Author: Jay Wile

Please…Discard the Dogma!

Evolutionists have dogmatically insisted that pseudogenes are genes that were broken by mutation and are now useless. Some are now pleading with their colleagues to actually look at the data.

It always troubles me when I read other scientists who ignore the data in order to cling to their cherished dogmas. As a scientist, I know that this holds back the progress of science. As a result, I was heartened to read three scientist calling on their colleagues to abandon evolutionary dogma when it comes to pseudogenes. If others heed their call, we will most certainly learn more about DNA.

What am I talking about? Let’s start with what a pseudogene is. It is a region of DNA that looks like a known gene, but is different enough that it can’t do what the known gene does. As a result, it has become evolutionary dogma that pseudogenes are “broken” genes – genes that became non-functional due to duplication and mutation. Here, for example, is how the Encyclopedia of Genetics definitively describes a pseudogene:

A pseudogene is a nonfunctional genomic region that originated by duplication of, and is still homologous to, an ancestral gene.

In other words, a pseudogene is the result of a gene being copied and then broken. Creationists have long argued that pseudogenes are functional; they just don’t function the way evolutionists expect them to. The three authors of the paper I mentioned above have arrived at that same conclusion (at least for many pseudogenes), and they are asking their colleagues to pay attention to the data and do the same.

To emphasize the point that this evolution-inspired dogma is wrong, they list many pseudogenes that have been demonstrated to have an important function. They then make this important statement:

The examples of pseudogene function elaborated on here should not imply that pseudogene functionality is likely to be confined to isolated instances.

In other words, you can’t say that the known functional pseudogenes are exceptions to the rule. There are enough functional pseudogenes to call into question the assumption that they are mostly non-functional.

At the same time, however, these authors are cautious:

The purpose of this article is not to discard the pseudogene concept or to suggest that all pseudogenes are functional. The majority of currently annotated pseudogenes are neither robustly transcribed nor translated. Such regions fit well the original descriptions of pseudogenes as ‘similar, but defective’. Rather, we argue that their labelling as pseudogenes is not constructive for advancement of understanding of genome function and misdirects experimental design.

In other words, the authors are simply telling their colleagues to follow the data. Do not assume that a pseudogene is non-functional just because it has been identified as a pseudogene. Instead, investigate it to find out whether or not it actually is. The progress of science is hindered when you assume non-functionality because of the way the sequence has been identified.

I not only completely agree with that sentiment, I would also add this: following any dogma (evolutionist, creationist, or other) hinders the progress of science. Scientists should be willing to follow the data wherever they lead. Unfortunately, such scientists tend to be the exception, not the rule.

Are Hydroxychloroquine and Azithromycin Effective Against COVID-19?

Dr. Didier Raoult, French physician and microbiologist who thinks he has an effective treatment for COVID-19 (click for image source)
Two weeks ago I wrote about a possible treatment for COVID-19, the pandemic disease that is affecting most of our lives. It has been championed by French physician and microbiologist Dr. Didier Raoult. So far, he has written two papers about it (here and here). I was excited about his initial report, and I was hoping for a serious follow-up study. When I saw that he had written a second paper, I eagerly read it. Unfortunately, it wasn’t the serious study that I had hoped for. Nevertheless, it has gotten some media attention and seems to have influenced the FDA, so I decided to share my thoughts on it.

The results seem very exciting. He and his colleagues treated 80 patients with the malaria-fighting drug hydroxychloroquine and the antibiotic azithromycin. They note that they saw “clinical improvement” in 78 of them. One of the other two (an 86 year-old patient) died, and the other (a 74 year-old patient) was still in intensive care when the paper was written. While that sounds really good, there are a couple of “red flags” that make me hesitant to think that the treatment is as effective as it seems.

The first problem is that there is no control group. In a serious medical study, there needs to be a similar group of patents who do not receive the treatment. The treated group can be then measured against the untreated (control) group. Without that, it is very difficult to determine what the actual effect of the treatment is. Of course, I understand why there is no control group. Dr. Raoult wants to save lives. He thinks his treatment is effective, so he wants to give it to as many people as he can. He would have to “withhold” his life-saving treatment from some people so that he could have a control group, and that could lead to more deaths. I can understand why a physician would shudder at that idea.

However, the control group is important, because we really have no idea what would have happened to the 78 people who recovered had they not been given the treatment. While we still don’t know, the fatality rate of this disease is thought to be 1-2%. In 80 people, then, you would expect only one or two (0.8-1.6 to be precise) deaths, so this group of patients has the fatality outcome we expect had there been no treatment at all.

Now, of course, Dr. Raoult and his colleagues did more than just track whether or not the patients died. They tracked the amount of virus in each patient’s nasal cavity and found that the amount of virus dropped significantly for most of them. Once again, that sounds nice, but without a control group, we simply don’t know whether or not that was because of the treatment.

The second problem is the profile of patients who got the treatment. They mostly seemed to have a mild case of the disease. Only 15% had fever. Only 53% showed signs of lower respiratory tract infection. Worse, 5% showed no symptoms at all. Once again, it isn’t surprising that most of these patients recovered – most of them fit the profile of people who are expected to recover.

There is a third problem. A scientific study has been done in China with a control group. It is very small, and I can’t read it, since it is in Chinese. However, based on a Forbes article, the study had 30 patients. Half were given hydroxychloroquine, and half were not. That study showed no significant difference between the control group and the treatment group. Thus, if that study is correct, hydroxychloroquine is not an effective treatment for COVID-19.

Now, of course, that study didn’t include the antibiotic, so it’s possible that Dr. Raoult’s treatment is better than the treatment assessed by the study. It’s also possible that because of problems with the Chinese study’s design (small number of patients and no placebo, for example), the Chinese study is wrong. From a scientific point of view, then, we simply do not know whether or not Dr. Raoult’s treatment (or hydroxychloroquine by itself) is effective against COVID-19.

Nevertheless, the FDA has approved using hydroxychloroquine and other, similar drugs to treat COVID-19. This is probably a good plan, since the risks of using the drugs are low. However, until serious, controlled studies are done, we have no idea whether or not they are doing any good.

A Cool Variation on an Experiment

In my elementary science book, Science in the Beginning, I explain to students that many things in science are counter-intuitive. To make this point clear, I have them do an experiment with unexpected results. In one lesson, students learn that salt melts ice. In the next lesson, they are presented with this question:

In which situation will an ice cube melt more quickly:
Floating in hot freshwater or floating in hot saltwater?

I then have them do the experiment. They put hot freshwater into two glasses. They then add salt to the water in one of the glasses. Afterwards, they put ice cubes of roughly the same size in each. Unlike most people expect, the ice cube in freshwater melts more quickly. Here is how I explain the results (keep in mind they have already seen that freshwater floats on saltwater):

So, why did the experiment produce counter-intuitive results? Because of another fact that you know but probably didn’t think was important enough to consider: freshwater floats on saltwater. Why did the ice cubes melt so quickly? Because you put them in hot water. The water was so hot that the ice cubes had to melt. But when the ice cubes melted, where did the water that was formed by the melting actually go?

Let’s start with the freshwater. Remember that cold freshwater is just a bit heavier than an equal volume of warm freshwater. What does that tell you? It tells you that cold freshwater sinks in warm freshwater. Well, as the ice cube melted, the water that was formed by the melting process was still pretty cold. Thus, it sank in the hot water, getting out of the way. This allowed the warm freshwater around the ice cube to stay very warm, which kept melting the ice cube.

What happened in the saltwater was a completely different story, however. Remember that freshwater floats on saltwater. This effect is so strong that cold freshwater floats in hot saltwater. So,in the end, when the ice cube started to melt, the cold freshwater that was formed from the melting ice cube floated on the top of the saltwater, along with the ice. It didn’t sink like it did in the cup that had freshwater in it. For the ice cube to continue to melt, then, the hot saltwater had to heat up the newly formed freshwater that floated on the surface. That took time, and as a result, the ice cube melted a bit more slowly.

So, the counter-intuitive results were caused by the fact that freshwater floats on saltwater, but cold freshwater sinks in hot freshwater. That probably wasn’t something you thought about when I initially asked you the question, but you probably understand why it is important now that I have explained it to you. It turns out that a lot of science is like this because God created an incredibly complicated world for us. Often, we don’t think about all the different things that are important when we try to analyze a situation. As a result, many experiments end up showing us counter-intuitive results. Regardless of how counter-intuitive, however, as a scientist, you must follow what the experiments show. After all, we can’t always take into account all the complexities of creation, so when we do an experiment and find counter-intuitive results, unless we find something wrong with the way we did the experiment, the results are more important than what we think the results should be!

A homeschooling mother, Leah, recently shared a variation that she and her son, Parker, made to this experiment, and it is pictured above. They made ice cubes out of water that had blue food coloring in it. The first picture on the left is of the ice cube in freshwater. You can clearly see the cold water from the melted ice cube sinking in the warm freshwater. The middle picture shows you both ice cubes, and it is really clear that the water coming from the melting ice cube is floating on the saltwater, while it is mixing well with the freshwater. The last picture shows you what is left after both ice cubes melt. Once again, you can see that the water from the ice cube has mostly stayed floating on the saltwater.

The impressive thing about this variation is that Leah came up with the idea on her own. When she suggested it to Parker, he immediately understood what it would show. I would have never thought to do this kind of variation, but it really illustrates the process well. I will probably add a note about doing this in the next printing of the course so that others can benefit from it.

Ignoring the Log for the Speck

The Parable of the Mote and the Beam by Domenico Fetti (c. 1589 – 1623)

A reader sent me an article from the Home School Legal Defense Association (HSLDA). It is about a summit being held by Harvard Law School. Scheduled to happen in June of this year, the summit is supposed to address problems that exist within the homeschooling community. As the HSLDA article indicates, the lineup of speakers is a “Who’s Who” of anti-homeschooling advocates and advocates of strict governmental regulation over home education. HSLDA is rightly worried about this conference, especially since there don’t seem to be any homeschooling advocates among the speakers.

The HSLDA article provides a link to the summit’s website, and I was struck by the title: “Homeschooling Summit: Problems, Politics, and Prospects for Reform.” When I read that title, I couldn’t help but think of Jesus’ words, recorded in Matthew 7:1-5:

“Do not judge so that you will not be judged. For in the way you judge, you will be judged; and by your standard of measure, it will be measured to you. Why do you look at the speck that is in your brother’s eye, but do not notice the log that is in your own eye? Or how can you say to your brother, ‘Let me take the speck out of your eye,’ and behold, the log is in your own eye? You hypocrite, first take the log out of your own eye, and then you will see clearly to take the speck out of your brother’s eye.”

The organizers of this summit are behaving exactly the way Jesus describes. They are worried about the problems associated with homeschooling, when those problems are incredibly rampant in the public schooling system. What are these problems? The website says:

The focus will be on problems of educational deprivation and child maltreatment that too often occur under the guise of homeschooling, in a legal environment of minimal or no oversight.

The irony should be obvious. Educational deprivation and child maltreatment are RAMPANT in the government-regulated public schools, but the organizers of this summit think that government regulation is needed to keep it from happening in home schools!

If you don’t understand the severity of these problems in government-regulated public schools, you haven’t looked at the data. Students in our public schools routinely experience educational deprivation. It is estimated that about one-fifth of high school graduates are functionally illiterate. Testing indicates that seniors in public school perform well under the international average in mathematics. Performance on the ACT indicates that more than 25% of high school graduates who plan to go to college are not prepared for it. The list could go on and on.

What’s even more alarming is the rate of child maltreatment in the public schools. A government report estimates that 1 out of every 10 children will suffer sexual abuse in the public schools. If you weren’t aware of how rampant sexual abuse is in our public schools, I suggest you spend some time at Stop Educator Sexual Abuse Misconduct & Exploitation. The stories are heart-wrenching, and unfortunately, the public schools have a pattern of covering up these incidents, which leads to them becoming even more common.

Now please understand the point I am trying to make here. I am not saying that we shouldn’t try to address the issue of educational deprivation and child maltreatment in home schooling. What I am saying is that government regulation isn’t very effective at getting the job done. After all, government regulation is much, much easier in public schools, where the students are regularly in the presence of government employees. Even in such an environment, however, educational deprivation and child maltreatment are rampant.

In the end, if these speakers and the organizers of this summit are really interested in the welfare of homeschooled students, they should work with homeschooling organizations, not against them. Homeschooling organizations know the homeschooling population better than government organizations. As a result, they would be more effective at helping to correct educational deprivation and child maltreatment among homeschoolers, which I suspect is significantly less common than it is in the public schools.

Unfortunately, based on the list of invited speakers at this summit, my guess is that the participants will advocate working against homeschoolers, which will ultimately produce more educational deprivation and child maltreatment, not less.

A Possible Treatment for COVID-19

A transmission electron microscope image of the coronavirus SARS-CoV-2. The spikes surrounding the virus make it look like a crown, which is where it gets its name. (click for credit)

While countries are scrambling to prevent the spread of COVID-19 (the disease caused by the new coronavirus), doctors are trying to find the best treatment for it. In three separate studies, a surprising candidate has been found: the anti-malarial drug chloroquine. In a letter that was published on February 19th, three Chinese scientists reported that more than 100 patients were given the drug. Based on the patients’ responses, they write:

…chloroquine phosphate is superior to the control treatment in inhibiting the exacerbation of pneumonia, improving lung imaging findings, promoting a virusnegative conversion, and shortening the disease course…

The authors also report that there were no adverse side effects noted in the patients.

A report in Spanish (translation here) concurs. It discusses both the results seen in patients and the results of experiments where primate cells are infected with the virus and then treated with chloroquine. The conclusion is as follows:

Chloroquine can both prevent and treat coronavirus in primate cells…According to South Korean and China human treatment guidelines, chloroquine is effective in treating COVID-19. Given chloroquine’s human safety profile and existence, it can be implemented today in the U.S., Europe and the rest of the world.

Finally, a study published in the journal Nature confirms that when primate cells are infected by the virus that causes COVID-19, both chloroquine and an antiviral drug known as remdesivir were effective at fighting it. The researchers state:

Our findings reveal that remdesivir and chloroquine are highly effective in the control of 2019-nCoV infection in vitro. Since these compounds have been used in human patients with a safety track record and shown to be effective against various ailments, we suggest that they should be assessed in human patients suffering from the novel coronavirus disease.

Now, of course, these studies are far from conclusive. However, I expect that doctors will judiciously test the treatment on patients who volunteer for it. Hopefully, that will allow us to learn more. Perhaps an effective treatment is on the horizon!

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.

Continue reading “No Other Explanation: Dinosaur DNA!”

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.

Continue reading “68% of the Universe May Not Exist!”