Saturday, August 06, 2005
The Creationist Model
I spent a considerable amount of time writing this post on FreeRepublic, so I thought I would post it here as well for future keeping. It was in response for someone asking me how I thought biodiversity occurred:
"Really? Let's see it, in your own words. What is your ID hypothesis?"
It's actually fairly simple. There are three basic mechanisms for biodiversity for a creationist:
* heterozygous fractionation -- basic mendellian speciation
* darwinism -- this is usually deleterious
* genomic modularity -- this is the innate ability of a genome to reconfigure itself in response to environmental stress.
The first has been fairly well proved. It was found by a creationist (Mendel) and no one doubts that it occurs. The second is also fairly standard, the difference being that creationists do not think that Darwinism has any significant creative power.
For example, if you set off fireworks, the direction of the fireworks is set mostly by the direction you aim the firework, and the explosive properties of it. The wind can modify the course a little bit, but it would be silly for someone viewing the interplay of a spark with the wind to say that the wind was the ultimate cause for the direction of the spark. The primary direction was set by other factors. I've also related it to breaking in a shoe. Breaking in a shoe changes the shoe itself, and sometimes even gives a better fit. But it would be futile to try and view the creation process for the shoe as a continuous breaking-in process -- it just doesn't work.
The final mechanism proposed by creationists is genomic modularity -- the ability of genomes to modify themselves. This goes under quite a few names, including natural genetic engineering, altruistic genetic elements, the AGE-ing process, and genomic modularity. Basically, it says that the cell and the genome can work together to reconfigure the genome in response to the environment. In fact, this is the primary role of transposons. There are several ways that this can happen:
1) some genes remain inactive in the genome until they are needed, these are pre-coded adaptations that simply get switched on
2) organisms can create new genes in response to specific environmental stresses
3) organisms can exchange DNA with their environment to better adapt to the organisms living in the area
4) probably some other ways people haven't thought of yet.
An example of (1) is in photosynthesis. There are two primary types of photosynthesis - C3 and C4. Evolutionary trees would have C4 photosynthesis being developed 16 different times! However, in many genuses examined within families that have C4 photosynthesis, it is found that even the genuses that do not have C4 photosynthesis still contain all of the genes necessary to pull it off. The difference being the promoter regions of the C3 and C4 genes. So, not only did C4 photosynthesis evolve 16 times, some of the plants have all of the genes necessary to do C4 photosynthesis and yet do not. C4 is quite a complicated pathway, needing an entire new set of organnelles to perform. The creationist explanation is that these families (or technically, holobaramins, but I will use family since its a more familiar term and is roughly correct) were created with both sets of genes, and the cell is able to activate different types of photosynthesis under environmental stress (likely related to a drop in available C02 gases).
Evidence of (2) is available in looking at pseudomonas. This has a highly adaptable genome, and in fact is able to manufacture _systems_ of genes for adapting to new food sources in less than 9 days. You might wonder, "if genomes can manufacture their own genes, then why would one even need to make a polyphyletic hypothesis?" As I explain in http://crevobits.blogspot.com/2005/08/genetic-algorithms.html the only way to make variation algorithms work is to have a significant portion of the algorithm be non-varying. In fact, it is the constraints imposed by the non-varying part of the algorithm that is most important to the algorithms function, even for those algorithms which rely on codal change to work. In fact, they would in fact be functionless if _everything_ could change. Error catastrophe would occur in just a few generations. In fact, not only can pseudomonas manufacture genes for food production in new environments, it will place these newly manufactured genes onto plasmids for transmission to the rest of the population. Likewise, there is a general mechanism in many bacteria called the SOS mechanism, which induces such change in times of extreme stress for the population, much like the bacteria is performing a full search of its variable capacity in order to find a pattern that works in the environment. As evidence that process does not change the basic patterns of the organism, note that pseudomonas was discovered in the 1800's and STILL is readily identifiable by the same description as it was then, despite its ability to manufacture new gene _sets_ in less than 9 days.
3) This one is not as fully fleshed out yet (none of them are very much, due to the very limitted amount of money available for creationist research), but Orchids are able to adapt morphologically to the insects that are nearby. There are several organisms that appear to "know" how to adapt to the local environment. One mechanism of this is likely interspecies gene transfer along mechanized lines. Viruses are thought to be genetic carriers designed to help this process along faster.
In the young-earth creationist model, the general trend of life is downward, because since the fall we no longer have God sustaining us as He once did. Therefore, random mutations have a generally deleterious effect on the harmony that these systems have. Viruses have gone from being beneficial components to harmful because they have lost the specificity they once had -- whether site specificity, organismal specificity, or lost their ability to constrain reproduction. For example, a virus which may be beneficial in one family may be harmful to another. If the mechanisms for keeping family specificity is broken, then the virus goes from being beneficial to harmful. Likewise, mutations on the transposons or on other components that deal with activation/deactivation of genes or with the natural genetic engineering have caused these mechanisms to not be quite as able as they have been in the past. While it is possible for an "unexpected" mutation to confer an advantage in some cases, in most cases it is deleterious, but not deleterious enought to affect propogation. Especially mutations within an adaptive mechanism, since that would not directly affect the organism's fitness within an existing environment, and thus could easily spread throughout the population.
Anyway, I discuss how one might weigh the benefits of each approach here:
http://crevo.blogspot.com/2005/06/evolution-chance-and-design-to-cb940.html
Also, the link I pointed out earlier in this post is also relevant in such a discussion.
"Really? Let's see it, in your own words. What is your ID hypothesis?"
It's actually fairly simple. There are three basic mechanisms for biodiversity for a creationist:
* heterozygous fractionation -- basic mendellian speciation
* darwinism -- this is usually deleterious
* genomic modularity -- this is the innate ability of a genome to reconfigure itself in response to environmental stress.
The first has been fairly well proved. It was found by a creationist (Mendel) and no one doubts that it occurs. The second is also fairly standard, the difference being that creationists do not think that Darwinism has any significant creative power.
For example, if you set off fireworks, the direction of the fireworks is set mostly by the direction you aim the firework, and the explosive properties of it. The wind can modify the course a little bit, but it would be silly for someone viewing the interplay of a spark with the wind to say that the wind was the ultimate cause for the direction of the spark. The primary direction was set by other factors. I've also related it to breaking in a shoe. Breaking in a shoe changes the shoe itself, and sometimes even gives a better fit. But it would be futile to try and view the creation process for the shoe as a continuous breaking-in process -- it just doesn't work.
The final mechanism proposed by creationists is genomic modularity -- the ability of genomes to modify themselves. This goes under quite a few names, including natural genetic engineering, altruistic genetic elements, the AGE-ing process, and genomic modularity. Basically, it says that the cell and the genome can work together to reconfigure the genome in response to the environment. In fact, this is the primary role of transposons. There are several ways that this can happen:
1) some genes remain inactive in the genome until they are needed, these are pre-coded adaptations that simply get switched on
2) organisms can create new genes in response to specific environmental stresses
3) organisms can exchange DNA with their environment to better adapt to the organisms living in the area
4) probably some other ways people haven't thought of yet.
An example of (1) is in photosynthesis. There are two primary types of photosynthesis - C3 and C4. Evolutionary trees would have C4 photosynthesis being developed 16 different times! However, in many genuses examined within families that have C4 photosynthesis, it is found that even the genuses that do not have C4 photosynthesis still contain all of the genes necessary to pull it off. The difference being the promoter regions of the C3 and C4 genes. So, not only did C4 photosynthesis evolve 16 times, some of the plants have all of the genes necessary to do C4 photosynthesis and yet do not. C4 is quite a complicated pathway, needing an entire new set of organnelles to perform. The creationist explanation is that these families (or technically, holobaramins, but I will use family since its a more familiar term and is roughly correct) were created with both sets of genes, and the cell is able to activate different types of photosynthesis under environmental stress (likely related to a drop in available C02 gases).
Evidence of (2) is available in looking at pseudomonas. This has a highly adaptable genome, and in fact is able to manufacture _systems_ of genes for adapting to new food sources in less than 9 days. You might wonder, "if genomes can manufacture their own genes, then why would one even need to make a polyphyletic hypothesis?" As I explain in http://crevobits.blogspot.com/2005/08/genetic-algorithms.html the only way to make variation algorithms work is to have a significant portion of the algorithm be non-varying. In fact, it is the constraints imposed by the non-varying part of the algorithm that is most important to the algorithms function, even for those algorithms which rely on codal change to work. In fact, they would in fact be functionless if _everything_ could change. Error catastrophe would occur in just a few generations. In fact, not only can pseudomonas manufacture genes for food production in new environments, it will place these newly manufactured genes onto plasmids for transmission to the rest of the population. Likewise, there is a general mechanism in many bacteria called the SOS mechanism, which induces such change in times of extreme stress for the population, much like the bacteria is performing a full search of its variable capacity in order to find a pattern that works in the environment. As evidence that process does not change the basic patterns of the organism, note that pseudomonas was discovered in the 1800's and STILL is readily identifiable by the same description as it was then, despite its ability to manufacture new gene _sets_ in less than 9 days.
3) This one is not as fully fleshed out yet (none of them are very much, due to the very limitted amount of money available for creationist research), but Orchids are able to adapt morphologically to the insects that are nearby. There are several organisms that appear to "know" how to adapt to the local environment. One mechanism of this is likely interspecies gene transfer along mechanized lines. Viruses are thought to be genetic carriers designed to help this process along faster.
In the young-earth creationist model, the general trend of life is downward, because since the fall we no longer have God sustaining us as He once did. Therefore, random mutations have a generally deleterious effect on the harmony that these systems have. Viruses have gone from being beneficial components to harmful because they have lost the specificity they once had -- whether site specificity, organismal specificity, or lost their ability to constrain reproduction. For example, a virus which may be beneficial in one family may be harmful to another. If the mechanisms for keeping family specificity is broken, then the virus goes from being beneficial to harmful. Likewise, mutations on the transposons or on other components that deal with activation/deactivation of genes or with the natural genetic engineering have caused these mechanisms to not be quite as able as they have been in the past. While it is possible for an "unexpected" mutation to confer an advantage in some cases, in most cases it is deleterious, but not deleterious enought to affect propogation. Especially mutations within an adaptive mechanism, since that would not directly affect the organism's fitness within an existing environment, and thus could easily spread throughout the population.
Anyway, I discuss how one might weigh the benefits of each approach here:
http://crevo.blogspot.com/2005/06/evolution-chance-and-design-to-cb940.html
Also, the link I pointed out earlier in this post is also relevant in such a discussion.
Permanent Link posted by crevo @ 5:47 AM 
