Tag Archives: biotechnology

January 2018 in Review

Most frightening stories:

  • Larry Summers says we have a better than even chance of recession in the next three years. Sounds bad, but I wonder what that stat would look like for any randomly chosen three year period in modern history.
  • The United States is involved in at least seven wars: Afghanistan, Iraq, Syria, Yemen, Libya, Somalia, and Pakistan. Nuclear deterrence may not actually the work.
  • Cape Town, South Africa is in imminent danger of running out of water. Longer term, there are serious concerns about snowpack-dependent water supplies serving large urban populations in Asia and western North America.

Most hopeful stories:

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

precision nutrition

Lancet has an article on precision nutrition and diabetes. Precision nutrition is the idea of a diet tailored specifically to an individual based on analysis of factors such as their genetics, proteins, and gut bacteria.

Precision nutrition for prevention and management of type 2 diabetes

Precision nutrition aims to prevent and manage chronic diseases by tailoring dietary interventions or recommendations to one or a combination of an individual’s genetic background, metabolic profile, and environmental exposures. Recent advances in genomics, metabolomics, and gut microbiome technologies have offered opportunities as well as challenges in the use of precision nutrition to prevent and manage type 2 diabetes. Nutrigenomics studies have identified genetic variants that influence intake and metabolism of specific nutrients and predict individuals’ variability in response to dietary interventions. Metabolomics has revealed metabolomic fingerprints of food and nutrient consumption and uncovered new metabolic pathways that are potentially modified by diet. Dietary interventions have been successful in altering abundance, composition, and activity of gut microbiota that are relevant for food metabolism and glycaemic control. In addition, mobile apps and wearable devices facilitate real-time assessment of dietary intake and provide feedback which can improve glycaemic control and diabetes management. By integrating these technologies with big data analytics, precision nutrition has the potential to provide personalised nutrition guidance for more effective prevention and management of type 2 diabetes. Despite these technological advances, much research is needed before precision nutrition can be widely used in clinical and public health settings. Currently, the field of precision nutrition faces challenges including a lack of robust and reproducible results, the high cost of omics technologies, and methodological issues in study design as well as high-dimensional data analyses and interpretation. Evidence is needed to support the efficacy, cost-effectiveness, and additional benefits of precision nutrition beyond traditional nutrition intervention approaches. Therefore, we should manage unrealistically high expectations and balance the emerging field of precision nutrition with public health nutrition strategies to improve diet quality and prevent type 2 diabetes and its complications.

I don’t want to be cynical, but I can imagine a scenario where this technology really catches on, but is accessible only to the rich. The result would be the rich living much longer than the rest of us (and they already live longer).

where gene therapy is heading

The “J.P. Morgan Healthcare Conference” provided some clues on where biotechnology may be going next.

After decades of setbacks, gene therapy—a loosely defined umbrella term for any technique that uses genes to treat or prevent disease—is finally here. In December, the field got its very first FDA approval with Luxturna, which corrects a defective gene in a rare, inherited retinal disease. With a half dozen more treatments in late-stage trials and an unusually open-minded FDA commissioner in Washington, the industry is expecting a flurry of new approvals this year…

Lambert’s lobbying roadmap for 2018 includes helping insurance companies understand what to do with a new gene therapy like Luxturna, which cures blindness with a single, $850,000 injection into the eye. Ranked by sticker price, it’s the most expensive medicine in America. Spark Therapeutics, the company that makes Luxturna, argues that the six-figure price tag isn’t actually that unreasonable, if you factor in all the costs that patients with the inherited retinal disease would have racked up in a lifetime of seeking better care.

But because their clinical trial patients haven’t been followed long enough to determine if the treatment benefits are actually durable for a whole lifetime, Spark has received significant pushback from insurers. As a result, the company is already exploring a some creative new pricing models. It announced last week that it’s offering a rebate program based on the treatment’s effectiveness at 30 to 90 days and again at 30 months with one East Coast provider, and is in talks about expanding it to other insurers, Spark CEO Jeffrey Marrazzo said at JPM. He said Spark is also in discussions with the Centers for Medicare and Medicaid Services on a multi-year installment plan option. Either of these could soon serve as a model for how gene therapies might be made available to patients without cutting the legs out from under the healthcare system.

The article also mentions one study that has some potentially bad news about the effectiveness of CRISPR in humans, but it sounds like the jury is still out on that.

2017 in Review

Most frightening stories of 2017:

  • January: The U.S. government may be “planning to roll back or dilute many of the provisions of Dodd-Frank, particularly those that protect consumers from toxic financial products and those that impose restrictions on banks”.
  • February: The Doomsday Clock was moved to 2.5 minutes to midnight. The worst it has ever been was 2 minutes to midnight in the early 1980s. In related news, the idea of a U.S.-China war is looking a bit more plausible. The U.S. military may be considering sending ground troops to Syria.
  • MarchLa Paz, Bolivia, is in a serious crisis caused by loss of its glacier-fed water supply. At the same time we are losing glaciers and snowpack in important food-growing regions, the global groundwater situation is also looking bleak. And for those of us trying to do our little part for water conservation, investing in a residential graywater system can take around 15 years to break even at current costs and water rates.
  • April: The U.S. health care market is screwed up seemingly beyond repair. Why can’t we have nice things? Oh right, because our politicians represent big business, not voters. Also, we have forgotten the difference between a dialog and an argument.
  • May: We hit 410 ppm at Mauna Loa.
  • JuneThe Onion shared this uncharacteristically unfunny observation: “MYTH: There is nothing mankind can do to prevent climate change. FACT: There is nothing mankind will do to prevent climate change”. It’s not funny because it’s probably true.
  • July: Long term food security in Asia could be a problem.
  • August: The U.S. construction industry has had negligible productivity gains in the past 40 years.
  • September: During the Vietnam War the United States dropped approximately twice as many tons of bombs in Southeast Asia as the Allied forces combined used against both Germany and Japan in World War II. After the Cold War finally ended, Mikhail Gorbachev made some good suggestions for how to achieve a lasting peace. They were ignored. We may be witnessing the decline of the American Empire as a result.
  • October: It is possible that a catastrophic loss of insects is occurring and that it may lead to ecological collapse. Also, there is new evidence that pollution is harming human health and even the global economy more than previously thought.
  • November: I thought about war and peace in November. Well, mostly war. War is frightening. The United States of America appears to be flailing about militarily all over the world guided by no foreign policy. Big wars of the past have sometimes been started by overconfident leaders thinking they could get a quick military victory, only to find themselves bogged down in something much larger and more intractable than they imagined. But enemies are good to have – the Nazis understood that a scared population will believe what you tell them.
  • December: A lot of people would probably agree that the United States government is becoming increasingly dysfunctional, but I don’t think many would question the long-term stability of our form of government itself. Maybe we should start to do that. The Consumer Financial Protection Bureau has been doing a decent job of protecting consumers and reducing the risk of another financial crisis. The person in charge of it now was put there specifically to ruin it. Something similar may be about to happen at the Census Bureau. A U.S. Constitutional Convention is actually a possibility, and might threaten the stability of the nation.

Most hopeful stories of 2017:

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

  • January: Apple, Google, and Facebook may destroy the telecom industry.
  • February: The idea of growing human organs inside a pig, or even a viable human-pig hybrid, is getting very closeTiny brains can also be grown on a microchip. Bringing back extinct animals is also getting very close.
  • March: Bill Gates has proposed a “robot tax”. The basic idea is that if and when automation starts to increase productivity, you could tax the increase in profits and use the money to help any workers displaced by the automation. In related somewhat boring economic news, there are a variety of theories as to why a raise in the minimum wage does not appear to cause unemployment as classical economic theory would predict.
  • April: I finished reading Rainbow’s End, a fantastic Vernor Vinge novel about augmented reality in the near future, among other things.
  • May: The sex robots are here.
  • June: “Fleur de lawn” is a mix of perennial rye, hard fescue, micro clover, yarrow, Achillea millefolium, sweet alyssum, Lobularia maritima, baby blue eyes, Nemophila menziesi, English daisy, Bellis perennis, and O’Connor’s strawberry clover, Trifolium fragiferum.
  • July: Ecologists have some new ideas for measuring resilience of ecosystems. Technologists have some wild ideas to have robots directly counteract the effects of humans on ecosystems. I like ideas – how do I get a (well-compensated) job where I can just sit around and think up ideas?
  • August: Elon Musk has thrown his energy into deep tunneling technology.
  • September: I learned that the OECD Science, Technology and Innovation Outlook named “ten key emerging technology trends”: The Internet of Things, Big data analytics, Artificial intelligence, Neurotechnologies, Nano/microsatellites, Nanomaterials, Additive manufacturing / 3D printing, Advanced energy storage technologies, Synthetic biology, Blockchain
  • October: Even if autonomous trucks are not ready for tricky urban situations, they could be autonomous on the highway with a small number of remote-control drivers guiding a large number of tricks through tricky urban maneuvers, not unlike the way ports or trainyards are run now. There is also new thinking on how to transition highways gradually through a mix of human and computer-controlled vehicles, and eventually to full computer control. New research shows that even a small number of autonomous vehicles mixed in with human drivers will be safer for everyone. While some reports predict autonomous taxis will be available in the 2020s, Google says that number is more like 2017.
  • November: It’s possible that the kind of ideal planned economy envisioned by early Soviet economists (which never came to pass) could be realized with the computing power and algorithms just beginning to be available now.
  • DecemberMicrosoft is trying to one-up Google Scholar, which is good for researchers. More computing firepower is being focused on making sense of all the scientific papers out there.

I’ll keep this on the short side. Here are a few trends I see:

Risk of War. I think I said about a year ago that if we could through the next four years without a world war or nuclear detonation, we will be doing well. Well, one year down and three to go. That’s the bright side. The dark side is that it is time to acknowledge there is a regional war going on in the Middle East. It could escalate, it could go nuclear, and it could result in military confrontation between the United States and Russia. Likewise, the situation in North Korea could turn into a regional conflict, could go nuclear, and could lead to military confrontation between the United States and China.

Decline…and Fall? A question on my mind is whether the United States is a nation in decline, and I think the surprisingly obvious answer is yes. The more important question is whether it is a temporary dip, or the beginning of a decline and fall.

Risk of Financial Crisis. The risk of another serious financial crisis is even scarier that war in some ways, at least a limited, non-nuclear war. Surprisingly, the economic effects can be more severe, more widespread and longer lasting. We are seeing the continued weakening of regulations attempting to limit systemic risk-taking for short-term gain. Without a pickup in long-term productivity growth and with the demographic and ecological headwinds that we face, another crisis equal to or worse than the 2007 one could be the one that we don’t recover from.

Ecological Collapse? The story about vanishing insects was eye-opening to me. Could global ecosystems go into a freefall? Could populous regions of the world face a catastrophic food shortage? It is hard to imagine these things coming to a head in the near term, but the world needs to take these risks seriously since the consequences would be so great.

Technology. With everything else going on, technology just marches forward, of course. One technology I find particularly interesting is new approaches to research that mine and attempt to synthesize large bodies of scientific research.

Can the human species implement good ideas? Solutions exist. I would love to end on a positive note, but at the moment I find myself questioning whether our particular species of hairless ape can implement them.

But – how’s this for ending on a positive note – like I said at the beginning, the one thing about 2017 that definitely didn’t suck was that we didn’t get blown up!

more on gene circuits

This is pretty dense, but what it is talking about is the idea of programming genes like circuits.

Enzyme-free nucleic acid dynamical systems

Abstract chemical reaction networks have been proposed as a programming language for complex dynamics, along with their systematic implementation using short synthetic DNA molecules. We developed this technology for dynamical systems by identifying critical design principles and codifying them into a compiler automating the design process. Using this approach, we built an oscillator containing only DNA components, establishing that Watson-Crick base-pairing interactions alone suffice for complex chemical dynamics and that autonomous molecular systems can be designed via molecular programming languages.

Gene Editing 2.0

Before CRISPR even becomes a household word (er, acronym?), it is already being replaced by newer and more precise methods, according to Wired.

Usually, when we’ve referred to Crispr, we’ve really meant Crispr/Cas9—a riboprotein complex composed of a short strand of RNA and an efficient DNA-cutting enzyme. It did for biology and medicine what the Model T did for manufacturing and transportation; democratizing access to a revolutionary technology and disrupting the status quo in the process. Crispr has already been used to treat cancer in humans, and it could be in clinical trials to cure genetic diseases like sickle cell anemia and beta thalassemia as soon as next year...

But this year, newer, flashier gene editing tools began rolling off the production line, promising to outshine their first-generation cousin. So if you were just getting your head around Crispr, buckle up. Because gene-editing 2.0 is here.

 

December 2017 in Review

Most frightening stories:

  • The U.S. has lost ground relative to its peers on road deaths, and is now well below average. I noted that something similar has happened with respect to health care costs, life expectancy, infant mortality, education, drug addiction and infrastructure. Maybe a realistic goal would be to make America average again.
  • A lot of people would probably agree that the United States government is becoming increasingly dysfunctional, but I don’t think many would question the long-term stability of our form of government itself. Maybe we should start to do that. The Consumer Financial Protection Bureau has been doing a decent job of protecting consumers and reducing the risk of another financial crisis. The person in charge of it now was put there specifically to ruin it. Something similar may be about to happen at the Census Bureau. A U.S. Constitutional Convention is actually a possibility, and might threaten the stability of the nation.
  • Daniel Ellsberg says we are very, very lucky to have avoided nuclear war so far. There are some tepid ideas for trimming the U.S. nuclear arsenal, and yet it is being upgraded and expanded as we speak. The North Korea situation is not getting better. Trump may be playing to religious fundamentalists who actually are looking forward to the Apocalypse.

Most hopeful stories:

  • Exercise may be even better for your brain than it is for your body, and exercising your body may be even better for your brain than exercising your brain itself.
  • Macroeconomic modeling is improving. So, just to pick a random example, it might be possible to predict the effects on a change in tax policy on the economy. Now all we need is politicians who are responsive to logic and evidence, and we could accomplish something. At least a few economists think the imperfect tax plan the U.S. Congress just passed might actually stimulate business capital investment enough to move the dial on productivity. The deliberate defunding of health care included in the bill is going to hurt people, but maybe not all that dramatically.
  • Moody’s introduced a new methodology for assessing climate risk in municipal bonds.

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

  • There are life forms surviving in space right now, most likely of Earth origin. I wondered if maybe we should purposely contaminate other planets with them.
  • Microsoft is trying to one-up Google Scholar, which is good for researchers. More computing firepower is being focused on making sense of all the scientific papers out there.
  • Futuristic technologies keep coming along. Something vaguely like the “liquid metal” from Terminator 2 is being used for experimental aircraft parts. Vital signs might be monitored soon using a simple RFID device. A tiny electric shock of just the right size to just the right part of your brain might cure you of bad habits. And Magic Leap may finally release…something or other…in 2018.

electroshock therapy for the brain

Someday you might be able to have a device implanted in your brain which can give it a little electric shock each time it is thinking about reaching for that junk food. This has just been treid in mice.

Closing the loop on impulsivity via nucleus accumbens delta-band activity in mice and man

Reward hypersensitization is a common feature of neuropsychiatric disorders, manifesting as impulsivity for anticipated incentives. Temporally specific changes in activity within the nucleus accumbens (NAc), which occur during anticipatory periods preceding consummatory behavior, represent a critical opportunity for intervention. However, no available therapy is capable of automatically sensing and therapeutically responding to this vulnerable moment in time when anticipation-related neural signals may be present. To identify translatable biomarkers for an off-the-shelf responsive neurostimulation system, we record local field potentials from the NAc of mice and a human anticipating conventional rewards. We find increased power in 1- to 4-Hz oscillations predominate during reward anticipation, which can effectively trigger neurostimulation that reduces consummatory behavior in mice sensitized to highly palatable food. Similar oscillations are present in human NAc during reward anticipation, highlighting the translational potential of our findings in the development of a treatment for a major unmet need.

Maybe pedophiles could be given this option in exchange for getting out of jail. Or maybe it won’t be an option. Maybe it could be implanted at birth and used, just as an example, if someone is thinking of pulling the wrong lever in a voting booth.

North Korea and biological weapons

Harvard Kennedy School has a new report on North Korea and biological weapons. It is not as alarming as it maybe could be. They almost certainly have the ability to produce them, as does any country, company, or institution with modern agricultural technology. There is no clear evidence that they have made a large-scale attempt to weaponize or deploy them.