Writing in Biology

Feedback loops are something that occur in many different aspects of life. They are an observation found in all different scientififc studies. This year alone I've learned about them in terms of human physiology and in climatology. Feedback loops are kind of like cycles. There is a signal that starts a chain reaction that leads to a response. Sometimes the response inhibits the initial siglanl, a negative feedback, and sometimes the response leads to an increase in the signal. An example of a positive feedback loop is chidbirth. The contraction leads to a nerve impulse that signals the hypothalamus to release the hormone oxytocin. The release of oxytocin leads to more contractions. Which then lead to more production of the hormone. The initial contraction leads to a stimulus that in the end results in more contractions. Blood clotting is another example of positive feedback because when a vessel is damaged platelets start to cling to it and when they cling they release a hormone that attracts more platelets. So the initial blood clotting leads to more blood clotting. The initial stimulus leads to an increase in the final product. 

Negative feedback has the opposite result. Negative feedback most often keeps something more towards equilibrium whereas positive feedback escalates, so usually only occurs in special instances. An example of negative feedback is thermoregulation. If a body temperature increase, measures are taken in order to try and lower the body temperature. So the initial increase leads to a decrease in body temp, therefore a negative response. Another example is blood sugar levels. When glucose levels are high, insulin is released to decrease levels. When levels are low, gllucagon is released to increase levels. The initial stimulus results in something trying to lower the signal. 

Methods and procedures play a huge role in scientific writing and research. Most of the information and knowledge we have obtained through history is because of scientific research and the ability to replicate that research. Experiments are an important aspect of science that allows us to obtain new knowledge and understand the world around us. In order for an hypothesis/experiment to be accepted, it must be able to be replicated. In order to do this, scientists must include a clear procedure of how they achieved their results. Within an experiment, there are variables that are changed as well as variables that must be controlled. The goal of this project is to practice writing informative and descriptive methods so others can understand and replicate an experiment. While we are not designing an experiment, we will be creating a multi-panel figure of a spider web found on the UMass campus as well as writing the methods we did to capture and create the figure. Once the methods are complete, each student will receive another student’s methods from their own and follow the procedure to hopefully create the exact same multi-panel figure as that student. The original multi-panel figure and the replicated multi-panel figure will be compared to see how accurate and descriptive the original methods were. This exercise allow students to see where they may need to be more descriptive in their methods and improve their scientific writing overall.

In this lab, the diversity of plant species in different environments were observed. The diversity of plant species were collected on a hill and a flatland. Depending on the slope of the environment, the plant diversity differed. Diversity is beneficial in an environment due to the stability it creates, making organisms more suitable for fighting disease and responding to other changes to its surroundings. An environment is healthy when it is very rich. Richness is the number of species in a community. The most common way to determine whether an environment is diverse is by calculating the Shannon Diversity Index. The Shannon Diversity Index is a method to mathematically measure a community’s diversity (Beals). This is important to biologists, enabling them to observe how rare or common a species is in an environment (Beals). Different enviornments were observed in order to see if the type of topography resulted in a difference in plant diversity. On a hill, the nutrients and soil ran down to the bottom, preventing plants from using them. The assumption can be made that there will be less diversity on a hill than there would be on a flatland due to the lack of nutrients.

The hydronium concentrations was found by using the pH halfway through the jump in pH change and using logarithms to isolate the concentration. The hydronium concentration that was calculated for the Sprite and NaOH reaction was 8.91E-9 M. This concentration was correlated, yet not similar to the citric acid concentration found in the previous experiment: 4.027E-9 M. This could be due to human error, such as adding too much base when trying to control the pH measurements. The calculated hydronium concentration in Coke and NaOH reaction was 1.02E-8 M. This concentration was similar to the phosphoric acid concentration found in the previous experiment: 1.07E-5 M. The hydronium concentrations that were calculated equal the Ka of half of the reaction. This is why we were able to solve for the hydronium concentrations by looking at the jumps in pH change as the volume of base increased.

Gnathostomes are a group of organisms which have true jaw structures, rather than a simple mouth. It is believed that these jaw structures developed from modified gill arches in fish. The first arch, the premandibular arch, is thought to have moved upward, forming the beginnings of the braincase as a plate underneath the brain itself. The second gill arch, the Mandibular arch, bends forward into two seperate sections. The top, which would eventually form the upper jaw, is called palatoquadrate cartilage. The bottom, forming the lower jaw, is mandibular cartilage. Eventually these cartilaginous structures would ossify in some organisms, giving them boney jaws. The third gill arch, the hyoid arch, forms a structure which supports the jaws themselves, providing a foundation to rest or directly connecting to the jaws. This also serves the purpose of anchoring the jaw to the braincase. Of course this anchoring method differs, or is entirely absent depending on the form of jaw suspension that develops in a particular organism.

A radioimmunoassay is a technique used to detect levels of different substances, usually antigens or hormones in the blood, by using antibodies and forming an antibody-antigen/hormone complex. For example. a radioimmunoassay could measure insulin levels of a particular patient. An antibody-insulin complex would be created (they will bind to each other), but the insulin used will be radioactive labeled insulin. A bunch of these antibody-insulin complexes would be created on a slide, and then the sample of the patients serum will be added in with the slide. If insulin is present in the serum, it will replace some of the radioactively labeled insulin in the previously formed antibody-insulin complexes on the slide. If it is high, it will replace more of them, so there will be more antibodies attached to non-radioactive insulin, and more free radioactive insulin that has been displaced. The antigen-insulin complexes will be precipitated out by the use of a second antibody that attaches to the complex. Then, the radioactivity of the supernatant, which contains all of the free insulin, will be measured. The level of radioactivity quantifies the amount of radioactive insulin that was displaced, which quantifies the level of insulin in the patient.

The purpose of this project is to generate a multipanel scientific figure of a local spider web. In order to do so, three pictures were taken; one of the web, one of the surrounding environment, and one of its location on a detailed map. These pictures were taken with a great deal of thought as later on, a peer will be tasked with replicating the figure based on my methods. When selecting a web to photograph, it was important to choose an area that my peers would have regular access too so that they would be able to replicate the figure as best as possible. For example, the spider webs in my basement werent photographed because not everyne would have access to my basement. The figure presented was set up in order to provide a smooth flow between photographs so that it would be easy for the reader to visualize the location, size, and environment which you can find said spider web. A lot of thought and detail was put into the project so that it would be relatively easy to replicate the figure.

    The two photographs were taken on the front-right side of the Student Union building at the University of Massachusetts Amherst at approximately 3 PM. A bike rack with an overhang was in the close proximity. Between the building and bike rack, an air filtration unit could be seen. On the right side of that was a small metal box with the words “Elect IN rm. 208” written on it in marker. The web was located under that box, and it extended to the right.

The web was large and relatively flat, so I decided to only focus on the right most potion. To take the photo, the camera was held about eight inches above it and pointed directly downwards. A quarter, held between the pointer finger and middle finger of my left hand, was held at the level of the web and positioned so that it would show up in the bottom left corner of the image. Flash was turned on. Once a satisfactory photo was taken, I moved back towards the bike rack. I then positioned myself between the windows of the Student Union and the second pillar of the bike rack structure. The camera was pointed directly at the location of the web. The shot was framed so that the air filtration unit was at the center. Finally, the second photo was captured.

Northern Blotting Analysis is a procedure used to detect a specific RNA molecule/specific group of RNA molecules within a larger group of RNA molecules. It is commonly used in research to study gene expression. It is similar to the Southern blotting Analysis, but detects RNA rather than DNA. First, RNA molecules are extracted, usually from cells. The RNA molecules are then separated by gel electrophoresis, which separates them based on their size. RNA molecules have a negative charge, so they travel towards the positive side. The smaller molecules will travel faster and thus, the molecules will end up in an order than ranges from big to small, from negative to positive. The gel that is used is a formaldehyde gel which denatures the RNA so that it is single-stranded rather than double stranded, so that it can be effectively probed later on. Next, a blotting procedure is used to transfer the RNA from the gel to a membrane, in which the RNA can be probed. The last major step is the probing/hybridization, where a DNA molecule (usually cDNA) with a sequence that is complementary to the desired RNA strand, is used to probe the RNA. Then the excess probes are washed off so that the results can be visualized in an autoradiograph.

Polymorphisms can occur due to many reasons. The main type of polymorphism is RFLP (or restriction fragment length polymorphism). RFLP's are a result of a change of length fragments. They can occur due to SNPs (single nucleotide polymorphism) mutations, Indels (insertion and/or deletions) mutations, or VNTR mutations (variable number of tandem repeats).