DNA Archives

January 6, 2026December 29, 2025

Orphan Genes Challenge Darwinism

The DNA in every cell in your body is made up of shorter strands called genes, which contain the instructions to produce various proteins. Neo-Darwinian evolutionary scientists look for genes with very similar sequences to others to show that one gene evolved from another through random genetic mutations. However, researchers are discovering genes that don’t resemble any other known gene. The technical term for these is taxonomically restricted genes (TRGs). These so-called orphan genes challenge Darwinism.

If all of life evolved from a common ancestor through small genetic mutations, orphan genes don’t fit this model. They either shouldn’t exist or should be extremely rare. A few years ago, evolutionists argued that only a small percentage of species’ DNA had been sequenced, and that with more research, the mystery of orphan genes would be resolved. However, the number of orphan genes continues to grow. The trend indicates that orphan genes challenge Darwinism.

Even closely related species that share a common trait can have their own unique orphan genes. In other words, the evidence does not support gradual changes caused by small mutations but instead points to entirely new, unique genes that have not been seen before. Evolutionists respond by saying natural selection can explain this, but they are unable to specify how. The research continues, but for now, it seems to me like an “evolution-of-the-gaps” argument.

As Jonathan Witt wrote in Salvo magazine, “Our uniform and repeated experience tells us that generating significant amounts of novel, functional information doesn’t happen by chance. It requires a mind. Our uniform experience tells us this, and probability calculations applied to everything from English text and software code to DNA confirm it.”

It’s safe to say that orphan genes challenge Darwinism and will likely continue to do so.

Reference: “Darwin’s Orphan Nemesis” by Jonathan Witt, in Salvo magazine, Spring 2025.

September 23, 2025September 22, 2025

First Responders in the Body

David Coppedge wrote a very interesting article about the body’s “first responders.” He described four instances where the body has its own superheroes ready in advance to handle and prevent crises that could lead to life-threatening diseases, such as cancer. These first responders in the body had to be present before they were needed. They are like police or firefighters who need the skill and training to come to the rescue when necessary. Planning and preparation indicate design.

One line of defense against infections is provided by cilia, which sweep the airways clean with wave-like motions. These hair-like structures are familiar, but recent research has shown that they provide upward as well as lateral flow to push fluids away from the airway surface. This action helps prevent bacteria, viruses, and harmful particles from reaching the cells of the airways and causing infections.

Another first responder removes toxic waste called reactive oxygen species (ROS) that develop in the cell’s mitochondria. Since these are toxic substances, ROS must be handled carefully. Organelles called peroxisomes detoxify these dangerous chemicals, sparing mitochondria from oxidative stress. This process requires two proteins that are resistant to toxins and produce a bridge that allows ROS to move safely between organelles.

This line of defense has been compared to the comic superhero, the Incredible Hulk. Dendritic cells that are part of the immune system travel through tissues looking for problems to solve, like cops on a beat. Usually, they slip through tissues, removing “bad guys” one at a time. However, when they come across a “mob” in their way, these narrow and flexible immune cells expand like the Incredible Hulk, with bulging muscles to push obstacles out of the way.

One of the first responders in the body is compared to Spartan warriors. It is the critical enzyme SPRTN. Before a cell divides, its DNA must be copied for the new cell. Unwanted proteins can latch onto the DNA strand and clog the copying machinery with cross-links called DPCs. That can lead to premature aging, cancer, or other problems. The SPRTN enzyme finds and repairs the clogs by degrading the proteins that cause them. SPRTN must degrade the clog without harming the surrounding tissue, and it does that by detecting ubiquitin tags that the DPCs carry. Understanding how SPRTN works enables scientists to develop strategies to enhance defense against age-related diseases and tissue damage caused by cancer therapies.

All of these discoveries were made through empirical observation by competent and respected scientists and reported in science journals. The first responders in the body are ready and prepared to serve and protect the human body. Like first responders to natural disasters, they are not there by accident but by a designed plan for defense and protection.

Reference: evolutionnews.org

September 19, 2025September 18, 2025

The Homochirality of Organic Molecules

Yesterday, we discussed the chirality, or handedness, of molecules, especially amino acids and proteins. The homochirality of organic molecules refers to their requirement for the same handedness, a mystery that has puzzled scientists since 1848, when Louis Pasteur first observed that some life-essential molecules had mirror-image forms. Amino acids used by living cells and the proteins they build have left-handed chirality, while DNA, RNA, and the sugars forming their building blocks are all right-handed. These facts raise a question for those who believe life arose spontaneously.

Left-handed proteins and right-handed DNA are found in all living organisms. The spiral structure of DNA needs to twist in a specific direction to function properly, but what caused the right-handed sugar molecules to come together? When half of all amino acid molecules in nature exhibit right chirality and the other half left, what force could have gathered only the left-handed ones to form the first proteins?

Scientists have speculated that cosmic rays or polarized light might have triggered this process. However, even if such forces created an initial bias for the same-handedness, they could not sustain and amplify it enough to produce a significant number of homochiral molecules to form the first living cells. In 1999, researchers proposed that electron spin created magnetism, causing left-handed peptides (short chains of amino acids) to bind to magnetic surfaces like magnetite. But this still did not explain how the homochirality of organic molecules could be amplified sufficiently to generate living cells.

Some scientists consider RNA to be the key to the origin of life. In 2009, a group of researchers studying RNA molecules suggested that a crystal called RAO could react to produce two of RNA’s four nucleotides. In 2023, other researchers used magnetism to produce RAO crystals with homochirality. However, this process required a magnetic field 6,500 times stronger than Earth’s magnetic field. Additionally, RAO has only been shown to produce two of RNA’s four nucleotides, still falling short of generating the complete homochirality of molecules needed for life.

As 2024 ended, NASA-funded research identified a problem with the so-called “RNA world” hypothesis. Simulating early Earth conditions, they found that RNA did not show a chemical bias toward selecting homochiral amino acids. The current thinking is that the homochirality of organic molecules “could have emerged through later evolutionary pressures.” In other words, we have the “evolution-of-the-gaps” theory because, of course, evolution can do anything you can imagine.

Currently, NASA scientists are analyzing samples brought back from asteroid Bennu, hoping that molecular evidence from meteorites and asteroids will demonstrate that the building blocks for life came from beyond Earth. I suspect that the force responsible for bringing life to Earth did originate outside our planet, and even beyond the universe.

References: science.org and nasa.gov

June 13, 2025June 13, 2025

Fruit Flies and Humans

The genetic data contained in DNA is rich in information. The DNA in living cells contains molecular genes that direct the synthesis of proteins necessary for the development of an organism’s body during embryonic development . As we mentioned in a previous post, the DNA of a fruit fly is 60% similar to that of a human. How can we explain the significant difference between fruit flies and humans?

How can similarities exist in the DNA of organisms that look and function very differently? According to Stephen C. Meyer, “scientists have found that the larger informational context in which genes are expressed often determines the specific function of the proteins they produce.” For example, Meyer notes that a corresponding gene in insects and vertebrates regulates the production of appendages. However, in fruit flies, it regulates the development of compound limbs with exoskeletons and multiple joints. In sea urchins, it regulates the development of spines. In vertebrates, it regulates the development of limbs with internal bony skeletons and multiple joints.

Orthodox evolutionary theory suggests that since genes control the development of anatomical structures, the corresponding genes should produce corresponding structures in various organisms. That would eliminate the differences between fruit flies and humans. Clearly, genes perform different functions based on the larger context of information in the organism. The context contains specified information that is key to the differences.

You could compare this context variability to words in an English text. The same words used in a different context can convey a very different meaning. Words can convey their intended meaning when they are used in a systematic, organized structure composed by an intelligent mind. A hodgepodge of random words can result from non-intelligent actions, but only intelligence can create a meaningful paragraph. What does that tell us when we apply that principle to genetics? Only intelligence can create a meaningful paragraph, and only intelligence can create fruit flies and humans.

Reference: Signature in the Cell by Stephen C. Meyer, pages 471-472

May 7, 2025May 28, 2025

Evidence for Design in Nature

On our websites, we often talk about evidence for design in nature. When average people see the amazingly organized structures in living organisms, they can’t help but feel that they must be designed. Even Richard Dawkins, the evolutionist best known for his worldwide atheism campaign, said that living systems “give the appearance of having been designed for a purpose” (The Blind Watchmaker, page 1). Of course, he adds that it is only an illusion. Atheist Francis Crick, who with James Watson, discovered the helical structure of DNA, warned biologists that they must “constantly keep in mind that what they see was not designed, but rather evolved” (What Mad Pursuit, page 138).

The intuition of design is nothing new. Plato and Aristotle saw evidence for design in nature and thought there must be a mind behind it. Of course, they could not know about the information-rich DNA molecule and the intricate structures within every living cell. They didn’t even know about cells. Even Charles Darwin thought that cells were just jelly-like protoplasm. He had no idea that there are machines, transportation vehicles, gates, duplicators, inspectors, and trash collectors within the cell wall in a city-like structure.

The more we learn about the inner workings of living things, the more we see design evidence not even imagined in previous years. Every living cell has a DNA molecule containing the instructions for building the proteins and structures required for that living creature. Computer pioneer Bill Gates wrote, “DNA is like a computer program, but far, far more advanced than any software ever created” (The Road Ahead, page 188). Even Richard Dawkins wrote, “The machine code in the genes is uncannily computer-like” (River Out of Eden, page 17).

Is there evidence for design in nature? Let me ask another question. Has any computer program ever created itself by chance, or did an intelligent mind write it? Apply that thought to the living things you see every day.

February 13, 2025February 10, 2025

Neanderthal DNA and Being Human

The 1856 discovery of human-like specimens that looked different from modern humans baffled scientists. Anthropologists named the specimens Neanderthals after the place where they were discovered, the Neander Valley in present-day Germany. The Neanderthals had a larger brain than modern humans, but the head was flattened, and the skull had a heavy bone structure. The media portrayed the find as a missing link between apes and humans. Atheists jumped on the discovery by saying it proved human evolution and showed that the biblical account was fantasy. Today, Neanderthal DNA reveals their relationship to modern humans.

In 1912, Jim Thorpe won two gold medals at the Summer Olympic competition. Thorpe was a native American member of the Sac and Fox tribe. He was exceptionally strong and had numerous physical characteristics similar to the fossil remains of the Neanderthals. Thorpe was racially different but not a different species.

In 2010, researchers published the Neanderthal DNA genome sequence. Comparisons between that data and modern humans confirm that modern humans have Neanderthal DNA in their genome. In addition to the new genetic information, when researchers dig into places where they found Neandertal remains, they also discover the remains of complex tools, plant-based medicines, and storage of staples such as flour for making food. Evidence also suggests the use of symbols to communicate and ritual treatment of the dead. These things indicate that Neanderthals are not a missing link but an early race of humans.

The Bible does not define humans based on their physical makeup. Artists have depicted Adam and Eve as white-skinned, blue-eyed, six-foot-tall, attractive Caucasians. In my travels around the world, I have seen Adam and Eve portrayed as people of color, orientals, and even pygmies. What defines humans is not our physical appearance but our spiritual makeup. That is how we are created in the image of God.

The Bible’s description of how God created the physical human body is that we are made from the dust of the earth. (See Genesis 2:7 and 3:19.) No matter what our physical bodies are like, we are all one and are all created in God’s image. (See Genesis 1:27 and 9:6.) That concept permeates the biblical account. It helps us understand the teachings of Christ, that we are to love (agape) our neighbors and even our enemies.

— John N. Clayton © 2025
Reference: Scientific American magazine for February 2025, pages 43 -47 and scientificamerican.com

April 12, 2024April 10, 2024

Then It Would Be Alive!

Origin of life research has occupied scientists for years. The media often exaggerates claims that science is getting close to creating life. “Creating RNA life in a lab” is a headline in a recent issue of The Week magazine. The story is about the Salk Institute in La Jolla, California, developing a molecule of ribonucleic acid (RNA) “that could generate accurate copies of another type of RNA.” The article went on to say, “This brings the researchers one step closer to their ultimate goal of creating an RNA molecule that can make accurate copies of itself.” The study’s co-author Gerald Joyce said, “Then it would be alive.”

Ribonucleic acid (RNA) is a polymeric molecule essential for most biological functions. It has a structure similar to deoxyribonucleic acid (DNA), which carries the genetic information in every living cell. The scientists have created the macromolecule RNA in the laboratory by combining smaller molecules. To say that if an RNA molecule could reproduce itself, “then it would be alive” is an exaggeration.

As an analogy, let’s suppose I want to make a new car, which I would call a Claytonmobile. I get an engine out of a Ford, a transmission out of a Honda, a chassis out of a Chevy, and an interior out of a Royals Royce. I put these together and announce to the world that I have created a car. In reality, what did I do? I took things already created and assembled them, but I didn’t create anything. Some of you old timers may remember the Tucker automobile, which was very much like what I just described.

This same process is happening in the scientific community attempting to create life. The goal of the group at La Jolla is to form an RNA molecule that can make copies of itself. The researchers say, “Then it would be alive.” That means they are changing the definition of life that most of us learned in biology classes from high school through graduate school. That definition says life is that which can move, breathe, respond to outside stimuli, and reproduce. When researchers can get RNA to reproduce, they will have satisfied one of the parameters, but they certainly will not have created life.

The more we know of the creation, the more we understand the wisdom and power of the Creator. In Proverbs 8:17-23, Wisdom, personified as a woman, says that those who seek her will find her and that her fruit is better than gold or silver. In verse 22, she says, “The Lord possessed me in the beginning of His way before His works of old. I was set up from everlasting, from the beginning before the earth was.” The complexity of RNA and DNA and of life itself is a great apologetic for the existence of God. We need to listen to the words of Wisdom.

Reference: The Week for March 29, 2024, page 21, reporting on a Washington Post story.

December 28, 2023December 27, 2023

Major Factors for Rejecting Faith in God

Polls show that belief in God among Americans has declined over the past few years, and most dramatically among Gen-Zers. Generation Z is the term used to describe those born between the late 1990s and early 2000s (approximately 1997 to 2012). This generation grew up with access to the internet and portable digital technology. What are some major factors for rejecting faith in God?

Stephen C. Meyer said that the Discovery Institute surveyed people if they agreed with this statement: “The findings of science make the existence of God less probable.” Among self-proclaimed atheists, 65% agreed, and 43% of agnostics agreed. What these people perceive about science has influenced their belief in God. However, as we have said before, science supports faith in God.

In recent years, scientific discoveries have given us more reasons to believe in God. One significant discovery is that the material universe had a beginning. Evidence for that appeared in the 1920s, was confirmed in the 1960s, and further reinforced in the 21st century. The Bible tells us that in verse 1, but it took scientists years to accept the evidence. Anything that begins to exist must have a cause. The cause of the material universe must be outside of time and space and, therefore, immaterial. Science recognizes that time, space, matter, and energy all had a beginning, but they could not have created themselves.

A second discovery that points to an intelligent Creator is that the universe was fine-tuned for life from the beginning. Many physical constants must be precisely as they are for life to exist. More than that, without precision fine-tuning of the physical laws and constants, the universe itself would not exist. Chance cannot explain the precision because so many precise factors must work together.

A third discovery that came into a fuller understanding in the 21st century is the design of the digital code in the DNA molecule that makes life possible. This design has been there since the emergence of the first living cell. We have no examples of information being created without a mind to create it. Information does not happen by chance.

In those three recent discoveries, science rediscovers God. Then what are the major factors for rejecting faith in God? More on that tomorrow.

Reference: Stephen C. Meyer on “Has Humanity Forgotten God” on YouTube

December 13, 2023December 12, 2023

A Pleasing Concert – The Parable of the Piano

When a piano performance concludes, who gets the applause? Is it the piano or the pianist? The piano is designed to create specific musical sounds, but without the pianist, the piano does nothing. The pianist’s skill makes a piece of furniture become a musical instrument to produce a pleasing concert that brings joy to everyone.

Let’s think of the piano as the DNA that provides a blueprint for our bodies. The human genome is the complete sequence of the information the DNA supplies. It includes genes that code for proteins as well as non-coding genes. This is a greatly simplified description of something infinitely more complex than a piano. The piano’s keys, hammers, and strings cannot be an adequate comparison to the human genome, but it will suffice for our parable.

So, in the piano concert, the pianist is the one who ultimately determines whether the performance is good or bad. The actions of the pianist can produce a pleasing concert that brings joy and pleasure to the audience. Or the pianist can make everyone uncomfortable. The pianist is the person everyone sees and applauds or the one that people boo.

If the piano is the DNA, then we are the pianists. Our DNA does not determine the quality of our lives. It may give us opportunities for success or have defective parts that make success in life more difficult. But we choose how we play the concert, and how we play can bring joy to others despite our limitations.

However, it is not just people to whom we can bring joy or pain. There is a piano Designer. In this life, He has not given each of us the same quality piano. The parable of the talents tells us that. But the Creator expects us to use what we have to make music pleasing to those around us and, ultimately, to Him.

How can we present a concert that even the Creator will applaud? He hasn’t left us without guidance. The Creator also gave us the musical score to follow. Read it, learn from it, and practice it every day. And when people applaud the pleasing concert, remember to give the credit to the One who created the piano and wrote the music.

April 21, 2023April 19, 2023

What Are the Chances?

Advocates of unguided naturalistic evolution say that evolution could have gone in many directions, and we are lucky to be here. But what are the chances of evolution producing you and me as we are today? Evolutionists would say the changes are 100% since we are already here. But, if we go back to the cosmic creation event, or “big bang,” the chances that we would have evolved are nil. On the other hand, if God planned and guided the creation because He had us in mind, the chances are 100%.

The DNA that makes us who we are physically is a highly complex strand of information. What are the chances that it could have written itself by chance? First of all, information comes from intelligence, not chance. Calculating the likelihood of something after it has happened is a statistical fallacy. After all, DNA is here, and so are we, so the chances are 100%. But what are the chances if we go back before the fact? What are the chances that non-living chemicals could come together in a just-right way to form the first living cell? Then what is the statistical evidence for that first cell multiplying and modifying by random chance mutations and natural selection to create humans?

One imagined scenario involves a billion chimpanzees typing on a billion keyboards for a billion years, accidentally typing one line of Shakespeare. What are the chances of that? Well, the short answer is that it will never happen. Computer keyboards have various numbers of keys, but the old-fashioned typewriters had 58, so let’s go with that number.

Forget Shakespeare. Look for the line “I love you more.” without quotation marks. That is a total of 16 letters, spaces, and a period. With 58 keys and 16 letters, what are the chances of accidentally typing that line? To compute that, you would have to multiply 58 X 58 X 58 X 58 X 58 X 58 X 58 X 58 X 58 X 58 X 58 X 58 X 58 X 58 X 58 X 58. That is a total of 16 times. If you want to try it, go ahead, but it will probably exceed the capacity of your calculator. The answer would be 16.4 trillion quadrillion typing attempts.

Typing continuously at a speed equivalent to 45 words per minute, it would take 2,100 trillion years to have a 50/50 chance that one of those chimps would type that phrase. Absolutely nobody thinks that the Earth is anywhere close to 2,100 trillion years old. Nobody even suggests that the universe is that old. For this thought experiment, we are only looking for one short line of text, “I love you more.” That is nothing compared to the complex system of life on this planet.

The bottom line is that we can’t explain life or the fine-tuned physical constants of the universe by chance alone. But we can explain those things if God planned and guided the creation because He had us in mind. With God, our chances of being here were 100% from the beginning. (See Genesis 1:1.)

Reference: “Chances are…” by Bob Berman on Astronomy.com

For more on this topic see “Arranging Books on a Shelf“