Genetic engineering is a rapidly progressing scientific discipline, with tremendous current application and future potential. It’s a bit dizzying for a science communicator who is not directly involved in genetics research to keep up. I do have some graduate level training in genetics so at least I understand the language enough to try to translate the latest research for a general audience.

Many readers have by now heard of CRISPR – a powerful method of altering or silencing genes that brings down the cost and complexity so that almost any genetics lab can use this technique. CRISPR is actually just the latest of several powerful gene-altering techniques, such as TALEN. CRISPR is essentially a way to target a specific sequence of the DNA, and then deliver a package which does something, like splice the DNA. But you also need to target the correct cells. In a petri dish, this is simple. But in living organism, this is a huge challenge. We have developed several viral vectors that can be targeted to specific cell types in order to deliver the CRIPR (or TALEN), which then targets the specific DNA.

Now I would like to present a different technique I have not previously written about here – alternative splicing. A recent study presents what seems like a significant advance in this technology, so it’s a good time to review it. “Alternative splicing” refers to a natural phenomenon of genetics. Genes are composed of introns and exons. I always thought the nomenclature was counterintuitive, but the exons are actually the part of the gene that gets expressed into a protein. The introns are the part that is not expressed, so they are cut out of the gene when it is being converted into mRNA, and the exons are stitched together to form the sequence that is translated into a protein. Alternative splicing refers to the fact that the way in which the introns are removed and the exons stitched together can vary, creating alternative forms of the resulting protein. This dramatically increases the number of different proteins that an organism’s genes can code for, because each gene can potentially code for multiple protein variants through alternative splicing.

Continue Reading »

At this point there is little question that a giant asteroid, 10 kilometers across, impacted the Earth about 66 million years ago. Evidence for this impact began with an iridium layer discovered at the Cretaceous-Paleogene, or K-Pg, boundary. Something deposited an unusually high level of iridium in a brief event all around the world. Later the likely crater resulting from this impact was found in Chicxulub, Mexico. Multiple other discoveries have supported this conclusion, including the fact that this impact was the likely cause of the dinosaur extinction. There was also massive volcanic activity at that time, and dinosaur populations may have been in decline, but that was likely a side show. The main event was the impact.

Such an impact would have released a tremendous amount of energy (10^23 joules), equivalent to a 100 million megaton bomb. There were multiple effects of that impact. One is that a lot of Earth crust material would have been melted and thrown up into the atmosphere, but at less than escape velocity so ultimately raining back down to Earth. Some of these molten droplets cooled into glass spherules as they fell, raining tiny glass beads onto the Earth – creating another geological marker for the impact.

The asteroid impact was essentially in the Gulf of Mexico, causing a massive tsunami that swept over North America. My favorite geological find resulting from this is at the Tanis site in Hell’s Creek. The massive tsunami washed lots of fish and other sea life across the continent, and deposited them in a valley, creating a large jumble of fossils all deposited at once. Scientists know they are from the day of the impact because the fish have glass spherules stuck in their gills – they breathed them in while still alive.

Continue Reading »

It is difficult to project costs into the future, because there are many variables and small errors magnify over time. But still, statistical modeling can be done and validated to produce reliable estimates that can at least inform our discussion. There have been many methods of modeling the cost of global warming vs the cost of transitioning to net-zero carbon.  In general they find that, while there will be costs to transitioning to green technology, there will also be overall savings from reducing global warming.

A new study takes a different approach from previous one – they do not consider the effects of global warming at all, but rather only consider the cost of energy itself. This is basically an ROI approach – we will need to invest a lot of money in new infrastructure, but as a result we will have cheaper electricity, so how does that net out. The bottom line is that under every scenario they consider, transitioning to green energy technologies will save billions of dollars per year in energy costs, and trillions over the entire transition. But let’s look at some of the variables they have to consider.

One thing they did different than prior economic analyses was to try to more accurately model the future costs of green technologies (wind, solar, batteries). Other studies take a conservative approach, but they have all underestimated the decreasing costs of these technologies. So the researchers in the new study more accurately modeled past predictions compared to actual costs and came up with a more accurate model that they validated with historical data. More accurately modeling the likely future decrease in the costs of these technologies increased the likely savings from transitioning to them.

Continue Reading »

I have to be honest, I don’t believe it. Whenever research seems to show a phenomenon that defies the known laws of physics, that is my initial reaction. It’s a good default approach, and so far it has proven correct. I didn’t believe it when researchers claimed they found neutrinos traveling faster than light. It turns out, it was a flaw in the equipment. In fact, I have not believed the many claims over the years of faster than light phenomena, all of which have fallen away. I did not believe the countless claims of free energy or perpetual motion, all of which have failed. I did not believe claims of cold fusion, and still don’t. I did not believe it when engineers claimed to have produced propellantless acceleration (the EM drive). That one crashed and burned as well.

These claims typically have two features in common. They are based on an observed anomaly, and that anomaly is very tiny. It’s just more likely that a tiny anomaly that appears to break the laws of physics is the result of a tiny error, not that the laws of physics as we currently know them are wrong. This is especially true when talking about conservation laws, which are so well established that we can treat them as – laws.

I always acknowledge that our understanding of the laws of physics is incomplete, and there could be some phenomenon hiding in the parts we have not figured out yet (quantum gravity is a good example) that could allow for these apparent anomalies. I’m just not holding my breath. Also, the bar we set for the threshold of evidence before accepting the anomaly as real should be incredibly high. Again, history has proven countless times that this is a good approach.

Continue Reading »

The US is about to pass into law the first real action on climate change in decades. Obviously there is a lot of politics involved, and I don’t want to get sucked into that, but rather I want to discuss the strategy of this approach to mitigating climate change. Here is a summary of the climate-related provisions in the bill. The bill provides tax incentive and grants for states, industry, and individuals to purchase electric vehicles, install green energy, make buildings energy efficient, convert cement, steel, and agricultural industries to more green methods, reduce leaks from methane pipes, and accelerate research in green technologies and manufacturing. Proponents estimate these measures will reduce US carbon emissions by 40% by 2030.

This projected reduction, however, is not compared to zero reduction, but rather what would happen without the bill:

Recent modeling by Rhodium Group highlights the substantial emissions reduction impact of these provisions. Under a business-as-usual scenario, the United States is on track to reduce greenhouse gas (GHG) emissions by between 24% to 35% by 2030 compared to 2005 levels. Should the IRA become law, this would increase to between 31% to 44% by 2030.

So it looks like the provision will produce an additional 10% reduction. Critics would also argue that this is only for the US and therefore as a percental of global GHG emissions, this is small potatoes. In a tradeoff to get support, the bill also would increase leasing for more oil and gas drilling:

“…it requires the U.S. Department of the Interior to lease 2 million acres in federal lands onshore and 60 million acres offshore each year for oil and gas development (or whatever acreage the industry requests, whichever is smaller).”

This has some environmentalists upset (aren’t we supposed to be reducing fossil fuel production). I don’t think they should be. There is a very deliberate strategy to this bill, and I think it is the correct one. At the top level, strategically there are two basic approaches to reducing GHG emissions, or specifically the burning of fossil fuels (which is the major contributor) – either we reduce supply of fossil fuels or we reduce demand. These, of course, are not mutually exclusive, we can do both, but specific measures usually fall into one or the other category.

Continue Reading »

This is a great idea, and in fact is long overdue. The NIH is awarding various grants to establish educational materials and centers to teach principles of scientific rigor to researchers. This may seem redundant, but it absolutely isn’t.

At present principles of research are taught in basic form during scientific courses, but advanced principles are largely left to individual mentorship. This creates a great deal of variability in how well researchers really understand the principles of scientific rigor. As a result, a lot of research falls short of scientific ideals. This creates a great deal of waste in the system. NIH, as a funding institution, has a great deal of incentive to reduce this waste.

The primary mechanism will be to create teaching modules that then can be made freely available to educational and research institutions. These modules would cover:

biases in research; logical fallacies around causality; how to develop hypotheses; designing literature searches; identifying experimental variables; and reducing confounding variables in research.

Continue Reading »

It should come as a surprise to no one that the fossil fuel industry has been financing a vast public relations campaign over the last three decades to sow confusion and doubt about human-caused climate change. This is already well established. One Harvard study, for example, focusing on ExxonMobil, found:

That analysis showed that ExxonMobil misled the public about basic climate science and its implications. They did so by contributing quietly to climate science, and loudly to promoting doubt about that science.

Now, the BBC reports on two people who worked with a PR firm specifically to deny the science of climate change who are now telling their story, adding some more details and focus to the tale. Don Rheem and Terry Yosie worked for E Bruce Harrison, an industry PR guru, who, starting in 1992, landed the campaign to work for the Global Climate Coalition (GCC), an industry group comprised of oil, coal, auto, utilities, steel, and rail industries. What do all these industries have in common? They all contribute significantly to green house gas emissions. And why 1992? Because that is the year of the election that would replace an oil-friendly president with one more friendly to environmental causes, and with a vice president who was a climate change activist. The handwriting was on the wall.

And Harrison had a vision – he had honed his tactics fighting auto industry regulations and spreading doubts about the harms of smoking for the tobacco industry. He recruited a team and made climate change denial his primary focus. The tactics his firm used for the GCC were largely the same – they put out constant opinion pieces, background pieces for journalists, and paid advertising emphasizing doubt about climate science. For example, in a 1994 booklet they claimed:

The greenhouse effect is a natural phenomenon produced by naturally occurring atmospheric gases. To date, there is no evidence to demonstrate the climate has changed as a result of any “enhancement” to this natural phenomenon by man-made greenhouse gases.

Continue Reading »

On the most recent season of Love Death and Robots (which is excellent, btw) the first episode sees the return of the three robot explorers from previous seasons. They are looking over the remains of human civilization trying to figure out what went wrong. It’s a clever and funny commentary on some of our more irrational social ills and how fragile civilization can be. And while the apocalypse is primarily a plot device for survivalist and zombie movies, it is a serious issue and something we can plan for.

No one wants to think about the worse-case scenario, or confront it as a real possibility. There are survivalists and preppers who seem to romanticize the idea – if you put so much time and effort into preparing for something, it can be seen as anti-climactic if it never happens. But it does make sense to prepare for contingencies that you truly hope never happen. Also, preparing for a global catastrophe should in no way detract from our attempts at preventing catastrophe. It should not be a form of giving up. Rather, we’re just hedging our bets. We should spend the majority of our efforts preventing disaster, but just in case.

One example of this is the Svalbard global seed vault. In case there is some agricultural apocalypse, such as a blight, or some other collapse of global civilization, a large stock of seeds of all agriculturally important plants are kept preserved in the vault. We could use this as an emergency supply to reboot our agricultural system. Hopefully we will never need to crack open the vault (metaphorically) but in case we do, it’s nice to know that it’s there.

A recent paper (expanding on prior research) explores the practicality and utility of civilization refuges as a hedge against global catastrophe. The authors argue that we should at least think about which locations in the world would be most resilient in the face of, for example, a global pandemic. What if we have a pandemic similar to COVID except ten times or even a hundred times more deadly. COVID is now at 6.3 million global deaths. What if it were 63 million, or 630 million? These are plausible scenarios, and we would be foolish not to take reasonable steps to prevent them, mitigate them, and prepare for them. Again, prevention is the best option, but we need to prepare for failure leading to a worst-case scenario.

Continue Reading »

What if there were a change we could make in our society that would save, in the US alone, more than 50,000 lives per year and avoid more than $600 billion every year in health care costs and lost productivity? How much should we invest each year to make the necessary changes? Even if we invested $3 trillion over the next 10 years, that would only be half as much as we would save over the same length of time (in addition to preventing have a million premature deaths). Would you say that was worth it? It sounds like a good deal, but of course we have to delve into the details.

I am talking, as you probably guessed from the title, about clean energy. Burning fossil fuels releases particulate matter into the atmosphere, which causes respiratory illness and increases the risk of stroke and heart attack. Coal is worse than oil is worse than natural gas, but they are all a problem. A newly published study set out to estimate the societal costs just from the perspective of health to the energy, transportation, and manufacturing industries and their use of fossil fuel. Here are the key findings from the abstract:

In this study, we estimate health benefits resulting from the elimination of emissions of fine particulate matter (PM2.5), sulfur dioxide, and nitrogen oxides from the electric power, transportation, building, and industrial sectors in the contiguous US. We use EPA’s CO-Benefits Risk Assessment screening tool to estimate health benefits resulting from the removal of PM2.5-related emissions from these energy-related sectors. We find that nationwide efforts to eliminate energy-related emissions could prevent 53,200 (95% CI: 46,900–59,400) premature deaths each year and provide $608 billion ($537–$678 billion) in benefits from avoided PM2.5-related illness and death. We also find that an average of 69% (range: 32%–95%) of the health benefits from emissions removal remain in the emitting region.

Even if these estimates are off by a factor of two or three, which is unlikely, we are still talking about 2-3 hundred billion dollars per year. Therefore, from a purely economic perspective, investing in clean energy is a good deal for the US, its people, and our economy. It would be economically irresponsible if we did not heavily invest in making the transition to clean energy as quickly as possible. It is important to realize the bottom line here – we can justify heavy investment in clean energy just from a health and health-related cost perspective alone. Even if you are a denier of global warming and its impacts, you should still support clean energy and rapidly phasing out fossil fuels.

Continue Reading »

This is one of the coolest science news stories of the last decade, and I’m a bit surprised it’s not getting more play. Paleontologists have discovered and been examining a fossil deposit from the exact day that the asteroid hit 66 million years ago, at the K-Pg boundary. The site is in Tanis (isn’t that where the Ark of the Covenant was found?) North Dakota (Oh, so no).  Actually it’s the Tanis site within the Hell’s Creek formation, which is a productive fossil bed. How can scientists be sure what they are looking at comes from the time of impact? That’s one of the interesting parts of the story.

What appears to have happened is that a large asteroid, about 12 km wide, struck the Yucatan peninsula in the Gulf of Mexico. The crater (Chicxulub crater) from the impact can still be seen. The impact threw a lot of material up into the atmosphere. It also caused a massive tidal wave that spread out, sending material along the Gulf shore, across Mexico, and up along the coasts. But part of this wave also snaked north along a riverbed that led inland to where modern day Tanis is, 3,000 km away. There the water came to rest in a large basin. The wave had swept up sea and land creatures, depositing them in a jumble in the basin. That is one of the lines of evidence that this fossil deposit is a direct result of the impact, the mix of land and sea creatures so far inland, and the fact that the deposit appears to be the result of a sudden chaotic event. It would take something massive to do that, like a meteor impact in the gulf.

An interesting technical detail is that the wave was likely only partly a tidal wave phenomenon from the “splash” of impact. Published evidence indicates that the deposit also likely coincided with a seismic wave – a harmonic wave in the body of water resulting from the impact. So it was more like a megatsunami.

Continue Reading »