Category: Modern Science

DNA Is Even More Complex Than We Thought!

An Illustration of DNA.
Author: Kevin Spear
James D. Watson and Francis Crick are credited with determining the basic structure of DNA. They had been studying an enormous amount of data that had been collected on DNA, and in a brilliant flash of insight, they came to the conclusion that DNA is shaped like a spiral staircase. The “stairs” on the staircase were composed of two nucleotide bases linked together. There are four nucleotide bases in DNA: adenine (A), thymine (T), cytosine (C), and guanine (G). In their model, A could only link to T and C could only link to G. This has become the generally-accepted view of DNA’s molecular structure, and a simplified illustration is shown on the left.

One of DNA’s elegant features is that the nucleotide bases are linked together with hydrogen bonds. Unlike their name implies, hydrogen bonds aren’t really chemical bonds at all. Instead, they are very strong attractions that exist between a hydrogen atom on one molecule and another atom (typically oxygen or nitrogen) on another molecule. Because hydrogen bonds are not true chemical bonds, they are not nearly as strong as chemical bonds. As a result, they can be “broken” with only a small amount of energy.

It turns out that this is the perfect design, because in order for DNA to code for proteins, the double helix must “open up” to expose the nucleotide bases. To do this, the link between the nucleotide bases must be broken. If the nucleotide bases were held together with chemical bonds, it would take a lot of energy to break the link, and that energy could easily damage the other bonds in DNA. Since the nucleotide bases are linked with hydrogen bonds, however, it takes only a small amount of energy to break the link. As a result, DNA can “open up” very easily, and the rest of the molecule is not harmed when that happens.

Watson and Crick determined all this, including exactly where the hydrogen bonds formed. Not surprisingly, the way in which the links form is called Watson-Crick pairing. Well, it turns out that there is another way the nucleotide bases can pair up, and a recent study shows that this is yet another amazing design feature of DNA.

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Here’s How Desperate Naturalists Are Becoming

This illustration shows that some molecules form two isomers that are like hands. They are mirror images but are not superimposable.
(Image courtesy of NASA)
Naturalistic evolutionists face many problems, most of which are the result of the fact that science doesn’t support what they want to believe. As a result, they must make up desperate explanations to work around what science clearly says. Nowhere is this more true than in origin-of-life research. Serious scientists understand that life comes only from other life. That’s what all the data clearly demonstrate. However, a naturalistic evolutionist simply cannot believe that. As a result, he or she must cook up wild scenarios by which nonliving chemicals can react with one another to magically create life.

Of course, there are countless problems with such wild scenarios. Demski and Wells recount many of them in their book, The Design of Life. Simon Conway Morris has an even more devastating review of the various origin-of-life scenarios in his book, Life’s Solution. One of the many intractable issues in any naturalistic origin-of-life scenario is chirality.

There are many molecules that have the same chemical formula but are quite different chemically. Glucose, for example is the sugar found in green, leafy vegetables. Fructose, on the other hand, is the sugar found in fruit. They are chemically quite different (which is why they taste different), but they have the exact same chemical formula: C6H12O6. They are chemically different because despite the fact that they contain exactly the same complement of atoms, the atoms arrange themselves into differently structured molecules. We call such molecules isomers.

There are many kinds of isomers, and one specific kind is a stereoisomer. Consider your hands. They are mirror images of one another. If you hold them together at the palms, your fingers and thumbs all match. However, if you try to lay one of your palms on the back of your other hand, your fingers and thumbs will not match. Your thumbs, for example, will be on opposite sides. In other words, while your hands are reflections of each other, they cannot be superimposed on one another. There are molecules like that as well. They are mirror images of each other, but there is no way you can turn one of the molecules around and make it look exactly like the other molecule. Such molecules are called stereoisomers. Because they are like your hands, we actually refer to one stereoisomer as the “left-handed” isomer and the other as the “right-handed” isomer.

An example of such a molecule is shown in the sketch above. The amino acid alanine can be formed two ways. Like your hands, those two molecules are mirror images of each other, but there is no way you can turn one of those images into an exact replica of the other. If a molecule has a stereoisomer, it is called a chiral molecule, and chiral amino acids cause all sorts of headaches for those who want to believe that life sprung from nonliving chemicals.

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If You Thought Some of My Other Posts Were Geeky…

A tortoiseshell cat helps explain genetics in light of X-inactivation. (Click image for credit)
A few posts back, I commented on some experimental genetic results that throw a real monkey wrench into the generally-accepted view of the evolution of gender. Part of that post dealt with the concept of X-inactivation, the process by which one of a woman’s X chromosomes is inactivated so that she has no more functional X chromosomes than a man. A commenter known as jsilverheels then asked an excellent question, which I attempted to answer.

All of that discussion related to chromosomes, dominance, recessiveness, etc. got me thinking about sex-linked inheritance. It’s a common subject taught in high school biology, and it is something I discuss in my biology textbook. However, X-inactivation seemed (in my mind) to contradict something that is routinely taught in most high school biology courses. I searched the web for an answer to this apparent contradiction, but to no avail. No matter what kinds of keywords I used, I couldn’t find an article that addressed this particular problem.

As a last resort, I ended up E-MAILing my sister-in-law. My wife is brilliant, and she comes from a family of brilliant people. Her oldest sister is not only an accomplished molecular biologist, she is also a dedicated college professor. I knew she would have the answer to this question, but I hate to bother people who are busy doing such productive things. Nevertheless, I really wanted an answer, so I broke down and sent her the question. Not surprisingly, she answered it straightaway. I thought I would blog about it, mostly so I would remember it later on.

WARNING: If you thought what I have posted before was geeky, you probably won’t like what appears below the fold!

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Who Cares About The Data? Don’t Question the Dogma!

Sterile worker ants tend their queen (the large one), her eggs, and her developing young
(Click image for credit)

Some of the most successful animals in creation have complex social structures. Consider the picture above. The queen ant (the large one in the picture) is the only one that can reproduce. The worker ants that tend the queen, care for her young, gather food, clean the nest, and protect the nest are sterile. They typically live short, dangerous lives so that the queen can live a long, safe life and produce many offspring.

When you look at the world through the simplistic lens of evolution, one obvious question is, “How could such social structures evolve?” If evolution is based on the idea of the survival of the fittest, why would individuals evolve to protect and care for some other individual? Worse yet, why would they evolve to become sterile, so that only the individual they are protecting and caring for can reproduce? Darwin tried to answer these questions with the concept of “group selection.” He thought that under certain circumstances, natural selection could work on a group of organisms instead of just on individuals. Evolutionists pursued this idea for quite a while, but then a more fashionable idea came along.

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Oh No! He’s Wrong Again!

Susumu Ohno is famous for postulating the existence of “junk DNA.” In his paper introducing the term, here is what he wrote about DNA sequences that he thought were nonfunctional:1

Our view is that they are the remains of nature’s experiments which failed. The earth is strewn with fossil remains of extinct species; is it a wonder that our genome too is filled with the remains of extinct genes?

Of course, as time went on, we slowly learned how wrong Ohno was in this assessment. While many DNA sequences are not used to produce proteins, specific functions have been found for much of this supposed “junk.” Indeed, as more and more functions have been found for more and more “junk” sequences, it is becoming increasingly clear that very little junk exists in the genome.

While Ohno did some marvelous work in his illustrious career, much of it was hampered by the blinders of evolution. When you are compelled to believe that nothing but natural processes are responsible for life, you simply cannot see the deep complexity of creation. As a result, you force simplistic ideas on science, whether the data support them or not. The idea that much of an organism’s genome could be filled with “junk DNA” is a perfect example of how evolutionary thinking produces absurd conclusions.

Recently, Yuanyan Xiong and colleagues have laid to rest another evolution-inspired idea that originated with Susumu Ohno.

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Should I Feel Stupid FOR Running or Just AFTER Running?

Runners in the Zurich Marathon of 2008. Click Image for credit.

An infrequent but enjoyable commenter (Black Sheep) recently asked a question that I thought I would answer with a post. The relevant portion of the comment is:

A friend and I are always puzzled by the way our bodies, or rather minds, react after a run. This really only tends to happen when we do longer runs, like when we were training for a half marathon. After we finish, whether it be a race or just a training run, we feel completely stupid…why the diminished mental capacity?

Some might argue that a person who wants to do such a long run is actually starting out with a diminished mental capacity. However, there is actually a very good reason for why you can feel stupid after a long run, even if you started with a keen mind. You will find the answer below the fold.

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The Amazing Design of Human Tears

Tears do some amazing things!
(click image for credit)
You probably don’t think about them very often, but tears are amazing. They are produced continually by your body’s lacrimal glands in order to lubricate your eyes as well as various tissue membranes associated with your eyes. They generally drain away through two structures called the lacrimal punctua. This is why you normally don’t notice your tears. However, if your lacrimal glands start producing tears too quickly for them to be drained away, they collect in your eyes until they eventually fall down your cheek. At that point, you (and other people) notice them, because you are crying.

There are two reasons for crying: eye irritation and strong emotions. If dust or other debris gets into your eyes, your lacrimal glands start producing a lot of tears in order to flush out the debris. All creatures with moveable eyes can cry because of irritation. I will call the tears produced by this kind of crying “irritant tears.” The chemical content of irritant tears is not all that surprising. In addition to oils for lubrication, water, and salt, they contain a powerful enzyme called lysozyme. This broad-spectrum antibiotic helps to prevent eye infections.

The second reason for crying has inspired today’s blog. A friend of mine sent me a news story regarding some new research that has been done on tears that are the result of emotion. Interestingly enough, she I and disagree strongly on what should trigger emotional tears (I am an old sap – she rarely cries for emotional reasons), but she knew the story would be of interest to me. When I looked a the study that generated the news story, it reminded me of some old research that was done on tears. Together, the old and new research tell us a lot about how amazing tears are.

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Exaggeration about the Great Pacific Garbage Patch

This Good Morning America segment is typical of the ridiculous exaggeration regarding a real problem
In my previous post, I promised to discuss two scientific frauds that have recently come to light. The first had to do with research related to vaccines. The second one is the topic of this post, and it has to do with an environmental issue. The environmental issue is a real one, but unfortunately, it has been exaggerated to such an extent that many will pass it off as just another environmental extremist scare now that the science related to it is better understood. To get an idea of the exaggeration, you can click on the YouTube video and see how Good Morning America reported on it.

The man being interviewed in the video is oceanographer Charles J. Moore. He is generally credited for discovering the “Great Pacific Garbage Patch,” which is a real environmental problem. Oceans have constant circular currents called gyres. When a bit of plastic gets caught in such a current, the current tends to trap it there. Over time, this leads to a large concentration of plastic in that area of the ocean.

In general, most ocean travelers avoid the gyres, as they are a nuisance to navigate through and do not hold a wealth of the kind of ocean life people typically want to see or harvest. However, he and his team decided to travel through the gyre that exists in the North Pacific. He calls it a “subtropical high,” and here is his description as found in the journal Natural History1

Yet as I gazed from the deck at the surface of what ought to have been a pristine ocean, I was confronted, as far as the eye could see, with the sight of plastic. It seemed unbelievable, but I never found a clear spot. In the week it took to cross the subtropical high, no matter what time of day I looked, plastic debris was floating everywhere: bottles, bottle caps, wrappers, fragments.

This is what was eventually named “The Great Pacific Garbage Patch.” In his article, Moore says that another marine researcher, Curtis Ebbesmeyer, estimates the size of the garbage patch to be roughly that of the state of Texas. He and some colleagues also published a paper that supposedly measured the mass of plastic found in the Great Pacific Garbage Patch and found that it is six times the mass of the plankton found there.2

Now all this seems incredibly dire. However, it is nothing more than a fraud.

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Anti-Vaccine Researcher Andrew Wakefield Committed Fraud

Science is self-correcting. Over time, mistakes made by scientists are generally uncovered by other scientists. Sometimes, the mistakes are found quickly. Often, the mistakes take a long time to uncover. But mistakes are simply that: mistakes. Creation is very complex, and as scientists, we can often be fooled by that complexity. What we see as the “obvious” conclusion from a study might not be the correct conclusion at all, because there is often an underlying complexity that was not considered. So while many, many mistakes happen in the course of doing science, it is to be expected. Thus, when a scientist is found to have made a mistake, it doesn’t mean the rest of the scientist’s work is worthless. Even very good scientists make mistakes.

Scientific fraud is another matter altogether. While no scientist should be condemned for making mistakes, all scientists who commit fraud should be strongly and vigorously denounced. There have been two reports of scientific fraud that have come out over the past two days, and I consider it my duty as a scientist to make sure my readers are informed of them. I will discuss the first (and most egregious) in this post.

It involves the nonsensical idea that vaccines cause autism. This idea has been thoroughly tested by various scientific studies, and it is simply wrong. Indeed, I debated a proponent of this idea recently. The debate was hosted, produced, and heavily advertised by an anti-vaccination group. It went so poorly for my opponent that all mention of it has been wiped away from the anti-vaccine site.

Despite the fact that the conclusions of science could not be clearer when it comes to vaccines and autism, there are many people who still believe that vaccines cause autism. Many of them are followers of Andrew Wakefield, the one responsible for the the fraud I wish to discuss in this post.

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What Makes Bone So Strong?

Even this electron microscope image of hydroxyapatite crystals in bone doesn't reveal its amazing secret.
(Public domain image)
Bone is a truly incredible substance. It is as strong as steel but at as light as aluminum. Not only is it strong, but it is surprisingly flexible as well. As is the case with most things God made, human technology cannot come close to producing something with bone’s amazing properties. Consider, for example, the work of Antoni Tomsia at Lawrence Berkeley National Laboratory in California. He and his colleagues are trying to artificially produce something with the characteristics of bone, but they simply cannot come up with anything as elegant and sophisticated as bone. He says:

People want a strong, light, and porous material, which is almost a contradiction in terms, but nature does it…Bone is made from calcium phosphate and collagen, which are both extremely weak. But nature mixes them together at room temperature and without toxic chemical [sic] to create something that is very tough — this fascinates us.

What makes bone so special? The short answer is that we don’t really know. However, we are learning. For quite some time now we have known that bone is a mixture of many things, principal among them a protein called collagen and a calcium compound called hydroxyapatite. The collagen gives bone its flexibility, while the hydroxyapatite gives bone its strength.

However, the hydroxyapatite in bone is stronger than hydroxyapatite made in the lab. Why? It has to do with the size of the crystals. When hydroxyapatite is made artificially, the individual crystals that form are very large. In bone, the crystals are very small, on the order of 3 billionths of a meter long. These nanocrystals have long been thought to be the reason that hydroxyapatite in bone is so strong. However, scientists haven’t been able to understand why the nanocrystals stay so small in bone.

Now Klaus Schmidt-Rohr and his colleagues might just have figured that part out!

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