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bio 551 take home

Submitted by kruzzoli on Fri, 12/14/2018 - 13:31

They sampled sound pressure levels directly from recording for one second before the randomly selected song and looked at the dB when the song was present and when it was not present. They looked at the difference in pressure to assess whether the noise had an effect on song structure. To look at the relationship between vegetation and structure on song structure,  they calculated the proportion of area around the males that contained structures of vegetation. The structure variables contain the percent of vegetation and reflective surfaces of concentric circles extending from the location of the bird.

They found that noise levels varied considerably with the proportion of urban and vegetative structure, but noise levels were not correlated with urban structure. They found that males from group one produced significantly higher maximum frequencies, broader bandwidths, and significantly slower trill rates than the group 2 males. Minimum frequency and bandwidth were the only traits that showed group specific responses to structure and noise. In males from both groups, peak frequency decreased, and the time between songs increased as urban structure increased. In general, vocal performance declined across all males with increasing noise and increasing urban structure. Peak frequency decreased with increasing urban structure; males put more energy into low frequency songs so it is more expensive to create low frequencies. This shows that unless it is beneficial to produce low frequency songs, like in the case of increased urban structure, males will produce higher frequencies because it requires less energy.


bio 551 take home

Submitted by kruzzoli on Fri, 12/14/2018 - 13:07

Males sing with different trill rates during the morning and during the day. When unpaired during the afternoon, they sing at a much higher rate than in the early mornings when they are paired and calling out to other males. This study was interested in the effects of noise and structure on the male song used to broadcast signals to other females, so only recordings from the day were used and none from the early dawn when they are calling to other males. They took recordings between 7 am and noon in April and May of 2011 and 2012 from the same area in Michigan. Taking recordings from the same time of day and the same season ensures consistency in the behavior of bird calls because calls can change seasonally depending on breeding or taking care of young or finding new habitat. Using the same location also ensure population similarities and that the differences found are not based on different environments or population differences. The sites of recordings varied from large rural areas with little noise and only a few man made structures to to sites that were highly urbanized and contained a lot of noise and a high proportion of sound reflecting surfaces and structures. One to three males were recorded from each site and each site was separated by at least .5 m to ensure there was not overlap and there was a reduced chance that the same male was recorded more than once. During song analysis, the birds were assigned random numbers so that they were unaware of the location of the bird to avoid bias on analysis.

bio 551 take home

Submitted by kruzzoli on Fri, 12/14/2018 - 12:36

Past studies show that species tend to increase their maximum frequency of signals as noise increases in an attempt to minimize the amount of their noise that would be masked by the increase in noise. This however, is contradicted by the idea that urban structure would select for lower frequency signals because lower frequencies have a better ability to bend around structures and are less prone to reverberation and they are less likely to develop echoes.

    In this, they focused on male chipper sparrows when they broadcast songs to females specifically. They were curious as to whether chipper sparrows with different song variants would adjust their songs differently to an increase in both noise and structure, whether noise and structure affected different features of song, and if vocal performance was affected by noise and structure. They looked at species in urban environments to explore how individuals in the same population responded to noise and structure, they wanted to know if they would respond in a similar way. They found that male sparrows fell into two different categories. The second group had higher trill rates, lower maximum frequency, narrower bandwidths, and higher trill rates than the first group. They predicted that the first group of sparrows would increase their minimum frequency in the presence of more noise in order to minimize the masking and decrease their maximum frequency in the presence of increased structure to maximize reverberation. They did not expect any change in temporal traits. They expected group two males that had higher trill rates to decrease their trill rate with increasing structure but they did not expect any changes in response to noise. This is because they were already not susceptible to noise masking from the environment.


bio 551 take home

Submitted by kruzzoli on Fri, 12/14/2018 - 12:04

This paper focused on the effects of anthropogenic noise, urban structure, and vegetation on the song structure of a historically open habitated bird.  They studied chipping sparrows, which evolved in an open grassland habitat. Species that evolve in closed environments, such as forests, tend to produce shorter and more tonal signals than those is open habitats, such as grasslands. This is because of attenuation and reverberation distorting sound and masking certain pitches and frequencies. Attenuation means that a sound will be fainter the further away from the source it becomes. Higher frequencies show a more excess attenuation than lower frequencies because they are more likely to be absorbed by the environment and they are more scattered since they are a higher energy, so they are more likely to be distorted in their path in the presence of a closed habitat. Degradation also plays a role in sound production as well and is more important in habitats with a lot of cover. Reflection and echoes make it difficult to differentiate different vocal elements.

    This study focused on song sparrows in the closed habitat of an urban environment. Urbanization has a lot of anthropogenic noise, which is  noise that has both a high amplitude and low frequency. This noise masks a lot of animal sounds and reduces the space that animals have to communicate. Built structures in urban areas are also highly reflective, sounds that reflect off of buildings in urban environments hold more energy than when they are reflected off of structures in forests because urban structures tend to be very smooth and flat in comparison so there is less sound absorption. Past studies show that


more reflection writing

Submitted by eehardy on Fri, 12/14/2018 - 11:56


When I began the “METHODS” assignment, I initially underestimated how much work it would be. In terms of most things, I am not very detail-oriented, and this project required high levels of attention to detail. In addition to that complication, I encountered a few random obstacles. It was actually more difficult than I had imagined to find a spider on campus in the first place. I looked in several corners and crevices indoors, before I finally headed outdoors and found one nested in its web on a plant pot outside of a central building on campus. When I was doing my write up initially, I was describing things pretty vaguely, jotting down my description as the way that I had the steps listed in my head. However, as I edited it and tried to think about it from an outsiders perspective, I realized that I was missing several details that were necessary for someone following my methods to get to the right place to find the spider. The way that I recalled things in my head was not naturally that detailed, although I did remember the details, I would not originally think of saying them, so I had to focus extra on that. I tried to put in every detail that I could think of so that the person following in my Methods would be able to obtain similar results. This is very important in a scientific Methods section: replicability is key. If a person cannot utilize a scientific methods section to repeat the experiment, the results cannot be tested a second time and thus cannot be verified. Even after adding all of the details that I could think of, when one of my classmates repeated my experiment there were still some differences between their end product and mine due to a few key details missing from my Methods that I had not thought of. In the end, this project really taught me and reiterated the importance of a very detailed scientific Methods section. I learned that the more detail, the better.



My teammates and I underestimated how much planning we should have done when working on the PROPOSAL. We did spend a solid amount of time doing the actual writing, but we did not read enough into how our PROPOSAL should be written so that we could plan accordingly. We did not read enough into how each section should be structured, and we did not collect enough background information before we started writing it. Our abstract ended up being much too long and our background information section was much too short. Our paragraphs were also not structured very well. We were a bit surprised when we got a grade lower than what we wanted, but looking back we had done a lot of things incorrectly and not planned well. It was unfortunate, but it it drove us to put a lot of extra effort into the PROJECT and learn from our mistakes.

Cancer draft

Submitted by curbano on Fri, 12/14/2018 - 10:22

Cancer research is so challenging because there are SO many different influences. Many things we encounter in our lives, such as radiation, technology, red meat, smoking, etc., are said to cause cancer, yet we still expose ourselves to those things. Clearly we can't avoid everything that is said to cause cancer, but I find it interesting that only 1% of cancers are found to be hereditary. In cancer, I would expect to see p53 mutations or there could be many other signaling/survival/etc pathways influenced in cancers. For example, we talked about the Bcr-AbI mutation that leads to a certain type of leukemia.


Reflection on PROJECT

Submitted by eehardy on Fri, 12/14/2018 - 00:08


Entering the class project titled “PROJECT,” I was feeling overwhelmed. My  group realized that our Project Proposal, which laid out all of the details of our project, and much of which could be used for the project itself, was insufficient, meaning that we would have to do extra work on our project since we couldn’t extract much of it from the proposal. The first time we met up to discuss the Project, we were all feeling overwhelmed, knowing we needed to work on the write up and do the actual research of measuring the spider webs itself.

We tried to work things out and made a little bit of progress. After meeting a couple more times and developing a solid plan, we were feeling a lot better and realized that the Project was not as much work as we had thought that it was. Planning out the project with my team helped me develop and learn about some time management and organizational skills. We had to plan what were appropriate times to use the necessary equipment, like the high technology microscope, based on when it was available, and then leave ourselves sufficient time to do the write up. I also learned to collaborate better and communicate effectively as a teammate. Sometimes I am quiet and do not voice all of my thoughts, but I think that I did a good job pointing out when something needs to be changed, and I think that I did a good job listening to my teammates as well. We were all very satisfied when we were able to effectively see and measure the spider webs under the microscope. I also learned a lot about how to consolidate information, because we had to cut down the text on our poster. Over all, I learned a lot doing this project and was very satisfied.


Submitted by eehardy on Thu, 12/13/2018 - 20:48

Biological factors are usually the most obvious and well-known factors involved in diseases. There are many different biological factors that can increase the risk of obesity for individuals. Although genetic factors have been linked to obesity, this does not seem to explain the sudden proliferation of obesity that we are seeing today. There is another factor, however, that seems to connect quite perfectly in the scheme of our current generation and obesity: sleep deprivation. Over the past century, the average amount of sleep per night in the United States has plummeted from 9 hours to about 6.5 hours, and seems to be decreasing even more. Recent studies have suggested that maybe the coinciding of the current sleep deprivation epidemic and the obesity epidemic is really no "coincidence" at all. Sleep deprivation has actually been linked to obesity. The research done has not only identified correlation, but specific factors caused by sleep deprivation that can cause obesity. In a study where subjects received 4 hours of sleep, remarkable changes in their hormone levels were noted and their glucose tolerance was impaired (this can be a marker of insulin resistance and diabetes). Sleep deprivation reduced levels of the hormone Leptin by 18%. Leptin is key for the regulation of energy and hunger. Leptin sends signals to the hypothalamus that suppress appetite, so when levels of Leptin are reduced appetite and cravings increase. While Leptin decreased with sleep deprivation, another hunger-regulating hormone, ghrelin, actually increased. Unfortunately, the increase of ghrelin actually has just about the same effect as the decrease of Leptin: an increase in appetite. Ghrelin is a hormone made in the stomach that sends a message to the brain that increases appetite and actually increases cravings for high carbohydrate, high-calorie foods. The craving of these fattening foods caused by ghrelin is likely adaptive and related to evolution and the foods that once kept our ancestors alive and provided them with enough energy, but today these excessive cravings induced by extra ghrelin are certainly not favorable. Not surprisingly, the subjects who were sleep deprived and subsequently had fluctuations of these hormones gained weight. Another study using brain scans further supports the link between sleep deprivation and obesity. A group of neuroscientists and psychologists used functional magnetic resonance imaging (fMRI) to study the brains of two groups of individuals: one who had been sleeping well and one who had not. For those who were deprived of sleep, the fMRI showed increased activity in the more primitive areas of the brain, such as the amygdala. These areas regulate the desire to fulfill the base biological needs: food, sex, and sleep. The more “higher order” areas of the brain controlled in decision making, like the frontal and insular cortexes, showed significantly less activity. So with an increased desire for food and decreased reasoning and decision-making abilities, the outcome is pretty clear. The sleep-deprived subjects wanted junk food. With the ridiculously jam-packed schedules of both adolescents and adults these days, sleep is declining, and clearly at a price. Sleep deprivation and the following hormonal changes clearly illustrate the roles biological factors play in obesity. Hopefully, people can learn from these studies about the importance of sleep and reduce obesity and the various other damaging effects of sleep deprivation.


Submitted by kruzzoli on Thu, 12/13/2018 - 20:19

Our group overall learned a lot about how be a better teammate and how to work together as a cohesive unit with our final project. We planned multiple meet ups throughout the week to work on the project which was something we did not do for the proposal. Because of the extra effort put into the project by everyone in the group, we had a much easier time collecting data, writing the report and creating a very nice poster. We grew a lot as a team from the proposal to the project and because of this I can now see myself being better at group work in the future. I already learned that I need to spend more energy when it comes to group work and I know how important it is to communicate, so I don’t think this will be something I struggle with in the future as much. Our final project was also really cool and being able to look at microscopic images of the webs was super interesting. I learned a lot about how to create a research plan and then how to carry it out, so the final project taught me a lot about myself academically.  

Finally, the reflection was a good way for me to reflect on everything this class has taught me this semester and allowed me to reconsider my feelings as a student in this class. I have not had to write a reflection since high school so it was definitely a reminder on how to evaluate the new skills sets that I have gained this semester. It was a rather quick and easy assignment but it allowed me to recollect my thoughts and really focus on the improvements I’ve made this semester which is something I probably would not have done if I did not write this reflection.



Submitted by kruzzoli on Thu, 12/13/2018 - 20:09

The first assignment of this semester was definitely unique and I think a good demonstration of how important  a well detailed and structured methods section really is. Creating a figure was important in itself because this is something needed for scientific writing and papers. I also wrote what I thought was a super detailed methods however the recreation of my image showed that I did have some errors and some areas that I could have been more clear on. I realized that all details, even if you think it might be common knowledge or common sense, need to be included and specified if you want a second person to be able to recreate what you did. This will help my future research and scientific papers because I am aware of how careful my word selection has to be and I know the importance of word choice and detail choice. I had two research projects in other classes this semester that I feel I wrote better than I would have before this assignment because I did my best to include all important details as well as getting rid of details that are unnecessary.

    The proposal project tested my abilities to work as a member of a group and at first posed a challenge between my group members and myself. We struggled at first to work together in order to complete the written sections and background research. Eventually we finished out proposal however it was not to the best of our abilities because we had failed to be a cohesive unit all working on the same project. We were able to turn this around come time for the final project.



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