Letter to a Biology Student

Dear incoming biology student,

        Hello! I am Michael Tang, a current freshman who has finished my year of Biology. As a student, I strive to excel in the subjects I like and also branch out into other areas of study, taking electives in Spanish language and computer science, and participating in extracurricular activities like piano and golf. I value quality and balance, preferring to hone my skills in a few specific areas while maintaining a broad balance across all the topics I am exposed to. To me, biology specifically is an intriguing subject; I have always felt drawn toward the unique processes and mechanisms it introduces, as well as its endless applications and explanations that keep it perpetually both relevant and interesting.
        Like you probably are, I was somewhat unsure on the first day of the expectations and workflow that Mr. Orre's class would bring. However, I soon learned that the class would be unlike most other classes I had previously taken: the course implements a "flipped classroom" model, which allows more flexible learning and more labs and activities. I definitely believe this is advantageous, and although it did mean more work to do for homework, the benefits significantly outweighed the costs. For example, the format allows additional class discussion on the lecture topics, as there is usually some time during the beginning of each class where we discuss the more complex aspects of the material. This normally follows a "Do Now," a warm-up of sorts involving an individual write-up answering some presented question related to the material. The bulk of class time is often used for different activities like watching videos, working on projects, or doing labs. In addition, we keep a biology blog over the course of the year (this letter is posted on mine), where we post unit reflections, lab write-ups, and similar content. Writing posts is sometimes part of the homework, though the homework usually consists of taking notes on vodcasts and working on textbook notes that are due at the end of each unit. These notes (on vodcasts and textbooks), as well as the "Do Nows" are written and kept in a notebook; as time passes, your notebook will slowly evolve into an essential study tool and resource, so make sure you maintain and organize it! Overall, the year is definitely packed with engaging topics, from cellular biology to molecular biology, from ecology to evolution to genetics. I learned a profusion of knowledge from the class, as I am sure you will, and even garnered some "soft skills" relating to time management, organization, and (fast and efficient) note-taking.
        I am sure you can apply most of your general "study skills" and similar school knowledge to get the most out of this class, although make sure to keep up with deadlines and coursework. Due to the "flipped classroom" model, the homework becomes especially important, so do not neglect it! It is responsible for teaching you the concepts (though they are generally reviewed during class) and bequeathing most of the information, and also accounts for a significant portion of your grade. To prepare for tests, make sure to review your vodcast notes and summaries, as virtually all of the test material is based on it. (although occasionally knowing some textbook or outside information can prove essential) Another large part of the class (and your grade) is labs, and writing effective analyses is important. Additionally, make sure to follow all of Mr. Orre's directions during a lab, especially during clean-up, as he is very particular about lab performance, and not following directions is one of his largest pet peeves.
        In conclusion, this class is a whirlwind of information and learning, though a whirlwind full of memorable experiences for me. It was one of my most enjoyable classes this year, and I also learned a great deal; next year I will be taking Chemistry Honors, and I hope to find a similar experience waiting there. I am sure you will take interest in this class just as I did, through the numerous blog reflections, vodcasts, and topics. All in all, good luck on your journey, and take care!

Best regards,
Michael Tang

Pig Dissection Lab

        In the pig dissection lab, we explored the different organs and processes in the body of a fetal pig and connected them to how the human body functions. We asked the essential question of "how can we see the workings of the human body systems in the pig?"; in the dissection, we found organs of the digestive, respiratory, circulatory, urinary, reproductive, and endocrine systems. These included the trachea and esophagus in the pig's throat; the pig's pancreas, gallbladder, liver, stomach, and intestines; and endocrine glands like the thyroid gland and the spleen. Furthermore, we recorded (and I edited) a video highlighting and explaining various organs in the pig. Watch the video below or here.

        The most interesting part of the dissection was identifying the different organs, as it was surprising how good of a representative the pig was for a human body; also, it helped bring to life the concepts we learned in the vodcasts, such as seeing the path the food might go through inside the pig's digestive tract or observing the blood vessels that connect the heart to the different parts of the body.
        In addition, the dissection itself was a valuable experience, as it was quite a different and unique lab. The careful taking apart and cutting open of the pig was unlike any lab we had done before, and working with a once-living organism was an interesting experience, though it did not pose any major obstacles with me or my group members. Overall, it was an enjoyable and educational experience (that I might repeat if I take A&P or a similar course later on) and provided a new and much-needed perspective on the unit material.

Unit 9 Reflection

        This unit was a whirlwind of different taxa, from the simple cell colonies of Porifera to the modern Mammalia. It covered many different kingdoms, phyla, and classes, organized in accordance with Linneas's binomial nomenclature system in different levels of organization.

Levels of organization

        The 3 domains are Bacteria, Archaea, and Eukarya. Bacteria are single-celled prokaryotes with flagella and cell walls made of peptidoglycan; they are somewhat comparable to the non-living viruses, which have capsids with DNA or RNA, and infect by taking control of cell machinery. The mysterious archaea domain are extremophiles and are difficult to compare with other taxa, a domain once thought to be part of Bacteria.
        In the domain Eukarya, some kingdoms include Plantae and Fungi, which have cell walls made of cellulose or chitin and have unique characteristics that help them survive in different environments. Our own kingdom, Animalia, is made up of phyla like Porifera, the sponges, and Cnidaria, the radially symmetrical polyps and medusas. Other phyla show the evolution of the digestive system, from the incomplete guts of Platyhelminthes, to the complete digestive tracts of Mollusca, to the coeloms of Annelida. The most common invertebrates are Arthropoda, which have segmented bodies with appendages, made up of a head, thorax (or cephalothorax), and abdomen). Of course, the phylum Chordata is one of the most advanced, featuring amniotic sacs and eggs, as well as a notochord and other embryonic features. The classes of Chordata go from the earliest fish (Agnatha, Chondrichthyes, Osteichthyes) to the first terrestrial vertebrates (Amphibia, Reptilia). From the dinosaurs evolved the phylum Aves, which had hollow bones, feathers, and fused collarbones to allow for flight. Of course, the phylum Mammalia eventually developed, composed of active endotherms including monotremes, marsupials, and eutherians (like us!).

A circular diagram of the tree of life

        In general, this unit was deeply satisfying to explore, as it covered one of my favorite topics in biology. The web of life is so infinitely complex, and its connections and history open our eyes to how everything, no matter how different, is so intricately linked. As deep as we have delved, I still have a plethora of questions brimming in my mind, from how anatomy and skeletal structures evolved, to the geological shifts that have facilitated the adaptation of these organisms. (learn more about Earth's history in my 20 Time here!) How did complex adaptations like the eye and the wing form? What were the intermediate structures, and what role did they play in the evolution of the taxa that possessed them? What were the key factors in coevolution and symbiosis, and in what cases was it thwarted by some other factors? Hopefully, my future academic endeavors will bring me answers to those questions, and beyond.

        In this unit, we completed the "What on Earth Evolved?" project, each exploring a specific species or group of organisms, in order to introduce various influential organisms in Earth's history. (we explored the history of the Earth in this project) I was given the task of researching stony corals, and I created (and presented) the above presentation. Take a look at the presentation above: corals are fascinating both internally and externally, and I gained quite a bounty of knowledge from this project. Additionally, I was able to practice designing a balanced presentation, and I improved my slide-making skills, juxtaposing images with researched information. I also learned how to embed the presentation into this blog, a skill I might find useful in the future. Ultimately, I was surprised at the ease with which I could convey my ideas to the class, which goes to show how important the practice I did was. In the future, however, I might try to enlarge the font to make the slides easier to read, and also research some additional background information in order to be able to better answer people's questions.
        All in all, this unit provided a very rewarding and eye-opening experience, and I look forward the next (and last) unit of Biology, which should provide a close-up perspective of the human body systems, in contrast with the "wide-lens" taxonomy we have been studying in this past unit.

Geologic Timeline Reflection

        This unit, I worked in a group and created a geologic timeline of the history of the Earth. The timeline gave a sense of the magnitude and major events of the past, as well as how insignificant of a time we humans have occupied. I have organized some thoughts below as a sort of reflection on the project and what we learned.

Mesozoic Era and the K-T extinction

         In the Earth's history, some significant events were the oxygen revolution, Cambrian explosion, and K-T extinction. The oxygen revolution, which occurred in the Proterozoic Eon, had a lasting and important impact on the Earth. Scientists have found that there was a radical increase in oxygen levels due to the photosynthetic actions of cyanobacteria; it has been estimated that the amount of oxygen went from 1% to 15% of current levels, and changed. Thus, this event affected the future of the Earth and made possible the proliferation of oxygen-respiring organisms afterward. The Cambrian explosion was also one of the most important events: it consisted of a burst of immense evolution and diversification that took place in an "explosion." The organisms arose in a mere 30 million years, and began many of the lineages that persisted for millennia, and that we see today. This was the cause of the development of both terrestrial flora and fauna, but also the marine life of the Ordovician and Devonian Periods. Lastly, the K-T extinction was highly influential to the development of the following Cenozoic Era. It saw the extinction of all dinosaurs and many other species, and allowed the adaptive radiation of the unaffected species and organisms, such as mammals. Thus, it made possible much of what exists today, including our own species, that would otherwise not have risen to such a degree.

Cenozoic Era and the blink of an eye that is us

        The scale of Earth's history is simply colossal, what with our own written and evolutionary history not even a blink of an eye in the planet. Though I had some idea of this comparison, especially as I had researched the topic as part of my 20 Time project, I was unaware of the vast difference of the eons and epochs. That said, we have had a surprising impact on the planet during our relatively short time here: we have changed the climate, the temperature, the geography, the topography; we have decimated many species, and allowed others to become widespread to further our own ends; we have spread and sought in space, and plumbed the deepest trenches of the Earth. As much as we have learned, we have destroyed, and there is no question that we will continue to do so. Perhaps through this, we are our own demise; just another species that formed, thrived, and died out as it made way for others to dominate. Are we just another Dinosauria? In all the ways we think ourselves superior, certain adaptations bequeathed similar advantages upon other species of the past. Flight, camouflage, speed, different senses: they all shone through and thrived, though the species changed and diverged. Are we different from all that came before us? What will come after us? Will we ever know? Perhaps not. But that is, inherently, our advantage: the unceasing yearning to know, to learn, to grow.

Unit 8 Reflection

        In this unit, we learned about evolution and its related processes and patterns. Evolution is a theory supported by numerous sources of evidence, such as analogous structures, where different species develop the same structures in different ways due to its benefits; developmental evidence, which can show processes shared in common by related species; homologous structures, which can show structures that have been adapted differently by diverging species; and fossils, which form a fossil record that can be used to track evolution across time. Evolution is mostly dependent on natural selection, though it is also affected by genetic drift, random changes in the population; gene flow, the movement of alleles; mutations, which influence and are acted on by natural selection; and sexual selection, a similar process involving selection for traits advantageous for mating success.

Result of artificial selection in carrots

        Like artificial selection, a process involving breeding a population for certain traits favored by humans, natural selection is a change in allele frequency in a population over generations. It occurs due to survival benefits certain traits give individuals. In addition, though the gene pool changes continuously over time due to natural selection, lethal alleles can remain as recessive alleles that may be influential in the event of changing conditions.
        As the population changes, patterns such as stabilizing selection, directional selection, and disruptive selections can appear. These relate to how different phenotypes become more less common, favoring an extreme, the intermediate, or both extremes. Disruptive selection is also a cause of speciation. Speciation occurs as new species rise due to behavioral, geographical, or temporal isolation. This can occur continuously, through gradualism, or in uneven stretches, as in punctuated equilibrium.

Allele frequency change over time in Hunger Games lab

        In a nutshell, this unit has been a whirlwind of ideas that tie in old concepts and new ones alike. (e.g. genetics, inheritance, populations) It has given many answers, though questions do not equally abound. For example, the information about homologous structures and fossils provoked questions about how these fossils actually change, and what genes control them. Partaking in the Hunger Games lab was particularly interesting, as it demonstrated real-time (or sped-up time really) how different factors play into the change in a population. Even the unexpected outcome still showed how genetic drift and new behaviors can affect what happens.Additionally, the vodcast on the history of life makes one wonder what exactly occurred that changed things so much. (go to my 20 time project to learn more!)
        In the last unit reflection, I made it a goal to more assertive, after exploring some of the different conflict styles. (e.g. passive, aggressive, assertive) Since then, I have put some effort into that goal, trying to put out a clearer opinion during group projects and, to some extent, in my life. For example, during a PE project, I made sure to maintain my priorities and to ensure we finished on time by keeping the group on schedule. I will continue to work toward this goal in the coming weeks, and I hope to be successful.
        All in all, I am looking forward to the next unit, and learning more about......kingdoms and phyla? That proves to be an adventure, and we shall see what it holds.

Hunger Games Lab

1. In this lab, we simulated real-life natural selection patterns through an experiment involving picking up food (corks) in various ways based on three different phenotypes: stumpies (AA), knucklers (Aa), and pinchers (aa).

   

   Lab overview and procedure

2. Knucklers and pinchers were the best at catching food, as knuckles or fingers were better for picking up food, and thus survived the most. The small a allele increasing significantly in frequency supported this, going from 50% of the gene pool to 0.74% of the gene pool in round 5.
3. In our experiment, our population evolved, as the allele frequencies shifted significantly due to differences in individual phenotypes.  The frequencies of the large A and small a alleles went from 0.5 and 0.5 to 0.38 and 0.62 over the course of the experiment. In addition, at the end of the experiment, there were 14 knucklers, 6 pinchers, and 1 stumpy from the 10-10-10 makeup of the beginning; all of the data points to a gradual shift in the gene pool of the population. 



Graph of allele frequency over time in experiment

4. Much of the changes in this experiment were due to non-random factors (e.g. natural selection). However, random events also impacted the experiment; genetic drift caused by changes in the food dispersion, as well as cheating to survive both affected the data. When the food was gathered in piles near some individuals, they were able to collect more food and thus survive and reproduce better. Additionally, some individuals resorted to cheating (i.e. grabbing technique) when selective pressures were high, and thus had an advantage unrelated to their traits.
5. In nature, when resources and conditions change, individuals and populations are affected: adaptations come into effect, and some individuals die out as a result of being unfit for the new conditions. For example, if an invasive species were to be introduced into the area, it might kill off or compete with the population, thus causing fewer individuals to survive. Similarly, the results of the lab may have been different if some key factors were changed. If the food was larger, the stumpies may have fared better, with an easier time picking up the food. On the other hand, if the food was smaller, it might benefit the pinchers, as they have an advantage picking up smaller food over the other phenotypes.
6. If there were not incomplete dominance, then there would be many more stumpies (making up 75% of the potential genotypes from a double heterozygous cross), as they are a result of the dominant big A allele. Conversely, without the knuckler phenotype, the pinchers would quickly outcompete the stumpies and dominate the population.
7. In this lab, we saw how natural selection is a major driving force of evolution, as it changes populations to make traits beneficial for survival more common over generations. Our beneficial allele was the small a allele, as pinchers and knucklers were better at surviving, so over time that allele became increasingly prevalent. Therefore, there were more pinchers and knucklers at the end.
8. Individuals adopted new techniques during the experiment. When selective pressures were high, they often cheated with a grabbing technique to increase their chances of survival. This likely led to there being more individuals with inferior phenotypes (i.e. more stumpies survived). Thus, it would have also increased the frequency of large A alleles. In nature, adaptations over time would play a similar role, beneficial mutations leading some to survive while others died off. An example would be the peppered moth: the black phenotype let the moth better camouflage from predators during the Industrial Revolution, and thus individuals with that phenotype had an advantage.
9. Natural selection acts on populations over many generations, and occurs due to beneficial traits of individuals. This can be seen in this lab: the beneficial traits that pinchers and knucklers had to pick up food caused their genes to be passed on more often (survived more often), and thus the population's gene pool was affected.

Unit 7 Reflection

        This unit was a tour in the essential "study of house," a branch of biology that grows in importance every day due to the numerous causes of damage to the environment. Ecology can be studied on many levels, from the smallest niches, full of factors and adaptations species need to survive; to complex food webs, structures linking hundreds or even thousands of producers and consumers of every trophic level, transferring less and less energy until apex predators get close to none; to entire ecosystems, rich with different organisms and the abiotic factors that affect their lives, as well as cycles of the nutrients they need; to the biosphere itself, extending worldwide and encompassing all life on earth.

Human population growth diagram

        Likely the most directly linked topic to humans is human population, which, like populations of any animal, is affected by factors such as immigration, disease, density, and dispersion. Like any population in its initial stages, the human population is also growing exponentially, though the carrying capacity of the earth can only support about 10-15 billion in total.

        One of the largest concerns currently is humans' effect on the planet. Through climate change, overexploitation, and introduced species, and habitat loss, we have created the sixth mass extinction, and have endangered a large percentage of all species. Unless we work as individuals and a society to conserve and restore resources and save biodiversity, the world as we know it will surcease.

Ball-and-stick model for polyethylene terephthalate (PET)

        This unit has indeed left me with some unanswered questions, such has how exactly our harmful, as well as restorative, processes work. (e.g. power plant and engine emission chemistry, properties of plastics and recycling for different plastics) A further exploration into basic economics and manufacturing could also help me broaden my knowledge, as would knowing more about the largest threats to the environment. What are the main causes of introduced species in the modern world? What industries and specific techniques should be targeted to reduce habitat loss and overexploitation?

        Much of the time we spent in this unit was working on a Conservation Biologist Project. In my group, we worked to create an effective presentation (see above) covering the environment and threats of the Ecuador cloud forests, as well as attempting to formulate solutions directed at these threats. Most of the time, we worked together well as a group, fulfilling group goals and individual tasks on schedule, and we were equally successful with our research. It was a bit difficult to coordinate large tasks as a group, such as putting together the works cited and getting the individual recordings done for editing, but in the end we were able to keep everyone, for the most part, on schedule, and wrapped up the work on time. If I were to do a similar project in the future, I would probably be more specific and break down goals. Furthermore, I would try to enforce goal deadlines better so that group members finished tasks on time without fail.
        A concept we learned was the different conflict management types: assertive, passive, aggressive, and passive-aggressive. After taking a self-assessment on the topic, I determined that my leading types were assertive (35%) and passive (27%); my goal is to be more assertive, which would entail being more clear and straightforward with my ideas, as well as keeping my priorities in mind as I communicate.
        In general, I look forward to learning more in the realm in biology, whatever it may be. On a side note, I will also work toward improving my writing, whether it be in biology reflections, or in any number of other applications.