Tag Archives: biotechnology

gene editing

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Here is a long article in MIT Technology Review about gene editing.

“Germ line” is biologists’ jargon for the egg and sperm, which combine to form an embryo. By editing the DNA of these cells or the embryo itself, it could be possible to correct disease genes and to pass those genetic fixes on to future generations. Such a technology could be used to rid families of scourges like cystic fibrosis. It might also be possible to install genes that offer lifelong protection against infection, Alzheimer’s, and, Yang told me, maybe the effects of aging. These would be history-making medical advances that could be as important to this century as vaccines were to the last.

That’s the promise. The fear is that germ-line engineering is a path toward a dystopia of superpeople and designer babies for those who can afford it. Want a child with blue eyes and blond hair? Why not design a highly intelligent group of people who could be tomorrow’s leaders and scientists?…

All this means that germ-line engineering is much farther along than anyone imagined. “What you are talking about is a major issue for all humanity,” says Merle Berger, one of the founders of Boston IVF, a network of fertility clinics that is among the largest in the world and helps more than a thousand women get pregnant each year. “It would be the biggest thing that ever happened in our field,” he says. Berger predicts that repairing genes for serious inherited disease will win wide public acceptance, but beyond that, the technology would cause a public uproar because “everyone would want the perfect child” and it could lead to picking and choosing eye color and eventually intelligence. “These are things we talk about all the time,” he says. “But we have never had the opportunity to do it.”

How far out are practical applications in humans? Reading farther down, some are saying 10-20 years.

what’s new with drugs

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Drugs are not immune from the current wave of seemingly accelerating innovation (from Pacific Standard Magazine):

New psychoactive substances are coming out so quickly that it’s not possible to ban them fast enough to keep up, let alone police or scientifically understand them. When one substance is outlawed, another is born, just chemically distinct enough from the last one to evade its ban…

Not since the 19th century—when an earlier wave of globalization rapidly accelerated the spread of opium, cocaine, marijuana, and hazily defined “patent medicines”—has there been such a burgeoning and unregulated pharmacopeia. And by all indications, the future promises only more acceleration. Last year, a research lab at Stanford demonstrated that it’s possible to produce opioid drugs like morphine using a genetically modified form of baker’s yeast. Soon, even the production of traditional illegal drugs or illicit versions of pharmaceuticals could become a highly decentralized cottage industry, posing the same kind of regulatory challenge that the specter of 3-D printed firearms poses to the project of gun control.

In 2013, the U.N.’s World Drug Report summed up the global situation this way: “The international drug control system is floundering, for the first time, under the speed and creativity of the phenomenon known as new psychoactive substances.” Testifying before Congress that same year, the DEA’s Joseph Rannazzisi said that his agency could not keep up with “the clandestine chemists and traffickers who quickly and easily replace newly controlled substances with new, non-controlled substances.”

New Zealand is starting to regulate recreational drugs more like food: with labeling, consumer notices, and so on. Sometimes I wonder how long this will stay a mom and pop business – once it’s legal, won’t big drug and chemical companies try to get in on the game? It’s a brave new world.

February 2015 in Review

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This blog got 173 hits in February! Pretty cool, considering I really just meant it as a place to collect my own scattered thoughts and refer back to them later. If 173 out of the 6 billion people out there like it, I am flattered. Okay, I understand there may have been a few repeat visitors. Also, judging from the most popular posts, there is one thing I mention occasionally that people really like: robots!

Negative trends and predictions:

  • Fresh Air had an interview with Elizabeth Kolbert, author of The Sixth Extinction. The idea here is that what humans are doing to other species is equivalent in scope to events that have killed off most life on Earth in the past.
  • The drought in the western U.S. continues to grind on.
  • There are some depressing new books out there about all the bad things that could happen to the world, from nuclear terrorism to pandemics. Also a “financial black hole”, a “major breakdown of the Internet”, “the underpopulation bomb”, the “death of death”, and more!
  • Government fragmentation explains at least part of suburban sprawl and urban decline in U.S. states, with Pennsylvania among the worst.

Positive trends and predictions:

  • Libraries are starting to go high-tech using warehouse robot technology.
  • I had a rambling post on technologies to watch: carbon fiber, the internet of things, self-driving cars and trucks, biotechnology for everything from carbon sequestration to cancer treatment to agriculture, and of course more automation, robots, and artificial intelligence. And yes, Clark W. Griswold’s cereal varnish is a real thing!
  • U.S. utility solar capacity is slowly ramping up.
  • A new study suggests a sudden, catastrophic climate tipping point may not be too likely.
  • Robots can independently develop new drugs.
  • According to Google, self-driving taxis are only 2-5 years away.
  • Complex ecosystems can be designed.
  • Compost toilets may save the world…if we can get over the ick factor and the sawdust problem.
  • There are lots of cheap new options for the aspiring high-tech handymen (and women and children) among us. Even better news, we may have reached the point where if you build a robot with your kid in the basement, and he then tells other kids about it, he might not get beat up on the playground.
  • New York City has some good examples of green stormwater infrastructure integrated in sidewalk and street design.

One thing that strikes me is that we keep hearing about biotechnology, but we haven’t seen big, obvious impacts in most of our daily lives yet. I suspect biotechnology is like computers and robots in the 70s, 80s, and 90s – slow but steady progress was being made in the background, the pressure was building, and then the wave suddenly broke onto the commercial and public consciousness. I suspect biotechnology is the next big wave that is going to break.

human head transplants

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Human head transplants may be possible this century, neuroscientist says

Sometimes a headline says it all. The article says this technology is not far off, although it would be expensive.

The separation of head and body would have to occur on two humans simultaneously, Canavero writes… The procedure, Canavero writes, would have to take place within an hour… He adds that the surgery would take a team of 100 surgeons roughly 36 hours to complete, at an estimated cost of £8.5-million ($128-million).[*]

“The problem” of this surgery, Canavero told ABCNews.com, “is not really technical but is completely ethical.”

It’s hard to imagine any situation where this would be ethical. To have a donor, someone would have to die in a way that leaves their otherwise healthy body completely intact, except for the head. Grafting heads onto executed prisoners might solve the ethical problem for some, but not for me. All I can think of is if we could grow human bodies with no brain at all, or all but the most primitive part of the nervous system that keeps basic organs functioning. Even that sounds ethically dubious. But you figure, if there is a black market for individual organs now, some dying rich person somewhere will try this eventually whether it is ethical or not. I wonder, if we somehow solved all non-brain-related diseases like heart disease and cancer, and we perfected the technology of cloning brainless bodies in some ethical way, how long could we live? How long could the brain actually last, considering that we hear constantly that we start losing brain function as early as our 30s?

I can’t help thinking of the awful 1991 movie Body Parts, in which this sort of thing doesn’t turn out well, and that was just an arm!

* yes if the operation cost 8.5 million British pounds, it should be 12.8 million US dollars above, not 128 million. Either that, or they meant 85 million pounds. It doesn’t really change the point of the article.

“robot scientist”

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This article is about a robot that can somehow develop its own experiments to test new drugs.

There is an urgent need to make drug discovery cheaper and faster. This will enable the development of treatments for diseases currently neglected for economic reasons, such as tropical and orphan diseases, and generally increase the supply of new drugs. Here, we report the Robot Scientist ‘Eve’ designed to make drug discovery more economical. A Robot Scientist is a laboratory automation system that uses artificial intelligence (AI) techniques to discover scientific knowledge through cycles of experimentation. Eve integrates and automates library-screening, hit-confirmation, and lead generation through cycles of quantitative structure activity relationship learning and testing. Using econometric modelling we demonstrate that the use of AI to select compounds economically outperforms standard drug screening. For further efficiency Eve uses a standardized form of assay to compute Boolean functions of compound properties. These assays can be quickly and cheaply engineered using synthetic biology, enabling more targets to be assayed for a given budget. Eve has repositioned several drugs against specific targets in parasites that cause tropical diseases. One validated discovery is that the anti-cancer compound TNP-470 is a potent inhibitor of dihydrofolate reductase from the malaria-causing parasite Plasmodium vivax.

December 2014 in Review

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At the end of November, my Hope for the Future Index stood at -2.  I’ll give December posts a score from -3 to +3 based on how negative or positive they are.

Negative trends and predictions (-12):

  • When you consider roads, streets, and parking, cars take up more space in cities than housing. (-2)
  • The latest on productivity and economic growth: Paul Krugman says there is risk of deflationary spirals in many countries, and the U.S. economy is nothing to right home about. (-1)
  • There are a few legitimate scientists out there warning of sudden, catastrophic climate change in the near future. (-1)
  • Automation (meaning robots and AI) is estimated to threaten 47% of all U.S. jobs. One area of active research into automation: weaponry. Only one negative point because there are also some positive implications. (-1)
  • Margaret Atwood’s Year of the Flood is a depressing but entertaining reminder that bio-apocalypse is possible. (-2)
  • Before the recent rains, the drought in California was estimated to be a once-in-1200-years event. Major droughts in major food growing regions are not good news, especially with depletion of groundwater, and loss of snowpack and glaciers also in the news. (-2)
  • William Lazonick argues provides evidence that the rise in the gospel of shareholder value correlated with the growth slowdown that started in the 1970s – his explanation is that before that, retained earnings were a cornerstone of R&D and innovation in the economy. Loss of a point because it’s good to hear a dissenting voice, but the economy is still run by disciples of the profits for now. (-1)
  • Elizabeth Warren and Bernie Sanders are warning that the U.S. financial system may still be dangerously unstable. (-2)

Positive trends and predictions (+6):

  • There are some new ideas out there for teaching computer programming, even to young children: Loco Robo, Scratch, and for-profit “programming boot camps”. (+1)
  • You can now get genetically customized probiotics for your vagina. (+1)
  • There are plenty of ideas and models out there for safe, walkable streets, some as simple as narrower lanes. But as I point out, the Dutch and Danish designs are pretty much perfect and should just be adopted everywhere. (+1)
  • I linked to a new video depicting Michael Graves’s idea for “linear cities“. These could be very sustainable ecological if they meant the rest of the landscape is left in a mostly natural condition. I am not as sure about social sustainability – done wrong, they could be like living in a mall or subway station. This was one of my all-time more popular posts. (+1)
  • There are new algorithms out there for aggregating and synthesizing large amounts of scientific literature. Maybe this can increase the returns to R&D and help boost innovation. (+1)
  • There will be several international conferences in 2015 with potential to make real progress on financial stability and sustainability. The phrase “deep decarbonization” has been uttered. (+1)
  • Some evidence suggests that the oceans have absorbed a lot of global warming over the past decade or so, preventing the more extreme range of land surface warming that had been predicted. This is a good short- to medium-term trend, but it may not continue in the long term. (+0)

change during December 2014: -12 + 6 = -6

Hope for the Future Index (end of December 2014): -2 -6 = -8

best of best of 2014

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This time of year, you pretty much have to do a “best of” post. I’ll get to a review of some of my own posts eventually, but in the meantime here are a handful of “best of” posts. I actually don’t know if they are the best of the best of, but they are just a few that caught my eye.

  1. from Wired, The Best and Worst in a Tumultuous Year for Science: Despite the annoyingly un-reader-friendly slide show format, there are some serious eye openers here, such as synthesis of completely new, man-made DNA base pairs; custom-designed monkeys with a “gene-editing system”; a potentially huge breakthrough on diabetes; and a study concluding that the number – not the number of species, but the actual number of wild animals – has decreased by half in the last 40 years.
  2. Longreads Best of 2014: Business Writing: This links to some great articles on education reform, the status and future of Microsoft, and Airbnb. But be warned, these are some seriously long reads!
  3. Economist Money talks podcast, End of year edition. I would always rather read the transcript, but still this goes through some major trends from the year like oil prices, financial regulation, Uber and Lyft, and is worth a listen.
  4. from Wired again, The Best Science Visualizations of the Year. Some interesting ones depict “genetic activity of ocean bacteria”, loss of Arctic summertime sea ice, and the origin and early spread of AIDS.
  5. From Urbanful, Film’s 6 coolest (fictional) hydrid cities. Yes, the Los Angeles version of Blade Runner makes it. So do Gotham City and Metropolis, which are described as “New York by night” and “New York by day”. Finally, “Big Hero 6, the first collaboration between Disney and Marvel, takes place in the futuristic city of San Fransokyo, a fusion of San Francisco, California and Tokyo, Japan.”
  6. One more from Wired: The Craziest Sci-Fi Fantasies That Got Closer to Reality This Year. There’s plenty of Star Wars vs. Star Trek here, but my favorites are that you can now get your dog cloned in South Korea, and a “cheetah robot”.

Happy new year!

The Year of the Flood

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I finally got around to reading The Year of the Flood, the second book in Margaret Atwood’s MaddAdam trilogy. And I liked it. I remember not loving the first book, Oryx and Crake. Sometimes whether or not you love a book depends on where you are and what you are doing when you read it. Often, I remember exactly where I was and what I was doing when I read a book I loved. And I don’t remember where I was when I read Oryx and Crake, which is a telling sign. However, I remember exactly when I read The Space Merchants by Frederik Pohl – 2009. And I remember thinking that Margaret Atwood lifted themes directly out of that book, only didn’t use them quite as well, so I guess I read Oryx and Crake after that. And I remember being annoyed that Atwood would not admit that the book was a work of science fiction, and that serious people were reading and positively reviewing the book who thought they were too serious for science fiction. Well, I have news – it was science fiction all along, and not only that, it’s cyberpunk. Well, I’ve decided to forgive all this. I can give her the benefit of the doubt, or else I can decide that she was paying homage to an earlier science fiction master and give her credit for that. As I’ve gotten more into science fiction, I’ve seen that done several times, obviously on purpose, and it seems to be acceptable where it might not be acceptable in another genre. So, I’ve decided since then that both books are pretty good after all, and I plan to read the third book.

In The Year of the Flood, there are themes that seem like they are taken right out of The Hunger Games. I found this interview online where Atwood says she has never heard of The Hunger Games, and forgives the author of The Hunger Games for taking her idea.

Have you had a chance to read or see The Hunger Games? The games are designed for the districts to pay back the Capitol for a past rebellion, via the lives of their children, like the heroine Katniss Everdeen. It seems to be inspired in part by elements of The Handmaid’s Tale, Oryx and Crake, and Year of the Flood, especially in terms of the structure of postapocalyptic society, how the disenfranchised are “chosen” for an honor that is anything but …
In kind of a game show? So, basically it’s Painball from Year of the Flood in which people are pitted against other people so other people can watch it on TV? And the origin of that of course is paintball, which is a real thing! It’s always nice to have people see the beauty of one’s ideas. I’m flattered. [Chuckles.] It sounds interesting. Some of these things go way back, mythologically. How did she end up in this position?

Because there’s a lottery, and her sister was chosen, and so she volunteers to take her place.
Shirley Jackson! How old are they?

Between the ages of 11 and 18.
Theseus and the Minotaur! Love it. And so they put these people in a very large area? It’s Painball. Same idea. If you survive, will they let you out?

I don’t want to spoil it too much for you.
That’s okay — I can guess. I haven’t written my third one yet, so whatever’s in it can’t be used in The Hunger Games.

The original Hunger Games novel was released in 2008, and The Year of the Flood in 2009. So it’s plausible that it was a coincidence and I’ll give her the benefit of the doubt again. Anyway, maybe she’s right and there are only a certain number of themes and plots out there, and good fiction is all about how you apply them to your characters and your time.

The MaddAdam books present a near-future dystopian society in a very entertaining way, and I was entertained by that. I don’t think I would be giving away too much if I told you there is a collapse of industrialized, urbanized civilization in this story. You find that out in the first few pages of the first book. Then the rest of the story is really about who, how, and why that happened. The first book focuses more on consumer society and dangerous technology in the hands of amoral – in fact immoral – private corporations, while the second mixes that with a bit of climate change, habitat and species loss.

You find out pretty early what actually caused the collapse, but the more interesting part to me, which Margaret hints at but ultimately leaves to our imaginations, is how the society got to the point it was at before the crash. Any sort of representative government seems to be completely absent, but you don’t get the sense that the corporations muscled it aside through any sort of armed means. Maybe they simply starved it of resources to the point where it gave up. The entire society is designed to accumulate wealth and power at the top, but it is a bit of a puzzle how that works. The corporations themselves create new value through their research into the new technologies, but then they have to make the whole society want to buy those things from them. They have to let just enough wealth trickle down to enough people so they can spend the wealth and let it be gathered back up. So there must be a very, very large number of relatively poor people working hard to support the elite few, without realizing they are doing that. I say relatively poor because they can’t be so poor they decide to drop out of the consumer system entirely (as a few people do, which is the focus of the second book.) They can’t realize how poor they are, and they have to have a little bit of income that they can spend on all the things the corporations provide, which is everything – food, shelter, clothing, drugs, even access to reproduction. They have to believe in money, and want to accumulate money, but they have to want the products and services of the corporations so much that they never actually accumulate much money but spend it all. Of course, the corporations are exploiting not just all these people but the natural environment, so at some point that is either going to catch up to them, unless there is an accident or deliberate act to help the process along first…

genetic sequencing: what’s it good for?

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Do you find genetic sequencing interesting, but you’ve been struggling to find a practical application? Look no further:

According to Hutchinson, Sweet Peach will provide women with kits allowing them to swab their vaginas at home, then mail the swab into a lab which will sequence the genomes of their vaginal bacteria. Sweet Peach will then create a personalized probiotic — targeting UTIs and yeast infections — based on each woman’s swab. Women will be able to purchase a monthly regimen or a longer “subscription” based on their needs. More information will be available when the company launches their crowdfunding campaign this coming week.

“It’s nothing about scent,” Hutchinson told The Huffington Post in a phone interview. “A vagina should smell like a vagina, and anyone who doesn’t think that doesn’t deserve to be near one.”

Okay, touche, nothing about scent… but I can think of plenty of applications above the waist that do involve scent. Bad breath and armpit odor are caused mainly by sulfate reducing bacteria, I think, so introduce another harmless organism that can out-compete them, and problem solved – in fact, showering too often might tend to disrupt your perfectly balanced armpit ecosystem. How about some genetically customized pro-biotic mouthwash and deodorant? You could come back from your next camping trip smelling better than when you left! Or on a more serious note, how about healthy teeth and gums without brushing?

freezing eggs

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It’s becoming more common to freeze human eggs. The implications are interesting. A woman can freeze eggs when she is young for later use, obviously. What if a young woman learns that she is not able to have children? Could she choose to be implanted with eggs her sister has frozen? Sure, that seems okay. What about eggs her mother chose to freeze decades earlier? The baby could be someone’s daughter and granddaughter at the same time. But still just a baby. I imagine these things will all happen within families, if they haven’t already. What about buying and selling eggs though? What about a couple paying a stranger to have their genetic child because they are just too busy or don’t want to be bothered with a pregnancy. That’s slightly more troubling, but I’m sure that too will happen if it hasn’t already.