Archive for the 'General Science' Category

Mar 14 2022

De-Extinction of the Tasmanian Tiger

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The last known thylacine, commonly known as the Tasmanian tiger, was in captivity in 1936. This marsupial predator was wiped out by human hunting. At the time Europeans colonized Australia the range of the thylacine was limited to Tasmania, but it did not survive contact with Europeans for very long.

The thylacine is now one of the primary targets for de-extinction – literally bringing the species back from extinction using cloning technology. This effort has just received a significant boost. The University of Melbourne just received a $5 million grant to develop their Thylacine Integrated Genetic Restoration Research (TIGRR) Lab. Scientists love their clever acronyms, and I wonder how long they had to work on this one.

The researchers at the lab have a specific plan in terms of how to bring back the thylacine. They have already completed the first step, which is to completely sequence the thylacine genome. Now they need to study this genome to understand it as best as they can. They will need to synthesize a complete genome, and then place it in stem cells prepared from another marsupial. This is where the cloning process comes in. You remove the DNA from the stem cell, insert the new DNA, and then coax the cell into dividing to form an embryo. They then plan to implant the embryo into a living host, such as a Tasmanian devil, who will then give birth to a live thylacine.

The process is tricky. We have cloned large mammals before, but not of an extinct species. Also, the process is not done when we have one thylacine. The goal is to create a breeding population. That means we need many individuals, both male and female, with sufficient genetic diversity. Once they have established a breeding population in captivity, the ultimate goal is then to reintroduce them back into the ecosystem of Tasmania.

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Mar 03 2022

Exuviae and Frass for a Circular Farming System

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What are exuviae and frass? These are terms I just learned and are probably new to you as well, but they may become more familiar in the future. Exuviae are molted exoskeletons from insects and are primarily made of chitin. Frass is undigested food from insects, so basically bug poop. Frass could make a good fertilizer for plants because it is high in nitrogen. Exuviae would not serve as fertilizer, but there are species of soil bacteria that can break down chitin for food. Adding exuviae to soil increases the population of these soil bacteria, which are beneficial to plants and make them more resilient to pests.

Exuviae and frass, therefore, can be extremely useful for farming. But where are we going to get the massive quantities of these materials that would be necessary to have any significant impact on our agricultural system? Well, we could farm insects for food and use the waste products of insect farming for plant agriculture. This could be the basis for a circular agricultural system. Organic matter from plant and animal farming can be used to feed insects which are also grown for food. The exuviae and frass from the insect farming can then be fed back into plant farming as fertilizer. This would not be a totally closed system, of course. Humans would be removing calories and nitrogen from the system to feed themselves, and human waste is typically not recycled as fertilizer (this is a separate issue – the risks and benefits of using humanure).

Insects are increasingly recognized as an important source of food. They have several advantages, the biggest being that they are small. This translates into a high food output to land use ratio. Raising insects also uses far less water than other food sources. Insects can also be easily farmed indoors, meaning they can be farmed year-round and in urban settings. Already there is significant farming of crickets, grasshoppers, mealworms, waxworms, and other insects for food. The insects are not generally consumed whole (although they can be), they are ground up and used as protein powder (such as cricket flour).

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Feb 28 2022

Some Good News on Climate Change

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One of the challenges of being a science communicator is keeping up to date. About 2.5 million scientific papers are published every year. Most of this is noise, preliminary studies, speculations, etc., but the end result is that most fields of science are constantly changing. This became very concrete for me while writing my next book (shameless plug alert), The Skeptics Guide to the Future, coming out this Fall. A big part of the book is examining cutting edge science and technology and then extrapolating it into the near, midterm, and far future. During the editing process there were constantly science news items that required small updates to the book. In fact I had to ask my editor, after the final submission, if I could please squeeze in one more update, and promised it would be the last one.

If you are not paying obsessive attention to a particular field of science, it’s really difficult to keep completely up to date. There is also a substantial delay, sometimes decades, between changes to the consensus of scientific opinion based on new evidence and when that new consensus filters down to the public’s general consciousness. Sometime the delay is forever, as outdated ideas persist indefinitely. This is especially true if an outdated scientific conclusion has a rhetorical utility, either in marketing a product or promoting a political ideology. We figured out a quarter of a century ago that consuming anti-oxidants were not good for your health, but don’t hold your breath for the supplement industry to alter their promotion of anti-oxidant products.

One idea that has become a standard part of the conversation on climate change is that once CO2 is released into the atmosphere it will cause continued warming for decades. So, the argument goes, even if we stopped all release of greenhouse gases today, full net-zero, the climate would continue to warm for many decades, perhaps a century or longer. That was the scientific consensus, although it was never a very firm one, just the best estimate based on existing evidence. That conclusion, however, started to crack as early as 2008, and by 2020 was updated with new and better science. This is a rare instance of good climate news. In an interview, climate scientist Michael Mann said:

“This really is true,” he said. “It’s a dramatic change in the paradigm that has been lost on many who cover this issue, perhaps because it hasn’t been well explained by the scientific community. It’s an important development that is still under appreciated. It’s definitely the scientific consensus now that warming stabilizes quickly, within 10 years, of emissions going to zero.”

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Feb 01 2022

DNA Microfossils and the Woolly Mammoth

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About 12 thousand years ago the late Pleistocene was transitioning to the current Holocene. This transition was marked by the end of the last glacial period, and turnover of entire ecosystems to a new homeostasis. Specifically in the Arctic North America, the mammoth-steppe biome was transitioning to the boreal forest we know today. As the name suggests, the most famous of the megafauna of the late Pleistocene was the woolly mammoth, and a lot of research has focused on nailing down the exact date when the woolly mammoth went extinct.

Dating the lifespan of a species is always a matter of finding the earliest and latest evidence for its existence. Such date ranges are always an underestimation, because it’s unlikely that we have discovered the very first or very last specimen, so it is very common for new fossil discoveries to expand the known date range. This is why headlines such as, “Woolly Mammoths Survived Longer than Previously Thought” are extremely common. Of course they did – most extinct species survived longer than we currently think.

However, it is not common that scientists hit upon an entirely new method for exploring the past and dating species, but that is what is happening now. Researchers from the McMaster Ancient DNA Centre are pioneering a technique to explore ancient environmental DNA. This is made possible by the extreme advances in genetics technology over the last few decades. Already environmental DNA is giving us a new powerful tool to explore ecosystems. We no longer have to track and tag representatives of all the species in an environment to get a sense of what plants and animals live there. We can just take a few scoops of soil and water and sequence the environmental DNA that we find. Every living things sheds DNA into the environment, and as their remains decay into the soil and water it spills their DNA for scientists to find later. My favorite application of environmental DNA technology is a survey of Loch Ness showing the complete absence of DNA from a plesiosaur or any similar creature.

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Jan 18 2022

Are We In a Sixth Extinction

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There have been five recognized mass extinctions in the history of life on Earth, and a number of smaller ones. They include, in order:

  • Ordovician (444 million years ago; mya) – climate change caused by continental drift
  • Devonian (360 mya) – volcanic eruptions
  • Permian (250 mya) – unknown, could be asteroid strike, eruptions, climate change
  • Triassic-Jurassic (200 mya) – volcanic activity
  • KT (65 mya) – asteroid strike

Many scientists believe we are now in the middle of a sixth mass extinction, this time cause entirely by anthropogenic factors – human activity. We are warming the atmosphere and oceans, acidifying the oceans, polluting the environment, overfishing, hunting some species to extinction, converting ecosystems to farmland and living space, and spreading invasive species. The evidence of a slow-rolling mass extinction seems to be obvious, but still there are those who question if it is really happening. That questioning ranges from healthy scientific skepticism to outright denial.

The reason for the debate is our ability to rigorously document the extinction rate over time. It’s not enough to point out that extinctions are happening. The current estimate is that there are 8.7 million species of plants and animals extant today. Extinction is also a natural part of the evolution of life over time, and biologists also estimate that the background extinction rate is about 10% every million years. This can also be expressed as one extinction per million species years (one extinction per million species per year). This means the background rate should be about 870 extinctions per century. Over the last century there have been recorded about 500 animal extinctions. This is the basis for the argument that we are not in the middle of a mass extinction.

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Jan 10 2022

A Quantum Gravity Experiment

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Perhaps the greatest challenge of current theoretical physics is to come up with a testable theory that unites the principles of general relativity with quantum mechanics. This has proven to be a very challenging problem, one that may take generations of physicists to crack. Right now physicists are mostly stuck in the theoretical realm, trying to come up with theories (like string theory) that may be internally mathematically consistent, but are challenging to falsify experimentally. However, Rana Adhikari, professor of physics at Caltech, and her colleagues are trying to come up with a way to do just that. Their approach derives from another weird concept within theoretical physics – that the universe may be pixelated, and may even be a hologram (three dimensions projected from a two dimensional surface).

For background, prior to the 19th century we comfortably lived in what we now call a classical universe. Our models of how the universe works were based upon our observations and experiments within the frame of macroscopic creatures living on the surface of a planet. Galileo and Newton developed, for example, laws of motion that defined how objects move and behave, including Newton’s theory of gravity. However, classical physics started to break down in the 19th century. For example, astronomers making more and more precise measurements of the orbits of the planets were finding that the orbit of Mercury was different than what our classical equations predicted. Those equations work extremely well, but there was something off about Mercury. Attempts at finding an explanation, such as a hidden planet on the other side of the sun, failed. Eventually we had to conclude that our classical equations were not quite right, or at least could not account for the special case of Mercury.

This is where Einstein comes in. First he proposed in theory of special relativity, which fixed some vexing problems in physics by proposing that the speed of light is an absolute constant regardless of frame of reference, and that it was space and time that are variables which can change based upon frame, specifically with respect to relative velocity. This was considered “special” relativity because it only referred to the speed of light. Einstein would have to work for years more before he was able to account for gravity in a theory of general relativity. His new equations not only solved the problem of Mercury’s orbit (it is close enough to the sun that relativistic effects from the sun’s gravity are measurable) but also made a large number of predictions. Over the last century Einstein’s theories have been confirmed to an extremely high degree.

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Dec 03 2021

Using CRISPR For Sex Selection

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Each year 6-7 billion male chicks are culled, because only females are needed for egg laying. Many other animals are also culled because one sex is desired either for food production or research. There are many research questions that are sex specific, and therefore large numbers of a single sex of a specific strain of mice may be required. Culling is a crude way to achieve these ends, and raises concerns about humanely treating animals.

For these reasons researchers have been looking for ways to achieve high degrees of sex selection in animals more efficiently and humanely. A new study published in Nature Communications seems to have made a significant advance in this direction, using CRISPR-Cas9 (a gene-editing system) to create a sex-selection system for either male or female mice that operates with 100% efficiency. The idea is clever – insert one half of a CRISPR-Cas9 kill switch into the X-chromosome of a female mouse, then insert the other half into either the X or Y chromosome of a male mouse. Only those embryos that get both halves of the CRISPR-Cas9 system (either XX or XY) will be killed at the early embryo stage.

This approach has been used before, in insects and zebrafish, but never in mammals. There are also other methods for sex selection that don’t rely on culling, such as sperm sorting, but this approach is not very efficient, and doesn’t work in birds where the females gametes determine sex. This new system has proven 100% effective in mice, and should easily port to other mammals such as pigs and cattle. The researches targeted a gene, the Top 1 gene, that codes for an enzyme critical for early DNA replication in a developing embryo. Inactivating this gene is a “suicide switch” for the embryo. This gene is also highly conserved, and the reason why it should work in all mammals, not just mice.

The researchers discovered that the early activity of this suicide switch has a specific advantage in sex-selection systems – it actually increases the yield (not just the ratio) of the desired sex compared to unselected litters. This happens because is many mammals with litters of multiple offspring, the females overproduce eggs, and not all eggs implant in the uterus. Therefore, if the eggs of the undesired sex are killed very early on more eggs from the desired sex can implant in the uterus and develop.

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Nov 15 2021

What Came Out of COP26

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The world met in Glasgow at the COP26 summit to see if politicians could put their heads together and work out a deal to limit global warming. The outcome was as much of a mess as you probably think it was. I suspect this is because their entire approach to the problem was flawed. That doesn’t mean it was hopeful or fruitless, just that it was highly problematic, and yielded highly problematic outcomes.

As an analogy, the psychological literature indicates that the best way to achieve a goal is not to focus on the goal but on the steps you need to achieve that goal. Richard Wiseman points this out in his book, 59 Seconds. Imagining yourself having achieved your goal is not helpful, and may even be counterproductive. Rather, you should outline the precise steps you need to take in order to achieve your goal. Chart a path, don’t just indicate your destination. I might humbly suggest that our world leaders would take this advice when they approach the problem of climate change.

As far as I can tell from all the reporting from COP26 (and the Paris agreement, and other climate agreements), the focus is primarily on the goal. We want to limit climate change to 1.5 C temperature rise above pre-industrial levels. That’s a great goal – now how are we going to achieve it? This latest agreement goes a bit further. It lays out several actual steps that are critical to achieving the temperature goal. One is to “phase down” coal. At the last minute India objected to the agreement to “phase out” coal and a watering down of the language was necessary to get an agreement. There was also an agreement to reduce deforestation, an admirable goal that is vital to tackling climate change.

While this language is one step closer to laying out actual policy changes, it is still not quite there. Politicians are straining to come up with language to portray the deal in a positive light, preferring the word “progress” over all others. But few are willing to use the word “success”, which is an indication that many think the conference was essentially a failure. But I think the failure was baked into the process. This is because you can’t just tell countries like India, who are banking on coal to develop their nation and reduce poverty, to phase out coal.

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Nov 01 2021

The Sri Lanka Organic Experiment

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Cautionary tales are extremely useful, as long as we take the right lessons away from them. As the saying goes, the best way to learn is from mistakes, but even better is to learn from someone else’s mistake without having to commit it yourself (and suffer the consequences). Sri Lanka has now made itself into a cautionary tale, and I would like to amplify any learning that can come from it. The primary conceptual lesson here is that – when ideology trumps science, the outcome is likely to be very bad.

There is also a specific lesson here. Organic farming may sound good in principle (if you just listen to the ideological marketing), but in practice it is a disaster. Sri Lanka has decided to do what other countries have done before, namely impose from above a commandment on how to run an industry based entirely on the philosophical beliefs of the leader. Perhaps the most famous example of this is Lysenkoism in the former Soviet Union, where the archaic ideas of geneticist Trofim Lysenko were given official support and decimated Soviet agriculture, costing millions of lives.

President Gotabaya Rajapaksa of Sri Lanka has done something similar – banning agrichemicals in Sri Lanka and forcing all farmers to farm organically. The result was absolutely predictable, a crash in agricultural output. While Sri Lanka is a net food importer, they still are dependent on local rice and other staple crop productions. Their exports are also mainly agricultural, such as tea, rubber, and many spices. Some reporting has focused on the timing of the change, during a fragile recovery from a pandemic. Also some have pointed out that going suddenly full organic is a problem because most farmers don’t know how to do it, and there was no adjustment period.

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Oct 29 2021

What Kind of Problem is Global Warming

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Framing is important, and often exists below our conscious awareness. If we are not even aware that we are framing an issue in a certain way, and that other framings are possible, this will influence our thinking in ways that we cannot anticipate or correct for. Sometimes a particular framing is deliberate, a strategy for propaganda and rhetorical advantage. This is often done in order to win a debate before it even begins, by rigging the intellectual venue. It’s therefore critical to keep on the alert for how you and others frame particular issues.

Framing has come up quite a bit in the recent comment discussions on global warming, so I would like to address the framing issue directly. The question is – what kind of a problem is global warming, from the perspective of how we can solve it. One framing, of course, is that it is not a problem, that it’s some kind of hoax, but I will simply reject that framing outright. There is an overwhelming scientific consensus that anthropogenic global warming is happening and is already causing problems, with big problems likely ahead. The question we should focus on now is, how should we mitigate AGW?

I have encountered four different ways to approach this question: scientific, economic, political, and social. If we ask, is AGW primarily a scientific, economic, political, or social problem, the answer is, “Yes”. It’s all of them at the same time, and there is interaction among these different factors. Human psychology, however, tends to favor oversimplification and moral purity, so there is a tendency to frame the issue from only one perspective. There is also a tendency to then stake out that framing as the one “correct” view, and then criticize the other perspectives by making straw men out of them, partly by pointing at their most fringe elements as if they were mainstream. But let’s take a more thorough and nuanced approach.

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