Tag Archives: biotechnology

more news from the yeast vats

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This article in Scientific American is about using fungus to generate everything from building materials to human organs to meat to substitutes to plastics.

Mycelium’s fast-growing fibers produce materials used for packaging, clothing, food and construction—everything from leather to plant-based steak to scaffolding for growing organs. Mycelium, when harnessed as a technology, helps replace plastics that are rapidly accumulating in the environment.

Mycelium also provides a cruelty-free way to create meatlike structures with a much smaller environmental footprint than traditional livestock, reducing greenhouse gas emissions, the use of food crops for feed and land use conversion. All these benefits come with little environmental cost: the process of growing mycelium results in limited waste (mostly compostable) and requires minimal energy consumption.

February 2019 in Review

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Most frightening and/or depressing story:

Most hopeful story:

  • Here is the boringly simple western European formula for social and economic success: “public health care, nearly free university education, stronger progressive taxation, higher minimum wages, and inclusion of trade unions in corporate decision-making.” There’s even a glimmer of hope that U.S. politicians could manage to put some of these ideas into action. Seriously, I’m trying hard not to be cynical.

Most interesting story, that was not particularly frightening or hopeful, or perhaps was a mixture of both:

  • We could theoretically create a race of humans with Einstein-level intelligence using in-vitro fertilization techniques available today. They might use their intelligence to create even smarter artificial intelligence which would quickly render them (not to mention, any ordinary average intelligence humans) obsolete.



Superintelligence

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I’m reading (listening to, actually) Superintelligence by Nick Bostrom and finding it unexpectedly very interesting. The book focuses on artificial intelligence, but early on he talks about possibilities for enhancing biological intelligence using current or near-future technology. Here’s an online paper where he talks about the same concept. Just using current in vitro fertilization technology, which creates about 10 embryos at a time, you could theoretically boost IQ by about 11 points if you pick just the smartest of the 10. (This is just a thought experiment so let’s not worry about the other 9. Of course, some otherwise reasonable people are going to have an ethical problem with this.) Do that 10 times in a row and you could theoretically boost IQ by 100 points or more. Einstein had an IQ of about 160. So you can produce a race of super-Einstein’s using current technology. Now, it would take 250 years to do this, and you would have to get everybody to do it, both to make a real impact at the societal level, and to avoid disturbing implications of those left behind.

Using a likely near-future technology called iterative embryo selection, you can theoretically extract the DNA from one or more embryos, move it to sperm and egg cells, combine them again to make a new set of embryos, and do it again. This might take a few years or months to go the 10 generations of 1-in-10, rather than 250 years. Now it’s potentially something big.

I’m a bit worried about super-villains. I don’t see any reason to think twice-as-smart humans will automatically be twice as ethical or twice as empathetic, and it might only take one really bad apple to ruin whatever utopia our newly brilliant problem solving selves come up with.

Like I said, the book is really about artificial intelligence. He believes that even humans enhanced to have, say, double the current average IQ will eventually be far outclassed by machines. It is not going to take 250 years for that to happen, so creating smarter humans in 250 years won’t make a lot of sense. If we create smarter humans in the short term, he thinks they will just use their smarts to make smarter machines even sooner.

This is just scratching the surface. It’s really a fascinating book, and somewhat like when I first read The Singularity is Near, I kind of feel like I am being let in on secrets that nobody else around me knows.

2018 in Review

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Most frightening and/or depressing stories:

  • JANUARY: Cape Town, South Africa looked to be in imminent danger of running out of water. They got lucky, but the question is whether this was a case of serious mismanagement or an early warning sign of water supply risk due to climate change. Probably a case of serious mismanagement of the water supply while ignoring the added risk due to climate change. Longer term, there are serious concerns about snowpack-dependent water supplies serving large urban populations in Asia and western North America.
  • FEBRUARY: Cape Town will probably not be the last major city to run out of water. The other cities at risk mentioned in this article include Sao Paulo, Bangalore, Beijing, Cairo, Jakarta, Moscow, Istanbul, Mexico City, London, Tokyo, and Miami.
  • MARCH: One reason propaganda works is that even knowledgeable people are more likely to believe a statement the more often it is repeated.
  • APRIL: That big California earthquake is still coming.
  • MAY: The idea of a soft landing where absolute dematerialization of the economy reduces our ecological footprint and sidesteps the consequences of climate change through innovation without serious pain may be wishful thinking.
  • JUNE: The Trump administration is proposing to subsidize coal-burning power plants. Meanwhile the long-term economic damage expected from climate change appears to be substantial. For one thing, Hurricanes are slowing down, which  means they can do more damage in any one place. The rate of melting in Antarctic ice sheets is accelerating.
  • JULY: The UN is warning as many as 10 million people in Yemen could face starvation by the end of 2018 due to the military action by Saudi Arabia and the U.S. The U.S. military is involved in combat in at least 8 African countries. And Trump apparently wants to invade Venezuela.
  • AUGUST: Noam Chomsky doesn’t love Trump, but points out that climate change and/or nuclear weapons are still existential threats and that more mainstream leaders and media outlets have failed just as miserably to address them as Trump has. In related news, the climate may be headed for a catastrophic tipping point and while attention is mostly elsewhere, a fundamentalist takeover of Pakistan’s nuclear arsenal is still one of the more serious risks out there.
  • SEPTEMBER: A huge earthquake in the Pacific Northwest could be by far the worst natural disaster ever seen.
  • OCTOBER: The Trump administration has slashed funding to help the U.S. prepare for the next pandemic.
  • NOVEMBER: About half a million people have been killed in Iraq, Afghanistan, and Pakistan since the U.S. invasions starting in 2001. This includes only people killed directly by violence, not disease, hunger, thirst, etc.
  • DECEMBER: Climate change is just bad, and the experts seem to keep revising their estimates from bad to worse. The Fourth National Climate Assessment produced by the U.S. government is not an uplifting publication. In addition to the impacts of droughts, storms, and fires, it casts some doubt on the long-term security of the food supply. An article in Nature was also not uplifting, arguing that climate change is happening faster than expected due to a combination of manmade and natural trends.

Climate change, nuclear weapons, and pandemics. If I go back and look at last year’s post, this list of existential threats is going to be pretty much the same. Add to this the depressing grind of permanent war which magnifies these risks and diverts resources that could be used to deal with them. True, we could say that we got through 2018 without a nuclear detonation, pandemic, or ecological collapse, and under the circumstances we should sit back, count our blessings, and wait for better leadership. And while our leadership is particularly inept at the moment, I think Noam Chomsky has a point that political administration after political administration has failed to solve these problems and this seems unlikely to improve. The earthquake risk is particularly troublesome. Think about the shock we felt over the inept response to Katrina, and now think about how essentially the same thing happened in Puerto Rico, we are not really dealing with it in an acceptable way, and the public and news media have essentially just shrugged it off and moved on. If the hurricanes, floods, fires and droughts just keep hitting harder and more often, and we don’t fully respond to one before the next hits, it could mean a slow downward spiral. And if that means we gradually lose our ability to bounce back fully from small and medium size disasters, a truly huge disaster like an epic earthquake on the west coast might be the one that pushes our society to a breaking point.

Most hopeful stories:

I believe our children are our future…ya ya blahda blahda. It’s a huge cliche, and yet to be hopeful about our world I have to have some hope that future generations can be better system thinkers and problem solvers and ethical actors than recent generations have been. Because despite identifying problems and even potential solutions we are consistently failing to make choices as a society that could divert us from the current failure path. And so I highlighted a few stories above about ideas for better preparing future generations, ranging from traditional school subjects like reading and music, to more innovative ones like meditation and general system theory, and just maybe we should be open to the idea that the right amount of the right drugs can help.

Fossil fuels just might be on their way out, as alternatives start to become economical and public outrage slowly, almost imperceptibly continues to build.

There is real progress in the fight against disease, which alleviates enormous quantities of human suffering. I mention AIDS, diabetes, and Alzheimer’s disease above. We can be happy about that, of course. There are ideas about how to grow more food, which is going to be necessary to avoid enormous quantities of human suffering. Lest anyone think otherwise, my position is that we desperately need to reduce our ecological footprint, but human life is precious and nobody deserves to suffer illness or hunger.

Good street design that lets people get around using mostly their own muscle power. It might not be sexy, but it is one of the keys to physical and mental health, clean air and water, biodiversity, social and economic vibrancy in our cities. Come to think of it, I take that back, it can be sexy if done well.

Good street design and general systems theory – proof that solutions exist and we just don’t recognize or make use of them. Here’s where I want to insert a positive sentence about how 2019 is the year this all changes for the better. Well, sorry, you’ll have to find someone less cynical than me, and/or with much better powers of communication and persuasion than me to get the ball rolling. On the off chance I have persuaded you, and you have communication and/or persuasion super powers, let me know.

Most interesting stories, that were not particularly frightening or hopeful, or perhaps were a mixture of both:

Whatever else happens, technology and accumulation of human knowledge in general march on, of course. Computer, robotics, and surveillence technology march on. The human move into space is much slower and painful than many would have predicted half a century ago, and yet it is proceeding.

I’ll never drop the waterless sanitation thing, no matter how much others make fun of me. It’s going to happen, eventually. I don’t know whether we will colonize Mars or stop defecating in our water supply first, but both will happen.

The gene drive thing is really wild the more I think about it. This means we now have the ability to identify a species or group of species we don’t want to exist, then cause it not to exist in relatively short order. This seems like it could be terrifying in the wrong hands, doesn’t it? I’m not even sure I buy into the idea that rats and mosquitoes have no positive ecological functions at all. Aren’t there bats and birds that rely on mosquitoes as a food source? Okay, I’m really not sure what redeeming features rats have, although I did read a few years ago that in a serious food crunch farming rats would be a much more efficient way of turning very marginal materials into edible protein than chicken.

The universe in a bottle thing is mind blowing if you spend too much time thinking about it. It could just be bottles all the way down. It’s best not to spend too much time thinking about it.

That’s it, Happy 2019!

23 is not enough for me

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This article in Wired explains how there is a lot more to sequencing the whole genome than just 23 genes. The cost of full sequencing has dropped to $1000, which is considered an enormous breakthrough, and it is expected to continue to fall. One company is even offering a $200 black Friday special even though they admit it is a loss leader.

Today, slightly more than a million people have had their whole genomes sequenced. Compare that to the 17 million estimated to have had their DNA analyzed with direct-to-consumer tests sold by 23andMe and Ancestry. They use a technology called genotyping, which takes about a million snapshots of a person’s genome. That might sound like a lot, but it’s really less than 1 percent of the full picture. Genotyping targets short strings of DNA that scientists already know have a strong association with a given trait. So say, for example, scientists discover a new gene that increases your risk of developing brain cancer. If that gene is not one that 23andMe looks at (because how would it know to look if the gene hasn’t been discovered yet), then you’d have to get tested all over again to learn more about your brain cancer risk. Whole genome data on the other hand, once you have it, can be queried with computer algorithms whenever a new genetic discovery gets made.

Here’s a good example of just how much more info is in a whole genome: Earlier this year, 23andMe got FDA approval to give consumers information about their BRCA1 and BRCA2 genes. More than 1,000 mutations in these genes are known to increase women’s chances of breast and ovarian cancers by as much as 75 and 50 percent, respectively. 23andMe’s test picks up the three BRCA mutations most commonly found in individuals of Ashkenazi Jewish descent, and geneticists have voiced concern that the results could leave people with a false sense of security. Veritas’ tests, on the other hand, scan for all of them and, according to the company, turn up five to seven variants of varying concern in those two genes for the average customer.

October 2018 in Review

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Most frightening stories:

  • The Trump administration has slashed funding to help the U.S. prepare for the next pandemic.
  • I read more gloomy expert opinions on the stability and resilience of the global financial system.
  • A new depressing IPCC report came out. Basically, implementing the Paris agreement is too little, too late, and we are not even implementing it. There is at least some movement towards a carbon tax in the U.S. – a hopeful development, except that oil companies are in favor of it which makes it suspicious. There is a carbon tax initiative on the ballot in Washington State this November that the oil companies appear to be terrified of, so comparing the two could be instructive, and the industry strategy may be to get a weaker law at the federal level as protection against a patchwork of tough laws at the state and local levels.

Most hopeful stories:

  • There is no evidence that kids in U.S. private schools do any better than kids in U.S. public schools, once you control for family income. (Okay – I admit I put this in the hopeful column because I have kids in public school.)
  • Regenerative agriculture is an idea to sequester carbon by restoring soil and  protecting biodiversity on a global scale.
  • Applying nitrogen fixing bacteria to plants that do not naturally have them may be a viable way to reduce nitrogen fertilizer use and water pollution.

Most interesting stories, that were not particularly frightening or hopeful, or perhaps were a mixture of both:

  • New tech roundup: Artificial spider silk is an alternative to carbon fiber. Certain types of science, like drug and DNA experiments, can be largely automated. A “quantum internet” could mean essentially unbreakable encryption.
  • Modern monetary theory suggests governments might be able to print (okay, “create”) and spend a lot more money without serious repercussions. What I find odd about these discussions is they focus almost entirely on inflation and currency exchange values, while barely acknowledging that money has some relationship actual physical constraints. To me, it has always seemed that one function of the financial system is to start flashing warning lights and make us face the realities of how much we can do before we are all actually starving and freezing in the dark. It could be that we are in the midst of a long, slow slide in our ability to improve our physical quality of life, but instead of that manifesting itself as a long slow slide, it comes as a series of random shocks where one gets a little harder to recover from.
  • I read some interesting ideas on fair and unfair inequality. Conservative politicians encourage people not to make a distinction between alleviating poverty and the idea of making everybody equal. These are not the same thing at all because living just above the poverty line is no picnic and is not the same thing as being average. There is a strong moral case to be made that nobody “deserves” to live in poverty even if they have made some mistakes. And simply “creating jobs” in high-poverty areas sounds like a nice conservative alternative to handouts, except that there isn’t much evidence that it works.

nitrogen fixing bacteria as an alternative to fertilizer

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The invention of nitrogen fertilizer is a key reason the Earth is able to support so many humans, but it has also taken a huge toll on our natural water bodies and climate. Grist has an interesting article on the possibility of using nitrogen-fixing bacteria, either naturally occurring or genetically engineered, on a much wider range of crops and on a much larger scale to help solve this problem.

A pack of startups is racing to market with a means of fixing nitrogen without polluting the Earth. One of them, Pivot Bio, just garnered a $70 million vote of confidence in a funding round led by Breakthrough Energy Ventures, the coalition of big-name billionaires — Bill Gates, Jeff Bezos, Michael Bloomberg, Richard Branson — hoping to power climate change-beating innovation…

Next year, Pivot plans to start getting farmers nitrogen-fixing bacteria — which efficiently delivers fertilizer to crops, no fossil fuels required. Farmers will spritz seeds with a liquid probiotic as they bury them in the ground. Another startup, Azotic Technologies based in England, is racing to bring a different bacterium to market around the same time. Intrinsyx Bio — a spin-off from a company that supplies NASA with bacteria and other critters for experiments — plans to put yet another bacterium on the market in 2020. And at least one other, the Bayer-backed Joyn Bio, is just ramping up. If any of them is able to provide a viable alternative to the international fertilizer industry, it could be the most significant environmental breakthrough since Haber figured out a way to synthetically release nitrogen from its natural bonds.

So this could be a big deal. Of course, I can’t help thinking of Donella Meadows talking about “layers of limits”. Remove one layer and continue to grow and expand, and you will eventually bump up against the next one.