Tag Archives: biotechnology

silicon-based life

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Scientists can now synthesize proteins that could be incorporated in silicon-based life forms.

Directed evolution of cytochrome c for carbon–silicon bond formation: Bringing silicon to life

Enzymes that catalyze carbon–silicon bond formation are unknown in nature, despite the natural abundance of both elements. Such enzymes would expand the catalytic repertoire of biology, enabling living systems to access chemical space previously only open to synthetic chemistry. We have discovered that heme proteins catalyze the formation of organosilicon compounds under physiological conditions via carbene insertion into silicon–hydrogen bonds. The reaction proceeds both in vitro and in vivo, accommodating a broad range of substrates with high chemo- and enantioselectivity. Using directed evolution, we enhanced the catalytic function of cytochrome c from Rhodothermus marinus to achieve more than 15-fold higher turnover than state-of-the-art synthetic catalysts. This carbon–silicon bond-forming biocatalyst offers an environmentally friendly and highly efficient route to producing enantiopure organosilicon molecules.

November 2016 in Review

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Sometimes you look back on a month and feel like nothing very important happened. But November 2016 was obviously not one of those months! I am not going to make any attempt to be apolitical here. I was once a registered independent and still do not consider myself a strong partisan. However, I like to think of myself as being on the side of facts, logic, problem solving, morality and basic goodness. Besides, this blog is about the future of our human civilization and human race. I can’t pretend our chances didn’t just take a turn for the worse.

3 most frightening stories

  • Is there really any doubt what the most frightening story of November 2016 was? The United Nations Environment Program says we are on a track for 3 degrees C over pre-industrial temperatures, not the “less than 2” almost all serious people (a category that excludes 46% of U.S. voters, apparently) agree is needed. This story was released before the U.S. elected an immoral science denier as its leader. One theory is that our culture has lost all ability to separate fact from fiction. Perhaps states could take on more of a leadership role if the federal government is going to be immoral? Washington State voters considered a carbon tax that could have been a model for other states, and voted it down, in part because environmental groups didn’t like that it was revenue neutral. Adding insult to injury, WWF released its 2016 Living Planet Report, which along with more fun climate change info includes fun facts like 58% of all wild animals have disappeared. There is a 70-99% chance of a U.S. Southwest “mega-drought” lasting 35 years or longer this century. But don’t worry, this is only “if emissions of greenhouse gases remain unchecked”. Oh, and climate change is going to begin to strain the food supply worldwide, which is already strained by population, demand growth, and water resources depletion even without it.
  • Technological unemployment may be starting to take hold, and might be an underlying reason behind some of the resentment directed at mainstream politicians. If you want a really clear and concise explanation of this issue, you could ask a smart person like, say, Barack Obama.
  • According to left wing sources like Forbes, an explosion of debt-financed spending on conventional and nuclear weapons is an expected consequence of the election. Please, Mr. Trump, prove them wrong!

3 most hopeful stories

3 most interesting stories

breakthroughs in antibiotic resistance

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There are potential breakthroughs against antibiotic-resistant bacteria, which I think is good as I’ve been coughing up some kind of alien green goo for about a week now.

An anti-infective synthetic peptide with dual antimicrobial and immunomodulatory activities

Antibiotic-resistant infections are predicted to kill 10 million people per year by 2050, costing the global economy $100 trillion. Therefore, there is an urgent need to develop alternative technologies. We have engineered a synthetic peptide called clavanin-MO, derived from a marine tunicate antimicrobial peptide, which exhibits potent antimicrobial and immunomodulatory properties both in vitro and in vivo. The peptide effectively killed a panel of representative bacterial strains, including multidrug-resistant hospital isolates. Antimicrobial activity of the peptide was demonstrated in animal models, reducing bacterial counts by six orders of magnitude, and contributing to infection clearance. In addition, clavanin-MO was capable of modulating innate immunity by stimulating leukocyte recruitment to the site of infection, and production of immune mediators GM-CSF, IFN-γ and MCP-1, while suppressing an excessive and potentially harmful inflammatory response by increasing synthesis of anti-inflammatory cytokines such as IL-10 and repressing the levels of pro-inflammatory cytokines IL-12 and TNF-α. Finally, treatment with the peptide protected mice against otherwise lethal infections caused by both Gram-negative and -positive drug-resistant strains. The peptide presented here directly kills bacteria and further helps resolve infections through its immune modulatory properties. Peptide anti-infective therapeutics with combined antimicrobial and immunomodulatory properties represent a new approach to treat antibiotic-resistant infections.

Zuckerberg vs. disease

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Mark Zuckerberg and his wife have decided to set a modest goal of curing all disease.

Facebook co-founder Mark Zuckerberg and his wife, Priscilla Chan, on Wednesday announced a $3 billion effort to accelerate scientific research with the wildly ambitious goal of “curing all disease in our children’s lifetime.”

The many components of the initiative include creating universal technology “tools” based on both traditional science and engineering on which all researchers can build, including a map of all cell types, a way to continuously monitor blood for early signs of illness, and a chip that can diagnose all diseases (or at least many of them). The money will also help fund what they referred to as 10 to 15 “virtual institutes” that will bring together investigators from around the world to focus on individual diseases or other goals — an idea that has the potential to upend biomedical science…

September 2016 in Review

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3 most frightening stories

  • The U.S. and Russia may have blundered into a proxy war in Syria. And on a loosely related war-and-peace note, Curtis LeMay was a crazy bastard.
  • The ecological footprint situation is not looking too promising: “from 1993 to 2009…while the human population has increased by 23% and the world economy has grown 153%, the human footprint has increased by just 9%. Still, 75% the planet’s land surface is experiencing measurable human pressures. Moreover, pressures are perversely intense, widespread and rapidly intensifying in places with high biodiversity.” Meanwhile, as of 2002 “we appropriate over 40% of the net primary productivity (the green material) produced on Earth each year (Vitousek et al. 1986, Rojstaczer et al. 2001). We consume 35% of the productivity of the oceanic shelf (Pauly and Christensen 1995), and we use 60% of freshwater run-off (Postel et al. 1996). The unprecedented escalation in both human population and consumption in the 20th century has resulted in environmental crises never before encountered in the history of humankind and the world (McNeill 2000). E. O. Wilson (2002) claims it would now take four Earths to meet the consumption demands of the current human population, if every human consumed at the level of the average US inhabitant.” And finally, 30% of African elephants have been lost in the last 7 years.
  • Car accidents are the leading cause of death for children ages 5 to 24. The obsession with car seats may not be saving all that many lives, while keeping children out of cars as much as possible would be 100% guaranteed to save lives. And one thing that would be guaranteed to help us create more walkable neighborhoods and therefore save children’s lives: getting rid of minimum parking requirements in cities once and for all. And yet you don’t hear this debate being framed in moral terms.

3 most hopeful stories

3 most interesting stories

  • Monsanto is trying to help honeybees (which seems good) by monkeying with RNA (which seems a little frightening). Yes, biotech is coming.
  • Some people think teaching algebra to children may actually be bad. Writing still seems to be good.
  • There have been a number of attempts to identify and classify the basic types of literary plots.

Theranos

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This is the story of Theranos, a biotech startup that was supposed to have a revolutionary blood-testing technology but ultimately turned out to be a scam. It turned out the technology didn’t work. It probably didn’t start out as a scam. They probably thought they were close to getting it to work, sold investors and consumers on the idea, thought if they could hide the problems for awhile they could buy some time to make it work and get away with it. But, it never worked and they eventually couldn’t hide the problems.

The most interesting part of the story, to me, is whether the tech startup model will translate to the biotech sector. The article has a little bit to say about that:

Holmes had indeed mastered the Silicon Valley game. Revered venture capitalists, such as Tim Draper and Steve Jurvetson, invested in her; Marc Andreessen called her the next Steve Jobs. She was plastered on the covers of magazines, featured on TV shows, and offered keynote-speaker slots at tech conferences. (Holmes spoke at Vanity Fair’s 2015 New Establishment Summit less than two weeks before Carreyrou’s first story appeared in theJournal.) In some ways, the near-universal adoration of Holmes reflected her extraordinary comportment. In others, however, it reflected the Valley’s own narcissism. Finally, it seemed, there was a female innovator who was indeed able to personify the Valley’s vision of itself—someone who was endeavoring to make the world a better place…

Holmes subsequently raised $6 million in funding, the first of almost $700 million that would follow. Money often comes with strings attached in Silicon Valley, but even by its byzantine terms, Holmes’s were unusual. She took the money on the condition that she would not divulge to investors how her technology actually worked, and that she had final say and control over every aspect of her company. This surreptitiousness scared off some investors. When Google Ventures, which focuses more than 40 percent of its investments on medical technology, tried to perform due diligence on Theranos to weigh an investment, Theranos never responded. Eventually, Google Ventures sent a venture capitalist to a Theranos Walgreens Wellness Center to take the revolutionary pinprick blood test. As the V.C. sat in a chair and had several large vials of blood drawn from his arm, far more than a pinprick, it became apparent that something was amiss with Theranos’s promise…

Silicon Valley, once so taken by Holmes, has turned its back, too. Countless investors have been quick to point out that they did not invest in the company—that much of its money came from the relatively somnolent worlds of mutual funds, which often accrue the savings of pensioners and retirees; private equity; and smaller venture-capital operations on the East Coast. In the end, one of the only Valley V.C. shops that actually invested in Theranos was Draper Fisher Jurvetson. Many may have liked what Holmes represented about their industry, but they didn’t seem to trust her with their money.

I think we are on the cusp of some kind of biotech boom. The question is, what will it look like, who exactly will it benefit, and who will want it? The health care and agricultural sectors are the most obvious fields. In fact, I think it is already pervasive in those fields. We are starting to here about biotech methods of fighting mosquitoes, and I suspect we will pull out all the stops when diseases like dengue and Zika start to affect people in the rich world. Agricultural pests won’t be far behind. Maybe stingless, pesticide resistant bees to replace our lost pollinators. Food science may weigh in with yeast vats that produce food without photosynthesis and animal protein without animals, although consumers are going to be very wary of these products at first. Viruses targeting specific bacteria might be the answer to antibiotic resistance. We may see cures for diseases that have alluded us until now, and a steady uptick in total life span and healthy life span at least among the moderately affluent. New fertility treatments, ways to preserve egg and sperm cells for long periods of time or even across generations, organ and whole organism cloning, ways for same-sex couples to have biological children, children carried by surrogate mothers, etc.

But these technologies all seem like they will benefit a few big corporate players, not the kind of broad-based startup ecosystem we have seen with information technology. Maybe that is okay. The idea of dorm room and garage genetic engineering labs is a little scary after all. But if there was a kind of broad-based, consumer-focused biotech innovation ecosystem, what would it look like? Maybe novel pets and houseplants. Maybe novel bioelectrical devices like radios, batteries, chargers, night lights, phones, computers, watches and other things that glow in the dark. Maybe energy-related devices like solar cells, fuel cells, oil-producing algae and bacteria that produce methane, methanol or other useful organic products from garbage. Maybe new forms of water and wastewater treatment that can work at many scales. Maybe new forms of biodegradable packaging. Maybe building materials and machines that can grow and heal. New forms of manufacturing. Maybe somebody will figure out how to put DNA in a computer or a computer in DNA.

This all sounds like nutty stuff now, when we are just starting to yawn at the wonders of the infotech age that seemed nutty a decade or two ago. They are such a part of our lives now that we have already forgotten life without them, and we think we saw them coming all along. I think biotech is already here behind the scenes, much as infotech was in the 80s and early 90s, and at some point it is going to seem to burst into the public consciousness just as infotech did in the mid-90s with the advent of the internet. I just don’t know what the biotech equivalent of the internet is going to be.

anti-aging pill

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This MIT professor thinks he has discovered an anti-aging pill.

The product contains a chemical precursor to nicotinamide adenine dinucleotide, or NAD, a compound that cells use to carry out metabolic reactions like releasing energy from glucose. The compound is believed cause some effects similar to a diet that is severely short on calories—a proven way to make a mouse live longer…

Scientists have shown they can reliably extend the life of laboratory mice by feeding them less, a process known as “caloric restriction.” That process seems to be mediated by biological molecules called sirtuins. NAD is important because it’s a chemical that sirtuins need to do their work and is also involved in other aspects of a cell’s metabolism. In worms, mice, and people, NAD levels fall with age, says Guarente, so the idea is to increase levels of the molecule.

“NAD replacement is one of the most exciting things happening in the biology of aging,” says Nir Barzilai, director of the Institute for Aging Research at the Albert Einstein College of Medicine in New York, who has coauthored scientific papers with Guarente but is not involved in Elysium. “The frustration in our field is that we have shown we can target aging, but the FDA does not [recognize it] as an indication.”

 

RNA interference

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Monsanto is trying to use genetic technology to kill honeybee pests.

RNA can also “silence” specific genes, preventing an organism from using them to make proteins. In 1998 scientists discovered that they could engineer stretches of double-stranded RNA to do the same thing. As a lab technique, RNA interference—or RNAi—turned out to be useful for learning about genes by turning them off. It also showed promise in fighting viruses, cancers, and even harmful pests and parasites. The researchers at the seminar were talking about using RNAi to prevent mosquitoes from spreading malaria, but that gave Hayes another idea. “I thought, could this be adapted to honeybee predator control?” In other words: to kill mites…

Traditional pesticides act like chemical backhoes, killing their targets (beetles, weeds, viruses) but harming good things along the way (beneficial insects, birds, fish, humans). RNAi, in theory, works instead like a set of tweezers, plucking its victims with exquisite specificity by clicking into sequences of genetic code unique to that organism. “If you could design an ideal pesticide, this is the stuff you’re looking for,” says Pamela Bachman, a toxicologist at Monsanto.

 

June 2016 in Review

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3 most frightening stories

  • Coral reefs are in pretty sad shape, perhaps the first natural ecosystem type to be devastated beyond repair by climate change.
  • Echoes of the Cold War are rearing their ugly heads in Western Europe.
  • Trump may very well have organized crime links. And Moody’s says that if he gets elected and manages to do the things he says, it could crash the economy.

3 most hopeful stories

  • China has a new(ish) sustainability plan called “ecological civilization” that weaves together urban and regional planning, environmental quality, sustainable agriculture, habitat and biodiversity concepts. This is good because a rapidly developing country the size of China has the ability to sink the rest of civilization if they let their ecological footprint explode, regardless of what the rest of us do. Maybe they can set a good example for the rest of the developing world to follow.
  • Genetic technology is appearing to provide some hope of real breakthroughs in cancer treatment.
  • There is still some hope for a technology-driven pick-up in productivity growth.

3 most interesting stories

gene circuits

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Here’s another article on the idea of designed biological circuits.

Synthetic mixed-signal computation in living cells

Living cells implement complex computations on the continuous environmental signals that they encounter. These computations involve both analogue- and digital-like processing of signals to give rise to complex developmental programs, context-dependent behaviours and homeostatic activities. In contrast to natural biological systems, synthetic biological systems have largely focused on either digital or analogue computation separately. Here we integrate analogue and digital computation to implement complex hybrid synthetic genetic programs in living cells. We present a framework for building comparator gene circuits to digitize analogue inputs based on different thresholds. We then demonstrate that comparators can be predictably composed together to build band-pass filters, ternary logic systems and multi-level analogue-to-digital converters. In addition, we interface these analogue-to-digital circuits with other digital gene circuits to enable concentration-dependent logic. We expect that this hybrid computational paradigm will enable new industrial, diagnostic and therapeutic applications with engineered cells.