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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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And Now For Something Completely Different

An infrequent but very entertaining commenter on this blog is known for thinking that there is just too much science at this stop on the information superhighway. While I disagree, I can at least understand the substance of the complaint. As a result, I would like to post something quite different today. For those who don’t know, I was (at one time) a professional actor, and I have dabbled from time to time in the writing of scripts. Recently, my church asked me to write and produce a “sermon-length” play. I have always been fascinated by the great men and women of Christendom, so I chose to honor the church’s request by writing a play about John Newton.

There is quite a lot of artistic license in the play, but I tried to be faithful to at least the broad strokes of Newton’s life and his abolitionist work. If you are looking for something completely different from genetics, radioactivity, and evolution, perhaps you might enjoy a 30-minute interlude by clicking on the link below.

Please note that the original link that was presented in this article no longer works. This is an updated version of the play. Unfortuantely, the main camera went out during the presentation, so the video ends in very poor quality.

Amazing Grace: The Script

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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Sorry, “Black Sheep.” Science IS Sexy

In a recent comment, the poster known as “Black Sheep” stated, “No matter what you think, science isn’t sexy.” I beg to differ. Just read these chemistry pickup lines, listed in the December 20, 2010 edition of Chemical and Engineering News (p. 56):

“I’m cobalt and you’re nickel. Let’s make an alloy.”

“I’d like to form a covalent bond with you.”

“If I could rearrange the periodic table, I’d put U and I together.”

“You’re lutetium and I’m vanadium. Together, we’re in LuV.”

“Our love will be like sodium in water: brief, explosive, and hot.”

And here’s my favorite:

“You’re so hot, your electrons are changing state.”

If that’s not sexy, I don’t know what is!

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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Discriminating Homeschoolers Lead to Excellent Curriculum

This news segment discusses the errors in some school textbooks.
A Facebook friend of mine (I honestly thought I would never use that term) recently posted the video on the left. It discusses several errors that are found in U.S. school textbooks. With the post, she noted, “I am so thankful and blessed we are able to homeschool!” As I reflect on her comment, I realize that there is a profound truth expressed there.

Several of my posts related to home education discuss the fact that homeschool graduates are, on average, head and shoulders above their peers. That was my experience when I taught at the university level, and it is the conclusion of many academic studies. There are several reasons that a home education tends to produce superior students, and I have explored some of them in the posts linked above and in articles I have written for homeschool magazines. However, I think my Facebook friend’s post provides yet another: Homeschooling materials are, on average, superior to what you find in most schools.

Like many true statements, this one is a bit counter-intuitive. After all, teachers choose the materials that are used in schools. While teachers are generally not experts in their field, they are at least more knowledgeable in their field than most parents. As a result, you would expect teachers to choose better educational materials than parents. Nevertheless, as someone who has examined the science texts used in schools and the science texts used in homeschools, it is my opinion that the ones used in homeschools are, on average, superior.

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A New Kind of Vaccine

The mosquito that carries dengue
(Click Image for credit)
As I have mentioned previously, vaccines are one the greatest medical advances God has allowed us to discover. They work by “pumping” your immune system so that it is ready to repel a pathogen (like a virus or bacterium) before you are infected. That way, your immune system doesn’t have to figure out how to fight the pathogen. It already knows what to do, and that gives it a head start, making your body much less likely to succomb to the disease.

Of course, the best way to prevent infectious disease is to prevent the infection to begin with. We try to do that with good sanitary practices, but they can only go so far. Regardless of how well we clean our surroundings, pathogens still manage to infect our bodies. In fact, some research is now indicating that we might be a bit too sanitary for our own good.

Medical historians are convinced that the rise in polio the U.S. experienced in the late 1940s and early 1950s was caused by good sanitary practices. When sanitary practices were rather poor, people were regularly exposed to small amounts of the polio virus, usually when they were babies and therefore had the extra protection given to them by the antibodies they received through their mothers’ milk. Their immune systems were able to conquer the weak exposure to the virus with the help of their mothers’ antibodies, and thus they became immune. As sanitary practices improved, however, fewer people were exposed to small amounts of the virus as infants. As a result, when they were exposed to concentrated amounts of the virus (from a person who already had the disease, for example), they would succumb to the disease.1

Some medical researchers take the lesson from the history of polio a step further. They believe in the hygiene hypothesis, which suggests that if a child grows up in an environment that is too clean, he or she will be more likely to contract a host of diseases later on in life, because the child’s immune system was not challenged enough early in life. While the data are not clear enough to determine whether or not the hygiene hypothesis is reasonable, there are some interesting studies that lend support to it.

So…is there a way to prevent infection of a specific parasite without making our surroundings “too clean” and without injecting something into people? The surprising answer might be, “Yes!”

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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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