Tag Archives: biotechnology

bacteria vs. cancer

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Here’s a bizarre article in New Yorker about curing a terminal brain tumor by purposely causing a serious but treatable brain infection.

The tumor had spread to his brain stem and was shortly expected to kill him. Muizelaar cut out as much of the tumor as possible. But before he replaced the “bone flap”—the section of skull that is removed to allow access to the brain—he soaked it for an hour in a solution teeming with Enterobacter aerogenes, a common fecal bacterium. Then he reattached it to Egan’s skull, using tiny metal plates and screws. Muizelaar hoped that inside Egan’s brain an infection was brewing…

For four weeks, Egan lay in intensive care, most of the time in a coma. Then, on the afternoon of November 10th, Muizelaar learned that a scan of Egan’s brain had failed to pick up the distinctive signature of glioblastoma. The pattern on the scan suggested that the tumor had been replaced by an abscess—an infection—precisely as the surgeons had intended. “A brain abscess can be treated, a glioblastoma cannot,” Muizelaar told me.

I almost called this post “shit for brains”, then I grew up just a little bit.

the yeast vats are here

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Asimov’s 1953 novel Caves of Steel featured food grown in vats by genetically modified yeast. It took awhile, but that’s here.

Cargill’s new product is an example of synthetic biology, a form of genetic engineering that uses modified organisms to manufacture compounds that would never be produced naturally. What makes EverSweet taste sweet is not stevia; it is a compound produced by a bioengineered yeast…

Ingredients that are being replaced or are likely to be exchanged for products made through synthetic biology include vanilla, saffron, coconut oil, patchouli, olive squalene, and rose oil. Indeed, the world’s largest cosmetics, flavor, and fragrance companies are hoping that synthetic biology will help them replace more than 200 natural botanical extracts.

This particular article is most worried about large food and chemical corporations replacing products formerly produced by small farmers. That’s a shame. It also talks about the growing backlash from the anti-GMO crowd. But the fact is, the backlash is probably growing because the technology has reached commercial viability. There may be a silver lining – if we are worried about ultimately hitting photosynthetic limits on food production, this may be a way around it. I think yeast will eat pretty much anything organic – mine like barley and honey, but I suspect you could feed them garbage, sewage, etc. in a severely resource constrained world. The dark cloud to the silver lining is always that if you remove one constraint, your ecological footprint will tend to keep growing until you encounter another one. The people in the caves of steel weren’t doing all that well as I recall.

August 2015 in Review

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Negative stories (-12):

  • About 7-19% of cancers are caused by chemicals in the environment. (-1)
  • Steven Hawking is worried about an artificial intelligence arms race starting “within years, not decades”. (-2)
  • The anti-urban attack continues, based on the false idea that crowded, stressful living conditions are the only type of urban living conditions available, and people are being forced into them against their will. This is naked, obvious propaganda that must be rejected. (-1)
  • The more ignorant our species is, the more confident we tend to feel. (-3)
  • According to Naomi Klein, “Our economic system and our planetary system are now at war.”  In related news, July was the warmest month ever recorded by humans, and carbon dioxide concentrations are the highest seen for millions of years. (-3)
  • The media buzz about a worldwide recession seems to be increasing. (-2)

Positive stories (+12):

  • The suburban vs. urban culture wars continue. Suburban office parks are tanking as young people prefer more urban job settings. Entrepreneurs are working on the problems of being car-less with children. (+1)
  • Steven Hawking has a plan to figure out if there is any intelligent life out there. (+1)
  • There are straightforward, practical ideas for dealing with the issues of loading, deliveries, and temporary contractor parking in dense urban areas. (+1)
  • Economists have concluded that preventing human extinction may be economical after all, because “reducing an infinite loss is infinitely profitable”. Is this kind of thinking really useful? (+0)
  • “gene drive” technology helps make sure that genetically engineered traits are passed along to offspring. (+0)
  • Technology marches on – quantum computing is in early emergence, the “internet of things” is arriving at the “peak of inflated expectations”, big data is crashing into the “trough of disillusionment”, virtual reality is beginning its assent to the “plateau of productivity”, and speech recognition is arriving on the plateau. And super-intelligent rodents may be on the way. (+1)
  • Honeybees may be in trouble, but they are not the only bees. (+0)
  • Robotics may be on the verge of a Cambrian explosion, which will almost certainly be bad for some types of jobs, but will also bring us things like cars that avoid pedestrians and computer chips powered by sweat. I for one am excited to be alive at this moment in history. (+2)
  • Dogs can be trained to smell cancer. (+1)
  •  There’s promise of a vaccine for MERS. (+1)
  • It may be possible to capture atmospheric carbon and turn it into high-strength, valuable carbon fiber. This sounds like a potential game-changer to me, because if carbon fiber were cheap it could be substituted for a lot of heavy, toxic and energy-intensive materials we use now, and open up possibilities for entirely new types of structures and vehicles. (+3)
  • Robot deliveries and reusable containers could be a match. (+1)

You might think I rigged that to come out even, but I didn’t.

The Secret of N.I.M.H.

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I remember going to see the rats of N.I.M.H. way too young and being terrified (perhaps second only to my fear of the Wicked Witch of the West). Anyway, the secret is out…

Wong FK, Fei J-F, Mora-Bermúdez F, Taverna E, Haffner C, Fu J, et al. (2015) Sustained Pax6 Expression Generates Primate-like Basal Radial Glia in Developing Mouse Neocortex. PLoS Biol 13(8): e1002217. doi:10.1371/journal.pbio.1002217

The evolutionary expansion of the neocortex in mammals has been linked to enlargement of the subventricular zone (SVZ) and increased proliferative capacity of basal progenitors (BPs), notably basal radial glia (bRG). The transcription factor Pax6 is known to be highly expressed in primate, but not mouse, BPs. Here, we demonstrate that sustaining Pax6 expression selectively in BP-genic apical radial glia (aRG) and their BP progeny of embryonic mouse neocortex suffices to induce primate-like progenitor behaviour.

NIMH stood for “National Institute of Mental Health”. Which was, of course, secretly creating super-intelligent rats.

July 2015 in Review

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I’m experimenting with my +3/-3 rating system again this month, just to convey the idea that not all stories are equal in importance. The result is that July was a pretty negative month! Whether that reflects more the state of the world or the state of my mind, or some combination, you can decide.

Negative stories (-21):

  • In The Dead Hand, I learned that the risk of nuclear annihilation in the 1980s was greater than I thought, and the true story of Soviet biological weapons production was much worse than I thought. (-3)
  • Elon Musk and Stephen Hawking, among others, are concerned about a real-life Terminator scenario. (-2)
  • I playfully pointed out that the Pope’s encyclical contains some themes that sound like the more lucid paragraphs in the Unabomber Manifesto, namely that the amoral pursuit of technology has improved our level of material comfort and physical health while devastating the natural world, creating new risks, and leaving us feeling empty somehow. (-1)
  • Bumblebees are getting squeezed by climate change. (-1)
  • The Cold War seems to be rearing its ugly head. (-2)
  • There may be a “global renaissance of coal”. (-3)
  • Joel Kotkin and other anti-urban voices like him want to make sure you don’t have the choice of living in a walkable community. (-2)
  • I think Obama may be remembered as an effective, conservative president, in the dictionary sense of playing it safe and avoiding major mistakes. Navigating the financial crisis, achieving some financial and health care reforms, and defusing several wars and conflicts are probably his greatest achievements. However, if a major war or financial crisis erupts in the near future that can be traced back to decisions he made, his legacy will suffer whether it is fair or not. (-0)
  • We can think of natural capital as a battery that took a long time to charge and has now been discharged almost instantly. (-3)
  • James Hansen is warning of much faster and greater sea level rise than current mainstream expectations. (-3)
  • Lloyd’s of London has spun a scenario of how a food crisis could play out. (-1)

Positive stories (+7):

chemicals and cancer

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I’ve tended not to obsess over chemicals and cancer, because I think there are other risks that are much higher and much more clearly proven (like the high odds of death every time you set foot in or anywhere near a motor vehicle, to give one example.) I also tend to accept some chemicals, like water disinfectants, food preservatives, drugs, even pesticides, as somewhat necessary evils – we actually know they have a downside, but they do more good than harm on balance. In a sense, it is a “luxury” that many of us avoid violence and infectious diseases long enough to get old and die of cancer. Cancer is at least to some extent a random phenomenon. That doesn’t mean we shouldn’t be looking for safer alternatives to these chemicals that do the same good. If we don’t look we won’t find them. And then, there are chemicals that are known to be harmful, and have no positive effects. Triclosan comes to mind. The companies using cynical fear-based marketing to force these on people should be punished.

All that aside, our food, water, air, and consumer products are full of chemicals, with the result that our bodies are full of chemicals. We don’t have good information on what most of them are doing to us, and especially what combinations of them may be doing to us. Here’s an interesting article that estimates what fraction of cancers are caused by chemicals in the environment, as opposed to lifestyle choices, genetics, and plain old bad luck.

Assessing the carcinogenic potential of low-dose exposures to chemical mixtures in the environment: the challenge ahead

Lifestyle factors are responsible for a considerable portion of cancer incidence worldwide, but credible estimates from the World Health Organization and the International Agency for Research on Cancer (IARC) suggest that the fraction of cancers attributable to toxic environmental exposures is between 7% and 19%. To explore the hypothesis that low-dose exposures to mixtures of chemicals in the environment may be combining to contribute to environmental carcinogenesis, we reviewed 11 hallmark phenotypes of cancer, multiple priority target sites for disruption in each area and prototypical chemical disruptors for all targets, this included dose-response characterizations, evidence of low-dose effects and cross-hallmark effects for all targets and chemicals. In total, 85 examples of chemicals were reviewed for actions on key pathways/mechanisms related to carcinogenesis. Only 15% (13/85) were found to have evidence of a dose-response threshold, whereas 59% (50/85) exerted low-dose effects. No dose-response information was found for the remaining 26% (22/85). Our analysis suggests that the cumulative effects of individual (non-carcinogenic) chemicals acting on different pathways, and a variety of related systems, organs, tissues and cells could plausibly conspire to produce carcinogenic synergies. Additional basic research on carcinogenesis and research focused on low-dose effects of chemical mixtures needs to be rigorously pursued before the merits of this hypothesis can be further advanced. However, the structure of the World Health Organization International Programme on Chemical Safety ‘Mode of Action’ framework should be revisited as it has inherent weaknesses that are not fully aligned with our current understanding of cancer biology.

CRISPR

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Here’s some more info on CRISPR, a genetic engineering technique some people are saying will be revolutionary.

 The Bacterial Origins of the CRISPR Genome-Editing Revolution
Sontheimer Erik J. and Barrangou Rodolphe. Human Gene Therapy. July 2015, 26(7): 413-424. doi:10.1089/hum.2015.091.

Like most of the tools that enable modern life science research, the recent genome-editing revolution has its biological roots in the world of bacteria and archaea. Clustered, regularly interspaced, short palindromic repeats (CRISPR) loci are found in the genomes of many bacteria and most archaea, and underlie an adaptive immune system that protects the host cell against invasive nucleic acids such as viral genomes. In recent years, engineered versions of these systems have enabled efficient DNA targeting in living cells from dozens of species (including humans and other eukaryotes), and the exploitation of the resulting endogenous DNA repair pathways has provided a route to fast, easy, and affordable genome editing. In only three years after RNA-guided DNA cleavage was first harnessed, the ability to edit genomes via simple, user-defined RNA sequences has already revolutionized nearly all areas of biological science. CRISPR-based technologies are now poised to similarly revolutionize many facets of clinical medicine, and even promise to advance the long-term goal of directly editing genomic sequences of patients with inherited disease. In this review, we describe the biological and mechanistic basis for these remarkable immune systems, and how their engineered derivatives are revolutionizing basic and clinical research.

artery-drilling robot

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Happy July 4 to the Americans reading this. As we eat our cheeseburgers and hot dogs, here’s a robot designed to drill through your blocked arteries, modeled after…the bacteria that causes Lyme disease. The article says it’s about 5 years out, so given my age and health I should be able to start eating all the junk food I want right now, and this technology should be available well before my arteries start to get into serious trouble.