Writing in Biology - Section 1

One of the most interesting things about scientific writing is that almost by definition, should not cultural contexts. The reason for this is that scientific writing is often done by people who learn English as a second language. I thought that this was always quite interesting because languages are one of the reasons why people end up going to the sciences rather than the humanities, and yet in the sciences, people are more often forced to write in a foreign language and need to convey the information more clearly. specifically in the context of writing, there should be no reason why scientific writing should have complicated language, or literary references because they are read mainly by those who speak English as a second language and the fact that the language needs to be relatively clear.  At least that was what I was thinking when I was smart behavior of true slime mold in a labyrinth. it has nothing to do with the actual assignment, but I thought that it was interesting that the article was written by someone at Hokkaido University in Japan who presumably learned English as a second language. On first glance, the writing was really simple, with words that would never be found in an English class book. Then I remembered that once on a website teaching Japanese scientists how to read in English that writing a scientific article in English is slightly more different than actual English, which due to the fact that it is an actual language change quite constantly, and the accepted norms for English does not necessarily mean that it is a norm with normal English. 

How are plants classified? It’s a fairly straight-forward question one might assume would produce a straight-forward answer, but in fact there are many grey zones. There are four basic criteria that allow scientists to classify an organism as a plant. First, the organism in question must have a cell wall that uses cellulose. This cell wall provides mechanical strength, a protective barrier, an expandable frame, and exoskeleton for turgor pressure changes, and is made of cellulose. The second criteria is the cell must be able to store starches. Specifically store them in organelles known as plastids. These plastids may be for only storage production or can actually produce certain chemicals depending on the type of plant. The third criteria is the organism must contain both plasmodesmata and phragmoplasts. Plasmodesmata are channels which connect adjacent cells protoplasts to one another. The protoplast of a plant cell is the fluid in the cell similar to the cytoplasm in an animal cell. Phragmoplasts mediate cell separation during mitosis. They provide the scaffolding needed that allows a clean separation to occur properly. The fourth and final criteria to be classified as a plant is the organism must undergo photosynthesis and contain chlorophyll a and b. Each type of chlorophyll absorbs a different wavelength of light. Many organisms are able to fit one two or three of these criteria and some all. Ultimately it comes down to the scientist's interpretation of the organism. Some believe that only land plants should be considered while others believe some green algae should be included as they do meet all the criteria.

At first glance, the overall structure of the two articles is similar in the sense that they have sections that are titled. The article written by Boomsma JJ, Timmermans H, Corvers CPM, and Kabout J. about monogamous leaf mining larvae has a clear abstract, introduction, methods, results, and discussion. Within each of those are sub-sections that are clearly titled regarding their subject. The article written by Nakagaki about the smart behavior of slime molds has an abstract that is seemingly shorter in length than the abstract in the leaf mining article. The sections to the article written by Nakagaki are not labeled with the terms introduction, methods, results, discussion but rather labeled with the information and subjects that are within the corresponding paragraphs. Both articles have two columns of writing rather than the writing being in paragraphs that span the whole page. They are both visually pleasing overall and both take on a “textbook-like” look with figures and graphs located neatly within the columns of information. The level 1 headings in the article about leaf miners are the titles introduction, methods, results, discussion which are also numbered. For example, the level 1 heading “2. Methods” has a section below it that is “2.1 Field Collections” and so on until the last section of the methods which is titled “2.3 Within Leaf Feeding Stratification.” The article about smart slime mold behavior seems to only have level 1 headings. Both articles list references for the cited information. The leaf miner article is significantly longer than the slime mold article and thus has many more references. It is obvious that both articles are scientific in nature and are examples of scientific writing; even though they show various differences. Most paragraphs in each article show a clear “what” and “why” for a first sentence. Those sentences answer what the section is going to talk about and why it is talking about it. In the results section of the leaf mining article, the beginning of the section discusses that it is talking about “A substantial variation in hostplant characters” and specifically mentioned that “Betula pu- bescens appeared to have a broad distribution in the lower scale range, whereas Betula pendula was charac- terised by a narrow peak of high.” These statements indicate that section was going to discuss substantial variation between the hostplant characters and then specified what species had a broad range and what species had a narrow peak in the data. This first paragraph of this sentence gets to the point of what the section is discussing and why it is discussing it.

At first glance, the overall structure of the two articles is similar in the sense that they have sections that are titled. The article written by Boomsma JJ, Timmermans H, Corvers CPM, and Kabout J. about monogamous leaf mining larvae has a clear abstract, introduction, methods, results, and discussion. Within each of those are sub-sections that are clearly titled regarding their subject. The article written by Nakagaki about the smart behavior of slime molds has an abstract that is seemingly shorter in length than the abstract in the leaf mining article. The sections to the article are not labeled with the terms introduction, methods, results, discussion but rather labeled with the information and subjects that are within the corresponding paragraphs. Both articles have two columns of writing rather than the writing being in paragraphs that span the whole page. They are both visually pleasing overall and both take on a “textbook-like” look with figures and graphs located neatly within the columns of information. The level 1 headings in the article about leaf miners are the titles introduction, methods, results, discussion which are also numbered. For example, the level 1 heading “2. Methods” has a section below it that is “2.1 Field Collections” and so on until the last section of the methods which is titled “2.3 Within Leaf Feeding Stratification.” The article about smart slime mold behavior seems to only have level 1 headings. Both articles list references for the cited information. The leaf miner article is significantly longer than the slime mold article and thus has many more references. It is obvious that both articles are scientific in nature and are examples of scientific writing even though they show various differences. Most paragraphs in each article show a clear “what” and “why” for a first sentence. Those sentences answer what the section is going to talk about and why it is talking about it. In the results section of the leaf mining article the beginning of the section discusses that it is talking about “A substantial variation in hostplant characters” and specifically mentioned that “Betula pu- bescens appeared to have a broad distribution in the lower scale range, whereas Betula pendula was charac- terised by a narrow peak of high.” These statements indicate that section was going to discuss substantial variation between the hostplant characters and then specified what species had a broad range and what species had a narrow peak in the data. This first paragraph of this sentence gets to the point of what the section is discussing and why it is discussing it.

Agriculture is a process that impacts everyone worldwide, yet most people do not consider the science that goes into efficient agriculture, not only in terms of crop yield but in the way that the farmland is used and how farmers maintain their crops. An important aspect of crop growth as well as the growth of many other plants, is the relationship that the plant has with mycorrhizae fungi. About 70% of plant species have a relationship with a type of fungi called arbuscular mycorrhizae (AM). These fungi take up residence in the roots of a plant and can provide the plant with essential nutrients for survival as well as water, and in return the plant supplies the fungi with the sugars that it produces. A paper I read today reviewed why farmers should consider the number and types of mycorrhizae that might reside in the soils being used for agriculture. Not only can the mycorrhizae improve the quality of the yield, they also contribute to soil structure as well as reduced nutrient loss in the soil. AM fungi have been shown to increase yields in crops such as potato and cassava, and intermediate response levels in cereals such as wheat. For these reasons, the paper argues that farmers should have more interest in managing the levels of mycorrhizae in the soil. Using products like fertilizers and fungicides can disturb the soil make-up and inhibit mycorrhiza growth, which can lead to poor soil quality and nutrients, which is not sustainable in long-term production of food. The goal of this paper is to bring forth the idea that when we reconsider how agriculture is practiced, we should take into account more than just increasing yields of crops. The soil, the relationships of biota within the soil, and their well-being are just as important for agriculture as obtaining high yields to feed the growing population.

My topic for this blog is again medically related because that is my interest. I'm thinking about the social and economic hinderences in getting into medical experiencial opportunities. Firstly, through word of mouth about how people I know have obtained shadowing positions and other low-level hospital jobs that provide them with basic knowledge and exposure to the medical field, most people get it through family connections. Examples I know include an uncle who runs an ER, a parent who knows a friend that is a cardiologist, a close family friend thats a nurse, having parents that are both doctors, giving away a dog to someone who works high up at BayState, the list goes on. Knowing somebody in the medical field extremely increases your likelihood of being considered for experiential opportunities and gives you an advantage in the field, boosting your future and youre resume. Of course, people who make careers in the medical field are often well off because it requires money to go through schooling and education to obtain those types of jobs. This alone creates an economic barrier on the ladder to the top, the metaphorical top being, say, being a doctor. If you come a lower class family, you are less likely to have connections with well-off families that could afford to send children to medical schooling. Of course, there are always acceptions, and contemporaneously there exists programs and funds to send the less fortunate to schools, and opportunities are becoming more even. This still exists however, because the system has always benefitted on the lower class and that hasn't changed. And so, if the top is hardest to reach, the entry level is more difficult than you might initially think. You might think that an easy way to be involved in medicine is EMT-ing. It is one of the classic go-to jobs for undergraduates trying to get hours and exposure and experience. This requires nearly a thousand dollars towards the class, not to mention time and effort to study, learn and pass. Then on top of that you need hundreds of dollars to take the state and national exams to become certified to work after passing the class. Everything has a pay wall.

How does the body at an embryonic stage even know where to place all the organs in such perfect order? The drosophila's dorsoventral axis formation is a good model system to give us a general idea. At a very early stage, the drosophila undergoes syncytial specification – in short, it is one cell full of nuclei in the same cytoplasm and they signal each other. Along the cytoplasm, there are genes creating proteins in different concentrations to establish different axes, including the dorsoventral axis. Gurken is a protein that starts off a signaling cascade that leads to the determination of the ventral identity. Dorsal protein controls the ventral identity of the embryo. Toll protein assists in transporting dorsal into the nucleus of the ventral side, where it acts a transcription factor to establish the identity. Another protein called cactus helps by preventing dorsal from entering and hence dorsalizing that end. To prove this theory, Roth et al had performed immunolocalization and Western blots to find location of the proteins in the wildtype, dorsalized and ventralized embryo. In short it is the difference in concentrations of dorsal in the cytoplasm and the nucleus that creates the morphogenic gradient, which leads to the embryo to have a dorsoventral axis. In fact, the morphogenic gradient is a concept that can be seen in other settings too. For example, when our hands our forming, the the placement of our fingers from our thumb down to our little finger depends upon morphogenic gradient of a certain protein. 

One longstanding debate in the field of biology is whether or not viruses should be considered alive.  Viruses are composed of a protien coat with some form of genetic material contained on the inside.  Unlike all other species not debated as "living," viruses lack the ability to reproduce on their own because of their simple design.  Instead, viruses are only able to reproduce or replicate within a host.  They use the machinery present in their host cells to replicate and spread the virus.  For those who believe viruses are not alive, this is the main point they cite.  Without a host cell, virsuses would not be able to survive therefore should not be considered alive.  The opposition believes viruses should be considered alive because of the success they have at infultrating thier hosts and reproducing.  Like all other species considered alive, success by a virus should be determined by their reproductive fitness.  Those who are not fit are removed from the population while those fit to survive pass on their ability to the next generation.  The niche that viruses find themselves in the ecosystem is one that they have remained in since their discovery.  Yes, they need a host but a host is their niche.  If they were not fit for this niche they would not survive or exist in the living world but they do.

The act of phytophagy is the act of eating plants. In some way or another almost all living things depend on the feeding of plants. This ranges from herbivores that directly eat plant matter to carnivores that eat other organisms who may depend on plants. Species as large as an elephant depend on plants to feed and species as small as a beetle depend on plants for food. In some cases, it is easy to find a plant that shows evidence of phytophagy by insects. Leaves may be discolored and brown and show patterns of an insect eating its way through the leaf while other may show large holes in the leaf. In the case of the a Blue Vervain plant located in the back of the parking lot in Lot 12 at University of Massachusetts Amherst, there was clear indication of an insect eating many holes through the leaves of the plant. The stem was untouched, the pinnacles with small flowers were also untouched, yet the leaves where nearly destroyed by the insect using them as its food source.

In the field of biology, understanding the field of genetics can unlock many great things for fields outside of science. An example can be understanding how DNA fingerprinting can be used to convict a criminal. These ideas are sometimes not well-received by the general public at first, but these small ideas can lead to something big. Mammalian cloning is a subject that allows us to dip our toes into what the rest of the world can do with cloning. Dolly the Sheep is the first mammal to ever be cloned. Now, we clone all sorts of animals for both experimental and sentimental reasons. By sentimental, I am referring to the cloning of pets. There are companies that can clone your pet after it has passed away. It probably brings up the question, what more can our modern scientists do? Human cloning is on the line, and it brings up a debatable idea of whether we should be doing so. According to the NHGRI, no solid scientific evidence has been shown that human embryos have been cloned. Furthermore, the drawbacks of cloning are immense. Of 277 cloned embryos, only Dolly the Sheep was born. This does not touch the topic of modifying the genome itself! There has been a lot of drama around a scientist who used the CRISPR/CAS9 gene-editing system to make two twin babies who are supposedly HIV-immune. Although the scientist delivered data that shows he was successful, ethical repercussions are up in the air.