More Thoughts on the New Coronavirus

An infographic adapted from one produced by the CDC (click for larger version)

A few readers have sent me questions regarding the coronavirus that is spreading across the world, so I thought I would make a post answering those questions and providing some resources you can use to deal with the issue. Please note, however, that I am neither a medical doctor nor a biologist. As a result, I don’t claim any expertise on the matter. However, there are some misconceptions about the virus that are easily cleared up, and there are some facts that anyone who can understand the scientific literature should share.

First, a few facts. The term “coronavirus” refers to a very large group of viruses that circulate mostly among mammals and birds. However, some are able to infect people. Most coronaviruses that infect people produce mild illnesses, but some (like this one) produce potentially fatal ones. The coronavirus that is in the news right now is one that has not been seen before. This is not unusual. When an animal is infected with two different versions of the coronavirus, they can mix together, producing a new (usually called “novel”) coronavirus. This particular novel coronavirus has been charmingly named SARS-CoV-2, and it causes the disease referred to as COVID-19. Because of that, it is sometimes referred to as the “COVID-19 virus.”

The reason it has been given the name SARS-CoV-2 is that its genetic sequences indicate it is very similar to the virus that caused the SARS outbreak of 2003. Based on that sequence, it is thought that the virus originated in bats, but it might have passed through another animal (possibly a scaly anteater) before infecting people. Most importantly, there is strong evidence against the idea that it was genetically engineered. This is because the way it infects people is quite different from what would have been predicted given our current knowledge about these viruses. In other words, it is very hard to believe that anyone knowledgable enough to engineer a virus would purposefully make the genetic sequences that end up allowing the virus to be so good at infecting people.

The illness caused by this virus is flu-like, but it is much more serious than the flu. The death rate caused by the flu changes from year-to-year, depending on the strains that circulate. However, on average, the flu has a death rate of about 0.1%. That means for every 1,000 people who get the flu, 1 will die. Even though that is a low death rate, a lot of people get the flu. As a result, millions of people die from the flu every year. We don’t know the death rate for this new virus, since we don’t really know how many people have actually been infected, but the best estimate so far is that the death rate is about 2%. That means this virus is thought to be 20 times more deadly than the flu virus.

Second, the resources. The infographic above has been adapted from one that was produced by the CDC. The university at which I teach has asked all its professors to post this electronically as well as wherever students might be found. It is basic, but nevertheless, it does contain some helpful information. This link will take you to the latest information regarding where the virus has been detected, how many people have been infected, and how many people have died.

In general, the best way to avoid being infected by this virus is to avoid other people and avoid going to places where it has been found. The virus spreads most effectively when an infected person is within a few feet of an uninfected person. However, it might also be transferred by surfaces. If someone sneezes on a surface and someone else touches that surface, the virus can be transferred to the hand. Then, if that person touches his or her mouth, nose, or eyes, it is possible for the virus to begin an infection. Thus, you need to wash your hands a lot and avoid touching your eyes, nose, and mouth in between washings.

The most important thing to remember is that while the illness caused by this virus has a death rate that is thought to be about 2% on average, it is significantly higher for elderly people, people who are already sick with something else, and people with weakened immune systems. Thus, if you show any of the signs of the illness (fever, cough, shortness of breath) and think you might have been in contact with someone who has the virus, you should seek medical help.

While there are several groups working on a vaccine to prevent the spread of the virus, the earliest a vaccine could possibly be ready would be at least a year from now. My guess, given that I am anything but an expert about these things, is that it will not be needed. The disease seems to have already plateaued in China, and I expect other countries to be a bit better at reducing the spread. Thus, I expect that the spread of the disease will slow down significantly before a vaccine can be approved for use. I could easily be wrong about that, however.

No Other Explanation: Dinosaur DNA!

Cells In two different stages of mitosis. The dark areas represent DNA, which is most likely damaged but still at least partially arranged in chromosomes.
(image from paper being discussed)

Despite the overwhelming evidence, there are some who are skeptical that soft tissue can be found in dinosaur fossils. Even among those who think that there may be soft tissue in some dinosaur fossils, there are those who think that there is no way complex molecules like DNA could possibly be found in that tissue. Well, Dr. Mary Schweitzer and her colleagues have recently published a study that, as far as I am concerned, should put all doubts to rest. Yes, dinosaur fossils do contain soft tissue and original dinosaur biomolecules, including DNA.

The study involves a detailed investigation of fossils from duck-billed dinosaur (Hypacrosaurus stebingeri) nestlings that are supposed to be 75 million years old. The authors examined cartilage tissue under the microscope and found what were obviously cells. Of course, that’s nothing unusual. The Dinosaur Soft Tissue Research Institute has some really great examples of dinosaur cells and other delicate structures from dinosaur fossils. They also have evidence for RNA in the fossils (see here, here, and here).

What’s new (and in my mind definitive) about this study is that they applied two different DNA stains to the tissue. The stains are designed to bind only to DNA, and when you use two different stains and see them both bind to the same structures, you have doubly confirmed the presence of DNA. Of course, what they saw could be DNA stains binding to DNA that contaminated the fossil, right? Wrong! The image at the top of the post indicates why. If I ask anyone who has taken a good high school biology class what the red box is drawn around, he or she should be able to tell me.

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A Newly-Discovered Component of Blood!

This transmission electron microscope image shows the structure of the newly-discovered blood component: functional mitochondria enclosed in vesicles.
(click for credit)

I have been teaching science for 34 years. I have been writing science textbooks for 27 years. I can’t tell you how many times I have written about blood and its components. Indeed, I am writing a 7th-grade textbook right now (Science in the Atomic Age), and it has a couple of sections on the properties and characteristics of human blood. As usual, I discuss the cellular components of blood (red blood cells, white blood cells, and blood platelets) as well as the chemical components of blood (blood clotting factors, water, electrolytes, various proteins, etc.). I honestly thought we understood blood pretty well. However, God’s creation is so complex and intricate, it still surprises us. In a recently-published paper, scientists have found that blood contains something no one ever noticed before, and it is neither cellular nor chemical. It is something in between!

To understand what was found, you need to know that cells in fungi, plants, animals, and people contain small structures that are responsible for burning chemicals from your food and packaging the resulting energy into small units that the cells can use. Those structures are called mitochondria. While most of a cell’s DNA is held in the nucleus of the cell, there is some DNA found in the mitochondria. Not surprisingly, it is called mitochondrial DNA (mtDNA) to distinguish it from the DNA found in the nucleus, which is called nuclear DNA (nDNA).

I had learned quite some time ago that there was a lot more mtDNA in blood than nDNA, but that always made sense to me. Red blood cells have neither, because they eject their nucleus and mitochondria when they mature. However, white blood cells have both. When someone extracts DNA from blood, he or she is getting the nuclear DNA from the white blood cells. Well, each cell has several mitochondria and only one nucleus, so the white blood cells will contribute more mtDNA than nDNA to blood. In addition, blood platelets have mitochondria but no nucleus, so they are contributing a lot of mtDNA and no nDNA.

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Our Best Computer is Positively PRIMITIVE Compared to the Human Brain

A small selection of the connections in the human brain (left) and the world’s most powerful supercomputer (right).
Image on left by the PIT Bioinformatics Group. Image on right by the OLCF at ORNL.
Creative commons licensing. Click for specifics.

I have been working on my new book, Science in the Atomic Age, which (Lord willing) will be published this summer. In the section where I cover the nervous system, I compare a mouse brain and a human brain to computers. It’s rather fascinating. Below, you will find a slightly-edited excerpt from that discussion. Please note that the students have already learned that neurons are cells found in nervous tissue and that the integumentary system is the system of organs that makes your skin:

The brain has three major divisions: the cerebrum (suh ree’ brum), the cerebellum (sehr’ uh bell’ uhm), and the brain stem. The cerebrum is in charge of most of the really complicated things that the brain does. For example, it receives signals from your eyes and interprets them so that you can see. It receives signals from your ears and interprets them so you can hear. It receives signals from all the nervous tissue in your integumentary system so that you can figure out what you are touching as well as things like whether you are too warm, too cold, or comfortable. It also helps you learn, and it stores your memories. All this takes a lot of work, so it requires a lot of neurons.

How many neurons? The average adult cerebrum contains about 20 billion neurons. That number doesn’t mean very much by itself, so by comparison, the average adult mouse cerebrum contains about 2.5 million neurons. So the human cerebrum contains about 10,000 times as many neurons as a mouse’s cerebrum. Of course, a mouse is much smaller than a person. By weight, a person is about 3,000 times as heavy as a mouse. At least part of the difference between a mouse’s cerebrum and a person’s cerebrum is due to that. But people are much more intelligent than mice, and the number of neurons in the cerebrum must also be related to that.

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68% of the Universe May Not Exist!

The history of the universe, according to the standard model of cosmology (click for credit)

Unsuspecting students are often taught “facts” that are anything but actual facts. Consider, for example, what NASA says about the nature of the universe:

It turns out that roughly 68% of the universe is dark energy. Dark matter makes up about 27%. The rest – everything on Earth, everything ever observed with all of our instruments, all normal matter – adds up to less than 5% of the universe. Come to think of it, maybe it shouldn’t be called “normal” matter at all, since it is such a small fraction of the universe.

What is this thing called “dark energy” that supposedly makes up more than half of the universe? NASA honestly says that no one has any idea. However, NASA assures students that we know that 68% of the universe is made up of it.

Of course, what NASA (and most astrophysicists) neglect to tell students is that the entire existence of dark energy, including its amount in the universe, is based on a myriad of assumptions, some of which are almost certainly not true. Nevertheless, they assure students that they know dark energy exists and that most of the universe is made up of it. The cold, hard truth, however, is that everything we know about dark energy is based on models, and those models are built on assumptions. If the assumptions are wrong, the models could be wrong, and if the models are wrong, the whole idea of dark energy could be wrong.

This issue was brought front and center with the recent publication of a paper that challenges one of the assumptions that is instrumental in the conclusion that dark energy exists. If the results of this paper are confirmed, dark energy will be thrown into the same trash bin as phlogiston, luminiferous ether, and the impossibility of quasicrystals.

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The Inquisition Is Furious About Brazil!

The logo of the Intelligent Design Research Institute at Mackensie University in Brazil. (click for source)

Bill Nye says and writes a lot of ignorant things (see here, here, here, here, and here, for example). While it is hard to choose the most ignorant statement he has ever made, this one has to be in the top five:

Denial of evolution is unique to the United States.

I have already shown how that statement is 100% false, and anyone who even casually investigates the issue would know that it is false. However, as the links above show, investigation is definitely not one of Nye’s strong suits! I was reminded of his incredibly ignorant statement when I read this article, from the journal Science.

Like Bill Nye, the author of the article doesn’t seem to understand how to investigate an issue. Nevertheless, the article has some interesting content. It seems that the federal government in Brazil has appointed Dr. Benedito Guimarães Aguiar Neto to head an agency called CAPES, which oversees Brazil’s graduate study programs. This is noteworthy, because Dr. Neto was instrumental in forming an Intelligent Design Research Center at Mackenzie Presbyterian University in Brazil. Of course, this infuriates the Scientific Inquisition, because Intelligent Design has been officially declared as heresy by the High Priests of Science. To have someone who believes in heresy positioned in a powerful educational office is unthinkable! As the article tells us, one Brazilian biologist has said:

It is completely illogical to place someone who has promoted actions contrary to scientific consensus in a position to manage programs that are essentially of scientific training.

Of course, that very statement is incredibly anti-science, because almost all of the great scientific advancements in history come from the very act of questioning the scientific consensus. I would think that every institution of higher education should have many high-level officials who challenge the scientific consensus.

As I said, the author of the article doesn’t seem to be able to investigate an issue, since he calls Dr. Neto a “creationist.” I realize that the term is very broad, but there is no indication that Dr. Neto is a creationist. In fact, all he has stated is that Intelligent Design should be introduced in Brazil’s basic educational curriculum. I suspect that he is an advocate of intelligent design for that reason, but that doesn’t make him a creationist. Dr. David Berlinski is an advocate of Intelligent Design, and he doesn’t even believe in God. However, if you are a lazy writer, it is easier to falsely label a person than it is to actually investigate what that person believes.

In any event, I can’t help but see this as a step in the right direction. The progress of science depends on questioning the scientific consensus. Whether or not it was intentional, Brazil’s government decided to appoint someone who is skeptical of the consensus in a position of influence when it comes to science education. Not only does this further demonstrate that Bill Nye’s statement is breathtakingly ignorant, but it also gives us more indication that the biological sciences are slowly emerging from the quagmire of NeoDarwinism and getting ready to truly advance.

That Virus in China

People in China wearing surgical masks. Photo copyright shutterstock/testing.

If you haven’t been paying a lot of attention to the international news, you might not know that there is a serious virus spreading in China. As of yesterday at 3 PM Eastern, 640 people have been infected, and 17 have died. Most of the cases are in China, where the virus originated, but there have been four cases in Thailand, two in Vietnam, and one each in Japan, South Korea, Singapore, and the United States. While there is always a chance that the virus could produce a pandemic, officials in China seem to be doing all they can to keep that from happening.

Several cities have suspended bus and train service in an attempt to keep people the virus from spreading through travel. The city in which it originated (Wuhan) has been completely shut down. A colleague of mine says that her son is in that city, and all transportation has ceased. Businesses (even grocery stores) are not allowed to open. People must make do with the food they currently have until the government decides that it is safe for businesses to open again. Currently, they are hoping to allow businesses to open on Tuesday. The virus is very dangerous, but the Chinese government seems to be taking it seriously. Only time will tell if their efforts will be enough.

What is this virus? It is a strain of coronavirus, which causes respiratory infections. It usually gets spread from animal to human, but in some cases, it can be spread from human to human as well. This version of the virus seems to be one of those. Most coronavirus infections produce mild symptoms. In fact, nearly everyone has had a coronavirus infection at one time or another. However, the severity of the infection depends on the proteins that the virus carries. The SARS epidemic of 2003 was caused by a particularly virulent coronavirus, resulting in more than 770 deaths worldwide. The hope is that the spread of this coronavirus can be better contained.

Why did it just appear? When the cell of an organism is infected with two different viruses, a new virus, called a recombinant virus, can be produced, mixing characteristics from each. That seems to be what has happened here. According to a study that was just published, it looks like the virus is a combination of a bat coronavirus and another one that cannot be identified. The study looked at the way the proteins are coded, and the authors claim that the most likely animal that spread the virus is a snake. That would be odd, since coronaviruses are only known to infect mammals. However, Wuhan does have open markets where live snakes are sold, and since that’s where the virus originated, it could have come from a snake.

Regardless of what animal it came from, once this new virus (which is really just a combination of two old viruses) was produced, it then was transmitted to a person. Once again, that’s usually the way a coronavirus is spread to people, but this one has been confirmed to spread from human to human, which is why China is clamping down on travel. The virus can be spread through the air, through personal contact, or from touching a surface that has the virus on it and then touching your mouth, nose, or eyes before washing your hands. Because of this, many people in China are wearing masks like you see in the photo above (which was taken a long time ago), and they are washing their hands regularly. Currently, there is no cure for the viral infection. The best thing that can be done is to treat its symptoms (fever, cough, and breathing difficulties) so that the body’s immune system has time to conquer it.

We should pray that the Chinese government is taking this situation as seriously as it seems to be, so that a deadly epidemic is averted. Also, we should pray for the people in the cities that are on lockdown. Not only are they the ones most at risk for the infection, but their lives have also been severely disrupted. Some may even have to deal with hunger or thirst caused by the precautions that are being taken.

UPDATE (02/26/2020): Here is an analysis from the WHO. If it is correct, then the epidemic is declining, and the fatality rate outside Wuhan is much less than what was originally feared.

UPDATE: My colleague, whose son is in Wuhan, says that the grocery stores were open on Sunday (January 26th) and well stocked. He was able to buy enough food to last a month if necessary. According to him, there was no panic. However, the city is still on lockdown, and the infection is still spreading. As of the morning of Monday, January 27th, there have been five confirmed cases in the U.S. Not of the U.S. cases have resulted in death, but at least 56 are dead in China.

A Dirty Childhood Can Lead to a Healthy Life

A happy child plays in a muddy river (photo copyright Shutterstock/Christin Lola)

One of the proposed explanations for the rise in allergies seen in the industrialized world is the hygiene hypothesis. It argues that many children who live in industrialized nations are raised in an environment that is just too clean. Because of this, they are not exposed to infectious and foreign agents that properly “train” their immune system. In addition, they miss out on some of the good bacteria and fungi that would take up residence in their body and support their immune system. As a result, the natural development of the immune system is stunted, and the body doesn’t know how to properly respond to certain assaults.

While there is a lot of good indirect evidence to support the hypothesis, the only controlled studies that support it have been done on mice. Of course, it is hard to do a controlled study on people, because you would have to get two similar groups of people and force them to live in different environments (one clean and one dirty) for a long period of time, and that’s just not practical. However, I recently came across a study which comes close to doing that, and the results strongly support the hygiene hypothesis.

The authors cleverly made use of an artificial separation of people that occurred more than 70 years ago. At the end of World War II, Finland had to give up some of its land to Russia, creating a new border between the two countries. Over time, the people who lived on either side of the border developed very different lifestyles. The Russian side of the border stayed largely agrarian, while the Finnish side became more urban. Since these two populations started out very similar but ended up very different, the authors decided to compare their susceptibility to allergies, and the results were rather astonishing.

In 2003, the authors randomly selected 98 Finnish children and 82 Russian children who were 7-10 years of age. They took skin samples and nose mucus samples, and they asked the parents to report on the childrens’ susceptibility to certain allergies. They also measured the sensitivity to certain allergens by looking at chemical levels in their blood. They then did a follow-up study of the same children roughly 10 years later. The results remained consistent between the initial and follow-up studies: The Finnish children were three to ten times more likely than the Russian children to have allergic reactions like asthma, hay fever, eczema, and a runny nose.

When the authors examined the skin and nose mucus samples, they found that the Russian children had a lot more bacteria in their skin and mucus than the Finnish children. In addition, the diversity of bacterial species was much greater in the Russian children. So the children who had more bacteria and lots of different species of bacteria living in and on their bodies were less likely to have allergies!

The authors specifically note that the largest disparities between the two groups were in bacterial species from the genus Acinetobacter. As the authors state:

Our results also suggest that high abundance and diversity of Acinetobacter might contribute to the low allergy prevalence in Russia. Implications of early‐life exposure to Acinetobacter should be further investigated.

In other words, the authors think that at least part of the reason that the Finnish children had more allergies is that they weren’t exposed to enough Acinetobacter. Where do these bacteria live? In dirt and water. So based on the results of this study, children who grow up doing things like the child in the picture at the top of the post are less likely to develop allergies later in life!

As a creationist, this doesn’t surprise me at all. God created us to interact with His creation, and when we try to isolate ourselves from it, we suffer.

How Can a Planet Orbit Two Stars?

An artist’s interpretation of the planet TOI 1338b, which orbits a binary star system. The planet is on the left. The two stars are the two white spheres. (NASA image)

If you haven’t seen it, there is a viral story about a high school student, Wolf Cukier, who made a significant discovery. During a summer internship, he was looking through data that had already been flagged as coming from binary star systems. In these systems, two stars orbit one another. While this may sound unusual, most stars in the universe (as far as we can tell, anyway) are a part of a system in which two or more stars orbit one another. Solitary stars like our sun are the exception, not the rule.

In most binary star systems, one star is much brighter than the other. As a result, if earth’s orbit is aligned with the orbital paths of the two stars in a binary star system, when the dimmer star passes between earth and the brighter star, the light we get from that star system gets dimmer. This is called an eclipsing binary. The data that Wolf Cukier was studying had already been noted as representing eclipsing binaries, but Wolf noticed another periodic dimming in the light coming from a binary star system charmingly named “TOI 1338.” The dimming was weaker than the dimming seen from the eclipsing binary, but it was regular. It was determined that this weak dimming was the result of a planet coming between earth and the brighter star in the binary system. In other words, this young man had found a planet orbiting two stars! Such planets are rare, but not unheard of. There were seven such planets confirmed before this one, but this is the first one discovered using this particular telescope, which is called TESS.

If you can’t quite visualize what is going on here, NASA has made a helpful animation, which I have included below. As you can see from the animation, when the dimmer star in the system passes between earth and the brighter star, the amount of light earth receives from the system decreases a lot. When the planet comes between earth and the brighter star, it dims a little.

The student and several scientists have co-authored a paper that has been submitted for publication. Years ago, I had a high school student co-author a scientific paper with me because of a discovery she made under my supervision, and it was very exciting. I hope that their paper gets published as well!

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Once Again, Don’t Get Your Science from Facebook!

A visualization of the Australian fires that have happened recently (by Anthony Hearsey and Creative Imaging: click for more info)
I have made two posts so far cautioning people to be very skeptical of science-related Facebook posts (see here and here). In general, you should be skeptical of anything on any social media site, but science is easily skewed and misrepresented, especially when people are trying to show their own virtue by championing some cause.

One case in point comes from the Australian bushfires that are wreaking havoc throughout the country. My Facebook feed recently showed me the image you see on the left. The person posting wanted to make me aware of how devastating the bushfires in Australia have become, so he posted this picture. While it does indicate an incredible level of devastation, it isn’t really true. There are two problems with the image. First, it looks like a satellite photo that is showing the fires burning right now, but it is not. It is an image that was developed on a computer, and it doesn’t show how Australia is burning right now or at any other time in the past. Each “flame” in the image represents a fire that burned sometime this season. In other words, it shows any region of Australia that had a fire this season, but it shows that region as on fire right now. In fact, many of the fires depicted on this image have been extinguished.

There is a bigger problem that is common with all visualizations of this kind. When you make an image like this, you need to add “fire” in the region where there is or was a fire. However, the image represents something very, very large. Suppose there was a fire that burned three square miles. That’s a big fire, but in this image, it would be represented by a red dot that is one millionth the size of the image. Thus, it wouldn’t show up. In order to make it show up, you need to make it bigger. However, that makes it look like more than three square miles were burned.

This issue is called “gridding.” When dealing with a large object, it must be partitioned into small sections by drawing a grid. If the sections in your grid are very large compared to the areas that you are depicting, the resulting depiction is deceptive. So, in fact, even considering all the fires that have happened so far this season (extinguished or not), they haven’t covered as much of Australia as the “flames” on this map.

Now don’t get me wrong. I am not saying that the fires in Australia are nothing to be worried about. They most certainly are devastating! They probably represent the worst bushfires in the past hundred or so years. That’s a bit hard to tell, because some of the most devastating fires in Australia occurred in the past, when news coverage wasn’t very good. We know, for example, that in 1851 widespread bushfires killed at least 12. In 1939, bushfires killed at least 71. While it does look like the current bushfires are burning a larger area than any of the previous ones, it is hard to say that with certainty. Regardless, the image above definitely overstates their severity.

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