Cladogram
In this project, we were given a small container of hardware pieces, including washers, nails, and screws. Pretending they were fossils of different organisms, we made a cladogram based on their traits, as well as a story behind their environment and why they evolved.
Timeline
For this project, we picked a living organism (in our case, the great white shark) and traced its evolutionary history. We started our timeline in the Silurian Era, when some fish started to develop cartilage skeletons. We then followed it into the Devonian Era, where these fish lost their scales, a distinct feature of the modern shark. In the Cretaceous Era, some sharks developed the white underbelly of the great white. Although it has been long believed that the great white evolved from the megalodon, new evidence suggests that it actually evolved from mako sharks. The modern great white shark's cartilage skeleton and serrated teeth show its long evolutionary timeline.
PCR Lab
Purpose
The purpose of this lab was to learn about common lab procedures, as well as to trace our own genetic history using PCR and gel electrophoresis.
Hypothesis
If what I have been told about my ancestry is correct, then the lab should show that I am European.
Procedure
We followed a lab procedure provided by BABEC. After swishing 10mL of saltwater around our mouths, we used pipettes to transfer 1.5mL of the solution into a plastic tube. We centrifuged it for 1 minute, creating a pellet of cells, and poured off the excess liquid. After resuspending the pellet in the leftover 100μL, we added it to a tube containing 5% Chelex beads. Then, we left the tube on a 99℉ heat block for 10 minutes. We then centrifuged it for another minute, then transferred 50μL of the solution to another tube. We put 20μL of a “master mix” into a PCR tube, then added 20μL of primer mix. We then transferred 10μL of our DNA solution into the PCR tube. After putting it in a thermal cycler, we added 10μL of loading dye to the solution. Shown in the image, we ran 150 volts through a 2% agarose gel for 20 minutes, then stained it with gel red for 72 hours. Lanes A1 and B1 were loaded with a 100 base pair ladder, and the rest of the lanes were loaded with 20μL of a 50μL DNA / 10μL loading dye solution. My sample was in lane B8.
Data and Observations
None of the lanes on our gel gave us results. The pellet of cells looked more like a flat disc than an actual pellet. Our gel,besides the ladders, had only a single speck of dyed substance in one of the lanes. However, this did not correspond to any Alu length.
Analysis
This data shows that we made at least one major error during the lab because we did not get results. This was probably on the day where we had to use ice cubes instead of crushed ice to keep the PCR tubes cold. The process was likely interrupted by us having to keep removing the tube from the ice to add in reactants. Because the results were inconclusive, my hypothesis can neither be shown right nor wrong. In the future, it would be beneficial to have finely crushed ice for PCR. It would be interesting to investigate what else may have compromised our results.
Conclusion
We did not execute the lab procedures properly. For our lab, we were attempting to copy our Alu repeat using a DNA copying process called PCR. We did this by extracting cells from our cheeks and mixing them with various reactants. For the middle phase of this process, it requires the reactants to constantly be cold. Unfortunately, we not have enough results to consider our data set an accurate representation of the frequency of the repeats. This means that we made a mistake in our lab. The most likely cause was that, when we had to keep the PCR tubes cold, we did not have crushed ice. Instead, we had to hold the tubes against whole ice cubes, and had to lift them off for fluid transfer. This likely caused the tubes to warm up, stopping the PCR reaction. Another reason we did this lab incorrectly is that we did not set up a control sample. This means that we had no baseline for whether the error in the lab was a mistake we made or a failure in the chemical process.
The purpose of this lab was to learn about common lab procedures, as well as to trace our own genetic history using PCR and gel electrophoresis.
Hypothesis
If what I have been told about my ancestry is correct, then the lab should show that I am European.
Procedure
We followed a lab procedure provided by BABEC. After swishing 10mL of saltwater around our mouths, we used pipettes to transfer 1.5mL of the solution into a plastic tube. We centrifuged it for 1 minute, creating a pellet of cells, and poured off the excess liquid. After resuspending the pellet in the leftover 100μL, we added it to a tube containing 5% Chelex beads. Then, we left the tube on a 99℉ heat block for 10 minutes. We then centrifuged it for another minute, then transferred 50μL of the solution to another tube. We put 20μL of a “master mix” into a PCR tube, then added 20μL of primer mix. We then transferred 10μL of our DNA solution into the PCR tube. After putting it in a thermal cycler, we added 10μL of loading dye to the solution. Shown in the image, we ran 150 volts through a 2% agarose gel for 20 minutes, then stained it with gel red for 72 hours. Lanes A1 and B1 were loaded with a 100 base pair ladder, and the rest of the lanes were loaded with 20μL of a 50μL DNA / 10μL loading dye solution. My sample was in lane B8.
Data and Observations
None of the lanes on our gel gave us results. The pellet of cells looked more like a flat disc than an actual pellet. Our gel,besides the ladders, had only a single speck of dyed substance in one of the lanes. However, this did not correspond to any Alu length.
Analysis
This data shows that we made at least one major error during the lab because we did not get results. This was probably on the day where we had to use ice cubes instead of crushed ice to keep the PCR tubes cold. The process was likely interrupted by us having to keep removing the tube from the ice to add in reactants. Because the results were inconclusive, my hypothesis can neither be shown right nor wrong. In the future, it would be beneficial to have finely crushed ice for PCR. It would be interesting to investigate what else may have compromised our results.
Conclusion
We did not execute the lab procedures properly. For our lab, we were attempting to copy our Alu repeat using a DNA copying process called PCR. We did this by extracting cells from our cheeks and mixing them with various reactants. For the middle phase of this process, it requires the reactants to constantly be cold. Unfortunately, we not have enough results to consider our data set an accurate representation of the frequency of the repeats. This means that we made a mistake in our lab. The most likely cause was that, when we had to keep the PCR tubes cold, we did not have crushed ice. Instead, we had to hold the tubes against whole ice cubes, and had to lift them off for fluid transfer. This likely caused the tubes to warm up, stopping the PCR reaction. Another reason we did this lab incorrectly is that we did not set up a control sample. This means that we had no baseline for whether the error in the lab was a mistake we made or a failure in the chemical process.
Biology
Evolution is the process in which species traits alter over time. The main force driving evolution is natural selection. Natural selection is the process in which organisms with adaptions (beneficial mutations) beat out their competition, allowing them to survive and reproduce.
Speciation is the process of creating a new species. Sympatric speciation occurs when a small population within a species develops a new adaption and eventually becomes its own species. Allopatric speciation occurs when a species is split by a physical barrier, and the two parts adapt differently to their environments.
Geographic isolation is when a species is split by a physical barrier, such as a mountain or body of water. Behavioral isolation is when organisms cannot reproduce due to differences in their natural behaviors, such as being nocturnal or diurnal. Temporal isolation is when organisms do not reproduce because of a difference in mating season. Reproductive isolation is when species cannot interbreed due to a significant difference in genetic code, such as the number of chromosomes. Isolation usually results in speciation.
Speciation is the process of creating a new species. Sympatric speciation occurs when a small population within a species develops a new adaption and eventually becomes its own species. Allopatric speciation occurs when a species is split by a physical barrier, and the two parts adapt differently to their environments.
Geographic isolation is when a species is split by a physical barrier, such as a mountain or body of water. Behavioral isolation is when organisms cannot reproduce due to differences in their natural behaviors, such as being nocturnal or diurnal. Temporal isolation is when organisms do not reproduce because of a difference in mating season. Reproductive isolation is when species cannot interbreed due to a significant difference in genetic code, such as the number of chromosomes. Isolation usually results in speciation.
Reflection
During this project, I was able to significantly improve my cooperation with the rest of my team. I was more open to others' ideas and compromises than I have been in the past. However, I also maintained my leadership in the group by making sure everyone was on task when they needed to be.
While it has improved, I still need to work on my empathy. I have a natural tendency to push for my ideas without fully considering everyone else's, a bad habit that need to be replaced. I also need to work on communication because I sometimes will do work on the project without approval from the rest of the group.
While it has improved, I still need to work on my empathy. I have a natural tendency to push for my ideas without fully considering everyone else's, a bad habit that need to be replaced. I also need to work on communication because I sometimes will do work on the project without approval from the rest of the group.
I worked on the cladogram with Sadie Ikeda, Luis Jasper, and Matt Jones.
I worked on the timeline with Bryce Bernales.