Intelligent Design Archives : Page 8 of 17 : Proslogion

Desperately Seeking Innovation

One of the biggest problems facing evolutionists is the explanation of how brand new information can be added to a genome. After all, if flagellates eventually evolved into philosophers, an enormous amount of truly original information had to be added to flagellates’ (and their descendents’) genomes. However, genomes are so well-designed and highly-structured, it is difficult to imagine a naturalistic process that could add information to them. Nevertheless, evolutionists have tried their best. One of the more popular notions is gene duplication followed by mutation. We know that genes can be duplicated. It happens quite frequently. The thought is that when a gene is duplicated, one of the copies can continue to produce the protein it is supposed to produce, while the other copy is free to mutate and find some completely new function.

While the thinking behind this idea is logical, experimental evidence to support it has been hard to find. As a result, evolutionists tend to jump on any experimental finding that might suggest the idea is accurate. This is well illustrated by an article that was linked by a commenter on a previous thread. The article claims that researchers have finally shown how a gene can pick up a brand new function, which can then be amplified and modified over time.

Unfortunately, the article’s claim is not accurate. I had already read the scientific paper on which the article was based ¹, so when I read the article, I understood how incorrect its claims are. However, I am sure the commenter and many other readers of Science Daily do not. As a result, I want to discuss the study’s actual findings. They are very interesting, and they tell us a lot about the genetics of bacterial adaptation. However, they don’t tell us anything about how genes acquire brand new functions or about how information can be added to a genome.

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An Atheist Who Rejects Materialist Neo-Darwinism

Dr. Thomas Nagel is a Professor of Philosophy and Law at New York University. He has a long list of academic publications, which include books and journal articles. He is a Fellow of the American Academy of Arts and Sciences as well as the British Academy. He has been awarded both the Rolf Schock Prize for his work in philosophy and the Balzan Prize for his work in moral philosophy. Oh…and he is an atheist. He recently wrote a fascinating book entitled, Mind and Cosmos:Why the Materialist Neo-Darwinian Conception of Nature is Almost Certainly False.

The book is fascinating on many levels. Probably the most obvious is the fact that while he is an atheist, he speaks very highly of the Intelligent Design movement. In fact, he credits the Intelligent Design movement for stimulating his thinking on the subject of origins. He disagrees with their belief in a Designer, but he has given them a fair hearing, and he says this:

Even if one is not drawn to the alternative of an explanation by the actions of a designer, the problems that these iconoclasts pose for the orthodox scientific consensus should be taken seriously. They do not deserve the scorn with which they are commonly met. It is manifestly unfair. (p.10)

But wait a minute. Aren’t the Intelligent Design arguments fatally flawed? Don’t they rest on an incredibly poor understanding of the nature of science? Not according to this philosopher. He has read both the Intelligent Design advocates and their critics, and he says:

Those who have seriously criticized these arguments have certainly shown there are ways to resist the design conclusion; but the general force of the negative part of the intelligent design position – skepticism about the likelihood of the orthodox reductive view, given the available evidence – does not appear to me to have been destroyed in these exchanges. (p. 11)

But wait a minute, isn’t the only motivation behind Intelligent Design the desire to “prove” the existence of God? Nagel says that’s certainly part of the motivation, but not all of it. After all, he mentions David Berlinski as someone who is sympathetic to the negative claims of the Intelligent Design movement but has no desire to believe in a Designer. He also says:

Nevertheless, I believe the defenders of intelligent design deserve our gratitude for challenging a scientific world view that owes some of the passion displayed by its adherents precisely to the fact that it is thought to liberate us from religion. (p. 12)

In the end, then, religious motivations exist on both sides. Some Intelligent Design advocates are motivated by their desire to lend evidence to their belief in a Designer, but some evolutionists are motivated by their desire to be liberated from religion. This even-handed observation is obviously true, but it is rarely made by those who do not believe in God.

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The ENCODE Data and Pseudogenes

As I mentioned in two previous posts (here and here), the coordinated release of scientific papers from the ENCODE project has produced an enormous amount of amazing data when it comes to the human genome and how cells in the body use the information stored there. While the majority of commentary regarding these data has focused on the fact that human cells use more than 80% of the DNA found in them, I think some of the most interesting scientific results have gotten very little attention. They are contained in a paper that was published in a journal named Genome Biology, and they relate to the pseudogenes found in human DNA.

For those who are not aware, a pseudogene is a DNA sequence that looks a lot like a gene, but because of some details in the sequence, it cannot be used to make a protein. Remember, a gene’s job is to provide a “recipe” for the cell so that it can make a protein. Well, a pseudogene looks a lot like a recipe for a protein, but it cannot be used that way. Think of your favorite recipe in a cookbook. If you use it a lot, it probably has stains on it because it has been open while you are cooking. Imagine what would happen if the recipe got so stained that certain important instructions were rendered unreadable. For someone who has never looked at the recipe before, he might recognize that it is a recipe, but because certain important instructions are unreadable, he will never be able to use the recipe to make the dish. That’s what a pseudogene is like. It looks like a recipe for a protein, but certain important parts have been damaged so that they cannot be used properly anymore. As a result, the recipe cannot be used by the cell to make a protein.

Pseudogenes have been promoted by evolutionists as completely functionless and as evidence against the idea that the human genome is the result of design. Here is how Dr. Kenneth R. Miller put it back in 1994:¹

From a design point of view, pseudogenes are indeed mistakes. So why are they there? Intelligent design cannot explain the presence of a nonfunctional pseudogene, unless it is willing to allow that the designer made serious errors, wasting millions of bases of DNA on a blueprint full of junk and scribbles. Evolution, however, can explain them easily. Pseudogenes are nothing more than chance experiments in gene duplication that have failed, and they persist in the genome as evolutionary remnants…

Obviously, Dr. Miller didn’t understand intelligent design or creationism when he wrote that, as they can both explain nonfunctional pseudogenes. Before I discuss that, however, I need to point out that since 1994, functions have been found for certain pseudogenes. As far as I can tell, the first definitive evidence for function in a pseudogene came in 2003, when Shinji Hirotsune and colleagues found that a specific pseudogene was involved in regulating the functional gene that it resembles.² Since then, functions for several other pseudogenes have been found. In fact, a recent paper in RNA Biology suggests that the use of pseudogenes as regulatory agents is “widespread.”³

Even though functions have been found for many pseudogenes, the question remains: Are most pseudogenes functional, or are most of them non-functional? Well, based on the ENCODE results, we might have the answer. While the ENCODE results indicate that the vast majority of the genome is functional, they also indicate that the vast majority of pseudogenes are, in fact, non-functional.

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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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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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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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