You aren’t just an observer looking at the universe; you are a piece of the universe that has become capable of understanding itself

-A conversation with Dr James Aguirre 

By the time I finally connected with Professor James Aguirre, he was already settled in the David Rittenhouse Laboratory at UPenn, coffee in hand, surrounded by the quiet hum of machines and equations. He greeted me with the kind of relaxed warmth that instantly cuts through any formality. For someone who spends his days wrestling with the birth of the universe, he was surprisingly down-to-earth. 

“It’s always exciting to connect with fellow researchers,” he said, “especially those bridging the gap between engineering and the environmental sciences.” That line stayed with me. In a way, that’s exactly what this conversation was about: building a bridge, not just between disciplines, but between ordinary readers and a universe that can feel impossibly far away. 

I told him a bit about Nature Insights, how we’re trying to create a platform where people from all over the world can send messages to each other through stories, ideas, and science. This issue, I explained, was all about space, and after going through his research and watching his lectures, it felt obvious: if anyone could send a meaningful message from the universe to our readers, it was him. 

The universe as a glowing map 

When I asked Dr James to start with the “big picture” of the universe, he didn’t reach for equations. Instead, he reached for something we all know: a map of Earth at night. 

“Imagine you’re looking at a map of the world in the dark,” he said. “You see bright clusters of lights, cities, connected by highways, with huge dark patches in between, like oceans or deserts. The universe is organized in a very similar way, just on a scale that’s almost impossible to wrap your mind around.” 

In his world, this glowing map has a name: the Cosmic Web. Galaxies don’t just float around randomly; they line up along long, thin filaments made of galaxies and dark matter, like strands in some invisible three-dimensional spiderweb. Where those filaments intersect, you get enormous clusters of galaxies. In between, there are vast “voids”, huge bubbles of almost nothing. 

For Professor James Aguirre, this structure is not just pretty to look at; it’s the universe’s autograph. The way matter is arranged today, he explained, is a fossil record of the Big Bang itself. If you map where everything is right now, you can, in a sense, rewind the clock and watch the universe grow from tiny fluctuations in density into the enormous web we see today. 

He broke it down into three ideas. First, it’s our origin story: those filaments grew out of microscopic ripples in the early universe, so studying them means studying the physics that shaped everything we see. Second, it’s where the invisible players, dark matter and dark energy, show themselves, because the large-scale structure acts like a laboratory big enough to reveal their influence. And third, it gives context for life: you can’t fully understand a single star, or a planet like Earth, without understanding the environment it was born into. 

“We live in a tiny corner of a vast, interconnected web that’s been evolving for 13.8 billion years,” he said. “In my work, I’m trying to see the scaffolding of that web.”  He and his collaborators use instruments that let them look back to when this cosmic infrastructure was just starting to form. “It’s like trying to find the first few bricks in a skyscraper that now spans the entire horizon,” he told me. It’s poetic, but also literal: he is, in a very real way, hunting for the first building blocks of everything. 

The universe’s “teenage years” 

When we shifted to the evolution of stars and galaxies, his focus sharpened. The era Dr Aguirre cares most about has two names that sound like something out of a sci-fi novel: the Cosmic Dawn and the Epoch of Reionization. If the Big Bang was the universe’s birth and today is its adulthood, this period, he said, is its adolescence, and he is obsessed with it. 

For a few hundred million years after the Big Bang, the universe was a dark, featureless place, filled mostly with neutral hydrogen gas, a cold, thick “cosmic fog.” No stars, no galaxies, no light. Astronomers call this period the Cosmic Dark Ages. 

Then gravity started winning. Somewhere between about 200 and 500 million years after the beginning, clumps of gas collapsed to form the very first stars and black holes. These first objects were huge, unstable, and unbelievably bright. Their intense ultraviolet light began chewing holes in the hydrogen fog, stripping electrons from atoms in a process called reionization. Bit by bit, the fog lifted, and the universe went from dark and murky to transparent and illuminated. 

Dr Aguirre calls this era the “missing link” in our own story and gives three reasons why it matters so much. 

• It’s the forge of elements. The early universe only had the simplest elements, mostly hydrogen and helium. Those first stars were factories that built heavier elements like carbon, nitrogen, and oxygen. The atoms in your body, and even the steel in a campus building, can trace their lineage back to those first stellar “polluters.” 

• It’s when the universe became see-through. Before reionization, light couldn’t get very far without hitting neutral gas. Afterward, the universe effectively “cleared the air,” allowing light to travel freely. Without that shift, we wouldn’t be able to see distant galaxies at all. 

• It’s the blueprint of galaxies. The way those first bubbles of light formed and merged shaped how galaxies like the Milky Way would later look. Studying this era is like reading the DNA of our own galaxy. 

  
  

One of Professor James Aguirre’s major efforts involves HERA, the Hydrogen Epoch of Reionization Array, which sits in the Karoo Desert in South Africa. Interestingly, they are not trying to see the first stars directly, they’re too faint. Instead, he said, they look for the holes those stars carved into the hydrogen fog. 

“It’s like looking at a piece of Swiss cheese to understand where the bubbles came from,” he laughed. “We’re trying to catch the exact moment when the universe ‘turned on’ and became the complex, light-filled place we call home.” 

That’s also where, he added, the story of “us” really begins. 

Building a cosmic time machine 

At some point, Dr James Aguirre’s inner engineer took over, and the conversation shifted from big ideas to the tools that make those ideas testable. If the “what” of cosmology is the story, the “how” is the incredibly intricate machine we use to read it. 

To human eyes, the night sky looks like dark velvet dotted with stars. But that’s only a tiny slice of reality. JA works mostly in the millimeter and radio parts of the spectrum, far beyond visible light. There are two main reasons for that. 

First, there’s cosmic redshift. Because the universe is expanding, light from the very first stars and galaxies has been stretched as it travels across billions of years. What began as high-energy ultraviolet or visible light has been pulled out into longer wavelengths. By the time it reaches his lab, that light has shifted into the infrared and millimeter-wave range. If we only used visible-light telescopes, the most interesting parts of the early universe would remain literally invisible. 

Second, space is dusty. Clouds of tiny carbon and silicate grains act like smoke, blocking visible light. Millimeter waves, with their longer wavelengths, can slip through that dust. That lets astronomers peer into stellar “nurseries,” regions where new stars are being born, that would otherwise stay hidden. 

But knowing where to look is one thing; actually detecting those signals is another. When I asked him about the biggest challenge in building these instruments, he didn’t hesitate: sensitivity. 

The signals from the Epoch of Reionization are unimaginably faint. Over an entire year, the radio energy collected from a distant galaxy can be less than the energy released when a single snowflake hits the ground. To detect something that weak, you need a system that is almost absurdly quiet and stable. 

He outlined three major hurdles. 

• Radio Frequency Interference (RFI): Our world is loud. Phones, GPS satellites, microwaves, everything screams in radio frequencies. Those human-made signals are millions of times stronger than the cosmic whispers he’s trying to hear. That’s why telescopes like HERA sit in remote deserts, far from cities and their noise. 

• The “instrumental ghost”: The instruments themselves are so sensitive that they can end up “seeing” their own heat. The electronics in a telescope can drown out the signal from space, so the detectors often need to be cooled to near absolute zero, colder than deep space, just to stay quiet enough. 

• Precision calibration: Arrays like HERA are not just cameras; they’re huge, carefully tuned scientific instruments. If a single antenna shifts by a few millimeters because of wind or temperature changes, the data can be distorted. Keeping everything stable over years is a constant battle. 

  
  

“In short,” he said, “my job is to build an ear that’s quiet enough to hear a whisper from 13 billion years ago, while standing in a world that won’t stop shouting.” 

Then he smiled and added, “Honestly, astronomy is as much about being a plumber and a coder as it is about being a physicist.” 

Riding balloons, chasing first light 

When I asked what current projects excite him most, his answer made it clear that we are living through a turning point. For decades, astronomers were focused on simply detecting faint signals. Now, he said, we’re moving into an era where we can actually map them in detail. 

He talked about several projects that feel poised for breakthroughs. HERA, in its second phase in the Karoo Desert, is now a field of 350 fixed radio dishes. Instead of pointing it like a traditional telescope, they let Earth’s rotation sweep the sky across the detectors. The hardest part at the moment is “foreground removal”, stripping away the bright radio noise from our own Milky Way so the faint 21-centimeter signal from early hydrogen can emerge. It’s some of the toughest data analysis he’s ever done. 

Then there’s the BLAST Observatory, a balloon-borne telescope. They launch it into the stratosphere to get above most of Earth’s water vapor, which usually absorbs the light they want to observe. With BLAST, they use polarimetry, the measurement of light’s polarization—to study dust and magnetic fields in our galaxy and beyond, helping them understand how stars are guided into existence. 

He’s also deeply involved with the Simons Observatory in Chile’s Atacama Desert, designed to study the Cosmic Microwave Background (CMB), the afterglow of the Big Bang. One of its goals is to look for “B-modes,” tiny swirls in the polarization of the CMB that could betray the presence of primordial gravitational waves from the universe’s first instant. If detected, those patterns would give us direct clues about what happened in the first fraction of a second after everything began. 

Back at Penn, his group is working on something called the QUASAR project, developing quantum-dot-based spectrometers. These devices aim to detect individual photons with extremely fine resolution, a marriage of quantum engineering and cosmology that lets physics at the smallest scales illuminate the largest ones. 

When he talked about technological change, he described the shift from “single-pixel” detectors—where mapping the sky meant painfully scanning one point at a time, to huge arrays with thousands of detectors that can take in wide swaths of sky at once. Technologies like MKIDs, Microwave Kinetic Inductance Detectors, have made it possible to put thousands of sensors on a single chip and read them out with just a few wires. 

“So is this a golden age?” I asked. 

“Yes,” he said, “but with a catch.” We now have more data than ever and instruments more sensitive than previous generations could have imagined. At the same time, we’re “data-rich and information-poor”: the challenge has shifted from building detectors to building algorithms smart enough to find the needle in a multi-terabyte haystack. 

“We’re at the threshold where we stop wondering if we can see the beginning of time,” he said, “and start asking what those first moments are trying to tell us about the laws of physics.” 

Cosmic connectivity and a door waiting to open 

As our conversation turned toward teaching and the future, his tone softened. These are the questions, he told me, that follow him on late walks across campus or through quiet nights in the lab. 

If he could give people one fundamental idea about our place in the cosmos, it would be cosmic connectivity. Many of us look at the stars and feel small, maybe even insignificant. He wants us to flip that perspective. 

“You’re not just an observer looking at the universe,” he said. “You are a piece of the universe that, after billions of years of evolution, has become capable of understanding itself.” 

Every atom in your body once lived inside a star that exploded long before Earth formed. When we study the large-scale structure of the universe, we’re not just looking at anonymous points of light; we’re looking at our own origin story. Realizing that we all share the same ancestral home, a small, pale blue dot inside a vast web, should, in his view, inspire both humility and a shared sense of responsibility. In a world that often feels divided, the sky is, quite literally, something we all have in common. 

For young researchers, especially in fields like engineering, his advice is simple: don’t be afraid of the “hard” hardware. We may live in a digital age, but the universe still speaks in physical signals. We need people willing to get their hands dirty building the next generation of sensors and telescopes. 

When I asked him to imagine one breakthrough over the next five years, he didn’t hesitate. He wants a direct detection of the 21-centimeter signal from the Cosmic Dawn, the moment when the first stars turned on. Right now, we have theories and indirect hints, but not a clear, direct measurement. 

“It’s like knowing there’s a party behind a closed door because you can hear the music,” he said. “But you haven’t opened the door yet.” 

Detecting that signal with HERA would be that door opening. It would tell us when the first stars formed, how big they were, and how quickly they changed the universe. It would carry us from the Dark Ages into the light of certainty. 

He’s also watching the Simons Observatory closely. A confirmed detection of B-mode polarization in the CMB, the fingerprint of gravitational waves from the universe’s earliest instant, would shake our understanding of gravity and the Big Bang. 

As we wrapped up, JA circled back to the mission of Nature Insights. Sending “a message from everyone to everyone,” he said, is exactly what the universe has been doing for 13.8 billion years. It has been broadcasting its story in light and radiation all this time. It just took us a while to build the right antennas, and the right questions, to finally start listening.