An early triumph for the infant synthetic biology?
Do you suppose Science‘s Breakthrough (Arrrrgh!) of the Year for 2015 has already arrived? In January, no less? Via two papers in Nature? Which venue, I suppose, might take it out of the running for being a Science B***********.
These are reports on genetically recoded organisms, GROs, rather than genetically modified organisms, GMOs. In the organisms’ genomes, all instances of a particular codon have been replaced by another. The amino acid the new codon calls for during protein synthesis is lab-created and does not exist in nature.
The scientists have altered the genetic code of that favorite experimental bacterium, Escherichia coli. These are not just organisms that have never existed before. “We do consider this a new class of organism,” the redoubtable George Church, senior author of one of the papers, told reporters. “It’s not just a new species. In a way it’s a new kingdom.”
“We now have the first example of genome-scale engineering rather than gene editing or genome copying,” Church told Stephanie Dutchen at Phys.Org. “This is the most radically altered genome to date in terms of genome function. We have not only a new code, but also a new amino acid, and the organism is totally dependent on it.”
Genetic recoding is quite a big deal for a number of reasons
First, and this is what media accounts mostly emphasized, it’s the most intriguing, and apparently effective, idea so far for building an escape-proof firewall between genetically modified organisms and the environment. The technique’s virtues have been demonstrated so far only in the lab. But there are giddy speculations about the potential for oil-spill cleanup microbes that could be dismissed from the planet the moment their work was done and, eventually, genetically engineered crops whose foreign genes could not transfer successfully to other plants in the wild.
Also, the bugs can resist infection by viruses. Viruses survive by commandeering a host’s genetic machinery to make their own proteins. But they are stymied by the never-before-encountered genome of the recoded E. coli. This trait might be applied fairly soon to fermentation and other industrial microbiological processes like manufacturing drugs via bacteria, where contaminating viruses can be a serious problem.
At D-brief, Kari Lydersen said the technique could also provide biotechnologists with built-in intellectual property protection. They could make their own organisms dependent on specific synthetic amino acids. Other companies would have trouble replicating those recoded organisms.
Frankenbug Failsafe Promises Synbio Safety
The technical details of how these miracles are to be accomplished are pretty intricate, which is why most accounts (including this one) leave them out. Take advantage of the explanatory labor of others. See, for example, this post at DNA Science by Ricki Lewis, my colleague here at the PLOS Blog Network. See also this nicely written but unbylined piece from Genetic Engineering News. I stole its alliterative hed for this section. Also consult the ever-reliable John Timmer at Ars Technica and Ian Sample at Guardian Genetics.
The initial stages of recoding experiments were published starting in 2013, and Lewis points out that the approach was considered (and rejected) for Science‘s B*********** of the Year last year. She thinks the idea that GMOs can be made safer will make no difference at all to anti-GMO activists. She’s almost certainly right about that. They talk safety when it suits them, but by and large they aim their vitriol at other targets, like industrial agriculture and global megaconglomerates.
The future of genetic recoding, and of life-as-we-know-it
The researchers’ ideas about the future implications of genetic recoding were not received with universal huzzahs. The Verge quoted Cambridge University plant scientist Alison Smith, who pointed out that complex organisms like plants have a lot more genes than E. coli, and will be much harder to recode. The optimistic speculations about where this work could go, she said, “might be an extrapolation too far.”
There was also skepticism about how much of a failsafe recoding will turn out to be. These cautionary moments were frequently coupled with reference to Jeff Goldblum’s prediction in Jurassic Park: Life finds a way.
Toward the end of Carl Zimmer’s long post at The Loom, he muses briefly about how genetic recoding affects the definition of life. Scientists, he says, have wondered if life-as-we-know-it takes up only a tiny portion of the space of all possible forms of life. Recoded E. coli tell us those speculations are likely true. In just a few years humans have created organisms never before seen–never before possible–on Planet Earth. Yet, he says, within their constricted Universe of artificial amino acids, these inventions are as alive as we are.
It’s a small world when the measles virus is around
A measles epidemic that erupted at Disneyland and is spreading from the Happiest Place on Earth eastward across the US. How irresistible a story is that? The number of confirmed US cases is now creeping toward 100 people, already more than the median annual number for the first decade of this century. Most cases have been linked to Disneyland.
The vaccination status of only a minority of the cases is known. Of those, most of those who caught the disease had never been vaccinated. Some are proclaiming that this is the beginning of the end for the anti-vaccine movement.
Perhaps that will turn out to be true. But, Steven Novella says at Neurologica, the anti-vaxxers are fighting back, crowing that a number of people infected had been vaccinated. That’s not at all weird. The vaccines don’t seem to work in a small percentage of people.
At Wired, Katie Palmer explains. Take a bunch of people and crowd them together in a confined space with someone who has contracted measles elsewhere. (For example, Disneyland in mid-December.) Statistically, about 90% of them will have been vaccinated, but, also statistically, about 3% of the vaccinated will become infected anyway. Of the 10% who weren’t vaccinated, about 90% will come down with the disease. And of the few who were vaccinated but got infected anyway, many will have quite mild cases.
Steven Novella concludes, “The numbers are very clear. This outbreak would not have occurred at all, or would have been much smaller, were it not for the large numbers of unvaccinated people in the population.”
Novella also notes that the anti-vaxxers dismiss measles as a disease of no consequence. But it certainly can be. Pediatrician Claire McCarthy, blogging at MD Mama, points out that 1 in 10 people with measles will get an ear infection or diarrhea, 1 in 20 will get pneumonia, 1 in 1000 will get encephalitis, which can lead to seizures, deafness, or mental retardation, and 1 or 2 in 1000 will die.
There can be side effects of the vaccine, she acknowledges. One in 6 will get a fever, 1 in 14 will get some temporary pain or stiffness in the joints, 1 in 20 will get a rash, 1 in 75 will get swollen glands. These are all temporary conditions, but there are also more serious, although rare, side effects: 1 in 3000 will get a seizure from a fever, and 1 in 30,000 will have a drop in platelet count, possibly leading to bleeding. Still, McCarthy concludes, “The risks of all of these serious side effects are smaller than the risk of dying of measles.”
Maybe the anti-vaxxers aren’t to blame, exactly?
2014, it turns out, was our worst year for measles in this century so far: 644 cases. Hardly any can be blamed on Disneyland, which didn’t begin until December, and it’s not clear how influential the anti-vaxxers have been. Nearly 60% of last year’s cases were in Ohio, triggered by an Amish farmer who had contracted measles on a visit to the Philippines.
This convoluted tale from Julia Belluz at Vox, who says that only 2% of the population refuses vaccinations outright. The government claims the measles vaccination rate has held steady for a decade at about 92%. She quotes an official of the Centers for Disease Control and Prevention thus, “The people getting measles are those that travel abroad, come back, and live in a community among people who weren’t vaccinated.”
So the reappearance of an exceptionally contagious disease that had all but disappeared from the US is due to a toxic combination of increased foreign travel and the existence of isolated unvaccinated populations.
You don’t need to be part of a religious community to live in one of those isolated populations. A study published last week in Pediatrics showed that geographic clusters of unvaccinated children existed all over the state of California, for instance “a 1.8-mile area in Vallejo, where 22.7 percent of kids were under-vaccinated,” says Liza Gross, who blogged about the study at Shots. You can see how misinformed gossip about vaccines causing autism and suchlike can be passed easily around to parents of kids in neighborhood play groups and nursery schools.
The Ohio Amish do not refuse vaccination as a matter of religious principle. Members of this community have avoided getting vaccinated because, in the 1990s, two Ohio kids got sick, allegedly after the measles vaccine.
Now, Belluz reports, as a result of the 2014 outbreak the Amish seem to be changing their minds. After watching serious measles cases among their friends and relatives, they are getting vaccinated once again.