came online in 2019, fully operational, producing open ecological data across nearly two hundred data products.
The data in our 2020 paper came from NEON.
I don’t say that to take credit for the paper’s existence — the science belongs far more to my collaborators, and NEON’s data is freely available to anyone. I say that because it illustrates how federal science infrastructure works on timescales longer than any administration or initiative. The NEON I helped rescue produced the data that underpinned microbiome research I did after leaving government — research that sat within a scientific ecosystem the National Microbiome Initiative had helped legitimize and accelerate. These threads connect in ways that no press release captures and no budget line reflects.
I thought about that call with Dr. Handelsman more than once while we were working. She had done her job. I had done mine. The arithmetic had added up. And somewhere downstream of that transaction — through the relabeled dollars, through the rescued observatory, through the open data and the collaboration with Colwell — there was a team of scientists doing the work the headline had promised.
That team included me.
The money wasn’t new. But the science was.
Discoverers and Discoveries 