Archive for October, 2019

Oct 31 2019

Tracing Human Origins

Published by under Evolution

When and where did fully modern humans first emerge? That is an interesting question that paleontologists have been chasing for decades. Now a new genetic study claims to have pinpointed that origin to northern Botswana 200,000 years ago. The claim is already getting some pushback from other experts, but the new data does add to our understanding of human origins.

The study looks at mitochrondrial DNA, a technique that has been used before. This is DNA outside the nucleus, in each mitochondria of the cell (the power factories). They are almost exclusively passed down through the maternal line, because the egg provides all the mitochondria to the embryo, while sperm generally contribute none (although one may sneak through from time to time). You can therefore use mDNA to trace maternal lines.

When this type of analysis was first done researchers found that all humans have a common female ancestor going back to about 200,000 years in Africa. This result was widely misinterpreted in the press, not helped by the fact that this alleged ancestor was deemed the “mitochondrial Eve.” If you go back far enough, everyone is related to everyone. Therefore we all have many common ancestors. What the analysis shows really is a couple of things. First, that only one mitochondrial line from this time survived to the modern day. That doesn’t mean we only have one common female ancestor. But every time a woman has only sons, her mitochondrial line dies out. This finding does suggest, however, that the human population when through a relative bottleneck at this time. Our ancestors were not spread around Africa or the world, because then each region would have its own mitochondrial lineage.

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Oct 29 2019

Hygiea May Be a Dwarf Planet

Published by under Astronomy

Hygiea is the fourth largest asteroid in the asteroid belt, after Ceres, Vesta and Pallas. Recent observations of Hygiea are now challenging the distinction between an asteroid and a dwarf planet.

For some context, Ceres is the largest asteroid and is also the only one that is unambiguously a dwarf planet, by current definitions. Actually, when first discovered in 1801 it was considered a planet. It was the first asteroid discovered in the asteroid belt between Mars and Jupiter, but when more were discovered it became increasingly obvious that Ceres was part of a swarm of objects in a similar orbit. In the 1850s it was then demoted to an asteroid, although was the king of the asteroids, if that is any consolation.

Then in 2006 the International Astronomical Union (IAU) created the new category of dwarf planet and redefined the threshold for being a planet. According to the IAU, in order to be a planet you have to be large enough for gravity to pull your shape into a rough sphere (called hydrostatic equilibrium), not be a moon, orbit the sun, and dominate your orbit. A dwarf planet, rather, is an object with the first three criteria, but has failed to clear out its orbit of other objects. That last bit is what caused Pluto to famously be demoted to a dwarf planet, because its largest “moon”, Charon, was considered to be too large to be just a moon. Pluto and Charon orbit each other around a center of gravity (barycenter) that is outside both worlds.

However, the Pluto-Charon situation shows what a mess the classification system is. For now the five official dwarf planets are Pluto, Ceres, Eris, Makemake, and Haumea. There are many candidate dwarf planets that await further characterization. Charon is controversial. Some astronomers argue  that Pluto-Charon should be considered a double dwarf planet system, largely because the barycenter is outside both worlds. However, other argue that the location of the barycenter is not a strict criterion, because it depends on distance. For example, the barycenter of the Jupiter-Sun system is outside the surface of the sun, because of Jupiter’s distance. For now Charon is a moon, and its “promotion” to dwarf planet is in limbo. Also, the New Horizon data has called into question whether or not Charon is in hydrostatic equilibrium, but that is a separate issue.

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Oct 28 2019

The Golden Rice Saga

Published by under General Science

Science Writer Ed Regis has recently published a book, Golden Rice: The Imperiled Birth of a GMO Superfood, in which he tells the tragic story of golden rice. In his telling he does not come off as an ideologue, or someone who kept with an initial dramatic narrative regardless of the facts. Rather, he wished to find the truth, which is often messy and nuanced.

Golden rice is a genetically modified form of rice that is enriched with beta carotene, the precursor to vitamin A. It was developed by a non-profit humanitarian collaborative, is free of patents, and was produced with the intention of making it freely available to farmers in developing worlds. The first version of golden rice was produced in 2002, but this version had very low beta carotene levels. The latest versions, however, have sufficient levels that if current diets containing rice as the staple source of calories were switched to golden rice, it would be enough to avoid vitamin A deficiency.

Vitamin A deficiency is a global pandemic. According to the WHO:

An estimated 250 000 to 500 000 vitamin A-deficient children become blind every year, half of them dying within 12 months of losing their sight.

Golden rice has the potential to significantly reduce this disease burden by fortifying a daily staple with beta carotene. This sounds like a solid win for science, so what turns this into a tragic tale? Of course you know the answer, irrational resistance based on misplaced fears.

Greenpeace has lead the charge against the development and adoption of golden rice, mainly out of their generic resistance to all things GMO. Regis writes:

Over the years since the prototype version was announced, Greenpeace had issued a practically endless stream of press releases, position papers, and miscellaneous other statements about Golden Rice that were filled with factual inaccuracies, distortions, and wild exaggerations of the truth.

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Oct 25 2019

Mystery of the Hubble Constant

Published by under Astronomy

76.8 kilometers per second per megaparsec.

A megaparsec is about 30 million trillion kilometers, or perhaps better stated as 30 exameters. Given the significant figures, and the massive denominator, that makes this constant extremely precise. But is it accurate? Other measures using different methods come up with 74.03, 71.9, 69.8, and even 67.4.

We are talking about the Hubble constant, the rate of expansion of the universe. Edwin Hubble first proposed that the entire universe is expanding in 1929. This was based initially on observations by Harlow Shapley that other galaxies appear to be moving away from us. Their color is red-shifted from the doppler effect on the light coming to us from those galaxies. (As an aside, this applies to galaxies outside our local galaxy cluster, which are not uniformly moving away from us because we are gravitationally bound.) Hubble then made an extensive measure of the red shift of galaxies, and found that the farther away galaxies were, the more red shifted they were. This could be explained if the entire universe were expanding.

In 2011 three astrophysicists were awarded the Nobel prize for their discovery that, no only is the universe expanding, this expansion is accelerating. This means there must be an unknown force overcoming gravitational attraction and pushing everything apart – a force now called dark energy. But dark energy is not the mystery I am referring to in the title.

The mystery of the Hubble Constant is why different astronomers and different methods come up with different numbers? There are a few generic possibilities here – whenever different measurements disagree. It’s possible that the measurements themselves are simply inaccurate. This is always the first assumption and needs to be explored and ruled out before other explanations are seriously considered.

What generally happens is as more and more careful and thorough measurements are made, or the techniques or instrumentation are refined, the measurements start to converge on the real answer. Problem solved. However, that is not what is happening with the Hubble Constant. It is perhaps too early to tell for sure, but so far measurements have not been steadily converging. This, in fact, is essentially the mystery.

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Oct 24 2019

Another Damning Organic Study

Published by under General Science

A recent study looks at the carbon emission impact if England and Wales switched entirely over to organic farming. They found:

We predict major shortfalls in production of most agricultural products against a conventional baseline. Direct GHG emissions are reduced with organic farming, but when increased overseas land use to compensate for shortfalls in domestic supply are factored in, net emissions are greater. Enhanced soil carbon sequestration could offset only a small part of the higher overseas emissions.

In their model organic farming did not use fossil-fuel based fertilizer. The nitrogen comes from natural sources, like manure, and also rotation crops that fix nitrogen, such as legumes. This does result in a direct reduction in green-house gas (GHG) emissions, but also results in about a 40% decrease in crop production. That shortfall would have to be made up with increased imports, mostly from Europe. So then we have to calculate what it would take to replace the shortfall in production. This is where there is some variability in the model, because it depends exactly what land is converted to crop production. In the most likely scenarios there would be a net increase in GHG emissions of about 20%.

This is a great example of the law of unintended consequences. When dealing with any complex network, like agriculture, you have to consider the effects of any one change on the overall system. This is not the first study to show that organic farming is a net negative for the environment, and so it is in line with previous research. Further, the disadvantages of organic farming get worse as you try to scale it up.

For example, consider the nitrogen cycle – agriculture is largely a system of recycling nitrogen into food. So for any system you have to consider where all the nitrogen is coming from. Organic farming uses manure, but when the world’s agriculture was limited to manure as a source of nitrogen, that severely limited food production. The green revolution was largely created by the ability to make artificial fertilizer and therefore a non-manure based source of nitrogen. Bottom line – we cannot support the world’s population on manure.

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Oct 22 2019

Prime Editing the Genome

Move over CRISPR – enter Prime Editing.

Maybe. What we can say is that the pace of technological advancement in genetic editing is advancing so quickly it’s hard to keep up. Now a new study, published in Nature, details a new method for editing called prime editing. The authors write:

Here we describe prime editing, a versatile and precise genome editing method that directly writes new genetic information into a specified DNA site using a catalytically impaired Cas9 fused to an engineered reverse transcriptase, programmed with a prime editing guide RNA (pegRNA) that both specifies the target site and encodes the desired edit.

So actually this is built off of CRISPR technology, using a Cas9 component, and then pairing it with a bit of RNA (pegRNA) that both targets the bit of the genome you want to edit and also has the new code you want to insert. Insertion is accomplished by the enzyme reverse transcriptase. How does this compare to existing methods for gene editing? The authors again:

“Prime editing offers efficiency and product purity advantages over homology-directed repair, complementary strengths and weaknesses compared to base editing, and much lower off-target editing than Cas9 nuclease at known Cas9 off-target sites. Prime editing substantially expands the scope and capabilities of genome editing, and in principle could correct about 89% of known pathogenic human genetic variants.”

It is more precise and has fewer errors, and is able to target 89% of known genetic diseases. It cannot fix errors where a gene is entirely missing, or where there are too many copies of a gene. They tested the method on two human genetic diseases in human cells, Tay Sachs and sickle cell anemia, with success.

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Oct 21 2019

Aluminum Air Batteries

Published by under Technology

An article about a new battery is making the rounds and I am getting a lot of questions about it – Ex-Navy officer turned inventor signs a multi-million deal to produce his electric car battery that will take drivers 1,500 miles without needing to charge. As stated, that sounds like a significant advance, about a 5 fold improvement over the current lithium-ion batteries powering a Tesla, for example.

That would certainly be a huge advantage and give the electric car industry a significant boost. Increased range would alleviate “range anxiety” and also mean the recharging could happen once a week rather than every night. It would also make electric vehicles easier to use on long trips. Further, increased range is the same as smaller batteries. Instead of a range of 1,500 miles, you cold have a battery with a 300 mile range that weighs one-fifth as much. (I am assuming that when they state the range they are comparing batteries of the same size.) That would make the vehicle more efficient and potentially cheaper.

But as always, the devil is in the details. What exactly are they talking about? There are lots of red flags in this article, starting with the fact that it is in the Daily Mail, which doesn’t exactly have a good reputation for high quality journalism. Also it makes it seem like this is the invention of one guy, rather than a lab, company, or even industry. That’s not realistic. There is also this:

Few will have heard of Jackson’s extraordinary invention. The reason, he says, is that since he and his company Metalectrique Ltd came up with a prototype a decade ago, he has faced determined opposition from the automobile industry establishment.

Sorry, but this conspiracy theory does not pass the smell test. New battery tech would not threaten the automotive industry, it would be a new option.

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Oct 18 2019

Diffusion of Responsibility

Published by under Culture and Society

I still remember the PSA of the crying American Indian, sad because of all the trash that the modern world was spreading in the previously pristine environment. It was powerful, and it had a real impact on me. The ad was sponsored by Keep America Beautiful, and I (like most everyone else) assumed this was an environmental group interested in keeping America beautiful.

Actually the piece was a clever bit of propaganda, which relates to the topic of this post – the diffusion of personal responsibility. I wrote yesterday about the letter from celebrities admitting that they are environmental hypocrites for living a high carbon footprint lifestyle while campaigning against climate change. The conflict is between personal and collective responsibility, and my basic conclusion is that both are important. Many excellent points were raised in the comments, and two points in particular I think deserve additional exploration. The main one, mentioned by townsend, is that this all relates to the diffusion of personal responsibility. This was implicit in my previous post, but it is an important social psychological principle that is worth discussing further.

I first learned about this in my Social Psychology class in college – this is a long well-established psychological principle. The broad brushstrokes are this – humans are social creatures. We evolved emotions of justice, reciprocity, shame, and guilt in order to modify our behavior to be compatible with our social structure. If everyone maximally pursued selfish interests, we could never have a functioning society.

However, problems arise when the sense of personal responsibility is diffused, because this shortcircuits the feedback loops of guilt, shame, and a sense of responsibility. If something is equally everyone’s responsibility, then it is essentially no one’s responsibility. I experience this every time I travel is large groups. Once you get north of about 6-7 people, the group is paralyzed and can’t seem to do anything. Even walking together from point A to point B becomes an exercise in herding cats. However, if you assign someone as the group leader (or wrangler, or whatever) then the group can function as a unit. The same is true on any project – there needs to be clear lines of responsibility.

This lesson was learned with public housing. Common areas soon fell into disrepair and utter filth. This is because no one was responsible for them. If, however, housing was designed with no common spaces – where an individual owner was responsible for their own space, the situation was much improved.

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Oct 17 2019

Are We All Hypocrites?

Published by under Logic/Philosophy

Recently celebrity supporters of Extinction Rebellion, a protest group calling for aggressive action on climate change, signed a letter admitting to being hypocrites. They state:

“Dear journalists who have called us hypocrites. You’re right. We live high carbon lives and the industries that we are part of have huge carbon footprints.”

But they go on to say:

“Like you, and everyone else, we are stuck in this fossil-fuel economy and without systemic change, our lifestyles will keep on causing climate and ecological harm.”

Their letter highlights an interesting conflict between personal responsibility and collective responsibility. How much is it on all of us as individuals to make sacrifices, or at least make a reasonable effort, to limit our carbon footprint? Coincidentally there was an interesting take on this question in the latest season of The Good Place (spoiler ahead). The lead characters discover that no one has made it into the Good Place in over 500 years. At first they think that the Bad Place has managed to hack the system in their favor, but ultimately discover that this reality is just an unintended consequence of modern life.

Cosmic points are awarded to individuals based on their actions, but the point system considers all consequences, intended or not, no matter how remote. So buying flowers for your grandmother may earn you points, but you lose more points because the money for those flowers found their way ultimately to a corporation using child labor. The interconnectedness of our global economy has made it literally impossible to be good.

So what do we do? Are we all hypocrites?

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Oct 15 2019

Impossible Bug Burger

Published by under General Science

The market is innovating some burger alternatives in order to reduce demand for beef.  There are potentially three reasons to reduce beef consumption – health, environmental, and ethical. How successful are these replacements?

First let me quickly review the reasons for reducing beef. The health effects of eating red and processed meat are, at present, controversial. I reviewed this question recently at SBM. There is evidence for increased cancer and heart disease from eating large amounts of red and especially processed meat, but the absolute risk is low and the quality of the evidence is low. You can make of this what you will, and that’s the controversy. My take is that if you keep your total calories where they should be for weight maintenance, and eat plenty of fruits and vegetables, the rest takes care of itself.

The ethical concerns are complex and reflect personal values. Again, personally, I don’t have a problem with eating animals after they are dead, as long as they were treated humanely while they were alive and they were slaughtered in a humane way. However, I understand the points on the other side and respect the views of those who wish to avoid meat for ethical reasons. I currently file that away as a personal choice. I don’t think there is ethical justification for outlawing meat, however.

The environmental concerns are also complex, but it is clear that producing a lot of meat is very inefficient. Potatoes, for example, produce 17 times the amount of calories per acre than beef. But some land is better suited for grazing than farming. Cows also produce a lot of methane. Water usage from animals is also high. This does not mean the best thing to do is eliminate meat completely. Rather, as one study indicates, we should use land optimally. Some land is best for growing a certain kind of crop, while another might be best for grazing, while still other land is best left untouched for natural ecosystems.

Whether or not you think we should reduce meat consumption to zero or not, the evidence does suggest that industrialized nations are eating too much meat. So it is reasonable to moderate our meat consumption at the very least.

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