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 based1, 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.
A beanbug, Riptortus pedestris (click for credit)Mutualistic symbiosis, the process by which organisms of different species interact so that all of them benefit, is a very common phenomenon in creation (see here, here, here, here, and here for a few examples). A recent study in the Proceedings of the National Academy of Sciences, USA highlights a very interesting case of mutualistic symbiosis that not only has some important implications for farmers, but also relates to the creation/evolution controversy.
The study examined insecticide resistance in bean bugs (Riptortus pedestris) and similar insects. The authors considered one of the most popular insecticides used by farmers across the world, fenitrothion. It has been known for some time that certain insects, such as the bean bugs in the study, can develop resistance to that insecticide. This is a problem, since bean bugs not only damage bean crops, but also some fruit crops.1 The authors were interested in what causes this insecticide resistance. As they state in the introduction to their paper:
Mechanisms underlying the insecticide resistance may involve alteration of drug target sites, up-regulation of degrading enzymes, and enhancement of drug excretion, which are generally attributable to mutational changes in the pest insect genomes.
In other words, when an insect develops resistance to an insecticide, it is generally assumed that there was a change in the DNA of the insect. A mutation might have damaged the site where the insecticide is supposed to bind; the activity of a gene involved in the destruction of unwanted chemicals might have been enhanced so that the insect destroys the insecticide; or perhaps the activity of a gene involved in getting rid of waste is enhanced so that the insect just excretes the insecticide.
The authors show that for the specific case of fenitrothion resistance in bean bugs and similar insects, none of these mechanisms play a role.
The cover of Fodor and Piattelli-Palmarini's bookNot long ago, Dr. Jerry Alan Fodor (a professor of Philosophy) and Dr. Massimo Piattelli-Palmarini (a professor of cognitive science) wrote a book entitled What Darwin Got Wrong. I haven’t read the book, but what I have read about it indicates that the authors strongly believe Darwin was right when it comes to the idea that all species descended from a common ancestor. However, they strongly disagree with the mechanism that Darwin proposed (and most Neo-Darwinists accept) for the process by which that happened. While most modern evolutionists contend that mutation acted on by natural selection is the main process by which species adapt and change, the authors argue that it is only one of many considerations. In fact, they go a step further and claim that there is no scientific reason to elevate natural selection above these other processes which it comes to their relative importance.
Since I have not read the book, I cannot comment on the validity of their arguments. However, I ran across a quote from the introduction that makes me want to read the entire book. They call their introduction “Terms of Engagement.” After laying out the terms and outlining the contents of the book, the authors write:
So much for a prospectus. We close these prefatory comments with a brief homily: we’ve been told by more than one of our colleagues that, even if Darwin was substantially wrong to claim that natural selection is the mechanism of evolution, nonetheless we shouldn’t say so. Not, anyhow, in public. To do that is, however inadvertently, to align oneself with the Forces of Darkness, whose goal it is to bring Science into disrepute. Well, we don’t agree. We think the way to discomfort the Forces of Darkness is to follow the arguments wherever they may lead, spreading such light as one can in the course of doing so. What makes the Forces of Darkness dark is that they aren’t willing to do that. What makes science scientific is that it is.
[Jerry Fodor and Massimo Piattelli-Palmarini, What Darwin Got Wrong, Farrar, Straus, and Giroux, First American Edition 2010, p. xx]
I couldn’t agree more. When those who call themselves scientists want to shut off debate on an issue, they are exposing themselves for what they are: rabidly anti-science. Science is all about following the evidence, regardless of where that evidence might lead. It is unfortunate that some (if not many) in the scientific community attempt to silence those who are simply trying to follow the evidence.
Thomas Nagel teaching at New York University (click for credit)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.
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.
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.
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.
The basic unit of heredity (the gene) has been defined as a stretch of DNA that codes for a protein. In plants, animals, and people, genes are made of introns and exons. The ENCODE results suggest this definition might need to be changed. (Click for credit)
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.
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!
Many evolutionists think that body hair in humans is useless. The data say otherwise. (Click for credit)One of the many reasons scientists are rejecting the hypothesis of evolution (see here and here, for example) is that many of its predictions have been falsified (see here, here, here, and here for even more examples). The more we learn about the world around us, the more clear it is that the predictions of the evolutionary hypothesis just don’t work. This is probably most apparent when it comes to “vestigial organs,” biological structures that are supposed to serve no real purpose; they are simply leftover vestiges of the evolutionary process. As Darwin himself said, they are like the silent letters of a word. They don’t serve a purpose in the word, but they do tell us about the word’s origin.
I have written about vestigial structures many times before (here, here, here, here, here, here, and here) because they are so popular among evolutionists. However, as the data clearly show, the evolutionists are simply wrong about them, and the more research that is done, the more clear it becomes. The latest example is human body hair. This has always been a favorite among evolutionists. Here are two evolutionary descriptions of human body hair. The first comes from a book specifically designed to help the struggling evolutionist in his attempt to convince people that his hypothesis has scientific merit.1
Humans, like all other organisms, are living museums, full of useless parts that are remnants of and lessons about our evolutionary histories (Chapter 6). Humans have more than 100 non-molecular vestigial structures. For example, our body hair has no known function.
Body hair is another functionless human trait. It seems to be an evolutionary relic of the fur that kept our distant ancestors warm (and that still warms our closest evolutionary relatives, the great apes).
As is the case with most evolutionary ideas, serious scientific research has shown that such statements are simply wrong.
