Nov 06 2020

How the Brain Predicts Outcomes

This is a really interesting study trying to work out one of the brain regions involved in decision-making. The researchers are studying mice, and using a technique know as calcium imaging and optogenetics to view the activity of brain cells in a living animal in real time. The short version is that a brain region known as the anterior cingulate cortex (ACC) is necessary for model-based decision making. But let’s back up a bit and talk about decision making.

There appears to be two basic ways that vertebrates make decisions – model-based decision making and model-free decision making. The former involves creating an internal model of what is likely to happen in the world as a consequence of our specific actions. This approach also updates that model based upon experience. For example you may have a mental model of what is likely to happen if you slap people without provocation. If you ever decided to actually slap someone, their reaction would be used to update your model and inform future model-based decisions.

Model-based decision making is very effective, as it can take into consideration many variables and constantly updates itself with real-world experience. But this approach is also very labor-intensive. One of the basic principles of neuroscience is that brains are lazy, meaning that they tend to choose the pathway of least energy expenditure to get to a desired outcome. What this means on a neurological level is that the brain is generally wired with mechanisms to reduce energy expenditure, by which I mean thinking. As we learn, pathways form that make actions, thoughts, and behaviors more automatic. This often literally means laying down subcortical pathways that can carry out the procedure automatically without having to engage higher cortical processing, which is very energy intensive. For example, when you drive to work, which you have done hundreds or thousands of time, you will likely be on “automatic pilot”. You don’t have to think about your route, or when to turn, you just drive there from memory. It’s so easy, your brain can engage in other tasks, to the point that you may not even remember the drive.

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Nov 05 2020

Crop Yield with Higher CO2

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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Nov 03 2020

Magic Amulets Do Not Prevent COVID

Retraction Watch has an interesting article about a very curious paper published in Science of the Total Environment. In fact, the paper and communication from the lead author are so bad I have to wonder if its a Sokal-like prank. If not, it is more evidence that the world has become so weird there are many things which are beyond satire. But let’s take this at face value. The title of the paper is: “Can Traditional Chinese Medicine provide insights into controlling the COVID-19 pandemic: Serpentinization-induced lithospheric long-wavelength magnetic anomalies in Proterozoic bedrocks in a weakened geomagnetic field mediate the aberrant transformation of biogenic molecules in COVID-19 via magnetic catalysis.”

Many scientific publications are extremely technical and require very long technical descriptions, but my “gratuitous jargon” alarm went off at this title. The paper itself is worse – I get the distinct impression it is using jargon not to be precise, but to impress and befuddle. But wading through the jargon, the claim here that has caught attention is this – “Nephrite-Jade amulets, a calcium-ferromagnesian silicate, may prevent COVID-19.” What? Wearing a jade amulet may prevent COVID-19? You are going to have to do better than dazzling with jargon to make that claim stick, or even to get it taken seriously. The fact that the authors reference Traditional Chinese Medicine (TCM) does not help either.

The co-founder of Retraction Watch, Ivan Oransky, wanted to get to the bottom of it also, so he wrote the following e-mail to the corresponding author, Moses Turkle Bility, PhD. Oransky wrote:

“Dr. Bility
I blog at Retraction Watch. Can you confirm that you co-authored this paper?”

That was it – a very simple query to confirm authorship. This is pretty standard in academia, just dotting all the i’s. This was Dr. Bility’s response:

Dear Dr. Ivan Oransky, yes, I published that article, and I kindly suggest you read the article and examine the evidence provided. I also suggest you read the history of science and how zealots have consistently attempted to block and ridicule novel ideas that challenge the predominant paradigm from individuals that are deem not intelligent enough. I not surprised that this article has elicited angry responses. Clearly the idea that a black scientist can provide a paradigm shifting idea offends a lot of individuals. I’ll be very candid with you; my skin color has no bearing on my intelligence. If you have legitimate concerns about the article and wish to discuss, I’ll address; however, I will not tolerate racism or intellectual intolerance targeted at me.

Whoa, where is that coming from? I suspect that Dr. Bility has already received some pushback prior to getting the very innocent query from Retraction Watch, but such a response is extremely telling. Bility immediately goes for the “small minded bigots can’t appreciate my paradigm-shifting brilliance” card. Sorry, Dr. Bility, but with that reaction you just branded yourself a crank and a pseudoscientist. Perhaps that’s not fair, but neither is this massively out-of-proportion response.

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Nov 02 2020

Earth-Sized Rogue Planet Discovered

Published by under Astronomy
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I like to keep my mental model of the universe updated as much as possible. One of the things I learned not too long ago about the universe is the frequency of “rogue” planets. These are planets that are not bound to any star. The dominant current theory is that most of these rogue planets formed in stellar discs just like bound planets but then at some point in their history interacted with another large body and were flung out of their stellar system. In fact, most planets that form in a stellar system may have unstable orbits that will doom them over the cosmological short term to either collide with another body, fall into their parent star, or get flung out of the system. Only those planets with stable orbits remain, and so eventually systems will settle down with a relatively few planets in stable orbits.

How many rogue planets (also called FFPs for free floating planet) are there in the Milky Way? We don’t know, and estimates vary wildly. The most cited recent estimate based upon computer simulations suggest that there are at least 50 billion rogue planets in the Milky Way. This is not much, actually, as there are between 100 and 400 billion stars, so that’s less than on per star. Still, that is a lot of rogue planets wandering the vast darkness of interstellar space. But other estimates of the number of rogue planets are much higher. At the high end one estimate put the number at 100,000 times greater than the number of stars. That seems implausible. But it suggests the number could be much higher than 50 billion. Even if on average there are several rogue planets for each stellar system, that would create hundreds of billions of such planets in our galaxy. And we have to include all the dead stars whose planets are still roaming interstellar space.

As an aside, any such estimate has to include a size parameter – how many FFPs of size greater than or equal to X. The estimates above use Pluto as the lower end of the size range. The lower you go, however, the greater the number.

What we need is some observational data to supplement the theoretical simulations. If we can do a survey looking for rogue planets then the number of such worlds we find can be plugged into our simulations to come up with better estimates for the total number. But how, you may be wondering (if you don’t know already) can we find a cold dark planet at the vast distances of interstellar space? Right now we find exoplanets by using a few methods. One method is the transit methods – we look at the dip in light output from a star as a planet passes in front of it. Another is the wobble method – we look for the wobble in the path of a star that indicates it is being tugged by a large planet going around it in its orbit. We might also be able to directly image a planet by looking at the reflected light off of it and removing the glare from the parent star. None of these methods will work for a rogue planet.

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Oct 30 2020

Evolution of Dogs

Published by under Evolution
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The evolution of dogs from wolves is a long and complex one. A recent study adds some further information to this tale – as long as 11,000 years ago there were already at least five different distinct breeds of dog. These different breeds partly tracked along with human populations, but not completely. But let’s back up a bit and see where this new information fits into the story.

Experts actually don’t agree on exactly when and where dogs first appeared, or even if it was one event or multiple independent origins. What is clear is that dogs are essentially domesticated wolves. Their likely origin was in Europe sometime between 19 and 32 thousand years ago. This makes dogs the first domesticated animal. I have often considered (being a life-long dog owner myself) how useful dogs would have been to ancient people. They are excellent guardians, sending up an alarm when anything strays too close to camp. My dog will let me know when racoons are poaching the bird feeder at 3am. They are territorial and will keep critters small and large out of the area. And in an emergency they will even fight for their masters. More developed and trained dogs can also do all sorts of jobs, from herding to hunting.

The extreme usefulness, not to mention companionship, of dogs to humans lead to the early hypothesis that humans domesticated wolves, probably by first raising wolf pups. Tamed wolves are more aggressive than dogs, but they can bond with humans and function in the human world. We know from the silver fox experiments that some mammal species can be significantly domesticated in just a few generations. So it would not take long for these tamed wolves to become more docile, loyal, and obedient. But experts now suspect this is not what actually happened.

The history of human and wolf interaction is mainly one of competition and eradications. Humans have always treated large predators as a threat. Wolves specifically have mostly been eradicated where humans flourish, often deliberately. This still does not preclude the exception of tamed wolves, but it did give rise to an alternate hypothesis – perhaps wolves domesticated humans rather than the other way around, meaning that it was the wolves who changed the nature of our relationship first. In this scenario wolf populations living near humans may have learned to poach at the edges of settlements, perhaps eating the bones or other refuse that humans discarded. The more cute and friendly wolves would have had more success at this strategy, while the more aggressive wolves would have been killed or driven off. This could have led to a subpopulation of friendly wolves mostly living off of human refuse. Selective pressures could have then quickly domesticated these proto-dog wolves, who were only later taken as companions by humans. Human selection would then have taken them the rest of the way to modern dogs.

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Oct 29 2020

Brain-Machine Interface with Stentrode

Brain-Machine interface (BMI) technology continues to incrementally but steadily progress, and I do think this is one of the technologies that will transform our future. Studies have already demonstrated that there are no biological or theoretical limitations to such technology – the brain happily communicates with computers and seamlessly incorporates signals to and from them through the existing process of brain plasticity. The real limitation with practical applications of BMI is technological, mostly in designing electrodes that can safely work for a long time.

As I have discussed before, there are numerous approaches. Scalp surface electrodes are safe and easy, but have no resolution because the skull attenuates signals to and from the brain. Brain surface electrodes work much better, but they are invasive and tend to form scar tissue which can limit their lifespan. Microwires are a cutting edge approach, very thin hair-like wires that penetrate the brain, and can have both high resolution and long term safety. There is also the clever approach of putting the electrodes inside blood vessels in the brain. One company, Synchron, has been developing this technology since 2010 and their device, the Stentrode (a portmanteau of stent and electrode), has now completed a preliminary human trial.

The idea is to insert electrodes the way a stent would be placed inside a blood vessel to treat a blockage. The advantage here is that the endovascular stent technology already exists. They just had to make the stent out of electrodes, which they did. The huge advantage here is that you can get electrodes inside the skull and next to the brain without opening the skull or doing brain surgery. The brain itself is never penetrated. The electrodes are not as intimate with brain tissue as brain surface or penetrating electrodes, but that’s the tradeoff. The question is – how much efficacy can we get from endovascular electrodes?

Much of the research previously has been done on animals, mostly sheep and pigs. Initially the electrodes were connected directly to an external control device that also provides power. But this requires wires to go through the blood vessel to the outside, which is an infection risk. The latest design, the one studied recently, communicates wirelessly to a control box worn by the subject. The only mention I could find of how the electrodes are powered suggests they are powered wirelessly through this control box. This setup could potentially send and receive signals from the Stentrode.

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Oct 27 2020

Water on the Moon

Published by under Astronomy
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A new paper published in Nature Astronomy presents further evidence for significant water near the surface of the Moon. This is exciting news for the prospects of a lunar base, especially since NASA is planning on returning permanently to the Moon by 20204.

The Artemis program (Artemis is the twin sister of Apollo) plans to put the first woman and the next man on the lunar surface by 2024. Even if they don’t meet this ambitious timeframe, they will likely succeed sometime this decade. Unlike the “flags and footprint” mission design of Apollo, Artemis is designed for sustained exploration of the Moon. Artemis will use the space launch system, which will be the most powerful rocket in the world. In fact, the most powerful configuration of the SLS will be more powerful than the Saturn V rocket. This is because the SLS was designed no only to return to the Moon, but to be powerful enough to get to Mars, which is the ultimate goal.

On top of the SLS will be the Orion capsule, NASA’s deep space capsule. Orion can accommodate up to four astronauts, and is designed for multi-week missions. It will have exercise equipment, radiation shielding, and on board waste disposal. When they get to the Moon they will have a new lunar lander, currently in development. But unlike Apollo, NASA also plans on building the Gateway – a lunar orbiting platform for long term occupation and exploration of the Moon.

After the initial Artemis missions, NASA plans to create a basecamp near the south-pole of the Moon for long term occupation and exploration of the Moon. Why the south pole? In NASA-speak the poles, “may contain mission-enhancing volatiles.”  In addition “These sites may also offer long-duration access to sunlight, direct-to-Earth communication, surface slope and roughness that will be less challenging for landers and astronauts.”

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Oct 26 2020

Murder Hornets Found and Destroyed

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 23 2020

Randi vs The Psychics

My skeptical colleague, James Randi, died earlier this week at the age of 92. He led a long, happy, and rich life and died with few meaningful regrets, and that is something to be celebrated. But we will also miss his wit and keen mind. He was one of the founders of modern skepticism, focusing his attention mainly on the consumer protection angle. He particularly delighted in exposing frauds and hucksters.

Randi came at skepticism through the magician path, which is not uncommon. Houdini, perhaps the most famous stage magician of all time, began this tradition by setting to expose the fake mediums of his time. Houdini realized that many of them were using standard magician stage tricks in order to fake seances. This is fine as a form of entertainment, but they were essentially tricking people into thinking they were contacting lost loved-ones in order to relieve them of excess cash. This practice continues to this day. As a magician himself, Houdini knew how to detect and expose their tricks.

Randi’s career in many ways is similar to Houdini’s but he helped spawn an entire movement of people, including scientists and philosophers, to help in the task. Randi told a story of his youth when he attended a faith-healing session. The pastor had people fill out “prayer cards” with their basic information and the ailment for which they sought healing. The pastor would appeal to the angels to bring him divine information about the next person who needed help. One person in the audience would cry out in joy and the pastor, seemingly through divine means, rattled off very specific information about them – information he could not have known.

Randi instantly recognized this as the old “one ahead trick”. The pastor was simply reciting the information he just read on the previous card, as if it were for the next person. This is a mentalism trick, meant to entertain, but being used to deceive. So Randi exposed the pastor for the trickster that he was, but those present did not thank him. They yelled at him, called him names, and ran him off. They were surprisingly ungrateful that Randi had popped their bubble of illusion and deception.

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Oct 22 2020

COVID-19 Becoming Less Deadly

Over the course of the pandemic the death rate in people diagnosed with COVID-19 (the case-fatality rate) has declined. Unpacking all the reasons this may be the case can help us better understand and fight this disease. A few recent studies shed some light on this question. While there might be some encouraging news here, it highlights that this is still a “novel” virus and we have a lot to learn about the illness it causes.

One recent study looking at the case fatality rate in the New York region from March to August found that the death rate for those admitted to the hospital dropped from 27% to 3%. They also found many possible reasons for this dramatic decrease. One is the fact that in March New  York hospitals were overwhelmed with COVID cases. They did not have enough ICU beds or ventilators, and doctors were crushed beneath the initial wave of cases of a disease they had no experience with. So simply “flattening the curve” and reducing pressure on hospitals is one important factor.

The most encouraging reason for the decline is the steep learning curve of knowing how to treat those who are seriously ill with COVID. Doctors have learned through direct experience how to better manage COVID patients, and many interventions became standard practice between March and August. For example, it is better to rest patients on their stomach than their back, and it is better to delay ventilation as long as possible. The discovery that steroids can reduce the risk of cytokine storm was perhaps a significant improvement. Some patients now get convalescent plasma, something that obviously could not have happened early on. Remdesevir was given emergency use authorization, but a recent study by the WHO found no survival benefit from this drug (or from hydroxychloroquine, a combination of the anti-HIV drugs lopinavir and ritonavir; and interferon).

While we still do not have a cure for COVID-19 or a proven effective anti-viral, management has significantly improved and this has definitely contributed to survival. However – this is not the only effect, and may not even be the major effect.

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