Writing in Biology - Section 1

ATP itself does not give energy directly to a process that may need it, rather it is the breaking down of ATP that gives a reaction the energy it needs to proceed. The energy that ATP gives comes from energy released by breaking the bonds in its structure. The three phosphate groups attached to each other all have the same charge, and like charges prefer not to be close to one another. Given this relationship, a lot of energy is required to bond these phosphate groups together. When a reaction needs energy, the bond between the second and third phosphate group of the ATP molecule is broken, which releases a large amount of energy that can be used by reactants. Because mitochondria produce the cell’s major energy source, ATP, mitochondria are referred to as “the powerhouse of the cell”.

Competition amongst organisms in the same environment is a major force that drives species to adapt and evolve. Competition is at the foundation of the saying "survival of the fittest", as those who are best fit can compete with other organisms in their environment better and have a better chance of reproducing. Organisms in competition with each other are battling to gain control of a particular resource, whether that be food, shelter, or some other resource. The battle for these resources forces organisms to adapt and overcome the challenges that they may face when vying for control of these resources. If one organism is unfit to compete with another, it will lose easy access to resources in the area, and unless the less-fit organism can move to a new area where it can access the same resources without such fierce competition, the numbers of that organism will decline and may eventually go extinct if it cannot adapt.

Game theory is a field of scientific modelling that is most often employed, in simple situations, when the optimal choices of one player depend on the optimal choices of another player. More complex game theory models are described as dynamic and not only take into account the optimal choices of the players but also their respective conditions. A simple game theory model that describes interactions between two players is prisoner’s dilemma. The classic prisoner’s dilemma example involves two prisoners who are under interrogation and have two choices: to cooperate with one another, or to defect and betray on another. This leads to a payoff matrix as follows: 

Thus, in a one-off interaction, the optimal strategy is always to defect, as either you go free or you get a 5 year sentence. Whereas, if you were to cooperate you would either get a 1 year sentence or a 10 year sentence, both of which are worse payoffs than the defecting payoffs. However, over many interactions, cooperation is the best strategy as it has the best average payoff. This model is often used in economics. However, it can also be used in animal behaviour in determining the nature of short-term and long-term group interactions and the development of altruism in a species.

The occupations people held determined their standing in society. Archaeologists uncovered only a few seals, which indicate it is likely that they were used by individuals or communities with considerable power, such as landowners, merchants, and religious leaders (Kenoyer). If everyone in the society were equal, then many seals would have been found because everyone would have the opportunity to have one, yet this is not the case. Instead, a select few were discovered. This implies a small group of people interacted with these items and possibly received more economic gains than others in society. Reports on early Harappan settlers say they, “seem to have exploited the rich agricultural and grazing lands along the Ravi River to sustain themselves as they built economic and political power through craft production and trade” (Kenoyer). A system of trade, or economy, is a capitalistic idea and capitalism encourages the summation of wealth, usually by individuals. Some initial settlers must have made good livings off trading goods while others not so much. Over time, as these settlers became the Harappan people we know today, it is possible wealth disparities increased amongst the population. Again, if there are disparities in wealth, there are disparities in social class and therefore a social hierarchy is present.

Human civilizations tend to possess similar characteristics even across religious, linguistic, spatial barriers. Civilizations such as Harappa and Sumer may appear to be completely different, and there are many reasons why they were. However, similar traits can be observed through artifacts found at these ancient sites, one of which is a social hierarchy. In general, a polarized social hierarchy develops due to power dynamics from a ruling class legitimized by another social factor. In the case of the Harappans, their social hierarchy was much less polarized than ancient Sumers and was legitimized through the economy rather than a ruling class.

    Archaeologists studying Harappan civilization in the Indus river valley have uncovered many artifacts which, I believe, show society to be a hierarchy. Some artifacts were identified as jewelry or luxury goods which were likely used by an upper class “to demonstrate their wealth and status” (Kenoyer). A society without a hierarchy implies there is little to no social stratification among the people and everyone has similar opportunities. If these luxury goods and jewels were used to demonstrate status and wealth then there must have been a disparity in wealth. Interestingly, children, commoners, or both, were found to be wearing terra-cotta items whereas members of the upper class wore exotic stones (Kenoyer). If there weren’t a disparity then demonstrating their wealth would be pointless because everyone would have had the same jewelry. However, commoners and the upper class did not have the same jewelry, likely due to a disparity in wealth. Where there are wealth disparities, there are social disparities. After some time, I believe social classes based on wealth gaps evolved in Harappan society forming a hierarchy. 

When I had finished reading “At the Full and Change of the Moon”, I had an array of thoughts, and did not know where to begin by expressing them in a response paper. I began thinking closely of the characters and realized Marie Ursule reminds me of my mother, as she would do anything for the security of her daughter, and Bola reminds me of myself as she been through a lot and is handed a series of unfortunate events. This mother-daughter connection helped me with my response as Marie Ursule sees such promise in her daughter’s eyes, that she can see any promise, is an undeniable sign of hope but one that acknowledges the pain and suffering bound up with hope. This reminds me of my mother’s sufferings, as I was the second Mariam born in the family, as the first Mariam passed away when she was four, but my mother still sees promise in me and has hope for me. This hope and prosper is shown in the passage on page 44 when the narrator says “Marie Ursule had seen in her child’s eyes, the sea, and the journey to be made that melts the body. She had seen the child in the sea.” Marie Ursule sees through her child as any mother would. She knows Bola more than Bola may think, and even with her death, she will always be watching her and her every move. It would be false of me to point this out in an analysis because ultimately, without Marie Ursule and her intentions, Bola and Bola 2 would have never could experience the world like no other, without slavery. And … “Marie Ursule saw water in the child’s eyes. So much water she dabbed it away...” These two small but significant quotes show that Marie Ursule had the best eye for her daughter. Metaphorically, she used water as “tears” as Marie’s past has indirectly haunted Bola, but it was but the sea, in Bola’s eyes. This definitely relates to me as my sister’s passing haunts me indirectly, as I have never met her, but because I live in the present, it is but my current existence of the “second Mariam” that I can truly see. 

According to the NIH genetic inheritance reference and OMIM, the mode of inheritance is autosomal dominant or recessive inheritance pattern. 

An attempt to discover the gene that is responsible for retinitis pigmentosa was made in the 1970s, which the discovered gene was named to be RP1. more concrete evidence that the gene causes the disease was made in 1999, where two different research confirmed the gene on chromosome 8. For a disease that we are studying, the mutation was first found in a large Irish family in 1989. The RHO gene was discovered in 1992, in a study that studied 12 families that had retinitis pigmentosa. In the 1989 paper, the researchers attempted to identify the mutation through linkage study with a gene in chromosome 3. In 1990, a paper established that the mutation is in pro23 to His mutation in the RHO gene. In 1992, another paper established that retinitis pigmentosa can also be caused by an arg207 to met mutation In RHO gene. So far, there have been 9 mutations in the RHO genes that cause retinitis pigmentosa.

The mutation that we are specifically studying is related to the mutation in the gene that codes for the RHO protein (3q22.1). However, there are other mutations that are associated with the disease, such as in the gene coding for RPGR, (xp11.4), CRB1 (1q31.3), and IDH3B(20p13).

    No, because retinitis pigmentosa can be caused by multiple genes, and many of the symptoms are similar and cannot be distinguished clinically. Because of this, there is no clear cut association between the genotype and phenotype.

Clinically,  in a patient with retinitis pigmentosa, the eye, specifically, the cone cell is affected. In a patient with retinitis pigmentosa, the symptom starts with often  childhood, starting with the loss of night vision and gradual loss of peripheral vision and then the loss of central vision, ending in complete blindness usually around 30 to 40

    In a less clinical sense, the patients of retinitis pigmentosa are aware of their potential to become blind through one or both of their parents and other family members because they have other family members that have a similar disease, there is an expectation that the patient will go through life with a similar sight loss pattern as that for their parents. From the description that the patients give on how it feels to have the disease, the sight is mostly light and dark with very little details. Another description is that their vision is slowly being smudged by vaseline, or it’s like wearing a pair of sunglasses in the dark.  The onset of symptoms often start with childhood, but the symptoms can manifest at a later life stage. Similarly, while it is common that the patients would be completely blind by 40, it is not unheard of for people to retain vision until their 80s. The decrease in vision and later, complete loss of a vision is a major disability and often results in the patients unable to do certain jobs and for those who do not have complete blindness, patients often pause before telling their bosses and managers about their condition, fearing repercussion. While most patient’s vision will degrade to the point where they are unable to drive, because it is a progressive disease, the patients are aware that this will happen, and that they may have to use walking stick eventually. The patients also have a harder time adjusting their sense of self compared to those that were born blind.

The restriction digests for Agouti and TYRP1 are then analyzed by running an agarose gel. Agouti and TYRP1 restriction digests are performed in separate gels. Gel electrophoresis is performed by first pouring 3.0 g high-resolution agarose into a prepared gel box. A comb is immediately inserted into the gel and removed when the gel has solidified. The gel is then covered with 1x TAE buffer until the top of the box is covered. The ladder is premade and given by Assistant Gregory Teicher. Restriction digest products are prepared by adding 3 µL of SmartGlow (a dye). 12 µL of digests and ladders are loaded in any order, being sure each lane is labeled and given the correct solution. The settings for the gel are set to no timer (infinite) and a voltage of 115 V. The gel is stopped when looked Assistant Teicher approves of the gel.