Proslogion : Page 58 of 113 : Thoughts from a scientist who is a Christian (not a Christian Scientist)

DNA Is Even More Sophisticated Than We Thought!

DNA_wide — The information in DNA is stored in sequences of four different nucleotide bases (A, T, C, and G). In a gene, three nucleotide bases code for a specific amino acid, and that three-nucleotide-base sequence is called a 'codon.' (click for credit)

Over the years, scientists have learned a lot about DNA. Nevertheless, the molecule continues to surprise us with its exquisite design. Not long ago, scientists demonstrated that a single gram of DNA can store about 500,000 CDs worth of information. It has also been shown that the code used by DNA to store this information has been specifically designed to allow living organisms to respond to their environment in many different ways. In addition, we know that DNA stores its information in “modules” that can be rearranged in many different ways. This allows a single stretch of DNA to contain many different meanings, depending on how the modules are put together.

In the December 13 issues of Science, researchers have demonstrated yet another incredible design feature of DNA, and according to the University of Washington, the scientists who made the discovery were “stunned.” To understand what was done and what the discovery means, however, you need a little bit of background information on DNA and how it is used by the cell.

DNA stores its information in sequences of nucleotide bases called adenine (A), thymine (T), guanine (G), and cytosine (C). As shown in the illustration above, those nucleotide bases link together to hold DNA in its familiar double helix shape. The meaning of each sequence depends on where it is in the molecule. In many organisms, a small fraction of the DNA is made up of genes, and in most of the organisms with which you and I are familiar, the genes consist of two regions: exons and introns. The exons of a gene contain the recipe that tells the cell exactly how to make a protein. This recipe is given in groups of three nucleotide bases, which are called codons. Each codon specifies a certain chemical called an amino acid. When the cell stitches amino acids together in the sequence given by the codons, it makes a useful protein.

Introns are “spacers” that exist between the codons in a gene. Once derided by evolutionists as “junk DNA,” we now know that introns are a powerful means by which the exons are split up into functional information modules. The cell can stitch the modules together in different ways, so that a single gene can instruct the cell on how to make many different proteins. This is called alternative splicing, and it is a incredibly powerful design feature that allows DNA to store its information with amazing efficiency. Indeed, thanks to alternative splicing, there is a single gene in fruit flies that can tell the cells to make 38,016 different proteins!¹

Now don’t get lost in all the terminology. Think of it this way: genes tell the cell how to make proteins. However, to increase the information storage capability of DNA, these genes are split into two regions: exons and introns. The introns separate the exons into modules of useful information, and the cell stitches those modules together in different ways so that a single gene can tell the cell how to make lots and lots of different proteins.

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Some “Vegetative” Patients are Probably at Least Partially Aware

coma — An EEG image of a person in a vegetative state listening to a list of words that contains the word to which he is attending and a bunch of distractor words. (click for credit)

The Royal College of Physicians defines a vegetative state as:¹

a clinical condition of unawareness of self and environment, in which the patient breathes spontaneously, has a stable circulation, and shows cycles of eye closure and opening that may simulate sleep and waking

When I read this definition, a question immediately arises: How do you know whether or not a person is aware of himself or his environment? You might ask him a serious of questions, but if he doesn’t have the ability to move his mouth or other parts of his body, how can he make you aware of his responses?

A few years ago, Dr Steven Laureys made headlines with his pronouncement that a man in a coma was able to communicate with people when given the aid of a keyboard and someone to support his hand as he typed. Based on Dr. Laureys’s work, it seemed that the man was describing exactly what you might think is going on in the mind of a person who is aware of himself and his surroundings but cannot communicate with the outside world. However, as skeptics started pointing out the flaws in Dr. Laureys’s method, further tests were done, and it turns out that the person supporting the patient’s hand was actually directing the patient’s hand. In other words, the patient wasn’t communicating; the helper was.

So what can we say scientifically about such patients? If they cannot do anything to communicate with the world, how do we know whether or not they are aware of it? A collaboration of scientists from Cambridge University, the University of California at Los Angeles, and the University of Western Ontario have gotten us a step closer to answering that question. They have published a study in the journal NeuroImage: Clinical that might help us produce a method by which an aware patient can communicate, even if he is not able to do so by traditional means.

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Chromosome Fusion? It’s Getting Harder and Harder to Believe.

People have 23 pairs of chromosomes, for a total of 46 chromosomes. Most apes have 24 pairs of chromosomes, for a total of 48 chromosomes. One very popular piece of genetic evidence for the idea that humans and apes have a common ancestor is that human chromosome 2 looks like two chimpanzee chromosomes that have been stitched together. As the evolutionary story goes, the common ancestor between apes and humans had 24 pairs of chromosomes, and it initially passed them to those animals that began evolving into apes and humans. The apes kept that number of chromosomes, but after the human lineage split off from the chimpanzee lineage, something happened to fuse two of the chromosomes, leading to only 23 pairs of chromosomes in humans. As Dr. Francis Collins puts it:¹

The fusion that occurred as we evolved from the apes has left its DNA imprint here. It is very difficult to understand this observation without postulating a common ancestor.

This idea has been around for a long time, but I never put much stock in it. Why? Because even if human chromosome 2 is the result of two independent chromosomes being fused together (an example of which is shown in the illustration above), I don’t see why this can only be understood in the context of evolution. After all, we know that chromosome fusion events happen in human beings today.² Thus, if human chromosome 2 really is the result of a fusion of two chromosomes, it could have happened early in the history of human beings. It need not have happened to some hypothetical evolutionary ancestor. Any event that restricted the human population to those who arose from the people who originally experienced the chromosomal fusion would then fix that chromosome in the population. A worldwide Flood in which a single family was saved would be one example of such an event.

Regardless of whether or not human chromosome 2 is evidence of common ancestry, it’s getting hard to understand how it could even be the result of two chromosomes fusing.

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Insults Do Not an Argument Make

darwins_doubt — This book by Dr. Stephen Meyer has elicited a lot of insults from its critics, but not much reasoned response.

Nearly two years ago, I wrote a review of double-doctor Alister McGrath’s book Why God Won’t Go Away. It ends with an amusing anecdote about a young man who meets Dr. McGrath and asks him to sign one of his theology books. The young man tells Dr. McGrath that he has Richard Dawkins to thank for his conversion to Christianity. He had read Dawkins’s The God Delusion and thought it was so unfair and one-sided that he had to look at the other side. When he did, he become convinced of the reality of Christianity.

While one might pass this off as an isolated incident, it’s not clear that’s the case. Not long ago, I blogged about another person who was raised Catholic but became an agnostic in her teens. She read The God Delusion and similar works, thinking it would drive her to atheism. Once she read Dawkins and his fellow New Atheists, however, she read authors on the other side of the debate. In comparison, she found the arguments of Dawkins and his ilk intellectually deficient, so she returned to her Catholic faith.

Note what happened in both of these cases. Each person decided to look at both sides of the issue. They looked at the arguments of those who claimed there is no God, and they looked at the arguments of those who claimed there is a God. Both decided that those who argued against the existence of God had a significantly weaker position. As a result, they ended up believing in God.

But what makes the arguments of the New Atheists so weak? It’s not just that they have little evidence to back up their claims. It’s more than that. I think one of the reasons their arguments are so weak is that they try to make up for their lack of evidence with insults and bluster. Somehow, they think they are making their case stronger, but to most reasonable people, it has the opposite effect. A few days ago, I ran across a story that makes this very point.

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An Explanation that is Not Exactly Iron-Clad

tyran1 — Tyrannosaurs like this one were thought to have gone extinct 65 million years ago, but soft tissue has been found in one Tyrannosaurus rex fossil. Soft tissue has also been found in several other fossils that are supposed to be millions of years old. (click for credit)

In 2005, Dr. Mary Schweitzer shocked the scientific world by reporting soft tissue in a Tyrannosaurus rex fossil that is supposed to be 68 million years old.¹ While many scientists who are more interested in their preconceptions than they are in the data tried to dismiss her findings, several other examples of soft tissue in fossils that are thought to be millions of years old have been found (see here, here, here, here, and here). In the end, it has become nearly impossible for a thoughtful scientist to conclude anything other than the fact that there is soft tissue present in some fossils which are thought to be millions of years old.

Now, for someone who truly believes in an ancient earth, it’s very hard to explain how soft tissue can remain in a fossil that has been in the ground for millions of years. Even for a young-earth creationist like myself, it is still a difficult thing to understand. Soft tissue tends to decay in a matter of days or weeks. From a chemical point of view, it is hard to understand how it can stay soft for even a few years, much less hundreds, thousands, or even millions of years. Fortunately, Dr. Schweitzer has continued her studies on soft tissue in dinosaur fossils, and she has found at least one chemical mechanism by which soft tissue can be preserved for significantly longer than anyone expected.²

She and her colleagues began by examining soft tissue from her T. rex fossil as well as a Brachylophosaurus canadensis fossil. While the T. rex fossil is supposed to be about 68 million years old, the B. canadensis is supposed to be about 76 million years old. Nevertheless, under a transmission electron microscope, both are seen to harbor soft vessels that are probably blood vessels. Interestingly enough, however, the vessels have tiny particles of iron embedded in them.

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The Plastisphere

plastic_ocean — What happens to the plastic floating in the oceans? It turns out, quite a lot! (click for photo credit)

Quite a while ago, I wrote an article about the Great Pacific Garbage Patch, which ended up being included in a book entitled Opposing Viewpoints Series – Garbage & Recycling. While the magnitude of the problem is severely overstated in nearly every popular treatment of the subject, it is a real problem. It came about as a result of the fact that some of the plastic which is not disposed of properly ends up in the oceans. A lot of that plastic gets stuck in gyres – permanent circular currents that exist in distinct regions of the seas. In most cases, once the plastic gets stuck in the gyre, it doesn’t leave.

So what happens to this plastic over time? Does it decay? Does it just float there forever? How badly is it affecting the ecosystem of the gyre? A new paper published in Environmental Science and Technology attempts to partially answer these questions. The authors sampled plastic marine debris (PMD), as well as the water in which it was floating, from several different spots in the North Atlantic. They then studied it with a scanning electron microscope (SEM), Raman spectroscopy, and DNA sequencing. The results were fascinating!

The authors found a rich diversity of microscopic organisms living on the plastic.¹ In fact, the diversity was so rich that they have decided the plastic supports its own little biological community. As a result, they call the plastic and the organisms living on it the Plastisphere. It’s probably correct to think of it this way, because the organisms living on the plastic are quite different from the ones living in the water where the plastic floats.

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An Odd View of an Old Debate

Carl Strock is a journalist-turned-columnist who recently retired from the Schenectady Gazette after 25 years of service. After he traveled to Israel and wrote some decidedly anti-Israel columns, the Gazette received numerous complaints. In response, his editor told him to stop writing about Israel for a while and submit all of his columns to her for editing. This bothered Strock, because he saw it as censorship. After continuing his columns with less frequency, he eventually retired. However, he has not stopped writing. He has a blog at the timesunion.com and has written a book, From D’burg to Jerusalem, The Unlikely Rise and Awful Fall of a Small-Town Newsman.

Why am I writing about Mr. Strock? Because in his book, he mentions a debate he had with me back in 2006. I had actually forgotten about the debate, but when a reader in Schenectady told me about being mentioned in his book, I recalled the event. I got his book and planned to read the entire thing, but it just isn’t my cup of tea. However, I did read some parts of the book, including the chapter that discusses the debate. I found his view of that event to be very odd.

Here’s what prompted the debate: Strock had written some columns in the Gazette regarding creationism and intelligent design. Since he obviously knew little about either subject, his columns provoked some rather heated responses, which he seemed to find surprising. Eventually, he tired of people pointing out his ignorance, so he said:

I will meet any of them in open forum, and we’ll see who’s ignorant of what. (p. 161)

A student who was using one of my textbooks at the time contacted me, and (of course) I agreed to meet Mr. Strock in open forum. Strock was surprised, but he agreed to the debate. I thought the debate was amatuerish but informative. Based on what he has written in his book, he obviously disagrees.

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The Bacterial Flagellum: More Sophisticated Than We Thought!

flagellum1 — This is a schematic of a bacterium's flagellum (image in the public domain).

The bacterial flagellum is a symbol of the Intelligent Design movement, and rightly so. After all, bacteria are commonly recognized as the “simplest” organisms on the planet. Nevertheless, their amazingly well-designed locomotive system has continued to amaze the scientists that study it. In 1996, Dr. Michael Behe highlighted the intricate design of the bacterial flagellum in his book, Darwin’s Black Box. While some have tried to explain it in terms of Neo-Darwian evolution, they have not come close to succeeding.
Not only is the bacterial flagellum amazingly well-designed, it is far more versatile than anyone imagined.

Some bacteria (like Escherichia coli) have multiple flagella, which makes it very easy for an individual to navigate in water. All the bacterium has to do is adjust which flagella are spinning and how they are spinning, and the single-celled creature can do acrobatics in the water. However, the vast majority of bacteria have only one flagellum. It was thought for a long time that because of this, it is difficult for them to make sharp turns in the water.

Two years ago, this thinking changed abruptly when a group of physicists from the University of Pittsburgh showed that the bacterium Vibrio alginolyticus, which has only one flagellum, can make sharp turns with ease. They showed that in order to execute such a turn, the bacterium backs up, lurches forwards, and swings its flagellum to one side.¹ The entire maneuver takes less than a tenth of a second and results in a 90-degree turn. So not only is the bacterial flagellum an exquisite “outboard motor” that propels the bacterium through the water, it is also a rudder that allows the bacterium to make sharp turns at will!

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Sofishsticated Swimming

This is a glass knifefish like the one used in the study (click for credit)

Many aspects of nature are a mystery to science, and at least part of the reason is that nature has been designed so incredibly well. There are systems running in nature that are simply too complex for us to understand and, as a result, their functions remain a mystery. Not all that long ago, for example, many biologists were silly enough to actually think the human genome was mostly junk, simply because they couldn’t understand what the vast majority of the human genome does. Of course, as we have learned more about DNA, we have learned that what was once considered “junk” is vitally important (see here, here, and here, for example). Since the Encode project published its first major results, most reasonable biologists have slowly started to realize what creationists have said all along – there really isn’t much (if any) junk DNA.

Even on a larger scale, there are many aspects of nature that are very hard to understand. A recent article in the Proceedings of the National Academy of Sciences of the United States of America provides an example:¹

Animals often produce substantial forces in directions that do not directly contribute to movement. For example, running and flying insects produce side-to-side forces as they travel forward. These forces generally “cancel out,” and so their role remains a mystery.

Why would a moving animal expend energy to produce forces that are perpendicular to its motion? Those forces don’t contribute to the animal’s forward motion, and they tend to cancel each other out. As a result, they are often called “antagonistic forces.” Such forces seem like an utter waste of energy. Nevertheless, lots of animals do this. In addition, some animals exert antagonistic forces even when they are not moving in a given direction. Hummingbirds, for example, produce antagonistic forces when they are hovering over a flower.

To understand the purpose of antagonistic forces, the authors of the study examined the glass knifefish (Eigenmannia virescens). When this fish is “hovering” in the water, it uses its fins to produce antagonistic forces. It has been thought that these forces might improve the fish’s ability to control its position and orientation in the water, but no one understood how.²

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Overly Honest Moments in Science

I don’t tweet. If you have been reading this blog for any length of time, you know why. I have a hard enough time constraining my writing to a few hundred words, much less 140 characters. Nevertheless, it is interesting to see how scientists use Twitter to communicate what they are doing. For example, I recently wrote about a particle physicist who used Twitter to explain to people what was happening in the Fukushima nuclear power plant disaster. He became a bit of a celebrity as a result and has used that platform to do some serious science related to the level of radioactive contamination in Japan’s food supply.

Why in the world am I discussing a social media tool that I don’t even use? Because a reader posted a link on my Facebook page. It contains a series of tweets posted with the hashtag #overlyhonestmethods, which was started by a scientist known as “dr. leigh.” The hashtag has become a bit of a phenomenon. Essentially, scientists use it to explain the real reasons behind some of their methods.

The picture at the top of the post is a classic example of a tweet that contains the hashtag. I immediately related to it, because as a nuclear chemist, I have built a lot of systems that blew up or failed in some other spectacular way. However, when I finally got a version of the system to work, I would refer to it as “representative.” That’s just the way it is done.

If you have some time, scroll through a few of the tweets. Some of the language can be a bit foul, but the tweets give you a brief glimpse into the real world of scientific research. You might be a bit surprised at what you read!