Ode to Biology

The Study of Life

It’s time to get back to the basics.

As a scientist who has found inconvenient things throughout COVID, I’m proud of my discoveries yet saddened by what I experienced as the inefficiencies of science. From when my forecasts suggested a pandemic could lead to surges in NYC in March/April 2020 and I was told I was not an epidemiologist to when I helped Drs. Bruttel and Van Dongen quantify just how unnatural SARS-CoV-2 is as an Ikea virus with a built-in reverse genetics system, I’ve gone so far in the frontiers of knowledge that it feels rather lonely, distant and unrelatable. My inconvenient findings have thrust me into an epistemological warzone of science, and, in the fog of academic war, it feels at times as if I’ve lost sight of the beauty of biology, the awe and wonder that drew me to science in the first place.

In the madness of the mosh pit, I’ve forgotten about the music.

Yesterday, as I hopped out of my car from an invigorating day at work, I saw a lizard on the fence, and I heard the music again. The lizard was a Sceloporus undulatus, or Western fence lizard, a short, stubby, smooth-looking but spiny-feeling lizard that often has a bright blue throat and belly. This particular lizard was a baby. Just a few months ago, I remember seeing a pregnant (‘gravid’) mother on our fencepost and I told my wife: that’s one pregnant lizard. Sidebar: my wife thought it was ridiculous that I could tell a lizard was pregnant from half a yard away, but these are some of the fun things you learn from years spent raising and catching lizards. Now, there’s a baby lizard running around our fence. The baby lizard looked me in the eye briefly until instinct kicked in and it ran like its life depended on it.

Life. Life is so subtle and complex in its beauty, it’s easy to take it for granted. It’s easy to get so caught up in our human affairs that we lose sight of the miracle of life. Yet, whenever I feel like I’m losing sight of the beauty, I remember when I was a kid riding on a train to my grandparent’s house in Iowa and my mom pointed to the world outside the train. “Everything you see out there is wild”. She told me all about how the sun is a giant ball of fire, shooting energy in the form of light all the way across space to hit our planet, how plants breathe in C02 and use that energy to make sugars, breathing out the oxygen that we breathe in.

Take a deep breath. Your diaphragm is a muscle fueled by sugars, many of which were made by plants, and that muscle helps your lungs expand to take in the air around you. Feel the satisfaction as oxygen moves from your lungs to your blood, as carbon dioxide moves from your blood to your lungs. That oxygen bound to hemoglobin and pumped through your veins to all your grateful cells has its own biological story. Every single molecule of oxygen you’ve ever breathed in came from a plant somewhere. Now, exhale. That carbon dioxide you breathe out is used by plants to make the sugars you eat and the oxygen you breathe. We breathe out a molecule that plants breathe in to give us the oxygen we breathe. Every single breath we take is an ode to Earth’s living systems, to plants that produce oxygen and sugars.

It’s easy to forget that. How many breaths have we taken without thinking about the community of plants that made the oxygen for us?

A lot of animals eat plants. Strictly herbivorous animals often have big bellies because they need to host a bunch of microbes in a vat inside themselves to degrade the tough sugars in plants. Every time you see a cow eating grass, look at its massive belly and think about the microbes living inside that belly. The cow owes its life not just to the plants that make oxygen it breathes, but also to the plants it eats and the microbes that help the cow digest it. Every time you eat a plant, you are also not able to digest the tough sugars alone, but rather microbes in your GI tract break down the plants from complex and tough sugars into simpler compounds that we can absorb through the lining of our intestines. If you are a vegetarian, you owe your life to the easy-to-overlook microbes that help you convert those plants into nutrients your body can use.

Animals that eat plants are often afraid of other animals that eat animals. The predators that eat other animals will go to great lengths of speed or stealth to completely end the life of another animal, not from malice but merely need. An animal that eats another animal will consume its tissues, convert the tissues of its food into the blood and muscle that powers it, and prowl on. Every carbon and nitrogen and phosphorus atom in that animal’s body came from another plant or animal. Atomically, we are what we eat.

Your muscles contain fibers whose contractions help you run, swim, climb, move your eyes across the page, or smile. The muscle fibers are made of amino acids, amino acids have nitrogen, and every nitrogen atom in every amino acid in every muscle fiber of your being came from something you ate at some time in your life. How easy is it to forget that every step I take is guided by nitrogenous muscle fibers assembled from the food you ate last week, last month, and even last year? Think of a single meal containing either beans or meat that you ate over a week ago - nitrogen from that exact organism is now lodged inside your muscles, and you may carry such nitrogen with you for as long as you live.

There are herbivores, there are carnivorous predators, and there are pathogens. From the eyes of a pathogen, the world is full of titans. Some pathogens seek out massive single-celled bubbles while others seek out multicellular metropolises of many massive cells. Pathogens are nifty little rogues that slip through the seams and defuse the defenses of cells, find some way to enter the giant bubbles and divert all the machinery in the cellular metropolis to the task of making the pathogen’s babies. You have been infected by pathogens before, and lived to tell the tale. That victory was made possible by an immune system too complex to tell in today’s story, but perhaps we can take a moment to appreciate those unsung immunological heroes whose song we’ll sing another day.

There are parasites, much like pathogens, that feed off massive hosts. Parasites, like mosquitoes or hookworms, must evade the host in every way as they suck blood or extract nutrients without the host’s permission. One misstep, one misplaced bite, one flight past the host’s eyes or ears, one wrong movement to alert the host of the parasite’s presence, and the parasite is dead, squished, gunned down by the immune system, dissolved into atomic dust, never to be seen again.

Herbivores and carnivores, predators and prey, mutualistic microbes, pathogens, and parasites… We’re so fortunate to look outside the window of a train today and see such remarkably complex living systems. It wasn’t always this way. The history of how we got here can help one appreciate the present even more.

All of the life on Earth came from a common ancestor. The common genetic code and the common housekeeping genes like RNA polymerase and ribosomes that all organisms share tell the story of the evolution of life from a common ancestor into every living thing we see today.

Living things reproduce. Parents make babies. However, whether a baby bacterium, a baby plant, a baby cricket, a baby lizard, a baby virus or a baby mosquito, the babies of every generation are mutated slightly from the parents and those mutations can change the structure and function of the babies over their whole lives. For any slice in time, life on Earth is an entire universe of organic molecules in motion, big bags of enzymes seeking to consume resources, survive, and reproduce to make other bags of enzymes just like it. At the end of any one organism’s life, their molecules disperse like atomic dust and become one with everything, integrated into the blood, muscles, and bones of the animal that ate it and dissolved into nothing to become nutrients in the soils. However, if the organism reproduced then there is a slightly mutated replica of that organism that goes on to survive, reproduce, and make similarly mutated babies even farther removed from the common ancestor. Over long stretches of time, the cyclical molecular machines we call living organisms start off as babies, consume resources, make more babies, and die. The babies that are better at consuming more resources make more babies than the rest. Slowly, imperceptibly to any one bag of enzymes, life evolves.

What used to be simple bags of enzymes doing the bare minimum enzymatic work to survive over 3 billion years ago slowly diversified into complex food webs of microbes. Oxygenic photosynthesis evolved 2.6 billion years ago in a world whose atmosphere was full of carbon dioxide, but the oxygen we love to breathe in today was toxic to life, forcing babies everywhere to adapt to use oxygen as we do, adapt to hide from oxygen like the “anaerobic” microbes in our guts, or die. Eventually, oxygen itself enabled different kinds of metabolism like what we use - we breathe in oxygen and use it to light sugars on fire, releasing carbon dioxide, water, and energy. The molecular innovation of oxygen allowed other forms of life to evolve.

At some point in the distant past, single cells joined forces to form multicellular masses, biofilms that could produce public goods and survive storms or prowling tribes able to eat lesser microbes. Power in numbers. The cellular tribalism sparked an arms race of multicellular life, kicking off the Cambrian Explosion of animal forms 500 million years ago, an evolutionary biological Big Bang in which simple multicellular forms experimented with different forms of symmetry, different numbers of arms and legs, different orientations of their mouths and anuses (I shit you not), and more.

The explosion of animal life in the water slowly led to the evolution of bones. Enzymes evolved the ability to make bones, and babies with those enzymes were able to swim faster, avoid getting eaten, and reproduce more.

With time, some photosynthesizing algae were crowded out of the sea and they found solace first in the intertidal zone, then they thrived in tidal pools, then over generations and generations of a biological Manifest Destiny they colonized land. But land is different from the sea. All of our ancestors, all of our contemporary cousins, all of life (besides viruses) boils down to soap-bubbles called cells filled with water, demanding enzymes, and DNA. When delicate water-filled bubbles go onto land, there is far less water than in the sea, and cells dry up like a tomato or grape that shrivels in the sun. In order to survive on land, cells need some kind of waterproof shell. With time, enzymes in early algae evolved to make the ‘cuticle’, a waterproof shell that helped algae colonize land.

As algae colonized land, they grew taller but cells at the top of the stack, close to the sun and capable of photosynthesizing more, were farther from water on the ground and even with cuticles they would dry out. With time, experimentation, and natural selection, plants evolved roots to draw water from the soils and, with more time, experimentation, and natural selection, they evolved systems to pump water from soils all the way to cells at the top of the plant. So-called “vascular” plants were born, enabling leaves to form and focus on photosynthesis while root and shoots pumped water and sugars to the towering communes of cells.

But how did plants reproduce? How did one commune of cells become another? Algae and basal vascular plants, to this day, still reproduce with motile sperm. They dedicate particular cell lines to reproduction, but those cell lines haven’t evolved much from plankton in the sea. Algae and ferns and more literally send swimmers into water at the base of the plant to find eggs. Thus, the algae, mosses, and ferns need to live close to water or in places where it rains regularly enough that their sperm can swim to find eggs and make babies.

Clearly, there is more to land than the streams and rainy places where motile sperm can swim. Some plants evolved the ability to live farther and farther from water. Continents drifted and climates changed such that deserts arose where once there was plentiful rain. With time, experimentation, and selection of babies, plants pressured by the unreliability of water eventually innovated pollen, a durable, waterproof-ish coat around their sperm, enabling them to send their sperm wafting through the air. The “gymnosperms” or seed plants like the junipers, pines, redwoods, and more all send their sperm wafting through the air, often leaving massive yellow piles of fertile dust on our windshields to this day.

At some time during the early evolution of plant life to land, animals also got crowded out at sea and some made their way to land. Unlike plants, animals have to swim or run around to get their food, and all that running & swimming takes a lot of energy. Animals are able to burn so much energy by eating sugars, breathing oxygen, and just like oxygen helps fire burn wood it helps animals break down sugars to release energy, helping us swim, run, move our eyes across the page, or type the stories of our ancestors on Substack. To evolve to life on land, some animals - the ‘tetrapods’ - evolved lungs to breathe and limbs to run.

The early tetrapods, however, were slimy and still rather fish-like. They were like salamanders and frogs that needed to spend most of their time in the water or they would dry like a prune, like a moss without its cuticle. They also needed to lay their watery eggs in the water, much like the ferns. With time, some salamanders evolved something like a cuticle and became something like newts capable of straying farther from water. The same happened with some cousins of frogs evolving a more waterproof skin to become toads. Newts and toads are like the mosses of tetrapods - they have a cuticle that prevents them from drying out, but they still need to reproduce in the water.

By a stroke of evolutionary brilliance, by pure happenstance, I like to imagine that some babies in eggs had slightly more waterproof eggs, and they survived to hatch whenever the pools of water dried up. Over time, more and more waterproof eggs evolved until suddenly we had something like lizards running amok, laying hard-shelled, water-proof eggs and eating insects with similar waterproof exoskeletons and all manners of evolutionary tools to avoid desiccation.

For any cross-section of evolutionary time, species are interacting with one-another and their evolutionary success is determined by their ‘ecological’ interactions, their interactions with other living things and non-living aspects of their environment like water, rainfall, heatwaves and more. While we see sharks eating fish, cows eating grass, corn growing in a field, or a lizard on a fence looking me in the eye, when we zoom in we see a symphony of symphonies of molecules driving cell division and embryonic development yielding multicellular metropolises from a single sperm and a single egg.

There’s so much more to the evolutionary story I haven’t covered, and that will always be the case. Our words, our scientific understanding, our brains, are not capable of grasping it all. This isn’t to diss our brains - that we know of the Big Bang, the Cambrian Explosion, and our own existence is yet another wonder to behold. That I can sit here and type the stories of our ancestors - yes, our ancestors, as you and I probably have common ancestors dating back to 10,000 years ago, maybe 100,000 years ago if we’re unlucky. But it’s all the same - at some point in the not too distant past, you and I can trace our DNA to a common ancestor who persevered, had babies, and made us possible. Even that lizard on the fence that looked me in the eye is but a distant cousin. So, too, is the mosquito I just killed and even the grapes in the wine I’m drinking. We are all related, we are all threads in an evolutionary tapestry going back to the beginning of life on Earth, and that is beautiful.

When we look at the DNA, we can see the story of our ancestors written in every single cell of our body.

When I listen to the music, I remember why I became a biologist. While I am endlessly fascinated by mathematics, physics, chemistry, astronomy, and more, I personally fell in love with the beauty of life at a young age, sitting on my mom’s lap as she told me all about the wild things that lived outside the train. The enzymes that photosynthesize, the microbes that live inside of us, the algae, the ferns, the pines & junipers, the flowering plants, the invertebrates, the vertebrates, the tetrapods, the salamanders and the newts, the lizards, the birds that evolved to swim through the air, the hominids, our language, our technology, and more - life is everywhere you see it.

I went on from that train ride to breed lizards, study enzymes, catch lizards like Sceloporus species in the arid grasslands outside Albuquerque, study the molecules that flow through ecosystems, understand the mathematics of evolution, climb pine trees and admire plants in a tropical rainforest, and study a virus that entered a human population tethered to the internet, typing with their evolving tongues.

Sure, humans, like other primates, can make a ruckus when they’re aroused. We’re all mischievous hominids really, bags of bitchy, demanding enzymes, typing furiously as our brains burn sugar to comprehend some complex fact, admire a work of art, or conceive the right order of words to inspire someone. However, whenever I get too sucked-into our human affairs, I find my awe & wonder by zooming out, by tuning in and listening to the music, remembering the story of our ancestors and marveling at a lizard on the fence made by the photosynthesis of an ancient pinon pine.

Biology, the study of life, feels to me a bit like being the family historian with the broadest definition of family our DNA, and the mathematical axioms of life, will allow.

This Biologist’s Guide to Life was never intended to be a battleground over epidemiological policy nor the origins of a virus; I just got sucked into those scientific debates by the misfortune of following my scientific feet into the warzone and playing some role in discovering inconvenient things. The things I discovered are far less pleasant than the lizard on the fence, although they are beautiful in their own tragic way - humans evolved the ability to make viruses in a lab, and one of those viruses now floats through the air among us, infecting upper respiratory cells, and we desperately try to build defenses against it.

The Biologist’s Guide to Life was intended to be my love letter to living things. I hope to get back to that as soon as possible. As we deal with the tragedy of a pandemic, we can use some beauty to feel more inspired by - and in love with - the world around us.