Writing in Biology

Gene therapy and optogenetics are used to treat blindness that was caused by retinitis pigmentosa (RP) and advanced dry-aged related macular degeneration. The two conditions cause the photoreceptors of the retina to die off, gradually. Which would cause difficulty seeing especially in low light. Eventually the loss of vision would be complete and would result in blindness. In the experiment, researches utilized a virus that was modified to contain a gene for an algae called Channelrhodopsin-2 (ChR2). ChR2 is a light sensitive protein. Researchers hypothesized that when ChR2 is injecting into the subjects eye, ChR2 would start expressing and taking over the dead opsins. Since ChR2 is light sensitive, the patient would be able to regain some eyesight, even though it might be in black and white and blurry.

Amyotrophic Lateral Sclerosis is a neurodegenerative disease that affects nerve cells in both the brain and spinal cord. These neurons are interconnected from the brain to the spinal cord and the spinal cord to our muscles. As these motor neurons progressively die, the ability of our brain to control muscle movement is diminished. With voluntary muscle movement being affected, many patients lose the ability to control simple everyday actions. Scientists around the world have been completing studies towards discovering various treatments for this disease. ALS affects both patients neurologically and physically and that is where my interest in the disease stems from. As I have been completing research regarding muscle function and muscle fatigue, I would love nothing more than to develop a better understanding of ALS and gain first-hand experience in the clinical research and care of the disease in relation to muscle function. 

The primary goal of the Methods project is to compare and contrast observational differences between the original and recreated figures as followed by someone to develop critical skills used in science. Being able to reproduce the same results that were obtained by the researcher, distinguish between observation and inference and identify control factors within an experiment are all essential skills needed for scientific research. Interspecific interactions vary between being identified as mutualistic, antagonistic or competitive. These interactions can be long term, transitory and are extremely dependent on the species external factors.

    Replicability is an essential component to this project and not only will my peers be reproducing my figure, but I will be reproducing one of theirs. When brainstorming for this project, different factors had to be taken into consideration including both the location and accessibility of the species. The two species that I documented for my interspecific interaction include both a Crab Cutleaf tree and moss. When creating my figures and writing my methods, various factors including the weather, the background, other subjects in my photo, the angle, distance and type of camera that were used all had to be kept in mind. In order for my partner to accurately reproduce my image, I understood that all the detail needed to be organized in clear-cut and definitive steps.

As part of my Writing in Biology class at the University of Massachusetts Amherst, we were tasked with developing a multipanel figure, writing a methods for said figure and having someone follow our methods to replicate the figure. Not only did someone follow my methods, but I was also assigned someone elses to follow. The purpose of this project is to illustrate the importance of detail when writing a methods section and the significance of this detail in scientific replicability. After receiving my partners replicated panel, it was apparent that there were significant differences in comparison to my original figure. These differences were due to unclear explanations in the methods along with some factors that were uncontrollable.

As far as temperature compensation in the organism-level processes Clarke argues that studies are focused too much on the cellular level and that we do not have an adequate understanding at the molecular level. He proposes to examine the thermodynamic characteristics of the growth processes at a molecular level in order to expand our knowledge on the subject. Temperature compensation is not the only adaptation that Clarke feels is worth understanding. Just as important are the costs of temperature adaptation that come along with compensation. A major cost is the turnover of proteins based on the outcome of temperature, molecular stability, and physiological function. A way to examine these costs is to look at the total costs of existence for an organism excluding reproduction, growth, and activity. These costs have shown to vary with temperature and studies have provided data that point to organisms living in cold temperatures having protein degraded more than those in warmer temperatures.

In the reading by Andrew Clarke, the author gives his own personal opinions on the effect that evolutionary temperature adaptation has on life history theory, food-web dynamics, biological diversity, and biotic response to climate change. His two main goals of the paper are to identify important gaps in our general knowledge of evolutionary temperature adaptation and secondly to explore the consequences of the adaptation of temperature for ecology. Clarke points to a simple model of evolutionary temperature compensation in cellular models to propose two questions. One being how has evolution altered physiology at different temperatures and the other being to what extent has full compensation been achieved? He claims that organisms maintain physiological rates by three different strategies: quantitative, qualitative, and modulation. He then points to the relationship between enzyme function and organism performance as a way of looking into the compensation required. The changes in temperature can potentially cause for metabolic imbalances. However, he points out that in order to have a full understanding of this effect we need to understand the dynamic behavior of the metabolic system in order to know cellular responses to thermal change.

An exergonic reaction is a reaction where there is a net negative change in free energy. This type of reaction is considered to be spontaneous, meaning that no energy has to be put into the system for a reaction to occur. This type of a reaction is favored because it releases energy that can be used by the cell. You can relate this concept to catabolism. Catabolic reactions start with reactants that have a high free energy and end with products that have a low free energy. Catabolism is the type of process in which ATP is generated. An endergonic reaction is a reaction in which there is a net positive change in free energy. This type of a reaction is not spontaneous and requires the input of energy to proceed. You can relate this concept to anabolism. Anabolism starts with reactants that have a low free energy and end with products that have a high free energy. This process take ATP to complete and for that reason is not favorable for the cell to carry out. A trick that I use to remember whether the reaction uses ATP is that anabolism and ATP both start with the letter A.

Recently, astronomers have discovered a galaxy that is blowing gas bubbles. These gas bubbles stretch a couple thousand light-years across and are crackling with charged particles 100 times more energetic than anything on earth. These bubbles were detected in the galaxy NGC 3079 which is 67 million light-years away from earth. The bubbles that are spewing are known as superbubbles because they are quite large. Superbubbles form when shock waves shove gases released by stars far into space leaving a “bubble-shaped” cavity behind. It is still unknown about how these cavities are truly formed but scientists intend on finding out more about them and the possible dangers they could pose.

Tumors become metastatic when they leave their primary site of development and travel throughout the bloodstream to start new growths over the body. This can lead to complications in treatment as it is challenging to eradicate the tumor completely if it is mobile. Metastatic ancer cells also have the ability to modify their genomic expression patterns. This allows them to behave like stem cells, remain quiescent, and express a broader range of genes to further their survival. They are also then able to differentiate into a different cell type at any moment. This lack of consistency in cell identity renders metastatic cancer difficult to fully treat. Metastatic cancer cells can also create an environment known as the premetastatic niche, an environment where the cancer can modify to its advantage and eventually spread to. These cancer cells additionally have the ability to induce angiogenesis in other cells in order to maximize nutrient flow to their population and increase their survivability.