Question 1. What were the main findings of the ENCODE project?
Only a small percent of the 3.2 Gb human genome encodes for genes but much of the remainder was chalked up a junk. However, the ENCODE project suggests that up to 80% of the genome consist of various active regulatory, and structurally significant regions.
Question 2. Define “junk DNA.”
Junk DNA plays no active role in influencing an individual organism’s survival or reproduction, i.e. it does not code for or regulate transcription.
Question 3. Define the “C-value paradox,” and give one example of it in a group of organisms. What might account for this paradox?
Under the C-value paradox, we note that as genome size increases an increase in the complexity of the organism is …show more content…
Define a “functional element (FE).” In the ENCODE project, what biochemical activity makes up most of the newly described FEs?
All parts of the genome that encode for a protein, or RNA are the classical genetic elements that fall under the ENCODE description of functional elements. However, if a given region preforms any repeatable biochemical process it can be defined as an FE, including structural code or protein binding sites.
Question 5. What are Doolittle’s two outcomes of his thought experiment? Which outcome seems most likely, and why?
The first of Doolittle’s outcomes is that functional elements are relatively consistent across a range of C-values. Secondarily, he suggests that as C-value increases the number of functional elements in the genome increases. The latter would suggest that organisms with larger genomes would therefore be more complex based on the increase in non-informational functionality. This pattern is not clear in eukaryotic genomes where drastically different genomes can result in similar levels of complexity (frog and salamander) or amoeba genome’s can dwarf more complete organism’s genomes.
**Reread and reassess
**Second one
Question 6. How does Doolittle define …show more content…
Beyond the examples listed by Doolittle we could infer that stomach sound would be considered an exaptation as well because they are not, likely, under selective pressure but evolved nevertheless.
Question 8. What method does Doolittle think is the most reliable way to infer true function? Why? What is the other acceptable way? Why? And what is the least desirable way? Why? Which did ENCODE use?
Selected effect, or evolutionary conservation is the most reliable method for inferring functionality according to Doolittle. This method is based on a logical assessment that if an element is functional it will be maintained in divergent lineages as the result of purifying selection. Another common method is experimental ablation, a perturbation of a system experimentally allows for a connection to be made between the activity of a region and the organisms phenotype, however, such a method can result in the formation of unsubstantiated causations (i.e. a given gene causes a phenotype). Finally, the least desirable way, and the one on which ENCODE is based on is that function is assumed bases solely on existence in a genome. This is a dangerous based on the affiliated assumption that selection is the only major driver of genome evolution, which is very unlikely. Moreover, this assumption fails to tell us anything about what the function may
Only a small percent of the 3.2 Gb human genome encodes for genes but much of the remainder was chalked up a junk. However, the ENCODE project suggests that up to 80% of the genome consist of various active regulatory, and structurally significant regions.
Question 2. Define “junk DNA.”
Junk DNA plays no active role in influencing an individual organism’s survival or reproduction, i.e. it does not code for or regulate transcription.
Question 3. Define the “C-value paradox,” and give one example of it in a group of organisms. What might account for this paradox?
Under the C-value paradox, we note that as genome size increases an increase in the complexity of the organism is …show more content…
Define a “functional element (FE).” In the ENCODE project, what biochemical activity makes up most of the newly described FEs?
All parts of the genome that encode for a protein, or RNA are the classical genetic elements that fall under the ENCODE description of functional elements. However, if a given region preforms any repeatable biochemical process it can be defined as an FE, including structural code or protein binding sites.
Question 5. What are Doolittle’s two outcomes of his thought experiment? Which outcome seems most likely, and why?
The first of Doolittle’s outcomes is that functional elements are relatively consistent across a range of C-values. Secondarily, he suggests that as C-value increases the number of functional elements in the genome increases. The latter would suggest that organisms with larger genomes would therefore be more complex based on the increase in non-informational functionality. This pattern is not clear in eukaryotic genomes where drastically different genomes can result in similar levels of complexity (frog and salamander) or amoeba genome’s can dwarf more complete organism’s genomes.
**Reread and reassess
**Second one
Question 6. How does Doolittle define …show more content…
Beyond the examples listed by Doolittle we could infer that stomach sound would be considered an exaptation as well because they are not, likely, under selective pressure but evolved nevertheless.
Question 8. What method does Doolittle think is the most reliable way to infer true function? Why? What is the other acceptable way? Why? And what is the least desirable way? Why? Which did ENCODE use?
Selected effect, or evolutionary conservation is the most reliable method for inferring functionality according to Doolittle. This method is based on a logical assessment that if an element is functional it will be maintained in divergent lineages as the result of purifying selection. Another common method is experimental ablation, a perturbation of a system experimentally allows for a connection to be made between the activity of a region and the organisms phenotype, however, such a method can result in the formation of unsubstantiated causations (i.e. a given gene causes a phenotype). Finally, the least desirable way, and the one on which ENCODE is based on is that function is assumed bases solely on existence in a genome. This is a dangerous based on the affiliated assumption that selection is the only major driver of genome evolution, which is very unlikely. Moreover, this assumption fails to tell us anything about what the function may