Category: Modern Science

Could This Be a Clue About the Origin of Pathogens?

A house finch, which is now susecptible to a new eye infection. (Click for credit)
The origin of pathogens is of particular interest to creationists. When God finished creating the world, he pronounced it “very good.” Now as I have pointed out previously, the term “very good” does not mean perfect. Nevertheless, it is hard to understand how disease-causing pathogens could fit into to a “very good” creation. So where did pathogenic organisms come from? One of the first steps toward an answer to that question came in 2003, when J.W. Francis proposed that microscopic organisms were created to serve as a link between macroscopic organisms and their physical environment. This link helped to channel necessary chemicals from the environment to the macroscopic organisms. However, when the Fall occurred, mutations began happening, and those mutations ended up turning beneficial microorganisms into pathogenic microorganisms.1

This makes sense in light of certain forms of cooperation between organisms. For example, a while ago I wrote about a relationship that exists between a grass that flourishes in hot soils, a fungus, and a virus. Scientists don’t know the details of the relationship, but they know that in order for the plant to grow in hot soils, it must be infected by a specific fungus. However, that fungus will not do the plant any good unless it is infected by a virus. Obviously, the fungus supplies some necessary chemicals to the plant, allowing it to live in hot soil. However, in order for the fungus to be able to do that, the virus must be providing necessary chemicals to the fungus. So in this situation, you have a viral link between the environment and a fungus, and then a higher-level link between the fungus and the plant. Obviously, if one of those links was corrupted, it could turn a beneficial relationship into a deadly one.

Over time, other creationists have suggested ideas for the origin of other pathogens. Dr. Peter Borger, for example, has a very interesting hypothesis on the origin of RNA viruses. He suggests that the genomes of all creatures were originally created so that they could produce fast adaptations to changes in their environment. As a result, all genomes contain variation-inducing genetic elements – sections of DNA that are specifically designed to produce changes that will aid in adaptation. He postulates that RNA viruses have been produced as a result of a corruption in certain variation-inducing genetic elements. This idea is intriguing because it solves the the RNA virus paradox, a recognized problem in the evolutionary literature.2

The real question, however, is what are the specific mechanisms by which this might happen? Exactly how could a beneficial microorganism (or genetic element) become pathogenic? As I was perusing the scientific literature the other day, I ran across an article in PLoS Genetics that might help us begin to answer that question.

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Arched Necks In Dinosaur Fossils: Is Water to Blame?

The position of the head and neck in this fossil is common among dinosaur fossils (Click for credt).
Relatively complete dinosaur fossils are fairly rare. Additionally, fossils in which the bones are essentially preserved in their proper arrangement (called fully articulated fossils) are even more rare. However, among these rare, fully-articulated fossils, there is a common feature: the head is often thrown back, curving the neck, as shown in the fossil on the left. This is so common it has its own scientific term. It is called the opisthotonic posture. Since it is so common among dinosaur fossils, it has been recognized for a long time. Indeed, the first reference to it in the scientific literature can be traced to a German paper that was written by A. Wagner back in 1859.1 Since then, paleontologists have been trying to figure out what causes this unusual “death pose.”

This investigation has produced a lot of speculation, but in the end, a study that was published in 2007 seemed to have settled the issue. It was done by a veterinarian, Dr. Cynthia Marshall Faux, and a vertebrate paleontologist, Dr. Kevin Padian. That seems like a perfect team when it comes to figuring out what’s going on here. The veterinarian would understand the various physiological and anatomical features of living vertebrates and how they would change during the death process, and the paleontologist would understand the details regarding the fossilization process. Their conclusion was:2

It is not postmortem contraction but perimortem muscle spasms resulting from various afflictions of the central nervous system that cause these extreme postures.

So according to Faux and Padian, the opisthotonic posture occurs at or near the time of death (perimortem) due to problems related to the central nervous system. It has nothing to do with what happens after death (postmortem). Their study got a lot of press and was considered by some to be the final say on the matter.

That is, until last year.

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Where the Conflict Really Lies, Part 2

In part 1 of my review of Dr. Alvin Plantinga’s book, Where the Conflict Really Lies: Science, Religion, and Naturalism, I spent all my time discussing how he deals with the superficial conflict between theism and science. That’s because Plantinga spends most of his book discussing the issue. When it is time to move on to the deep concord that exists between science and theism, you have reached page 191 of 350. I suppose he spends so much time on the issue because there is so much discussion of it in today’s society.

When Plantinga moves on to discussing what he sees as the deep concord between science and theism, he brings up many familiar arguments. He starts with the “fine tuning” argument, which says that science has found many, many aspects of the universe that would forbid life if they were much different from how we actually observe them:

For example, if the force of gravity were even slightly stronger, all stars would be blue giants; if even slightly weaker, all would be red dwarfs; in neither case could life have developed. The same goes for the weak and strong nuclear forces; if either had been even slightly different, life, at any rate life even remotely similar to the sort we have, could probably not have developed (p. 195)

Thus, it really does look like the universe was “rigged” to produce life, as the theist believes.

Plantinga also discusses the argument that turned me from atheist to creationist – the argument from design. When we observe nature, we see instances of the most exquisite design, which generally implies the existence of a designer. He says that the design argument isn’t an irrefutable argument for theism. After all, there are ways around it. However, they “add to the pile” of evidence for theism. Here is how he puts it:

…design discourses do support theism, although it isn’t easy to see how much support they offer. I realize that this is a wet noodle conclusion: can’t I say something more definite and exciting? Well, I’d love to; but my job here is to tell the sober truth, whether or not it is exciting. That obligation can sometimes interfere with telling a good story, but what can I say? (p. 264)

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Where the Conflict Really Lies, Part 1

I have written about Dr. Alvin Plantinga before (here, here, and here). He is arguably the most important Christian philosopher alive today and is largely responsible for the revitalization of Christian philosophy that took place in the mid-to-late 1900s. As my previous posts indicate, I don’t always agree with Dr. Plantinga. However, each time I have read one of his books or listened to one of his lectures, I have learned a great deal. As a result, I was thrilled to receive a copy of his newest book, Where the Conflict Really Lies: Science, Religion, and Naturalism for Christmas.

Like any serious book on science or philosophy, this is not an easy book to read. It’s not that Plantiga is hard to understand – quite the opposite. It’s just that he thinks very, very deeply. As a result, when you read his books, you also have to think deeply. Of course, the hard work is rewarded if you stick with it, but make no mistake about it – reading this book in its entirety is hard work. Now Dr. Plantinga has made it a bit easier for you if you don’t want to work quite so hard. The book is written in two fonts: a large one and a small one. If you read just the large font, you can understand the message of the book, but you won’t get bogged down by certain details. If you read the small font as well, you get the message of the book in all its philosophical depth. While that is challenging, it is well worth it.

Dr. Plantinga encapsulates the message of his book in an elegant phrase. He says that his overall claim can be summed up as follows:

There is a superficial conflict but deep concord between science and theistic religion, but superficial concord and deep conflict between science and naturalism. (p. ix)

Needless to say, I wholeheartedly agree with this statement. Interestingly enough, however, I agree with it for slightly different reasons from those that are given in the book.

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Silver Foxes Change Rapidly… and in Surprising Ways

In the experiment, farm-bred silver foxes went from being agressive towards people (left) to being friendly (right) in as little as six generations. (Photos from reference 1)

I recently read about a fascinating experiment that has been going on in Russia for the past 50 years. Dmitry K. Belyaev acquired some silver foxes from a farm that breeds them for their fur. The farm started about 50 years prior to the experiment, so several generations of foxes had experienced human contact to some degree. However, the foxes still did not care for human contact and were quite aggressive if they were forced into such contact.

Belyaev took this group of foxes and began trying to develop a new trait: tameness. Each fox was exposed to a human for a specific amount of time at specific ages. The fox was then evaluated based on how well it reacted to the human, and only the foxes with the best overall reactions to humans were bred. In a mere six generations, some foxes were born that not only enjoyed human contact, they actually craved it! This behavior became characteristic of the entire population, so that the foxes now behave like dogs – wagging their tails, whimpering, licking people, and generally doing all they can to interact with people.1

Now these results are cool on at least two levels. First, I was shocked at how quickly the foxes adapted to human socialization. For human-friendly foxes to appear in a mere six generations just astounds me. I know that dogs were domesticated from wolves, but I always imagined that it took a long, long time. After all, a lot has to change in order to take an animal that avoids people and is aggressive towards them and turn it into an animal that not only jumps up on your lap to cuddle with you but begs to be able to do so! According to this experiment, however, the change can happen quickly. Second, I just think it would be incredibly cool to have a pet fox. From time to time, I see a wild red fox in the neighborhood where I live. I would love to have such a beautiful animal as a pet!

Those are the cool aspects of the experiment. However, there are a lot more interesting aspects to the experiment, and they indicate that we still have a lot to learn when it comes to genetics.

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The Debate is Settled on Another “Vestigial Organ”

The Guiana dolphin's vibrissal crypts, which some thought were vestigial remains of whiskers (photo from reference 3)
Most dolphins are born with hairs on their rostrum. However, those hairs quickly fall out, leaving empty pits behind. The photograph on the left gives a rather striking example of these pits, which are often called vibrissal crypts. For a long time, there has been controversy in the scientific literature regarding what these pits are. Some have contended that they are leftover vestiges from when the ancestors of dolphins had whiskers1, while others have suggested that they serve some sort of sensory purpose.2

Wolf Hanke and his colleagues set out to settle this controversy for at least one species – the Guiana dolphin (Sotalia guianensis). As they say in the introduction to their study3

These vibrissal crypts are often described as vestigial structures lacking innervation and the characteristic blood sinuses [15,16], which are probably reduced in favour of the sonar system.

However, they indicate that there are some data that contradict this this idea, so they decided to do a detailed study of the Guiana dolphin’s vibrissal crypts. First, they examined the microscopic structure of the tissue. They noticed that each crypt had about 300 nerves plugged into it, which is more than the number of nerves plugged into a rat’s whisker. It seems obvious that there wouldn’t be such a large amount of nerve tissue wasted on a useless structure.

In addition, the tissue looked a lot like the electroreceptors found in the bill of a platypus which allow the platypus to detect electrical fields in the murky water where it lives. Why would the platypus want to sense electrical fields? Because whenever a muscle contracts, it sends out a weak electrical signal. As a result, a platypus can find prey without seeing or smelling it. All the platypus has to do is find the electrical signals being emitted by the prey’s contracting muscles.

So the microscopic structure of the tissue in the vibrissal crypts makes it look like the Guiana dolphin uses them to detect electrical signals, just as the platypus does. The scientists decided to put this idea to the test, and the results were astounding.

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You Never Know What They Will Discover…If You Let Them!

Tetrakis(nitratoxycarbon)methane, a theoretically-possible molecule discovered by ten-year-old
Clara L. Lazen.
Back when I was on the faculty at Ball State University, I was cleaning some platinum foils that I was using in my research. I brushed them with ethanol and then put them in a flame until they glowed red hot. By accident (which is often the way scientific truths are discovered), I found that if I passed a platinum foil back over (but not into) the ethanol while it was hot but no longer glowing, it would start to glow red hot again. When I pulled it away from the ethanol, it would stop glowing, but if I put it near the ethanol soon enough, it would once again begin to glow. I was fascinated by this effect and played with it for quite a while. The next day, I was teaching chemistry to a class of gifted-and-talented high school juniors, and I showed them what I had found. Then I gave them the “explanation” for it.

Platinum is a known catalyst, which means it tends to speed up a reaction without being consumed. In addition, alcohols are known to decompose into another class of organic molecules called “aldehydes,” and that happens quickly in the presence of the right catalyst. Thus, it was “obvious” what was going on: the platinum was catalyzing the decomposition of ethanol vapors into aldehyde vapors (specifically, acetaldehyde vapors), and the energy released by that reaction heated the already-hot platinum sufficiently to start it glowing red again. The students oohed and ahhed over the effect, and they dutifully wrote down my explanation in their notes. At the end of class, however, one of the students patiently explained to me that my analysis couldn’t be correct.

You see, she had done something I hadn’t bothered to do. She used the appendixes in the back of her book to calculate the energetics of the decomposition of ethanol into acetaldehyde, and she found that the reaction actually absorbed energy. It did not release energy. Thus, it could not be heating the platinum! Needless to say, I was rather impressed with this young lady’s analysis. The next class period, I told all the students that I was wrong and that I would look into the real explanation. However, I couldn’t find anything in the chemical literature that was relevant. As a result, I asked the young lady if she would work under my NSF research grant that summer and figure out what was really going on. She was surprised that I thought she could figure something like that out, but she said she would be happy to try.

It took her only a few weeks to learn what was really going on. Yes, the platinum was catalyzing the decomposition of ethanol into acetaldehyde, but that wasn’t what was causing the effect. Instead, the other product of that decomposition, hydrogen, was reacting with the oxygen in the air to make water. That reaction released the energy which caused the platinum to heat up enough to glow red hot again. This young lady’s work was so solid and elegant that we published a paper on her explanation of the effect.1

Why am I telling you this story? Because a friend of mine alerted me to an article that brought it all back to me in vivid detail.

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Motherhood Has a Lasting, Cellular Impact!

In pregnancy, the placenta is a barrier between the baby and the mother (Gray's Anatomy Image)
A very interesting writer named Amanda Read is a Facebook friend of mine. She has an amazingly diverse reading list, and she often posts things that she has read and found interesting. A while back, she posted a story about how a baby’s cells reside in his or her mother long after the baby is born, and that they may aid the mother in healing certain kinds of tissues. When I read the story she posted, I immediately expressed my skepticism. After all, we have an amazing immune system that fights any cells that are identified as foreign. Even though the baby develops in the mother’s body, there is a placenta that forms a barrier between the mother and the baby. It was obvious to me that a baby’s cells could not pass across the placenta, because the mother’s immune system would immediately attack them as foreign cells.

Well…it turns out that I was dead wrong. When I actually looked into the story, I found that while the story was a bit biased, the fact is that a baby’s cells do, indeed, cross the placenta, and they do, indeed, stay with the mother for a long, long time. In addition, the mother’s cells cross the placenta and stay with the baby for a long, long time. This phenomenon is called fetomaternal microchimerism, and believe it or not, scientists have known about for quite some time.

The first paper that discussed this phenomenon was written by Herzenberg and his colleagues in 1979. Published in The Proceedings of the National Academy of Sciences USA, the paper details how they found cells with Y chromosomes in mothers after pregnancy, but only if the baby was a male.1 Since a woman has no Y chromosomes, it was clear that the cells they found didn’t belong to the woman. The authors didn’t have the ability to use genetic testing to confirm that the cells belonged to the baby, but they showed that these Y-chromosome-containing cells appeared only when the mother had a baby boy. Thus, it was clear that the cells must be coming from the baby.

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The Appendix: More Evidence That the Creationist Prediction Is Correct

The Human Appendix (Gray's Anatomy Image)
For many, many years, evolutionists have called the human appendix a vestigial organ. In their view, our supposed ancestors needed a large cecum for digestive purposes. Over time, however, we evolved so that we didn’t need such a large cecum anymore. However, mutation and natural selection never got around to completely removing the large cecum and, as a result, we have a leftover, useless, small version called the appendix. As one evolutionist put it:1

…we have an appendix (a small remnant of a prior ancestor species’ intestinal sack) which not only is of no use to us but which can sometimes kill us when it gets clogged up and infected! What kind of god or other “intelligent designer” would design organisms with such useless, imperfect, wasteful, and sometimes even harmful physical features?

As I wrote previously, there is strong evidence that this evolution-inspired idea is incorrect. Evidence indicates that the appendix acts as a safe reservoir of the beneficial bacteria that usually populate your intestine. That way, when you have a disease that wipes out those bacteria, they can quickly repopulate your intestine so as to restore your normal level of health. This function conforms quite nicely to a creationist prediction made several years before this evidence began to mount.

Of course, a few pieces of evidence do not make a clear-cut case. As a result, it is important to test the idea that the appendix has a vital function in the human body by making predictions based on that assumption and then seeing whether or not the predictions are confirmed by the data. This has recently happened. In 2007, some medical scientists wrote a paper suggesting that the appendix served as a reservoir for the beneficial bacteria that live in our intestines.2 As a result, they predicted that if specific intestinal diseases were investigated, it should be found that people who have those diseases are better able to fight them if they have an appendix.

Well, a study that tested this prediction was recently published, and the prediction was dramatically confirmed.

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More on Comparing the Human and Chimpanzee Genome

A schematic representation of DNA, concentrating on the nucleotide bases that encode biological information. (Click for credit)
How similar is the human genome to the chimpanzee genome? Since both genomes have been fully sequenced, you would think that would be an easy question to answer. Unfortunately, it is not. After all, how do you compare the genomes of two different species? You might think that the most straightforward way would be to simply line the two genomes up and see how much they overlap. If that’s the way you are comparing the genomes, then the answer is relatively easy. Based on the analysis done by the Chimpanzee Sequencing and Analysis Consortium, about 75% of the two genomes overlap well. There is an error rate of about 3% within that overlap, however, so the two genomes are 72% similar based on this kind of analysis.

The problem is that simply lining two genomes up and looking for overlap might not be the best way to compare them. After all, it seems that genomes have been designed to change. Genes and their regulatory agents can move around, be copied to different parts of the genome, etc. As a result, when you compare genomes between species, you might need to be a bit more careful in how you do it.

One popular means by which geneticists compare genomes today is by looking at chunks of DNA in one organism and comparing them to the genome of the second organism. One common way to do this is to use the computer program called BLAST (Basic Local Alignment Search Tool). This program takes a chunk of DNA from one organism and splits it into a series of short sequences called “words.” It then looks through the genome of the second organism, trying to find regions where there is a lot of similarity with the words generated from the first organism. If the similarity is above a specified threshold level, BLAST scores it as an overlap, keeping track of precisely how similar the two sections of DNA are within that overlap.

In other words, rather than looking for long stretches of DNA that overlap between two organisms, BLAST looks for smaller regions of overlap. This makes sense, of course, since a given gene or a given regulatory piece of DNA takes up only a small part of the total genome. By comparing small parts of two genomes rather than the genomes in their entirety, you are better able to find the functional units within the DNA that are similar.

So…when scientists use a comparison method such as BLAST, how similar are human and chimp DNA? Surprisingly, the jury is still out on the definitive answer to that question!

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