The Science Behind the Glow

Before the science there was a child, and that child was afraid of insects. He was born with a compromised immune system and had severe allergic reactions to any insect bite. Everything that flew or crawled in his neighbourhood in Abra Honda could hurt him. He was always fascinated by how the smallest things could hurt him so much. Until one night he caught a cucubano, a firefly, and it walked across his palm without stinging him. For many months he escaped his bed at night to go into the woods just to play with this wonderful thing that lit up but would not hurt him. One night his father saw him and followed him, and when he realized what his son was doing, he told him fireflies were a gift from Papá Dios, and that if he liked them so much he was going to take him to a place where many more lit up at night, but in the water. Several weeks later his father kept that promise and took him to La Parguera, and he sat by the glass bottom of a boat watching tens of thousands of green points race past underneath him. He asked his dad if they were also fireflies, and his dad told him that they were like them, but smaller, and that it was God’s presence revealing itself in front of them. That kid was nine and had no other explanation for what he was seeing, and he believed it. And that kid was me.

After almost forty years, life brought me back to the bioluminescent bay as I scouted places for my private experiences. And since then I stayed.

I am a man of faith, raised between a Catholic and a Methodist family. And since my father introduced me to it, the bay has been a place where I truly feel connected with the universe in a way only faith can explain.

But as I started curating what is today my most regarded private tour, I began learning how the glitter and the glow behaved and changed. Slowly I started to see patterns, noticing small changes, making notes about everything I saw. And without really noticing it, I started studying the bioluminescence, and the glow became my teacher long before the research did. Most of what I eventually read served to confirm something I had already watched happen.

This page aims to give you both: what the science says, and what and how I saw first.

The full story

It was the obvious one. How many places like this are there?

The first thing I found surprised me, because it was the opposite of what I expected. A single organism making light is not rare at all. Roughly three quarters of the animals living in the deep sea make their own light. But be honest with me, how many times have you seen it? In an aquarium, snorkelling, diving? Ever?

That did not make any sense to me. If it is so common, why does almost nobody ever get to see it, and why do we get to see it here every single night?

And that was the genesis of my years of research.

I quickly discovered that what is rare is not the light. It is that the conditions hold permanently enough to keep them at the density we have here. Rare enough that it manifests this intensely. Rare enough that on a bad night it is still unmistakable. And rare enough that when one of these bays dims for a few days, it makes the news.

Sit with that last one for a second. Nobody writes an article because the ocean did not glow last night. Here, going dark is a newsworthy event.

There are only five places on earth like that. Some sources add one in Costa Rica, and then another twelve to fifteen places where it happens seasonally.

But of the five, three of them are ours. Mosquito Bay on Vieques, Laguna Grande in Fajardo, and La Parguera in Lajas.

I sat with that for a long time. Puerto Rico is about three thousand five hundred square miles. You could drop this island into any one of the Great Lakes between two and nine times over and still have room. And this little piece of land holds more than half of the permanently bioluminescent bays on the planet.

And I will say the rest of it plainly, because I am a man of faith and I would rather be honest than neutral. Three of the five, on an island this small. It is difficult for any Puerto Rican to look at that and not feel we were blessed by the Creator of the universe with what may be one of the crowning jewels of His creation.

As a historian I am trained to be careful with the word miracle. As a Puerto Rican standing in that water, I have never found a better one.

That is the fact everybody repeats. Nobody ever seems to get to the question underneath it, which is the one that kept me reading for years. Why five? Why not five hundred? Why here?

The answer, when I finally assembled it, was almost uncomfortable to look at. It is not one condition. It is a stack of them, all of which have to be true at the same time, in the same place, in the same water, and if any single one is missing, the bay does not hold.

My research taught me these organisms want tropical temperatures, roughly twenty-four to twenty-nine degrees Celsius. I also learned that what I call regular water temperature is not that common, and it rules out most of the planet immediately. Warmth also slows down some of the things that eat them, which means the population lives under less pressure than it would anywhere cooler.

This one I had already felt without understanding it. I noticed it my very first time swimming there. Not only was I more buoyant, but one bit of water in my mouth felt like pure salt. It was after doing all three that I realized they were all extremely salty. At La Parguera we even have salt flats behind the mangroves. But why were they so salty? I did what since my school days I have always done best: research, and find out why. And was I in for a surprise.

What I found is that the salt is doing something far more important than holding us up. It is a filter. Very few competitors and very few predators can tolerate it, so one species gets to dominate that water in a way it never could out in the open ocean. The thing that makes you float is the same thing that makes the bay possible.

This is the condition most people underestimate or misunderstand, and it is the one I find most beautiful. Entering the bay before the night went dark made me realize the entrance was so shallow you could see the bottom, and one day I asked my captain to let me jump in there, and it was so shallow I could stand with my shoulders still out of the water. Again, that was something new to me, and I spent the next few days buried in the web looking for an answer.

What I found was that the opening to the sea has to be small enough and shallow enough that the population does not simply wash out with every tide, but not so closed that the water goes stale. It has to allow enough exchange to renew, and not so much that the bay empties itself. And it made me realize that balance, like in life, is the whole thing. A few feet wider or a few feet deeper and there is no bay, there is just a cove.

Another thing I discovered after visiting all three is that they are all ringed in red mangrove. That took me back to my computer, and again research taught me that those mangroves were part of the delicate equilibrium required to have bioluminescence all year long. I learned that the leaf litter breaking down in that water is actually the food source of the dinoflagellates.

And learning this taught me that it is the one I want people to sit with, because it is the one that, by being careless, we can destroy. No mangrove, no bay. It is that direct. Clearing mangrove off a coastline is not a landscaping decision, it is a decision about whether we want the light to stay.

So: warm, salty, enclosed but breathing, mangrove-fringed, tropical, with exactly the right hydrodynamics. Put all of that on a map at once and the map gives you five places, and three of them are close enough to my house that, well planned, doing all three in a single night is a doable challenge, one I will soon prove can be conquered.

I thought I had the list and that I understood it all. I did not.

I have to confess I have always been the go-to man when anyone wanted to know something. From winning the science fairs in my school years, to calling out history teachers when they said something I knew not to be true, or repeated outdated information. I was the one kid who would read every book he was handed in a few days, and who would still remember what he read forty years later. I still am.

My fascination with the bay has me researching bioluminescence all the time, and I even have AI bots that scan weekly for new research and scientific papers about it. That continuous learning process allowed me to discover a sixth condition, one that only a handful of scientists even know about, and one that nobody, myself included, would ever have guessed. I found it buried in a six-year monitoring study of Laguna Grande, and it stopped me cold in my tracks.

After six years, the researchers found that the strongest blooms line up with periods when the salinity drops slightly. Not fresh water, still very much the sea, going from about 35.5 parts of salt per thousand down to 34.4. That is the equivalent of about one tenth of a percentage point. A change so small we would never feel it. And yet it is the single strongest environmental correlation they found to the bloom periods.

Immediately I assumed that meant rain, but as I kept reading I discovered it does not. Then I thought about the nearby river, and I found out the scientists had checked the river discharge into that lagoon and it correlated with essentially nothing. Neither local rain nor river flow is what causes that minuscule but so significant change in salinity.

I was intrigued, and as I dug deeper into the study the true source emerged in an incredibly surprising way. The water comes from South America.

I read it and could not credit what my eyes were seeing. I went back to check whether I was missing or misunderstanding something, but I was not. As I kept reading I learned that plumes of lower-salinity water from the Orinoco and the Amazon push north through the Caribbean between August and November, driven by the trade winds, and they arrive here, and our two bays in the east respond.

I want to say that plainly, because I have not stopped thinking about it since I read it. Incredible as it sounds, the high season of the bioluminescent bays of Puerto Rico is set by the Amazon River. Rain falls on a continent I have only visited a handful of times, runs down rivers I will never see, crosses an ocean, and weeks later I watch the bays reach their peak as we paddle over water whose salinity has been very slightly diluted by the mighty Amazon.

After this, all I can say is that you might want to question my faith. What you cannot question is how incredible this single fact is.

For a long time I explained to my guests that the mangroves were fertiliser. Leaves fall in, they break down, they release nutrients, the organisms use those nutrients to photosynthesise, and the bay glows. I said it more than a hundred times. It is not wrong. It is just incomplete, and the part I was missing, which I learned through never-ending research, turned out to explain something that had been bothering me for years.

I am always coming up with questions. That is my nature. And by observation I had realized that if these organisms lived, as I believed, on sunlight alone, three overcast days in a row would flatten a bay completely. But even having watched La Parguera, my bay, dim on runs like that many times, the reality is I had never once watched it go out, and I could not account for how they were still generating any charge at all.

And then again, this six-year study showed me the light. These organisms are mixotrophs. It is a fancy word that simply means mixed feeding, mixo, mix, and troph, feeding, or that they have two ways of feeding. I already knew they charged through photosynthesis. They carry chloroplasts and they run on sunlight like a plant. And I also knew they fed on the decaying leaves from the mangroves. But what I did not know is that when they cannot use photosynthesis to charge, they can still take energy from the organic matter suspended in the water. That explained what I had already noticed and experienced. They have two engines, not only one.

And the research that established this for our species was done in part at La Parguera. My bay.

And here is what it explained. A second way to eat is part of the answer. When the sun fails them, they are not helpless. They use what the mangroves give them.

The species responsible in our bays is Pyrodinium bahamense. They are single-celled dinoflagellates, twenty to fifty microns across, which means you would need somewhere between five hundred and thirteen hundred of them lined up to span a single inch, depending on the size of the cell.

They are not static. They swim with two whip-like tails called flagella, one wrapped around the middle and one trailing behind, and the combination makes them spin as they move. That detail matters more than it sounds. These things are not drifting. They are going somewhere, on a corkscrew path, all night long, under everybody. How, and why it matters, is worth explaining.

A drifting particle goes wherever the water takes it. A swimming organism can hold its position, climb, or drop. Part of why a bay holds its density is that the cells are actively staying, not passively accumulating.

Many dinoflagellates also migrate vertically, rising toward the surface at night and sinking during the day. If that holds true here, it would explain something practical about my bay, where the light sits in the water column, and why so much of what we see happens in the top few feet at the hour we are in it.

And now I have to admit something.

I have spent more than three hundred nights in the water with these organisms. I have filmed them for years. I have had thousands of them sitting on my skin, blinking, close enough to my eyes to touch. And I have never once seen one.

Not one. Not ever. They are far below anything the human eye can resolve. I first saw what they actually look like in a photograph, years into all of this, and later through a microscope.

So everything I know about them from the water, and I know a great deal, I learned entirely from their light. That is the only part of them any of us will ever see with our own eyes. We have all been staring at something invisible and calling it beautiful.

I am a historian by training and by temperament, which means I have a low tolerance for a record that stays wrong because nobody bothered to check it. This is one of those, and for several years I helped spread it. You will read in many places, including things I wrote years ago, before I knew better, that the word dinoflagellate comes from Greek words meaning fire and whirling. It is repeated on tour sites, in articles, on signs. But as always, research showed me that I, and everyone else, had it wrong.

Dinoflagellate is dinos, Greek for whirling, and flagellum, Latin for whip. Whirling whips. It describes how the thing swims, and there is no fire in it anywhere.

The fire is in the other name. Pyrodinium is pyr, fire, and dinos, whirling. The whirling fire. That is the genus, not the group, and whoever christened it in 1906, working in the Bahamas with nothing like the instruments we have now, understood exactly what he was holding. He gave it the better name.

This part I got wrong for a few years, and through those years I explained it equally wrong, because it is still wrong on most of the internet today. So let me be careful with it.

I knew the reaction needs two things to happen. Luciferin, the molecule that emits light when it is oxidised, and luciferase, the enzyme that drives the reaction. I also knew both are stored together inside tiny compartments called scintillons, which sit along the inside of the cell membrane.

What I used to say, because it is what we will still read almost everywhere, is that the cell releases luciferin and luciferase into the water. It does not. My continuous research taught me that nothing leaves the cell. Not one molecule. I finally had it right: the entire reaction happens inside the scintillon, in a space too small to picture, and what reaches our eyes is light passing out through the cell wall.

That is not a mere technicality. Think about what it would mean if the other version were true. If every one of those organisms were dumping its chemistry into the bay each time you moved your arm, the whole thing would burn itself out in a single night and there would be nothing left by morning. Instead every cell keeps its machinery, opens and closes the door to let the reaction happen internally, and does it again. And again. And again, all night, for as long as you keep moving.

What triggers the reaction is entirely mechanical, and explaining it defies our understanding because of the scale at which it happens. The dinoflagellates are whirling close to one another, and something deforms the cell. Your arm passing through the water. A fish. A paddle. The hull of a boat.

That deformation fires an electrical signal across the membrane, which opens channels and lets protons flood into the scintillon. The protons drop the pH inside it sharply, and that drop in acidity is the switch. It turns the luciferase on. The enzyme goes to work on the luciferin in the presence of oxygen, the molecule oxidises, and it lets go of its energy as a photon of blue-green light at around four hundred and eighty nanometres.

All of that complicated sequence takes about a tenth of a second, which is why it reads to us as a spark and not a glow.

I remember exactly where I was when I understood that the switch is acidity. I was at the Vanderbilt hotel, waiting for some guests, and when I read it, it gave me such a eureka moment that I almost jumped out of my chair. For years I had assumed it was something like an electrical contact, a simple on and off. Discovering that it was not was an experience in itself. Now I knew that every one of those sparks is a change in pH inside a compartment smaller than a wavelength of the light it makes. And I understood that when I move my arm through that water I am not flipping a switch. I am changing the whole chemistry of several hundred thousand tiny rooms at once, and each of them answers me with a burst of light.

Then I found something that I still think is the strangest fact in all of this. They do not simply glow because it is dark. They run on a circadian clock, which means they have adapted to where they live and already know when it is day and when it is night. Take them to a dark spot during the day and you cannot trick them into glowing.

Yes, exactly as you read it. Scientists have taken them into a laboratory, held them in total darkness around the clock, removed every cue about what time it is, and they still did not flash during what should have been daytime. Not that they could not. Their clock told them it was still daylight.

They are, in the most literal sense available to a single cell, asleep.

This means the bay keeps its own hours. It knows when it is daytime and when it is night, and it does not depend on the sun to tell it. I still find that more amazing than the chemistry itself.

For years I explained the glow the way everybody does. It is a defence mechanism, I would say. The flash startles the predator and the predator refrains from eating them. A burglar alarm.

Research taught me that this is almost certainly not what is happening, and that the real answer is far better.

A copepod eating dinoflagellates is not frightened by a flash of light. Why would it be? But that flash makes the copepod visible, in an ocean that is otherwise completely dark, and there are fish out there whose entire diet consists of eating copepods.

The light, I learned, does not save the cell by scaring off its attacker. It saves the cell by getting its attacker eaten.

So I was right about the alarm. But it is not an alarm that frightens the burglar. It is one that calls the police.

And that helped me understand something about what we are doing out there that I had only partly understood. When we are swimming or treading water in the bay and every movement lights up around us, we are triggering several hundred thousand distress calls, from organisms that, having no eyes, have mistaken the flow of water created by our arms for something coming to eat them, each one screaming for help in the only voice it has.

That is what all that beauty is. And now that I fully understand it, I cannot help being moved by it, even after more than three hundred times in there.

There is one more thing about Pyrodinium bahamense, and it is the one that keeps me humble about all of this.

In much of the world this species is not a wonder. It is a problem. It is a well-known cause of harmful algal blooms, and in some regions it produces saxitoxin, which accumulates in shellfish and causes paralytic shellfish poisoning. Fisheries get closed over it. Livelihoods end. People have died from eating contaminated shellfish where this organism blooms.

The same creature. The same machinery. Put it in the wrong water and it is a public health emergency. Put it in ours, under the conditions I described above, and it becomes something people cross oceans to experience.

I do not think that is an accident of luck. But I am a man of faith, so I would say that.

Is the water safe?

Everything above this line is published, and I am only reporting how I learned it and how it helped me understand our bays. What follows is not, and I want to be honest about the difference, because a page like this is only worth anything if you can tell which is which.

These are three things I have watched happen that I have never found written down anywhere.

They charge by day, through photosynthesis, and they only discharge when something moves the water. So the state of the bay on any given night is not really about that night. After several overcast days with boats going in and stirring them up every single evening, the whole bay reads dim, not because of the clouds overhead right then, but because of the accumulated draw of the nights before. A quiet bay after three cloudy days behaves nothing like a busy one. You cannot see that unless you are there for all of it, night after night, which is exactly why nobody has written it.

The worst night I ever had, four inches of rain had fallen in a day. Fresh water is lighter than salt water, so all of it sat on top like a lid, and from the surface that bay looked dead. Flat black. Nothing. I got underneath the platform and the light was all still there, below the fresh layer, exactly where the salt water was, completely untouched. A bay that looks dark from six feet above the surface is not necessarily a dark bay. It may only be a bay you are looking at from the wrong side.

The Laguna Grande study recorded monthly lows of a few thousand cells per litre, which is effectively off, and that is where the bioluminescent blackouts you may have read about in the news come from. In three hundred nights I have never seen La Parguera off. It goes down. It has slow stretches. But it does not fall through.

I believe the answer is geography. Laguna Grande sits up where the Atlantic and the Caribbean meet and depends on currents pushing lower-salinity water up to it, while La Parguera is already in the Caribbean, not waiting on a delivery. It is the same reason the sargassum current runs past us to the south and never comes in. But I want to be very clear that this is what the empirical data from three hundred nights gives me, not a finding in a scientific study. Nobody has studied it. I wish somebody would, and I would hand them everything I have.

After all of it, the chemistry, the clocks, the salinity, the Amazon, this is the part I keep coming back to.

If somebody had written this into a novel, an editor would have sent it back for being too much. Water that answers your body. Invisible things that scream in light. A bay that sleeps by day even when you lock it in total darkness. It reads like science fiction, except nature does it.

And it is literally out in my backyard. That is how small this island is. Lajas is my backyard, and so is Fajardo, and so is Vieques. We all share the same one.

I will close by sharing what my father told me: the bay is a divine manifestation revealing itself in front of us. I was nine years old. Neither of us had ever heard the word luciferin.

I have spent the decades since learning about proton gradients and scintillons and circadian clocks and salinity budgets and the plumes of the Amazon River. I have read every study I have found. I have taken hundreds of notes. I have filmed it more than three hundred times, documenting it, trying to understand a bit more of what I am looking at.

Every single thing I have learned has made it more remarkable, not less.

Nothing I have read has given me the slightest reason to think he was wrong.