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Sunday, November 23, 2014

Defending the Indefensible, Part 2

Posted by jlwile on September 16, 2012

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.

There are two problems with Mr. Karlsson’s argument. First, I ignore nothing that Nye says. In fact, I concentrate on exactly what he says. He says that evolution denial is unique in the U.S. It most certainly is not. He describes the U.S. as a technologically-advanced nation, to be sure, but he also uses that same description for Japan. Thus, as I said before, Nye’s use of that phrase is not a qualifier for his statement. It is simply a description of both the U.S. and Japan.

The bigger problem, of course, is that Mr. Karlsson uses neither of the approaches he describes in his attempt to make excuses for Nye’s ignorance. Instead, he uses a third approach, in which he invents things that Nye didn’t say. Mr. Karlsson claims that Nye didn’t mean that evolution denial was unique to the U.S., only that the U.S. is unique among technologically-advanced nations because of the large proportion of people who deny evolution. Of course, Nye doesn’t use the phrase “large proportion” at all, and he says nothing about evolution denial being unique “among technologically-advanced nations.” In his hypothetical interrogation, then, Mr. Karlsson’s method would result in the interrogator saying, “Ah…I see. Hundreds of people saw you in a cafeteria all day, and that cafeteria was in a completely different country. Obviously, then, you must be innocent.”

I understand why Mr. Karlsson wants to put words in Nye’s mouth, but doesn’t excuse the fact that he is doing just that. Mr. Nye said nothing about the U.S. being unique in evolution denial because of the fact that it is technologically advanced and because it has a larger proportion of people who deny evolution. Instead, he said that evolution denial is unique in the U.S., and that statement is demonstrably false, even for technologically-developed nations.

Mr. Karlsson also seems to have trouble admitting to the reality of the data in the study that he himself presents. The study clearly shows that evolution denial in technologically-advanced nations is rather common. In several technologically-advanced nations, more than 20% of the population deny evolution. He claims that because the U.S. has less than twice the percentage of evolution deniers as those countries, that somehow makes it unique. The problem with such a statement is obvious. There is nothing unique about a country having a large fraction of people who promote a view that is common in nearly every technologically-advanced country in the world!

In order for the U.S. to be unique among technologically-advanced nations, its proportion of evolution-deniers would have to be incredibly different from that of other technologically-advanced nations. As is the case with most of Mr. Karlsson’s assertions, the data show quite the opposite. The data are clear – the U.S. simply has a slightly higher percentage (not even twice as many, in most cases) of evolution-deniers than the other technologically-advanced nations.

Still Trying to Claim That Creationism Represents False Balance

Mr. Karlsson wants people to believe that creationism doesn’t have the scientific support that evolution does. Of course, the facts say something quite different. Indeed, since creationism is significantly more consistent with the vast majority of the scientific data, it is clearly the better scientific description of origins. You can find many excellent overviews that demonstrate this fact, such as this one. Interestingly enough, in order to attempt to make his case, he gives a link entitled 29+ Evidences for Macroevolution: The Scientific Case for Common Descent. Of course, anyone who is familiar with the creation/evolution controversy knows what a scientifically-flawed document that is. This article is an excellent overview that points out its most obvious flaws.

Mr. Karlsson also can’t seem to admit the obvious fact that my textbooks produce excellent university students. He says that the anecdotes I present are “hardly convincing.” That may be true for someone who doesn’t want to look at the data, but to anyone who is interested in evidence, the fact that there are many, many students who use my textbooks who go on to excel at university-level science is direct evidence that my textbooks produced excellent university-level science students.

He then goes on to say that even if my textbooks produce excellent university-level students, that doesn’t mean they are error-free. After all, there are other reasons these students might be good at university-level science. For example, maybe the excellence of the other materials in the books is dwarfed by the supposed mistakes made when it comes to evolution. Perhaps the effectiveness of home education renders all those supposed mistakes about evolution irrelevant. Of course, that doesn’t work, because many of these students go on to excel in biology, and evolution is rampant throughout university-level biology courses. If my books were littered with mistakes on evolution, it wouldn’t produce excellent university-level biology students. In addition, not one of these university students, who have excelled specifically in biology, has mentioned these supposed mistakes. Instead, they recommend my courses as excellent preparation for university-level biology. I understand why Mr. Karlsson wants to believe that my books are full of errors. However, once again, the data do not support his contention.

Still Stuck on Gene Duplication

Mr. Karlsson continues to argue (in spite of the evidence to the contrary) that gene duplication followed by mutation is a reasonable mechanism for evolutionary innovation. He claims that I “ignore” most of the evidence he supposedly cited, but of course that is not true. I gave the problems associated with his first two citations and then explicitly said that the other citations had similar problems.

He then proceeds to discuss his second citation in-depth. Notice that he says he will not discuss the other citations because it would take too long. Of course, that’s why I didn’t discuss his other citations in depth. However, it is fine for him to “ignore” his other citations, but he claims I am doing something wrong when I do exactly the same thing. As you can see from reading my previous article discussing Mr. Karlsson’s errors, this is a common tactic that he uses.

In discussing his second citation, he claims that it shows multiple lines of evidence that the RAG1 and RAG2 proteins (often lumped together and called just the RAG protein) are the result of an “invasion” of a transposon from a pathogen. Of course, the evidence doesn’t point to that at all. He says that the sequences of the RAG genes are similar to that of some bacterial transposons. This, of course, is completely false. The RAG2 gene has no similarities to any transposons. As this paper demonstrates, the RAG1 protein has a small “core” that is similar to a group of transposons found in eukaryotes. However, as anyone who has taken freshman biology knows, bacteria are not eukaryotes!

More importantly, the idea that a gene is similar to another gene and therefore must be related to that gene is demonstrably false. As I pointed out quite some time ago, there are genes in dolphins and bats that are nearly identical, and no evolutionist suggests that they are related to one another. Instead, they are similar because they perform a similar function. It’s not surprising that there is a core of RAG1 that is similar to some transposons, since the actions of the RAG1 enzyme have similarities to the actions of some transposons.

Mr. Karlsson seems to think that the fact that genes are close to one another in the genome means they must have been both inserted into the genome via the same event. Of course, that is not true. Genes that work together are often close to one another in the genome, because when one is transcribed, the other is often transcribed as well. Please note that the very paper Mr. Karlsson cites postulates that only the RAG1 gene is the result of a transposon invasion. It says the RAG2 gene was probably already there and “then lost its original function and was co‑opted to the VDJ rearrangement process.” Thus, even the paper he cites doesn’t support his supposed second line of evidence!

Mr. Karlsson also thinks that the RAG proteins only cause the insertion of DNA in vitro. Obviously, he needs to read the scientific literature more frequently, because we have known for several years that this is not true. They also do this in vivo, indicating that it is a part of their function. Thus, they do it not because they come from bacteria (remember, the similarity isn’t found in bacteria, anyway), but because they are designed so as to be able to perform that function.

In the end, he asks why these several lines of “evidence” make such a “powerful case” for the transposon-invasion model. In fact, I have shown that none of them make the case for such a model. It’s not surprising, then, that even some evolutionists doubt it. As this paper tells us:

Since the “RAG-transposon” has not been located despite an extensive search, it is time to evaluate the origins of the acquired immune system critically and experimentally rather than as dogma.

If there is such a powerful case for the transposon-invasion model, why does this author (to whom the paper that he cites refers) propose a completely different model?

Mr. Karlsson then tries to claim that the evidence shows that vertebrates have gone through two whole genome duplications, using a quote from his second citation. The problem, of course, is if you look at the paper that is referenced to support this statement, you don’t find such confident wording. Here is what you find:

The relatively few surviving gene duplicates from the vertebrate stem provide evidence for ancient paralogous relationships between groups of human chromosomes10, 11, 12, 13, 14 that plausibly arose from multiple rounds of whole-genome duplication before the emergence of modern vertebrates. However, the number, the timing and even the genomic scale of the duplication events, and their consequences for subsequent genome evolution, are poorly understood (for a review, see ref. 15), in part because the tunicate genomes are highly rearranged relative to the unduplicated early chordate karyotype (see below). [emphasis mine]

While I agree that a double genome duplication is a plausible explanation, as the paper indicates, the conclusion is built on a lot of speculation and only a bit of evidence.

Now that I have corrected Mr. Karlsson’s errors you can see that the reference Mr. Karlsson cites does exactly what I said it does in my first post. It simply postulates what might have happened. It provides no convincing evidence, and what evidence that is provided is not the result of direct observation.

After mangling the science related to the one citation Mr. Karlsson chose to discuss, he then mangles the science in the BIO-COMPLEXITY study that I cited. He claims:

Actually, the paper shows that this particular gene duplication did not result in adaptive evolution. But that says nothing about gene duplication generally.

Of course, nothing could be further from the truth. The paper shows that when a gene mutates even slightly from its functional form, it gets downregulated to the point where it is no longer used. As the authors clearly note, this has direct application to the supposed mechanism of gene duplication followed by mutation as a source of evolutionary innovation:

Our results show that competition between reductive and constructive paths may significantly decrease the likelihood that a particular constructive path will be taken. This finding has particular significance for models of gene recruitment, since weak new functions are likely to require costly over-expression in order to improve fitness. If reductive, cost-cutting mutations are more abundant than mutations that convert or improve function, recruitment may be unlikely even in cases where a short adaptive path to a new function exists.

I understand why Mr. Karlsson wants to ignore these data. They demonstrate exactly the opposite of what he claims. As a science educator, however, I cannot allow others to close their eyes to the importance of such work.

As I pointed in my previous discussion of Mr. Karlsson’s errors, he refuses to discuss the science in the CMI article I cited, because it also discusses data that show gene duplication followed by mutation cannot be the source of evolutionary innovation. Instead, he uses the “search for ammunition” method he accused me of using when discussing Mr. Nye’s ignorance about worldwide evolution denial. He claims that because the CMI article says that gene duplication can be beneficial to plants, it refutes the common creationist claim that gene duplication never produces anything beneficial.

Of course, in writing this, Mr. Karlsson once again shows that he doesn’t know the creationist position at all. Creationists don’t claim that gene duplication cannot be beneficial. They don’t even claim that gene duplication followed by mutation cannot be beneficial. What they claim, because the evidence demonstrate this, is that gene duplication followed by mutation cannot insert new information into a genome. This, of course, is the point of the CMI article, and Mr. Karlsson cannot argue against the data in the article that demonstrate this fact. As a result, he tries to distract the reader by mischaracterizing what the article actually says.

Still Confused About the C-Value Paradox.

Mr. Karlsson seems to think that the c-value paradox has no bearing on gene duplication as a source of evolutionary innovation, but it clearly does. He claims that I view evolution as a “ladder,” but that is completely false. Indeed, all one has to do is read this blog to see that I most certainly understand that evolutionists see all current life as the “tips of the branches” on the “tree” of evolution. This, however, does nothing to exempt gene duplication followed by mutation from its prediction.

Mr. Karlsson doesn’t understand that because he doesn’t seem to understand the evolutionary process. He claims:

The organisms alive today that we consider “simple” have had exactly the same amount of time to diverge from a common ancestor as extant organisms we consider “complex”.

The problem with this view is that while these organisms have had the same amount of time to diverge from a common ancestor, many of them have not been diverging much at all. Quite a while ago, for example, I noted that eyes which are supposedly 515 million years old look like modern insect eyes. Recently, paleontologists found gall mites in amber that is supposed to be 230 million years old but are “dead ringers” for modern gall mites.

So the issue is not time. It is how much supposed evolution has taken place. If an organism has experienced a lot of supposed evolutionary innovation, that means it had to have a lot of gene duplication followed by mutation. Thus, it should have a large genome. If an organism hasn’t experienced much supposed evolutionary innovation, it should not have experienced as much gene duplication followed by mutation. As a result, it should have a smaller genome. This, of course, is not the case, which is strong evidence against the idea that gene duplication followed by mutation can produce evolutionary innovation.

Still Applying a Double Standard

As I noted previously, Mr. Karlsson is adept at applying double standards. He tried to claim that there was something wrong with me only discussing a couple of representative citations that he produced and only commenting briefly on the rest. Then, of course, he did exactly the same thing, focusing on only one of his citations. In his first attempt to explain away the problems with Nye’s video, he was annoyed that evolution was portrayed as random mutation plus natural selection. When I pointed out that evolutionists use the exact same description, he said that it was understandable, since they were giving only an introductory view of evolution. I pointed out that the creationists were simply giving an introductory view as well, so Mr. Karlsson was clearly using a double standard.

He claims that this isn’t relevant, because the creationists were providing “their view of what evolution was.” However, that’s exactly what the evolutionists I presented were doing. They were giving their view on what evolution is, in an introductory manner due to the audience to whom they were writing. The creationists were doing exactly the same thing. As we can see, then, Mr. Karlsson is so fond of using double standards that he doesn’t seem to notice when he uses them!

Still Relying on Incomplete Lineage Sorting

Mr. Karlsson claims that incomplete lineage sorting is “Hardly a new and radical idea.” However, it most certainly is. Indeed, the earliest reference I can find to it comes from 1993. If you read the paper, you will see exactly why it is brought up – a mitochondrial DNA analysis was not consistent with the evolutionary expectations, so an ad hoc explanation had to be invented to account for it. As I said in my previous post, a good theory should not have to explain around the data. The data should support it. That is why comparing DNA sequences produces some of the strongest evidence against evolution, contrary to Mr. Karlsson’s original claim.

Still Not Understanding the Creationist Position

Mr. Karlsson attempts to explain away the fact that he did not understand the creationist position in his first reply to me. He claims that when he said creationists believe that God created the organisms we see in “pretty much” the same form that we see today, he was allowing for variation within Biblical kinds. Of course, that’s not true. As perusal of any serious creationist literature will make clear, the variation within the Biblical kinds can be quite significant. As a result, creationists suggest that many organisms today bear only a slight resemblance to the originally created kind.

He then tries to claim that it would be impossible for wolves, coyotes, dogs, etc., to have been produced by a pair of dogs that were preserved on the ark, because there simply wasn’t enough time for that to happen. He says that creationists must postulate a ridiculously high mutation rate to accomplish that kind of diversification. Like most of what Mr. Karlsson says, this is quite false.

In fact, wolves, dogs, and coyotes can mate and produce fertile offspring. As a result, the genetic differences between them are very small. Thus, it would not take any significant time for such minor differences to accumulate. Indeed, an experiment that has been going on for only about 50 years has demonstrated just how fast such diversification can take place. Once again, then, observational evidence supports the creationist position.

He also claims that because the creationist view started off with only two dogs, there would have been a problem with the accumulation of recessive and harmful mutations during inbreeding. Once again, however, this ignores the genetic data. Since dogs, coyotes, and wolves can mate and produce fertile offspring, we know that there is little difference in them genetically. Thus, there is no need to postulate the accumulation of a large amount of recessive mutations.

Still Not Understanding The Supernatural and Science

Mr. Karlsson claims that I have not responded to his charge that belief in a supernatural being undermines the concept of the uniformity of nature. Once again, like most of what Mr. Karlsson says, this is simply not true. I have, in fact, shown that it was belief in the Christian God that produced the concept of the uniformity of nature. As the quotes I gave in my initial reply to the commenter demonstrated, because Christians believed that one God created the entire universe, and because they viewed that God as a Lawgiver, they were able to postulate that the entire universe operated under one set of uniform laws. This, of course, is what birthed modern science.

He claims that the proper God concept was not necessary to produce science, and he supports that claim in two ways. First, he says that “Ancient Greece and China made great scientific advances, even without the belief in the deity of the bible.” However, that’s precisely the point. They did not. Ancient China, for example, was way ahead of ancient Europe technologically, but Europe produced the scientific revolution, not China. Why? Dr. Joseph Needham spent several years studying China’s development to answer that question. He gave three reasons. The first two dealt with Chinese jurisprudence and bureaucracy. Here is the third:

Third, the autochthonous idea of a supreme being, though certainly present from the earliest times, soon lost the qualities of personality and creativity. The development of the concept of precisely formulated abstract laws capable, because of the rationality of the Author of Nature, of being deciphered and re-stated, did not therefore occur.

In other words, the proper god concept was, indeed, crucial to the development of modern science. China did not have it, so China did not produce modern science.

The second way Mr. Karlsson tries to deny this obvious fact is to quote Dr. Richard Carrier. In the quote, Dr. Carrier claims that science didn’t flourish for about a thousand years after Christianity began to dominate the Western World. However, that is simply false. Historian Dr. James Hannam shows quite clearly that science progressed steadily throughout Christianity’s reign, and it was specifically because of the Christian concept of God. Instead of being an impediment to science, then, the Christian concept of God was absolutely necessary to its development.

It is unfortunate that Mr. Karlsson mangles science and history as much as he does in order to promote an idea that many scientists are rejecting. I do hope that he learns from this exchange. If nothing else, those who read both sides will see rather clearly that science supports the creationist position, and that history clearly shows that science is a product of Christianity.

Comments

11 Responses to “Defending the Indefensible, Part 2”
  1. Jason says:

    Dr Wile

    Your response(s) have certainly taught me a lot, thank you once again.

    One can only hope as Mr. Karlsson licks his wounds, after the beating you’ve given him again, that at least something you’ve touched on here might sink in.

    Evolution seems to have become a kind of religion for many, I can understand why Mr. Karlsson would disagree with you and defend his beliefs.

  2. jlwile says:

    Jason, I just hope he learns the actual science so that his view will be an informed one.

  3. D. Perrine says:

    Well, not only did you give me a enjoyably long article to read, you gave me several sources to back check and read as well. Thank you.
    I am always looking for more information on this debate as it twinges a personal note.

  4. jlwile says:

    That’s my goal, D. Perrine. I want to give people the information they need to make an informed choice. It seems Mr. Karlsson would rather mischaracterize the science in order to persuade people to agree with him. I am more interested in educating people so that they can make their own decision.

  5. Jason says:

    Having exchanged a number of messages with you, both on and off your blog, I believe you to be an honest “teacher” genuinely trying to help where you can.

    Thank you for your time, effort and patience Dr Wile.

  6. jlwile says:

    Thank you, Jason.

  7. Evan says:

    I am using your textbook “The Human Body, Fearfully and Wonderfully Made!” and find I learn much faster from this textbook than others BECAUSE it is from a logical creationist perspective. Rather than confusing me by trying to explain how things evolved using weak evidence and paradoxes, you and Marilyn M Shannon explain why God created the various systems of the body the way that he did. I am thoroughly enjoying your curriculum and hope you write more textbooks in the future.

  8. jlwile says:

    Thanks so much, Evan. I am glad that the course is working out so well for you!

  9. D. Perrine says:

    I believe, in the first part of this article, you mentioned that you ignored horizontal gene transfer because it was an ad hoc rationalization of the data. Then again in this post you said that incomplete linage sorting was another example of an ad hoc rationalization.

    How do you distinguish between a real concern, something that might actually make the data harder to interrupt or explain the data and something that is indeed ad hoc?

  10. jlwile says:

    D. Perrine, I didn’t say that horizontal gene transfer is an ad hoc rationalization. In my first response to Mr. Karlsson, I pointed out that horizontal gene transfer is not a valid explanation for the problems that I cited, because the problems I cite had to do with animal evolution, and animals rarely participate in horizontal gene transfer, at least as far as we can tell. Horizontal gene transfer is a real concern, because it has been observed. However, it is mostly observed in bacteria and rarely observed in animals. Thus, as an explanation for why genetics doesn’t agree with morphology when it comes to the evolution of animals, it doesn’t work.

    I say that incomplete lineage sorting is an ad hoc rationalization because it was undreamed of until the data failed to confirm the evolutionary prediction. In addition, we have never confirmed that it actually happens. Evolutionists only think it happens because it’s the way they explain around the fact that the evolutionary prediction failed. Compare that to horizontal gene transfer in bacteria. We knew about it long before anyone tried comparing the genes of bacteria to one another to determine evolutionary relationships, so it wasn’t something that came up after the fact. In addition, we have actually seen it, so we know it happens.

  11. D. Perrine says:

    I am so sorry for misrepresenting your argument. Thank you for clearing that up.

    So, it is really just a hypothesis that has been formed in order to explain data that is incongruent with another supposed hypothesis or theory.

    Thank you for explaining that.

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