Writing in Biology - Section 1

Today, I had two classes. One in the morning and the other during early afternoon. After class today, I studied for my plant biology exam that is tomorrow during class. The exam covers the first eight lectures that we had in class and covers the topics of photosynthesis, different light receptors, plant pathogens and their defense sytem, and crop diversity. An interesting yet shocking fact I learned during one of the lectures is that undernutrition contributes to nearly half of all deaths in children under 5 and is widespread in Asia and Africa. Knowing that many children are dying from undernutrition is an important reason for studying the plants and crops that are produced to feed a population. Knowing how to effectively speed up the process of growing crops to feed a population who are being underfed can lead to a lower percentage of children under 5 being affected by undernutrition.

Whaling has been a practice for thousands of years. About 4000 years ago whaling was practiced by Norwegians and most likely the Japanese as well. Whaling was also practiced by many Inuit communities in the artic. During that time the entire whale was used. Blubber was used as a source of vitamins and protein for people to eat. Bones where made into tools. Baleen was used for basket weaving, roofing material, and fishing line. As whaling became more and more popular and profitable, European communities began the practice and eventually America began the practice. Whaling in America was rather wasteful and excessive. There is an oil gland in the head of most whales that is called the melon. This melon contains oil that people sought after for lighting lamps. There were some other uses for the oil such as cosmetics, lubricants, and heating but mainly it was used to lamp oil.

                In the 1800’s whaling had reached its climax and people became more efficient in killing whales. Harpoon guns were much more efficient and steam ships were faster. Since humans were becoming more populated and more efficient at killing whales, their populations began to plummet. In the 1900’s people became less reliant on whale oil due to the new use of petroleum. Later in the 1900’s whales started to become recognized as endangered. Fortunately, in 1971 the U.S. outlawed whaling. Since then, some species of whales rebound. As time goes on, whaling has become more and more unpopular allowing some species of whales to continue to recuperate.   

It is funny how the first thing that comes to my mind is Parkinson's diseases whenever someone says deep brain stimulation (DBS). DBS has proven to be helpful in treating several other movement disorders, one of them being Tourette's. Tourette's causes somebody to make involuntary movement and noises called tics. This usually happens due to abnormal connections in the basal ganglia of the brain. DBS allows two small electrodes implanted into the brain and delivering electrical impulses to potentially change the connections and prevent the impulses causing the tics. The patients are usually awake during the procedure because the activity can be measured while they are awake rather than under sedation. It is quite mind boggling whenever I think about the patients just aware of their surroundings while there are holes being drilled through their skulls. 

Songbirds have the capacity for species-specific recognition and individual recognition. The mechanisms of species-specific recognition generally involve recognition of invariable song features rather than variable ones. For example, though European robins produce hundreds of songs, they all follow the same syntactic rules. The robins’ songs must be composed of different phrases, phrases must alternate in pitch, and during bouts, all of the songs must be different. Experiments were performed where the speakers played songs using sounds that robins can’t produce but followed their song’s syntactic rules and they responded as if the speaker were another male. However, the robins didn’t respond to the speaker when the song was changed to include only low-pitched phrases. This supports the inference that the environment may degrade pitch and different individuals will use differently pitched notes, but that syntactic rules will remain the same, allowing for conspecific recognition. Another example of this invariability phenomenon is in the indigo bunting, which recognizes conspecifics by element composition. Indigo bunting song consists of a single element repeated quickly to produce a trill. As opposed to the robin where manipulating syntactic elements changes response rate, changing the element results in much lower conspecific response in the indigo bunting. Individual recognition is a more complicated story, and is very species specific. Colonial birds tend to have the ability to recognize individual calls, as is the case with bank swallows and emperor penguins. As these species live in colonies, parents have to be able to recognize the calls of their offspring in order to feed them. In the zebra finch, females seem to recognize their father’s calls, as they tend to choose mates which have similar but not identical songs, a behaviour that is likely to have arisen in order to avoid incest. Songbirds have the capacity to recognize individuals, and not only respond differently to neighbours and strangers but have different levels of response to different neighbours. A male will respond less strongly to a neighbour’s song from a familiar location than a stranger’s song from that same location. Should the neighbour’s song be played from an unfamiliar location, the male will respond just as strongly to it as it would a stranger’s song. This response seems explicable from a territoriality point of view. The male will respond more aggressively to new individuals who pose threats as opposed to neighbours with pre-established boundaries, and will respond aggressively to expansionary neighbours.

I woke up at 9 AM on Saturday to get ready for lab at 10 AM. I went to the bathroom, brushed my teeth, and returned to my room. Here, I got changed and got my things ready to leave. These included a water bottle, my wallet, keys, and my phone. In the kitchen, I filled my water bottle up and grabbed a few snacks so I didn't need to go to a dining hall for breakfast. I left my apartment and locked my door. We've never had an issue where we live, however, better be safe than sorry. I unlocked by my car, prayed, and started the car. Over the summer I had 2 times where my car did not start due to a faulty alternator. This left me often doubtful my car will start. I drove for 5 minutes to get to campus and parked near Tobin hall. I walked into the building and went to the lab to set up. 30 minutes passed before the participant showed up in the parking lot. I was there to greet and lead them to the proper room. The lab runs children aged 6-10 years old through a series of pictures and records their brain responses to those images via EEG caps. These caps have 64 nodes on them all over a cap which record the brain waves radiating from the participants head. An hour into the study, the participant viewed and responded to all the images. We rewarded that participant with a prize and the parent with a $20 compensation for their help. Clean up lasted another 30 minutes, after which I left the lab and went to a dining hall around 12:30 PM.

Humans have affected the world around us in innumerable ways. As humanity progresses, we further alter the world to our needs, which can sometimes create problems of its own. Despite human power and ingenuity, nature  and its laws continue to persist. Humanity has had a close relationship with bacteria since the first human encountered its first bacteria. It was only in recent history that the invention of antibiotics relieved the human race from the grip of harmful bacteria. The invention of antibiotics was an extremely important leap in medicine for humans and the animals we can give antibiotics too. They are used heavily in a variety of industries, which all contriburte to the process of natural selection. Antibiotic resistant bacteria have become a terror for doctors, researchers, and patients in the last few decades. Overuse of antibiotics has led to mutations for resistance becoming commonplace in some bacteria species. This threatens our modern medical system, as well as the lives of all humans exposed to these bacterias. These resistant bacteria cannot be killed by the most common antibiotics and even some which are used as a last resort. A few alarming strains have been appearing more and more in recent years, usually within the species of Salmonella typhi, Mycobacterium tubercluosis, Pseudomonias aeruginosa, and Neisseria gonorrhoeae. While not all of these bacteria lead to deadly diseases, antibiotic resistance in these strains make it nearly impossible to help relieve the symptoms of them, or help stop an individual from dying. However, we have not run out of options yet. One possibly alternative is to simply work on developing a new antibiotic which bacteria are not yet immune to. As the new antibiotic is administered and (hopefully) kills off the bacteria, the process of lowering antibiotic use can begin. This combined process would hopefully eliminate the possibility of resistance occurring, at least at such a high rate and across multiple species of bacteria. Of course, this process is not perfect, and could result in new resistances being developed and individuals not getting the antibiotics they truly need. There is still room for genetic changes to happen spontaneously and result in resistance, but by killing off the resistant bacteria there is hope that acquired AR in bacteria can be lowered, or at least controlled.  

Overuse of antibiotics has led to mutations for resistance becoming commonplace in some bacteria species. This threatens our modern medical system, as well as the lives of all humans exposed to these bacterias. These resistant bacteria cannot be killed by the most common antibiotics and even some which are used as a last resort. A few alarming strains have been appearing more and more in recent years, usually within the species of Salmonella typhi, Mycobacterium tubercluosis, Pseudomonias aeruginosa, and Neisseria gonorrhoeae. While not all of these bacteria lead to deadly diseases, antibiotic resistance in these strains make it nearly impossible to help relieve the symptoms of them, or help stop an individual from dying. However, we have not run out of options yet. One possibly alternative is to simply work on developing a new antibiotic which bacteria are not yet immune to. As the new antibiotic is administered and (hopefully) kills off the bacteria, the process of lowering antibiotic use can begin. This combined process would hopefully eliminate the possibility of resistance occurring, at least at such a high rate and across multiple species of bacteria. Of course, this process is not perfect, and could result in new resistances being developed and individuals not getting the antibiotics they truly need. There is still room for genetic changes to happen spontaneously and result in resistance, but by killing off the resistant bacteria there is hope that acquired AR in bacteria can be lowered, or at least controlled.  

Creating a new species of animal requires many generations of reproductive isolation leading to evolutionary divergence. Plants do not have this requirement for speciation, the process of becoming a new species. Instead, have the capacity to bring about a new species in one generation. In animals having more chromosomes than the baseline may cause inviability problems in the offspring and result in their death. However, in plants, if an offspring receives 2 copies of DNA from parent AA and 2 copies from parent BB then the offspring AABB is viable. It is a completely new species. One such example is the bread wheat we use today. It has 42 chromosomes and has genetic material from 3 other species. The first set of species to cross were Einkorn wheat and Wild Goat Grass resulting in a new species known as Durum wheat. 14 chromosomes AA from the Einkorn and 14 chromosomes BB from Wild Goat Grass came together making 28 chromosome Durum wheat AABB. A second crossing event occurred when 28 chromosome AABB Durum grass crossed with 14 chromosome DD T. tauschii to form 42 chromosome AABBDD bread wheat.

    How is it that plants generate new plants with different chromosome counts? There are 2 ways it may happen. Allopolyploidy, the crossing of 2 different plant species or Autopolyploidy, the self crossing of two gametes from 1 species. Allopolyploidy occurs when gametes of 2 plants are able to fertilize and form one cell that contains half the information from each parent plant. The chromosomes duplicate producing a new chromosome count and therefore a new species. Autopolyploidy requires a non-disjunction event in either the first or second split of the parent reproductive cell. A non-disjunction event is when all the genetic material is pulled towards one side or the other resulting in a cell that contains double the genetic material.

Plant pathology and animal pathology differ greatly. While animals have an adaptive immune system that allows them to generate defences as new infections arise, plants do not. Plant pathogens come in three general classes, necrotrophs, biotrophs, and hemibiotrophs. Necrotrophs are organisms that kill plant tissue through enzymes and tend to be generalists that can infect many plants. Biotrophs are parasitic organisms which, in order to complete their life cycle, require host survival. These pathogens will cause slowed senescence and build haustorums that usurp metabolites from plant epithelial cells. Hemibiotrophs are biotrophs in the first part of their life cycle and necrotrophs during the second part of their life cycle.. Pathogens have three main ways of egress into a plant. They can either directly penetrate the plant through the use of a pilus or penetration peg, enter through pre-existing openings such as stomata, or enter through wounds. Plants have a series of defencive strategies to resist infection. The first line of defence is physical, plants have a waxy cuticle and cell walls that aim to prevent direct access to the cytoplasm of plant cells. In addition to a physical barrier, plants produce toxins to kill certain pathogens or create papillae in the epithelial cell walls to prevent pathogenic penetration. The second line of defence is specific, and is known as resistance (R) gene immunity that follows a gene for gene model. Pathogens produce effectors that mask their presence, and plants produce proteins that are able to detect effectors. If a plant can detect an effector then it will engage a hypersensitive response that involves immediate cell death around the infected area. At the cost of a few cells, this method enables the plant to prevent the infection from spreading.

Similarities:

The plant in panel A of both figures can be deduced to be the same plant. It is a small potted plant with brown coloring to the leaves. Both figures have the same chart on the wall to the left of the plant, and background window behind. The pattern on the leaves of the plant are identical as well as the matching position of the leaf formations. Both figures have a ruler placed to the left of the plant to allow for height estimation of the fauna. The picture in both figures is oriented horizontally.

Panel B is a different plant from panel A, and again is the same plant from figure to figure. It is a potted plant with white color alteration to the center of the leaves. There is a wooden flat top in front of the potted plant, as well as a lowered dirt section between the flat top and the windowsill behind. Again the ruler is to the left of the potted plant, and both figures can be viewed to identify matching key descriptive factors (coloration of the leaves, position and overhang of the plant above the pot, leaf distribution) that confirms both figure makers have found the same plant. In both figures the picture is oriented vertically.

Panel C for both figures is a final, third plant that has a purple color tinting the leaves. The plant seems to have much more purple color on the leaves towards the top of the plant, and more traditional green towards the bottom. Both figures have matching plants, framed by the dark wooden flat top in front, a lowered dirt enclosure and a windowsill behind.  In this photo there is a tan clay pot to the back left of the plant, and the positioning, coloration and leaf health (holes and damage) match from plant to plant. There is a tag on the wooden flat top in front of the plant, that would most likely list the species of plant but it is not legible in either photograph. Its position in relation to the plant is identical in both figures. A ruler for height estimation is off to the left of the plant in both figures. 

Differences:

Panel A is taken from a much closer and lower angle to the plant. The pot is visible in the second figure, and not in the first. A human hand is visible holding the ruler on the left in the first Figure, while the second Figure is not suspended by anything in frame. The wooden flat top that is present in front of all of the plants is not visible in panel A of Figure 1, neither is the lowered dirt enclosure. Some of the lower leaves are not visible in the 1st Figure that are visible in the 2nd. Additionally, a tan wooden windowsill is visible behind the plant.

The photos for panel B are taken from opposing angles, the plant viewed from the right in Figure 1 and from the left in Figure 2. Figure 2 is taken from further back, and there is a tan potted plant visible to the right behind the center plant. The bars on the window behind are much more visible in Figure 2, and there is a name tag taped to the wooden flat top visible.

Panel C is notably different in that Figure 1 is a vertically oriented photograph and horizontal in Figure 2. The ruler is mostly obscured and out of frame in Figure 1, and the photographs are taken from different directions. Figure one is taken from the front, right side of the plant and Figure 2 is taken from the left. This changes what is visible, and the potted plant inthe background is much more visible in Figure 2.

Overall the picture quality is also different, with much higher saturation and fuzziness to the image quality of Figure 1. Figure 2 is much sharper, and has a colder image effect with more blue light hues than yellow. In all photos in Figure 2 they are taken from approximately the same difference from the subject, where the subjects in Figure 1 are variable from panel to panel. These may be attributed to camera type or quality, and hand dominance of the photographer. The demarcation of panels in Figure 1 and 2 is relatively the same in both figures, but consistently Figure 1 seemed slightly higher on the panel placement.