Book Extract | The Color of North: The Molecular Language of Proteins and the Future of Life

Book Extract

Excerpted with permission from the publishers The Color of North: The Molecular Language of Proteins and the Future of Life. Shahir S. Rizk and Maggie M. Fink, published by The Belknap Press of Harvard University Press/ HarperCollins Publishers India

ORIGIN

Shahir S. Rizk

Using her stone mortar and pestle, my grandmother crushed fresh garlic cloves with cumin, sea salt, and a drizzle of lime juice, filling the kitchen with a powerful aroma. On the small table to the side, half a dozen fish, cleaned and gutted, sat on a metal plate. She handed me the heavy stone container and instructed me to spread the paste on the fish, covering every inch, while she washed the rice. My hands would smell like garlic for the rest of the day, but I didn’t mind.

Though we didn’t rush this process, my grandmother and I needed to keep track of time. Soon my parents would return from work, hungry, and we would have a meal ready for them as we had done every day over the summer. Each meal took the entire day to prepare. I listened to my grandmother’s instructions and observed the methodical but relaxed way she dipped the fish in flour, slapping each one between her two palms to remove the excess and slipping them into a pan of sizzling oil.

My grandmother grew up in the south of Egypt in a rural town where she learned the culinary arts of the region. After marrying my grandfather, they moved north with the flow of the Nile River, living for several years in Cairo, where my mother was born. They ultimately settled farther north in Zagazig, a small city in the ancient land of Goshen, where Joseph and the Israelites had settled thousands of years before. Zagazig was my childhood home, too, and I lived just a short walk away from my grandmother’s apartment. Spending summers with her was an opportunity to learn the old ways of the world. It was a chance to grasp a piece of the past, a past that was getting pushed away by the modern world with its frozen meals, disposable culture, and digital toys.

I spent my summers watching, learning, and of course, cooking.Our seafood dishes often contained the Red Sea Moses sole, a strange fish that resembles a flounder. The eyes of the Moses sole point up from the top side of its flat body. Its mouth is tilted toward one side, and its lopsided gills give it a permanent grin. The bottom side is bare, devoid of any recognizable fish features. “It looks like a fish split in half,” I said. With a skeptical smile, my grandmother recounted how, when Moses parted the Red Sea, one unlucky fish happened to be caught in the middle of the action; it too was split in half, and that’s the ancestor of what we eat today. We both chuckled as she turned the burner down low under the steaming pot of rice.

The Moses sole lives near the bottom of the Red Sea, where the water is warm year-round and teeming with life, including hungry sharks. With both eyes pointing upward, the Moses sole is always watching for predators, and its dotted scales match the color and tex- ture of the sandy sea floor, providing camouflage. But if it’s not hidden well enough, and a hungry shark does spot it, the fish has another weapon: it secretes a powerful shark repellant known as pardaxin. When released from the Moses sole, pardaxin coats the inside of a shark’s jaw, causing temporary paralysis and preventing the Moses sole from becoming shark dinner.

Pardaxin is a protein, and, like all proteins, it is invisible to the naked eye. It would take about one million pardaxins, strung side-to- side, to equal the width of the period at the end of this sentence. Even the most powerful microscopes struggle to get a glimpse of proteins. Scientists must use x-rays and sophisticated machines, along with a lot of computations, to determine what proteins look like. Deciphering the structure of a protein is a heavy lift, but it’s worth it, because the secret to how any protein works lies in its unique structure.

When we zoom in on pardaxin, we see that it resembles two twisted spiral staircases connected by a short loop, making a “hairpin” shape that resembles a bobby pin.1 Each of the spirals is known as a helix. Pos- itive charges along the loops are attracted to negative charges on the surface of cells lining the inside of the shark’s jaw and gills. When the Moses sole senses an approaching shark, it releases a milky cloud containing millions of pardaxin molecules. Each protein becomes at- tracted to the shark’s jaw and gills much like a magnet jumps from your hand and onto a refrigerator. Once latched on, the pardaxin mol- ecules act like thousands of tiny thumbtacks, poking miniscule holes in the shark’s cells and causing their insides to leak out as salty ocean water rushes in. The disruption of the cell membrane and the imbal- ance of salts within the shark’s cells temporarily paralyze the pred- ator, giving the Moses sole enough time to escape. Having a shark repellent at the ready has helped the Moses sole survive in the Red Sea for millennia. But pardaxin is only one of thousands of proteins made by the fish, each with a specific structure and a precise function. Together, they make life at the bottom of the Red Sea possible.

Proteins are not unique to the Moses sole; they are found in every organism, from bacteria to bananas, birds to bees, algae to alligators, and mold to chimpanzees. We make our own proteins and use them for almost everything we need to survive. Each one of our 40 trillion or so cells is packed full of proteins swimming shoulder to shoulder in a solu- tion of salty water. In fact, proteins make up about half of the mole- cules in our cells. Most of the other half is water, and the tiny remaining percentage is comprised of DNA, sugars, and lipid (fat) molecules. If one of our cells was the size of an average American home, it would be filled with about 30 billion proteins, ranging roughly from the size of a grape to that of a watermelon. Each of these proteins carries a story of who we are and where we come from—and not just our family history, but also our evolutionary history, that is, how we are linked with every- thing around us. Proteins convey our origin story and potentially, the origin story of life itself.

INGREDIENTS FOR LIFE

My grandmother was born before World War I and left school after the fourth grade. She was married and already had several children when she survived the German air raids over Cairo during World War II. She didn’t understand the new fads of the 1980s. To her, my pixelated com- puter games seemed to be from a different world. But she knew many secrets rooted in science without having learned them at a lab bench or from a book. She knew that crushing garlic released its aroma. We now know that this breaks up the cells of the garlic plant, releasing a special protein—an enzyme that drives a chemical reaction, liberating molecules with that characteristic smell. She knew that if you boil stew for several minutes and leave it covered, it will keep for days.

We now know this as pasteurization: the high heat unravels and inactivates many toxin proteins, killing bacteria that would cause sickness. Without knowing anything about proteins or enzymes, my grandmother relied on ancient wisdom, wisdom that had flowed down from one generation to the next in stories, anecdotes, and food just as the Nile River had carved its way through desert rocks, transforming the sand into a narrow, lush valley of verdant farmland. And it was that ancient wisdom that I tried to soak up.

Throughout history, stories and traditions have been passed down to help future generations understand their world and thrive in it. How to crush garlic. How the Moses sole came to be. How to listen for the sound of the water reaching a boil. In this way, we inherit information from our ancestors, information as important as the genetic information we receive from our parents in the form of DNA.

Like a handwritten recipe, jotted down on a stained scrap of paper and passed from generation to generation, our inherited DNA is the instruction manual for making proteins. Every gene in DNA is a code for making one protein. Slight differences in the way our proteins are constructed give us curly or straight hair, make us short or tall, and determine how much of the pigment melanin our skin and eye cells make. But beyond our eye color or hair texture, our proteins are essential to every breath, heartbeat, and blink of an eye. Proteins dictate how we interact with the world around us. They signal when it’s time to wake up and when it’s time to sleep.

Proteins convert signals from light, scents, and tastes into a molecular language carried through a chain of hundreds of proteins that move and twist, resembling a microscopic Rube Goldberg machine. As it makes its way through our nervous system, this molecular language is translated and perceived as colors, shapes, flavors, and smells. Proteins are quite literally interpreters of our environment.

Humans have roughly twenty-five thousand different genes. Most of our genes contain the information to make a protein, or a segment of a protein, with a unique shape and a specific job.3 Even though al- most every cell in our bodies carries the same genetic material, not all twenty-five thousand proteins are made in every cell. The difference between a liver cell and a brain cell is not the genes they carry but which genes they “read” to make proteins. Liver cells will read only the parts of DNA required to make the proteins that a liver cell needs. The other genes remain dormant. The same is true for a brain cell, an immune cell, or a skin cell. Some genes can remain dormant for the entire life of a cell, while others are brought to life to create fully functioning proteins. And so, while the DNA within a cell can tell us whom the cell belongs to, the proteins the cell chooses to make tell us the type of cell it is. Each cell contains its own story, with proteins as the main characters acting out the directions of the DNA.

But proteins are not directly made from DNA. There is a go-between molecule that facilitates the translation of genetic language into functional protein language. This molecule is RNA, an essential compound in all organisms. In fact, it is RNA that assembles the building blocks of proteins, connecting them in a specific sequence based on the instructions encoded in DNA. In this manner, proteins in every cell are assembled by the action of RNA to carry out all the functions that cells need.

This flow of genetic information from DNA to RNA and into proteins is the central dogma of biology. Most of our understanding of this process has come from studying genes. Similarly, scientists have mostly looked at evolution through the lens of DNA and mutations in the genetic code. But as more tools and technology have allowed proteins to be studied, questions about the origins and evolution of life are now being looked at from the point of view of proteins, the final products of DNA. By shifting our attention to proteins, to the stories of evolution, adaptation, and inheritance they hold, our story and the story of all living things become clearer.

There is no known lifeform that does not rely on proteins, so the question of how proteins became integral to life is a question about the origins of life itself. We still know little about the conditions that made life possible on our planet, but these conditions were likely very different from today’s. Geologic records paint a picture of a harsh environment with volcanic eruptions spewing toxic gases of methane and ammonia. Without the atmosphere we have today, the Earth’s sur- face was bombarded with ultraviolet light, and intense storms covered large parts of the world. In this chaotic environment, simple, organic molecules began to come together, fusing to make more complex molecules, some of which may have become the building blocks of DNA, RNA, and proteins.

While it might seem unlikely that life could emerge in such harsh conditions, experiments conducted in the 1950s by Stanley Miller and Harold Urey at the University of Chicago suggest that this scenario was not far-fetched. Miller and Urey tried to recreate the conditions on our planet when life first began 3.5 to 4 billion years ago.4 In a sealed con- tainer, they mixed volcanic gasses of ammonia, methane, and hydrogen above saltwater that resembled an early ocean. Then they heated the mixture, periodically zapping it with an electric spark to simulate light- ning from a storm. Within one day, the color of the solution trapped in the reaction vessel began to change to a faint pink. After a week, it turned a deep red. When Miller and Urey opened the sealed con- tainer, they found that the mixture now contained five different amino acids, the building blocks of proteins. The experiment was ground- breaking, demonstrating the possibility that the molecules needed for life could have been made from basic substances likely found in a primordial Earth.

Even with the Miller-Urey experiment, many questions remain un- answered. What did the first protein look like? When and how was it made? We still don’t have the tools to answer these questions. But we do know that proteins are a part of every plant, animal, and even bac- terial molecular story—and that learning more about proteins can shed light on the numerous ways nature has used them to navigate the ex- treme ups and downs of the world and to ensure the survival of all organisms.

Proteins are incredibly versatile molecules that play a wide range of roles in living organisms. They support the basic functions that are common to all life. Every organism must eat, grow, reproduce, and excrete waste. Underlying these common functions are proteins that have not changed much across the kingdoms of life. For example, many of the proteins we use to digest our food are nearly identical to those used by bacteria, our most distant relatives. Likewise, most of the pro- teins that are used to duplicate DNA every time our cells divide are similar across all forms of life. Many proteins act as enzymes, facili- tating the chemical reactions within living cells.

These proteins synthe- size and recycle a wide range of molecules and generate energy from the food we eat. Structural proteins support cells and tissues under- lying the framework of skin, bones, hair, and nails. They also form the fibers of muscles and tendons, enabling us to move when our mus- cles contract. Transport proteins help move molecules throughout the body, delivering nutrients to cells, removing waste, and flushing out harmful toxins. Signaling proteins are involved in all cellular com- munication; many hormones are signaling proteins that regulate various physiological processes. Receptor proteins on our eyes, tongues, and noses help us see, taste, and smell. And immune-response proteins identify and neutralize foreign invaders such as bacteria and viruses.

Having such amazing molecular machines helps organisms adapt to their environment, survive, and proliferate. But when proteins go rogue, they can play a significant role in disease progression. One of the most devastating examples of proteins gone awry is cancer. The uncon- trolled cell growth eventually leads to tumors that often spread throughout the body. Proteins called oncoproteins can fuel this growth by promoting cell division or inhibiting natural cell death. Proteins known as tumor suppressors, which normally act as a check on cell growth, can be inactivated, allowing cancer cells to proliferate un- checked. Protein disfunction plays a significant role in neurodegener- ative diseases like Alzheimer’s and Parkinson’s, too. As proteins fail to take on the correct structure, they accumulate in the brain, where they form toxic clumps that disrupt normal cellular function.

Proteins also play a critical role in infectious diseases. Pathogens like bacteria and viruses often produce proteins to help them evade the immune system or to hijack host cells for their own reproduction. The spike protein on the surface of the SARS-CoV-2 virus, for example, allows it to enter human cells and cause COVID-19. Once inside our cells, the virus can make copies of itself using the cell’s own protein- making machinery. Without the action of the proteins produced by our immune cells, the virus spreads without control, causing disease and even death. Understanding the role of proteins in disease progression is crucial for developing effective treatments.

Just as so many proteins have mostly remained unchanged through- out evolution, some have come to possess truly incredible properties that defy our own imaginations. Proteins help bacteria survive inside nuclear reactors and protect microorganisms from the immense pressure and scorching temperatures found near deep-sea vents miles below the ocean’s surface. They keep birds in sync with the magnetic field of the Earth as they migrate each year and give fireflies their ghostly glow on warm summer evenings. And for a select few organisms that live in cold climates, proteins prevent them from being frozen solid. By looking closely at these miracle-performing proteins, we can start to build an understanding of how all proteins, even those that have dramatically different tasks to perform, evolve.

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Shahir S. Rizk and Maggie M. Fink The Color of North: The Molecular Language of Proteins and the Future of Life The Belknap Press of Harvard University Press/ HarperCollins Publishers India, 2025. Hb. Pp.272

An awe-inspiring journey into the world of proteins—how they shape life, and their remarkable potential to heal our bodies and our planet.

Each fall, a robin begins the long trek north from Gibraltar to her summer home in Central Europe. Nestled deep in her optic nerve, a tiny protein turns a lone electron into a compass, allowing her to see north in colors we can only dream of perceiving.

Taking us beyond the confines of our own experiences, The Color of North traverses the kingdom of life to uncover the myriad ways that proteins shape us and all organisms on the planet. Inside every cell, a tight-knit community of millions of proteins skilfully contorts into unique shapes to give fireflies their ghostly glow, enable the octopus to see predators with its skin, and make humans fall in love. Collectively, proteins orchestrate the intricate relationships within ecosystems and forge the trajectory of life. And yet, nature has exploited just a fraction of their immense potential. Shahir S. Rizk and Maggie M. Fink show how breathtaking advances in protein engineering are expanding on nature’s repertoire, introducing proteins that can detect environmental pollutants, capture carbon dioxide from the atmosphere, and treat diseases from cancer to COVID-19.

Weaving together themes of memory, migration, and family with cutting-edge research, The Color of North unveils a molecular world in which proteins are the pulsing heart of life. Ultimately, we gain a new appreciation for our intimate connections to the world around us and a deeper understanding of ourselves.

In the extract that has been published, Shahir S. Rizk recounts watching his grandmother work in the kitchen and his childhood memories of growing up in Egypt. Later, he manages to connect the dots between traditional knowledge, passed across generations to that of scientific discoveries which proved these communities already knew. This is a theme that is carried throughout the book as the authors share personal and professional experiences/case studies linking it to the information being gathered about proteins.

Maggie M. Fink puts it very well when she says:

Our bodies will stop functioning one way or another. We cannot cheat death. But as we learn more and more about the great symphony of proteins that make us who we are, we can better understand ourselves and the world around us. And with that knowledge comes the ability to create new notes – to design something that nature has never seen before. For the hope of gene editing doesn’t end with correcting mistakes, but rather with doing the miraculous: inventing entirely new proteins.

Biotechnology is a fascinating area of science. It has multiple applications. There are many experiments taking place – whether for medical advancement as The Color of North details and in other spheres, such as was recently showcased at a fashion show. Iris van Herpen's recent Autumn/Winter 2025 couture collection, titled "Sympoiesis," featured a dress made from man-made bio-based protein fibers, developed by the Japanese company Spiber. The dress is made from man-made protein fibers, the brainchild of Japanese firm Spiber. CEO Kazuhide Sekiyama. This innovative fabric is part of a growing trend of using sustainable, bio-based materials in high fashion, with the goal of reducing the fashion industry's environmental impact. The collection also included a "living dress" made from bioluminescent algae, showcasing the potential of biotechnology in fashion.

Shahir S. Rizk is Associate Professor of Biochemistry at Indiana University South Bend and the Indiana University School of Medicine. The recipient of the Cottrell Scholar Award, he is an illustrator and poet whose work has appeared in Acorn, Modern Haiku, and Twyckenham Notes. He cohosts the podcast Rust Belt Science.

Maggie M. Fink is Adjunct Professor at Indiana University South Bend and a postdoctoral researcher at the University of Notre Dame, where she divides her time between science communication and studying bacterial genetics. She is an artist and poet whose work has appeared in Landlocked Lyres and been featured in exhibits at the University of Notre Dame. She cohosts the podcast Rust Belt Science.