Tuesday, March 21, 2006
Genome Decay
Genome decay is an interesting topic for creationists. The basic idea is this:
There are several sources on this subject, and I have not had time to read all of all of them. Jerry Bergman gave an excellent overview of this subject in Darwinism and the Deterioration of the Genome (membership to CRS required, if you don't have a membership, the abstract is here). Todd Wood gave a good overview of a specific instance in Genome Decay in the Mycoplasmas, where he hypothesized that pathogenicity in many instances is the result of the loss of regulatory genes. This study (summarized here and pointed out to me by MikeGene) indicates that a disruption of a single gene can cause a relationship to go from symbiotic to parasitic. John Sanford wrote a whole book on this (which I have not yet had the opportunity to read) called Genetic Entropy & the Mystery of the Genome.
This post is mostly a summary of Bergman's paper. The rest will likely be dealt with at greater length as I have time.
Bergman starts by pointing out that in neo-Darwinistic theory, the only source of real biological novelty is in random mutation. Minor variation can be explained through sexual recombination, but the real stuff of evolution is in the mutations.
Note that Bergman uses slightly different definitions than what are standard. He uses "mutation" to refer to genomic change which is not specific responses to stress. In papers where he is discussing genomic changes which are in response to specific stresses, he uses the term "recombination". I think that is a much better terminology than the standard usage of "mutation" for both directed and undirected change.
Bergman's first point, however, is that mutations are not random -- they show several distinct biases. Such biases over long periods, even balanced by natural selection, would produce a genome that was dominated by a few amino acids -- serine, arginine, leucine, valine, proline, threonine, alanine, and glycine. However, the patterns found in the genome are in opposition to what would be expected from mutation. This is even more striking when we examine DNA that has no known function. This indicates that mutation has only had a small effect in producing the modern genome.
Bergman also discusses mutational hotspots, showing that the locations where mutations are likely to occur are limitted. Personally, I think he did not do a good enough job explaining the difference between a mutational hotspot and a hotspot that is the result of adaptive recombination, and perhaps even a hotspot that is the result of a now-failing, disfunctional recombination system (genome deterioration will also bring about a deterioration in adaptive mechanisms).
He surveyed the beneficial mutation literature, and found almost all of them to be loss of function mutations. I.e. -- it was an instance of genome degredation, but one which happened to be useful to a certain degree. This supports, not negates, the hypothesis of genome degredation.
Bergman has an excellent table listing the biases of mutations, and perhaps I will see if I can reproduce it here.
My main criticisms are Bergman are these:
We really need to stop focusing on taking down Darwinism (honestly, this is already complete -- it will just take a generation for the old guard to step down), and start work on positive models of creation.
Anyway, the paper is much better than I could do it justice for here. The Creation model of an initially very good creation which has suffered from the fall works well with the concept of genome decay. Wood has pointed out that the decrease in speed of adaptation since after the flood could be the result of the decay of adaptation mechanisms.
- The copying mechanism for cells is excellent, but not perfect
- The double-helix is likewise good at maintaining integrity, but not perfect
- The distribution of these random (as opposed to adaptive) mutations are well-known
- Natural selection is good at removing bad codes, but not degraded or neutral codes
- Therefore, the genome will slowly degrade and lose information over time
There are several sources on this subject, and I have not had time to read all of all of them. Jerry Bergman gave an excellent overview of this subject in Darwinism and the Deterioration of the Genome (membership to CRS required, if you don't have a membership, the abstract is here). Todd Wood gave a good overview of a specific instance in Genome Decay in the Mycoplasmas, where he hypothesized that pathogenicity in many instances is the result of the loss of regulatory genes. This study (summarized here and pointed out to me by MikeGene) indicates that a disruption of a single gene can cause a relationship to go from symbiotic to parasitic. John Sanford wrote a whole book on this (which I have not yet had the opportunity to read) called Genetic Entropy & the Mystery of the Genome.
This post is mostly a summary of Bergman's paper. The rest will likely be dealt with at greater length as I have time.
Bergman starts by pointing out that in neo-Darwinistic theory, the only source of real biological novelty is in random mutation. Minor variation can be explained through sexual recombination, but the real stuff of evolution is in the mutations.
Note that Bergman uses slightly different definitions than what are standard. He uses "mutation" to refer to genomic change which is not specific responses to stress. In papers where he is discussing genomic changes which are in response to specific stresses, he uses the term "recombination". I think that is a much better terminology than the standard usage of "mutation" for both directed and undirected change.
Bergman's first point, however, is that mutations are not random -- they show several distinct biases. Such biases over long periods, even balanced by natural selection, would produce a genome that was dominated by a few amino acids -- serine, arginine, leucine, valine, proline, threonine, alanine, and glycine. However, the patterns found in the genome are in opposition to what would be expected from mutation. This is even more striking when we examine DNA that has no known function. This indicates that mutation has only had a small effect in producing the modern genome.
Bergman also discusses mutational hotspots, showing that the locations where mutations are likely to occur are limitted. Personally, I think he did not do a good enough job explaining the difference between a mutational hotspot and a hotspot that is the result of adaptive recombination, and perhaps even a hotspot that is the result of a now-failing, disfunctional recombination system (genome deterioration will also bring about a deterioration in adaptive mechanisms).
He surveyed the beneficial mutation literature, and found almost all of them to be loss of function mutations. I.e. -- it was an instance of genome degredation, but one which happened to be useful to a certain degree. This supports, not negates, the hypothesis of genome degredation.
Bergman has an excellent table listing the biases of mutations, and perhaps I will see if I can reproduce it here.
My main criticisms are Bergman are these:
- He fails to mention recombination as a source of genetic variation
- He fails to note that many previously identified "mutations" wound up being just more recombinational activity
- He uses genome decay as more of a criticism of Darwinism than as a useful step towards understanding Creation. For instance -- what can we expect the genome to look like 100 years down the road? How does genome decay in certain parts of the genome affect different systems? How is the adaptive recombination systems in the genome affected by genome decay?
We really need to stop focusing on taking down Darwinism (honestly, this is already complete -- it will just take a generation for the old guard to step down), and start work on positive models of creation.
Anyway, the paper is much better than I could do it justice for here. The Creation model of an initially very good creation which has suffered from the fall works well with the concept of genome decay. Wood has pointed out that the decrease in speed of adaptation since after the flood could be the result of the decay of adaptation mechanisms.
Permanent Link posted by crevo @ 5:31 AM 
