Perfect Paragraph

Both articles seem to contain level 1 headings for the main title of each article (centered and bold-faced) however, the sub-titles for each section of the articles contain level 2 headings that are left-aligned and bold-faced. Each section of the articles are structured in steps, such as the steps and processes the scientists took to develop and conduct their experiments. It breaks down the processes of the experiment so it is much easier to read, understand, and analyze. Each section identifies what part of the experiment has been conducted and gives a detailed analysis of what occurred or what results were recorded. The first paragraph of each section gives a small intro into what the section will discuss a little background knowledge and a transition from one paragraph to another. It appears that the paragraphs in both articles contain a logical flow of ideas as the ideas are organized in almost a chronological order of occurrence during the experiment. However, I would say that the first article has better flow of topic sentences, while the second article is more chopped and could be read in sections without going through the entire article.

Structure of Scientific Literature

The similarities of these two pieces of literature are the level 2 headings, this includes the abstract, introduction, discussion and conclusions. Although the article about the non-native species in the Baltic Sea, if read one can see that they are included. On the other hand, the article on the wide spread and different traits of these species specifically states these headings. The abstract is used in these pieces of literature to give a quick summarizing background on the topic of discussion. The following section is the introduction which is a more in-depth background configuration which includes the original thought and ending with the hypothesis which will try to be validated or invalidated in the research. Materials and methods are to follow. This section is used to give specific details about how they retrieved their data in order for other scientists who are interested in the topic to perform the research on their own to validate the authors results. The results section is where they include all of their data, including well organized tables and graphs to connect all of their data in a simple and efficient display. Finally, the discussion and conclusion section is used to discuss the results point out any major setbacks or notable data they expected or did not expect. This is also where they connect it back to their hypothesis and validate or invalidate it in a clear and concise way.  

In this specific study, the researchers are trying to correlate the cavitation effect on a popping bottle to brain injuries. Cavitation is when water at rest is all of a sudden sped up with a force of acceleration, causing a destructive wave to shatter the bottle or container that the liquid is sitting in. Similar to liquid trapped inside a bottle, the brain is surrounded by fluid, so a hit to the head could cause a similar effect to our brains. Our brain is essential to almost every function that happens throughout our body and during a concussion your brain is damaged or bruised. Although one concussion might not cause long term damage, repeated amount of concussions can cause long term memory loss and diseases like CTE, like we see many football players having. With this information, researchers are able to create better safety equipment to minimize the amount of trauma our brain sustains. In conclusion, if the force of the hit to the brain is above a certain margnitude, there is no safety equipment that researchers can create to protect the person.

The novel Your Inner Fish: A Journey into the 3.5-billion-Year History of the Human Body by Neil Shubin explores the origins of humanity. Shubin makes it clear from the start of the novel that humans have changed over time through evolution, and the fossil record has secrets of our past hidden inside of it. Even though only a miniscule fraction of organisms are fossilized, fossils can be used to glimpse into the past and study our ancestors. Shubin focuses on how similar humans are to other animals, both morphologically and genetically. For example he highlights that all animals have heads, even fish, a trait that can be adequately explained through common descent. It is by far more likely that having a head is a shared trait, than it is that it independently arose in numerous recent lineages. This is one of the main themes of the book, highlighting similarities humans share with other animals. Darwin used the same method in On the Origin of Species, but here Shubin can built off of Darwin’s foundation by using modern discoveries.

This week we had to read Chapter 3 and 7 from the “Writing in the Biological Sciences” text. In my opinion, the most important factor to remember when writing is to always write with the reader in mind. After you have already formulated your hypothesis, performed all the necessary experiments and research, it is time to focus on who is going to be reading your writing. Ask yourself: “what is the most important piece of information you would like to convey to your audience?” Remember to write clearly. For instance, the first paragraph of this chapter mentions that we need to take into account how the reader is going to interpret our writing. If we were trying to appeal to a feeling or evoke some kind of emotional response from our reader then we would lean towards using fancy, and flowy language and phrases. However, when trying to communicate scientifically, that kind of writing is unecessary and instead it makes more sense to use precise, clear language that is easy to understand and is correctly worded. It is important to establish importance in a sentence as well. Depending on where a certain phrase is placed and what punctuation is used, it can be viewed as something negative or as something positive. Old information is placed at the beginning of a paragraph and new information that needs more emphasis, is placed at the end of a sentence. Last, but not least, we need to remember to use past tense for observations, unpublished results, and specific interpretations and to use present tense for general rules, accepted facts and established knowledge.

The organism being observed consists of a body and tail structure covered by a translucent coating. The length of both the tail and body are roughly 15mm and the height of the body is roughly 3mm. The organism is able to move in a wave-like manner, utilizing its ability to contract and expand as well as six leg-like stumps on the bottom of the organism that seem to provide added traction. The six legs counted on the bottom of the organism also seem to provide stabilization and help to turn the organism over when on its back. Also observed through the translucent underside of the organism were white intestine-like organs lining the body, that could have digestive or nervous system functions. Despite being able to move, the organism seemed to lack direction and some sensory skills, moving around the perimeter of the container primarily, and frequently running into the edge. The organism is clearly aware of its surroundings however, when the container was shaken or moved, the organism stopped moving and only resumed when presumed safe. This stopping of movement when in presumed danger could be an important mechanism for evading the detection of predators. Many questions remain about the development of the organism as well as its habitat, place in its ecosystem and sensory and physiological capabilities. 

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. 

When a couple is expecting a child, they wonder what gender it is and what defects it could possibly have. In the past, the best method to answer these question was a procedure called amniocentesis. Amniocentesis is a technique where a needle is inserted into a women’s amniotic sac through her abdomen in order to collect amniotic fluid which could then be analyzed. This process gives results with a high degree of certainty, however it has some flaws. Since a long needle is being injected into the womb, there is the risk that it could poke something that it is not supposed to. Therefore, there is miscarriage in about 1% of amniocentesis patients. That being said, there is now a new method of determining the genetic information of the fetus, and it is much less invasive. The new test goes by the name of free fetal DNA testing, and all the mother has to do is get blood taken. By collecting the blood of the mother, companies like Harmony can separate out the fetal DNA and examine it to find birth defects and determine the gender, to a lesser degree of certainty than amniocentesis. The blood of the fetus and the mother do not directly mix, however, the placenta sheds tissue into the mother’s blood stream daily. Because of the placental shedding, fetal DNA can find itself leaking into the mother’s blood stream and mixing in with her blood and loose DNA. Once the scientists collect the blood sample of the mother, they then need to separate the fetal DNA from the mother’s DNA. Scientists have discovered that the fetal DNA fragments are much smaller than the mother’s DNA fragments. Using this knowledge, they use electrophoresis in order to separate the DNA fragments. In electrophoresis, the molecules are dragged through a gel matrix using an electric current causing the DNA fragments to arrange themselves by size. Once the fetal DNA fragments have been identified, they can then be used to determine things about the genetics of the fetus. 

The ability to perform early, non-invasive prenatal tests such as the Harmony Test is due to the discovery of cell free fetal DNA (cffDNA). As the name implies, cell free DNA can be found free floating in the bloodstream. In the blood of a pregnant woman, both maternal cell free DNA and fetal cell free DNA can be found in the mother's blood. The fetal DNA comes from trophoblastic cells, the cells on the outer layer of a blastocyst. Some of these trophoblastic cells go through apoptosis (programmed cell death), and the DNA can end up in the mother’s bloodstream. The fetal DNA is present in the mother’s blood after five to seven weeks of gestation, and the amount of cffDNA present increases as the pregnancy continues. One challenge of studying the cffDNA is that the majority of the free DNA in the bloodstream is maternal, not fetal. In order to accurately assess the karyotype of the fetus, it must be possible to analyze the fetal DNA without any of the maternal DNA. The ratio of maternal cfDNA and fetal cfDNA can vary greatly between each individual, with some reports claiming 3-6% of the DNA being fetal and others claiming 11-13.4% being fetal. The major difference allowing for differentiation between the two sources of DNA is that fetal DNA segments are around 200 base pairs long, which is significantly shorter than the maternal DNA fragments. To collect the DNA, the blood sample from the mother is spun down in a centrifuge to separate out the plasma, from which the cffDNA can be isolated and purified via methods such as PCR or use of a mass spectrometer.