mpetracchi's blog

Tropical jungles are found, as the name suggests, in the tropics between 10 degrees north and south of the equator. At these latitudes, precipitation rates are consistent, exceeding 2,000 mm or 79 inches annually with two peaks based on the intertropical convergence zone or ITCZ. The ITCZ is a region in the tropics with low average pressures due to the high uplift of warm air.  Temperatures don't vary much here, staying relatively stable around 25 degrees Celsius or 80 degrees Fahrenheit year-round. Given this very stable environment, with little change in both precipitation and temperature, species have been able to thrive with little to no stress or disturbance. Approximately 50% of the earth's species are present here, even though it covers only 11% of earths vegetation. 

The plant forms that grow here include broad-leaved evergreen and deciduous trees. These trees are able to photosynthesize all year long so instead of losing all their leaves, such as deciduous trees in Massachusetts, they can maintain the leaf year-round and expel it to immediately renew it. The abundance of plant life creates 5 layers of jungle known as the emergent layer, canopy, understorey, shrub layer, and forest floor. The forest floor, in particular, creates a paradox. It appears the soil here is very low in nutrients, so how could it support so much life? Unsurprisingly, the abundance of life is the reason why the soil is so nutrient-poor. Plants take in nutrients from the soil to grow, and if enough plants are growing then the soil gets leeched of all nutrients. 

Coral reefs may only span less than 0.01% of the ocean floor, but they house nearly a quarter of all known marine species. They are built using limestone produced by coral polyps in the warm shallow oceans near the tropics and are very complex and unique structures. Over the course of 1 year, a massive coral can expect to grow 2 cm, making the creation of such habitats incredibly slow. Smaller species of marine life use the densely populated corals as homes while predators such as cuttlefish and octopus use specialized techniques to draw them out. 

One particularly interesting mutualism is the clownfish and sea anemones. Found near the reefs, anemones are half-plant half animals that sting their prey such as fish and mussels. However, they seem to allow clownfish to inhabit the same space. It happens that clownfish clean the anemone of dirt and debris so keeping these kinds of fish around is actually very beneficial. Likewise, clownfish gain a home and a place to lay their eggs. The anemone provides protection to clownfish natural predators while clownfish do the same for anemones. Clownfish are normally eaten by larger fish, eels, and sharks, but having an anemone shelter can provide a secluded hiding spot. Anemones are eaten by starfish, eels, and other fish, which clownfish have the ability to ward off. They not only protect their home, but also the anemone. 

In almost any type of near-shore climate, whether it be polar, temperate, or tropical, kelp forests can be found. Kelp are large brown algae, with specialized tissues designed to live underwater. They require a rocky substrate present to which the kelp can use its holdfasts to root itself and begin growing. When large quantities of kelp bunch up in dense patches, the area can be called a kelp forest. The dense brush provides a unique habitat to a diverse selection of wildlife including sea urchins, lobsters, mussels, abalones, other kinds of seaweeds and sea otters.

These organisms form a symbiosis with kelp, helping regulate its growth and destruction making this a very dynamic ecosystem. Sea urchins and sea otters are key regulators of this biome on opposite ends of the spectrum. Sea urchins are omnivorous bottom feeders that eat away at any vegetation or dead animals in their path, kelp being a major source of this diet. Although it may seem counter-productive that sea urchins regulate this biome by destroying matter, they actually play a key role. Without their grazing the kelp would grow continuously without any means to stop and eventually would form a forest so dense, light could not pass through and photosynthesis in the deeper areas would cease. Simultaneously, if too many sea urchins are allowed to graze the kelp forest would be destroyed. This is where sea otters come in. These marine mammals dive down into the kelp forests in search of their food sources, clams, mussels, and most importantly, sea urchins. One species regulates another species that regulates another. Without the sea urchin, the kelp forest may overgrow, without the sea otter the forest may be decimated. All are important in maintaining a homeostatic environment that benefits all the parties present, including the rest of the community of wildlife. 

The third goal of this lab is to Identify potential variables that must be controlled for the replicability of the study. For the best results, I will be writing my methods using descriptive and explicit language. Specifying the path I took to the proper plant and taking a picture from the proper angle, will be the first part. I will determine a landmark as a starting point and give detailed notes on the pathing I took to find my plant. The photo angles, especially for the ‘distant shot', will have clear steps and notes on my positioning and height. I will also describe where I am in relation to the plant. This will require detail because it can be very easy to step back and take a photograph of the plant with a completely different background. Another variable to control is the time of day. It is important the person replicating my work takes the photos at a similar time of day to match the shadows and lighting. A third factor I can control is how the final figure will be constructed. Careful instructions will be written for each step, beginning from the software used to the final touches. Methods sections may seem dry and unnecessary, however, having proper notes for every step along the way separates an easily replicable experiment from another.

Panel A

Panel marker A is in the lower left-hand corner in Figure 1 while in Figure 2 it’s in the upper left-hand corner. The size of the letter in Figure 1 is larger and centered while the marker for Figure 2 is smaller and off-center. The image in Figure 1 is upright while the image in Figure 2 is sideways. The lighting in Figure 1 is brighter whereas the lighting in Figure 2 is darker. The leaf in Figure 1 is green and attached to a tree while the leaf in Figure 2 is brown and on the ground. The camera angle in Figure 1 is slightly downward while the angle in Figure 2 is directed straight downward.

Panel B

Panel Marker B is in the lower left-hand corner in Figure 1 while in Figure 2 it’s in the upper left-hand corner. The size of the letter in Figure 1 is larger and centered while the marker for Figure 2 is smaller and off-center. The image in Figure 1 is upright while the image in Figure 2 is sideways. The lighting in Figure 1 is brighter whereas the lighting in Figure 2 is darker. The size of the arrow in Figure 1 is skinny and long while the arrow in Figure 2 is short and wide. Lederle and the PSB are in the background of Figure 1 while Hotel UMass is in the background of Figure 2. The arrow in Figure 1 points upward, while the arrow in Figure 2 points downward.

Panel C

Panel marker C is in the lower left-hand corner in Figure 1 while in Figure 2 it’s in the upper left-hand corner. The size of the letter in Figure 1 is larger and centered while the marker for Figure 2 is smaller and off-center. The circle identifying where the plant was found is circular in Figure 1 and Ovular in Figure 2. The circle in Figure 1 is located in the upper-middle portion of the map, while the circle in Figure 2 is located in the lower left-hand corner of the map. The arrow pointing towards this circle is black in Figure 1 and red in Figure 2. Figure 1 includes landmarks such as the ISB, Hotel UMass and Hasbrouck while Figure 2 does not. Figure 2 includes landmarks such as the PSB, part of Lederle and part of Northeast Residential while Figure 1 does not. 

The primary goal of this project is to explore replication in a scientific setting. Studies in the scientific community are considered valid only if replicability is possible. Studies are replicable if they include detailed methods sections that explain exactly how to follow their own procedure. This type of writing may be challenging as assumptions must not be taken into account and there must be a balance of detail to the length of methods. This project seeks to explore these issues and make note of how to properly write replicable methods sections.

The secondary goal of this lab is to distinguish clearly between differences and inferences. Coming to a conclusion about two different pieces of data may be quick and easy for some, however, defining what a difference and inference is, may not be. For example, if two different fonts are used in two figures the difference would not be the different fonts. Rather the difference in the lettering style of the text itself. This is the observable difference. The inference then becomes ‘the fonts are different’. This statement requires previous knowledge of different font styles. This project helps explain the difference versus inference issue through the results and discussion section where the differences are kept to the results and inferences to the discussion.

The third goal of this lab is to Identify potential variables that must be controlled for the replicability of the study. In order to get the best results possible, I will attempt to control as much as I can in my descriptions. One important thing I can control is specifying the path I took to the proper plant and taking a picture from the proper angle. I will do this by describing the path they need to take from a set landmark to the intended location. The angles to use when taking pictures, especially for the ‘distant shot must be explained properly to get the best results possible. This one will require more detail because it can be very easy to step back and take a photograph of the plant with a completely different background. Likely, my methods will include some directionality and some description of what I fit in the background. Another basic thing I can control is when to take the photograph. It is important they do so at a similar time of day to match the shadows. A third factor I can control is how the final figure will be constructed. Careful instructions will be written for each step, beginning from the software used to the final touches.

A monoculture is the farming of one crop in a single area. The advantages of this process are three-fold. First, a single type of crop allows for the mechanization of the various farming process that goes into planting and harvesting foods. Heavy machinery replaces the hands of people and therefore increases the amount of possible cultivated food and the speed at which it occurs. We, as a species, prefer this method of farming because it allows us to feed the large and demanding global population we have today. Without it, we could not sustain the seven and a half billion people we have today. Second, uniformity in crops means that care of these large monocultures is kept low. This means that farmers don't need to have multiple different sprays and chemicals needed to combat disease and pests. A single product can be used for every need. Also having single crops in one field prevents the outcrossing of two species to create hybrids or new species. Third, monocultures can be cultivated by heavy machinery in large single batches and don't require separation by hand. The later processing of the food can also be industrialized from both the amount of volume brought in and the lack of contamination from another crop.

There are two key disadvantages to monocultures. First, a monoculture has increased susceptibility to disease. In a field of a single plant, the likelihood of a disease event where the entirety of a crop becomes wiped out is fairly high. A single new pathogen unknown to the plant's defense systems could infect one and eventually all the plants. Unfortunately, plants do not have an adaptive immune system so when a new pathogen is present they cannot defend themselves. If every plant in a field were to be identical and susceptible to a disease, then they all die. Second, a monoculture loses landrace diversity. Landrace diversity is the diversity of crops grown in one area. Similar to disease susceptibility, a decrease in heterozygosity prevents new beneficial mutations or hybrids from developing. A loss in ecological diversity can severely impact an ecosystem that may rely on disappearing species.

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.

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.