Study of Mice Highlights the “Junk DNA” Myth

Junk DNA is a crucial to evolutionary theory, despite the fact that it most likely doesn’t exist to any significant extent.
The concept of “junk DNA” is crucial to evolutionary theory. For example, the “gold standard” of evolutionary simulations doesn’t produce any evolution unless at least 85% of the simulated DNA is junk. This is why so many evolutionists are fighting against the straightforward conclusions of the ENCODE series of studies, which indicate that at least 80% of the human genome is functional. Dr. Dan Graur, for example, has famously said that if ENCODE is right, then evolution is wrong.

As is the case with most evolution-inspired ideas, the more we learn about the natural world, the more it becomes obvious that there is very little “junk DNA” in nature. A recently-published study of gender in mice highlights this fact. In the study, an international collaboration of scientists examined the development of sexual characteristics in mice. As you probably already know, in mammals there is a pair of chromosomes referred to as sex chromosomes. If an individual has an X chromosome and a Y chromosome in that pair, he is a male. If the individual has two X chromosomes, she is a female.

But the development of the proper characteristics associated with each sex depends on what happens during embryonic development. For example, as a mammal embryo develops, it starts out producing ovaries. However, there is a gene on the Y chromosome called Sry. It produces a protein that controls the production of another protein, called SOX9. The SOX9 protein turns developing ovaries into testes. A male develops testes, then, because of the action of a gene on the Y chromosome. But as this latest study shows, there is more to it than that.

The scientists removed a small section of DNA from genetically-male mice. This section is found in what the authors refer to as a “gene desert,” a section of DNA that is devoid of genes. Nevertheless, when that small section of DNA was deleted, the genetically-male mice developed ovaries and female genitalia. Now please understand that the genes involved in the production and regulation of the SOX9 protein were not removed; only a small portion of what many would call “junk DNA” was removed. Nevertheless, without that section of DNA, the genetically-male mice did not produce enough SOX9 protein, so the ovaries continued to develop into ovaries, which then caused the production of female genitalia. As a result, the authors refer to this small section of DNA as a SOX9 “enhancer.” It enhances the production of SOX9 at just the right time, so the males develop the correct gender characteristics.

While the results of this study are fascinating, they are not surprising. After all, it has become more and more clear that the concept of “junk DNA” is a myth. As a result, it makes sense that even small sections of DNA have important functions, at least in certain stages of development or under certain conditions. The reason I am blogging about the study is because of something the lead author said in an article that was published on his institution’s website:

Our study also highlights the important role of what some still refer to as ‘junk’ DNA, which makes up 98% of our genome. If a single enhancer can have this impact on sex determination, other non-coding regions might have similarly drastic effects. For decades, researchers have looked for genes that cause disorders of sex development but we haven’t been able to find the genetic cause for over half of them. Our latest study suggests that many answers could lie in the non-coding regions, which we will now investigate further.

Indeed. As Dr. John Mattick so aptly put it more than a decade ago:

…the failure to recognise the implications of the non-coding DNA will go down as the biggest mistake in the history of molecular biology.

Observations about Second-Generation Homeschoolers

One of several second-generation homeschoolers I have met this year.

This is “convention season” for homeschoolers across the United States, so I have been traveling to several different homeschool conventions, giving talks and speaking individually with lots of homeschooling parents. In some ways, these conventions never change. Many of the talks that I give are on the same topics that I spoke about at homeschooling conventions more than 20 years ago: how to “teach” science at home, why it is best for most students to be homeschooled through high school, and the fact that homeschooling produces graduates who are, on average, significantly better university students. Obviously, the details of the talks change every few years, but the basic points do not.

In the same way, many of the questions I get from homeschoolers are the same year after year and convention after convention. My son is only in 7th grade but is about to start Algebra 1. Should he really take high school biology? (In general, the answer is “yes,” but it depends on the student’s ability to work independently and how he reacts to academic rigor.) If he does take biology in 7th grade, can it be included on the high school transcript? (Once again, the answer is “yes.” See this article for more details.) My daughter is very talented in ballet and wants to pursue it as a career, but it requires a lot of rehearsal time. What should I do? (If a professional says that she has real potential, then you should scale back her other academic courses so that she can pursue her talents. Don’t neglect her education; just pare it down to the basic essentials so that she can have more time to hone her craft).

At the same time, however, each year brings a few changes. Some of the conventions that used to be large and well-attended are either very small or nonexistent. Other conventions that didn’t exist many years ago are now large and well-attended. Lots of new curricula are available, giving homeschoolers a wealth of choices for how to meet their children’s educational needs. The people you see at homeschooling conventions are also becoming more and more diverse every year.

This year, I noticed a new difference. Most likely, the difference has been slowly growing over a period of many years, but after speaking at the California Homeschool Convention this past weekend, it struck me that this year, I have interacted with a lot of second-generation homeschoolers (homeschool graduates who are now homeschooling their own children).

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Another Unsuccessful Attempt to Detect Dark Matter

This NASA image illustrates the fact that most astrophysicists think there is about four times as much dark matter as visible matter in the universe.

A couple of months ago, I wrote an article about a galaxy that has no “need” for dark matter. This is interesting, because most galaxies “need” dark matter to explain the motion of their stars. Based on the mass that is actually observed in most galaxies, the stars should not be moving the way that they do. Thus, scientists think there must be a lot of mass in those galaxies that cannot be seen (dark matter). To make their current theories work, scientists estimate that about 80-85% of the mass in the universe comes from dark matter. Since dark matter is thought to be so prevalent in the universe, scientists have tried to detect it directly, without any luck.

How do you detect something you can’t see? First, you have to have some idea of what you are looking for. Then, you design an experiment to see if what you think you might be looking for really exists. The most “promising” candidate for dark matter is a class of hypothetical particles called “weakly interacting massive particles” (WIMPs). These are particles that don’t interact with matter using the electromagnetic force. Since the electromagnetic force works via the exchange of photons, if a particle doesn’t use the electromagnetic force, it produces no light. Instead, WIMPs are thought to use only the gravitational force and the weak force, which works only at the subatomic level and is responsible for most of the natural radioactivity on planet earth.

Since all the matter we know of uses the electromagnetic force, WIMPs are obviously strange particles. However, they are allowed by the mathematics of the standard model of physics, which is why they are considered the most “promising” of the candidates for dark matter. How do scientist try to detect WIMPs? The most sensitive WIMP detector is called XENON1T, which is filled with liquid and gaseous xenon. The design of the detector allows scientists to identify electromagnetic interactions that occur between particles hitting the detector and the liquid xenon inside. They discard those interactions, and what’s left should be any interactions that use only the weak force. Those, of course, would be caused by the WIMPs.

The team of scientists using XENON1T reported their latest results at a seminar on May 28th, and so far, they have not seen a signal that is consistent with what is expected for WIMPs. I think their results argue strongly that WIMPs don’t exist, but that’s not the only explanation. The results could also mean that physicists don’t understand WIMPs as well as they thought, and these particles actually interact more weakly with matter than what the theories tell us.

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NASA Has NOT Found the Building Blocks of Life on Mars

A “self-portrait” of the Curiosity rover on Mars: a composite of several images taken with the rover’s Hand Lens Imager.

The headlines are screaming it. NASA Mars rover discovers ‘building blocks’ for life: 3-billion-year-old organic matter, Curiosity Rover Finds Ancient ‘Building Blocks for Life’ on Mars, Building Blocks of Life Found on Mars, etc. etc. There’s only one problem. The building blocks of life were not found on Mars. I wish they had been. I think it would be awesome to find evidence of life on other planets besides earth. However, what NASA’s rover discovered on Mars wasn’t even close to the building blocks of life.

So what was really found on Mars? Not surprisingly, the title of the scientific paper that was published in the journal Science comes close to the truth:

Organic matter preserved in 3-billion-year-old mudstones at Gale crater, Mars

Now, of course, I think the “3-billion-year-old mudstones” is scientifically irresponsible, but notice the difference between the scientific article’s title and the title of the articles written by “science journalists.” There is no mention of life in title of the scientific article.

But wait a minute. Isn’t that just semantics? Doesn’t “organic” refer to chemicals that come from living things. Absolutely not! As I tell students in my elementary science book Science in the Industrial Age:

While organic chemicals are generally associated with living things, it is possible to make them from nonliving things…Scientists still use the terms “organic” and “inorganic” today to classify chemicals, but they do so based on the elements that make them up, not based on where they come from.

Now, of course, the news articles I linked above eventually get around to saying that it is possible for the molecules discovered on Mars to have come about without the presence of life. Even with that caveat, however, the news articles are still wrong, because the molecules discovered are not, in any way, the “building blocks of life.”

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Study Demonstrates that Most Animal Species Came Into Existence at the Same Time?

Most of an animal’s DNA is in the nucleus of the cell, but there is DNA in the powerhouse of the cell, which is called the mitochondrion.
In a comment on a previous article, a reader informed me of a study that I had not seen. It was published in the journal Human Evolution and its results are consistent with the idea that 90% of all animal species came into being at roughly the same time. This is certainly not what the hypothesis of evolution would predict, so some creationists as well as some intelligent design advocates have presented the study as evidence against evolution. In my reply to the comment, I expressed skepticism, even though I would love for the conclusions of the study to be correct. Now that I have read the study itself, I am even more skeptical.

The authors of the study analyzed the DNA of many different species of animals. However, they did not look at the DNA found in the nucleus of the cell. That DNA, called nuclear DNA, is responsible for most of an organism’s genetically-defined traits. They looked at mitochondrial DNA, which is the small amount of DNA that is found in the mitochondrion, the structure that produces most of the energy that the cell ends up using. To give you an idea of how different mitochondrial DNA is from nuclear DNA, the nuclear DNA of a human being is over 3 billion base pairs long, while human mitochondrial DNA is just over 16,000 base pairs long. You don’t need to know what “base pairs” are to see that there is only a tiny, tiny amount of mitochondrial DNA in a human cell compared to nuclear DNA.

Now even though there isn’t a lot of mitochondrial DNA, some sections of it seem to be very characteristic of the species of animal from which the cell comes. For example, a 2016 study analyzed a section of mitochondrial DNA (called the COX1 gene) among different species of birds. It showed that the COX1 gene alone was enough to separate 94% of the birds into species. Similar studies indicate that the COX1 gene can separate other species of animals, so the sequence of the COX1 gene is often referred to as the DNA barcode of the animal. This is what the authors of the study I am discussing focused on.

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The Final Mother/Daughter Comparison Between My Chemistry and Apologia’s Chemistry

In case you missed out on the first installment of this review, a mother and daughter have been comparing my chemistry course, Discovering Design with Chemistry, to Apologia’s chemistry course, Exploring Creation with Chemistry, 3rd Edition. This review came about because they had originally started using Apologia’s course, and it just wasn’t working for them. They started using my course, and it worked much better, as you can see in the previous installment as well as what you can read below. The comparison starts with the daughter’s perspective and ends with the mother’s perspective:

From the daughter’s perspective:

Last January, I wrote a comparison review for 3 modules of Apologia’s Exploring Creation, 3rd Edition, to 4 chapters of Dr. Wile’s Discovering Design with Chemistry. My overall view was that Apologia was very thrown together and confusing, while Discovering Design was more organized and enjoyable. In May of this year, I completed studying Dr. Wile’s Discovering Design with Chemistry, as well as reading over Exploring Creation; my original opinions remain the same as before. Though, there are a few more things I’d like to add in.

As I went through both texts, I discovered that the order of information and tone of writing is very important to how the student copes with the material. For example, Discovering Design is in conversational tone as if Dr. Jay himself were the one talking. He will often add in quick, funny or humorous things throughout the text especially when the topic starts getting heavy, which I find helps to release “chemistry stress.” Exploring Creation is also in a conversational tone, but it gets to be a bit confusing when a paragraph is giving an example using the pronoun “I,” and the student in this case has no idea who ‘I’ is.

In Discovering Design, Dr. Jay explains things to the point, builds on top of the material as chapters go on, and balances the difficulties of that material so that it doesn’t seem like too much. I can’t say any of this for Exploring Creation. While a few explanations are easy to understand, too often the book contains wordy paragraphs and unnecessary rules, and it’s difficult to grasp how any of the chemistry concepts taught are connected. In Discovering Design, you can’t wait to read the next section. In Exploring Creation, you can’t wait until you’ve finished the module.

I did come across a few frustrating things while studying Discovering Design. One was not being able to successfully complete experiments, because I couldn’t get the materials in the country where I live, and sometimes getting generally confused because, well, chemistry can sometimes be confusing. However, having said that, the experiments I was able to complete were excellent and helpful (For example experiment 10.4), the extra helps website helped overcome some of the confusion, and overall the course was really what I was expecting when I wanted to learn about Chemistry. I didn’t study Exploring Creation all the way through (On Your Owns and tests), but after just reading it, I don’t imagine a student would have a very good idea of the beauty of what chemistry really is; as Discovering Design does so well.

The last thing I can say is that Exploring Creation is like learning a bunch of mixed up chemistry facts, while Discovering Design is taking a thorough chemistry course.

S. White, student

From the mother’s perspective:

As we worked through Discovering Design, I found my thoughts were about the same regarding the teacher’s material. The fact that concepts are well-explained in the Discovering Design teacher’s manual helped a lot, as it has been a very long time since I have studied chemistry. Comparing the tests of the two texts, I especially noticed a difference in the weighting of the points for the test questions. In the Discovering Design tests, I felt there was a healthy balance between grading the math and grading the understanding of concepts, whereas Exploring Creation seemed to put too much weight on the math questions so that even if a student got everything right but two of the math questions, he could fail the test, which doesn’t seem to be right when a student has clearly mastered the concepts.

I would like to note here that Dr. Wile’s text is designed to take a normal school year, and as you can see, my daughter completed the entire text in 5 months. This was not because the text was too easy, but rather that my daughter dedicated 5 or 6 hours a day (and in some cases more) to chemistry in order to finish it before her graduation. I would not recommend this schedule to the average student.

L. White, teacher

Do “Climate Change” Skeptics Behave in a More “Sustainable” Way?

A few days ago, I ran across an interesting study that I think is worth discussing. Like most studies that try to understand human behavior, its results are incredibly tentative. Nevertheless, they are interesting, and they also are consistent with a trend that I have noticed among my colleagues and friends.

The researchers wanted to probe how a person’s belief in human-induced “climate change” affects his or her personal behaviors. They recruited 600 people from Amazon Mechanical Turk (I had never heard of it until reading the study), and assessed both their beliefs about human-induced climate change as well as their behavior when it came to four types of “pro-environmental” activities: recycling, using public transportation, purchasing environmentally-friendly consumer products, and utilizing reusable shopping bags.

One very important aspect of this study is that the researchers didn’t just do this once. They did it seven times throughout one year. That way, they could track beliefs and behaviors as they ebbed and flowed. Unfortunately, it is hard to keep people interested in a study like this, so while they started with 600 participants, only 291 actually completed all seven evaluations. However, some participants missed just a few evaluations, so an average of 413 participants were evaluated in each of the second through seventh analyses.

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Why You Must Read Multiple Opinions When it Comes to Evolution

I ran across an old article by Dr. David Berlinski. He is one of the more interesting proponents of intelligent design, since he does not believe in God but nevertheless thinks the natural world is obviously the result of design. In addition, he is an entertaining writer whose keen wit and disciplined thought help him cut to the heart of the issues about which he writes.

The entire article is worth reading, but for the purposes of this blog post, I will just give you the “executive summary.” The eye has always been a problem for flagellate-to-philosopher evolution. Not only does it seem so obviously designed, but developing an evolutionary history of the various eyes we see in nature has led to the incredible conclusion that eyes must have evolved independently in multiple evolutionary lineages. Nevertheless, those who fervently believe in evolution as a creation myth are convinced that it must have happened somehow. As a result, they tend to jump on anything that might support their fervent belief.

Enter Dr. Dan-Eric Nilsson and Dr. Suzanne Pelger, who published a scientific article entitled “A Pessimistic Estimate of the Time Required for an Eye to Evolve.” In this article, they sketch what they think might be a path by which a small circle of light-sensitive cells surrounded by a dark pigment and covered with a protective layer of tissue might evolve into a camera-type eye. In a series of eight drawings that they came up with in their own minds, they show how that circle of light-sensitive cells might form a depression, add a lens, and eventually come to resemble some of the eyes that we see in nature.

They measured four aspects of each drawing and assumed that those aspects could each change by 1% for every evolutionary step that was taken towards the next drawing. In the end, they estimated that it would take 1,829 steps to get from the first drawing to the last one. Using a simple equation that tries to estimate how many generations it takes to produce each evolutionary step, they arrived at the conclusion that it would take only 363,992 generations to get the job done. Since some organisms with eyes have generations that last a only a year, they suggest that in some cases, eyes could evolve in a mere 363,992 years.

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DNA Is Even More Complex Than We Thought!

Illustration of the i-motif structure of DNA formed from the standard double-helix structure.
(This figure is from the scientific article being discussed.)

DNA is a wonderfully complex chemical that we are still a long way from fully understanding. Its ability to store information is amazing. Experiments indicate that a single gram of DNA (a gram is approximately the mass of a U.S. dollar bill) can store 500,000 CDs worth of information! It uses a complicated system of alternative splicing so that a single region of the molecule can store the information needed to produce many different chemicals (see here and here, for example). It is so complex that even the best chemistry lab in the world cannot produce a useful version of it. In the end, the best human science can do is make tiny sections of DNA and then employ yeast cells to stitch those segments together so that they become something useful.

In 1953, American biologist James Watson and English physicist Francis Crick published a landmark paper describing the structure of DNA that we have all come to know: the double-helix. Since then, however, scientists have discovered at least 10 other structures that DNA can take on. One of the more interesting ones is called the i-motif structure, which is illustrated above. Rather than the well-known double-helix, it is a four-stranded, interlocking ladder.

This rather bizarre form of DNA was first discovered as a structure produced in the lab, and many biochemists thought that it couldn’t exist in most living organisms (especially humans), because it tends to form in acidic conditions. Human blood is just slightly basic (pH between 7.35 and 7.45), so it was thought that i-motif DNA wouldn’t be found in human cells. However, a new paper provides very strong evidence that i-motif DNA not only exists in human cells, but that it is constantly forming and unforming based on what is going on in the cell!

The researchers decided to look for this form of DNA in human cells by making an antibody that would bind only to the i-motif form of DNA. They tagged the antibody with a fluorescent dye that would glow green when the antibody attached. They demonstrated that the antibody was faithful to bind only to that form of DNA, and they put the antibody in the nucleus of a human cell. Using a microscope, they were able to see antibodies glow in several different places, indicating that i-motif DNA was, indeed, present in the nucleus.

What’s even more remarkable, however, is that the glowing regions turned on and off. This indicates that the i-motif structure was being made from the double-helix form and then transformed back into the double helix form. Why? There’s no solid answer to this question, but the researchers noticed that i-motif DNA tended to form a lot during transcription. If you don’t recognize that term, in order to make a protein, the cell must read the “recipe” for that protein from the DNA and then send that recipe to another place in the cell to make the protein. The first part of that process (reading the DNA) is called transcription, and the second part (turning it into a protein) is called translation. That means i-motif DNA is formed more frequently when the cell is starting the process of making a protein.

Because of this, the researchers suggest that the i-motif form of DNA provides some sort of regulation in the production of proteins. After all, the cell not only needs to know how to make proteins, but it also needs to know when to make them and how much to make. The “how” part is something we know pretty well. The “when” and “how much” parts are still quite mysterious to modern science. We have uncovered (and partially understood) some of DNA’s regulatory mechanisms, but as this new discovery of i-motif DNA in human cells indicates, we still have a long way to go.

DNA is just one of the many marvels in Creation that testify to the design ingenuity of the Creator, and the more we learn about it, the more I stand in awe!

Another Mother’s Day Drama

“Following Mommy” by Heldara Baltica (click for credit and license)

Yesterday was Mother’s Day, and once again, I came up with a short skit for church in honor of the event. Over the years, I have created several Mother’s Day skits, and I have posted two of them (see here and here). Interestingly enough, the first link is my most-viewed post for this year. Since that indicates at least some interest in Mother’s Day skits for church, I thought I would go ahead and post this new one as well.

Before I share the script, I would like to make a couple of notes. The only “set” I used for this skit was a single chair at center stage. I had a spot on the chair, and it was “loose” enough for the father to be seen well as long as he stayed close to the chair. You can put crumpled-up sheets of paper around the chair to indicate that Jack has been working hard, but that’s not necessary. Also, both readings (the bad poem at the beginning and the heartfelt note at the end) can be written in Jack’s notebook already, so that he need not memorize either piece. Finally, there is no reason for Jack to be a young man. You could change the name to Jill and use a young woman instead.)

As always, you are free to use this skit in any way that might edify the body of Christ. I would like to be credited if possible, but more importantly, I would like Christ to be glorified.

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