Credits

Aryn Baker is a Rome-based foreign correspondent who has spent the past 25 years writing about the intersection of climate change, conflict, migration, science, culture and politics around the world.

It turns out playing God is neither difficult nor expensive. For about $2,000, I can go online and order a decent microscope, a precision injection rig, and a vial of enough CRISPR-Cas9 — an enzyme-based genome-editing tool — to genetically edit a few thousand fish embryos.

In addition to this, I’ll need the hand-eye coordination of a middling video game player, a stack of petri dishes and an insulated box that can keep my edited embryos in the Goldilocks temperature zone of around 28.5 degrees Celsius. In fact, the most difficult part is getting a reliable supply of freshly fertilized zebrafish embryos for my experiments. Fortunately, at the Marine Biological Laboratory in Woods Hole, Massachusetts, where I spent 10 days in May learning how to do genetic editing, it’s not a problem. The lab can produce a new batch every hour, so I have plenty to work with.

I line up dozens of single-cell embryos along the edge of a glass slide. Under the microscope, they look like a string of yellowed pearls. When I prod them with an ultra-fine glass syringe, they squish like tapioca balls in a boba tea. But if I get the angle right, I can inject them with a carefully calibrated dose of CRISPR-Cas9 designed to disable a gene associated with eye development. When they hatch into larvae a few days later, they will have no eyes. If I were to allow them to reach adulthood, which I won’t, they could theoretically breed with other similarly blinded adults to create a population of eyeless fish for an aquarium exhibit of unnatural wonders.

The process is deceptively simple; the implications are anything but.

Breaking The (Genetic) Code

In the 13 years since biochemist Jennifer Doudna, Emmanuelle Charpentier and their fellow collaborators harnessed an ancient mechanism of bacterial immunity to develop a genome-editing technology, CRISPR-Cas9 has become a powerful and infinitely customizable tool that allows humans to rewrite the language of life. It can target plant and animal genes, and promises a cure for any disease with a genetic component. It can alter heritable traits like eye color, size, strength and cognitive performance. It has already been used to make crops more productive, fruit sweeter and rice cultivation less water-intensive. 

The tool allows humans to genetically edit sterility into pests, like the New World screwworm — a flesh-eating maggot that preys on both cattle and humans — and the mosquito that carries malaria, potentially driving them to extinction. 

We can also edit animals out of extinction by using the same process to insert DNA derived from ancient forebears into their modern descendants. In April, the venture-backed biotech firm Colossal Biosciences introduced to the world a litter of what they said were “de-extincted” dire wolves brought back into existence after disappearing from the world for more than 10,000 years. Critics dubbed the wolves “dire-ish,” noting that only a few genes in the modern gray wolf — those that dictate coat color, size, musculature and jaw shape — had been altered, not the whole genome. Still, the technological advance offers a tantalizing glimpse of what else can be achieved with genetic editing.

It may also promise us the ability to prevent extinction in the first place, starting with one of the most threatened ecosystems on the planet: coral reefs.

Fixing Failure Through Genetic Editing

Coral reefs are fundamental to the health of our oceans. They cover less than 1% of the Earth’s ocean, but are home to a quarter of the ocean’s fish. They protect our coastlines from storm surges and rising sea levels and bring in hundreds of billions of dollars a year in tourism and fishing revenues. Without them, we would lose a major carbon sink. And they are on the brink of extinction, threatened by ocean acidification and rising temperatures that are outpacing their ability to adapt. The millions of tiny polyps that make up a reef rely on a symbiotic relationship with algae, which photosynthesize sunlight into food for both organisms. When stressed by high heat, coral expel their colorful symbionts, leaving behind a bleached white reef. Recovery is possible, but when bleaching events repeat in quick succession, the coral usually dies.

A recently published study in Nature finds that 70% of Atlantic coral reefs will be dead or dying by 2040 under current warming conditions. If warming exceeds 2°C degrees Celsius beyond pre-industrial levels, nearly all reef systems — at least 99% — will stop growing by 2100. We are already averaging 1.3°C, and could hit 1.7 °C as soon as 2027, according to the World Meteorological Organization.

“It turns out playing God is neither difficult nor expensive.”

If scientists could use CRISPR to engineer a more heat-tolerant coral, it would give coral a better chance of surviving a marine environment made warmer by climate change. It would also keep the human industries that rely on reefs afloat. But should we edit nature to fix our failures? And if we do, is it still natural?

Using the new field of biotech to save the natural world from the fallout of a previous technological romance has gained traction among scientists and conservationists who worry we have no time to waste. However, it remains a hotly debated topic, pitting those who say, “we can” against those who say, “we shouldn’t.” At the core is a fundamental divide over what makes nature natural, the risks of unintended consequences and the responsibility that comes with using a technology once relegated to the realm of a divine creator. 

“CRISPR presents us with new options,” Christopher Preston, an environmental philosopher from the University of Montana, told me. His book, “The Synthetic Age,” explores how humans are poised to radically reshape the natural world using CRISPR editing, de-extinction and climate engineering. “So the million-dollar question is, how do you decide? Which parts of the world should we leave to natural evolutionary processes, and which parts of the world should we grab hold of and design so that they work better?”

Evolution is not keeping pace with climate change, so it is up to us to give it an assist, he said. In some cases, the urgency is so great that we may not have time to waste on deliberations over ethics. “There’s no doubt there are times when you have to act,” Preston continued. “Corals are a case where the benefits of reefs are just so enormous that keeping some alive, even if they’re genetically altered, makes the risks worth it.” 

Not all genetic interventions are feasible for now. But eventually, say scientists, they will be, and it is better to start studying the implications before they are regularly deployed by citizens, scientists and venture capitalists trying to fix the mistakes of the past, at the risk of inadvertently making new ones. This is precisely why I ended up hunched over a petri dish, examining the results of my first experiment: rewriting the code of life for approximately 150 zebrafish embryos. 

CRISPR stands for clustered regularly interspaced short palindromic repeats, and it is an ancient bacterial defense system that identifies and fends off viral attacks. When bacteria are attacked, the survivors embed a snippet of the invading virus’s DNA into their own genome, which then serves as an internal mug shot that is passed down through generations. The next time the bacteria encounter that specific DNA sequence in an invading virus, they will cut it out by using an enzyme that works like a molecular scalpel, called Cas, which stands for CRISPR-associated protein, neutralizing the threat. It is this seek-and-destroy mechanism that Doudna and Charpentier repurposed into an elegant tool for manipulating DNA sequences. They published their breakthrough in 2012 and received the Nobel Prize in Chemistry for their work in 2020. 

CRISPR can be programmed to target specific patterns of genetic code, and once found, the Cas9 will cut it out. In most cases, this disables the gene’s function entirely; however, the same system can be used to replace a gene segment to purposely alter its function, or to repair a gene’s faulty mutation, much like a spell-check for DNA.

A day after the injections, I could see my zebrafish embryos starting to develop inside their eggs. The ones that had been successfully injected had no eyes. The un-injected embryos — my control group — did. This was to be expected. The zebrafish’s genome, like that of fruit flies and lab mice, is well understood, and I was working with a version of CRISPR-Cas9 designed to target the Rx3 gene, which governs eye development in most vertebrates. For a less-studied species, like coral, there is no map of what each gene does. To figure that out, scientists must knock out specific genes one by one, observe the impact and then deduce their role. Before CRISPR, this would have been near impossible. Even with CRISPR, it’s not exactly easy. 

Climate Proofing Coral

Unlike zebrafish, a freshwater species from Asia that spawns whenever the lights go on, coral only spawns at the beginning of the summer, in the middle of the night, for just a few evenings following a full moon. For Phillip Cleves, a principal investigator at the Carnegie Institute for Science’s embryology department who has dedicated his career to studying coral genetics, that meant packing up his lab and decamping to Queensland, Australia, while he waited for the Acropora millepora corals of the Great Barrier Reef to get it on.

“Should we edit nature to fix our failures? And if we do, is it still natural?”

Once they did, the process of injection was pretty much the same as with my zebrafish embryos: He collected the newly fertilized eggs, lined them up in petri dishes and then spent the next several hours injecting the embryos with a solution containing CRISPR-Cas9. Back in 2020, he was working on a hunch that disabling the HSF1 gene would decrease coral’s heat tolerance even further. HSF1, or Heat Stress Factor 1, is a gene that can be found in almost every species from yeast to humans, and is believed to influence how organisms respond to heat. Cleves’ hunch proved right.

Once his coral larvae hatched, Cleves exposed them to moderately high temperatures. Those whose HSF1 gene had been disabled via the CRISPR solution injection died. The others survived. Cleves’ identification of the gene in coral responsible for controlling thermal tolerance brings scientists one step closer to using genetically assisted evolution to engineer a more heat-resistant organism. Now that they know what HSF1 does, they could, theoretically, replace it or manipulate it to encode a higher heat tolerance. Cleves’ findings are among the first non-commercial applications of CRISPR-Cas9 for conservation purposes.

It’s one thing to disrupt a gene, and something else entirely to replace it with a different one, so this approach to climate-proof coral is still tantalizingly out of reach. “We know that knocking out one gene causes a decrease in tolerance, but it’s unclear what types of genetic changes we could make to increase it,” Cleves told me. “Finding genes that can enhance heat tolerance in corals is an essential research topic.”

He suspects that heat tolerance is polygenic, meaning that it is influenced by multiple genes. These genes may vary between species. And even different populations of the same species may express their genes differently, turning them off or on, depending on the environment. Targeting only one gene would be like genetically engineering a gray wolf to have white fur and calling it a dire wolf.

In the meantime, Cleves is optimistic that his quest will eventually bear fruit. “We’re seeing massive death of corals, and then, in some cases, recovery,” he says. “CRISPR helps us understand how this is happening. Because it’s an open question as to how coral will survive climate change. They need to adapt. We must find out how we can facilitate that.”

Cleves’ lab now has a domesticated coral farm that can produce embryos several times a year, so he no longer needs to wait for the first full moon of summer over the Great Barrier Reef to continue with his experiments. The accelerated pace couldn’t come at a better time: The past three years have seen back-to-back bleaching events that have all but wiped out coral in the Caribbean, and nearly half the species in the Indo-Pacific.

“Catastrophic is not a word I use lightly, but that is exactly what 2025 is shaping up to be,” Kate Quigley, a molecular ecologist and a principal research scientist at Australia’s Minderoo Foundation, told me. “There are only a few species left in the Caribbean, and my colleagues there are now saying words like functionally extinct, which means there are not enough individuals to have successful breeding. That is terrifying.”

Scientists still don’t understand why, exactly, coral expel their algae symbionts when the water heats up, but Quigley, who replicates bleaching events in a tank to test coral heat tolerance in her lab in Western Australia, can tell you what it smells like. “It’s awful, like rotting fish. You walk into the lab, and you know you have dead coral even before you look in the tank.”

In Quigley’s lab, scientists take coral to the extreme limits of heat tolerance to identify those that survive. Then they crossbreed the survivors to see if they can produce a more resilient organism. She feeds details of those findings into an AI model that helps identify parts of the reef most likely to produce hardier corals that could bolster any future breeding program. 

For all the research Quigley and Cleves have dedicated to climate-proofing coral, neither wants to see the results of their work move from experimentation in the lab to actual use in the open ocean. Needing to do so would represent an even greater failure by humankind to protect the environment that we already have. And while genetic editing and selective breeding offer concrete solutions for helping some organisms adapt, they will never be powerful enough to replace everything lost to rising water temperatures.

“Catastrophic is not a word I use lightly, but that is exactly what 2025 is shaping up to be.”

— Kate Quigley

“I will try to prepare for it, but the most important thing we can do to save coral is take strong action on climate change,” Quigley told me. “We could pour billions and billions of dollars — in fact, we already have — into restoration, and even if, by some miracle, we manage to recreate the reef, there’d be other ecosystems that would need the same thing. So why can’t we just get at the root issue?”

Given the persistent failure of governments to act with the urgency necessary to stem the burning of fossil fuels that are driving climate change, it is easier to look with hope towards techno-optimist solutions that promise to fix what society has already broken. Colossal Biosciences’ dire-ish wolf program aside, genetic editing is already offering concrete advantages in a conservation context.

A Genetically Edited American Chestnut Grows Roots

The American chestnut — a vital source of timber, food and shade for early Americans that once blanketed the eastern half of the United States with billions of trees — was nearly wiped out by a deadly invasive fungus in the early 1900s. The few remaining examples rarely reach maturity, and plant biologists consider the chestnut to be functionally extinct.

But over the past three decades, The American Chestnut Foundation, a non-profit hub for research and conservation efforts, has supported genetic editing to create a blight-resistant strain of this once keystone species. “The dire wolf is cool, but ecologically it’s not important,” Gregory Kaebnick, a senior research scholar at New York’s Hastings Center for Bioethics, told me. “The American chestnut, though, if you replanted those across Eastern forests, that could make a difference. And so it strikes me as worth the investment.”

Other programs are looking to use CRISPR not to save a specific species, but to save ourselves from our excesses. RemePhy, a company built by bioengineers from Imperial College London, has genetically modified plants to enhance their ability to draw waste metals and toxins from polluted soil, providing a cleanup service around mining sites. 

George Church, the Harvard Medical School professor of genetics behind Colossal’s dire wolf project, was part of a team that successfully used CRISPR to change the genome of blue-green algae so that it could absorb up to 20% more carbon dioxide via photosynthesis. Silicon Valley tech incubator Y Combinator seized on the advance to call for scaled-up proposals, estimating that seeding less than 1% of the ocean’s surface with genetically engineered phytoplankton would sequester approximately 47 gigatons of CO2 a year, more than enough to reverse all of last year’s worldwide emissions. 

But moving from deploying CRISPR for species protection to providing a planetary service flips the ethical calculus. Restoring a chestnut forest or a coral reef preserves nature, or at least something close to it. Genetically manipulating phytoplankton and plants to clean up after our mistakes raises the risk of a moral hazard. Do we have the right to rewrite nature so we can perpetuate our nature-killing ways?

“We’ve gone from talking about how to let nature carry on as best it can, to ‘How can we engineer it to provide this vital service?’” Preston, the environmental philosopher, told me. “We’re not trying to preserve a natural system. We’re just trying to find the best way to pull carbon out of the atmosphere. That requires a little bit more humility.”

It also requires caution. 

CRISPR-Cas9 enables us to hack the genetic code. But we still can’t build a reef from scratch. We have vague ideas about how the ocean works, and we don’t know how to replicate what does work. The possibilities of genetically editing a more resilient ecosystem are endless. But so too are the risks.

When my RX3-injected zebrafish embryos hatched, I noticed that many of them were stunted. A few had deformed flippers, and some could only swim in circles. It was unclear if the stunting was a result of injection trauma, a side effect of the CRISPR-Cas9 editing process, or if the gene that I had disabled would have otherwise contributed in some way to normal growth.

Amateur geneticists like me have probably done the zebrafish RX3 experiment thousands of times. The results are usually predictable, but the unexpected stunting side effect illustrates the need to allow for unintended consequences, either within the organism or the ecosystem it occupies. We don’t want to save one species only to ruin another part of the environment that we don’t quite understand yet.

“We don’t want to save one species only to ruin another part of the environment that we don’t quite understand yet.”

The CRISPR-edited American Chestnut trees demonstrated blight resistance, but a few of them appeared to be shrubbier than their unedited forebears, and many died from other diseases. A lab mix-up early on in the breeding process didn’t help. It led to the misidentification of several trees, accusations of a possible cover-up and commercial interference, and the withdrawal of support from the American Chestnut Foundation — an arboreal drama tailor-made for a true crime podcast. Researchers still don’t know why, exactly, the CRISPR’d trees are not flourishing, but they suspect that the editing process encoded a defect on a critical gene. The project continues.

CRISPR-Cas9 editing is not immune to human error, and it is never 100% accurate, noted Josh Rosenthal, a biologist at the Woods Hole Marine Biology Lab who taught me and other journalists how to use the technology. As with my stunted zebra fish, or the shrubby, disease-prone chestnuts, “There could be off-target changes,” he said. Most of them won’t appear as problematic, “But every once in a while, they’re going to change something in a detrimental way.” That’s acceptable in a lab. It could be hazardous in the environment.

My blind, stunted zebrafish probably wouldn’t survive in the wild, but escaped novelty zebrafish genetically altered to glow red or green for aquarium hobbyists are now flourishing in Brazilian rivers. The blacklight glow probably doesn’t give them a competitive advantage, but it does show that CRISPR-edited organisms can reproduce in natural environments, passing their altered genes down through generations.

Even a successful intervention could inadvertently set off a chain reaction. It could, for example, give the new organism a competitive advantage, depriving others of food, space and an opportunity to evolve climate resilience unassisted. A super coral might thrive in a warming ocean, but if there is only one species, the reef becomes a monocrop, devoid of biodiversity and vulnerable to disease. At a minimum, successfully climate-proofing a reef would require editing heat tolerance into hundreds, if not thousands, of coral species.

But then there is the complex interplay of growing acidity caused by excess CO2 in the water, and other organisms essential to reef function. A sense of humility is essential, Quigley told me, echoing Preston. “Engineering the ocean, or the atmosphere, or coral is not something to be taken lightly. Science is incredible. But that doesn’t mean we know everything and what the unintended consequences might be.” 

It is too late to put the genetic genie back in the bottle. The technology to alter organisms is not only widely available — you can buy a frog genome editing kit for the cost of a nice terrarium — its power is now amplified by AI. ChatGPT will, with the right prompts, suggest edits to render a virus more virulent. A quick Google search can take you to biotech companies willing to sell the basic components. Using CRISPR-Cas9 to manipulate heritable traits in humans is still frowned upon. But nothing really governs its application in other organisms other than one’s personal ethics or those of the lab sponsoring the science.

As knowledge of the technology spreads beyond the lab, anyone with a hand steady enough to inject an embryo can start knocking out genes. Knocking them in is still difficult, but that, too, will change. “We are as gods, and might as well get good at it,” wrote pioneering environmentalist Stewart Brand in 1968, describing humanity’s technological impact as a “force of nature” in his inaugural issue of the Whole Earth Catalogue magazine.

As with all powerful technologies, getting good at it means balancing the benefits of using it against the consequences. When it comes to preserving the planetary environment in the face of an all-but-certain climate-driven catastrophe, that also means weighing the cost of inaction. “Maybe gene editing isn’t appropriate for reefs that are still relatively healthy,” Quigley told me.

But in places like the Caribbean, where many reefs have already bleached into rubble-filled wastelands, it could be, she added. “I think people’s tolerance for risky endeavors will change relatively quickly once things start to rapidly decline.” As much as Quigley loathes the idea now, she doesn’t hold herself exempt. “It’s a terrible thing to imagine a world without coral.”