Wednesday, March 17, 2010

Dead Genes

On page 66, Coyne says that "when a trait is no longer used, or becomes reduced, the genes that make it don't instantly disappear from the genome: evolution stops their action by inactivating them, not snipping them out of the DNA." If these genes are dead and have no purpose in an organism, what is an advantage of passing them on to the next generation? Besides consuming unnecessary energy in the DNA replication process, what other negative effects could passing on dead genes have? Also, how can dead genes help scientists trace down certain aspects of evolution?


  1. While these dead genes may seem to serve no function, non coding segments have actually been found to aid in gene regulation. According to, "...ncRNAs produce functional RNA molecules rather than encoding proteins and have been found to have roles in a plethora of cellular processes including transcriptional regulation, RNA processing and modification, mRNA stability, and even protein degradation." The Campbell book suggests that these DNA coding segments play a role in RNA processing, mRNA degredation and the initiation of translation. During RNA processing, the non coding DNA will help regulate alternative RNA splicing, which is the process in which several different mRNAs can be derived from a single transcript segment simply by changing which parts are introns and exons. In eukaryotes, the non coding segments will activate or inactive the protein factors that initiate translation. One specific example is after an egg is fertilized, the non coding DNA will activate the translation initiation factors which will then start the process of translation. Overall, these non coding segments actually play a big role in gene regulation while at the same time helping us connect them to their evolutionary ancestors based on common genes.

  2. These "dead genes" appear to have no purpose to living organisms today other than the regulation of other genes, but at one point in time, they might have served a purpose necessary for the survival of the organism. For now, the gene is simply inactive, stored in the genome, but there is no definite guarantee that it will stay inactive in future generations. Because our environment is constantly changing, it could be a potentially greater cost to the species to dispose of an inactive gene and require it later as compared to spending the extra energy now in order to replicate the gene.

    However, holding on to this seemingly useless sequence of DNA could have negative effects on the species. It is believed that 3-8% of the human genome is composed of viral DNA which has been inserted into the genome in past generations. Since viruses cannot replicate their own DNA, they use other cells. Of the two types of replication, the Lysogenic Cycle implants viral DNA into the cell and allows the cell to divide naturally. If something triggered the activation of the viral DNA, changing it to the lytic cycle, it would result in the death of the cell. Carrying such DNA is a potential danger to the cell's survival.

    Whether the "dead genes" are necessary or a detriment to the survival of the cell, they aid in scientists mapping of our evolutionary past. With evolutionary trees, it is debated which branch diverged first. Early evolutionary trees focused on the anatomy of the species; however, modern technology allows scientists to look at the proteins made by different species. As a result, species can be grouped by unique proteins. Having "dead genes" allows scientists to connect species which are farther apart because the gene was utilized in the past when the two species would have been closer together.

  3. While once useful, dead genes are found in the genomes of many species, suggesting that these genes were once active in a common ancestor, and that natural selection has disposed of the need for these genes. This is one of Coyne's arguments in favor of natural selection and evolution, that a creator, in making “all species […] from scratch” (67) would not design these species to have such useless genes. Dead genes are the “recipe” for making once necessary proteins, and over time, these have ceased to be expressed, suggesting that making these proteins would not be beneficial towards the ability of the individual to survive and reproduce. By tracing these silenced genes back to a common ancestor, we can discover the evolutionary changes that have taken place, especially since, as Coyne states, that we still find these nonfunctional genes in related species (67). Noting this continuity in the gene pool, and given our astounding ability to sequence the genome of species, we may discover evolutionary relationships based on our genome. Coyne gives a very explicit example of this, on page 68, using the GLO pseudogene. Due to a mutation, the GLO gene is silenced in humans; primates are noted to have the exact same mutation (a deletion mutation) which suggests that humans and primates have descended from the same common ancestor. However, he makes an important distinction; guinea pigs also have the GLO gene silenced, yet they are supposed not to have descended from the same common ancestor as humans and primates because it was inactivated in a different way, probably due to similar environmental or situational circumstances (such as vitamin C already being in abundance in their diet) that allowed for this independent silencing of the GLO gene. Going along with the idea of natural selection, inactivating this gene and therefore preventing the process of transcription and translation would allow the organism to allocate more energy and resources towards other, more important metabolic pathways, rather than wasting energy maintaining one that is unnecessary.

    I take issue with something stated above, that “it could be a potentially greater cost to the species to dispose of an inactive gene and require it later as compared to spending the extra energy now in order to replicate the gene.” While thinking about it, this assertion is very sound, given the mechanism for natural selection, this is most likely not a valid proposal for why there is an advantage for passing these dead genes on to the next generation – it is probably much simpler than that. The mechanism for evolution, natural selection, acts in present time; that is, unsatisfactory genes, with respect to the current environment, are less likely to be passed on to the next generation. Natural selection does not take the future into consideration; it will do anything to improve the organism's fitness, and the fitness of the next generation, whose genes come directly from the present generation.

  4. (cont'd)
    Point mutations are much more likely to happen than entire segments of genes being deleted from the genome. The reason for this is, as stated in our textbook, that larger mutations tend to be lethal (298), because their effects are perpetuated throughout the gene. Many genes are found on the same strand of DNA, thus any kind of mutation may affect more than just the gene directly acted upon. As suggested by the book, a large-scale mutation or deletion would most likely not allow the organism to survive, due to the changing of multiple crucial genes. These organisms would most likely not survive to reproduce, therefore these changes in genes to create dead genes would be gradual and probably small-scale. Also, genes may overlap on the same chromosome; that is, the end of one gene may, in fact, be the beginning of another gene. Cutting out genes arbitrarily may destroy nearby genes.

    Since mutations are likely to happen, given evolutionary time, any of the harmless mutations that improve the individual's fitness (by allowing them to conserve or allocate energy better, or by allowing their reproductive fitness to increase) will tend to pass onto successive generations.