Below the Edge of Darkness Read online

  That tree is gone now, long ago chopped down and replaced by something more classically tree-like. My perception has outlived the reality. I can recall the shape and placement of its branches, the feel of its corrugated bark, the earthy smell around the base of the trunk where its roots extended toward the pond. Upon my return from the hospital, I saw that tree with much greater appreciation for the act of seeing, which made me think more deeply about what I was seeing.

  We connect to nature through our senses, but that’s not the only way to see. Over time I have added layers to the memory, greatly expanding my understanding of the how and why of treeness. Knowing how a tree carries water and nutrients from its roots to its leaves, and sugars from its leaves to its roots, and how willow bark harbors aspirin-like compounds adds layers of significance to the memory.

  It is easy to understand why a tree is the living thing most often used to symbolize the human need to connect to nature. Poets and conservationists pen odes to “a tree called life” because it is a living being that nearly everyone has experienced firsthand. But how do we connect to nature on the much broader scale upon which we are now impacting it? We live on an ocean planet, but we have very little understanding of what that actually means. Ours is a living, breathing water world, filled with creatures whose existences are so utterly alien to our own, it’s a significant struggle to relate to them.

  How we choose to perceive the world around us shapes our existence. We believe we see the world as it is. We don’t. We see the world as we need to see it to make our existence possible. At least that used to be true, but our world is changing so rapidly that we need a bigger picture of what makes life possible. We can’t just look to trees to understand the intricate workings of the natural world. We must include the ocean and its myriad astonishments in a wider, wilder view. To look at the surface of the ocean without knowing the sparkling web of life that is woven through its depths is to be blind to its wonders and the part it plays in making our existence possible.

  Skip Notes

  *1  In metric units, that’s ten microns and thirty centimeters, respectively; in American units, it’s one-tenth the thickness of a dollar bill for the former and one-fifth as tall as Danny DeVito for the latter.

  *2  Actually, at 103 acres this is more of a lake than a pond, but in New England “pond” is often used in reference to some of its lakes’ origins as “kettle hole ponds,” depressions left by receding glaciers.

  *3  The time between the traffic light turning green and the cab behind you starting to honk.

  *4  Dwight Harken (1910–1993), known as the father of heart surgery, was chief of thoracic surgery at Peter Bent Brigham Hospital in Boston and Mount Auburn Hospital in Cambridge from 1948 to 1970. That appointment meant that his and his team’s being at Mount Auburn that day was somewhat less of a miracle than I was originally led to believe—unless you factor in the traffic between Boston and Cambridge.

  *5  Nerd note: I wonder if NDEs might be an evolutionary adaptation allowing rational thought and calm in such extreme, life-threatening circumstances, where adrenaline and panic might otherwise result in further, self-inflicted damage.

  *6  Preferably with their permission.

  *7  Either they hadn’t administered enough local or my brain was interpreting pressure as pain. Much later, one of the surgical nurses who was on duty that night admitted that she had never seen anything like what they saw when they opened me up. After they cleared all the necrotic tissue away, she said, there was a cavity big enough to stick a man’s fist into.

  Chapter 2

  FIAT LUX*1

  Spitting into my mask, I scrubbed the inside of the faceplate to prevent fogging. The sun had just disappeared below the horizon and the sky’s light was rapidly fading. It was 2012, and I was off the Caribbean island of Saba with a bunch of folks who had come out on this dive boat because I suggested they might see bioluminescence, though I had never been diving here and couldn’t be sure. We all donned snorkel gear and slipped from the boat into the warm tropical waters.

  Floating at the surface, I eagerly scanned the sandy bottom ten feet below. Out of the corner of my eye I thought I saw something. Was that a glowing spot in the sand? When I looked directly at it, it seemed to disappear. But a little while later there was another, and another. Then I heard somebody shout, “Hey—look at that!” Someone else managed a muffled “Wow!” into their snorkel as more and more of the blue lights appeared and then began rising off the seafloor like strings of glowing champagne bubbles. In just moments we were surrounded by the ephemeral chasing lights that are the mating displays of sea fireflies.

  These remarkable little creatures are crustaceans called ostracods, which aren’t much bigger than sesame seeds but are capable of producing copious amounts of light. Their common name comes from the fact that they use their bioluminescent displays as fireflies do on land—to attract mates. It’s the males that put on the show; they emerge from Caribbean reefs, seagrass meadows, and sand just after twilight, and as they swim through the water they squirt out discrete globs of light that are a mix of their light-producing chemicals held together with a dab of mucus. The lights appear and then disappear sequentially. For some of the people on that boat, it was the first time they had ever seen bioluminescence, and they were totally captivated and awash with questions.

  The first time I saw bioluminescence was in my backyard. Mine is a quintessential childhood memory: fireflies flashing their lovers’ code on a warm summer’s eve as I ran barefoot in pursuit, stirring up the heady green smell of freshly mown grass. Catching these living lanterns was easy. I could hold one in my cupped hands and peek between my palms to watch its abdomen flare. How does it do that? I marveled. It’s a question not easily answered. If you try to take a firefly apart to see how it works, the first thing you have on your hands is a nonworking firefly.*2 However, holding it gives at least one clue to its sorcery. Bioluminescence is cold light. This seems surprising, because, based on our everyday experiences with the sun, candle flames, and incandescent lightbulbs, we associate light with heat. Nevertheless, they are not inseparable.

  All light comes from atoms. Picture the simple Bohr model of an atom, where negatively charged electrons orbit a positively charged nucleus and the orbits are represented as concentric shells. Different distances from the nucleus represent different energy levels. Electrons in the orbits nearest the nucleus have the least energy. If an electron absorbs enough energy, it jumps to an outer orbit and then, when it falls back down to its ground state, it gives up energy as a packet of light called a photon. All light is generated by this same basic process. The only distinction between different kinds of light is how the electrons get excited in the first place.

  In a candle flame, say, or an old-school lightbulb, the electrons are excited by thermal energy, in which case the light is called incandescence. The prevalence of such sources is why we associate heat with light. But there are other means of excitation, such as a chemical reaction, in which case the light is called chemiluminescence. Bioluminescence is a special case of chemiluminescence, distinguished by the fact that the light-producing chemicals are synthesized by living organisms. Light sticks, which emit light but not heat, are another example of chemiluminescence, one where the chemicals are manufactured by humans.

  Any light that isn’t caused by incandescence is lumped under the heading of luminescence. Besides bioluminescence and chemiluminescence, there are more obscure phenomena like sonoluminescence, caused by sound, and triboluminescence, caused by the breaking of chemical bonds.*3 Two more common examples of luminescence, fluorescence and phosphorescence, frequently get confused with bioluminescence, but they’re not equivalent, because their excitation energy comes from light rather than from a chemical reaction.

  Something that is fluorescent absorbs light of one color and re-emits a different, longer-wavelength
(i.e., lower-energy) color. Black-light posters, for example, absorb ultraviolet light that is largely invisible to our eyes—which is why it’s called black light—and re-emit it as a visible color. A fluorescent lightbulb is so called because the inside of the glass tube is coated with a fluorescent material that absorbs the UV photons emitted by gas atoms in the tube, and emits visible photons. This is accomplished with almost no release of infrared light (heat), which is why you can touch a fluorescent bulb without being burned.

  Phosphorescence is not bioluminescence, despite how often you hear the words equated. It’s a very common misconception that has been repeated so many times it borders on a disinformation campaign. Phosphorescence, like fluorescence, is excited by light, but with an added delay in the re-emission, making it the basis of the fearsome glow-in-the-dark decorations and toys sold at Halloween. Part of the confusion between phosphorescence and bioluminescence stems from descriptions of bioluminescence as resembling “liquid phosphorus.” Certain forms of chemical phosphorus produce a dim glow, and as a result, the word phosphorescence was originally coined to describe things that glow without burning, but, in fact, the glow of phosphorus is not phosphorescence but rather the result of a chemiluminescent reaction.

  I’ve often thought that it’s too bad there isn’t an alternate word for bioluminescence, because the fact that people find it difficult to spell and pronounce has contributed to its relative obscurity. Years ago, I worked with an artist to create a coloring book about bioluminescence that included glow-in-the-dark paints. Since the whole idea was to share the feeling of pure wonder, I struggled to find just the right title. I thought The Living Lights Coloring Book would do but then rejected it because it might be mistaken for something to do with religion and went with a more scientifically accurate but less approachable title, The Bioluminescence Coloring Book—which may be why we still have several thousand of these masterworks in storage.

  The names of the chemicals that produce the light in a bioluminescent reaction are a bit more manageable: luciferin and luciferase. That terminology was the invention of the French physiologist Raphaël Dubois (1849–1929), who is generally credited with ushering in the modern era of bioluminescence research. Working with a bioluminescent click beetle and later a bioluminescent clam, he demonstrated that their light-producing chemicals could be extracted using an experimental approach involving hot-water and cold-water extractions. When the tissues were ground with cold water, he got light emission for several minutes before it went dark. Hot-water extracts, on the other hand, did not produce light, but when the now-dark cold-water extract was mixed with the hot-water extract, he discovered that he could reactivate the light emission.

  Dubois called the substance from the hot-water extract luciferin and the substance from the cold-water extract luciferase. The terms were derived from lucifer, which means “light-bringing” in Latin (from lux, or “light,” and ferre, “to bring”). The suffix -ase is traditionally used to name enzymes. Enzymes are large, complex molecules that are destabilized by heat, while substrates are generally much smaller, more stable molecules. Therefore, Dubois made the following deductions: (1) While both the enzyme and the substrate were initially present in the ground-up cold-water extract, the substrate, which he called luciferin, was used up in a matter of minutes and the light extinguished. (2) The hot-water extract did not produce light initially, because the heat denatured the enzyme, leaving just the heat-stable luciferin. (3) Mixing the hot- and cold-water extracts was therefore the equivalent of mixing the heat-stable substrate, luciferin, with the heat-labile enzyme, luciferase.

  Dubois’s terminology is still used today, but it sometimes causes confusion because people believe the names refer to specific chemicals. They don’t. They are generic terms used for any bioluminescent substrate or enzyme, of which there is a surprising variety.

  That there are so many different bioluminescent chemicals is a testament to how important bioluminescence is. The ability to produce light is so critical to survival that it has been selected for independently more than fifty times during evolutionary history. This is known as “convergent evolution,” where creatures that aren’t closely related evolve similar traits in order to adapt to similar circumstances. For example, although sharks and dolphins share analogous streamlined body shapes and fins of comparable form and function, this is not because they are closely related genetically; sharks, after all, are fish, while dolphins are mammals. Rather, that particular body plan works well for maneuvering through water and therefore provides an advantage—allowing them to catch more food and evade more predators and thus survive long enough to pass on their DNA.

  In the case of bioluminescence, many very different animals solved the problem of how to survive in the dark the same way: Make your own light. In textbooks on evolution, the classic example given for convergent evolution is eyes, like those of squid and octopods (invertebrates) and those of fish and humans (vertebrates). In both cases, the eyes are camera-like in that they have an iris and a lens at the front that focuses light on the photoreceptors at the back. However, while the photoreceptors in the cephalopod eye face toward the lens, for vertebrates they face away—clear evidence of their independent origins.

  In fact, eyes have evolved independently more than fifty times, appearing in diverse animals like jellyfish, flatworms, flies, mollusks, fish, and whales, in a variety of forms, from simple pits or eye spots to more elaborate camera-like eyes and complex compound eyes (sometimes called bug eyes) consisting of thousands of individual light-gathering units. This is similar to how many different times it’s thought that bioluminescence evolved. However, there is one remarkable distinction. All eyes depend on the same chemistry—a light-sensitive protein called an opsin—while the luciferins and luciferases that make bioluminescence possible are unique in different groups of animals.

  The independent origins of such disparate chemical systems in so many different groups of animals are not only a stunning testament to just how critical bioluminescence must be to their survival but a treasure trove for science. Like Prometheus stealing fire from Zeus to give to mankind, scientists have found all manner of ways to harness living light—using chemicals extracted from bioluminescent organisms to illuminate the inner workings of cells and test for life processes and key molecules.

  One chemical, green fluorescent protein (GFP), extracted from a bioluminescent jellyfish, has so advanced human understanding of cell biology that the impact of its discovery has been equated to the invention of the microscope. Bioluminescent sea fireflies have provided the means to image tumor tissues and test the effectiveness of anticancer agents in a single animal, instead of having to sacrifice large numbers of animals at different times to study the effectiveness of the treatment. The bioluminescent chemistry of terrestrial fireflies is routinely used to test for bacterial contamination and, less routinely, to test for the presence of life on Mars. There are many more examples. There are also remarkable numbers of bioluminescent chemistries still awaiting discovery, and new applications to be invented that could lead to equally phenomenal breakthroughs.

  However, even where we have identified what chemicals are involved in producing bioluminescence, that still doesn’t answer the question How does it do that? Saying that we understand x because we know y would be akin to claiming that you understand how a car works because you know it runs on gasoline. There’s a bit more to it than that.

  The fact that I became involved in research that asked that very question of a different light-producing organism had nothing to do with my youthful musings on the subject. In fact, I think it’s safe to say that I gave no thought whatsoever to how animals make light for almost two decades after my childhood firefly encounters. Rather, my obsession with bioluminescence grew out of my brush with blindness.

  * * *

  —

  I saw the world very differently after I got out of the hospital. There were m
oments of surpassing joy for the act of seeing, but there were also moments of unfamiliar doubt. I had regained sight but lost the supreme confidence of youth that anything is possible. I learned the hard way that the two sides of the anything coin might include bad just as easily as good, which meant I felt the need to consider possible negative outcomes and try to always have a plan B.

  It is a measure of just how much my worldview had shifted that when I returned to Tufts in the fall of my sophomore year, I changed my major from marine biology to premed. As it turned out, this was a temporary detour, but at the time it was a significant upheaval of my life’s plan. I had held firm to the goal of becoming a marine biologist since I was eleven years old.

  That year, when kids my age would normally be in sixth grade, was transformative for me. Up until then I had been a mediocre student. I had always hated school and, as a result, had paid little attention to anything my teachers were saying, merely biding my time by daydreaming until I could get home and be outside. But the year I turned eleven was a year of travel that woke me from my reverie. My parents were Ph.D. mathematicians, and that year was a sabbatical year for my dad, who was a professor at Harvard. My mother, who had given up full-time teaching to raise my brother and me, resigned her part-time position at Tufts to spend the year abroad.*4

  My brother, eleven years older, was married by the time I was ten, so it was just me and my parents that year. The plan was to spend half the year traveling and half in Australia, where my dad had a Fulbright fellowship at the University of Melbourne. Since I would be out of school for most of the year, Mom and Dad would be my teachers. Homeschooling wasn’t a thing in those days, and this was considered a bit unorthodox. However, since the primary focus of the sixth-grade curriculum was world history and math, and I would be traveling around the world visiting historical wonders with a couple of mathematicians, my school grudgingly conceded that I might survive the academic deprivation and ultimately decided that I would be allowed to come back into the public school system without having to stay back a year.