Nov 20 2018

Possible New Branch of Eukaryotes Defined

Scientists report in Nature the indentification of two new species of Hemimastigophora, a predatory protist. What makes the paper newsworthy is that the authors are arguing that their genetic analysis suggests Hemimastigophora, currently categorized as a phylum, should instead be its own suprakingdom.

To make sense of this let’s review the basic structure of taxonomy, the system we use to categorize all life. All known life is divided first into three domains, the bacteria, archaea, and eukaryotes. Bacteria and archaea do not have a nucleus, while eukaryotes are larger and have a nucleus which contains most of their DNA.

Eukaryotes are divided into kingdoms, including plants, animals, fungus, protozoa, and chromista (algae with a certain kind of chlorophyll). Kingdoms are then divided into phyla, which are essentially major body plans within that group.

This is a simplified overview, because there is a lot of complexity here, with suprakingdoms, subkingdoms, and further breakdowns. Further, there is a lack of consensus on how to exactly divide up these major groups. Even in the cited paper, the authors say there are 5-8 “suprakingdom level groups” within the domain eukaryotes. The number of kingdoms depends on which scheme you use, and how you interpret the existing evidence.

The reason for uncertainty is that we have not yet done a full genetic analysis on every known group. Further, when we discover new species that lie outside of the existing scheme, we have to rethink how different groups are actually related.

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Nov 19 2018

No – Atlantis Has Not Been Discovered in North Africa

A video is making the rounds claiming “proof” that Atlantis existed in norther Africa. This video is by Jimmy from Bright Insight and it is an excellent example of crank pseudoscience. Jimmy has made himself into a social media brand, with lots of conspiracy and pseudohistory nonsense to sell, but let’s focus on this one video for now.

The video follows a familiar format – gather together lots of circumstantial evidence, exaggerate its significance and specificity, ignore anything that doesn’t fit, ignore all genuine scholarship, and create the impression that you’re onto something. Essentially – blow a lot of smoke to convince the naive that there’s a fire.

His argument is essentially that the Richat structure, or the Eye of the Sahara, fits Plato’s description of Atlantis so well, it essentially amounts to proof.

First, let me start out by stating that the consensus of actual scholarship is that Atlantis is a myth. Plato never intended his description of Atlantis to be an actual claim that the city existed. He used it as an obvious rhetorical device – the evil empire that was vanquished by the morally pure Athenians, and wiped off the Earth by the wrath of the gods. The notion that knowledge of a nine thousand year old city (at his time) somehow came only to Plato, of all people, is itself a huge stretch. Further, no one at the time reacted to his description of Atlantis as if it were a real claim. All his contemporaries understood it to be a device, not a claim. Jimmy does not even address this fatal flaw in his argument.

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Nov 16 2018

Changing the Kilogram

This is one of those items that at first does not seem like a big deal, and probably won’t get much play in the mainstream media, but is actually a significant milestone. Today, the international General Conference on Weights and Measures will meet in Versailles, France, to vote on whether or not to adopt a new standard for the kilogram. This is a formality, because this change has been worked on for years and the standard is now all set to change.

I have been reading a lot recently about the history of science and technology, and one common theme is that an important core feature of our modern society is infrastructure. If, for example, there were some sort of apocalypse, what would it take to reboot society? Theoretically, we would preserve much of our knowledge in books and would not have to start from scratch. The limiting factor would likely be infrastructure. Gasoline engines won out over electric engines for cars partly (and some believe primarily) because the infrastructure for distributing gasoline was put in place before the electrical infrastructure.

Science itself also has an infrastructure, which includes standard weights and measures. This sounds boring, but being able to precisely measure something, using standardized units that every scientist around the world can use, is critically important to both science and technology. Anything that makes doing science easier reduces the cost and increases the pace of science, with incredible downstream benefits.

In 1879 Le Grand K (or the International Prototype Kilogram – IPK) was created – this is a cylinder of platinum and iridium that is the ultimate reference for 1 kilogram. This hunk of metal is kept in a double bell jar, and never touched. Even a slight finger print would change how much it weighs. From this original kilogram, exact copies were made and distributed to countries to serve as their national standard. Occasionally these copies are sent back to France to compare to the original. These copies are then used to calibrate equipment used for precise measurement.

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Nov 15 2018

Spain Seeks to Ban Alternative Medicine

It’s nice to get the occasional good news, to know that there are other people out there who respect facts and science. The Spanish government announced that it plans to ban alternative medicine from state health centers. This is a bold move, and completely justified. In fact, any other approach is nothing short of outrageous.

In Spain there is a robust state health system, which covers all people living and working in Spain – about 90% of the population use public health care. About 19% use private health care to some extent. Spain is considered to have one of the best health care systems in the world, and has the life expectancy to go with it.

Now they want to make their health care system even better by purging it of harmful and wasteful pseudoscience. They have not yet provided a comprehensive list of what they consider “alternative” but gave homeopathy and acupuncture as examples (a good place to start). The Guardian reports:

The proposal, unveiled by the science and health ministers, aims to avoid the “potential harmful effects” of the practices when they are used as an alternative or a complement to treatment that is itself based on “proof and scientific rigour”, the government said in a statement.

At its core it is a simple and even obvious standard – provide health care that the best available scientific evidence says is safe and effective, and is the best option available, provided by licensed professionals. I have yet to hear even a semi-reasonable argument against this basic approach. The “alternative” is to use treatments that are not safe, not effective, or have been inadequately tested, provided by those who are not legitimate experts or professionals.

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Nov 13 2018

Engineering Photosynthesis

There’s some bad news, followed by good news, but partially countered by further bad news. The bad news is that our population is growing, and therefore our food requirements, and yet we are approaching the limits of our ability to increase crop yield with cultivation alone. Experts can quibble about whether or not we are at or near the limit, but it’s pretty clear that we are not going to double crop efficiency in the next 50 years through cultivation.

That, however, is pretty much what we need to do if we are going to meet humanity’s caloric needs. By 2050 yields will need to be 60% higher than 2005, and needs will likely continue to rise before they stabilize. Sure, there are some gains to be made in reducing waste, but not nearly enough. And sure, we need to take steps to stabilize our population more quickly, like fighting poverty and promoting the rights of women in developing countries.

But even under optimistic conditions – we simply need to grow more food. Further, as I recently reviewed, we are pretty much using all the good arable land available. Expanding into more land for growing food is not a good option.

So really we have one viable option if we are going to meet our food needs – genetically modifying crops. That is the good news – GMOs actually have the potential to significantly increase crop yields. One way to do that is through making photosynthesis more efficient. It turns out, there are several ways to do this.

First, there is a difference between C3 and C4 photosynthetic pathways. The C4 pathway is more efficient, and increases biomass production. Part of the efficiency is through better carbon concentration mechanisms. This pathway has independently evolved in many plants, and there are others that are part way between C3 and C4, but our major food crops all use C3.

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Nov 12 2018

Optimizing Wind Turbines

It’s pretty clear at this point that we need to be moving away from fossil fuels as quickly as possible. Fossil fuels essentially are stores of ancient carbon, long sequestered from the environment, that we are now releasing back into the environment, altering the balance of the carbon cycle leading to increased forcing of global temperatures.

The good news is that other forms of energy are advancing nicely. Wind and solar are now past the point of cost effectiveness in many situations – without even counting the cost of pollution, which I think should be counted. If you consider the health and environmental effects of fossil fuel pollution, all other forms of energy become much more cost effective. (This is the idea behind the carbon tax.)

Nuclear, it seems, is likely going to have to be part of any future energy infrastructure that uses minimal fossil fuel, but lags in cost effectiveness. The nuclear industry is responding, however, with safer and cheaper designs.

It is heartening to know that we essentially have the technology to phase out fossil fuel right now, if we had the political will to do so. It is, of course, disheartening that we lack the political will even in the face of a solid scientific consensus, and clear technology options. Further, whatever technology we choose to invest in will only get better over time.

This constant progress has made the conversation about renewable energies in particular interesting – because the facts on the ground are constant evolving. Solar and wind keep getting better and more cost effective. Wind power is particularly interesting because there are so many factors involved – in both the design of the turbines themselves and their placement.

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Nov 09 2018

Navigation May Be Fundamental to Thinking

Have you ever been in a semi-familiar location but couldn’t quite place where you were, then suddenly the landmarks line up and you know where you are? This might happen when entering a familiar location from an unusual direction, for example. Also (a seemingly unrelated question), when you visualize abstract ideas, do you arrange them physically. For example, do you visualize time (like days, weeks, months, years), and if so is there a particular physical relationship by which you mentally organize the progress of time?

Scientists from the Max Planck Institute for Human Cognitive and Brain Sciences (MPI CBS) and the Kavli Institute for Systems Neuroscience in Trondheim, Norway have published a paper in which they propose these two mental phenomena are directly related. One of the scientists, Edvard I. Moser, won the 2014 Nobel Prize for some of this work.

For background, researchers discovered that there are a type of neuron called place cells in the hippocampus (specifically area CA1) that store the memory for specific locations. When you are in a familiar location, a unique pattern of place cells will light up. Further, there is a second type of cell called grid neurons, which are arranged in a hexagonal pattern in the nearby entorhinal cortex. These grid cells light up in sequence as you move through your physical space – the physical arrangement of the grid neurons map to the physical arrangement of your environment.

This is an elegant system – your brain basically has a movable grid map, the grid keeps track of your local navigation, while the place cells keep track of where the map is.

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Nov 08 2018

Echinacea Does Not Work for the Cold

We are heading into cold and flu season, so Time magazine decided to helpfully tell us what the science says about echinacea and the common cold. Unfortunately, they completely bungled their report, getting the bottom line wrong. Exactly where they go wrong, however, is extremely common and instructive.

The terrible article is partly not the fault of the author. They spoke to experts and tried to do a balanced piece. Unfortunately, there are experts out there who are biased and just wrong. The author was not able to make sense of the evidence themselves, and so they helplessly just passed along whatever nonsense they were told. This is another manifestation of the infiltration of “alternative” medicine into our system – there are always going to be “experts” out there who are just alternative cranks, but they will get quoted along side more serious scientists.

For example, they write:

Other experts say there is evidence that echinacea can be helpful. “Echinacea is popular because it does work for at least some people,” says Kelly Kindscher, a professor of environmental studies at the University of Kansas who has written a textbook on echinacea. While some clinical trials have not shown echinacea to be effective, Kindscher says others have found benefits.

I understand listening to someone who wrote a textbook on the topic, but this conclusion flies in the face of published reviews. The next statement shows where they go wrong:

A 2010 study published in the Annals of Internal Medicine compared echinacea to a placebo and to no treatment at all. It found evidence that echinacea outperformed both when it came to reducing the duration of the common cold — but these benefits were too small to be considered statistically significant.

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Nov 06 2018

Electron Quantum Metamaterials

Material science is, in my opinion, one of the most underappreciated of the sciences. Perhaps because it is so wonky, it doesn’t seem to get much public attention, and yet the development of new materials arguably has the potential to change our civilization more than any other single advance. Our level of technology is largely defined by the materials we have mastered, and discovering a new material is literally a technological game changer.

It’s always hard to predict the next big advance, but there are some intriguing candidates. Interest seems to be clustering around anything on the nano scale – such as carbon nanofibers. Two-dimensional materials that are only one or a few atoms thick (which includes carbon nanofibers) is an area of intense research as well. There is also a relatively new class of materials called metamaterials, which do interesting things with light and other forms of electromagnetic radiation. Metamaterials essentially have emergent properties, and could have potentially exotic applications such as rendering objects invisible in certain frequencies.

A new paper attempts to codify and name one particular type of metamaterial that the authors (Justin C. W. Song & Nathaniel M. Gabor)  are proposing be called “electron quantum metamaterials.”

These types of materials are comprised of two or more layers of two-dimensional nanomaterial that are rotated with respect to each other so that special patterns emerge. This is likened to a moire pattern, where two sets of thin parallel lines are offset from each other by a certain amount and that creates an interference pattern. The interference patterns emerges from the specific relationship between the lines.

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Nov 05 2018

Oumuamua and the Alien Hypothesis

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One year ago, in October 2017, astronomers detected the first confirmed interstellar visitor to our solar system – an asteroid dubbed Oumuamua. The name is Hawaiian for “scout”, as if the asteroid is a messenger from a distant system. A Hawaiian name was chose because the object was discovered by the Panoramic Survey Telescope and Rapid Response System-1 (Pan-STARRS-1) in Hawaii. Determining that Oumuamua was an interstellar object was not difficult – the determination was based on its trajectory. It was traveling really fast, too fast for any object originating from our own system. It’s velocity would also take it out of our system – it was moving too fast to be captured by the gravity of our sun.

All of that is cool enough, but astronomers carefully analysing the trajectory of Oumuamua discovered (and published their findings in June 2018) that its acceleration could not be explained entirely by gravity. Some force was pushing, ever-so-slightly, on the object. This acceleration could be explained by outgassing, if there were any volatiles on Oumuamua that were heating up as it got closer to the sun. These gases would be like tiny rocket engines. Observations of the object did not detect any comet-like tail, which is why it was thought to be an asteroid. But if this new observation were correct, then it would have the ices and gases associated with a comet.

Oumuamua was discovered 40 days after its closest approach to the sun, when it was already on its way out of our solar system. At this point it should have been slowing down a bit from the pull of the sun’s gravity, but instead it was speeding up slightly. This could be explained by outgassing caused by heat from the sun.

This led to a debate about whether or not Oumuamua was an asteroid with a small amount of ice, or a comet that had lost most of its ice. It seems that the object exists in the gray zone between asteroid and comet (and we run into yet another definition demarcation problem). Further, close analysis showed that Oumuamua is very elongated (often described as “cigar-shaped”) and quickly tumbling end-over-end.

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