Tag Archives: genetic engineering

Bill McKibben

Bill McKibben has a new book called Falter: Has the Human Game Begun to Play Itself Out? In an interview with the Intercept, he expresses a lot of concern about climate change. Another interesting thing he talks about is the idea that genetic technology could mean that an individual human could become obsolete for the first time.

As things stand, these technologies will take the economic inequality presently in existence and encode it in our genes. This is so obviously going to happen if we continue down this path that no one bothers to argue otherwise. Lee Silver, a professor at Princeton University who is one of the leading proponents of genetic modification, has already said that in the future we will have two unequal classes of human beings: “GenRich” and “naturals.” He and many others have already begun taking such a future as granted.

April 2019 in Review

Most frightening and/or depressing story:
  • The most frightening and/or depressing story often involves nuclear weapons and/or climate change, because these are the near-term existential threats we face. Oliver Stone has added a new chapter to his 2012 book The Untold History of the United States making a case that we have lost serious ground on both these issues since then. In a somewhat related depressing story, the massive New Orleans levy redesign in response to Hurricane Katrina does not appear to have made use of the latest climate science.
Most hopeful story: Most interesting story, that was not particularly frightening or hopeful, or perhaps was a mixture of both:
  • Genetic engineering of humans might have to play a big role in eventual colonization of other planets, because the human body as it now exists may just not be cut out for long space journeys. In farther future space colonization news, I linked to a video about the concept of a “Dyson swarm“.

2018 in Review

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

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.

gene-edited soybean oil

Gene editing is starting to move into food, using CRISPR and something new (to me) called TALENs.

Calyxt’s soybean is the first of 23 gene-edited crops the Agriculture Department has recognized to date.

Scientists at Calyxt, a subsidiary of the French pharmaceutical firm Cellectis, developed their soybean by turning “off” the genes responsible for the trans fats in soybean oil. Compared with the conventional version, Calyxt says, oil made from this soybean boasts far more “healthy” fats, and far less of the fats that raise bad cholesterol…

Tripodi likes to say the product is akin to olive oil but without the pungent flavor that would make it off-putting in Oreos or granola bars. It has earned praise from the Center for Science in the Public Interest, a consumer group that says public health will benefit from ingredients with less trans and saturated fats, regardless of how they were developed.

I’m not really afraid of genetically engineered food, but when we monkey with whole foods in this way, it almost never ends up being healthier. Two good cases in point are vitamin pills and baby formula. If you want to be healthy, you should eat the actual soybeans rather than the Oreos or granola bars with soybean oil in them, whether genetically modified or not. And I happen to like olive oil, by the way.

My other concern is biodiversity. The more patented, altered, and homogeneous our food supply is, I wonder if it is more vulnerable to some pest or disease coming out of left field and wiping out the vast majority of it. This concern is not limited to genetic engineering either.

Alzheimer’s reversed in mice

An experimental genetic treatment has been able to completely remove the brain plaques that cause Alzheimers disease in mice.

BACE1 deletion in the adult mouse reverses preformed amyloid deposition and improves cognitive functions

BACE1 initiates the generation of the β-amyloid peptide, which likely causes Alzheimer’s disease (AD) when accumulated abnormally. BACE1 inhibitory drugs are currently being developed to treat AD patients. To mimic BACE1 inhibition in adults, we generated BACE1 conditional knockout (BACE1fl/fl) mice and bred BACE1fl/fl mice with ubiquitin-CreER mice to induce deletion of BACE1 after passing early developmental stages. Strikingly, sequential and increased deletion of BACE1 in an adult AD mouse model (5xFAD) was capable of completely reversing amyloid deposition. This reversal in amyloid deposition also resulted in significant improvement in gliosis and neuritic dystrophy. Moreover, synaptic functions, as determined by long-term potentiation and contextual fear conditioning experiments, were significantly improved, correlating with the reversal of amyloid plaques. Our results demonstrate that sustained and increasing BACE1 inhibition in adults can reverse amyloid deposition in an AD mouse model, and this observation will help to provide guidance for the proper use of BACE1 inhibitors in human patients.