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The Academic Jungle

The Organisms of Bellarmine College Preparatory

Producer—Toyon Berries

Heteromeles arbutifolia

This plant is supposedly the namesake of Hollywood. No wonder, given its fashionably bold red color. Native to California, this plant begs to be noticed by passing animals. When birds and coyotes spot and consume the berries, the plant’s seeds are dispersed in convenient packages of fertilizer.

IMG_0841.JPGPrimary Consumer—Domestic Chicken

Gallus gallus domesticus

From its convenient perch, the chicken survives on the offerings of her loyal servants, the humans. Subsisting on a diet of grains, her life is a fairly easy one. Admittedly, her eggs disappear every morning, but otherwise, her environment lacks predators and scarcity of food.

IMG_0861.JPGSecondary Consumer—Comet Goldfish

Carassius auratus

The fish too finds prey in the hands of its caretaker, the humans. A steady source of mealworms keeps its stomach filled and its fins swishing. Its tank may be in desperate need of expansion, but its elodea plants keep the oxygen levels high enough for comfort.

IMG_0875.JPGTertiary Consumer—Corn Snake

Pantherophis guttatus

The rat snake’s diet consists, as one would expect, mainly of rodents. The rodents, which are omnivorous, will eat almost anything that sits still long enough. Because some of the rodents’ prey are primary consumers (bugs and other small animals), the rodents are secondary consumers. This makes a snake a tertiary consumer. This means that much less energy is available to the snake population (by the ten percent rule), and therefore, each ecosystem can support very few snakes. They are native to California, but similar species can be found across North America.

IMG_0877.JPGDecomposer—Mealworms (Darkling Beatle)

Tenebrio molitor

These mealworms aren’t really worms at all! Instead, they are they larvae of the darkling beetle, a species that survives mainly other rocks, in dark, confined spaces. The darkling beetle consumes the dead waste of animals and plants, such as fallen leaves, to obtain energy. This returns resources of the ecosystem to a usable state by new organisms. It lives in temperate forest and grasslands worldwide.

IMG_0900.JPGHerbivore—Rhinoceros

Rhinoceros sondaicus

The rhinoceros, despite it frightening horn and skin resembling plate armor, is an herbivore at heart. It requires large territories so that it can forage for edible plants. However, land available to the rhinoceros has been shrinking in recent years, due to deforestation and development, leading to territories shrinking as well. This leads to competition between the rhinos, and lowers the number of individuals the habitat can support.

IMG_0847.JPGCarnivore—Northern Lynx

Lynx canadensis

The Canadian Lynx, or Northern Lynx, subsists off a variety of preys. It’s not afraid of large targets, and can hunt anything from grown dear to young rodents. Because of the large forested area available in Canada and the North United States, this species is not endangered.

IMG_0716.JPGOmnivore—Zayd

Homo sapiens

The Homo sapiens, despite being both meat and plant eater, is oddly picky. It often requires that foods be mixed together, thoroughly cooked, and served onto flat stones before choosing to consume them. Nonetheless, its enormous population spans the globe, and it grows much of its own food. Unfortunately, it is also considered the main reason for climate change, and the expansion of its cities and towns has destroyed many habitats.

IMG_0850.JPGThreatened species—Great White Shark

Carcharodon carcharias

The main threat to the Great White Shark today is commercial hunting. In search of shark fins to produce stew or other cuisine, hunters will often kill as many sharks as they can. Though shark fin soup has been proven to have no health benefit, many seek it as a supernatural cure for many ailments, chiefly cancer.

IMG_0896.JPGEndangered species—Tiger

Panthera tigris

The dense growth of human populations is the main concern for the tiger population, which is steadily decreasing. Other causes of its endangerment include poaching, and killing by humans out of fear. The tiger, while not being chased by angry humans, survives off a varied diet of meat. Consuming over 80 pounds of food at once, it will hunt gazelles, elk, or wild board

IMG_0853.JPGNon-native species—Unicorn

Equus unicornus

The unicorn seems slightly out of place in the Sobrato hallway for good reason. One has never before been spotted in the Bellarmine habitat, and it appears to be an invasive species. It might have displaced the local horse population, if there were one, but its presence seems mainly harmless.

IMG_0825.JPGPollution source—Car

Auto mobilus

The car is only one of the sources of pollution provided by humanity. By burning a fossil fuel, gasoline, it allows for easy and fast transport along public roads. However, in the process, it emits greenhouse gasses such as carbon dioxide. These, once in the atmosphere, trap heat and light from being re-emitted through the atmosphere, leading to globally higher temperatures. In addition, the exhaust of cars can contain particulate matter, which can damage the lungs of nearby animals, and cause smog.

 

In this Ecological study, I examined where each organism in the Bellarmine campus. Compared to environmental science, which is a much broader topic that covers all biotic and abiotic factors of an ecosystem, this was much more specific and focused. Humans indistinguishably shape the Bellarmine campus environment. The pavement and buildings limit the area usable by other organisms. These influences walk a fine line between biotic and abiotic factors. After all, they are the effect of humans, a living species, but they themselves have no organic material.

 

In the Bellarmine campus multiple food webs exist and intermingle. For example, trees can produce leaves, which, once decomposed, feed the Darkling Beetle larvae. These decomposers may then be consumed by rates, a secondary consumer. Finally, the top predator, the rat snake, feeds off the rats. Overall, the amount of biomass on each level of the pyramid decreases, in ccordance with the ten percent rule.

 

Of course, given the influence of humans, pollution also plays a key role in the ecology of Bellarmine. The climate change resulting from humans’ use of fossil fuels has led to the largest drought on record in California. In turns, this limits the water supply to many native plant species, such as native grasses, endangering new species. Pollution, which covers any waste that directly affects the ecosystem, also exists in Bellarmine in the form of sewage. However, because of the admirably extensive plumbing system, this is prevented from harming the outside environment. However, it cannot be denied that the ecology of Bellarmine is continually shaped by humans, both of the campus and of the world.

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One Long Timeline

Recently in class, we used a five meter long strip of paper to record significant events in Earth’s history. Call us self-centered, but we mainly focused in important developments of life on Earth. We divided the timeline into 5 billion-year long segments, and then plotted important events in Earth’s development using a scale of 1 cm to 10 million years.   
The result was, however, a mostly blank roll of paper. Though the last few hundred million years were packed full of important events, before that, there were huge gaps between notable changes. This served to remind us that, even if life has been around on Earth for most of this planet’s lifetime, life as we know it is an incredibly recent development. After all, even smallest gaps in our timeline spanned millions of years.

  
As life on Earth has diversified, it has become more difficult to fully comprehend all living organisms’ shared ancestry. And yet, while plotting back all the way to the first life on Earth, it became that most of our diversification has occurred in the (relatively) recent past. The billions of years separating all organisms from one common ancestor seem endless, and yet through all those years, similar traits have remained.

A Fashionable Snack

As my lab partners and I built our jellybean necklaces on Thursday, we were all suddenly very thankful that we did not control the transcription of RNA in our cells. The process was long, had multiple steps for errors to occur, and required a sufficient supply of patience and jelly beans. Given as many chances to go wrong as there are, and it’s quite surprising how accurate transfer of information from DNA to proteins is in our cells.As my lab partners and I built our jellybean necklaces on Thursday, we were all suddenly very thankful that we did not control the transcription of RNA in our cells. The process was long, had multiple steps for errors to occur, and required a sufficient supply of patience and jelly beans. Given as many chances to go wrong as there are, and it’s quite surprising how accurate transfer of information from DNA to proteins is in our cells. In my necklace, I used the following codon dictionary to translate to RNA sequence to protein.
  
Original DNA Sequence:

3′ tac aga cta tac atc tga taa aat acc aga atc tac gca ttt ata aga atc acc gta cga tga aga atc cta atc aca taa caa taa ttt atc cga aca acc atc 5′

First, the DNA sequence features a TATA box. This is a series of T and C bases that is not transferred to the RNA, but instead used to initiate transcription. Next, the TAC triple will become the AUG codon which triggers that start of amino acid translation at the ribosome. After the other sequences, the ATC triple will become the UAG stop codon to end the protein.

Resulting mRNA sequence:

5 ‘ (modified G cap) aug ucu gau aug uag acu auu uua ugg ucu uag aug cgu aaa uau ucu uag ugg cau gcu acu ucu uga gau uag ugu auu guu auu aaa uag gcu ugu ugg uag aaa aaa aaa aaa aaa aaa aaa aaa aaa aaa 3′

The mRNA, though it mainly matches the DNA sequence, has a few add-ons. First, the modified G cap on the 5’ end protects the mRNA from being disassembled by various enzymes. The poly-A tail does the same thing, and its length corresponds with how the the mRNA can exist without begin broken down by enzymes in the cell

Resulting protein sequence: Met Ser Arg Met S. Thr Iso Leu Try Ser S. Met Arg Asp Tyr Ser S. Try His Ala Thr Ser S. Asp S. Cys Iso Val Iso Lys S. Ala Cys Try S.

Using S. to denote each stop codon and the first three letters from each amino acid, this would have been the sequence of the resulting acid. I chose to ignore all stop codons except for the final one, so that the entire sequence could be translated. However, after the first stop codon, the sequence would be finished and the translation would end.

My jellybean protein necklace:

  
The key I used is here as well, so that you can see the code behind this highly fashionable accessory:

  
P.S. I used the same color for both Cysteine and Lysine, which occurs only once, due to a shortage of colors.

ALIEN LIFE DISCOVERY

Log 184.

User R19Remmel

    
This week, in our exploration, we discovered the remains of an unrecognizable organism. Levels of decay suggest that it died recently, most likely within the last few days. Given the superb condition of this alien creature, we couldn’t pass up the opportunity to pull it apart. I’ve attached out video transmission of the dissection here:

Video Transmission
Though this organism may initially seem bizarre and unrelated to life on earth, further examination revealed a striking number of similarities to animals on earth. The organism possessed 8 limbs, or tentacle, surrounding a central opening. Just inside this opening sat a solid, sharp beak. We believe the organism used this as mouth, and cut through food using its beak. The size and sharpness of the organ suggests this organism ate small animals for food. This is most revealing; if this is indeed a carnivore, then there must be multiple other organisms to discover on this planet. 

Multiple tiny suction cups covered one side of each tentacle, which the organism could use to latch on to prey, and pull its body to the beak. Following the esophagus, the digestive track continued into a large central organ(s). Unfortunately, possibly due to decay after the organism died, this central tissue was extremely fragile, and though this likely contained prominent parts of the digestive and respiratory, it broke apart at our first incision. We suspect buildup of “molecular acid” is also to blame.

Directly above this cavity was a membrane surrounding a sac filled with blood, white rounded organs, and minuscule curled tubes. We hypothesize this sac protected the male reproductive system. Sperm could easily have moved from the testes, through the seminiferous tubes, and out of the opening at the very top of the squid.

Enclosing both the central cavity and this sac was a thin but strong flap of skin. An addition flap enclosed the opening at the top of the organism and the sac containing the reproductive system. Finally, at the bottom of the organism, next to the mouth, we discovered two eyes, behind openings in their protective lids.

This discovery poses the question of whether this should be classified as “life” at all. Our dissections provides substantial evidence that it qualifies. This organism comprised of various tissues (and therefore, by extension, cells), such as connective, blood, and muscular tissue. In addition, we viewed multiple organ systems, which represent those of animals on Earth (such as the digestive system). The mouth suggested that this creature consumed food, intaking energy to perform life processes like all life. Finally, the reproductive system indicates that this species reproduces, allowing life to continue into further generations. All of this evidence leads us to believe that we have indeed discovered new alien life.

Meiosis Movie

This week, we modeled meiosis. Thankfully, after our recent cell cycle video, we had our process for making the stop motion down. We used two colors of DNA, red and yellow, to distinguish the maternal and paternal genes. To represent the cell membrane, we used colored clay. Though this initially created a large enough cell, as it divided in two, and then four daughter cells, the resulting cells were problematically small. This was a reminder that a large number of small cells has a larger surface area (clay) to volume (cell size) ratio than one large cell. This made it more difficult to illustrate Anaphase II and Telophase II, because the chromosomes did not fit inside the cell. This project also demonstrated that, even though meiosis divides one cell into 4, each of the four has an entire half the number of chromosomes as the original. This is because each of the initial chromosomes is double-stranded, unlike the chromosomes in the 4 daughter cells. Here’s our video:

Our Meiosis Video
Q&A
What is the function of meiosis? Meiosis splits a diploid cell, a cell with 2n number of chromosomes, into four haploid cells, which have n number of chromosomes. The haploid cells, called gametes, are used in reproduction,and in most cases must fuse with another gamete to create a new organism.

What events promote genetic variation during meiosis? In Prophase I when homologous chromosomes line up, certain corresponding pairs of DNA are switched between the chromosomes by enzymes, called crossing-over. This allows the genes an organism receives from its grandparents to be totally random: that is, if one gene is from their grandfather, the whole rest of the gene is not necessarily so. This allows natural selection to act on individual genes, instead of entire chromosomes.

What causes non-disjunction? Non-disjunction is caused by chromosomes that do not split during metaphase I or II.This can be because the centromeres did not break correctly following Metaphase II, leading haploid one cell to have n+1 chromosomes and its partners to have n-1.

Panda bears have 42 chromosomes compared to 74 chromosomes found in most bears. How could this occur? Explain in terms of non-disjunction. Non-disjunction creates gametes that have a different number of chromosomes than the previous n number. For example, if one gamete does not receive one of its chromosomes due to non-disjunction, it will create an organism with one less chromosome. So, among a bear population, non-disjunction could have eliminated certain chromosomes throughout the generations. This, along with other genetic variations, would create a new species, the panda bear.

What did you learn from this project? This project showed me just how many things can go wrong in meiosis. Ensuring that every chromosomes went to the right place, and that every spindle fiber was just the right length proved how complex of a process this is. We had a joke that if our group were in charge of all cell reproduction, no one would be healthy. Given that meiosis occurs so often in many organisms, this showed how complex the systems that regulate it must be (even if our diagrams are quite simple).

Cell Cycle Movie

Our Cell Cycle Movie
This week, we created our stop motion movie of the cell cycle. In particular, this gave us a chance to trace a cell’s DNA through the cycle. First, in the synthesis stage, the DNA is duplicated, creating two new identical strands where before there was one. However, ideally these news strands will be exact copies of the original, and thus carry no new information. Before Mitosis, the DNA condenses into chromosomes by winding around specialized proteins, histones. This allows DNA to split into two identical copies of the same information, called sister chromatids, which ensures that each daughter cell will have the same genetic information. These sister chromatids are attached by a groups of proteins called the centromere.
  
During Mitosis, mitotic cyclins peak in the cell and trigger kinases, which in turn trigger the breaking apart of the protein bonding the sister chromatids together. One of each chromatid, now called a chromosome, is pulled to each of the new daughter cells, ensuring that they recieve a full copy of DNA. If the sister chromatids fail to separate, they can end up both travelling to the same cell.
  
This results in aneuploid daughters cells, which are cells that do not have the correct amount of chormosomes. These cells often (but not always) cannot function properly because they are either missing genetic information or they have too many copies of certain genes. When genetic information is changed at any point in the cell cycle, this is called a mutation.
  
  This causes the DNA of the cell or daughter cells to change, sometimes by only tiny variations. Though this happens very rarely in regular cells, certain outside chemicals or radiation (called mutagenic factors) can cause mutations. For example, ultraviolet radiation can alter the structure of DNA, and caffeine can accidentally replace certain base pairs. When enough mutations occur to damage both tumor suppressing genes and protooncogenes, which are respectively in charge of regulating cell growth and promoting it, a cell can lose control of how often in divides. This out-of-control cell growth (cancer) can begin to interfere with surrounding tissues and, through metastasis, can spread to other areas of the organism. Given the drawbacks of this condition, it is clear why cells devote so much energy to ensuring that they replicate completely and accurately in the cell cycle.

Your Inner Fish

Though we often hear that all living things are somehow related, this documentary showed how many resulting similarities we have to other organisms. For example, the structure of the bones in our limbs matches that of birds, and even, yes, fish.
  
But that’s not where the similarities end. Human and fish embryos share early forms of gills, the same overall cells, and undescended gonads. But with all these similarities between species, it can be hard to imagine how our differences evolved. This documentary recounted the search for the first organisms to transfer from living underwater to living on land. Eventually, they it revealed Tiktaalik, a transitional flat-headed fish. Like fish, it had scales, fins and gills, but like mammals, it had a neck and lungs. It even matched the skeletal pattern of our limbs today. Other transitional organisms, like the animals between reptiles and mammals, would also share characteristics of both groups of organisms. An animal linking reptiles to mammals might have fur for insulation, but also be cold-blooded. In addition, it may have given live birth. Like both reptiles and mammals, it would have had a backbone. Here’s a drawing of one possible transitional animal: