Evolution is making us sick and for the first time we can stop it

Over billions of years, evolution has created a stunning variety of life on Earth, including us humans. Even now, it is helping wildlife adapt to the enormous changes we are making to the planet. But evolution has a dark side too. For a start, it can be a hazard to health: it is why the cancers that kill 1 in 5 of us grow ever more dangerous as they progress, and stop responding to treatments. It is also why antibiotic-resistant superbugs are becoming more common, and why killer diseases like malaria can evade drugs. It takes a toll on our food and the environment, too, as farmers battle to keep rapidly evolving pests and weeds under control. And it is behind the resurgence of infestations we thought were long defeated, including head lice, bedbugs and rats. It is no exaggeration to say that the future of civilisation depends on our halting these threatening kinds of evolution. This ambition may sound like hubris, but biologists have long been seeking ways to do just that. They have now come up with a whole array of approaches, including creating “immutable” genes, turning gene-editing tools into “anti-evolution” super-weapons, and making viruses mutate so fast that they cannot evolve. “We can even reverse antibiotic resistance,” says Lee Cronin at the University of Glasgow, UK. We tend to think of evolution as a process that happens over millions of years, not as something we need to worry about in practical terms. In fact, it can be rapid and has been causing problems for humanity since the dawn of civilisation. When early farmers started weeding by hand, the plants evolved to outwit them by looking more like crops. In the industrial age, evolution has become an industrial-scale problem. Almost as soon as we started using penicillin to treat infections, DDT to kill mosquitoes and herbicides to destroy weeds, resistance began to emerge. The reason is simple: when we try to wipe out pests and pathogens, we put huge pressure on them to evolve or die. If a poison isn’t totally effective, those individuals that survive are likely to have some resistance to it – and their offspring may acquire mutations that make them even more resistant. With repeated exposure to a poison, a population can evolve resistance very quickly. Warfarin was first used to kill rats in 1948 and the earliest report of resistance came just a decade later. In fast-reproducing organisms like viruses and bacteria, the process can take just days or hours. Evolution is happening right here, right now, all around us and even inside us; cancer is an evolutionary disease. As well as evolving to evade the drugs meant to kill them, cancer cells evolve to dodge the immune system’s attacks, to trick the body into supplying them with food and oxygen, and to spread. Evolution also explains why organisms we have domesticated or engineered to perform specific tasks sometimes go rogue. For instance, the oral polio vaccine is a weakened virus that has a habit of evolving back into the full-on disease-causing virus. And the bacteria and yeasts used in the manufacture of myriad products tend to evolve to do our bidding less well with time. It is an enormously expensive problem. Back in 2001, Stephen Palumbi at Stanford University in California calculated that evolution was probably costing the US more than $100 billion a year. This estimate has not been updated, but the figure would be far higher today, he says. So, what can we do? Lots, actually. “Evolution is not the dreaded enemy that the media makes out,” says Cronin. We have already won some notable battles in our struggle against it. Take triple therapy for HIV. In the 1990s, doctors began combining three drugs to make it very hard for the virus to evolve resistance to all of them at once. “Triple drug therapy is one of the first truly evolutionary treatment strategies,” says Palumbi. “This approach seems to have given life back to millions of people.” In fact, halting evolution can be as easy as removing the pressure that drives natural selection. For instance, the fungus that causes a crop disease called rice blast became resistant to a new fungicide within just three years. When farmers in Japan stopped using it, the resistant strain disappeared in four years. It isn’t even necessary to stop using a fungicide or pesticide: you just need to ensure that susceptible pests outbreed resistant ones. Where farmers grow crops genetically engineered to produce Bt toxin, an insecticide, pests become resistant within a matter of years. But if farmers plant mixtures of Bt and non-Bt plants, large numbers of Bt-susceptible pests survive. These mate with the fewer Bt-resistant pests, swamping any emerging resistance. The approach undoubtedly works; however, farmers are reluctant to grow lots of non-Bt plants.

Reverse the pressure

It is even harder to persuade people not to overuse antibiotics. Antibiotic resistance is getting rapidly worse and threatening to undo a century of progress in medicine. Yet, even here, there is hope. As paradoxical as it sounds, some researchers think we can use antibiotics to reverse the selection pressures on bacteria, and make them susceptible to antibiotics again. Cronin and his colleagues are among dozens of teams working on this. They have been experimenting with alternating two antibiotics that attack different aspects of bacteria. The basic idea is not new – alternating chemicals with different modes of action has long been used to prevent pesticide resistance arising – but it has not been applied to antibiotics before. Cronin’s team has developed a model to work out how to optimise the effect, and shown that it works in cells growing in culture. “We actually were able to reverse the resistance over time. We were not expecting that,” he says. What’s more, the model suggests this approach could help prevent cancers becoming drug-resistant, too. Meanwhile, CRISPR gene editing is allowing us to tackle evolution head-on in an entirely novel way. The technology can target and destroy specific DNA sequences, with all kinds of potential applications. “If someone told me several years ago we can do this, I would have said you’re crazy,” says Alejandro Chavez at Columbia University in New York. CRISPR involves two linked components: the Cas9 protein and a guide RNA. Cas9 scans a cell’s DNA until it finds a sequence that matches part of the guide RNA, and then cuts the DNA at that specific site. So, with the appropriate guide, CRISPR can chew up the DNA coding for antibiotic resistance (or other unwanted traits) without killing the bacterium carrying it. In other words, it can be used to reverse evolution. The tricky part is getting the CRISPR toolkit inside a bacterium. This can be done with viruses known as bacteriophages, which replicate themselves by injecting their DNA into bacteria. Geneticists hijack these phages, swapping viral DNA for DNA that codes for the CRISPR components. Several companies have successfully used the modified phages to treat antibiotic-resistant infections in animals, and human clinical trials could start soon. But there are some big limitations. For a start, specific phages infect specific bacteria, so each treatment must be customised. In addition, phages don’t survive in the bloodstream, so cannot be used to treat internal infections – although they could be sprayed on wounds or used to target bacteria in the gut.

Resistance is futile

Udi Qimron at Tel Aviv University, Israel, wants to use phages in a different way, to resensitise bacteria to antibiotics before they get a chance to infect people. His plan is to add the CRISPR phages to sprays for cleaning surfaces in hospitals and to the creams that medics use to wash their hands. “If we constantly use such creams, we can eventually reduce the ratio of resistant bacteria to sensitive bacteria,” he says. This won’t be easy, not least because the CRISPR phages will not spread in hospitals or elsewhere because they can’t replicate – they don’t carry viral genes. That is an advantage from a safety point of view, but it lessens their effectiveness. But Qimron has a cunning plan. He has engineered phages that are harmless to resensitised bacteria but can replicate “in the wild” and kill other bacteria. He hopes to use both kinds of phage together so that antibiotic resistant bacteria not resensitised by one are destroyed by the other. It will be very difficult to eliminate all resistant cells in complex environments, points out evolutionary biologist Jeffrey Barrick at the University of Texas at Austin. But it is hard with conventional methods too. Chavez is taking a different tack. Instead of using CRISPR to reverse evolution, his team wants to stop specific traits evolving in the first place. “We wondered if you can have CRISPR hide on a genome, be calm, do nothing and, when something arises you don’t like, have CRISPR snip it out,” he says. To find out, his team created a CRISPR system that targets a mutation known to make a specific strain of E. coli resistant to the antibiotic rifampicin. Next, they inserted this system into non-resistant E. coli. Then they put the bacteria in the guts of mice, which they dosed with rifampicin. Resistant mutants appeared within days in mice given unaltered bacteria, but not in those given the engineered strain. This “anti-evolution” system could be used in all kinds of ways. The most obvious is to stop unwanted mutations occurring in the microorganisms we use to manufacture a huge variety of products, from beer to insulin to vanilla flavouring. “A lot of times when you are growing stuff in large batch fermenters, over time the microbes lose the ability to make the substances of interest,” says Chavez. “That makes sense because making these substances is a huge metabolic drain on them.” But it is a headache for manufacturers. Barrick’s team is addressing this problem by creating “antimutators”: bacteria with a lower mutation rate. One way of doing this is by removing so-called genomic parasites, DNA sequences found in all organisms that provide no benefit but greatly increase the mutation rate. Another way is to improve the accuracy of the enzymes that copy DNA, which can reduce mutation rates up to 30-fold. It is also possible to make DNA itself immutable – or at least less prone to mutation. One way is to give a particular DNA sequence extra functions, making it more valuable, so that if it does mutate, the organism will be less likely to survive. For example, by weakening a “promoter” sequence so that it controls the action of two genes instead of one, researchers have reduced mutation rates tenfold. Other biologists are doing exactly the opposite. They are capitalising on the fact that very high mutation rates can stop organisms adapting and evolving, and even drive them to extinction. A few experimental drugs are thought to work in this way, including one that shows promise against viruses causing diseases ranging from flu to West Nile virus. This approach may be effective against only viruses that encode their genetic information in RNA, because they have very high mutation rates to start with. But Chavez’s “anti-evolution” system should work in a much wider range of organisms, perhaps even wild plants and animals such as mosquitoes and rats. CRISPR has already been adapted to make artificial gene drives – DNA sequences that copy themselves within the genome in such a way as to get passed on to all of an animal’s offspring, not just half of them. “Could you have this on a gene drive that spreads in a population, that’s in theory benign to the population, and just prevents them evolving something you don’t want? I think it’s totally reasonable,” says Chavez.

“Biologists are creating new ‘anti-evolution’ super-weapons”

CRISPR promises a whole new way to tackle the dark side of evolution. But the problem with reversing or preventing specific mutations is that others could arise that achieve the same thing. “Evolution oozes round any barrier,” says Barrick. Nevertheless, CRISPR-based approaches offer something new. They are not foolproof, but unlike with conventional drugs and pesticides, where you must start from scratch once resistance evolves, CRISPR components can just be tweaked to target new DNA sequences. “Sequence-specific antimicrobials could be very powerful,” says Chavez. With that power comes responsibility. “Genetically based tools really do change the evolutionary dynamic,” says Palumbi. “We need to be really sure that we don’t create unintended consequences.” And that is difficult: for example, it has recently been shown that some vaccines can drive the evolution of more dangerous viruses. “It requires a great deal of thought and experimentation, and appreciation of the power – and the unlikeliness at times – of evolution,” he says. One thing is certain: even with new weapons in our struggle against evolution, this is not a conflict that will ever end. “You will never completely solve the problem,” says Palumbi. “You need to be a step ahead of it the whole way.”

New Scientist, 29 August 2018 ; http://www.newscientist.com/