A Crack in Creation review – Jennifer Doudna, Crispr and a great scientific breakthrough

This is an invaluable account, by Doudna and Samuel Sternberg, of their role in the revolution that is genome editing

Scientific zeal … Jennifer Doudna.

It began with the kind of research the Trump administration wants to unfund: fiddling about with tiny obscure creatures. And there had been US Republican hostility to science before Trump, of course, when Sarah Palinobjected to federal funding of fruit fly research (“Fruit flies – I kid you not,” she said). The fruit fly has been a vital workhorse of genetics for 100 years. Jennifer Doudna’s work began with organisms even further out on the Palin scale: bacteriophages, tiny viruses that prey on bacteria.

Yoghurt manufacturers knew they were important, not least because bacteriophages can destroy yoghurt cultures. Research on the mechanism of this process began in the labs of Danisco (now part of the giant DuPont) in the early 2000s, before spreading through the university biotech labs. In 2012 Doudna and Samuel Sternberg’s team at Berkeley (they are co-authors of the book but it’s written solely in Doudna’s voice) came up with probably the greatest biological breakthrough since that of Francis Crick, James Watson and Rosalind Franklin.

Biologists had become intrigued by a curiosity in the genome of some bacteria: they had repeat patterns interspersed always by 20 bases of DNA, which turned out to match sequences found in the phages (as bacteriophages are always known) that prey on them. They had stumbled on a bacterial immune system, now known as Crispr (Clustered regularly interspaced short palindromic repeats) – a sequence reading the same forwards and backwards.

An astonishing story of molecular countermeasures against phage invasion was revealed; these enable the bacterium to recognise the phage next time it invades. More than that, Crispr guides a killer enzyme to cut the phage’s DNA at the point where the 20‑base sequence is found. Doudna then demonstrated that bacterial Crispr can be reprogrammed to cut any DNA from any organism. This is what has been sought for more than 30 years: an accurate (or almost accurate) way of editing DNA. And there has never been a better example of the unforeseen benefits of pure research because no one guessed that a technique of such power and universality would emerge from what appeared to be a fascinating but arcane corner of biology.

The Jurassic Park fantasy is kept alive by Crispr.
 The ‘Jurassic Park fantasy’ is kept alive by Crispr. 

Crispr is not just a triumph for unfettered scientific curiosity, it’s also a reminder that the secret of life lies in tiny things. The visible world can be beautiful but we are gulled into thinking it must be more important than what we can’t see. People have been making that mistake for a long time. In The Citizen of the World (1762), Oliver Goldsmith mocked the supposed pedantry of all who study the tiny creatures revealed by the microscope: “Their fields of vision are too contracted to take in the whole … Thus they proceed, laborious in trifles, constant in experiment, without one single abstraction, by which alone knowledge may be properly said to increase.” But, of course, it is precisely being able to “see” small things that has unlocked the biological treasure trove.

Very soon after Doudna’s paper on the technique appeared in 2012, labs all over the world tried it and found it was surpassingly easy to use; a gold rush began. It’s always difficult when something like this happens to sort the hope from the hype, but anticipation is now intense. Doudna does, though, sound many notes of caution. Yes, Crispr is the most accurate form of gene editing so far, but it isn’t perfect. There are 3bn bases in the human genome so there is always a chance of a stray 20-base match and a fatal cut in the wrong place. A debate is taking place on whether to allow gene edits only outside the body (with the edited cells reinserted) or to allow editing of eggs and sperm, which changes that germline forever. Doudna comes down cautiously for germline editing, pointing out that mitochondrial replacement therapy, which also leads to permanent genetic alteration, is already a reality in the UK.

For now the most exciting potential medical application is in single gene diseases, such as cystic fibrosis, sickle-cell anaemia and muscular dystrophy. This is the simplest possible task for Crispr. Just one base has to be corrected out of the 3bn and it’s not a needle in a haystack: Crispr can find and cut and repair it. Sickle-cell anaemia is caused by a faulty haemoglobin gene, so blood can easily be withdrawn from the body, the gene edited and returned to the body. But this approach demands extreme caution. Genes often have multiple effects and the sickle-cell gene is known to protect against malaria. So if you fixed the sickle-cell gene in the African population (where it is prevalent) there would be many new cases of malaria. But then Crispr can probably fix that, too; other researchers, with Gates Foundation funding, are urgently tackling that problem. There is hardly an area of medicine that could not benefit from Crispr, and on the fringe there is the Jurassic Park fantasy, kept tenuously alive by the work of Crispr’s other great name, George Church at Harvard, who is editing the elephant genome to create a creature more like a woolly mammoth.

If medical ethics loom large in debates around Crispr, money and patents loom even larger. Now that this apparently unpromising research has blossomed, the venture capitalists are gathering. Doudna recounts how, so soon after her triumph, “colleagues became rivals; papers were pored over for future patent battles”. The patent battle in question came to fruition after the book was completed. Doudna’s team lost this round, and it’s not clear what the future holds for Crispr’s intellectual property rights. It is unlikely that medical progress will be delayed but there will be some bruised participants and money spent along the way.



IN FEWER THAN five years, the gene-editing technology known as Crispr has revolutionized the face and pace of modern biology. Since its ability to find, remove, and replace genetic material was first reported in 2012, scientists have published more than 5,000 papers mentioning Crispr. Biomedical researchers are embracing it to create better models of disease. And countless companies have spun up to commercialize new drugs, therapies, foods, chemicals, and materials based on the technology.

Usually, when we’ve referred to Crispr, we’ve really meant Crispr/Cas9—a riboprotein complex composed of a short strand of RNA and an efficient DNA-cutting enzyme. It did for biology and medicine what the Model T did for manufacturing and transportation; democratizing access to a revolutionary technology and disrupting the status quo in the process. Crispr has already been used to treat cancer in humans, and it could be in clinical trials to cure genetic diseases like sickle cell anemia and beta thalassemia as soon as next year.

But like the Model T, Crispr Classic is somewhat clunky, unreliable, and a bit dangerous. It can’t bind to just any place in the genome. It sometimes cuts in the wrong places.And it has no off-switch. If the Model T was prone to overheating, Crispr Classic is prone to overeating.

Even with these limitations, Crispr Classic will continue to be a workhorse for science in 2018 and beyond. But this year, newer, flashier gene editing tools began rolling off the production line, promising to outshine their first-generation cousin. So if you were just getting your head around Crispr, buckle up. Because gene-editing 2.0 is here.

Power Steering

Crispr’s targeted cutting action is its defining feature. But when Cas9 slices through the two strands of an organism’s DNA, the gene-editor introduces an element of risk. Cells can make mistakes when they repair such a drastic genetic injury. Which is why scientists have been designing ways to achieve the same effects in safer ways.

One approach is to mutate the Cas9 enzyme so it can still bind to DNA, but its scissors don’t work. Then other proteins—like ones that activate gene expression—can be combined with the crippled Cas9, letting them toggle genes on and off (sometimes with light or chemical signals) without altering the DNA sequence. This kind of “epigenetic editing” could be used to tackle conditions that arise from a constellation of genetic factors, as opposed to the straightforward single mutation-based disorders most well-suited to Crispr Classic. (Earlier this month, researchers at the Salk Institute used one such system to treat several diseases in mice, including diabetes, acute kidney disease, and muscular dystrophy.)

Other scientists at Harvard and the Broad Institute have been working on an even more daring tweak to the Crispr system: editing individual base pairs, one at a time. To do so, they had to design a brand-new enzyme—one not found in nature—that could chemically convert an A-T nucleotide pairing to a G-C one. It’s a small change with potentially huge implications. David Liu, the Harvard chemist whose lab did the work, estimates that about half of the 32,000 known pathogenic point mutations in humans could be fixed by that single swap.

“I don’t want the public to come away with the erroneous idea that we can change any piece of DNA to any other piece of DNA in any human or any animal or even any cell in a dish,” says Liu. “But even being where we are now comes with a lot of responsibility. The big question is how much more capable will this age get? And how quickly will we be able to translate these technological advances into benefits for society?”

Putting On The Brakes

Crispr evolved in bacteria as a primitive defense mechanism. Its job? To find enemy viral DNA and cut it up until there was none left. It’s all accelerator, no brake, and that can make it dangerous, especially for clinical applications. The longer Crispr stays in a cell, the more chances it has to find something that sort of looks like its target gene and make a cut.

To minimize these off-target effects, scientists have been developing a number of new tools to more tightly control Crispr activity.

So far, researchers have identified 21 unique families of naturally occurring anti-Crispr proteins—small molecules that turn off the gene-editor. But they only know how a handful of them work. Some bind directly to Cas9, preventing it from attaching to DNA. Others turn on enzymes that outjostle Cas9 for space on the genome. Right now, researchers at UC Berkeley, UCSF, Harvard, the Broad, and the University of Toronto are hard at work figuring out how to turn these natural off-switches into programmable toggles.

Beyond medical applications, these will be crucial for the continued development of gene drives—a gene-editing technology that quickly spreads a desired modification through a population. Being able to nudge evolution one way or the other would be a powerful tool for combating everything from disease to climate change. They’re being considered for wiping out malaria-causing mosquitoes,and eradicating harmful invasive species. But out in the wild, they have the potential to spread out of control, with perhaps dire consequences. Just this year Darpa poured $65 million toward finding safer gene drive designs, including anti-Crispr off-switches.

Step On The Cas

Despite decades of advances, there’s still so much scientists don’t understand about how bugs in your DNA can cause human disease. Even if they know what genes are coded into a cell’s marching orders, it’s a lot harder to know where those orders get delivered, and how they get translated (or mistranslated) along the way. Which is why groups at Harvard and the Broad led by Crispr co-discoverer Feng Zhang are working with a new class of Cas enzymes that target RNA instead of DNA.

Since those are the instructions that a cell’s machinery reads to build proteins, they carry more information about the genetic underpinnings of specific diseases. And because RNA comes and goes, making changes to it would be useful for treating short-term problems like acute inflammation or wounds. The system, which they’re calling Repair, for RNA Editing for Programmable A to I Replacement, so far only works for one nucleotide conversion. The next step is to figure out how to do the other 11 possible combinations.

And scientists are finding new Cas enzymes all the time. Teams at the Broad have also been working to characterize cpf1—a version of Cas that leaves sticky ends instead of blunt ones when it cuts DNA. In February, a group from UC Berkeley discovered CasY and CasX, the most compact Crispr systems yet. And researchers expect to turn up many more in the coming months and years.

Only time will tell if Crispr-Cas9 was the best of these, or merely the first that captured the imagination of a generation of scientists. “We don’t know what’s going to wind up working best for different applications,” says Megan Hochstrasser, who did her PhD in Crispr co-discoverer Jennifer Doudna’s lab and now works at the Innovative Genomics Institute. “So for now I think it makes sense for everyone to be pushing on all these tools all at once.”

It will take many more years of work for this generation of gene-editors to find their way out of the lab into human patients, rows of vegetables, and disease-carrying pests. That is, if gene-editing 3.0 doesn’t make them all obsolete first.

Science and Morality

Science and Morality

science doesn’t give us a script for what to value or believe in, but it helps us write that script.

I am a faithful book buyer and an omnivorous reader, but one with a precocious streak—I like to look up authors and email them with questions about their books. Since penning a book about the CRISPR-Cas9 gene-modification system, readers are now writing to me with all sorts of middle-of-the-night thoughts. Many people think of science as a good thing—STEM has cachet, synonymous with our goodness—but the advance of the life sciences unnerves some people.

Matthew Endrizzi, a biology teacher in New Hampshire, suggested recombinant DNA research—including CRISPR—was dangerous enough in theory that he has proposed to move it all to the moon (he has not yet secured the funding or political will to do this). Margalit Laufer, a therapist in the Netherlands, has started a grassroots campaign to stop the application of CRISPR, a motivation which is linked to her views on the divinity of nature.

Science can discredit our speculations, folk science and illusions about how the world works and what to be afraid of; but the opposite, science as a positive script for what to value or believe has its limitations. Robert Oppenheimer was painfully aware of this when he concluded that “science is not all of the life of reason; it is a part of it.”

CRISPR may indeed be used to create bioweapons through the engineering of microbes, or create pathological strains through unscrupulous genetic manipulation. But the unleashing of dangerous microbes has been a concern at least since the 1970s when recombinant DNA first emerged, not to mention giving rise to films such as the Andromeda Strain and The Stand.

In fact, a temporary moratorium on gene engineering was tried in the 1970s, but many scientists already thought the risks of biohazard were overblown. British microbiologist Ephraim Anderson titled one paper Indiscriminant use of antibiotics has exerted more pressure on the bacterial population than could be wielded by all the research workers in the world put together. We cannot rule-out the prospect that a genetically modified microbe could cause a global threat to humans. But the risks are minute and simply worth enduring, most academics have concluded.

The argument that genes embody a sort of sacrosanct character that should not be interfered with is not too compelling, since artifacts of viruses are burrowed in our genomes, and genes undergo mutations with each passing generation. Even so, the principle that all life has inherent dignity is hardly a bad thought and provides a necessary counterbalance to the impulse to use in vitro techniques and CRISPR to alter any gene variant to reduce risk or enhance features, none of which are more or less perfect but variations in human evolution.

Indeed, the question of dignity is thornier than we might imagine, since science tends to challenge the belief in abstract or enduring concepts of value. How to uphold beliefs or a sense of dignity seems ever confusing and appears to throw us up against an age of radical nihilism as scientists today are using the gene editing tool CRISPR to do things such as tinker with the color of butterfly wingsgenetically alter pigs, even humans. If science is a method of truth-seeking, technology its mode of power and CRISPR is a means to the commodification of life. It also raises the possibility this power can erode societal trust.

In 2008, the President’s Council on Bioethics released a 555-page report, titled Human Dignity and Bioethics, which fielded essays by wide array of thinkers including the progressive philosopher Daniel Dennett and conservatives such as Leon Kass. As Dennett put the problem, “When we start treating living bodies as motherboards on which to assemble cyborgs, or as spare parts collections to be sold to the highest bidder, where will it all end?” The solution of rescuing human dignity from the commercial forces of science, Dennett noted, cannot involve resorting to “traditional myths” since this “will backfire” but instead concepts of human dignity should be based on our sovereign right to “belief in the belief that something matters.”

Dennett argues that faith is important in an everyday sense, such as most people have faith in democracy even as “we are often conflicted, eager to point to flaws that ought to be repaired, while just as eager to reassure people that the flaws are not that bad, that democracy can police itself, so their faith in it is not misplaced.” The point is also true about science, “since the belief in the integrity of scientific procedures is almost as important as the actual integrity.” In fact, we engage in a sort of “belief maintenance” insofar that “this idea that there are myths we live by, myths that must not be disturbed at any cost, is always in conflict with our ideal of truth-seeking” and even as we commit to ideas in public or just in our hearts, “a strange dynamic process is brought into being, in which the original commitment gets buried” in layers of internal dialog and counterargument. “Personal rules are a recursive mechanism; they continually take their own pulse, and if they feel it falter, that very fact will cause further faltering,” the psychiatrist George Ainslie wrote in the Breakdown of Will. If science can challenge beliefs, dignity is more primal—it is the right to hold beliefs, make use of science, and exercise belief maintenance.

Dignity is tricky to defend against the explication and engineering of human life by means of chemical processes, and it is complicated by the reality that many people increasingly look to science to shape their view and moral direction, as we are living in a new age of resurgent scientism—an assumption that science encodes values. A century ago, scientism appeared to be all but dead. The modernist break caused rupture between the moral and cultural commitments and sheer existence—hence it led to existentialism and the struggle over defining our commitments.

Whatever it meant to life a good life, it couldn’t be predefined by culture or science. In Anton Chekhov’s 1889 short story, “A Boring Story,” Nikolai Stepanovich, an internationally recognized scientist and professor of medicine, slips into melancholy near the end of his life. Despite his incredible success, his life seems evermore ambiguous, as the modernist movement comes to displace his authority. Katja, a young girl, a representative of the new generation, comes to him asking for advice and guidance, but Nikolai knows he has no way to tell her how to live. The irony is that freedom invoked a melancholy. His physician friend Mikhail Fyodorovich confides in Nikolai, “Science, God knows, has become obsolete. Its song has sung. Yes… Humanity has already begun to feel the need of replacing it with something else.”

In fact, we may be in the midst of a rebound to this break, whereby a resurgent scientism defines the moral directive, and data science is used to shape the arc of our decisions. Scientists can appeal to a mythos of bringing us closer to reality, as if peering into neuroimagery or analyzing the genome gives us information that is more true that life as we experience it. To some extent we learn bits and pieces of what makes us who we are. But ironically, it can weaken our sense of reality due to the obsession with statistical signals, which are often taken out of context, algorithms which speciously shape societal decisions, datingdecisions, or pick the next president—much of which fails us. More time and data is going to vastly improve the ability of science to regulate our lives, quite the opposite. This is because the life of the mind often involves the toggling between two opposing ideas, where there are no right decisions. As economist Thomas Sowell put it, “The march of science and technology does not imply growing intellectual complexity in the lives of most people. It often means the opposite.”

In his essay “The Virtue of Scientific Thinking” in the Boston Review, Harvard science historian Steven Shapin, who has also written on how much of our belief in science and the world is based on trust in the written word, has argued that trust in science has a critical role in morality, and that science, say climate science, can indeed be useful to shape values and direct policy decisions. But there are also obvious pitfalls to resurgent scientism. In recent decades, the free inquiry of science has been linked to technology, and thus to modes of institutional power, and monetization.

Therefore, scientific inquiry can be in jeopardy to the extent that it becomes put to the extreme uses of capitalization of the life sciences. Science, once a challenge to institutional authority, has increasingly been defined by status, finance and what look like hierarchical structures, which I think that people subconsciously like to see. But scientists, by close association with biotech, also risk a backlash that people make disengage with them, and begin to see credible facts as merely framing one more business venture. Importantly, we trust that what scientists say is probably true, but there is no guarantee of this trust or belief. In fact, trust is jeopardy as scientists connect their work to modes of technology as a means to personal power, half-million dollar cancer drugs, a billion-dollar CRISPR patent battle, and the like.

Science does not provide a positive script—but information to help build that script. For instance, a hypothesis is a proposition or belief that can be tested; but as Karl Popper once suggested, a hypothesis cannot be proven, only disproven (one black swan proves not all swans are white, but more white swans do not) since a given can never be completely proved—there is always the chance of a challenge by new data. Science offers no starting points, and there are questions of whether science is, in fact, leading us to any complete view of nature, which will be unchallenged, or, in some way, enlightened.

Increasingly, some scientists deny a Theory of Everything. Physical systems may be in a state of competition; in other words—there is no logic at the basis of reality. Therefore, while science is a useful tool, we have to at least entertain the prospect that it only leads to an abyss of time—an ongoing building and rebuilding of human histories. I suspect it will fail as a singular means to guide us to any conflict-free reality, and that we are far from done struggling with the consequences of the modernist break.


First U.S. Human Embryo Gene Editing Experiment Successfully “Corrects” a Heart Condition


A study published today in the journal Nature confirms earlier reports of the first-ever successful gene-editing of embryos in the U.S. Though controversial, the treatment could one day be used to address any of the 10,000 disorders linked to just a single genetic error.


Last week, reports circulated  that doctors had successfully edited a gene in a human embryo — the first time such a thing had been done in the United States. The remarkable achievement confirmed the powerful potential of CRISPR, the world’s most efficient and effective gene-editing tool. Now, details of the research have been published in Nature.

The procedure involved “correcting” the DNA of one-cell embryos using CRISPR to remove the MYBPC3 gene. That gene is known to cause hypertrophic cardiomyopathy (HCM), a heart disease that affects 1 out of 500 people. HCM has no known cure or treatment as its symptoms don’t manifest until the disease causes sudden death through cardiac arrest.

How CRISPR Works: The Future of Genetic Engineering and Designer Humans
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The researchers started with human embryos created from 12 healthy female donors and sperm from a male volunteer who carried the MYBOC3 gene. The defective gene was cut out using CRISPR around the time the sperm was injected into the eggs.

 As a result, as the embryos divided and grew, many repaired themselves using the non-edited genes from the genetic materials of the female donors, and in total, 72 percent of the cells that formed appeared to be corrected. The researchers didn’t notice any “off-target” effects on the DNA, either.

The researchers told The Washington Post that their work was fairly basic. “Really, we didn’t edit anything, neither did we modify anything,” explained Shoukhrat Mitalipov, lead author and a researcher at the Oregon Health and Science University. “Our program is toward correcting mutant genes.”


Basic or not, the development is remarkable.“By using this technique, it’s possible to reduce the burden of this heritable disease on the family and eventually the human population,” Mitalipov said in an OHSU press release.

However, gene editing is a controversial area of study, and the researchers’ work included changes to the germ line, meaning the changes could be passed down to future generations. To be clear, though, the embryos were allowed to grow for only a few days and none were implanted into a womb (nor was that ever the researchers’ intention).

In fact, current legislation in the U.S. prohibits the implantation of edited embryos. The work conducted by these researchers was well within the guidelines set by the National Academies of Sciences, Engineering, and Medicine on the use of CRISPR to edit human genes.

University of Wisconsin-Madison bioethicist Alta Charo thinks that the benefits of this potential treatment outweigh all concerns. “What this represents is a fascinating, important, and rather impressive incremental step toward learning how to edit embryos safely and precisely,” she told The Washington Post. “[N]o matter what anybody says, this is not the dawn of the era of the designer baby.”

Before the technique could be truly beneficial, regulations must be developed that provide clearer guidelines, according to Mitalipov. If not, “this technology will be shifted to unregulated areas, which shouldn’t be happening,” he explained.

More than 10,000 disorders have been linked to just a single genetic error, and as the researchers continue with their work, their next target is BRCA, a gene associated with breast cancer growth.

Mitalipov hopes that their technique could one day be used to treat a wide-range of genetic diseases and save the lives of millions of people. After all, treating a single gene at the embryonic stage is far more efficient that changing a host of them in adults.


CRISPR, Life Altering Genetic Innovation

The scientific community is in the midst of a gold rush in new technological applications all made possible by the CRISPR/Cas9 system. CRISPR, short for “clustered regularly interspaced palindromic repeats” is quite possibly the biggest innovation in biological science since PCR was developed over three decades ago. This is literally life altering genetic innovation.


Scientists have been modifying genomes for years, so what’s the big deal behind this new technology?

In the past, prior to 2010, in order to modify the genome of a mouse, researchers would transfer embryonic stem cells into a mouse embryo containing the genetic mutation of choice. It would then take three generations to see the desired mutation and actually start utilizing the mutation for research purposes. This resulted in large amounts of time and money spent on breeding two unnecessary generations of mice without the guarantee of success. If a researcher wished to modify five genes of interest, this process would be repeated, you guessed it, five more times.

Taking this into account, CRISPR only needs one generation. This system is precise, efficient, and flexible, allowing for multiple mutations to be made all at once. Its efficacy has been proven time and time again in mice, monkeys, and recently in non-viable human embryos by a group of researchers in China, which proves its potential to treat ANY genetic disease.

As applications of this system are developed, many billion-dollar opportunities will arise. With this much money at stake along with world changing potential, rights to the invention are sure to create a heated patent battle at the USPTO, begging the question; who owns the technology anyways?

Professor Jennifer Doudna of UC Berkeley and Emmanuelle Charpentier from Umea University in Sweden filed on March 15, 2013 – one day before the first-to-file rule took effect – and claimed a priority date of May 25, 2012. On the other hand, Feng Zhang of the broad institute of MIT and Harvard in Cambridge, Massachusetts filed on October 15, 2013 under the accelerated examination program. The Broad Institute received patent No. 8,697,359 in April of 2014 claiming priority to a provisional application filed in December 2012.

As the Broad Institute continued to file applications for the technology, Doudna filed a Suggestion of Interference claiming that the Broad Institute Patents interfered with Doudna’s previous application. Pre AIA gives right to who created the invention first, unlike the first-to-file rules of today. An interference procedure is underway with oral arguments set for November 2016.

At stake are the rights to exclusively make, use, license, and sell the invention. The CRISPR/Cas9 system has the ability to completely alter how we treat genetic diseases, and may lead to the actualization of ‘designer babies’ – babies born with their traits hand picked by the parents. The discovery of a lifetime is up for grabs and it will be interesting to see who emerges with rights to the technology. Each party has issued liscences to large biotech companies ready to use the technology in grand-scale implication, however these projects have been delayed, pending the USPTO decision of this patent battle.


CRISPR Is Rapidly Ushering in a New Era in Science

A Battle Is Waged

A battle over CRISPR is raging through the halls of justice. Almost literally. Two of the key players in the development of the CRISPR technology, Jennifer Doudna and Feng Zhang, have turned to the court system to determine which of them should receive patents for the discovery of the technology. The fight went public in January and was amplified by the release of an article in Cell that many argued presented a one-sided version of the history of CRISPR research. Yet, among CRISPR’s most amazing feats is not its history, but how rapidly progress in the field is accelerating.

A CRISPR Explosion

CRISPR, which stands for clustered regularly-interspaced short palindromic repeats, is DNA used in the immune systems of prokaryotes. The system relies on the Cas9 enzyme* and guide RNA’s to find specific, problematic segments of a gene and cut them out. Just three years ago, researchers discovered that this same technique could be applied to humans. As the accuracy, efficiency, and cost-effectiveness of the system became more and more apparent, researchers and pharmaceutical companies jumped on the technique, modifying it, improving it, and testing it on different genetic issues.

Then, in 2015, CRISPR really exploded onto the scene, earning recognition as the top scientific breakthrough of the year by Science Magazine. But not only is the technology not slowing down, it appears to be speeding up. In just two months — from mid-November, 2015 to mid-January, 2016 — ten major CRISPR developments (including the patent war) have grabbed headlines. More importantly, each of these developments could play a crucial role in steering the course of genetics research.


CRISPR made big headlines in late November of 2015, when researchers announced they could possibly eliminate malaria using the gene-editing technique to start a gene drive in mosquitos. A gene drive occurs when a preferred version of a gene replaces the unwanted version in every case of reproduction, overriding Mendelian genetics, which say that each two representations of a gene should have an equal chance of being passed on to the next generation. Gene drives had long been a theory, but there was no way to practically apply the theory. Then, along came CRISPR. With this new technology, researchers at UC campuses in Irvine and San Diego were able to create an effective gene drive against malaria in mosquitos in their labs. Because mosquitos are known to transmit malaria, a gene drive in the wild could potentially eradicate the disease very quickly. More research is necessary, though, to ensure effectiveness of the technique and to try to prevent any unanticipated negative effects that could occur if we permanently alter the genes of a species.

Muscular Dystrophy

A few weeks later, just as 2015 was coming to an end, the New York Times reportedthat three different groups of researchers announced they’d successfully used CRISPR in mice to treat Duchenne muscular dystrophy (DMD), which, though rare, is among the most common fatal genetic diseases. With DMD, boys have a gene mutation that prevents the creation of a specific protein necessary to keep muscles from deteriorating. Patients are typically in wheel chairs by the time they’re ten, and they rarely live past their twenties due to heart failure. Scientists have often hoped this disease was one that would be well suited for gene therapy, but locating and removing the problematic DNA has proven difficult. In a new effort, researchers loaded CRISPR onto a harmless virus and either injected it into the mouse fetus or the diseased mice to remove the mutated section of the gene. While the DMD mice didn’t achieve the same levels of muscle mass seen in the control mice, they still showed significant improvement.

Writing for GizmodoGeorge Dvorsky said, “For the first time ever, scientists have used the CRISPR gene-editing tool to successfully treat a genetic muscle disorder in a living adult mammal. It’s a promising medical breakthrough that could soon lead to human therapies.”


Only a few days after the DMD story broke, researchers from the Cedars-Sinai Board of Governors Regenerative Medicine Institute announced progress they’d made treating retinitis pigmentosa, an inherited retinal degenerative disease that causes blindness. Using the CRISPR technology on affected rats, the researchers were able to clip the problematic gene, which, according to the abstract in Molecular Therapy, “prevented retinal degeneration and improved visual function.” As Shaomei Wang, one of the scientists involved in the project, explained in the press release, “Our data show that with further development, it may be possible to use this gene-editing technique to treat inherited retinitis pigmentosa in patients.” This is an important step toward using CRISPR  in people, and it follows soon on the heels of news that came out in November from the biotech startup, Editas Medicine, which hopes to use CRISPR in people by 2017 to treat another rare genetic condition, Leber congenital amaurosis, that also causes blindness.

Gene Control

January saw another major development as scientists announced that they’d moved beyond using CRISPR to edit genes and were now using the technique to control genes. In this case, the Cas9 enzyme is essentially dead, such that, rather than clipping the gene, it acts as a transport for other molecules that can manipulate the gene in question. This progress was written up in The Atlantic, which explained: “Now, instead of a precise and versatile set of scissors, which can cut any gene you want, you have a precise and versatile delivery system, which can control any gene you want. You don’t just have an editor. You have a stimulant, a muzzle, a dimmer switch, a tracker.” There are countless benefits this could have, from boosting immunity to improving heart muscles after a heart attack. Or perhaps we could finally cure cancer. What better solution to a cell that’s reproducing uncontrollably than a system that can just turn it off?

CRISPR Control or Researcher Control

But just how much control do we really have over the CRISPR-Cas9 system once it’s been released into a body? Or, for that matter, how much control do we have over scientists who might want to wield this new power to create the ever-terrifying “designer baby”?

The short answer to the first question is: There will always be risks. But not only is CRISPR-Cas9 incredibly accurate, scientists didn’t accept that as good enough, and they’ve been making it even more accurate. In December, researchers at the Broad Institute published the results of their successful attempt to tweak the RNA guides: they had decreased the likelihood of a mismatch between the gene that the RNA was supposed to guide to and the gene that it actually did guide to. Then, a month later, Nature published research out of Duke University, where scientists had tweaked another section of the Cas9 enzyme, making its cuts even more precise. And this is just a start. Researchers recognize that to successfully use CRISPR-Cas9 in people, it will have to be practically perfect every time.

But that raises the second question: Can we trust all scientists to do what’s right? Unfortunately, this question was asked in response to research out of China in April, in which scientists used CRISPR to attempt to genetically modify non-viable human embryos. While the results proved that we still have a long way to go before the technology will be ready for real human testing, the fact that the research was done at all raised red-flags and shackles among genetics researchers and the press. These questions may have popped up back in March and April of 2015, but the official response came at the start of December when geneticists, biologists and doctors from around the world convened in Washington D. C. for the International Summit on Human Gene Editing. Ultimately, though, the results of the summit were vague, essentially encouraging scientists to proceed with caution, but without any outright bans. However, at this stage of research, the benefits of CRISPR likely outweigh the risks.

Big Pharma

“Proceed with caution” might be just the right advice for pharmaceutical companies that have jumped on the CRISPR bandwagon. With so many amazing possibilities to improve human health, it comes as no surprise that companies are betting, er, investing big money into CRISPR. Hundreds of millions of dollars flooded the biomedical start-up industry throughout 2015, with most going to two main players, Editas Medicine and Intellia Therapeutics. Then, in the middle of December, Bayer announced a joint venture with CRISPR Therapeutics to the tune of $300 million. That’s three major pharmaceutical players hoping to win big with a CRISPR gamble. But just how big of a gamble can such an impressive technology be? Well, every company is required to license the patent for a fee, but right now, because of the legal battles surrounding CRISPR, the original patents (which the companies have already licensed) have been put on hold while the courts try to figure out who is really entitled to them. If the patents change ownership, that could be a big game-changer for all of the biotech companies that have invested in CRISPR.

Upcoming Concerns?

On January 14, a British court began reviewing a request by the Frances Crick Institute (FCI) to begin genetically modified research on human embryos. While Britain’s requirements on human embryo testing are more lax than the U.S. — which has a complete ban on genetically modifying any human embryos — the British are still strict, requiring that the embryo be destroyed after the 14th day. The FCI requested a license to begin research on day-old, “spare” IVF embryos to develop a better understanding of why some embryos die at early stages in the womb, in an attempt to decrease the number of miscarriages women have. This germ-line editing research is, of course, now possible because of the recent CRISPR breakthroughs. If this research is successful, The Independent argues, “it could lead to pressure to change the existing law to allow so-called “germ-line” editing of embryos and the birth of GM children.” However, Dr. Kathy Niacin, the lead researcher on the project, insists this will not create a slippery slope to “designer babies.” As she explained to the Independent, ““Because in the UK there are very tight regulations in this area, it would be completely illegal to move in that direction. Our research is in line with what is allowed an in-keeping in the UK since 2009 which is purely for research purposes.”

Woolly Mammoths

Woolly Mammoths! What better way to end an article about how CRISPR can help humanity than with the news that it can also help bring back species that have gone extinct? Ok. Admittedly, the news that George Church wants to resurrect the woolly mammoth has been around since last spring. But the Huffington Post did a feature about his work in December, and it turns out his research has advanced enough now that he predicts the woolly mammoth could return in as little as seven years. Though this won’t be a true woolly mammoth. In fact, it will actually be an Asian elephant boosted by woolly mammoth DNA. Among the goals of the project is to help prevent the extinction of the Asian elephant, and woolly mammoth DNA could help achieve that. The idea is that a hybrid elephant would be able to survive more successfully as the climate changes. If this works, the method could be applied to other plants and animal species to increase stability and decrease extinction rates. As Church tells Huffington Post, “the fact is we’re not bringing back species — [we’re] strengthening existing species.”

And what more could we ask of genetics research than to strengthen a species?

*Cas9 is only one of the enzymes that can work with the CRISPR system, but researchers have found it to be the most accurate and efficient.


CRISPR pioneer muses about long journey from China to pinnacle of American science

That’s because of CRISPR, the gene-editing technique that lets scientists manipulate the genetic code of organisms almost like revising a sentence with a word processor. Zhang was one of its pioneers, and on Wednesday he emerged victorious after a bitter patent dispute.The ruling, by judges with the U.S. Patent Office, declared that Zhang’s work on living plant and animal cells was sufficiently original to deserve its own protection. It was a decisive outcome that will surely prove lucrative for Zhang and the Broad Institute, but he did not do anything special to celebrate. He made no immediate public comment. He did not even read the news coverage, he said.

“The patent stuff is not so interesting, and it can be distracting,” the soft-spoken scientist offered a day later, finally addressing the case as he sat down with a Washington Post reporter for a previously scheduled interview. “Now we can get back to work.”

The patent dispute was closely followed in the triangle of geography marked by the institute, Harvard University and the Massachusetts Institute of Technology. Here, in what has become the Silicon Valley of the life sciences, Zhang and his colleagues have spun off ventures that can commercialize their inventions.

CRISPR is an all-purpose tool that promises great advances in the prevention of diseases caused by genetic mutations. In China, Zhang’s birth country, it is already being used in human clinical trials.

Yet the technique has also raised unsettling possibilities for cosmetic human enhancements and “designer babies.” Earlier this week, the National Academy of Sciences and National Academy of Medicine produced a long report on the ethics of gene editing, arguing for extreme caution when dealing with heritable human traits but leaving open the possibility of use to remove disease-causing genes.

Some critics worry about a slippery slope, but Zhang thinks the bioethics committee got it just right.

“I think these are important issues, but I don’t think right at this second we should be overly concerned about it. It’s too far off,” he said.

The politics of science

Even with the patent case behind him, however, there is another significant distraction these days. It arises not through the courts but from the White House.

Science is inherently an international enterprise, built around a universal language of discovery and methodology. Zhang’s lab, like similar facilities across the country, has a large percentage of foreign-born scientists drawn to research opportunities in the United States.

President Trump’s executive order banning entry from seven Muslim-majority countries has alarmed this global community. The Broad, as it is commonly called, put out a statement of opposition, saying the order “turns its back on one of America’s greatest sources of strength: the flow of visitors, immigrants and refugees who have enriched our nation with their ideas, dreams, drive, energy, and entrepreneurship.”

 Zhang talks of his own life story when asked about Trump’s action.

“From my own experience, America has been an amazing place,” he said. “And it sort of gives opportunities for immigrants to realize what they want to do, to reach for their potential, and also, by doing that, make the world a better place. I’m very fortunate to have had the opportunity to move here.”

He was 11 when he first came to the United States in 1993. He spoke almost no English, arriving with his father to at last rejoin his mother. The teeming city of Shijiazhuang, in the north of China, was replaced by the alien landscape of Des Moines.

His mother had not intended to stay following her studies here, but Iowans embraced her. She got a good job with a company called the Paper Corp. She decided to start a new life and bring her son and husband to the United States. They each received a series of visas and green cards. She eventually became a citizen, as did her son. Her husband remains a Chinese citizen.

“I never felt I was discriminated against. I never felt we weren’t welcome there,” Zhang said of his youth in the heartland. And there were other immigrants, too, many of them Vietnamese refugees from war zones. He spent half the day learning English and then playing word bingo to hone his vocabulary.

He hung out with other kids interested in science. “We were all nerds,” he said. As a teenager, he got a position working after school at the Human Gene Therapy Research Institute. He could call himself a bench scientist, often working late into the evening while his mother waited for him in the parking lot.

Elite institutions soon recognized his brilliance. His résumé includes a degree from Harvard, then a doctorate from Stanford. He learned about the natural bacterial immune system, CRISPR, an acronym for clustered regularly interspaced short palindromic repeats.

Bacteria evolved a defense mechanism against viral invaders that would insert genetic material into bacterial DNA. The system functions like molecular scissors, snipping away the invasive material.

Two other researchers, who would become rivals in the patent case, published the first paper describing the gene-editing technique and applied for patents. Jennifer Doudna and Emmanuelle Charpentier showed how to turn the natural bacterial system into a laboratory tool, but initially they did not apply it to plant and animal cells. That was Zhang’s breakthrough, published in 2013 at the same time as a similar paper by Harvard geneticist George Church.

“Feng was very early in recognizing the importance of reducing it to practice in mammalian cells,” Church said this week.

Doudna and Charpentier can still receive patents on their original discovery. In an email Friday to The Post, Doudna wrote, “Obviously the Broad Institute is happy that their patent didn’t get thrown out, but we are pleased that our patent can now proceed to be issued.”

But she raised another concern. The judges’ decision was based in part on public comments she made, expressing uncertainty about whether CRISPR would work in cells with nuclei. Because of that, she fears the ruling could have a chilling effect on scientific communication.

“Must every scientist now factor in a potential patenting strategy and alter how transparent they are about their work?” Doudna wrote.

Doudna and Charpentier have already received the $3 million Breakthrough Prize funded by Silicon Valley tech tycoons. Then earlier this year they won the Japan Prize, each receiving the equivalent of about $420,000.

And lurking out there somewhere is the Nobel.

‘Why do we age?’

On Thursday, the morning after the ruling, Zhang drove his 2004 BMW to work as always, arriving at 7:30 to meet with a student and help him prepare for a class presentation. Then he had a call with an oil executive in the United Arab Emirates who is funding research on a genetic disease that affects the executive’s daughter.

He still has a spot in his lab for experiments, though he does those during the summer since right now he’s busy teaching two classes. The lab work is in the hands of about 20 researchers, some already with doctorates and medical degrees.

CRISPR gets all the publicity these days, but it is not the only game in town. Life is a complex chemical system that over billions of years has developed all sorts of tricks and mechanisms. Most of the microbes in the human gut have never been cultured or characterized. Basic questions remain unanswered.

“Why do we age?” Zhang asked.

The CRISPR system is itself a work in progress. It’s an inexact editor still.

“It cuts very well,” he said. “To insert something, it doesn’t work very well at all.”

But he’s working on that. Everyone stand by.



A new CRISPR breakthrough could lead to simpler, cheaper disease diagnosis

Scientists say SHERLOCK is a ‘game changer’

Scientists say SHERLOCK, a new CRISPR breakthrough and diagnosis tool, could be a game changer for the ability to identify infectious diseases like Zika.

The controversial laboratory tool known as CRISPR may have found a whole new world to conquer. Already the favored method of editing genes, CRISPR could soon become a low-cost diagnostic tool that could be used practically anywhere to determine if someone has an infectious disease such as Zika or dengue.

CRISPR — which stands for Clustered Regularly Interspaced Short Palindromic Repeats — is basically a bacterial immune system that uses “molecular scissors” to snip away genetic material from invasive viruses. Early in this decade, researchers figured out how to exploit the natural system to craft a relatively cheap, remarkably easy-to-use technology for editing genetic codes almost as readily as using a word processor to revise a paragraph.

On Thursday, Feng Zhang, one of the pioneers of CRISPR, and 18 colleagues published a paper in the journal Science showing how they had turned this system into an inexpensive, reliable diagnostic tool for detecting nucleic acids — molecules present in an organism’s genetic code — from disease-causing pathogens. The new tool could be widely applied to detect not only viral and bacterial diseases but also potentially for finding cancer-causing mutations.

CRISPR has been a sensation in the world of molecular biology, but the powerful tool has incited fears that it could be misused. Ethicists earlier this year released a report saying it should be limited in humans to treating diseases or disabilities, and with special caution when genetic changes would involve eggs, sperm or embryos and potentially be inherited by future generations. But CRISPR is already widely used in laboratory studies and has shown great promise in revealing the genetic origins of diseases, including cancer. This new application would propel CRISPR into the much less controversial realm of point-of-care disease diagnosis.

The new study has a whiff of marketing about it: Zhang and his colleagues have named their new tool SHERLOCK — for Specific High Sensitivity Enzymatic Reporter UnLOCKing.

“Nature is really amazing. Over the course of billions of years, it’s come up with all these very powerful enzyme systems, and by studying the basic biology of these systems, some of them will give rise to important applications — like genome editing, like diagnostics,” Zhang, of the Broad Institute of MIT and Harvard, told The Washington Post.

Co-author Jim Collins, also of the Broad Institute, said, “In this diagnostic application we are really harnessing the power and diversity of biology. … I view it as a potentially transformative diagnostic platform.”

They report that their technique is highly portable and could cost as little as 61 cents per test in the field. Such a process would be extremely useful in remote places without reliable electricity or easy access to a modern diagnostic laboratory.

“We showed that this system is very stable, so you can really put it on a piece of paper and it will survive. You don’t have to refrigerate it all the time,” Zhang said.

“My head is spinning a little bit because this looks very, very provocative. And exciting,” said William Schaffner, a professor of infectious diseases and preventive medicine at Vanderbilt University Medical Center, who was not involved in the new research. “If you had something that could be used as a screening test, very inexpensively and rapidly, that would be a huge advance, particularly if it could detect an array of infectious agents.”

Collins said the scientists behind SHERLOCK have filed for patents on the technology, and are discussing ways to move their new tool from the laboratory to the clinical arena.

Zhang is one of the key figures in the CRISPR patent fight between the Broad Institute and the University of California at Berkeley, the latter the homebase of CRISPR pioneer Jennifer Doudna. The patent board ruled in favor of Zhang and Broad earlier this year. Doudna and another researcher had published their CRISPR discoveries first, but Zhang took the technique another step, into cells with nuclei, and the patent board ruled that the second step was sufficiently different that both could be eligible for patent protection. On Thursday, Berkeley and other interested parties filed an appeal of that ruling.

Scott Weaver, an infectious disease researcher at the University of Texas Medical Branch at Galveston, who was not involved in the new research, said after reading the study, “It looks like one significant step on the pathway which is the Holy Grail, which is developing point-of-care, or bedside detection, which doesn’t require expensive equipment or even reliable power.”

Harvard geneticist George Church is one of the lead researchers propelling CRISPR, a breakthrough gene-editing technique, into the future.
CRISPR is capable of preventing congenital disease.

Kazuo Ishiguro: Soon, We Will Be Able to Create Humans Who Are Superior to Other Humans

  • Author Kazuo Ishiguro believes we are unwittingly walking into a dystopian future because the world has yet to give science and technology more than just peripheral interest.
  • He believes that we have yet to engage in meaningful conversations about where scientific advancements will take us, and the kind of impact they will have on our lives.


According to Kazuo Ishiguro, there are three areas of science that are set to transform how we live and interact with others over the next few decades: gene editing, robotics, and artificial intelligence (AI).

Ishiguro, granted, is best known as one of the most celebrated fiction writers today. He is behind the novel Never Let Me Go, the story of a dystopian future where humans are cloned to be organ donors. But the possibility of a future so fundamentally changed by scientific advancements could be more than the fruit of the author’s creativity and imagination.


He cites CRISPR as a primary example. The discovery of this gene editing tool gives scientists the option to modify pieces of the genome, paving the way for unprecedented applications in medicine. Right now, we can replace faulty genes with working ones, which is a great accomplishment unto itself. But moving forward, as we learn more about this new technology, the option to enhance functional genes to create intellectually and physically superior humans becomes a real possibility.

Think of it as like a real world Gattaca, where society is divided into two classes. Half will be populated with humans with genetically engineered genes that makes them healthier, smarter, stronger—designer babies, essentially. And the other half, with humans whose genetic sequence has been left to chance, untouched, leaving them biologically inferior.


Ishiguro believes we are unwittingly walking into this dystopian future because the world has yet to give science and technology more than just peripheral interest. Sure, we celebrate the headlines and acknowledge the accomplishments, but we have yet to engage in meaningful conversations about where these advancements will take us, and the kind of impact they will have on our lives.

Developments in AI and robotics for instance, mean a major part of intellectual capital will shift to what he refers to as “the Silicon Valley masters of the universe”—it will no longer be under universities or government funded labs. The lack of regulation regarding these rapid developments is also cause for concern. And of course, there is the ongoing debate about the ethics behind advancements in genetic sciences, like CRISPR.

The relevance of Ishiguro’s musings about the future comes in time for the opening of a new permanent mathematics gallery at the Science Museum in London. Included in the exhibit is the author’s father, oceanographer Shizuo Ishiguro, who created a machine that can predict coastal storm surges.

The author however, hopes that exhibits such as this will prompt more discussion about the trajectory of science and spur deeper interest. These breakthroughs have real implications that deserve to be discussed.



CRISPR pioneer Jennifer Doudna shines hope on the future of genetic modification at SXSW.

Jennifer Doudna, co-inventor of CRISPR Cas9 technology, or the ability to program genes using a special enzyme, spoke about the promises of this technology onstage at SXSW this afternoon. In a keynote today, Doudna noted that while this technology is very young (less than five years old), “it’s been deployed very rapidly for existing applications.”

For example, CRISPR Cas9 tech has important applications for treating diseases. One of the first applications we’ll see entering clinical trials, Doudna said, is using Cas9 gene editing tech to correct the mutation that causes sickle cell disease.

Another example is using the tech to create gene drives, which entails driving a trait through a population very quickly. Doudna said it’s already being deployed in the lab setting to make changes to insects that carry diseases, such as mosquitoes that carry certain pathogens.

“In the future, we could create mosquitoes impervious to infections and therefore prevent spreading diseases,” Doudna said.

Then, of course, there’s the use of gene editing in human embryos, which has attracted a lot of attention in the last few years. For example, the tech could be used to make changes to the immune systems of people with cancer, and make them more capable of fighting the disease.

The University of California Berkeley professor and founder of biotech startup Caribou Bioscience was until recently embroiled in a hotly contested two-year patent battle with the Broad Institute of MIT and Harvard over key portions of the technology, namely the ability to edit living cells.

 The Broad Institute won in that case last month, but, as Doudna pointed out to TechCrunch shortly after the decision went public, it still allows her team and the company she founded to work with the technology in a variety of ways.

CRISPR is a technology potentially worth hundreds of billions, if not trillions, as it could change entire industries. While the Broad Institute won the rights to its patent under a “no interference” ruling, UC Berkeley must still obtain the more basic CRISPR patent. Should that happen, companies interested in using the technology would likely have to pay both institutions for the rights.

During her keynote, Doudna noted how the development of this technology has been a very collaborative effort between professors, academic institutions, regulators, students, etc.

What ultimately creates the most stress for her is the fear that people will get out ahead of the tech, “getting so excited they start to deploy it before it’s even ready,” Doudna said. “I worry most about that kind of overextension that might lead to some sort of harmful effect that would then turn the public against it.”

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