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The title of the poster my lab partner and I created was, "Qualifying the Effect of Microscope Properties and Techniques". In a series of experiments we learned how to properly use a research quality light microscope. The experments were geared toward practicing the use of technical ascepts of the microscope. So this involoves the use of filters, shutters, and adjsuting numerical aperature. There were also a variety of methods we practice in order to capture a high quality image. These methods include setting up Kohler illumination, use of fluoroescent microscopy, and setting up an oil immersion lense. All these various experiments came together to encapsultate our main objective of qualifying the effect of microscope properties and techniques in order to create a high quality image.

A major part of our experiments was adjusting numerical aperature under a variety of different conditions in order to see its effect on the visualization of a sample. The following figure shows a change in numerical aperature when the magnification is kept constant  x100 and visualized with fluorescense. The fluorescent beads are figure A-C. The numerical aperature increases left to right: starting with 0.5, increasing to 0.875, and finally ending at 1.25. This is similar for the photos of the DAPI stained nuclei. Visually, we can conclude that both the DAPI stained nuclei and the fluorescent beads increase in image intensity as numerical aperature increases because we can see it gets brighter. This observation is quantified in the table because we mapped the fluorescent intensity of the five nuclei over the three different numerical aperature settings. The intensity of 1.25 is much greater than 0.5 proving that intensity increases as numerical aperature increases. It can also be argued that resolution increases too because the minimal loss of image light. 

A commonality among the most living things is their circadian rhythm. The circadian rhythm is one of the most important mechanisms and it works by regulating hormones and different cellular activities based off external cues such as light. Our body has a drop in melatonin and our blood pressure is higher when we wake up and it is light out. As the day goes by, our level of alertness increases along with our coordination. Between afternoon and evening, we have the greatest muscle strength and cardiovascular efficiency. As it gets darker, our melatonin levels start to rise preparing us for sleep. These changes occur due to the biological clock set by our zeitgeibers, i.e., time keeper. These zeitgeibers are located in the suprachiasmatic nucleus of the brain. Studies have shown that lesions in the SCN can cause disorders relevant to circadian rhythm. 

The replicated figure does in fact show an image of the same leaf as the original. It lacks a ruler in the photo to show size. The hand holding the leaf is also not orientated the same way as the original. The time of day seems to possibly be different in the replicate since the leaf and hand is within the shadow of the tree rather than being in the sunlight such as the original is. The figure A also showed the trunk to the chute in the photo whereas the replicate only shows the petiole of the leaf in addition to the leaf itself. The figure B that shows the entire chute and the bottom half of the tree is also completely shadowed rather than the tree casting a 90-degree shadow to the right of its trunk. The arrow in figure B is also slightly off in regards to the angle of the arrow in the original. It looks like the photo was captured while the photographer was standing closer to the tree than the photographer of the original photo. The figure C replicate also looks like it was a photo taken by someone standing closer than that of the original photo. Like the shadowing in figure A, the shadow of the trees is also different in the replicate than the original in figure C. It seems like the time of day when the photos were taken was different in the replicate than it was in the original. The tree on the left of the figure C photo is also cut off a little whereas in the original it is not cut off at all. The letters that label the figures are also a little different. The second figure which included the map had a smaller red X than the original figure 2. They are in smaller text boxes and located more in the left corner than they are in the originals.

To determine whether a student would be able to replicate a multi figure panel based on descriptive scientific writing alone we assigned the Methods Project. The Methods Project required that the student locate evidence of phytophagy on the campus of University of Massachusetts Amherst and take photos of that evidence. We took photos that included a close-up image of the evidence, then a image of the object from farther away to show location, and then a map of where that evidence was on the campus.  We found that with descriptive scientific writing in the form of a methods section of a scientific article the student was able to create a multi panel figure that closely resembled the original multi panel figure created by another student. Although they were similar there were some striking difference in the figures. Some of those differences included the orientation of the hand holding the leaf that displayed evidence of phytophagy, the absence of a ruler to show scale, and some difference in the time of day the photos were taken which resulted in a change in the shadows cast by the trees that showed the evidence. We concluded that with using descriptive scientific writing that the multi panel figures were close but not the same. These results suggest that the students could improve on their scientific writing skills.

Although there were striking similarities between the original figure and the replicate, there were differences and those difference can be accounted for. The figure A may be lacking a ruler if the replicator did not posses a ruler at the time of the photo being taken. The hand in the photo may not be in the correct orientation because of the lack of description as to how the hand was orientated while holding the leaf and the ruler. The difference in the time of day could be accounted for due to the replicator’s availability. It is possible that the replicator was not on campus around 4:00pm when the original photos were taken. Taking the photos for the figure at a different time of day also accounts for the differences in the shadows made by the tree. The replicate photos were also taken by a person standing closer to the tree than the person in the originals. This could be due to subjective understanding of how far away a certain amount of measurement is. One person might estimate 5 feet and be more accurate than the other person. Estimation of distance could also account for the tree on the left in figure C being cut off on the left side. The replicator might not have been standing far enough away to capture both trees and the entirety of the library in the background. The letters labeling the figures differed in the figures most likely due to lack of description of the size of the text box used to make the letter labels. Lack of description could also account for the red X being different on the second figure.

The auditory template model is the basic model for explaining song learning in birds, though there are many bird species who deviate from it. The model was developed by Peter Marler through experiments on chaffinches. He observed that chaffinches were only capable of learning song when they were hatchlings and during their first spring, and that they ceased to be able to learn when they reached a fully crystallized song or had high levels of testosterone. Additionally, the chaffinch hatchlings wouldn’t learn songs from heterospecifics, even when they hadn’t heard any other kind of song before. Lastly, when males were deafened they produced songs far more distorted than the ones produced by males without a tutoring song. From these data, Marler hypothesized that birds must possess some kind of crude template, and that they match this crude template to the songs they listen to until they hear their conspecific song, which then causes the template to crystallize into an exact template. Later, when chaffinches reach their first spring and testosterone levels begin to rise, they begin producing their own songs. With normal hearing, the birds can listen to themselves sing and match the song they produce to the template they’ve remembered. This explains the babbling phase most birds go through before reaching a crystallized song, as they need time to match the sounds they produce to the template sounds. Eventually, they reach a fully crystallized song that is a more or less faithful version of their species’ song. Though the data from several playback experiments seem to fit this model, there are many exceptions to it. For example, white-crowned sparrows will learn conspecific song played from a speaker, but will not learn heterospecific song learnt from a speaker. However, when the sparrow hatchlings are placed in social contact with heterospecific tutors they are able to learn heterospecific song, which seems to go against the idea of a crude template that filters heterospecific song. Another problem with this model has been highlighted in European robins which have an open-ended learning system. European robins have wide repertoirs spanning many hundreds of songs, each different from the last, and have no defining species specific song. In swamp sparrows, until shortly before full song crystallization, they produce 12 elements, which are then reduced to the number needed for their full song. These findings have led to the rise of another model known as the action model. In the action model, rather than having an auditory template, birds have pre-encoded elements that they must learn to put in the correct order to produce their species’ song. This model would explain the reduction in the number of elements used in swamp sparrow song. As for species with open-ended learning, one can only hypothesize that they have the capacity to learn throughout their lives and that they can learn as many elements as their syringeal muscles allow.

The replicated figure does in fact show an image of the same leaf as the original. It lacks a ruler in the photo to show size. The hand holding the leaf is also not orientated the same way as the original. The time of day seems to possibly be different in the replicate since the leaf and hand is within the shadow of the tree rather than being in the sunlight such as the original is. The figure A also showed the trunk to the chute in the photo whereas the replicate only shows the petiole of the leaf in addition to the leaf itself. The figure B that shows the entire chute and the bottom half of the tree is also shadowed rather than the tree casting a 90-degree shadow to the right of its trunk. The arrow in figure B is also slightly off in regard to the angle of the arrow itself. It looks like the photo was captured while the photographer was standing closer to the tree than the photographer of the original photo. The figure C replicate also looks like it was a photo taken by someone standing closer than that of the original photo. The shadow of the trees is also different in the replicate than the original in figure C. It seems like the time of day when the photos were taken was different in the replicate than it was in the original. The tree on the left of the figure C photo is also cut off a little whereas in the original it is not cut off at all. The letters that label the figures are also a little different. They are in smaller text boxes and located more in the left corner than they are in the originals. 

In order for any scientific work to become valid it must be replicated by other scientists who must be able to redeem the same results as the original experiment. The Methods Project is a way for students to practice descriptive scientific writing. After doing this project the student should be able to describe their method of completing a task to such extent that another student should be able to follow that method and replicate that task. The task in this project was to create a multi panel figure that displayed evidence of phytophagy at the University of Massachusetts Amherst campus. Although the students are mostly juniors in college, their ability to write a proper methods section in a scientific paper is unknown. To determine if the students were able to replicate the multi panel figure first created by a fellow student, they were assigned the Methods Project. The approach taken was to locate evidence of phytophagy, take pictures of it, and create a multi figure panel with those photos. Those photos were to be labeled properly, show a reference to the size of the evidence, and include any arrows or graphics necessary to show where that evidence was located on campus. The leaf that was selected that showed evidence of phytophagy was chosen because of its accessibility. It was located on a chute that was distinctive enough that another student following the methods would be able to find that exact leaf. The location was easy and convenient to access for anyone. The controlled factors would include weather and time of day that the photo was taken. With these factors considered another student should be able to replicate the figure after reading my methods.   

The third goal of this lab is to Identify potential variables that must be controlled for the replicability of the study. In order to get the best results possible, I will attempt to control as much as I can in my descriptions. One important thing I can control is specifying the path I took to the proper plant and taking a picture from the proper angle. I will do this by describing the path they need to take from a set landmark to the intended location. The angles to use when taking pictures, especially for the ‘distant shot must be explained properly to get the best results possible. This one will require more detail because it can be very easy to step back and take a photograph of the plant with a completely different background. Likely, my methods will include some directionality and some description of what I fit in the background. Another basic thing I can control is when to take the photograph. It is important they do so at a similar time of day to match the shadows. A third factor I can control is how the final figure will be constructed. Careful instructions will be written for each step, beginning from the software used to the final touches.

Humans have affected the world around us in a multitude of ways including changing the environments of the planet, the creatures that inhabit it, and the biotic and abiotic factors we interact with. As humanity progresses, we further alter the world to our needs which can sometimes create problems of its own. Changes we make to the world around us can often have unforseen (or forseen but trivialized) consequences which may change the world forever. Despite human power and ingenuity, nature and its laws continue to persist. Humanity has had a close relationship with bacteria since the first human encountered its first bacteria. Up until the last century, bacteria and their related effects on the human body were a global threat killing millions with little resistance. It was only in recent history that the invention of antibiotics relieved the human race from the grip of harmful bacteria. The invention of antibiotics was an extremely important leap in medicine for humans and the animals we can give antibiotics too. They are used heavily in a variety of industries, which all contriburte to the process of natural selection. Antibiotic resistant bacteria have become a terror for doctors, researchers, and patients in the last few decades. Overuse of antibiotics has led to mutations for resistance becoming commonplace in some bacteria species. This threatens our modern medical system, as well as the lives of all humans exposed to these bacterias. These resistant bacteria cannot be killed by the most common antibiotics and even some which are used as a last resort. A few alarming strains have been appearing more and more in recent years, usually within the species of Salmonella typhi, Mycobacterium tubercluosis, Pseudomonias aeruginosa, and Neisseria gonorrhoeae. While not all of these bacteria lead to deadly diseases, antibiotic resistance in these strains make it nearly impossible to help relieve the symptoms of them, or help stop an individual from dying. However, we have not run out of options yet. One possibly alternative is to simply work on developing a new antibiotic which bacteria are not yet immune to. As the new antibiotic is administered and (hopefully) kills off the bacteria, the process of lowering antibiotic use can begin. This combined process would hopefully eliminate the possibility of resistance occurring, at least at such a high rate and across multiple species of bacteria. Of course, this process is not perfect, and could result in new resistances being developed and individuals not getting the antibiotics they truly need. There is still room for genetic changes to happen spontaneously and result in resistance, but by killing off the resistant bacteria there is hope that acquired AR in bacteria can be lowered, or at least controlled.  For now, this is the most effective method at our disposal. Until humanity can find a more longterm and effective way to fight the ever evolving bacteria, the genetic and scientific armsrace will continue.