How LINEs and SINEs disprove Intelligent Design and Ben Stein
You can learn a lot from creationists. Attending creationist grade school, high school, college and medical school made me realize that the only possible reason to believe in creationism was if you believed the Bible simply couldn't be wrong in any way. Because even though all my teachers were creationists, the ones who knew science never really had very good arguments against common ancestry that weren't shot down by Darwin in his very first presentation of his theory of common descent by modification by means of natural selection.
In fact, one of my major professors in undergraduate once stated to me point blank, "If I didn't believe in the Bible, evolution is the only plausible explanation for life."
When people's jobs depend on their believing a certain way, they will on average tend to keep believing it, but I can't help but think the professor was tipping his cap a bit to his actual assessment of the evidence by that statement.
My professor made that statement back in the 1980s. Since then, the evidence has continued to roll in by the truckload. The only thing that seems to keep pace with it is the amount of willful denial of the facts by stubborn or misguided creationists. I try to keep track of the basic arguments for creationism and for it's bastard stepchild, Intelligent Design, so it was a surprise for me to see a post by DaveScot on Uncommon Descent (an ID blog) that tried to jiujitsu some of the strongest evidence for common descent by means of natural selection (which ID believes in to a degree not completely specified, but doesn't really believe completely explains every last detail) into an argument for intelligent design.
DaveScot makes a startling and sort of shocking admission far down the post:
Recently in a private forum where others are concerned with intelligent design I brought up the case of ERVs as evidence supporting common ancestry vs. common design. If common design instead of common ancestry the designer is evidently using existing species in situ as the template for new species. If that’s the case there’s effectively no difference whatsoever between common design and common ancestry.
Dave evidently is so ignorant he fails to distinguish between design and selection. For example. The wind blows. Which grains of sand will become blown dust that will pile up? The biggest ones or the smallest ones? Is the wind designing a sand dune? Yet DaveScot can't see that a sand dune is both non-random and not designed.
DaveScot makes a common fallacy that infuses bad thinking on the ID/Creationist side. There is no dichotomous state between randomness and design. There are things that were partly designed that have been subjected to random degeneration. If you throw your watch off a cliff, are you designing how it breaks? No. Do you intend it to break? Probably.
Is a Jackson Pollock painting designed or random? The answer is both. The painting has elements of randomness that are designed. Our genomes are the very best evidence for exactly how life works. It is a hodgepodge, a mishmash with elements of non-random natural selection vying for space with "parasitic" elements of the genome that do not actively create fitness for the organism (that we are currently aware of).
The best example of this mixture is the phenomenon of viral insertions into the genome.
The virus that strikes fear in the hearts of most people who break a condom is HIV. HIV is a retrovirus, which means that it has an enzyme, reverse transcriptase, which has a job to move the genome of the virus into the DNA strands of the host cell that it has infected. HIV does this all the time which is one of the reasons it is so difficult to eradicate or control.
The only uses of reverse transcriptase are the movement of gene sequences from one place to the other. They do not play a role in physiological processes of the body. Patients on drugs which suppress the activity of reverse transcriptase live reasonably long lives if the drugs work (Magic Johnson is, I imagine, on them).
Occasionally a retrovirus like HIV will insert itself into an egg cell of a mammal and become non-virulent but still replicate. It can place copies of itself or parts of itself back into the genome over time. These are called Endogenous Retroviruses (ERVs). ERVs show all the protein sequences of the original virus, but over time the original sequences degrade.
Some become Long Interspersed Nuclear Elements and Short Interspersed Nuclear Elements (LINEs and SINEs). Between them, ERVs, LINEs and SINEs make up about 8% of the human genome. The protein coded for most commonly in the human genome is reverse transcriptase. The LINEs and SINEs are genetic elements that are remnants of retroviral insertions. They are not used by our bodies or brains in any fashion we are aware of, although endogenous retroviruses appear to have played a role in the development of viviparity (the ability to give live birth).
DaveScot thinks this is evidence that God is a genetic engineer who tinkers with genomes. I am curious what John's argument from the scale of the universe would do with that deity. But the real treat on the DaveScot post is further down.
In the comments section, there's a link there to an absolute gem of a paper written by a very honest creationist named Todd Charles Wood. Todd believes in Noah's flood and thus believes that all of life descended from fixed kinds that existed less than 6000 years ago as pairs. Thus he talks about baraminology, which is the creationist term for the study of "kinds" and how they modify over time. But it gets better.
Todd examines the similarities between the chimp and human genomes. He carefully goes over the available evidence and comes out with this amazing statement:
Using a genomic argument, I previously proposed that Mycoplasma genitalium and Mycoplasma pneumoniae share a common ancestor, because both bacteria shared almost all of their genes, and the genes unique to M. pneumoniae could be explained by a chromosomal deletion in M. genitalium. As with the genetic diversity of cats, what is to preclude application of this same argument to chimpanzees and humans with the conclusion that we share a common ancestor with an animal?
To put this question another way, how can we maintain that felids or mycoplasmas share a common ancestor with their genomic differences, and deny that the smaller differences between humans and chimpanzees could not also arise from a common ancestor? The only way to do this is to favor other data in baraminology, and to deny the primacy of the genome in determining true phylogenetic or baraminic relationships. The alternative would be to scrap baraminology and revert to a position very close to species fixity.
Todd knows that species aren't fixed. That's got to be the case since there are more species alive today than could possibly have fit on the ark. But he's like my professor. The Bible comes first. This position forces Todd into the amazing statement that follows:
The similarity of the human and chimpanzee genomes offers evidence that the genome could primarily be a repository. If the fixed nucleotide mismatches between the chimpanzee and human genomes are 1.06%, then the original nucleotide identity could be as high as 99%. At that high level of similarity, perhaps it is not impossible to believe that God created humans and chimpanzees with identical genomes. The known differences between human and chimpanzee biochemistry (see Varki 2000; Varki and Atheide 2005) may well rule this out, but it is an intriguing possibility. Even at 99% identity, however, the biological and behavioral differences between chimpanzees and humans indicate that the source of these differences is not likely to be found entirely in the genome sequences. Theologically, the high similarity of humans and chimpanzees reinforces our spiritual – not physical (Ecc. 3:18-21) – distinctiveness from the animals. It is the image of God that makes us human not some intrinsically valuable genetic element.
When the facts are in your favor, argue the facts. When the law is in your favor, argue the law. When the law and the facts aren't in your favor, bang the table. In this case, Todd can't believe his senses, because the Bible tells him otherwise. So the Bible must be right, even though there's no evidence there to back it up. At least Todd is honest.
The entire premise of Intelligent Design is that it is different from modern science. Yet Ben Stein's film showed not one example of someone doing good scientific work that was contributing to a viable research program who lost a job because of it. The job of scientists is to make valuable contributions. A major difficulty in trying to make a valuable contribution to a field is not believing in its central points.
Imagine trying to get a job at CERN if you didn't believe quantum mechanics was true. Imagine trying to get a job at NASA if you thought the moon landing was faked. Imagine trying to get a job as a dentist if you thought that cavities came from masturbation.
That's all Ben Stein had to show in his film, with the exception of the insipid Hitler porn, and he tried to claim that it was discrimination. Ben didn't even have the honesty of Todd, who I hope one day quits trying to defend the indefensible.
I hope this examination of ID and creationism can show the tip of the iceberg that changed my mind.
In fact, one of my major professors in undergraduate once stated to me point blank, "If I didn't believe in the Bible, evolution is the only plausible explanation for life."
When people's jobs depend on their believing a certain way, they will on average tend to keep believing it, but I can't help but think the professor was tipping his cap a bit to his actual assessment of the evidence by that statement.
My professor made that statement back in the 1980s. Since then, the evidence has continued to roll in by the truckload. The only thing that seems to keep pace with it is the amount of willful denial of the facts by stubborn or misguided creationists. I try to keep track of the basic arguments for creationism and for it's bastard stepchild, Intelligent Design, so it was a surprise for me to see a post by DaveScot on Uncommon Descent (an ID blog) that tried to jiujitsu some of the strongest evidence for common descent by means of natural selection (which ID believes in to a degree not completely specified, but doesn't really believe completely explains every last detail) into an argument for intelligent design.
DaveScot makes a startling and sort of shocking admission far down the post:
Recently in a private forum where others are concerned with intelligent design I brought up the case of ERVs as evidence supporting common ancestry vs. common design. If common design instead of common ancestry the designer is evidently using existing species in situ as the template for new species. If that’s the case there’s effectively no difference whatsoever between common design and common ancestry.
Dave evidently is so ignorant he fails to distinguish between design and selection. For example. The wind blows. Which grains of sand will become blown dust that will pile up? The biggest ones or the smallest ones? Is the wind designing a sand dune? Yet DaveScot can't see that a sand dune is both non-random and not designed.
DaveScot makes a common fallacy that infuses bad thinking on the ID/Creationist side. There is no dichotomous state between randomness and design. There are things that were partly designed that have been subjected to random degeneration. If you throw your watch off a cliff, are you designing how it breaks? No. Do you intend it to break? Probably.
Is a Jackson Pollock painting designed or random? The answer is both. The painting has elements of randomness that are designed. Our genomes are the very best evidence for exactly how life works. It is a hodgepodge, a mishmash with elements of non-random natural selection vying for space with "parasitic" elements of the genome that do not actively create fitness for the organism (that we are currently aware of).
The best example of this mixture is the phenomenon of viral insertions into the genome.
The virus that strikes fear in the hearts of most people who break a condom is HIV. HIV is a retrovirus, which means that it has an enzyme, reverse transcriptase, which has a job to move the genome of the virus into the DNA strands of the host cell that it has infected. HIV does this all the time which is one of the reasons it is so difficult to eradicate or control.
The only uses of reverse transcriptase are the movement of gene sequences from one place to the other. They do not play a role in physiological processes of the body. Patients on drugs which suppress the activity of reverse transcriptase live reasonably long lives if the drugs work (Magic Johnson is, I imagine, on them).
Occasionally a retrovirus like HIV will insert itself into an egg cell of a mammal and become non-virulent but still replicate. It can place copies of itself or parts of itself back into the genome over time. These are called Endogenous Retroviruses (ERVs). ERVs show all the protein sequences of the original virus, but over time the original sequences degrade.
Some become Long Interspersed Nuclear Elements and Short Interspersed Nuclear Elements (LINEs and SINEs). Between them, ERVs, LINEs and SINEs make up about 8% of the human genome. The protein coded for most commonly in the human genome is reverse transcriptase. The LINEs and SINEs are genetic elements that are remnants of retroviral insertions. They are not used by our bodies or brains in any fashion we are aware of, although endogenous retroviruses appear to have played a role in the development of viviparity (the ability to give live birth).
DaveScot thinks this is evidence that God is a genetic engineer who tinkers with genomes. I am curious what John's argument from the scale of the universe would do with that deity. But the real treat on the DaveScot post is further down.
In the comments section, there's a link there to an absolute gem of a paper written by a very honest creationist named Todd Charles Wood. Todd believes in Noah's flood and thus believes that all of life descended from fixed kinds that existed less than 6000 years ago as pairs. Thus he talks about baraminology, which is the creationist term for the study of "kinds" and how they modify over time. But it gets better.
Todd examines the similarities between the chimp and human genomes. He carefully goes over the available evidence and comes out with this amazing statement:
Using a genomic argument, I previously proposed that Mycoplasma genitalium and Mycoplasma pneumoniae share a common ancestor, because both bacteria shared almost all of their genes, and the genes unique to M. pneumoniae could be explained by a chromosomal deletion in M. genitalium. As with the genetic diversity of cats, what is to preclude application of this same argument to chimpanzees and humans with the conclusion that we share a common ancestor with an animal?
To put this question another way, how can we maintain that felids or mycoplasmas share a common ancestor with their genomic differences, and deny that the smaller differences between humans and chimpanzees could not also arise from a common ancestor? The only way to do this is to favor other data in baraminology, and to deny the primacy of the genome in determining true phylogenetic or baraminic relationships. The alternative would be to scrap baraminology and revert to a position very close to species fixity.
Todd knows that species aren't fixed. That's got to be the case since there are more species alive today than could possibly have fit on the ark. But he's like my professor. The Bible comes first. This position forces Todd into the amazing statement that follows:
The similarity of the human and chimpanzee genomes offers evidence that the genome could primarily be a repository. If the fixed nucleotide mismatches between the chimpanzee and human genomes are 1.06%, then the original nucleotide identity could be as high as 99%. At that high level of similarity, perhaps it is not impossible to believe that God created humans and chimpanzees with identical genomes. The known differences between human and chimpanzee biochemistry (see Varki 2000; Varki and Atheide 2005) may well rule this out, but it is an intriguing possibility. Even at 99% identity, however, the biological and behavioral differences between chimpanzees and humans indicate that the source of these differences is not likely to be found entirely in the genome sequences. Theologically, the high similarity of humans and chimpanzees reinforces our spiritual – not physical (Ecc. 3:18-21) – distinctiveness from the animals. It is the image of God that makes us human not some intrinsically valuable genetic element.
When the facts are in your favor, argue the facts. When the law is in your favor, argue the law. When the law and the facts aren't in your favor, bang the table. In this case, Todd can't believe his senses, because the Bible tells him otherwise. So the Bible must be right, even though there's no evidence there to back it up. At least Todd is honest.
The entire premise of Intelligent Design is that it is different from modern science. Yet Ben Stein's film showed not one example of someone doing good scientific work that was contributing to a viable research program who lost a job because of it. The job of scientists is to make valuable contributions. A major difficulty in trying to make a valuable contribution to a field is not believing in its central points.
Imagine trying to get a job at CERN if you didn't believe quantum mechanics was true. Imagine trying to get a job at NASA if you thought the moon landing was faked. Imagine trying to get a job as a dentist if you thought that cavities came from masturbation.
That's all Ben Stein had to show in his film, with the exception of the insipid Hitler porn, and he tried to claim that it was discrimination. Ben didn't even have the honesty of Todd, who I hope one day quits trying to defend the indefensible.
I hope this examination of ID and creationism can show the tip of the iceberg that changed my mind.