Archive for the 'General Science' Category

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

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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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Oct 19 2020

Biodiversity Matters

I consider myself a skeptical environmentalist, which is why I was really annoyed by the book by the same name by Bjørn Lomborg. The problem with Lomborg’s book was not the notion of reviewing the science behind the big environmental issues, but rather that he did such a poor job his treatment amounted to denialism, not skepticism. It as so bad, in fact, that Scientific American was motivated to dedicate an entire issue to systematically debunking his claims. This, of course, is part of a larger trend of tainting the word “skeptic” by using it to refer to science deniers and contrarions (and yes, there is a difference and denialism is a thing).

I am an environmentalist in the way that we should all be environmentalists – we should care about the biosphere in which we live. It is literally the only one we have. It is probable that human civilization will never have another, ever. Think about that. Interstellar travel will likely never be practical, and even if we can figure out a way to get to nearby systems, we will not find another Earth. Finding a world that is “earth-like” would require science-fiction level faster-than-light travel which may never be possible, and if it is will not happen anytime soon. Even then, there is a huge difference between “earth-like” and Earth. Terrforming other worlds in our solar system is also very difficult, and will take thousands of years if it is practical at all. So except for far future unpredictable scenarios – this is it. Our efforts are best spent preserving the world that is literally perfect for us, because we evolved here.

Beyond just surviving, I also love nature, perhaps more than the average person. Although people in general have an affinity for nature, and studies show that people are generally happier and healthier when they have exposure to nature. But as human civilization has grown, especially in the las century, we have displaced many natural ecosystems and impacted the environment in such a way as to stress many natural ecosystems. This is a serious issue because of, in a word, biodiversity.

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Oct 06 2020

Undocumented Immigrants and Crime

Published by under General Science

We live in a democracy, and people have different perspectives, interests, and values. This means we can honestly disagree on questions about how to run our society, and the political process is supposed to work out those differences through compromise and democratic processes. However, the political process should be based on objective facts as much as possible. Senator Daniel Moynihan is quoted as saying, “Everyone is entitled to their own opinions, but they are not entitled to their own facts,” or some variation of that basic idea. If we lose the objectivity of facts, if everything is opinion, then the democratic process breaks down. There is no longer any common ground for discussion. In fact, what seems to be happening is that not only has fact devolved into opinion, opinion has become an alternate reality constructed and maintained through conspiracy theories.

Assuming we can get back to a world in which facts exist, let alone matter to some degree, they can very usefully inform public debate on political topics. Facts alone don’t determine political outcomes, because values can still differ, but they help. Let’s take the association between undocumented immigrants and crime as an example.

One of the prominent arguments put forward for aggressive policing of our borders is to stop undocumented immigrants, because they bring “large-scale crime and disease” across the border. But do they? Citing dramatic anecdotes will never give us a meaningful picture of reality. We are a nation of over 300 million people – everything happens somewhere. You can find anecdotes to support any narrative you wish. What we really need is data.

One problem is that undocumented immigrants are – undocumented. This makes it hard to track them and to get data on them. But we do have several lines of evidence that give us at least a partial picture. For example, some studies do surveys of individuals, asking their immigrant status and their involvement with crime. One such study, published in 2017, found that immigrants were 2-3 times less likely to report criminal behavior than demographically matched US born individuals. The two main weaknesses of this approach is that, first, it mixes documented and undocumented immigrants into one category. Second, this tells us only that immigrants report less crime, which may not be the same as engaging in crime.

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Sep 25 2020

Climate Change and Wild fires

Published by under General Science

Psychological research confirms what I have observed anecdotally – that people prefer simple answers to complex ones, and will often settle on a single cause of even complex events. This is why I often jokingly answer questions of, “Is the cause A, B, or C,” with “yes.” That is usually the correct (if unsatisfactory) answer, all of the options are correct to some degree. Assuming there is “one true cause” can also be considered a false choice fallacy, or a false dichotomy.

I most recently did this when asked if the increase in wildfires were are currently experiencing on the West Coast of the US are caused by global warming or bad forest management. The experts agree that both contribute, and a new review of the literature sheds some additional light on this question. The authors reviewed over 100 studies published since 2013. This same group published an earlier review on the causes of the Australian wild fires last year. The conclusion of the new review is that global warming has had an “unequivocal and pervasive” role in increasing the conditions that contribute to wild fires.

As they say, this is not rocket surgery. As the weather gets warmer we are experiencing a greater portion of the year with high temperatures, lower humidity, decreased rain, and increased winds. These are all conditions that contribute to starting and spreading wildfires, making them more likely and more intense when they occur. The result has been the worst fire season on record, with three of the four worst individual fires occurring this year.

Stepping back a bit to the bigger question – is there global warming – this fire season adds to the growing evidence that there clearly is. Average temperatures are increasing with the top 10 warmest years on record all being since 1998, with 2016 being the warmest. It is too early to tell for sure, but 2020 is on track to being one of the warmest years on record as well, and may even break the record as the warmest. Further, global ice is decreasing steadily. Hurricanes are getting stronger. Flooding is increasing. And of course, wild fires are increasing. You could claim that any one of these is a coincidence, or has a separate explanation. But given the totality of evidence, that amounts to little more than special pleading. Climate models predicted all of these things, and they are all happening. Trying to write off each individual item (and others I didn’t mention) may work rhetorically with some, but only when looked at in isolation. The probability that so many events predicted by climate scientists as a result of global warming are actually happening is not some grand coincidence or conspiracy. The Earth is warming.

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