Blog 12: Genetics Experiment Update

The fast plants are planted and growing rapidly! We planted them last Thursday (2/5/15), so they have been growing for almost a full week. A very important part of our planting process was doing the calculations for the amount of excess phosphorus and fertilizer that we were going to use while planting the seeds. After carefully weighing fertilizer pellets, calculating how much phosphorus we should use that would be proportional to both the fertilizer and soil, and doing more calculations and checking over our work, we finally mixed the soil, fertilizer, and extra phosphorus in four separate bowls and planted the seeds for our four different groups. Recap: There are 16 cells/group, and we have 4 groups. The first group is neutral, so there was no added phosphorus but just the fertilizer and soil. The small group had more phosphorus, the medium group had twice as much as the small group, and the large had twice as much phosphorus as the medium group. Doubling the amount of phosphorus made the most sense to us, and we felt that it would help our experiment succeed. Here is a low down of the measurements in a more clear and concise form: 
Added phosphorus to our plants:
small- 0.032g/group (0.002g/cell)
medium- 0.064g/group (0.004g/cell)
large- 0.128g/group (0.008g/cell)
Soil:
16.08g/group (64.32g total)
Fertilizer: 
0.384g/group (0.024g/cell & 6.144g total) 
Here are pictures that we took today when the plants were six days old. The stems all seem purple (may be hard to see in pictures), and we haven't really identified a huge change in' purpleness' between the four different groups. We are going to keep watching them and look more closely at the color intensities as we start wrapping up the experiment. This makes me question if we didn't add the appropriate amount of phosphorus or if phosphorus was not the variable to manipulate in our experiment. However, we did our research and are going to keep watching our data to see if it supports our hypothesis or not. Stay tuned! 

Blog 11: Annotated Bibliography for Genetics Experiment

Source 1:
Rhoades, H. (2009, August 6). The Importance Of Phosphorus In Plant Growth. Retrieved January 29, 2015, from http://www.gardeningknowhow.com/garden-how-to/soil-fertilizers/phosphorus-plant-growth.htm

This source is important because it demonstrates the importance of phosphorus and plant growth. Phosphorus helps produce healthy plants, and it is especially significant when growing plants in gardens to use fertilizer that has phosphorus in it because it makes them strong and beautiful. It also introduces the term 'phosphorus deficiency'.


Source 2:
Soils - Part 6: Phosphorus and Potassium in the Soil. (n.d.). Retrieved January 29, 2015, from http://passel.unl.edu/pages/informationmodule.php?idinformationmodule=1130447043&topicorder=2

This source provides additional information about phosphorus deficiency. It discusses coloring in plants (especially red/purple and dark green) in more depth than the previous source and emphasizes the importance of phosphorus in soil for growing plants. This element mainly promotes root growth and hastens maturity.

Blog 10: Genetics Experiment Update

We are all set up for our experiment, but we are waiting on the phosphorus to arrive before we can plant our fast plants. Therefore, we are doing research now and finishing up our planning and calculations. This is what our set up looks like:

We have four groups of plants: neutral, small, medium, and large. There are 16 cells per group, and we are planting three seeds per cell. We are also going to place 3 fertilizer pellets in each cell. Therefore, there will be 192 fertilizer pellets and seeds total in all four groups. As you can see, we have already added wisps in each cell (the blue rhombus-like materials). We have not yet determined the exact lighting or watering system yet, but we will have a better idea when we actually being the process of planting. We know that it will be a constant system. However, we have decided how much extra phosphorus we will be adding to the small, medium, and large groups. The neutral group will still have 3 fertilizer pellets in each cell, but we will not be adding any additional fertilizer. What we did was find the average amount of phosphorus in 3 pellets. We found the average weight of 3 fertilizer pellets is 0.071 g. Then we took that number and found the value that is 14% of that because the fertilizer is a 14-14-14% ration of nitrogen, phosphorus, and potassium. That number we determined was 0.001 g. Therefore, in each cell (with 3 fertilizer pellets and 3 seeds), there is 0.001 g of phosphorus. We decided that it makes the most sense and we will get good results if we double the amount of phosphorus for each group. That means that the small group will have 0.002 g of phosphorus added in each cell, medium group 0.004 g, and large group 0.008 g. I've never worked with fast plants before, so I'm excited and hoping to see some different lovely shades of purple!

Blog 9: Intro to Genetics Experiment

Olivia, Lucia, and I have decided to do our genetics experiment using fast plants. We chose this model organism because fast plants are easy to use while carrying out an experiment, and we designed a good experiment that we feel confident about. From preliminary research, we have decided to plant Wisconsin Fast Plants Purple Stem (Hairy seed, high anthocyanin expression) in our lab. We are unsure of exactly how many we are going to plant right now, but we do know that we want to have four different groups. Our variable that revolves around our experiment in Phosphorus. After doing research, we concluded that Phosphorus is the element that makes Wisconsin Fast Plants Purple Stem have purple stems. Therefore, our hypothesis is that the more Phosphorus in the soil that the fast plants are growing in, the more purple the stems will be. We are going to control the Phosphorus quantities by using a fertilizer that is 14-14-14 (NPK: 14% Nitrogen, 14% Phosphorus, 14% Potassium). We will put three fertilizer "seeds" in each plant and add more Phosphorus in different amounts. We are in the process of ordering raw Phosphorus and will measure it by weight before adding it in with the soil and 14-14-14 fertilizer. We are unsure of what form the raw Phosphorus is going to come in so that is why we are going to measure it by weight, whether it is a solid or liquid. The four groups I mentioned above will include a: Neutral group (only fertilizer- no added Phosphorus), minimal added Phosphorus, medium added Phosphorus, and large amount of added Phosphorus. As we go into more depth of experiment design, we may add or alter the groups of fast plants we are going to test. I'm hoping that we will be able to see a distinct difference between the plants that get more Phosphorus. More details and progress to come soon!

Blog 8: Evolutionary Tree

This is the modified evolutionary tree we created while studying the mammalian hibernation patterns of the Ursidae family (the bear family). Mammalian hibernation is defined as a type of hibernation that has a specialized, seasonal reduction in metabolism that is concurrent with scare food and cold weather. Therefore, bears that perform mammalian hibernation hibernate during the coldest periods of wintertime. If they did not, they would have a slim chance of surviving the brutal weather that winter brings. Our hypothesis was that bear hibernation is not ancestral. Therefore, it is not a trait found in the common ancestor.

Our data supports our hypothesis; bear mammalian hibernation is not ancestral. According to our data, only the Brown and American Black bear demonstrate mammalian hibernation; the Sun, Sloth, Andean bear, and Giant Panda do not mammalian hibernate to any extent; the Polar Bear and Asiatic Black Bear perform some characteristics of mammalian hibernation, but they do not fully mammalian hibernate. Clearly this behavior is not found in the common ancestor and therefore did not evolve over time. However, we discovered a reasonable answer as to why two bears in the Ursidae family fully mammalian hibernate, four do not at all, and two semi do. The bears that hibernate are bears that live in geographic regions where the winters are extremely cold. Thus, they hibernate for a few months in order to survive the winter months. They crawl into dens and remain in a tight ball until their hibernation period is over. The heart rate drops as well as the body temperature during this time. The bears that do not hibernate are bears that live in somewhat tropical regions where there is not a harsh winter. Therefore, there is no reason to hibernate if there is both food available and temperatures that don't reach below freezing all year round. For the two bears that semi-hibernate (the Polar and Asiatic black), it's slightly different. It's cold year round where Polar bears live, so the specie is already accustomed to surviving the cold temperatures. With that said, they do not perform mammalian hibernation like the Black and Brown bears do but rather remain in their dens for relatively long periods of time (several months). Asiatic black bears live in several different areas of southern Asia where there are two different climates with different temperatures. Therefore, only bears in the northern part of the region in their habitat mammalian hibernate whereas the bears in the southern part do not; some will sleep the whole winter, and some will sleep only during the harshest parts of it.  From our data, we concluded that bears use mammalian hibernation as a defense against the cold, harsh winter months. If bears live in areas where there aren't tough winters, then they don't hibernate. Therefore, the trait didn't start in the common ancestor (the Giant Panda according to our evolutionary tree) but emerged as the different bear species did. 

Blog 7: Intro to Evolutionary Tree Project

For the second bio research project of the year, Emma and I have decided to study the evolution of bears by analyzing and researching bear evolutionary trees and cladograms. To start, we have begun preliminary research on common bear behaviors. We discovered that most bears have very good sense of smell (their strongest sense), they see and hear well, and they can run at least 37 mph. Additionally, all mothers are very protective of their cubs, their intelligence is comparable with those of the great apes, and bears treat other bears like they would humans. Most bears are also not ferocious and have a fairly calm temperament. However, some characteristics tend to vary among the different bear species. Furthermore, we have decided to specifically research hibernation and how it changes for different bears. According to our tree, there are eight bear species. We did some research on each species and wrote down whether or not they hibernate fully, semi, or not at all. Here is what we have found:
Asiatic Black– semi-hibernate
Polar– do not hibernate
Sun– do not hibernate
Sloth– do not hibernate
American Black– do hibernate
Andean (Spectacled)– do not hibernate
Giant Panda– do not hibernate
Brown– do hibernate
We are going to do more research and are hoping to discover by the end what made some bears not hibernate anymore or start hibernating. Was it environmental or gene related? Are the bears that do hibernate closer to the common ancestor? Do the bears' common ancestor(s) hibernate? We hope to answer these questions and know more about bear hibernation and how it evolved. Will keep updated as we continue to research!

Blog 6: All About Cladograms

What are cladograms and evolutionary trees?

In science, biologists frequently use evolutionary trees to study organisms. Evolutionary trees, similar to cladograms, are essentially diagrams that show the evolution of organisms. The evolution is mainly based on similarities and differences between the characteristics of the organisms. Cladograms are basically the same as evolutionary trees; however, they do not show the ancestral aspect of organisms like the evolutionary trees do. Cladograms focus more on the relations of an organism. Therefore, the organism's descendents are not present or how it has changed over time. With that said, many single cladograms can be found in evolutionary trees. Evolutionary trees add the change over time aspect to the diagram. And both diagrams are based on phylogeny: the study of evolutionary relationships.

How can scientists use these?

Scientists can use cladograms and evolutionary trees to analyze organisms and the relationships they have with other organisms. They take into account various variables like molecular evidence, biochemistry, fossils, and DNA in order to create evidence for evolution. By looking at organisms' ancestors and descendents, they can have a better understanding of certain characteristics and predict why and how they change over time. After all, the relations among organisms change constantly. Therefore, it is useful to have a consistent and uniform diagram that can help keep track and analyze those changes by classifying organisms and their similarities and differences in character with others.

Example? 

 
Here is an example of a very simple cladogram. It is normal to have a straight line and have other lines connect off of it. The letters on the main line (in this case: A, B, C, F, G, H) are the characteristics of the organisms. Most cladograms are set up this way with the characteristics on the main line with the organisms branching off of it. *the letters D and E are an exception* For this cladogram, you are supposed to classify the characteristics with the appropriate organism. However, most cladograms give you the characteristics and organisms for efficiency purposes.

While doing this exercise, it is important to look at the characteristics and classify them with the organisms. The only organisms that has a curly antennae is the butterfly, so letter H corresponds with number 8. All the organisms and characteristics are different. However, when you look at just the organisms, they share similar characteristics and look related. For example, the dragon fly and the butterfly and the ant and the spider. In order to make a cladogram, it is important to determine characteristics that organisms share in common then to establish characteristics that make them unique.

Answers:
1. F
2. C
3. A
4. G
5. E
6. D
7. B
8. H

*Why is this not an evolutionary tree? Because it does not show the ancestry of the organisms.

Source:
Cladogram Analysis. (n.d). Retrieved November 8, 2014. http://www.biologycorner.com/worksheets/cladogram.html#.VF5vVIfVm8E