Published on 13 Mar 2017
Biohackers, much like their computer hacker forebears, prefer asking for forgiveness rather than permission.
March 14, 2017
October 8, 2015
In Wired, Sarah Zhang handicaps the horses in this year’s highly competitive Nobel Sweepstakes:
Nobel prize speculation, gossip, and betting pools kick off every fall around the time Thomson Reuters releases its predictions for science’s most prestigious prize. This year, one prediction was unusual: a genome-editing tool so hyped that it even got on the cover of WIRED.
(No, seriously, how often does molecular biology get to occupy the same space as Star Wars or Rashida Jones?)
The tool, Crispr/Cas9, is essentially a pair of molecular scissors for editing DNA, so precise and easy to use that it has taken biology by storm. Hundreds if not thousands of labs now use Crispr/Cas9 to do everything from making super-muscled pigs to snipping HIV genes out of infected cells to creating transgenic monkeys for neuroscience research. But the Nobel prediction stands out for two reasons: First, the highly-cited paper describing Crispr/Cas9 came out a mere three years ago, a blip in the timescale of science. Second, the technique is currently at the heart of a bitter patent fight.
Thomson Reuters bases its predictions on how often key papers get cited by other scientists. Here, the paper in question has as its authors Jennifer Doudna, a molecular biologist at UC Berkeley, and Emmanuelle Charpentier, a microbiologist now at the Max Planck Institute for Infection Biology. Missing is Feng Zhang (no relation to this writer), a molecular biologist at the Broad Institute and MIT, who actually owns the patents for CRISPR/Cas9 and says that he came up with the idea independently. So let’s say Thomson Reuters gets it right. Could the patent for a discovery go to one scientist, and the Nobel prize for the discovery to someone else?
The two groups — or their patent lawyers, really — are in fact fighting over credit for CRISPR/Cas9. At stake are millions of dollars already poured into rival companies that have licensed patents from the two different groups.
But putting aside all the lawyers and all the money for a moment, obsessing over finding the one true origin of Crispr/Cas9 gets science all wrong. Casting the narrative as Doudna versus Zhang or Berkeley versus MIT is a misapprehension of history, creativity, and innovation. Discovery comes not from a singular stroke of genius, but an incremental body of research. “I’m not a great believer in the flash-of-genius theory. If you are a historian —” says Mario Biagioli, who is in fact a historian of science at UC Davis — “you quickly will realize exactly how many times there are independent discoveries of the same thing.” The dispute over credit for CRISPR/Cas9 is not the result of exceptional coincidence and disagreement. In fact, it illuminates how science always works.
February 12, 2015
Last month, Matt Ridley ran down the benefits to farmers, consumers, ecologists and the environment itself that the European Union has been resisting mightily all these years:
Scientifically, the argument over GM crops is as good as over. With nearly half a billion acres growing GM crops worldwide, the facts are in. Biotech crops are on average safer, cheaper and better for the environment than conventional crops. Their benefits accrue disproportionately to farmers in poor countries. The best evidence comes in the form of a “meta-analysis” — a study of studies — carried out by two scientists at Göttingen University, in Germany.
The strength of such an analysis is that it avoids cherry-picking and anecdotal evidence. It found that GM crops have reduced the quantity of pesticide used by farmers by an average of 37 per cent and increased crop yields by 22 per cent. The greatest gains in yield and profit were in the developing world.
If Europe had adopted these crops 15 years ago: rape farmers would be spraying far less pyrethroid or neo-nicotinoid insecticides to control flea beetles, so there would be far less risk to bees; potato farmers would not need to be spraying fungicides up to 15 times a year to control blight; and wheat farmers would not be facing stagnant yields and increasing pesticide resistance among aphids, meaning farmland bird numbers would be up.
Oh, and all that nonsense about GM crops giving control of seeds to big American companies? The patent on the first GM crops has just expired, so you can grow them from your own seed if you prefer and, anyway, conventionally bred varieties are also controlled for a period by those who produce them.
African farmers have been mostly denied genetically modified crops by the machinations of the churches and the greens, aided by the European Union’s demand that imports not be transgenically improved. Otherwise, African farmers would now be better able to combat drought, pests, vitamin deficiency and toxic contamination, while not having to buy so many sprays and risk their lives applying them.
I made this point recently to a charity that works with farmers in Africa and does not oppose GM crops but has so far not dared say so. Put your head above the parapet, I urged. We cannot do that, they replied, because we have to work with other, bigger green charities and they would punish us mercilessly if we broke ranks. Is the bullying really that bad? Yes, they replied.
Yet the Green Blob realises that it has made a mistake here. Not a financial mistake — it made a fortune out of donations during the heyday of stoking alarm about GM crops in the late 1990s — but the realisation that all it has achieved is to prolong the use of sprays and delay the retreat of hunger.
April 28, 2014
I’m interested in life extension … I have no particular hankering to die any time soon, although I admit there is some truth in the aphorism “Many wish for immortality who don’t know how to spend a rainy Sunday afternoon”. Ray Kurzweil wants immortality, and he’s doing what he can to make that happen:
Ray Kurzweil — futurist, inventor, entrepreneur, bestselling author, and now, director of engineering at Google — wants to live forever. He’s working to make it happen. Kurzweil, whose many inventions include the first optical character recognition software (which transforms the written word into data) and the first text-to-speech synthesizer, spoke to Maclean’s for our annual Rethink issue about why we’re on the brink of a technological revolution — one that will improve our health and our lives, even after the robots outsmart us for good.
Q: You say we’re in the midst of a “grand transformation” in the field of medicine. What do you see happening today?
A: Biology is a software process. Our bodies are made up of trillions of cells, each governed by this process. You and I are walking around with outdated software running in our bodies, which evolved in a very different era. We each have a fat insulin receptor gene that says, “Hold on to every calorie.” That was a very good idea 10,000 years ago, when you worked all day to get a few calories; there were no refrigerators, so you stored them in your fat cells. I would like to tell my fat insulin receptor gene, “You don’t need to do that anymore,” and indeed that was done at the Joslin Diabetes Center. They turned off this gene, and the [lab mice] ate ravenously and remained slim. They didn’t get diabetes; they didn’t get heart disease. They lived 20 per cent longer. They’re working with a drug company to bring that to market.
Life expectancy was 20 a thousand years ago; 37, 200 years ago. We’re now able to reprogram health and medicine as software, and that [pace is] going to continue to accelerate. We’re treating biology, and by extension health and medicine, as an information technology. Our intuition about how progress will unfold is linear, but information technology progresses exponentially, not linearly. My Android phone is literally several billion times more powerful, per dollar, than the computer I used when I was a student. And it’s also 100,000 times smaller. We’ll do both of those things again in 25 years. It’ll be a billion times more powerful, and will be the size of a blood cell.
January 31, 2014
Another example of how sometimes we can benefit by using biomimicry:
Engineers intrigued by the toughness of mollusc shells, which are composed of brittle minerals, have found inspiration in their structure to make glass 200 times stronger than a standard pane.
Counter-intuitively, the glass is strengthened by introducing a network of microscopic cracks, according to a study published in the journal Nature Communications on Tuesday.
A team at McGill University in Montreal began their research with a close-up study of natural materials like mollusc shells, bone and nails which are astonishingly resilient despite being made of brittle minerals.
The secret lies in the fact that the minerals are bound together into a larger, tougher unit.
The binding means the shell contains abundant tiny fault lines called interfaces. Outwardly, this might seem a weakness, but in practice it is a masterful deflector of external pressure.
To take one example, the shiny, inner shell layer of some molluscs, known as nacre or mother of pearl, is some 3,000 times tougher than the minerals it is made of.
January 13, 2014
Nathanael Johnson says he has taken more abuse over his articles on genetically modified organisms than anything else in his writing career. And he says he learned something from his research: that it actually doesn’t matter at all.
It’s a little awkward to admit this, after devoting so much time to this project, but I think Beth was right. The most astonishing thing about the vicious public brawl over GMOs is that the stakes are so low.
I know that to those embroiled in the controversy this will seem preposterous. Let me try to explain.
Let’s start off with a thought experiment: Imagine two alternate futures, one in which genetically modified food has been utterly banned, and another in which all resistance to genetic engineering has ceased. In other words, imagine what would happen if either side “won” the debate.
In the GMO-free future, farming still looks pretty much the same. Without insect-resistant crops, farmers spray more broad-spectrum insecticides, which do some collateral damage to surrounding food webs. Without herbicide-resistant crops, farmers spray less glyphosate, which slows the spread of glyphosate-resistant weeds and perhaps leads to healthier soil biota. Farmers also till their fields more often, which kills soil biota, and releases a lot more greenhouse gases. The banning of GMOs hasn’t led to a transformation of agriculture because GM seed was never a linchpin supporting the conventional food system: Farmers could always do fine without it. Eaters no longer worry about the small potential threat of GMO health hazards, but they are subject to new risks: GMOs were neither the first, nor have they been the last, agricultural innovation, and each of these technologies comes with its own potential hazards. Plant scientists will have increased their use of mutagenesis and epigenetic manipulation, perhaps. We no longer have biotech patents, but we still have traditional seed-breeding patents. Life goes on.
In the other alternate future, where the pro-GMO side wins, we see less insecticide, more herbicide, and less tillage. In this world, with regulations lifted, a surge of small business and garage-biotechnologists got to work on creative solutions for the problems of agriculture. Perhaps these tinkerers would come up with some fresh ideas to usher out the era of petroleum-dependent food. But the odds are low, I think, that any of their inventions would prove transformative. Genetic engineering is just one tool in the tinkerer’s belt. Newer tools are already available, and scientists continue to make breakthroughs with traditional breeding. So in this future, a few more genetically engineered plants and animals get their chance to compete. Some make the world a little better, while others cause unexpected problems. But the science has moved beyond basic genetic engineering, and most of the risks and benefits of progress are coming from other technologies. Life goes on.
The point is that even if you win, the payoff is relatively small in the broad scheme of things. Really, why do so many people care?
June 12, 2013
At Marginal Revolution, Alex Tabarrok links to a new paper by Peter Huber:
[. . .]
The current regime was built during a time of pervasive ignorance when the best we could do was throw a drug and a placebo against a randomized population and then count noses. Randomized controlled trials are critical, of course, but in a world of limited resources they fail when confronted by the curse of dimensionality. Patients are heterogeneous and so are diseases. Each patient is a unique, dynamic system and at the molecular level diseases are heterogeneous even when symptoms are not. In just the last few years we have expanded breast cancer into first four and now ten different types of cancer and the subdivision is likely to continue as knowledge expands. Match heterogeneous patients against heterogeneous diseases and the result is a high dimension system that cannot be well navigated with expensive, randomized controlled trials. As a result, the FDA ends up throwing out many drugs that could do good:
Given what we now know about the biochemical complexity and diversity of the environments in which drugs operate, the unresolved question at the end of many failed clinical trials is whether it was the drug that failed or the FDA-approved script. It’s all too easy for a bad script to make a good drug look awful. The disease, as clinically defined, is, in fact, a cluster of many distinct diseases: a coalition of nine biochemical minorities, each with a slightly different form of the disease, vetoes the drug that would help the tenth. Or a biochemical majority vetoes the drug that would help a minority. Or the good drug or cocktail fails because the disease’s biochemistry changes quickly but at different rates in different patients, and to remain effective, treatments have to be changed in tandem; but the clinical trial is set to continue for some fixed period that doesn’t align with the dynamics of the disease in enough patients
Or side effects in a biochemical minority veto a drug or cocktail that works well for the majority. Some cocktail cures that we need may well be composed of drugs that can’t deliver any useful clinical effects until combined in complex ways. Getting that kind of medicine through today’s FDA would be, for all practical purposes, impossible.
The alternative to the FDA process is large collections of data on patient biomarkers, diseases and symptoms all evaluated on the fly by Bayesian engines that improve over time as more data is gathered. The problem is that the FDA is still locked in an old mindset when it refuses to permit any drugs that are not “safe and effective” despite the fact that these terms can only be defined for a large population by doing violence to heterogeneity. Safe and effective, moreover, makes sense only when physicians are assumed to be following simple, A to B, drug to disease, prescribing rules and not when they are targeting treatments based on deep, contextual knowledge that is continually evolving
September 28, 2012
Brid-Aine Parnell at The Register, talking about specialized electronic development:
When it comes to electronics, boffins are usually going one way — how to make them smaller, faster and longer lasting, but a few researchers are going against the tide — looking for electronics that can last just a moment and then disappear.
At the University of Illinois, with help from Tufts and Northwestern Universities, scientists have come up with biodegradable electronics that can do their job and then dissolve. Apart from reducing the amount of consumer electronics in landfills, the disappearing gizmos could also work as medical implants, before dissolving in bodily fluids, as environmental monitors or any other device that needs to disappear.
“From the earliest days of the electronics industry, a key design goal has been to build devices that last forever — with completely stable performance,” Illinois professor of engineering and project leader John Rogers said.
“But if you think about the opposite possibility — devices that are engineered to physically disappear in a controlled and programmed manner — then other, completely different kinds of application opportunities open up.”
June 27, 2012
California’s already bad economic situation could be made even worse by mandating that genetically modified foods be labelled to call attention to themselves:
The American Medical Association resolved this week that “there is no scientific justification for special labeling of bioengineered foods.”
The association has long-held that nothing about the process of recombinant DNA makes genetically engineered (GE) crop plants inherently more dangerous to the environment or to human health than the traditional crop plants that have been deliberately but slowly bred for human purposes for millennia. It is a view shared by the National Academy of Sciences, the World Health Organization, the Food and Agriculture Organization of the U.N., the European Commission, and countless other national science academies and non-governmental organizations.
And yet Californians will consider on their November ballots a law that mandates cigarette-like labeling of food derived from GE plants. Proponents claim to promote opportunities for consumers to make informed choices about the foods they eat. But to build support for the measure, they have played on consumer fears about a promising technology that is nevertheless prone to “Frankenfoods” demagoguery. If successful, they may well imperil the ability of Californians, and consumers around the world, to choose a technology that scientists contend could end hunger and malnutrition, lift hundreds of millions from poverty, and reduce the environmental impact of feeding an evermore populous world.
June 21, 2012
Sarah Zhang points out that people who want less damage to the environment should support GM technology in farming:
Genetically modified Bt crops get a pretty bad rap. The pest-killing Bacillus thuringiensis (Bt) bacteria protein these plants are bioengineered to make has been accused of harming monarch butterflies, honey bees, rats, and showing up in the blood of pregnant women.
Just one problem: None of that is true. (Click on any of those links to see a scientific refutation of each claim.) Seven independent experts in genetically modified crops I spoke to all confirmed that the science shows Bt crops to be safer than their alternative: noxious chemical insecticides.
[. . .]
But just as we do not blame a murder on, say, a knife, Bt technology is not to blame for the ills of industrial agriculture. After all, knives are pretty handy in the kitchen when we use them properly. Even critics will acknowledge that Bt crops have led to a sharp decrease in insecticide use, which is a huge net positive for the environment. Broad spectrum chemical insecticides kill often and kill widely, wiping out “natural enemies” that are helpful pest-eating critters like spiders. A massive 20-year study just published in the journal Nature found that using Bt cotton in China to control cotton bollworms closely tracked with a rebound in natural enemy populations, which in turn keep out secondary pests like aphids that usually proliferate when chemical insecticides kill the bollworms.
If that last sentence sounds complicated, it is. Integrated pest management is about recognizing the interconnected complexity of these ecosystems of plants and all the insects living on them. The Nature study found that pest control through Bt cotton even had spillover benefits to the non-Bt soybeans growing around them. Natural enemies like ladybugs, spiders, and lacewings keep pests unaffected by Bt at bay. “Maintaining the biological control agents we already have is one of the cornerstones of integrated pest management,” says William Hutchison, an entomologist at the University of Minnesota. In addition, a 2010 study by Hutchison in Science (PDF) showed that American farmers of non-Bt corn actually reaped two-thirds of the economic benefit (read: additional profit) from nearby Bt-related pest suppression.
November 22, 2011
No, it’s not some ferociously polluting corporation, or a dangerously powerful conservative politician or a candidate for the GOP nomination in the United States. It’s algae:
“We can engineer, humbly, like we have been domesticating plants for a long time,” one scientist told me. “We engineer the algae to do biochemically something quite different to what they’d be doing in the wild: they still take photons from the sun, and via biology, turn it into a useful captured molecule. We have them doing something similar but with stunning efficiency: it’s 40 to 100 times more efficient,” says Elbert Branscomb, chief scientist to the US Department of Energy.
There are (at least) around 60 startups hoping to produce oil and diesel biologically, with accelerated fermentation or photosynthesis techniques to produce an end product that is 100 per cent compatible with the existing infrastructure. Some, for example, tweak the algae to make them do photosynthesis anything from 40 to 100 times more efficiently. LS9 received $30m in funding and has a one-step process to convert sugar to create renewable petrol. It expects production within five years. If oil prices remain high, say over $40 or $50 a barrel, then it’s viable.
So why is this the biggest threat to the environmental movement?
But the greatest challenge cheap hydrocarbons poses is for people whose outlook is founded on what I call “End Times logic”. The most successful political movement in recent years is environmentalism, which expanded from specific concerns about pollution and conservation into an all-encompassing worldview, complete with very preachy appeals to changing parts of our lifestyles.
These ranged from “Don’t flush the loo too often”, to “Don’t fly for a weekend break”, to “Eat less red meat”. Very few politicians have felt courageous enough to contradict this. And the movement has achieved its ascendancy through urgent, apocalyptic appeals, rather than using calmer methods of rational persuasion which involve costs and benefits to be totted up. These new energy sources pose a profound problem: they saves the planet, and we carry on with minimum disruption.
I expect that one effect will be that environmentalism will become much more about everyday concerns such as pollution, and conservations again, back to where it started. But it grew into a vacuum, after the end of the Cold War, when great political ideas seemed to lose credibility. As a way of driving the political agenda, it will become currency without value. Buzzwords such as “sustainability”, founded on a resource-constrained view, will no longer be credible. People will simply laugh at them.
April 12, 2011
I had to check the date on this Guardian article, just to be sure it wasn’t an April Fools’ Day posting:
Bolivia is set to pass the world’s first laws granting all nature equal rights to humans. The Law of Mother Earth, now agreed by politicians and grassroots social groups, redefines the country’s rich mineral deposits as “blessings” and is expected to lead to radical new conservation and social measures to reduce pollution and control industry.
The country, which has been pilloried by the US and Britain in the UN climate talks for demanding steep carbon emission cuts, will establish 11 new rights for nature. They include: the right to life and to exist; the right to continue vital cycles and processes free from human alteration; the right to pure water and clean air; the right to balance; the right not to be polluted; and the right to not have cellular structure modified or genetically altered.
Controversially, it will also enshrine the right of nature “to not be affected by mega-infrastructure and development projects that affect the balance of ecosystems and the local inhabitant communities”.
I don’t know where the government is planning on moving all the Bolivians, because just by occupying the country, they’ll be violating these new rights on a moment-to-moment basis.
February 7, 2011
There’s been enormous progress in genomics; we’re now on the threshold of truly understanding how little we understand. While the anticipated firehose of genome-based treatments hasn’t materialized, we now know why it hasn’t materialized, and it’s possible to start filling in the gaps in the map. Turns out that sequencing the human genome was merely the start. (It’s not a blueprint; it’s not even an algorithm for generating a human being. Rather, it’s like a snapshot of the static data structures embedded in an executing process. Debug that.) My bet is that we’re going to have to wait another decade. Then things are going to start to get very strange in medicine.
Charles Stross, “Reasons to be cheerful”, Charlie’s Diary, 2010-12-31
October 21, 2010
The once-common American Chestnut tree fell victim to a blight during the last century, almost wiping out the species. The American Chestnut Foundation is hopeful of a revival:
By interbreeding the American with its Chinese cousin, tree lovers have created an American chestnut with some resistance to Asian blight and have developed a virus that can be injected into affected trees to combat the fungus. It’s a project that shows every sign of promise — with about 25,000 of the new chestnuts planted under the guidance of trained scientists and chestnut devotees.
If the hybrid plantings thrive, some envision huge tracts of strip-mined Appalachia one day being restored with lovely chestnut forests.
“We know we’re interbreeding resistance. Now we have to figure out, does it have enough resistance?” said Bryan Burhans, president of the American Chestnut Foundation, which has led the revival efforts.
He said it will take 75 to 100 years to know whether the tree can be reestablished as a mainstay of Eastern forests. But he said he’s “very optimistic” about the American chestnut’s future.
[. . .]
A fast-growing, hardy tree that thrives on rocky and acidic soil, the American chestnut served as an economic engine for Appalachia. Families fattened livestock with its nuts and used its wood for fuel, railroad ties, fence posts, musical instruments and furniture. It was a fixture along East Coast and Appalachian streets and highways, where its display of fingery white flowers was a springtime delight.
June 3, 2010
Joule Unlimited claims to have developed a new single-cell plant which can produce diesel fuel from sunlight and carbon dioxide:
Henry Ford, the father of the modern assembly line, predicted a future where fuel would be mass-produced from natural materials like fruit, weeds, or even sawdust — renewable alternatives to finite fossil fuels. Still, one energy technology being developed by Joule Unlimited, a company in Cambridge, Mass., might have surprised even him: a plant that sweats diesel.
Plants use the sun to convert carbon dioxide into energy, but Joule has designed tiny, gene-altered organisms (essentially single-celled plants) that use the photosynthetic process to create liquid fuel. Stored in brackish water enclosed in glass panels, they grow for a few days before a genetic switch is flipped, diverting their energy toward fuel production. The diesel, which they pump out continuously, is circulated away to a separator, where it’s extracted and sent to a storage tank. After several weeks, the plants are flushed away and the process starts over again. These microscopic organisms can be genetically engineered to secrete diesel or other chemicals the company plans on commercializing; president and CEO Bill Sims calls the technology an “above-ground oil well.”