Writing in Biology

Canis lupus familiaris (dogs), Canis lupus (wolves), and Canis latrans (coyote) are very similar animals, and often a topic of conversation if the species are under one species or separate. Although, these animals are different species, and should never be considered the same species.  Those who are in favor of the three animals being considered the same species, base that assumption because these three animals are able to interbred with each and produce viable offspring, which in past years was a sign that organisms are considered to be part of the same species. However, in an article Yes, eastern coyotes are hybrids, but the ‘coywolf’ is not a thing, the author points out that different species do not have to be completely reproductively isolated, as that notion is now disregarded by zoologists in present time. The article points out that in times when both the species of Canis lupus and Canis latrans were underpopulated and endangered that the different species would mate with each other along with the other species Canis lupus familiaris. Although, when each species is not in endangered they choose to mate with their respective species instead of interbreeding with other species. Therefore, because the animals choose to mate within their own type when there is no risk of extinction, shows that each animal is in different species. 

The phenomenon of oncogene addiction describes cancer cell dependence on individual oncogenes to sustain the malignant phenotype. There has been clinical evidence to support the idea of oncogene addiction. One area oncogene addiction has been seen is in Chronic myeloid leukemia also known as CML. In CML there is an abnormality in chromosome 22. A translocation event happens where RAG cuts some of the Abl gene and more of the Bcr gene. When they come together and combine, it forms an alternative chromosome 22 referred to as Philadelphia chromosome. CML is essentially driven by the BCR-ABL mutant oncogene as its addiction. This was demonstrated in patients through the clinical responses attained with the kinase inhibitor imatinb, which targets BCR-ABL. It is further supported by genetic mechanisms of resistance that vastly led to reactivation of BCR-ABL kinase activity. Another example is antiandrogens. These are used as a treatment for prostate cancer. They are also known to be ‘lineage addicted’ to AR and have recurrent AR amplifications or mutations upon resistance to first line therapeutic techniques.  Overall, medicine continues to advance and we are seeing other ways to support the phenomenon of oncogene addiction. 

High-schoolers are mainly taught to write creatively. The only scientific writing they do are lab reports. They only know that they have to state facts in scientific writings. They don't know much else about including structure within those facts when writing. They usually just answer the questions the teachers have them answer for various parts of the report. There are 4 main types of writing which include expository, persuasive, narrative, and descriptive. The scientific writing falls under the expository category. Despite scientific being only factual unlike the other types of writing, all writings need to take into consideration the readers. Every reader thinks differently so the writer has to be as clear as possible as to what he or she is trying to get into the readers' heads. I never thought that scientific writing would have to consider the readers and how they think. I thought it was just stating facts and hypotheses. What was true was true. What was observed was observed. Structure and function still matters in scientific writings. It seems to matter more than in other types of writing. Creativity can be many different things. Scientific writings sort of can't be many different things. Each sentence, paragraph, and section has a function. Each of those things matter. They do their own jobs in order for the readers to understand what points are trying to be put across. 

There is clinical evidence that oncogene addiction exists. This could be seen in CML.  CML is referred as Chronic myeloid leukemia. This involves chromosome 22 and an abnormality. A translocation event happens between chromosome 9 and chromosome 22 and there are RAG’s. When there is a mutation it causes RAG to cut some of the Abl gene and more of the Bcr gene. When combined it forms a changed chromosome 22 (Philadelphia chromosome).  CML is essentially driven by the BCR-ABL mutant oncogene so it is addicted. This was demonstrated in patients through the clinical responses attained with the kinase inhibitor imatinb, which targets BCR-ABL. It is further supported by genetic mechanisms of resistance that vastly led to reactivation of BCR-ABL kinase activity. Another example is antiandrogens and using them for the treatment of prostate cancers, which are known to be ‘lineage addicted’ to AR and have recurrent AR amplifications or mutations upon resistance to first line therapeutic techniques.  

Oncogenes are essentially dominant growth enhancing genes and if overexpressed can augment growth in one cell type but impede growth or stimulate programmed cell death in another cell type.  The phenomenon of oncogene addiction describes cancer cell dependence on individual oncogenes to sustain the malignant phenotype. Oncogenic functions are activated by them. Cancer cell survival relies on quite a few key genetic driver events. When an oncogene is turned off this means that the cancer cells will undergo programmed cell death. For instance, in transgenic mice when there is the expression of an inducible form of the H-ras oncogene it develops melanomas. When the ras gene was switched off apoptosis occurred and regressed. Another instance is with the expression of a Bcr-Abl fusion gene which results in the development of leukemia and killed mice. When switched off, even at advanced stages of disease, the leukemic cells underwent rapid apoptosis and this resulted in mice surviving. In cancer cells the regulation of signal transduction and gene expression is rather crazy and distinct of normal cells. Since they have a different form of regulation it is said that cancer cells may be more reliant on the activity of specific oncogenes. In addition, they are more sensitive to the growth-inhibitory effects of specific tumor suppressor genes like p53 versus normal cells. 

I found both articels that we were tasked with reading this week very interesting, they were also very similar in the way they were structured. After reading chapter 7 the reason for the similarities is quite obvious, it allows a logical and strong flow of ideas and makes it easier for the readers to understand the topics at hand. As for specific simlarites scene one example is the  the level one headers of both articles contained the title of the paper, the authors and the publication information. The level 2 headers of the papers preceded to contain the section descriptions, such as introduction or abstract and are placed when a new topic or study is about to be discussed. When each section was broken down and looked at the similarites continued to appear. For the papers each section is structured similar to the way of the whole paper is but in an abbreviated version obviously, they have intro paragraphs, normally the first paragraph of each section, to introduce the information and then the sections continue on, providing new statistics and information. Each section was also responsible for providing new information and statistics of the overall topic. As for the individual paragraphs they each had a topic sentence to either transition the paragraphs or introduce a new topic. This methodical structure and the similarities seen throughout the scientific field allow the ideas to be very logically organized and flow well. And the fact that each sentence continues to build on the idea presented in the second header and the topic sentence of the specific paragraph really assists the reader in understanding the overall point of the paper.

The next section of for the widely distributed native and non-native article is the materials where they first talk about the species they have selected for this and from what sources they were gathering the information from, followed by the traits that were relevant to the distribution of the species being observed. Finally, it mentions the trait interaction model which is used to determine the frequency of grid-cells a species occupied in connection to the train they have and interactions. This section went from broad to specific, from what species down to the specific trait interactions. The purpose of this section is to let the audience know where and how they were going about this problem or hypothesis so the audience could try to get the same results with the same sources and therefore data that the author used in this. The first paragraph of this section is used to give the audience the understanding of where they are gathering their main data from, from which outside database they used to get the data broad numbered data.

The article on the Baltic Sea have the same purpose for this section although it doesn’t explicitly administer that is the materials and methods. However, it still includes what is used in this section. It is also structured the same way by first mentioning how the non-native species were brought into the Baltic, then going into the rate of invasion currently and the number of species and their dispersal rate. The first paragraph in this section is used to give the origin of the problem, in contrast with the first article I mentioned, this article gives an even broader start to the problem, beginning with how this started. 

My first draft about the two assigned articles for this week talks about their structures. After reading chapter 7 in our books this morning on what the overall structure of our papers should conform to, I got a clearer understanding on the purpose of our assignment. The structures of the different sections play a big role in the flow, clarity and what we want our reader to know is important. In this draft, I would like to compare the introductions of both of the articles. Before doing that, I would like to point out the biggest difference between these articles. The article from the Ecology Matters journal is about an experiment performed by the researchers that includes a materials and methods section. The authors of the other article (the Biological Invasions publication) have not performed an experiment but rather have formulated a hypothesis, collected information from other articles and tried to "answer" their hypothesis. Therefore these articles will have different structures because of the underlying purpose of each. However, since I am comparing introductions, I am going to assume that they are similar since all introductions serve the same the purpose such as to contain the background information, state the hypothesis and introduce the purpose. Some things that our textbook points out that sound be included in the structure of the introduction are: funnel-shape organization with the known, first paragraph to be the background, the second to last paragraph to be unknown and the last paragraph to be the question/purpose and maybe the significance.
The first paragraph of the introduction in the article from the Ecology Matters journal starts with very general background information such as why one should study non-native species, funnels to a more specific background such as why/how this is being studied and by whom. The second to last paragraph contains phrases that are lead to be the unknown such as "should be." The structure of the last paragraph contains the the purpose and the hypothesis. However, it doesn't contain the experimental approach which I am going to assume is probably in the methods section. I liked the structure of their introduction but it would be helpful to know how they approached their question.
The first paragraph of the introduction of the other article also begins off broad and then the subsequent paragraphs become more specific with information that pertains to their research. It is interesting how their first sentence underlies their purpose just like in the other article. The second to last paragraph doesn't contain any unknowns which is probably because this is not an experiment. The last paragraph is very short and contains only the experimental approach.

The two articles, Origin matter: widely distributed native and non-native species benefit from different functional traits and Non-native species and rates of spread: lessons from the brackish Baltic Sea, both are similarly structured. The level one heading for each article is the title of the article and the authors who wrote the article. The level two heading are the different parts of the article such as the abstract, introduction, etc. Each section of the articles have an introduction into what the authors will be discussing in that section. At the end of each section there is transition sentence that leads into a new section. Overall, the flow of ideas is smooth and each section is connected even though the paragraphs present different information. The information in each paragraph help present all the points the author is trying to present to the reader. The way each paragraph is constructed is concise with precise language that presents the experiment and the findings of the experiment. 

One can determine an ancestral or derived trait based on the outgroup. The outgroup has a character state of zero for all traits listed in the data. The traits that are given the zero state are the ancestral traits which are present in the outgroup and used to disguise the morphology of the different animals. In the case of non-retractable and retractable claws, non-retractable claws was given the state of zero therefore in the out-group and ancestral.