Archive for the 'General Science' Category

Apr 23 2021

A “Decisive Decade” for Climate Action

Published by under General Science

After four years of backsliding on tackling climate change, it is good to see the US once again taking it seriously and trying to lead the world on climate action. Good intensions are necessary, but insufficient, however. The Biden Administration pledges a 50-52% decrease in CO2 emissions from 2005 levels by 2030. That sounds ambitious, and it is, but it is also not enough. It helps clarify how big the task is we have before us, but also how high the stakes are. Some recent studies also help clarify the picture.

First, a recent study yet again dispenses with the false dichotomy that dealing with climate change is about the environment vs the economy. Wrong. Climate change hurts the environment and the economy – so both of these concerns are in alignment. This study was done by a large insurance company (who are used to estimating risk and cost) and they concluded that climate change will cost the world economy $23 trillion in lost productivity by 2050 (compared to where we would be without climate change). Failing to tackle climate change is the costly option. Further, these costs will disproportionately affect poorer countries, increasing the wealth gap between rich and poor nations and likely causing political instability (not to mention a climate refugee crisis).

This does not even account for health care costs and lost productivity due to poor health from pollution. These costs are estimated to be hundreds of millions of dollars per year for the US and several billion worldwide.

Even if we just look at climate change through an economic lens, investing in clean energy is a no-brainer. Green technologies are the technologies of the future, and so it also makes sense for any country to invest in this industry to be competitive. Investing in these technologies would be a massive boost to our economy, with each dollar spent being returned many times over. Failure to do so is economic malpractice. Clinging to dirty 17th century technology is a loser’s strategy.

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Apr 13 2021

A CRISPR Genetic On-Off Switch

Published by under General Science

Our knowledge of genetics and the tools to engineer or modify genetics continues to rapidly progress. The most celebrated recent advance was CRISPR (clustered regularly interspaced short palindromic repeats), a bacteria-derived system that can easily target any sequence of DNA using a guide RNA. CRISPR is like the targeting system and it can be paired with various payloads, most commonly Cas9, which is an enzyme that will cut both strands of DNA at the desired location. CRISPR was actually discovered in 1993, but the CRISPR-Cas9 system was first used for gene editing in 2013, an advance that won the Nobel prize in chemistry in 2020.

We are still, however, on the steep part of the learning curve with this powerful technology, and now researchers have published perhaps the greatest advance since 2013 – a way to use CRISPR as an on-off switch for genes. At the very least this will revolutionize genetic research. But it also has incredibly therapeutic potential, although other hurdles remain for applications in living organisms.

Using CRISPR-Cas9 for gene editing basically comes in two forms, knocking in genes or knocking out genes. Knocking out genes is by far the easier of the two. CRISPR targets the gene you want to silence, or knock out, and Cas9 will make a double strand cut in the DNA. The cells natural repair mechanism, called non-homologous end joining (NHEJ), the joins to the two cut ends together. This repair mechanism, however, is very imprecise and frequently introduces errors. Many of those errors will cause a shift in the genetic sequence that essentially ruins to code, effectively turning off the gene. This change is permanent, and will be carried to all later generations.

Knocking in a gene is more difficult. You not only have to make the cut at the desired location, you have to provide the genes sequence you want inserted and you need a different DNA repair mechanism called homology-directed repair (HDR), which is more precise and preserves the genetic sequence so that the gene remains active. But NHEJ is much more common than HDR, and so the trick is finding ways to enhance HDR repair so that a new gene can be successfully inserted at the repair site.

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Apr 08 2021

Possible New Force

Published by under General Science

Physicists are all verklempt. Prof Ben Allanach, from Cambridge University said:

“This is the moment that I have been waiting for and I’m not getting a lot of sleep because I’m too excited.”

What could have scientists so excited? A muon that wobbled a little faster than it’s supposed to. In an experiment at the Fermi National Accelerator Laboratory (Fermilab) in Batavia, Illinois (the Muon g-2 experiment), physicists accelerated the subatomic particle muons and exposed them to a magnetic field. Muons are like electrons but 200 times heavier. They have a charge so should respond to a magnetic field by wobbling as they swing around the accelerator, and they did, but they did it a little faster than the standard model predicts they should. It was as if a force not contained within the standard model was acting on them. This experiment adds to another in Japan and yet another at the LHC also hinting at new physics. The statistical power of the Fermi results is at 4.1 sigma, or a 1 in 40,000 probability of being by chance alone. Five sigma (one chance in 3.5 million) is the threshold when the physics community accepts a claim as proven.

This is a big deal, perhaps even bigger than when the LHC confirmed the existence of the Higgs boson. That confirmed a prediction of the standard model, which is nice, but does not point the way to new physics. What physicists desperately want to do is break the standard model, to find some provable phenomenon that violates the standard model, which should lead to the discovery of a new particle or perhaps even a new force outside the current model. This is what would create the next great discovery in physics and perhaps solve some enduring mysteries, like what the hell is responsible for the acceleration of the expansion of the universe?

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Feb 19 2021

CRISPR-Edited Bananas

Published by under General Science

In the British Drama, Years and Years, they imagine the very near future. I do wonder what someone from 2010 would have thought about a tv show accurately depicting 2020. In any case, one of the throw-away lines of the show was that there are no more bananas. The writers did their research – that the Cavendish banana will disappear sometime in the 2020’s is extremely likely. It is being threatened by a fungus called Tropical Race 4 (TR4), which a century ago wiped out the previous commercial dessert banana, the Gros Michel (it’s not extinct, but cannot be grown commercially anymore).

TR4 is now on every continent that grows bananas. It is literally just a matter of time before the entire commercial Cavendish market is wiped out. TR4 and similar funguses also threaten other banana varieties (more like plantains) that provide a staple source of nutrition for large segments of the world (about 400 million people). So this is not just about no longer having access to a favorite dessert fruit – this can create a serious threat to food security in parts of the world.

Part of the problem is that all Cavendish banana plants are clones. The plants are triploid hybrids, which is why they don’t produce seeds. This also makes them sterile. They are reproduced by taking new shoots that grow off the underground bulb (or corm). For this reason the entire Cavendish industry is basically comprised of clones. This is the ultimate monoculture – which leaves them particularly susceptible to disease, such as TR4.

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Dec 21 2020

2020 One of Hottest Years

Published by under General Science

The year 2020 will be either the hottest year on record, or just behind the hottest year, 2016. The top 10 hottest years have all been from 1998 and later, with every year starting at 2013 being in the top 10. 2020 will now knock 1998 off the list, making the 10 warmest years all since 2005. The reason 1998 stuck on the list so long is because it was an outlier El Nino year, a weather pattern that tends to produce warmer weather. Next year, 2021, is likely to be a bit cooler because it is a La Nina weather pattern, which tend to be cooler. What does all this mean for the global warming debate?

First, it’s not much of a debate, at least not scientifically. There is a solid scientific consensus that average global temperatures are increasing, and that anthropogenic factors are mostly responsible for this forcing. Don’t believe the nonsense about there not being a consensus or that it is all based on one flawed paper – in fact, there is a consensus about the consensus. The debate is entirely cultural and political, not scientific. The evidence and the consensus are strong enough that any lay person who refuses to accept this scientific consensus is reasonably called a global warming denier.

The denier position is based on a number of logical fallacies and misleading arguments. They attack the very concept of a scientific consensus, and turn the technically true into a misleading point by saying that “science is never settled”. Well…yes, science is always open to revision by new data and new interpretations and theories. But that is not the point, making their argument a straw man. No one is talking about metaphysical certitude, or not being open to revising our climate models or projections with new data. Science, however, does not just exist in the abstract, sometimes we make important decisions based upon the current state of the science. The point is whether or not climate science is confident enough in its projections of global warming to use as a basis for policy. Saying that “science is never settled” is therefore a non sequitur. It is, in fact, a bit of deliberate misdirection.

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Dec 10 2020

The Decade of Climate Change

Published by under General Science

Of course there are many important issues facing the world, but arguably drastically reducing carbon emissions is near the top of the list. The 2020s is likely to be a pivotal decade for this effort, and will have a dramatic and long lasting effect. The reason for this is that we are nearing the end of our “carbon budget” – the cumulative amount of carbon we can release into the environment without causing warming >1.5C above pre-industrial levels. We are very close to exhausting this budget, and in fact most experts have set their sights on 2C as the goal, believing it is already too late to keep global warming below 1.5C. Without a major effort in this decade, we will miss the more liberal 2C target, we will have exhausted our carbon budget, and it will no longer be possible to avoid serious consequences of global warming. In fact, it’s possible it would then be too lake to stop a cascade of events that will eventually lead to 5-6C of warming through triggering threshold positive feedback events. This may take hundreds of years to play out, but it still may be unavoidable at that point.

This is really the last decade we have to ensure a high probability of avoiding significant global warming by drastically reducing our carbon emissions. This means transforming our energy and transportation sectors into mostly carbon free technology. Industrial emissions will be harder, and require various technological advances, but any such advances there will help as well. This means, at the very least, we have to stop burning fossil fuel. This in turn means electric vehicles (with perhaps some role for hydrogen and biofuel), and an energy infrastructure built on renewable sources (wind, solar, geothermal, hydroelectric) and nuclear with some grid storage. All of this is achievable with current technology, and will reap benefits beyond climate change, such as reduced health care costs and deaths from pollution.

Often, those who push back against the suggestion that we need to make this change to our civilization a priority frame the choice before us as a false dichotomy – the climate vs the economy. More people will be harmed by the economic costs of decarbonization than will benefit from reducing carbon emissions, they claim. Often this strategy is coupled with denial of climate change itself, or unsupported assertions that climate change will not be so bad. They will often point to the most extreme predictions of climate change and argue that the entire field is “alarmist”.

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Dec 01 2020

AI Mostly Solves Protein Folding

Published by under General Science

I wasn’t planning on writing about artificial intelligence (AI) two days in a row, but I also can’t plan the news. I also couldn’t pass up this item – London-based AI company, DeepMind, has mostly solved the extremely difficult problem of protein folding. If you are not already familiar with this issue, this may not sound like a big deal, but it is. So first lets’ give some background on the problem itself.

Biology is largely about proteins. Proteins are what genes code for, they make up enzymes, receptors, structural building blocks, antibodies, the basic machinery of cells, and more. Yes, lipids and carbohydrates are critical as well, but these are largely chaperoned by proteins. Proteins determine whether a cell is a liver or heart cell, and largely whether an organism is a human or sea cucumber.

Proteins are comprised of a sequence of amino acids, from a repertoire of 20 different amino acids. The specific sequence of amino acids is what is determined by the GATC genetic code in DNA, with three-letter codes for each amino acid. But a protein is more than just a sequence of amino acids. By itself a long chain of amino acids is a polypeptide – it doesn’t become a protein until that long chain is folded into a unique three-dimensional shape. Predicting how a long chain of amino acids will fold into a precise shape is the protein folding problem.

This is more difficult than it may at first seem. Imagine a chain with each link one of 20 possible different shapes, and that chain can be hundreds or even thousands of links long (titin is the largest known protein; its human variant consists of 34,351 amino acids). The number of possible ways to fold the protein gets magnified with each additional link. The resulting possibilities is staggering – too much for even the most powerful computer to crunch through. Determining how a sequence of amino acids actually folds is therefore determined mostly by direct laboratory study, using techniques such as X-ray crystallography and NMR spectroscopy. But this takes a long time – years for the largest proteins.

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Nov 12 2020

Biden’s Climate Plan

Despite Trump’s attempt to break US democracy in order to alter reality to his liking, Joe Biden will be sworn in as the next president. This has obvious implications for US’s plans for tackling climate change. The first is that we will now have an executive branch that recognizes science, that climate change is real, and will actually try to do something about it. Immediately this means rejoining the Paris accord, and appointing people to the energy and environmental agencies that are not climate change-denying coal executives.

Biden’s plan (which is not the green dew deal) is to have our energy infractructure be net zero carbon emitting by 2035 and the entire country to be net zero by 2050. That is ambitious, and if I had to bet I would say we will fall short of this goal (although I hope I’m wrong), but it is a reasonable goal. How, theoretically, will we get there?

First, although it is politically risky to say so bluntly, we have to wean ourselves entirely off of fossil fuel. Biden acknowledged this during the second debate – end fossil fuel subsidies, and phase out fossil fuels over time. Given his stated goal, that would mean phasing out coal, oil, and gas by 2035. Is that even feasible? Currently, if we look only at power production, the mix of sources in the US is: fossil fuels 62.6%, Nuclear 19.6%, and renewables (wind, solar, biomass, geothermal, hydroelectric) 17.6%. The question is, in 2035, what do we want our energy mix to look like and how can we get there?

The path to getting there is not insignificant, because we will be emitting carbon along the way. One controversy is fracking and natural gas, which is cleaner than coal, but still a fossil fuel. Should we phase out coal quickly by replacing it with natural gas plants, or skip over natural gas and go straight to renewables and nuclear? If we could skip natural gas that would be optimal, but realistically the perfect may be the enemy of the good. Natural gas may be an effective temporary measure to quickly eliminate coal while we are transitioning to net zero energy production. But I am open on this question.

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Nov 05 2020

Crop Yield with Higher CO2

Published by under General Science

One of the arguments often put forward by global warming deniers is that CO2 is not a pollutant, and in fact higher CO2 is good for crop yield. This point is invoked during their shifting defense – the planet is not warming; well, OK, it’s warming but it’s not due to humans; alright, humans are to blame but this won’t necessarily be a bad thing. See – CO2 is good for plants.

While this core claim is somewhat true, it needs to be put into perspective. First, as a risk vs benefit, raising global CO2, with all the downstream negative effects, is a terrible way to increase crop yield. But a new study looks at 30 years of data to address the underlying premise – what is the net effect of rising CO2 levels on crop production? The short answer is, while some crops increase yield, the overall effect is complicated.

The first distinction we need to make is between C3 and C4 crops, which refers to the type of photosynthesis used. In the C4 pathway some of the energy is used to concentrate CO2 in the chloroplasts, resulting in a higher efficiency of turning light into energy. C4 plants include corn and sugarcane. For these crops there is no benefit in yield from higher CO2 levels. C3 plants do not have this adaptation and they are more dependent on ambient CO2 levels, and they do benefit from higher CO2. But there are some important caveats to this.

What the study showed is that the overall average increase in yield among C3 crops to rising CO2 in the last 30 years is 18% “under non-stress conditions”. That last bit is important because that increase is significantly reduced if there is not enough nitrogen available to take advantage of the higher CO2, which is the case in most of the non-industrialized world. Further, the rising temperature that accompanies the higher CO2 decreases the yield, and also increases loss to pests. Wet conditions, which are also important for yield, reduce the benefit from CO2, however, which is greatest under drought conditions. So overall there has been a modest increase in yield in some crops in industrialized farming where increased nitrogen if available.

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Oct 26 2020

Murder Hornets Found and Destroyed

Published by under General Science

Invasive species can be a serious problem. They may lack predators to keep their populations in check, and some may be predators themselves, preying on species that cannot defend against them. Eventually a new equilibrium will be reached, but in the meantime this can be destabilizing and in the long term will reduce diversity. The “invasive species of the year” for 2020 has to be so-called “murder hornets”.

The proper name for this insect is the Asian giant hornet (Vespa mandarinia), and as the name implies it is native to temperate and tropical regions of Asia. It is the largest hornet species on Earth. As insects go, they are huge – “The hornet has a body length of 45 millimetres (1 3⁄4 inches), a wingspan around 75 mm (3 in), and a stinger 6 mm (1⁄4 in) long, which injects a large amount of potent venom.” Their nickname, “murder hornet”, derives from their behavior. They prey upon other insects, mainly honey bees, but also mantises and even other hornets. If they enter a honey bee nest, even a few hornets can wipe out the entire nest in several hours. They typically kill by decapitating the bees with their large mandibles. The bees defenses are all but useless – their stingers too small to penetrate the hornet’s armor.

They are not much of a direct threat to humans. Only about 40 people per year are killed in Asia from giant hornet stings. They are not generally aggressive, but will attack if they are threatened. They can sting multiple times, and their stinger is long enough to penetrate typical beekeeping suits. Their venom is known for producing incredible pain, and can cause some local tissue damage. So even if you don’t die, being stung will not be a pleasant experience. Their real threat to humans is indirect – from the threat they represent to our pollinators.

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