Thursday, April 2, 2009
Fossil Genes
On page 118, Carroll starts talking about a unique fish, Latimeria chalumnae, that was found many years ago but was preserved for the years to come. This fish has been labeled as a "living fossil" because the chances of finding and studying another one like it is very slim. Carroll compares this "living fossil" to the idea of "fossil genes". Why are fossil genes so important and how can they help us understand the behaviors and lifestyles of the species that are present in our world today?
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Fossil genes are genes that have decayed due to mutations and to the relaxation of natural selection. The relaxation of natural selection occurs because the gene no longer serves as an adaptation that increases an organism’s life fitness. The organism does not use the gene as its ancestors had, or the organism depends more on its other genes to replace the function of the fossil gene. Because natural selection no longer selects for organisms that contain the gene, mutations accumulate in the gene because there is no mechanism retaining the data of the gene. Fossil genes are important because they represent the shifts in lifestyles of different species over time. For example, the ancestors of the coelacanth had a functional SWS opsin; however, the coelacanth itself contains one fossil SWS opsin gene which contained a mutation the caused a premature termination. As we have learned, the nonsense mutation occurs when a codon is changed into a premature stop codon, which terminates the translation of the protein, making the protein nonfunctional. The fossil opsin gene came to be due to the living habitats of the coelacanth. Because the coelacanth live in deep waters, the coelacanth relies on a dim-light rhodopsin, as light is absent in deep waters. The coelacanth would not be able to detect color even if they possessed the SWS opsin gene due to the absense of light, so the SWS opsin gene decayed due to its uselessness. The influence of the environment relates to the theme of interaction with the environment. Because the environment does not provide the coelacanth with light, the SWS opsin gene becomes fossilized as its usefulness fades. The SWS opsin gene was also a fossil gene in whales and dolphins, which rely more on their dim-light opsin as well. In dolphins, a deletion of a base occurs early on in the SWS opsin gene. We have learned that such a deletion would throw off the three-base codons, and the protein would become nonfunctional due to the different amino acids that code for the new protein. The fossil gene of the whales and dolphins represent a shift in environment. Some whales and all dolphins descended from terrestrial mammals. Because their ancestors lived on land, they possessed a functional SWS opsin. As the whales and dolphins returned to the water, they did not use their SWS opsin, and the SWS opsin gene became fossilized. The loss of the SWS opsin relates to the theme of evolution because the dolphins and whales gained new adaptations when they shifted from a terrestrial to a marine environment. Their new adaptations included different opsin genes, and the SWS opsin gene was no longer needed. Fossil genes also depend on behavior. In humans, “about half of all our olfactory receptor genes are fossilized and incapable of making functional receptors” (128). The olfactory receptors can detect different types of odors, and the limited receptors of humans (5 out of 200) show that humans cannot detect smells as well as other animals. The fossilized olfactory receptors show that humans depend more on their sight than on their sense of smell. Because human sight is the more useful sense, replacing some functions of the sense of smell, the sense of smell is not used as much, resulting in fossilized olfactory genes.
ReplyDeleteAs Jennifer Ding stated in the above comment, fossil genes are the consequence of the continuing action of mutation over time - with the relaxation of natural selection. The purpose of my post is to expand upon the previous notions described in Ms. Ding's post: "The fossilized olfactory receptors show that humans depend more on their sight than on their sense of smell. Because human sight is the more useful sense, replacing some functions of the sense of smell, the sense of smell is not used as much, resulting in fossilized olfactory genes."
ReplyDelete"The fossilization and loss of genes are powerful arguments against notions of 'design' or intent in the making of species," (Carroll 136). Carroll makes a point that fossil genes are pieces of evidence that can be used to support the idea of natural selection. Natural selection is not an engineer, a designer, or a creator - it does not build a species to plan for the future or preserve what is not used. "Over time, chance mutations will accumulate, eventually disrupting the text of unused or unnecessary genes," (Carroll 136). Fossil genes are more open to be mutated because of the relaxation of natural selection. With so many genes in the genetic code of many species, one would think that many of them are useless. In fact, they are remnants - fossil genes - but their importance is to prove that "design" and "progression" are not the goals of natural selection. Natural selection acts to "make the fittest" so to say.
"Furthermore, the repetition of gene fossilization in different ancestors of entirely different groups of animals is striking evidence that, when selection is relaxed on a particular trait, the same events will repeat themselves in DNA," (Carroll 137) and these events contribute to the main message to be taken away from the chapter: evolution does not work in one single direction - it does not keep adding on bits of genetic code through mutations - there are losses along the way in the form of fossil genes.
To add to Ms. Ding's post of different behaviors and lifestyles of different species today, is the inclusion of the human gene MYH16. There is a two base deletion in the gene which causes an error in the reading frame of the DNA. To use an example from the Campbell textbook on page 308, consider the statement: "The red dog ate the cat." Group the letters incorrectly by starting at the wrong point and the result will be gibberish: "her edd oga tet hec at." A polypeptide will only be made correctly if the reading frame is correct. In humans, the gene had this error, but in chimps, gorillas, macaques, and orangutans the gene is still present. The MYH16 protein is made in a subset of muscles, particularly that of the temporalis muscle in the apes (which use the muscle as a part of their large jaws in chewing). The MYH16 protein forms part of the large fibers within the muscles. However, as a comparison, humans have a reduced version of the muscle and the muscle fibers are much smaller. If such a gene was instantly lost in one step, the organism would not be able to chew. In order for the gene to have been lost, it would have to take a series of steps where muscle mass was not lost in one step, "I think that the explanation for the fossilization of MYH16 is more likely to be similar to the history of globins in the icefish - that is, the muscle was becoming reduced by other genetic pathways and the fossilization of the MYH16 was most likely a later event after the gene became dispensable," (Carroll 136). Thus, fossil genes are necessary in order to understand our own lifestyle - we don't have the muscles to chew as much as an ape. The biological theme that this would relate to is obviously evolution, but also interaction with the environment and heritable information in that genetic info was lost and humans have to use the muscles to interact with their own environment to receive food.
Please refer to Campbell 308 to review reading frames.
Fossil genes are evolutionary markers on the genome that can be used to determine past behaviors and lifestyle of species present in our world today. The power of fossil genes to reveal an organism’s past life style stems from fossil gene’s creation. As the name implies, fossil genes are genes that have been fossilized – genes that no longer have any use in the current existing organism. However fossil genes were once functional genes in the ancestors of the current organisms. The cause of a gene to be fossilized is due to the shift in selection pressure from the environment. For example, when a population of Astyanax mexicanus began to live in caves, there was a relaxation in selection pressure on their eye sight and body color because “in the dark who cares what you look like” (Carroll 149). With selection pressure relaxed, mutations started to accumulate in the genes that code for eyesight and a black body color. Mutations could occur in many different ways. Nonsynonymous mutations are a change in the codon that results in the substitution of an amino acid. This would consequentially change the protein’s primary structure and the protein’s overall conformation. Base-pair substitution creates missense mutation but the effect on protein conformation could be either profound or inconsequential, depending on the substituted amino acid. For example if a stop codon substituted for a regular amino acid, the gene would terminate prematurely. A base pair insertion and deletion would cause a shit in the reading frame and become a nonsense mutation. These different type of mutations cause the genes that code for eyesight and body color to degenerate. As a result, cave population of the fish has become blind and albino. However, the fossilized genes can still tell a lot about the fish’s history. Because the genes once coded for eyesight and a black body color, biologist know that blindness and albinonism was not inherent in the cave fish. Biologist can deduce that the ancestors of the cave fish had once lived near the surface where there is light. A similar case could be made for the human olfactory system. The fact that humans “have only 5 functional V1r genes out of the more than 200 in our genome” is a good indication that our hominid ancestors relied much more on the sense of smell than humans today.
ReplyDeleteIn the previous response, Daniel Sheikh mentioned that fossil genes are an ostensible part of evolution. I agree with this statement and strongly believe that fossil genes provide solid evidence that evolution is a viable theory to any nonbeliever. On the contrary, if fossil genes did not exist, then there would be very legitimate reason to question the credibility of evolution. Nevertheless the existence of fossil genes is proof that organisms does change over time. When a feature of an organism is no longer needed, mutations in the gene that code for this feature will cause this feature will degenerate until it becomes no more than a token. This is evolution: organisms constantly modifying themselves due to selection pressure so that they are the fittest in their environment.