bthoole's blog

The proposal project was my favorite project of the semester. It was nice to work in a group and the openness of what the experiment could be was fun to play around with. The presentation that we gave to the class was easy to make and pulled a lot of information from what we had written for the final manuscript submission. I liked the collaboration around forming an idea for a project and finding other literature that was similar to our proposed experiment and could serve as a template for our methods construction. This will be an important skill for later in a scientific career when I have to think of and design a project. Next year I may have to do a literature review for an honors thesis and having done this project can help in my writing of a methods section for my project and for the overall aesthetic and layout of my thesis manuscript. It is my hope that I will have done publishable work and at the end of the year I can submit my research for review. Before that though, I have to propose a project and this project has helped show what goes into that process and how I can get ideas from similar projects to shape my own.

               The methods project had a couple had a couple difficulties but ultimately proved useful. This was the first time I had to use a computer image editor/ figure creator and Inkscape was difficult to understand in the beginning. Before I even had to generate an initial figure though, the methods section I wrote had to be changed to be less direct and giving directions to someone and more what exactly I had done. Usually, when I write a procedure for a chemistry lab report, it is direct “pour X amount in flask” but this had to be worded differently. The part of this project that replicated images was also helpful when we had the class and went over everyone’s comparison figures. It really showed how different perspectives and readings of methods can give different results and how exact the methods should try to be, including as many details as possible. The end manuscript for this assignment was also a challenge to write because its format was unlike anything I had previously composed. I never had to submit anything under manuscript guidelines, but given that I would eventually like to, this proved as a useful introduction to what that process may be like.

The perfect paragraph assignment gave cause to less stress than the drafts because I felt relatively confident in my paragraph writing. With the drafts, it was a matter of reaching a quota, but I felt that each draft could have served as a perfect paragraph so writing one for submission was not going to be a problem. As I did the project, leaving comments on other paragraphs gave me a better view into my own writing. Looking at other people’s paragraphs and leaving comments aimed at helping improve them gave me a lens to view my own stylistic approaches to writing. I realized how I would set sentences up or how I would phrase something was different than others. I also found that sometimes I would leave a comment and realize that I could do a better job of looking out for the things I was commenting on too. This allowed me to better edit my own writing. Reading your own writing is usually difficult because you know what it is you are trying to convey, but by using a different viewpoint to edit your writing is helpful in evaluating if it is as easy to read as it could be.

The weekly drafts assignment asked for blog posts throughout the week. At first it seemed that the weekly posts would be a lot to handle, making daily posts about science can cover a wide ground. I thought it was going to be especially difficult because I was not taking biology related classes this semester. However, the posts helped me review other classes that I had previously taken and remember important details that I otherwise would not have had to remember. The assignment helped showcase the need to be able to write an effective paragraph in a short amount of time. This was not a daily essay, but a way to mark what had happened. This helped show how helpful it is to take notes from classes that are usually bulleted or sentences that don’t always have a complete flow and reorient them into a more condensed paragraph with clearer meaning. It is helpful to rewrite the notes this way because it gives a review and better understanding of the subject when you are the one who has to write about a something that was taught/told to you.

Adaptive radiation is an evolutionary process that explains how organisms can rapidly evolve and diversify from one common ancestor into many different species. This is especially effective when the environment changes and creates new niche spaces for the once common ancestor to fill. The change in environment could be a physical boundary between the common ancestor group that separates them to change, but it could also be the introduction of a different food supply or new predator species. These forces act on the common ancestor and it fills different niche spaces and as they adapt to fill these new spaces, they also diversify enough to be different species. A well-known example of adaptive radiation is in Darwin’s finches. Although they present as different species on the outset, it is possible to trace them back to the same common ancestor. Their evolution occurred over a short period of time and their evolutionary adaptative difference can be explained by the island that the finches inhabit. Once the common ancestor was spread to the different islands of the Galapagos, different environmental pressures presented themselves, such as different food sources which would change the beak shape of the birds.

Adaptive radiation is an evolutionary process that explains how organisms can rapidly evolve and diversify from one common ancestor into many different species. This is especially effective when the environment changes and creates new niche spaces for the once common ancestor to fill. The change in environment could be a physical boundary between the common ancestor group that separates them to change, but it could also be the introduction of a different food supply or new predator species. These forces act on the common ancestor and it fills different niche spaces and as they adapt to fill these new spaces, they also diversify enough to be different species. A well-known example of adaptive radiation is in Darwin’s finches. Although they present as different species on the outset, it is possible to trace them back to the same common ancestor. Their evolution occurred over a short period of time and their evolutionary adaptative difference can be explained by the island that the finches inhabit. Once the common ancestor was spread to the different islands of the Galapagos, different environmental pressures presented themselves, such as different food sources which would change the beak shape of the birds.

The way that the soil is treated determines the ability it has to affect the cycle carbon. Carbon naturally cycles in and out of the soil, which is why agricultural lands are considered to be one of the major sinks of carbon. With that, comes the responsibility to suitably manage the land to improve the carbon sequestration and reduce any emissions that come from the land. However, agriculture is currently the third largest source of anthropogenic greenhouse gases that are released. To better understand how the land can be better managed for sequestration, it is necessary to understand how it currently managed to result in these large emissions. One of the largest culprits is the practice of liming soils, with the IPCC estimating that nearly 100% of the carbon stored in soils that are treated with lime is released as carbon dioxide. Lime and other fertilizers are applied to these soils to better crop production by changing the pH of the soil or providing necessary elemental nutrients like calcium or phosphorous that are commonly deficient in acidic soils. Often, limestone and dolomite are used as the sources of lime, which as discussed above also release carbon dioxide as they are broken and crushed. It has no been investigated whether this crushing could be coupled with a carbon capture technique, but studies have been done on how liming affects the release of carbon dioxide in soils treated with phosphate solubilizing bacteria and other phosphorous sources.

-Colors: We chose to test the colors white versus yellow and cyan versus green in our experiment. Some species of crab spiders are able to change their color from white to yellow, and yellow to white. We decided to use white and yellow as a control in our experiment and see which side the spiders would prefer. In the RGB model, the color white is made up of red, green and blue all at their highest intensities, which is 255. Yellow is made up of red and green both at their highest intensities of 255, with no blue is added. Cyan is made up of green and blue both at their highest intensities of 255, and no addition of red. Green is made up of only green at its highest intensity of 255.

-Set up: We used two spiders in our experiment, and each was given its own tank. One spider was placed in a yellow and white tank, and the other in a cyan and green tank. The color backgrounds in the tanks were split right down the middle and the other factors including light entering, materials and temperature were kept constant between the tanks.

-Procedure: To collect data we took measurements once a day for eight days in a row. Everyday we collected two measurements. The first measurement was what color side the spider was on when we first entered the room and before interacting with the spider. The second measurement was taken after moving the spider to the middle of the tank where the colors met. We gave the spiders a ten minute rest period before taking and recording the data on which color side background the spider chose.

There were three postulated methods of DNA replication that explained how genetic information was copied and passed down through the generations. The methods were semi-conservative, conservative and dispersive replication. Semi-conservative replication involved the double helix unwinding and each half becoming incorporated into a new strand of DNA while it served a s a template for what the other half should look like. Conservative replication suggested that the DNA double helix unwound to serve as a template for a new double helix, but that the original would wind back up and stay together and the replicated strand would be entirely new. Dispersive replication suggested that the double helix would be cut up and that the new strand would have pieces of the old strand of DNA and the newly synthesized DNA in it in no particular orientation. Meselson and Stahl investigated the idea of DNA replication and by using nitrogen markers, definitively showed that DNA replicated in a semi-conservative manner.

The carbon gases can be removed from the atmosphere and deposited in the land, but it is also known that there is a carbon process that involves the soils at surface level. Soil carbon is a large pool of terrestrial carbon and holds more than the atmosphere or that is held in biomass. Understanding how the soil carbon is cycled can help in any process in trying to keep it sequestered in the soil so that it is not released back into the atmosphere. One study took this outlook to compare the soil carbon pools at deforested coal mines to those that had been reclaimed. The reclaimed mines had been purposely afforested and were compared to the unreclaimed sites that remained barren and to older forests. The investigation into the differences in the carbon flow at the sites showed that there was an increase in carbon dioxide flux at the reclaimed sites, which was attributed to a higher root biomass presence. This increased the soil respiration rate, which is better for the reclamation of the environment and the eventual means to sequester carbon dioxide