Just as the novel coronavirus, which had brought large swathes of China and Europe to a standstill, began its wildfire migration through the wider US, a benign virus re-engineered to carry its cutting-edge CRISPR payload was injected into the eye of BRILLIANCE trial participant #1 at OHSU’s Casey Eye Institute. The goal: to treat and hopefully reverse the most common cause of inherited childhood blindness, Leber congenital amaurosis.

“Time slows down,” says Dr Mark Pennesi, chief of the Ophthalmic Genetics Division at the Casey Eye Institute, and primary investigator of the trial. “You watch the surgeon take this very, very tiny needle and just barely put it a few microns beneath the retina to inject the gene therapy product. It creates a little blister and it slowly grows. You’re holding your breath … and then it’s done and everyone exhales.”

News of the landmark procedure was announced, without much fanfare, at the beginning of March. By late summer, while the success of the operation had yet to be determined and its place in medical legend was still to be etched, the unnamed trial patient was reported to have experienced no significant complications, but Covid-19 dominated the news cycle.

“I think this has the potential to be game-changing,” says Stanley Qi, professor of bioengineering at Stanford University and one of the major players on the CRISPR landscape. “The promise behind CRISPR is that it can be used to treat diseases that have no cure yet. The sky is the limit, but the first step, proving it can safely be used in a human body with the desired effect, is crucial.”

In essence, CRISPR is a tool at the molecular scale, fashioned by visionary bioengineers to alter DNA. The results of these alterations could be wonderful, or terrify­ing. There are high expectations for modified foods that could end world hunger, treatments that could cure previ­ously unassailable diseases, and an improved quality of life for mankind. There is also the spectre of eugenics, bioterror and irreversible side effects. Like Arthur’s Excalibur, CRISPR is freighted with as much potential peril as promise.

Some of the most head-turning CRISPR stories, since its introduction to the scientific mainstream less than a decade ago, have played out in either the US or China. In 2013, researchers from Shanghai and Beijing used CRISPR to cure genetically caused cataracts in mice. The beneficial DNA alteration – to one single letter out of the 2.8 billion letters in the rodent genome – was inherited by the progeny of those mice.

In 2015, CRISPR was deployed in Shenzhen to create so-called micropigs – smaller versions of the already diminutive Bama breed. Some were sold as pets, sidestepping their intended fate as laboratory models for human disease. And at Harvard University in 2017, researchers used CRISPR to insert a digital moving image of a galloping horse into bacteria: something of a party trick but still proof that living cells can be repurposed as recording devices, allowing biologists to retrace and better understand their various functions.

These examples represent just the beginning of a journey that is likely to be both life-changing and hair-raising. In the CRISPR pipeline are a foil for malaria-spreading mosquitoes and a cure for huanglongbing, aka “yellow dragon disease”, scourge of the citrus industry.

On paper, given that CRISPR is nothing less than a way to rewrite the code of all living things, it should be possible to revive lost species – the woolly mammoth has already ambled into view on the CRISPR radar – and to design new ones. In theory, creation of a horned horse or a new species of winged lizard is not beyond its scope; the prospect of a fantastical bestiary including unicorns and dragons is not as fantastical as it sounds.

Compounding the affront to medical ethics, oversight of CRISPR’s unintended and unknown conse­quences was minimal. The vast majority of the scientific community and the public at large were outraged, and He is currently serving a prison sentence.

“There’s always the potential for the technology to get ahead of itself,” says Jennifer Doudna, professor of molecu­lar and cell biology and chemistry at the University of California, Berkeley, and founder of the Innovative Genomics Institute. “CRISPR babies is a good example that, yes, one can do that, but it shouldn’t be done for a lot of reasons. And so I think that’s going to be a challenge in this area where there’s so much capability and it’s advanc­ing incredibly quickly. The technology continues to improve. It continues to become easier and easier to make these very profound changes to the genomes of organisms, including humans.”

Co-authored with French professor Emmanuelle Charpentier, Doudna’s 2012 academic paper in the journal Science has long been regarded as a cornerstone in CRISPR’s evolution. It is also one reason, coupled with her public persona of being among the most visible and cautious of the scientists involved, that Doudna has been called “the mother of CRISPR”.

As she summarises in A Crack in Creation (2017), the book she wrote outlining the early years of the CRISPR saga, “We had built the means to rewrite the code of life […] Instead of remaining an unwieldy, uninterpretable document, the genome would become as malleable as a piece of literary prose at the mercy of an editor’s red pen.”

That kind of power would be enough to give anybody nightmares, and Doudna confesses she was not immune. In 2014, she had a dream in which a phantasmagorical, genetically freaky version of Adolf Hitler, human in form except for the face of a pig, inquired after the uses and implications of CRISPR. “With the whole circus around CRISPR babies and all of the media attention that came from that, I guess I’ve just become very aware of the public perception of this type of science,” says Doudna.

“I’m interested in making sure that there’s a counter story running at some level at least that says, look, CRISPR is an exciting, powerful technology: most people are using it responsibly and are working to make sure that it’s used for reasons that we would all agree are beneficial.”

CRISPR’s viral origins were first brought to light with the discovery in 1993 – by scientists working in the salt marshes of Spain’s Costa Blanca – of DNA fragments bearing a curious repeat pattern: the tongue-twisting palindromic structure baked into CRISPR’s acronym. After a series of separate investigations over the years that followed – uniting research into Saddam Hussein’s bacterial weapons programme with studies of a probiotic widely used to make yogurt – it became apparent that CRISPR was, in fact, a viral vaccination code written as segments of DNA.

Bacteria, like people, are susceptible to viral assault, and in an extraordinary feat of survival, they evolved a self-defence mechanism. Bacterial DNA “remembers” past viral attacks by stealing and storing a virus’ own DNA so that, in the event of a future invasion, the interloper can be recognised and destroyed.

CRISPR is bacteria’s way of protecting itself in the battle of life and death that rages constantly in the hidden universe of genes, cells and microbes – an all-natural kind of antiviral software.

It wasn’t until 2008 that CRISPR’s potential as a gene-editing mechanism was first formally articulated. Building on the yogurt probiotic studies, Professor Erik Sontheimer, from the RNA Therapeutics Institute at the University of Massachusetts Medical School, and postdoctoral researcher Luciano Marraffini, became the first scientists to show that CRISPR could be repurposed and added to the genome editor’s arsenal. “CRISPR came out of basic research that has nothing to do with genome editing,” says Sontheimer. “It was curiosity driven – and yet it gave us this fabulous set of tools.”

As described by Doudna and Charpentier in 2012, CRISPR-Cas9 – to give this original version its full name – is programmable, melding a protein called Cas9 with a strand of “guide RNA” (RNA is the molecule that acts as a messenger carrying DNA instructions for proteins) to form a precise DNA-seeking missile. But it looks less like a weapon than a misguided dessert.

Computer-generated animations and illustrations depicting CRISPR-Cas9 tend to reveal a Day-Glo lump of congealed creamed rice (Cas9) wrapped around a home-made macramé scarf gone horribly wrong (the guide RNA). Connected by forces non-chemists can barely imagine, let alone comprehend, this phlegmy ball of engineered genius appears to float in liquid caverns inaccessible to the human eye, guided towards its specific and minuscule DNA quarry by an innate impulse. Once in place, the soft machine snips apart the familiar twisted ladder of target DNA – so that what looks like a funky globular accident turns out to be a devilishly precise set of micro-scissors.

CRISPR-Cas9 was only the beginning. Primed by Doudna’s paper, the technology came hurtling out of the shadows and spawned an ongoing series of more accurate and versatile iterations. Chinese-American biochemist Feng Zhang, currently affiliated with the Broad Institute of MIT (Massachusetts Institute of Technology) and Harvard, produced a higher-fidelity version that upgraded CRISPR, by analogy, from a pair of scissors to the cursor on a word processor. By 2019, Zhang’s Harvard/MIT contemporary David Liu had further refined the technology into what he called a CRISPR “prime editing” system, able to search and replace DNA with even greater exactness.

By contrast, Qi at Stanford had seen an opportunity for a different kind of finesse, not by sharpening the scissors of CRISPR-Cas9, but by blunting them. His insight was to re-engineer the Cas9 protein to remove its slicing function, then adding the genetic equivalent of a switch. “It turns CRISPR into a completely new type of gene controller that lets me control any gene at any time by turning it on or off. This allows us to engineer cells and DNA in an unprece­dent­ed safe and useful way.” One of the main advantages of Qi’s CRISPR switches, which can also be used like lighting dimmers to control the degree of DNA function, is that the effects are reversible.

“I like to compare the human genome to a computer loaded with programmes and codes that control our behavi­our and our fate,” says Qi. “CRISPR is a programming language that allows us to rewrite the codes of the pro­grammes of DNA. Understanding the secrets and principles of how genes work is the basis of using CRISPR tools to reprogramme the DNA in the least invasive way possible.”

Qi’s dream of becoming a scientist took root early. At middle school, he was obsessed with molecules, “but what puzzled me most was life itself”, he says. “Why is a tree alive, but a rock isn’t? Can we make a tiny living synthetic cell from non-living components such as elements and mole­cules?” In 2006, after graduating from Tsinghua University, in Beijing, he moved to the US for graduate school at UC Berkeley. It was a lecture by Doudna in 2008 that sent him headlong down the CRISPR rabbit hole.

“As a synthetic biologist, I had always dreamed of a tool that allowed me to precisely control the code of DNA. I firmly believe that biotechnology is at the heart of how we will treat challenging diseases in the future. Many people are looking at genetic diseases such as sickle cell anaemia or Duchenne muscular dystrophy, which are inherited from parents. Most genetic diseases currently don’t have a cure and CRISPR holds promise for these types of conditions. I hold equal hope for treating lethal genetic diseases. I’m also excited about its use towards treating cancer and regener­ating damaged organs.”

Patrick Hsu, assistant professor of bioengineering at UC Berkeley and investigator at the Innovative Genomics Institute, sees “CRISPR-Cas9 like the Ford Model T – the first mass-produced car. Everyone had one, and they were cheap, but today we’re driving Teslas”.

Hsu has refocused CRISPR to look not at DNA, but RNA. “There are many diseases that are caused by defects at the RNA level,” he says. “With RNA-targeting CRISPR systems we can go after entire classes of diseases that are really difficult to address at DNA level.”

Hsu entered the CRISPR universe at its dawn, as a graduate student on Zhang’s Broad/Harvard team. He was born in Taiwan, raised in Canada, but moved to California for high school. A self-described synthetic biologist “interested in things that we cannot yet do rather than what biology does today”, his obsession with science extends back to his teenage side hustle with a laboratory investigating inner-ear hair cells.

His grandfather’s Alzheimer’s had left a deep and lasting impression on a pliant young mind naturally overstocked with curiosity. In CRISPR he found the means “to build better tools for asking these very same questions that I started asking when I was 11 years old. How can we actually draw causal links between a particular gene and an actual disease?”

It is through an extension of this inquiring lens that Hsu views the significance of the debut in-vivo eye trial at OHSU. “It was important because it allows us to go after a specific genetic disease that has a huge unmet need with no standard of care,” he says, referring to the current lack of treatment options for this kind of genetic condition. “It’s a pioneering trial for what could be developed into a new drug class – it’s all starting to just come together. And so I think it’s a very exciting time for the field.”

What is gene editing? Who’s doing it? And is it right?

The trouble and fascination with CRISPR is that it bleeds into so much more than state-of-the-art bioengineer­ing. Not surprising for a technology that has been described as the spark for the “industrial revolution of the human genome” and an “Ark of the Covenant […] hidden in the genome of bacteria”, capable of reshaping the human condition in a post-digital world.

Philosophically, CRISPR has reignited the debate over the direction and purpose of science, notably in the US, where after World War II, post-Manhattan Project distrust and scepticism towards scientists bled into explorations of genetics, leading to the current face-off: those who trust and expect that science can solve the world’s problems, and those who question the motives of scientists at every turn.

And splinter groups on both sides of the debate have emerged. Transhumanists hope that CRISPR turns out to be an important landmark in the self-guided evolution of mankind while, for bioconservatives, any meddling with the human genome should be treated with extreme caution or abandoned altogether. Those who find GMO crops to be highly suspect are likely to view the prospect of GMO people with even greater alarm.

Observers leaning towards science-scepticism can draw fuel for their position from the complex web of relation­ships that connect big money with academia, as illustrated by the landmark CRISPR operation at OHSU.

A knotty thread of sub-licensing deals, federal grants, venture capital and philanthropic gifting can be drawn between Editas Medicine, the pharmaceutical company behind the OHSU trial, and the non-profit Broad Institute of MIT and Harvard, which includes on its leadership team faculty vice-chair professor Liu – one of CRISPR’s most brilliant pioneers. Liu is also a co-founder, along with Zhang and Doudna among others, of Editas Medicine.

Here, the subplot thickens. Doudna cut ties with Editas six months into the company’s existence and co-founded genome-editing rival, Intellia Therapeutics, against the backdrop of a spat over the rights to CRISPR-based techno­logies. Legal battle lines were drawn between factions in the science hubs of the US. On the west coast, UC Berkeley and Intellia; facing them down from the east coast, the Broad Institute and Editas.

The visionaries at the cutting edge of CRISPR – by and large a reasonable and self-effacing group of people – play down the effects of the patent fight, presenting themselves as humble pioneers, elevated to great achievement on the shoulders of giants. Given that the stakes range from a slice of a multibillion-dollar industry to the prospect of a Nobel Prize, this default modesty may not represent the whole picture.

“When there’s money and potentially recognition involved in something, it does affect the way that people behave,” Doudna concedes. “And for some people, that becomes the end in and of itself. I think that was a very stark reality that I have had to face over the past few years, even with people in academia who I might have considered colleagues. The good news is that the science has not been impeded at all, in my view, by the patent dispute.”

Looking back on the rejection of an early CRISPR patent, Sontheimer could have ended up feeling like Pete Best, the Beatles’ drummer replaced by Ringo Starr on the eve of global stardom, but “it comes with the territory and that’s OK. I’ve wanted as much credit as I can get – this was a long and winding road and a lot of steps were necessary along the way, not just the last one or two. No one person ever discovers anything any more.

“That’s the way science goes: it’s sort of like the last person to screw the bolt onto the spaceship. Actually, it’s been great fun to watch it all play out. I mean, we had a feeling that we had found something pretty important, but, of course, we had no idea how big it was going to become.”

“CRISPR research is moving at light speed,” says Qi. “In 2012, I could finish reading almost all the papers written about CRISPR research in one afternoon. Now, I barely have time to scan the mountain of papers being released.”

Liu gave a TED talk in April 2019, noting that what had become possible thanks to CRISPR’s “molecular machines” would have been considered pure science fiction just five years earlier. In the spring and summer of 2020, studies were released showing that CRISPR had reversed diabetes in mice; pointed the way (via in-vivo primate trials) to a possible cure for heart disease; paved the way for studies of brain evolution by creating a new type of transparent squid; and alleviated “virtually all the complications” of a trial patient’s sickle cell disease. Simultaneously, the prime movers among the CRISPR cohort had diverted a large portion of their time and expertise towards Covid-19.

“Well, it seems that way, doesn’t it?” says Doudna, when asked whether CRISPR would make an ideal tool in the fight to defeat the coronavirus pandemic, given its viral roots. “It comes from a bacterial immune system, whose job is exactly that: find the virus and destroy it.”

Technically and practically, however, there’s a slew of obstacles that CRISPR has to overcome to produce an effective therapeutic for Covid-19. To explain, Qi heads for the amusement arcade. “I’ve always loved Pac-Man,” he says, about the video game in which a yellow puck consumes pixellated dots in a maze while pursued by ghosts. Qi’s bioengineered homage – Prophylactic Antiviral Crispr in huMAN cells (PAC-MAN) – works in a similar way.

“When players eat the big power pellet in the game, they no longer need to fear the ghosts. We studied CRISPR as a potential therapy for Covid-19 and realised that CRISPR can be our power pellet to help us fight this horrible virus. Unlike other antivirals such as a vaccine that boost our immune system to indirectly kill the virus, PAC-MAN uses the power of CRISPR to recognise specific targets – in this case, the viral RNA entering our cells – and directly destroys them. In this way, it is really like Pac-Man. It can chase down viruses and eliminate the threat.”

If tests progress as planned, the hope is to use PAC-MAN on multiple fronts. “I believe PAC-MAN is a broadly useful antiviral therapy,” continues Qi. “Of course, the technology is quite new, and it will take years to fully optimise. So whether it will have an immediate impact on the current Covid-19 pandemic is a question. Once it is developed in the clinics, it will be fast and easy to redesign it to fight another virus, for example, in weeks. This type of antiviral will be a key in the future to prevent another pandemic.”

Outside the race for a coronavirus therapeutic, CRISPR also holds great promise in diagnostics and testing. In July, Sherlock Biosciences – associated with Zhang and the east coast CRISPR posse – announced the world’s first CRISPR-based rapid, point-of-care test for Covid-19.

Earlier, in February, Zhang had tweeted approvingly that Sherlock’s Doudna-connect­ed competitor, Mammoth Biosciences, had openly shared its own studies of coronavirus diagnos­tics – evidence to back up the widespread claim among researchers that CRISPR rivalries are not harming the common good. “This is a really kind of cool place where, if your competitor wins, it can only be good for humanity,” says Hsu.

Even if a public triumph for CRISPR in the Covid-19 arena would go a long way to steadying the technology’s future course in terms of perceived benefits, roadblocks are sure to keep appearing. On the technical side, the “delivery problem” is one of CRISPR’s most stubborn challenges. Alternatives to the retooled virus – like the one used in the OHSU eye operation – are being explored.

Beyond the problems of CRISPR delivery, the human genome may just turn out to be too complex to master. “We don’t know which part of the genome went wrong for most diseases,” says Qi. “For example, in a cancer patient, which genes caused cancer? In the decay joint of the arthritis patient, which genes should we switch on to regenerate the joint? How many genes contribute to Alzheimer’s symptoms that we should target simultaneously?”

Hsu adds that even when the right genes are isolated, fixing them may not be as straightforward as a simple CRISPR cut-and-paste. “You can knock out a gene and maybe it is involved in this particular function that you’re trying to change, but it may well have many other functions that we just don’t yet know. When you actually do experi­ments in the lab you get this very hard-won appreciation for the complexity of biology.”

Despite all the problems that remain to be solved, “I’m an optimist,” says Sontheimer. “I don’t think that the prob­lems that currently still hold us back are insurmount­able. I think that the technological capabilities will continue to expand and get better and better all the time. I’m primarily focused on the biology and on trying to make it more possible to have the dream come true of therapeutic genome editing for patients who have a serious, otherwise unmet medical need.”

It might turn out that CRISPR and its spin-off techno­logies arrive too late to have any effective and lasting impact on the current pandemic. There could be a backlash against CRISPR’s darker potential that undermines the hope for the life-changing good it undoubtedly holds. Fear and scepticism could outmuscle reason and diligent inquiry as the CRISPR saga plays out against a backdrop of polar­isation and bias.

“In the old days, people came to herbs to find new medicine,” says Qi. “In the past century, people turned to chemistry. While human lifespans become longer, the quality of human life still needs to be improved. There are many age-related diseases which simply cannot be addressed using herbs or chemical drugs. The solution is likely in molecules – and CRISPR is probably one of them. One ultimate hope is that CRISPR can help to address ageing, and help people with age-related diseases.”

In some versions of local folklore, Portland’s Mount Hood was known as Wyeast, after the warrior involved in a bloody fraternal dispute over a beautiful woman named Loowit. Guardian of the only fire in the world, in the centre of the Bridge of the Gods, Loowit’s looks belied her true age. For her many years of service in the ember-tending depart­ment she had been offered eternal life by great chief Tyee Sahale, but told him that she did not want to live forever as an old crone. Youth and beauty were added to her immortality package as bonus gifts because, she reasoned, they would do exactly what Qi wants CRISPR to do: improve the quality of her life.