Four years ago, a few hundred miles off the coast of West Africa, a crane lifted a bulbous yellow submarine from the research vessel Poseidon and lowered it into the Atlantic. During half an hour of safety checks, Osborn watched water slosh across the submarine’s round window, washing-machine style. Then the crew gave the all-clear and the vessel descended. In the waters of Cape Verde, a volcanic archipelago that is famous for its marine life, Osborn felt the seasickness dissipate. She pressed her face against the glass, peering out at sea creatures until her forehead bruised. “You’re just completely mesmerized by getting to look at these animals in their natural habitat,” she told me.
Osborn was on a mission to find several elusive species, including a bioluminescent worm called Poeobius, and to sequence their genes for a global database of DNA. “We need the genome to figure out how these things are related to each other,” she explained. “Once we have that tree, we can start asking interesting questions about how those animals evolved, how they’ve changed through time, how they’ve adapted to their habitats.” Eventually, such genomes could inspire profound innovations, from new crops to medical cures. Osborn was starting to worry, however: she had already made several trips in the submarine and had not seen a single Poeobius. Each worm measures just a few centimetres in length and feeds on marine snow, or organic detritus that falls from the surface. Because it is yellow on one end, like a cigarette, it is sometimes called the butt worm.
As the pilot steered into deeper waters, Osborn operated a suction hose at the end of a robotic arm. Whenever she spotted organisms that she wanted to sample—crustaceans, sea butterflies, jellies—she’d suck them through a tube and into a collection box that was filled with seawater. She started to wish that the submarine had a rest room on board. Then, a few hundred metres down, she finally saw a group of Poeobius. “Oh, that’s what we want!” she remembers exclaiming. “Go! Go get that!” The pilot slowly turned the sub and Osborn sucked up the worms.
Back on the ship, even before using the rest room, Osborn deposited her boxes in an onboard laboratory. “It’s always exciting to climb out and go look at all the samplers, and take them into the lab and see what animals you’ve gotten,” she told me. She placed one of the Poeobius worms under a microscope, anesthetized it, sliced off a bit of gelatinous tissue, and placed it into a vial, which contained a liquid that would protect the DNA from deterioration. (The butt worm did not survive.) Back at the Smithsonian, a team would extract the genetic material and sequence it. It would soon become a new branch on a growing tree of life.
The evolution of life on Earth—a process that has spanned billions of years and innumerable strands of DNA—could be considered the biggest experiment in history. It has given rise to amoebas and dinosaurs; fireflies and flytraps; even mammals that look like ducks and fish that look like horses. These species have solved countless ecological problems, finding novel ways to eat, evade, defend, compete, and multiply. Their genomes contain information that humans could use to reconstruct the origins of life, develop new foods and medicines and materials, and even save species that are dying out. But we are also losing much of the data; humans are one of the main causes of an ongoing mass extinction. More than forty thousand animal, fungal, and plant species are considered threatened—and those are just the ones we know about.
For hundreds of years, biologists have roamed the globe in an epic effort to collect and categorize the life on Earth. In the seventeen-hundreds, after traversing Sweden to document its flora and fauna, Carl Linnaeus helped create the system that scientists still use to classify and name species, from Homo sapiens to Poeobius meseres. In 1831, Charles Darwin set out aboard H.M.S. Beagle to collect living and fossilized specimens, which inspired his theory of natural selection. The discovery of DNA, in the nineteenth century, offered a new way to classify species: by comparing their genetic material. DNA’s four building blocks—adenine (A), thymine (T), guanine (G), and cytosine (C)—encode profound differences between organisms. By studying their sequence, we might come to speak life’s language.
Scientists didn’t even begin to sequence a DNA molecule until 1968. In 1977, they sequenced the roughly five thousand base pairs in a virus that invades bacteria. And, in 1990, the Human Genome Project started the thirteen-year process of sequencing almost all of the three billion base pairs in our DNA. Its organizers called the endeavor “one of the most ambitious scientific undertakings of all time, even compared to splitting the atom or going to the moon.” Since then, researchers have been filling in gaps and improving the quality of their sequences, in part by using a new format known as a telomere-to-telomere, or T2T, genome. The first T2T human genome was sequenced only last year, but already scientists with the Earth BioGenome Project are talking about repeating this process for every known eukaryotic species. (Eukaryotes are organisms whose cells have nuclei.)
Because the E.B.P. Does not have its own funding, it does not sample or sequence species on its own. Instead, it’s a network of networks; its organizers set ethical and scientific standards for more than fifty projects, including the Darwin Tree of Life, Vertebrate Genomes Project, the African BioGenome Project, and the Butterfly Genome Project. This way, “when we get to the end of the project, it’s not the Tower of Babel,” Harris Lewin, an evolutionary biologist at the University of California, Davis, who chairs the E.B.P. Executive council, told me. “You know—your genomes are produced this way, and mine are produced that way, and they’re of different quality, so that, when you compare them, you get different results.”
Natural-history museums already have some of the samples needed to outline a genetic tree of life. The Smithsonian, for instance, has about fifty million biological samples. But, because DNA degrades quickly, it’s difficult to extract a high-quality sequence from, say, a frog in formaldehyde or an old taxidermy parrot. For this reason, the E.B.P.
After Osborn collected her butt worms, she had to transport them to her colleagues at the Smithsonian. This process can be more difficult than it sounds. Many researchers keep their samples intact by packing them with dry ice or liquid nitrogen in the field; airport-security workers sometimes flag these packages as suspicious, leading to delays that can spoil the DNA and waste an expedition. Osborn, for her part, checked a large insulated box on the flight from Cape Verde, and then waited a few hours in Newark for Fish and Wildlife officials to approve it for entry. As it turned out, her samples came from an entirely new species of Poeobius; a paper announcing the discovery is forthcoming.
The first stop in the journey from sample to sequence is a genetics laboratory such as the Vertebrate Genome Lab, at the Rockefeller University, on the eastern shore of Manhattan. On a drizzly day last May, I visited the V.G.L. To see how scientists turn a bit of animal tissue into a string of billions of letters. It was a kind of trophy wall on which inclusion signified not death but a kind of immortality.
Finally, the samples travel into refrigerator-size PacBio sequencing machines, which, in this case, were labelled with nicknames from “Star Trek.” Enzymes latch onto the adapters and traverse the strands, attaching a color-coded molecule to every building block of DNA. The machine detects the colors and “reads” the sequence that they represent.
This story appears in the August 2016 issue of National Geographic magazine.
If you took a glance around Anthony James’s office, it wouldn’t be hard to guess what he does for a living. The walls are covered with drawings of mosquitoes. Mosquito books line the shelves.
Hanging next to his desk is a banner with renderings of one particular species—Aedes aegypti—in every stage of development, from egg to pupa to fully grown, enlarged to sizes that would even make fans of Jurassic Park blanch. His license plates have a single word on them: AEDES.
“I have been obsessed with mosquitoes for 30 years,” says James, a molecular geneticist at the University of California, Irvine.
There are approximately 3,500 species of mosquito, but James pays attention to just a few, each of which ranks among the deadliest creatures on Earth. They include Anopheles gambiae, which transmits the malaria parasite that kills hundreds of thousands of people each year. For much of his career, however, James has focused on Aedes. Historians believe the mosquito arrived in the New World on slave ships from Africa in the 17th century, bringing with it yellow fever, which has killed millions of people. Today the mosquito also carries dengue fever, which infects as many as 400 million people a year, as well as such increasingly threatening pathogens as chikungunya, West Nile virus, and Zika.
Cow blood engorges an exposed mosquito’s gut in Anthony James’s lab. Versions of the species carrying Zika and dengue fever can be manipulated with CRISPR so that they give birth to sterile offspring, below.
Mosquito larvae in the laboratory of Anthony James at the University of California, Irvine pay witness to how a dreaded disease might be stopped. Both are Anopheles stephensi, a major carrier of the malaria parasite in urban Asia. Using a technique called CRISPR, James has edited a gene in the larva on the right so that the insect cannot transmit the parasite. A fluorescent protein signals that the experiment has worked. Released in the wild, mosquitoes engineered with CRISPR and a tool called gene drive could eventually replace the wild mosquitoes that carry the disease. But too much uncertainty still exists to put such science into practice.
In a widening outbreak that began last year in Brazil, Zika appears to have caused a variety of neurological disorders, including a rare defect called microcephaly, where babies are born with abnormally small heads and underdeveloped brains.
The goal of James’s lab, and of his career, has been to find a way to manipulate mosquito genes so that the insects can no longer spread such diseases. Until recently, it has been a long, lonely, and largely theoretical road. But by combining a revolutionary new technology called CRISPR-Cas9 with a natural system known as a gene drive, theory is rapidly becoming reality.
CRISPR places an entirely new kind of power into human hands. For the first time, scientists can quickly and precisely alter, delete, and rearrange the DNA of nearly any living organism, including us. In the past three years, the technology has transformed biology. Working with animal models, researchers in laboratories around the world have already used CRISPR to correct major genetic flaws, including the mutations responsible for muscular dystrophy, cystic fibrosis, and one form of hepatitis. Recently several teams have deployed CRISPR in an attempt to eliminate HIV from the DNA of human cells. The results have been only partially successful, but many scientists remain convinced that the technology may contribute to a cure for AIDS.
In experiments, scientists have also used CRISPR to rid pigs of the viruses that prevent their organs from being transplanted into humans. Ecologists are exploring ways for the technology to help protect endangered species. Moreover, plant biologists, working with a wide variety of crops, have embarked on efforts to delete genes that attract pests. That way, by relying on biology rather than on chemicals, CRISPR could help reduce our dependence on toxic pesticides.
No scientific discovery of the past century holds more promise—or raises more troubling ethical questions.. Many more will follow.
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No discovery of the past century holds more promise—or raises more troubling ethical questions.
“Scientists do not have standing to answer these questions,” Lander told me. “And I am not sure who does.”
CRISPR-Cas9 has two components. The first is an enzyme—Cas9—that functions as a cellular scalpel to cut DNA. (In nature, bacteria use it to sever and disarm the genetic code of invading viruses.) The other consists of an RNA guide that leads the scalpel to the precise nucleotides—the chemical letters of DNA—it has been sent to cut. (Researchers rarely include the term “Cas9” in conversation, or the inelegant terminology that CRISPR stands for: “clustered regularly interspaced short palindromic repeats.”)
The guide’s accuracy is uncanny; scientists can dispatch a synthetic replacement part to any location in a genome made of billions of nucleotides. When it reaches its destination, the Cas9 enzyme snips out the unwanted DNA sequence. To patch the break, the cell inserts the chain of nucleotides that has been delivered in the CRISPR package.
By the time the Zika outbreak in Puerto Rico comes to an end, the U.S. Centers for Disease Control and Prevention estimates that, based on patterns of other mosquito-borne illnesses, at least a quarter of the 3.5 million people in Puerto Rico may contract Zika. That means thousands of pregnant women are likely to become infected.
Currently the only truly effective response to Zika would involve bathing the island in insecticide. James and others say that editing mosquitoes with CRISPR—and using a gene drive to make those changes permanent—offers a far better approach.
Scientists used conventional genetic engineering to add genetic material from two other fish species to create the AquAdvantage Atlantic salmon (top), which can reach market size twice as fast as its natural counterpart. The fish consumes less feed and can be raised in isolation close to cities, reducing transportation costs and emissions, and eliminating any chance of escape into the wild. While the FDA has approved the fish as entirely safe for consumption, doubts over the safety of transgenic foods persist. In the future, CRISPR-engineered foods, which do not combine genes from different organisms, might find quicker acceptance.
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Gene drives have the power to override the traditional rules of inheritance. Ordinarily the progeny of any sexually reproductive animal receives one copy of a gene from each parent. Some genes, however, are “selfish”: Evolution has bestowed on them a better than 50 percent chance of being inherited. Theoretically, scientists could combine CRISPR with a gene drive to alter the genetic code of a species by attaching a desired DNA sequence onto such a favored gene before releasing the animals to mate naturally. Together the tools could force almost any genetic trait through a population.
Last year, in a study published in the Proceedings of the National Academy of Sciences, James used CRISPR to engineer a version of Anopheles mosquitoes that makes them incapable of spreading the malaria parasite. “We added a small package of genes that allows the mosquitoes to function as they always have,” he explained. “Except for one slight change.” That change prevents the deadly parasite from being transmitted by the mosquitoes.
How to Hack DNA
Learn—and visualize—how CRISPR technology works in this animated graphic video.
“I’d been laboring in obscurity for decades. Not anymore, though—the phone hasn’t stopped ringing for weeks,” James said, nodding at a sheaf of messages on his desk.
Combating the Ae. Aegypti mosquito, which carries so many different pathogens, would require a slightly different approach. “What you would need to do,” he told me, “is engineer a gene drive that makes the insects sterile. It doesn’t make sense to build a mosquito resistant to Zika if it could still transmit dengue and other diseases.”
To fight off dengue, James and his colleagues have designed CRISPR packages that could simply delete a natural gene from the wild parent and replace it with a version that would confer sterility in the offspring.
James is acutely aware that releasing a mutation designed to spread quickly through a wild population could have unanticipated consequences that might not be easy to reverse. “There are certainly risks associated with releasing insects that you have edited in a lab,” he said. “But I believe the dangers of not doing it are far greater.”
At Guangzhou General Pharmaceutical Research Institute in China, vet Long Haibin pets Taingou, one of two beagles grown from embryos edited to double muscle mass. Such experiments could eventually improve understanding ofmuscular dystrophy and other human diseases.
Research assistant Kou Xiaochen cradles a ferret at the Tongji University’s School of Life Sciences and Technology in Shanghai. The ferret’s genome was altered with CRISPR to give rise to microcephaly, a birth defect where the brain is smaller than normal. It’s a timely development: The Zika virus epidemic is directly linked to microcephaly. CRISPR may prove invaluable in building animal models to study Zika’s gravest consequence.
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It has been more than 40 years since scientists discovered how to cut nucleotides from the genes of one organism and paste them into the genes of another to introduce desired traits. Molecular biologists were thrilled by the possibilities this practice, referred to as recombinant DNA, opened for their research. From the start, however, scientists also realized that if they could transfer DNA between species, they might inadvertently shift viruses and other pathogens too. That could cause unanticipated diseases, for which there would be no natural protection, treatment, or cure.
This possibility frightened no one more than the scientists themselves. In 1975, molecular biologists from around the world gathered at the Asilomar Conference Grounds, along California’s central coast, to discuss the challenges presented by this new technology. The group emerged from the meeting having agreed to a series of safeguards, including levels of laboratory security that escalated along with the potential risks posed by the experiments.
It soon became clear that the protections seemed to work and that the possible benefits were enormous. Genetic engineering began to improve the lives of millions. Diabetics, for example, could count on steady supplies of genetically engineered insulin, made in the lab by placing human insulin genes into bacteria and then growing it in giant vats. Genetically engineered crops, yielding more and resisting herbicides and insects, began to transform much of the world’s agricultural landscape.
Yet while genetically engineered medicine has been widely accepted, crops produced in a similar fashion have not, despite scores of studies showing that such products are no more dangerous to eat than any other food. As the furor over the labeling of GMOs (genetically modified organisms) demonstrates, it doesn’t matter whether a product is safe if people refuse to eat it.
CRISPR may provide a way out of this scientific and cultural quagmire. From the beginning of the recombinant era, the definitions of the word “transgenic” and the term “GMO” have been based on the practice of combining in a laboratory the DNA of species that could never mate in nature. But scientists hope that using CRISPR to alter DNA could appease the opposition. It gives researchers the ability to redesign specific genes without having to introduce DNA from another species.
Each year up to half a million children in the developing world go blind for lack of vitamin A—but anti-GMO activists have interfered with research and prevented any commercial production of the rice. With CRISPR, scientists could almost certainly achieve the same result simply by altering genes that are already active in rice plants.
Scientists in Japan have used CRISPR to extend the life of tomatoes by turning off genes that control ripening. By deleting all three copies of one wheat gene, Caixia Gao and her team at the Chinese Academy of Sciences in Beijing have created a strain that is resistant to powdery mildew.
Chicago-based reproductive specialist (and Bulls fan) Ilan Tur-Kaspa collects a patient’s eggs using a needle and ultrasound for guidance. Screening embryos for genetic diseases prior to in vitro fertilization frees parents from having to make the agonizing decision of whether to abort an affected fetus or bring into the world a child who may suffer severely.
Both of Jack’s parents are carriers of a defective gene that imparts a 25 percent chance that their children will develop cystic fibrosis. Jack, 16 months old, is also a carrier but will never suffer from the illness. Ilan Tur-Kaspa, who performed the treatment at the Institute for Human Reproduction/Reproductive Genetics Institute in Chicago, has calculated that PGD could save $2.2 billion annually in cystic fibrosis treatment costs.
David Liittschwager
Farmers have been adjusting genes in single species—by crossbreeding them—for thousands of years. CRISPR simply offers a more precise way to do the same thing. In some countries, including Germany, Sweden, and Argentina, regulators have made a distinction between GMOs and editing with tools such as CRISPR. There have been signs that the U.S. Food and Drug Administration might follow suit, which could make CRISPR-created products more readily available and easily regulated than any other form of genetically modified food or drug.
The potential for CRISPR research to improve human medicine would be hard to overstate. The technology has already transformed cancer research by making it easier to engineer tumor cells in the laboratory, then test various drugs to see which can stop them from growing. Soon doctors may be able to use CRISPR to treat some diseases directly.
In the next two years we may see an even more dramatic medical advance. There are 120,000 Americans on waiting lists to receive organ transplants, and there will never be enough for all of them. Thousands of people die every year before reaching the top of the list.
For years, scientists have searched for a way to use animal organs to ease the donor shortage. . No regulatory agency would permit transplants with infected organs. And until recently, nobody has been able to rid the pig of its retroviruses.
Now, by using CRISPR to edit the genome in pig organs, researchers seem well on their way to solving that problem. A group led by George Church, a professor at Harvard Medical School and MIT, used the tool to remove all 62 occurrences of PERV genes from a pig’s kidney cell.
Researchers handle the lungs and heart removed from a gene-altered pig in the lab of Lars Burdorf at the University of Maryland School of Medicine, which has been developing and testing animal organs for human use since 2002. Once a painstaking slog—it took decades of research to successfully alter one sugar gene that is key to organ rejection—CRISPR has revolutionized the speed at which they can achieve results.
Please be respectful of copyright. Human blood filters through pig lungs in the lab of Lars Burdorf at the University of Maryland. Thousands of people die every year for lack of transplantable human organs. Scientists are experimenting with CRISPR to rid pig organs of viruses that harm humans.
When the scientists mixed those edited cells with human cells in a laboratory, none of the human cells became infected. That too would be a critical part of making this kind of transplant work.
Church has now cloned those cells and begun growing them in pig embryos. He expects to start primate trials within a year or two. Church told me he thinks this could happen in as few as 18 months, adding that for many people the alternative to the risk of the trial would surely be death.
And the conceit is that these people would not benefit from a transplant. But of course they would benefit. And if you had an abundance of organs, you could do it for everyone.”
The black-footed ferret is one of the most endangered mammals in North America. Twice in the past 50 years, wildlife ecologists assumed that the animals, which were once plentiful throughout the Great Plains, had gone extinct. They came close; every black-footed ferret alive today descends from one of seven ancestors discovered in 1981 on a cattle ranch near Meeteetse, Wyoming.
But the ferrets, inbred for generations, lack genetic diversity, which makes it harder for any species to survive.
Working with Oliver Ryder at the San Diego Frozen Zoo, Phelan and her colleagues are attempting to increase the diversity of the ferrets by introducing more variable DNA into their genomes from two specimens preserved 30 years ago.
Phelan’s work can address two immediate and interlocking threats. . And the plague is also fatal to the ferrets themselves, which become infected by eating prairie dogs that have died of the disease. A vaccine against human plague developed in the 1990s appears to provide lifelong immunity in ferrets. Teams from the Fish and Wildlife Service have captured, vaccinated, and released as many of the ferrets (a few hundred exist in the wild) as they can. But such a ferret-by-ferret approach cannot protect the species.
This technology could boost yields for the millions of people who depend on the crop as a staple. Unlike genetically modified organisms, CRISPR doesn’t introduce foreign DNA into a plant. Researchers hope CRISPR-modified foods won’t meet with the heated opposition that GMOs have triggered.
American chestnut trees blanketed much of the eastern U.S. Until an invasive fungus all but wiped them out in the early 20th century—a tragedy visible in a Virginia forest (left). William Powell of the State University of New York College of Environmental Science and Forestry and colleagues (including Kristen Stewart, right, tending a transgenic plant) have used a wheat gene to develop a blight-resistant chestnut. It may one day repopulate the eastern forest.
Library of Congress
With gene drives and CRISPRwe now have a power over species of all kinds that we never thought possible.
ByHank GreelyDirector of Stanford’s Center for Law and the Biosciences
Jack Newman is a former chief science officer at Amyris, which pioneered development of a synthetic form of artemisinin, the only genuinely effective drug available to treat malaria in humans. Now he focuses much of his attention on eliminating mosquito-borne disease in birds. The only current method of protecting birds from malaria is to kill the mosquitoes by spreading powerful chemicals over an enormous region. Even that is only partially successful.
“In order to kill a mosquito,” Newman says, “the insecticide actually has to touch it.” Many of these insects live and breed deep in the hollows of trees or in the recessed crags of rock faces. To reach them with insecticides almost certainly would require poisoning much of the natural life in Hawaii’s rain forests. But gene editing, which would result in sterile mosquitoes, could help save the birds without destroying their surroundings. “ “Avian malaria is destroying the wildlife of Hawaii, and there is a way to stop it. Are we really willing to just sit there and watch?”
In February of this year, U.S. . Many scientists considered the comments unfounded, or at least a bit extreme. There are easier ways for terrorists to attack people than to conjure up new crop plagues or deadly viruses.
But people will use the technology whether we know enough about it or not.”
The more rapidly science propels humanity forward, the more frightening it seems. This has always been true. Do-it-yourself biology is already a reality; soon it will almost certainly be possible to experiment with a CRISPR kit in the same way that previous generations of garage-based tinkerers played with ham radios or rudimentary computers. It makes sense to be apprehensive about the prospect of amateurs using tools that can alter the fundamental genetics of plants and animals.
But the benefits of these tools are also real, and so are the risks of ignoring them. Mosquitoes cause immense agony throughout the world every year, and eradicating malaria or another disease they carry would rank among medicine’s greatest achievements. Although it is clearly too soon to contemplate using CRISPR in viable human embryos, there are other ways of editing the human germ line that could cure diseases without changing the genetic lineage of our species.
Children born with Tay-Sachs disease, for instance, lack a critical enzyme necessary for the body to metabolize a fatty waste substance found in the brain. The disease is very rare and occurs only when both parents transmit their defective version of the gene to a child. With CRISPR it would be easy to treat one parent’s contribution—say, the father’s sperm—to ensure that the child did not receive two copies of the faulty gene. Such an intervention would clearly save lives and reduce the chance of recurrence of the disease.
When faced with risks that are hard to evaluate, we have a strong tendency to choose inaction. But with millions of lives at stake, inaction presents its own kind of danger. Last December scientists from around the world met in Washington to discuss the difficult ethics of these choices.
“With gene drives and CRISPR we now have a power over species of all kinds that we never thought possible,” says Hank Greely, director of Stanford’s Center for Law and the Biosciences. “The potential good we can do is immense. But we need to acknowledge that we are dealing with a fundamentally new kind of power, and figure out a way to make sure we use it wisely.
What do you think about editing the DNA of living organisms? Scientists have the tools—but how should they use them, and who should decide?
A recent European Journal of Clinical Nutrition study highlights some of the historical challenges associated with the assessment of body composition in the first two years of life.
Study: Body composition from birth to 2 years. Image Credit: didesigns021 / Shutterstock.Com
Background
Previous studies have identified associations between birth size and susceptibility to future illnesses as an adult. This suggests that the ‘quality’ of growth is a key determinant of the risk of later abnormal metabolic function.
