Creationism Archives : Page 15 of 30 : Proslogion

Time to Redefine the Concept of a Gene?

As I posted previously, a huge leap in our understanding of human genetics recently occurred due to the massive results of project ENCODE. In short, the data produced by this project show that at least 80.4% of the human genome (almost certainly more) has at least one biochemical function. As the journal Science declared:¹

This week, 30 research papers, including six in Nature and additional papers published by Science, sound the death knell for the idea that our DNA is mostly littered with useless bases.

Not only have the results of ENCODE destroyed the idea that the human genome is mostly junk, it has prompted some to suggest that we must now rethink the definition of the term “gene.” Why? Let’s start with the current definition. Right now, a gene is defined as a section of DNA that tells the cell how to make a specific protein. In plants, animals, and people, genes are composed of exons and introns. In order for the cell to use the gene, it is copied by a molecule called RNA, and that copy is called the RNA transcript. Before the protein is made, the RNA transcript is edited so that the copies of the introns are removed. As a result, when it comes to making a protein, the cell uses only the exons in the gene.

By today’s definition, genes make up only about 3% of the human genome. The problem is that the ENCODE project has shown that a minimum of 74.7% of the human genome produces RNA transcripts!² Now the process of making an RNA transcript, called “transcription,” takes a lot of energy and requires a lot of cellular resources. It is absurd to think that the cell would invest energy and resources to read sections of DNA that don’t have a function.

In addition, the data in reference (2) demonstrate that many RNA transcripts go to specific regions in the cell, indicating that they are performing a specific function. Since there is so much DNA that does not fit the definition of “gene” but seems to be performing functions in the cell, scientists probably need to redefine what a gene is. Alternatively, scientists could come up with another term that applies to the sections of DNA which make an RNA transcript but don’t end up producing a protein.

There is another reason that prompts some to reconsider the concept of a gene: alternative splicing. The ENCODE data show that this is significantly more important than most scientists ever imagined.

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Surprising? Only to Evolutionists!

dna1 — The human genome is the sum of all the DNA contained in the nucleus of a human cell.
(Click for credit)

In 2001, the initial sequence of the human genome was published.¹ Not only did it represent a triumph in biochemical research, it allowed us to examine human genetics in a way that had never been possible before. For the first time, we had a complete “map” of all the DNA in the nucleus of a human cell. Unfortunately, while the map was reasonably complete, scientists’ understanding of that map was not. Despite the fact that scientists had a really good idea of what was in human DNA, they didn’t have a good idea of how human cells actually used that material.

In fact, there were many scientists who thought that most of the contents of DNA is not really used at all. Indeed, when the project to sequence the human genome was first getting started, there were those who thought it would be senseless to sequence all the DNA in a human being. After all, it was clear to them that most of a person’s DNA is useless. In 1989, for example, New Scientist ran an article about what it called “the project to map the human genome.” In that article, the views of Dr. Sydney Brenner were brought up. As the director of the Molecular Genetics Unit of Britain’s Medical Research Council, he was considered an expert on human genetics. The article states:²

He argues that it is necessary to sequence only 2 percent the human genome: the part that contains coded information. The rest of the human genome, Brenner maintains, is junk. (emphasis mine)

This surprising view was probably the dominant view of scientists during the 1980s and 1990s. Indeed, the article represents the idea that the rest of the human genome might be worth sequencing as being the position of only “some scientists.”

Now why would scientists think that most of the human genome is junk? Because of evolutionary reasoning. As Dr. Susumu Ohno (the scientist who coined the term “junk DNA”) said about one set of DNA segments:³

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?

Indeed, evolutionists have for quite some time presented the concept of “junk DNA” as evidence for evolution and against creation. In his book, Inside the Human Genome: A Case for Non-Intelligent Design, Dr. John C. Advise says:⁴

…the vast majority of human DNA exists not as functional gene regions of any sort but, instead, consists of various classes of repetitive DNA sequences, including the decomposing corpses of deceased structural genes…To the best of current knowledge, many if not most of these repetitive elements contribute not one iota to a person’s well-being. They are well-documented, however, to contribute to many health disorders.

His point, of course, is that you would expect a genome full of junk in an evolutionary framework, but you would not expect it if the genome had been designed by a Creator. I couldn’t agree more. If evolution produced the genome, you would expect it to contain a whole lot of junk. If the genome had been designed by a loving, powerful Creator, however, it would not. Well…scientists have made a giant leap forward in understanding the human genome, and they have found that the evolutionary expectation is utterly wrong, and the creationist expectation has (once again) been confirmed by the data.

The leap began back in 2003, when scientists started a project called the Encyclopedia of DNA Elements (ENCODE).⁵ Their goal was to use the sequence of the human genome as a map so that they could discover and define the functional elements of human DNA. Back in 2007, they published their preliminary report, based on only 1% of the human genome. In that report, they found that the vast majority of the portion of the genome they studied was used by the cell.⁶ Now they have published a much more complete analysis, and the results are very surprising, at least to evolutionists!

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It’s Amazing What RNA Can Do!

A sunburn comes from micro-RNAs that are released by damaged cells. (Click for credit)

One of the truly remarkable things about creation is how one substance can be used in nature to do all sorts of different jobs. Take ribonucleic acid, for example. Commonly referred to as RNA, scientists have known for quite some time that it is an integral part of how the cell makes proteins. A particular kind of RNA, called messenger RNA, copies a protein recipe contained in DNA, and it takes that copy to a protein-making factory called a ribosome. Once the recipe is at the ribosome, two other kinds of RNA, transfer RNA and ribosomal RNA, interact with the messenger RNA to build the protein in a step-by-step manner.

Because RNA is such an important part of how the cell builds proteins, some scientists speculated that this was its only job. In 1993, however, Victor Ambros, Rosalind Lee, and Rhonda Feinbaum found another job for RNA. Short strands of RNA, which are now called microRNAs, sometimes regulate how much of a particular protein is made in the cell.¹ Since then, other forms of RNA have also been shown to regulate the amount of protein produced in a cell. In addition, scientists have found that some types of RNA perform functions that aren’t even directly related to the production of proteins. For example, some types of RNA serve as “molecular guides,” taking proteins where they need to be in the cell, while other types of RNA serve as a “molecular adhesives,” holding certain proteins to other RNA molecules or to DNA.

Now even though the last two jobs I mentioned are not directly related to protein production, they still involve proteins. So is it safe to say that while RNA performs several functions in the cell, all of them are related to proteins in some way? I might have answered, “Yes” to such a question if a student had asked me that just a few weeks ago. However, a new paper in Nature Medicine has found a function for some microRNAs that has nothing to do with proteins. Some microRNAs serve as radiation detectors.²

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Move Over, Kindle. This Scientist Stored His Book on DNA!

book_dna — DNA stores information more efficiently than any human technology. (montage of Art from Kevin Spear and the public domain)

Everyone has heard of DNA, but many don’t appreciate its marvelous design. It stores all the information an organism needs to make proteins, regulate how they are made, and control how they are used. It does this by coding biological information in sequences of four nucleotide bases: adenine (A), thymine (T), guanine (G), and cytosine (C). The nucleotide bases link to one another in order to hold DNA’s familiar double-helix structure together. A can only link to T, and C can only link to G. As a result, the two linking nucleotide bases are often called a base pair. DNA’s ingenious design allows it to store information in these base pairs more efficiently than any piece of human technology that has ever been devised.

What you might not realize is that pretty much any information can be stored in DNA. While the information necessary for life involves the production, use, and regulation of proteins, DNA is such a wonderfully-designed storage system that it can efficiently store almost any kind of data. A scientist recently demonstrated this by storing his own book (which contained words, illustrations, and a Java script code) in the form of DNA.¹

The way he and his colleagues did this was very clever. They took the digital version of their book, which was 5.27 megabits of 1’s and 0’s, and used it as a template for producing strands of DNA. Every time there was a “1” in the digital version of the book, they added a guanine (G) or a thymine (T) to the DNA strand. Every time the digital version of the book had a “0,” they added an adenine (A) or a cytosine (C). Now unfortunately, human technology cannot come close to matching the incredible design of even the simplest living organism. As a result, while living organisms can produce DNA that is billions of base pairs long, human technology cannot. It can produce only short strands of DNA.² So while a single-celled organism could have produced one strand of DNA that contained the entire book (and then some), the scientists had to use 54,898 small strands of DNA to store the entire book.

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More on Mercury’s Magnetic Field

One of the many scientific successes of young-earth creationism involves planetary magnetic fields. In 1984, Dr. Russell Humphreys produced a model of planetary magnetic fields that not only explained the data that were available at the time, but it also made several predictions.¹ Over the years, many of those predictions have been borne out by the data (see here and here, for example). Compare this to the old-earth theory, which continues to struggle in accommodating the data that we already know (see here and here, for example).

Not content to rest on his laurels, Dr. Humphreys has continued to use his successful model to make more predictions. One of his recent predictions involved what MESSENGER (the latest unmanned spacecraft to visit Mercury) would learn when it measured Mercury’s magnetic field. The last spacecraft to visit Mercury was Mariner 10 back in 1974-1975, and based on some assumptions, it was able to measure Mercury’s magnetic field. Since that measurement was made more than 35 years ago, and since the young-earth model predicts that all planetary magnetic fields should decay fairly rapidly, Humphreys used his young-earth model to predict that Mercury’s magnetic field should have decayed by 4-6 percent since Mariner 10’s previous measurement. By contrast, the old-earth model predicted no measurable change.

Nearly five months ago, I wrote about the scientific paper that had been written regarding MESSENGER’s measurement. The main conclusion from the paper was that the shape of Mercury’s magnetic field is completely unlike what was assumed in the Mariner 10 measurement. As a result, I concluded that the new measurement could not be compared to the old one. That, of course, was a disappointing conclusion, since I was very interested in finding if the young-earth planetary magnetic field model was successful in yet another one of its predictions.

Interestingly enough, the first comment on the post suggested that the old Mariner 10 data should be reanalyzed now that we know the shape of Mercury’s magnetic field. That way, a proper comparison of the two measurements could be made. At the time, I suggested that the raw data probably still existed, but it might be hard to retrieve because of the changes that had taken place in computer technology. As a result, I wasn’t sure whether or not such a reanalysis could be done.

Well, even though a reanalysis of the raw data hasn’t been done, Dr. Humphreys has done the next best thing, and it does seem that the data at least partially confirm his prediction.

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Once Again, It’s Just Not That Simple…

coco — Two versions of the same species of coccolithophore - the heavily-calcified one is on the left
(image from the paper being discussed)

A few months ago, I discussed the acidification of the ocean. It is often called global warming’s “evil twin,” because it is caused by rising carbon dioxide levels in the atmosphere. Unlike global warming, however, the connection between carbon dioxide levels in the atmosphere and increasing ocean acidity is straightforward and has been confirmed by many observations. Thus, while it is not clear that increased levels of atmospheric carbon dioxide will lead to global warming, it is very clear that increased levels of atmospheric carbon dioxide lead to an increase in the acidity of the ocean.

The question is, “How will increased ocean acidity affect the organisms living there?” Many who call themselves environmentalists answer that question by saying increased ocean acidification will produce catastrophic results, threatening many species of ocean life. The reason? Many organisms that live in the ocean have shells made out of calcium carbonate. To make those shells, the organisms use carbonate ions that are dissolved in the seawater. However, as the acidity of ocean water increases, the concentration of carbonate ions in the water decreases. Thus, it is thought that increased ocean acidification will make it harder for these organisms to make their shells. Here’s how one publication from the National Academies puts it ¹

As ocean acidification decreases the availability of carbonate ions, these organisms must work harder to produce shells. As a result, they have less energy left to find food, to reproduce, or to defend against disease or predators. As the ocean becomes more acidic, populations of some species could decline, and others may even go extinct.

Now if that’s true, ocean acidification is a major problem. Indeed, if several shell-making organisms go extinct, we could be in real trouble.

However, this is a very simplistic way of looking at things. Yes, the availability of carbonate in the ocean will affect how easily shell-making organisms produce their shells. However, there are a host of other factors involved in the process. To single out one factor without considering the others is not very scientific. When all the factors are considered, the picture is not nearly as bad.

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Stone-Age Animation

Thaumatrope — When you flip this thaumatrope back and forth, it looks like the flowers are in the vase. (public domain image)

It’s sad to see how evolutionary thinking causes so many misconceptions in the realm of science. For example, evolutionary thinking has produced the idea that “stone age” people were primitive and barbaric. Of course, as is the case with most evolution-inspired ideas, this one doesn’t stand up in light of the evidence. The more research is done, the more we know that “stone age” people had an advanced culture all their own.¹ A recent finding that I just read about in Science News adds more evidence to support the fact that there was nothing very “primitive” about ancient people.

The article starts out like this:²

By about 30,000 years ago, Europeans were using cartoonlike techniques to give the impression that lions and other wild beasts were charging across cave walls, two French investigators find. Artists created graphic stories in caves and illusions of moving animals on rotating bone disks…

While it’s very interesting that ancient artists were painting scenes that produced the impression of motion, the thing that really caught my eye was the part about the rotating bone disks. The article has three pictures that show how one of them worked (you can see them here), and when I saw those pictures, I immediately recognized it as a thaumatrope. However, according to everything I have read, the thaumatrope was invented in 1825. For example, here is how Ray Zone puts it in his book, Stereoscopic Cinema and the Origins of 3-D Film, 1838-1952:³

The fundamental principle behind the movies is persistence of vision, when a visual impression remains briefly in the brain after it has been withdrawn. This principle was demonstrated in 1825 with an optical toy called the “Thaumatrope,” invented by Dr. John Ayrton Paris.

Obviously, Mr. Ray is off by a few years!

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Animal Magnetism

Many species of fish, such as the brown trout pictured on the left, hatch in streams and then travel away from those streams in order to mature. However, when it is time to reproduce, they end up navigating back to the same stream in which they hatched so they can spawn there. How do they accomplish this? How do they know where they are and which way to swim in order to get back to that special stream? Based on behavioral studies, scientists have thought that these fish are able to sense the earth’s magnetic field and use it as an aid in their navigation. However, the specific source of this magnetic field sense has been elusive…until now.

A recent study has shed a lot of light on this magnetic sense, at least for trout (and presumably other similar fish, like salmon). The authors of the study set out to determine what gives the trout their magnetic sense, and they developed a rather ingenious method to aid them in their search. First, they took tissue samples from the trout’s nasal passages, because previous studies indicated that there was magnetite (a mineral that reacts strongly to magnetic fields) in those tissues.¹ Then, they put cells from the tissues under a microscope and exposed the cells to a rotating magnetic field. In response, some of the cells rotated with the field.² You can actually see a video of this happening here! Just click on the links for downloading the movies.

This is a very simple, very sensitive method for finding the cells responsible for the trout’s magnetic sense. As you can see from the video, the cells that are sensitive to the rotating magnetic field are smaller than the other cells in the tissue. Also, the authors found that only 1 in 10,000 cells in the nasal tissue have a magnetic sense. No wonder these cells haven’t been found until now! Of course, as the authors studied the cells more closely, they found evidence of thoughtful design.

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One Gene = One Protein? Not Even Close!

In a previous post, I discussed alternative splicing, an amazing aspect of our DNA that allows it to store information in a compact, elegant way. In brief, a gene is actually a recipe that the cell uses to make a particular protein. Since most of a cell’s DNA is in the nucleus, the “recipe” stored in that gene must leave the cell’s nucleus in order to be turned into a protein. To do that, the “recipe” is copied by a molecule called messenger RNA (mRNA). The mRNA then takes the copied “recipe” out of the nucleus to the ribosome, which is where proteins are made.

In eukaryotic cells (the kinds of cells found in plants and animals), however, something very interesting happens before the mRNA leaves the nucleus. Some parts of the mRNA are cut away, and the remaining parts are then stitched back together. The parts of the mRNA that are cut away never leave the nucleus, so they are called introns (they stay IN the nucleus). The remaining parts that are stitched together are called exons (they EXit the nucleus). For a while, geneticists didn’t know the purpose of introns, so in typical evolutionary fashion, many decided that they had no purpose, and introns were lumped into the category of “junk DNA.” Of course, as we have learned more about genetics, we have learned that the evolution-inspired idea of “junk DNA” is, itself, junk, although some evolutionists still cling to it.

Nowadays, of course, we know the reason that introns exist. It is part of the design of the Creator, allowing DNA to store information in an incredibly efficient way. Each exon represents a “module” of useful information. If the cell stitches the exons together in one way, it makes one protein. If it stitches the exons together in another way, it makes a different protein. As a result, a single gene can actually produce many different proteins. The introns not only serve as a means by which the cell can identify the exons, they also regulate the amount of the various proteins that are being made.

This process of alternative splicing is illustrated in the figure below:

alt_spice — Because of alternative splicing, a single gene can tell the cell to produce different proteins. (public domain image)

In the previous post about alternative splicing, I discussed how recent evidence suggests that up to 95% of the genes in the human genome participate in this process. However, I did not address how many different proteins a single gene can produce using alternative splicing. In some cases, the answer is truly astounding.

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Another Example of Three-Way Mutualism. Is This Just the Tip of the Iceberg?

Over two years ago, I wrote about an interesting three-way mutualistic relationship between a virus, a fungus, and a plant. Less than a year later, I wrote about how people are actually walking ecosystems, participating in a huge number of mutualistic relationships with many different species of bacteria. Last night, while reading the scientific literature, I ran across another example of a three-way mutualistic relationship, and it is equally as fascinating!

This three-way relationship starts with seagrasses. Coral reefs are the “stars” of the marine world, but seagrass communities can be considered its “workhorses.” While they make up only 0.2% of the ocean’s ecosystems, they produce more biomass than the entire Amazonian rainforest!¹ Why are they so productive? Because they form a wide variety of marine ecosystems that serve as nurseries for many developing fishes and homes to a wide variety of sea creatures including turtles, manatees, shrimp, clams, sea stars, etc. Because of their amazing ability to support such ecosystems, seagrasses have been studied by marine biologists for some time. However, there has always been a nagging mystery associated with them.

The roots of seagrasses trap sediments which form a rich mud that is often several feet deep. The mud is rich because it contains all manner of decaying organic matter. However, the reason the organic matter decays is because bacteria decompose it. One of the byproducts of this bacterial decomposition is sulfide, and if that sulfide were allowed to build up to high concentrations, it would actually end up harming the seagrasses themselves. However, it never does. No one has proposed a satisfactory explanation as to why this doesn’t happen.

Certainly, the seagrasses transport oxygen to the mud through their roots, and that oxygen can turn the sulfide into sulfate, which is harmless to the seagrasses. However, detailed studies show that the sulfide produced by the resident bacteria accumulates far faster than it can be removed by the oxygen that is added to the mud through the seagrasses’ roots, especially during warm seasons.² Thus, there must be some other way that sulfide is being removed from the mud.

Marine biologists had no idea what this other way was…until now.

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