September 2012 : Proslogion

The Great Debate

Last night, I debated Dr. Robert A. Martin on the question of creation versus evolution. I obviously took the creation side, and he took the evolution side. I debated him once before in 2009, and you can watch a video of that debate here. The format of this debate was a bit different from the one on the video. In this one, we each had 30 minutes to present our case, and then the audience asked us questions. The purpose of the questions was to focus the debate on what the audience found interesting in our presentations. Dr. Martin and I were each given a chance to address the question, and that usually led to more interaction between us. Everyone with whom I talked, including Dr. Martin, was very pleased with how it all turned out.

One thing I have to say up front is how appreciative I am of Dr. Martin. First, the fact that he was willing to do the debate at all is a testament to his commitment to real science education. I contacted several universities in Indiana, and none of them were interested in finding an evolutionist professor who was willing to debate. The common response by evolutionists is that they don’t debate creationists, because that would give the creationist view too much legitimacy. However, Dr. Martin realized that if no one came to give the evolutionary side, everyone at the conference would hear only one side of the story, and that’s not very good when it comes to science education. As a result, he was willing to drive from Kentucky to make sure that both sides were heard.

Second, Dr. Martin was incredibly gracious. He knew going in that this was a creationist event, so he knew that his view would be in the minority. In some ways, he was like a lion in a den of Daniels. However, he was very kind in how he treated everyone. Now don’t get me wrong – he took a strong stand for evolution. He often said things like the evidence for evolution is overwhelming, and that there is just no question about the age of the earth and the universe. But never once did he descend into the name-calling and other nonsense that is common among those who don’t care to discuss evidence. He limited his discussion to the science, and that was great.

Third, Dr. Martin was kind enough to stay longer than we had intended. Not surprisingly, there were a lot of questions, and at the scheduled end of the debate, the moderator stopped and said that we were officially out of time. However, Dr. Marin immediately said that he was willing to stay longer. As a result, everyone who stood up to ask a question was able to interact with us. Even after the debate was over, he stayed and talked with people one-on-one for quite some time. Clearly, Dr. Martin has a passion for science and science education. His demeanor and willingness to pleasantly engage people with whom he disagrees demonstrated that to me in no uncertain terms.

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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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Six Alaskan Cities in Six Days

I just got back from speaking with homeschoolers in six different Alaskan cities (Fairbanks, Kenai, Kodiak, Wasilla, Anchorage, and Juneau). In each city, I gave the same two talks: Homeschooling: Discovering How and Why It Works and Life is Amazing. I gave the first talk in the morning, and it was really for parents. However, there were some students in the morning sessions, and for the most part, they seemed to stay awake. The second talk was in the afternoon, and it was really for the students, but there were a lot of parents as well. Everyone enjoyed it, because I showed some amazing animations and videos (you can find links to them in the PDF linked above) and discussed in detail the science behind what the videos were showing.

Lots of great things happened during my time in Alaska, but two of them really stand out in my mind. In the morning talks, I showed several studies that indicate homeschooled students excel, both academically and socially. After I showed these data, I tried to offer some explanations as to why homeschoolers excel. You can see those reasons in the PDF file linked above. However, I also asked the audience to come up with their own ideas as to why homeschoolers tend to excel. I got many excellent replies, but I want to highlight one of them.

A homeschooling father mentioned a study that was done in 1957 by psychologist Dr. Harold McCurdy. What the father said about the study intrigued me, so I looked it up. The author investigated the lives of twenty geniuses like John Stuart Mill, Gottfried Wilhelm Leibniz, and Blaise Pascal. He wanted to see if he could find commonalities in their lives that might have aided their intellectual development. Who knows how effective such a study is, but I found his conclusions to be very interesting. Here is what he said:¹

In summary, the present survey of biographical information on a sample of twenty men of genius suggests that the typical development pattern includes as important aspects: (1) a high degree of attention focused upon the child by parents and other adults, expressed in intensive educational measures and, usually, abundant love; (2) isolation from other children, especially outside the family; and (3) a rich efflorescence of phantasy, as a reaction to the two preceding conditions.

By “phantasy,” the good doctor just means “imaginative play.”

Now as I said, I am not sure how effective such a study really is, so I don’t take these results to be conclusive by any means. However, what he describes sounds an awful lot like a homeschool! Homeschooled children are given a high degree of attention from their loving parents, often in the form of intensive educational endeavors. While not completely isolated from children outside the family, homeschooled students certainly have less contact with their peers than do non-homeschooled students. Finally, most homeschoolers I know severely limit the amount of television that their children can watch, which encourages imaginative play. In the end, then, it seems that homeschooling naturally provides a lot of what Dr. McCurdy thinks is necessary for the development of genius.

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Defending the Indefensible, Part 2

A blogger by the name of Emil Karlsson recently wrote an error-laden piece defending Bill Nye’s rant against creationism. A commenter on this site posted the piece, and as a science educator, I had to point out many of its errors. Mr. Karlsson responded by posting a piece with even more errors. Once again, as a science educator, I had to correct those errors. Well, Mr. Karlsson has attempted to reply to that post, and not surprisingly, he has done so with even more errors. In an effort to educate those who are interested in understanding science and how it works, I will once again correct Mr. Karlsson’s errors.

Still Trying to Get Around What Mr. Nye Actually Said

Mr. Karlsson is still trying to make excuses for Nye’s obvious ignorance when it comes to evolution denial around the world. In an attempt to explain around Mr. Nye’s own words, Mr. Karlsson sets up a hypothetical interrogation in an attempt to claim that I am looking for “ammunition” to use against Nye. Here is his hypothetical interrogation:

Interrogator: Did you smash the windshield of Mr. X’s car?

Innocent suspect: No. I mean, I don’t like the guy and he annoys me to no end, but I would never go so far as to destroy his property just because we did not get along. Besides, I was having lunch at the cafeteria when it happened.

He then says there are two ways you can interpret this. First, he claims that my way is to ignore the suspect’s statement of innocence and his alibi and instead focus on the fact that the suspect admits he didn’t like the victim. He claims that his way is to look at the suspect’s entire statement and conclude that the suspect is not guilty.

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Defending the Indefensible

Not long ago, I wrote a response to Bill Nye’s anti-science video. A commenter replied by posting a link to a blog that attempted to defend Nye’s indefensible statements. I quickly pointed out the many errors in the article, and the commenter obviously sent my response to the author, Emil Karlsson. He has now written another post in an attempt to defend his position. Unfortunately, it is more error-filled than his original post.

Here is my attempt to correct his errors, in the order he presents them:

1. Mr. Karlsson still tries to make excuses for Nye’s false statement about evolution denial being unique in the U.S.

In his reply to me, he gives Nye’s full quote from the beginning of the video. He then tries to claim that Nye was not saying exactly what he said – that denial of evolution is unique to the U.S. Mr. Karlsson claims:

So Bill Nye is not making the naive claim that denial of evolution is unique to the United States in the sense that it does not exist anywhere else, but rather the claim that United States is unique in being a highly technologically advanced society, yet have [sic] a large proportion of the population being creationist.

Of course, Nye is saying nothing of the sort. Nowhere in Nye’s statement can you find the words “large proportion.” In addition, while Nye certainly mentions technological advancement, he is using it as a descriptor for the United States, not a qualifier for his statement. Regardless of the mental gymnastics of Mr. Karlsson, Nye’s statement is unambiguously false.

However, let’s assume Mr. Nye really did mean what Mr. Karlsson claims, even though Mr. Nye said something completely different. Even if that’s the case, his statement is still a complete fabrication. Would Mr. Karlsson agree that Germany is technologically advanced? The study to which he refers indicates that more than 20% of its population denies evolution. The same is true of Italy, Spain, the Netherlands, and Switzerland. In the U.S., a larger percentage (roughly 40%) deny evolution, but that’s not drastically different from the percentage found in many other technologically-advanced nations. Even in the U.K., the percentage of people who deny evolution is greater than 15%.

In the end, then, even in technologically-advanced nations, denial of evolution is common. It is a bit more popular in the U.S., but it is certainly not unique to the U.S. Of course, the U.S. has always been on the cutting edge of science, so it’s not surprising that it holds a slightly higher percentage of people who see the serious scientific problems with evolution!

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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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Back To School? Add Doubt to Your Curriculum.

It’s that time of year again. Most students who attend public and private schools have started classes or are just about to start them. Even many home educated students take a summer break from their academic work and are facing the same situation. While there have been many different “back to school” articles written over the past few weeks, I think this one offers one of the more interesting messages. It talks about doubt and how you should not suppress it in your students.

The article is written by Dr. Kara Powell, who is on the faculty at Fuller Theological Seminary and is also the executive director of the Fuller Youth Institute. She talks about how it is natural for students to have doubts, and the last thing you should do is try to ignore those doubts or sweep them under the rug. Instead, you should encourage your students to express them, and you should address them as best you can. How does she come to this conclusion? She bases it on a study done by the Fuller Youth Institue. I wrote about a preliminary version of the study previously. It has grown since then, and the results are very interesting.

The study in its current form followed 500 youth-group graduates during their first three years in college. One of the main findings was that students who feel free to express doubts about their faith are more likely to be strongly active in their faith than those who do not. As a result, Dr. Powell says:

Doubt in and of itself isn’t toxic. It’s unexpressed doubt that becomes toxic.

That’s why she says that you need to foster an environment where students feel comfortable expressing their doubts. I couldn’t agree more.

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