Revising a Research Paper

        One part of writing a research paper not often talked about is the revision stage. After spending so much time researching, writing, editing, and formatting, it can feel like the paper is in its final form. However, it is rare that your first submission is your published version. Oftentimes, your paper will get feedback to help make your research paper stronger and more coherent. 

At first, reviewer comments can feel overwhelming. Seeing a long list of suggestions and questions can feel like the whole paper needs to be rewritten. In my own research paper on Diptericin, I received comments on parts of my reasoning, figures, citations, and explanations of my research methods. Some comments may point out major issues like unclear reasoning or problems with how data is interpreted. These comments take time because they require rethinking a section and going through the logic more carefully. 

Other comments are smaller but still important. These may include fixing citations, relabeling a figure, or changing the wording of a sentence. Although minor issues may not change the main argument of a paper, they still affect how professional and understandable the final version feels. A paper can have strong reasoning, but if the details are messy, its trustworthiness suffers. Tracking changes is also important because it shows honesty in the revision process by making every edit visible.

What helped me work through the pages of revision comments was realizing I needed to take things one step at a time. I organized comments that were related to each other or corrected the same section so I didn’t have to rework a section more than once. Sorting them into categories makes the process feel more manageable and more like a checklist of improvements rather than a giant problem. 

Revising a research paper also taught me patience. It can be frustrating to return to a paper after thinking it was done, but revision is where the real improvement happens. Each comment forces the writer to look at the paper from the reader’s point of view. Revising helps to make the research paper easier to understand. Detailed research methods are also important because they make the work reproducible, allowing someone else to understand and follow the same process to verify the results.

Dating Fossils

One of the most fascinating parts of studying anthropology is analysing fossils and determining how old they are. In Human Evolution: A Very Short Introduction, Wood explains that understanding the age of a fossil reveals details about how our ancestors lived and evolved.

One of the first methods to age fossils was looking at the surrounding rock and dirt. Generally, older sediment is found deeper in the earth and younger rocks are closer to the surface. This idea is called the law of superposition. If a fossil is found inside a certain layer, scientists can often assume it is around the same age as that layer of rock. However, this method is not foolproof as erosion and caves can move fossils or mix old and new sediments together.

As technology advanced, scientists discovered more absolute methods to date fossils. In East African fossil sites, many bones are found between layers of volcanic ash. These ash layers can be dated using potassium/argon or argon/argon dating because radioactive elements decay at a steady rate. Researchers also utilize palaeomagnetic dating, which analyzes changes in the earth’s magnetic field recorded in rocks. By comparing the magnetic pattern in sediments to known magnetic records, scientists can estimate the age of the fossils.

Other more specific methods help date fossils from different time periods. Ostrich eggshell dating uses changes in amino acids over time. Electron spin resonance and uranium series dating are often used for sites too old for radiocarbon dating but not old enough for potassium/argon dating. This plethora of techniques show that fossil dating is a careful process that combines geology, chemistry and biology to piece together the timeline of human evolution.

When I was younger, my family visited Salt Lake City in Utah and my brother and I had the opportunity to dig up fish fossils. Unfortunately, I wasn’t old enough to handle fossils so the most interesting specimen I dug up was fish poo. I remember being jealous of my brother, on the other side of the field, discovering fish bones while I uncovered their feces. Nonetheless, the trip inspired my fascination for archeology, and later anthropology.

Natural Selection

One of the most important ideas explained in Human Evolution: A Very Short Introduction by Bernard Wood is natural selection as it explains evolution. Darwin’s most influential contribution was not just stating that evolution existed, but explaining a possible mechanism.

Natural selection begins with variation and the notion that no two individuals are exactly the same. Some may be faster, stronger, or smaller, leading them to be better suited to their environment. These differences may be small, but they can create an edge that becomes vital when resources are limited and competition is fierce. If one individual has a trait that helps it survive long enough to mate, that trait will be passed down to its offspring.

Over time, useful traits will become more common in a population. This is due to individuals with those traits living longer and passing them on to future generations. Darwin connected this idea to artificial selection, where humans choose certain traits in plants and animals. He theorized that nature could “select” traits as well.

Natural selection helps explain why there are so many diverse organisms and how they are so well adapted to their environment. It also supports the branching in the Tree of Life, where different species are connected and evolve into different directions. Understanding mechanisms like natural selection is vital when exploring theories like convergence. Thus, the discovery of natural selection helped reveal that comparing features like the morphology of a subject is not always the most accurate method to determining evolutionary relationships. Learning about natural selection makes evolution feel less sudden and more like a slow process built on small differences.

Learning from Nature

Human Evolution: A Very Short Introduction by Bernard Wood encompasses many topics, but my favorite is about how scientists have viewed how humans fit into the natural world. In Ancient Greece, philosophers like Plato and Aristotle suggested that nature was one system. However, following the collapse of the Roman Empire, the idea that man was one with nature was lost until 16th and 17th centuries. As science developed, researchers began utilizing methods like induction, which began with observations that were tested with experiments, rather than deduction, which began with unproven beliefs, to understand where humans fit. Thus, human origins became something that could be studied through fossils, anatomy, geology, and eventually genetics.

Charles Darwin is arguably one of the most important figures in this shift of thinking. Influenced by other thinkers like Charles Lyell, who wrote about geology and how slow the earth changes, Darwin began to theorize about how minute changes over extended periods of time could also shape living things. Darwin noticed that animals and plants were not exactly alike. Even within the same species, individuals had small differences whether it be their beak was more stout or that they were different colors. These variations mattered because only the most well adapted survived in nature. Food and space were limited, so some had features that helped them live longer and reproduce successfully.

Reading about the development of the idea that humans are part of nature and Darwin’s journey helped me understand that science begins with paying close attention to the world. In classes like AP Biology and AP Chemistry, the importance of not leaving anything unquestioned is stressed. Darwin’s work with observing small details led to his theory of natural selection. By studying animals and the world around him, he helped change how people understood life and humanity’s place in it.

The Anatomy of the Brain Part 2

In addition to the major lobes we discussed before, there are several very important deep brain structures.  These small important structures are located near the center of the brain and part of the limbic system.

Thalamus is a relay station for all sensory signals, except for smell.  It also regulates sleep and awake cycles.

Hypothalamus is located above the pituitary gland.  It sends a chemical signal that controls the function of the pituitary gland, which is involved in processes such as sleep, body temperature, hunger. 

Pituitary gland is a small gland located behind the nose.  It is involved in control of many hormones produced by the thyroid, ovaries, and testicles.  It also receives chemical signals from the hypothalamus through a connecting stalk.

The amygdala is located under the cerebral hemisphere.  It is part of the limbic system and controls the “fight or flight” response when faced with danger.  It is also important in emotional memory and controlling emotions.

The hippocampus is a seahorse shaped structure located under the temporal lobe.  It is very important in new memory formation and spatial navigation.  This organ plays an important role in Alzheimer’s disease.

The basal ganglia coordinate movement and help us make decisions.  When the cells in this area die, patients can develop tremors and have a hard time with movement, leading to Parkinson’s disease.

The brainstem has three parts and connects the cerebrum, cerebellum, and the spinal cord.  The most superior segment is the midbrain.  The pons are located in the middle.  The medulla is the most inferior, connecting the brain to the spinal cord.  The brain stem function is very complex!  The midbrain is involved in motor functions such as eye movements, hearing, and visual information. The pons connects the cerebral hemisphere to the cerebellum and is involved in movements and balance. The medulla controls many basic life functions such as breathing, heart rate.  Many reflexes such as sneezing and coughing are also controlled by the medulla. In addition, cranial nerves III to XII originate from the brain stem.

Cerebellum is small and located at the back of the head.  It also has two hemispheres.  Its main function is to control balance and maintain posture.  But it is also involved in other functions such as learning skills and emotions. 

The brain is such a complex organ!  And we have barely started to understand it.  I think it is the most fascinating organ.  Underneath all this complex anatomy, the neurons generate tiny electric signals that form our thoughts, emotions, and sense of identity.

Analyzing Phylogenetic Trees

        Phylogenetic trees are one of the most useful tools a scientist can use for understanding evolutionary patterns. At first, they look complicated and confusing, with branches clustered everywhere and seemingly random numbers on lines. However, once you learn how to read them, they become a great visual way to understand relationships between species. In my paper, I used phylogenetic trees to compare diptericin sequences across different fly species.

A phylogenetic tree reveals how closely related different sequences are. Sequences that branch close together are more similar, while sequences separated by longer branches diverged more severely. For example, if several Diptericin copies from the same species appeared in a tight cluster, that pattern suggests recent duplication. If copies from one species appear in different parts of the tree, that suggests an older and more complicated evolutionary history.

I also compared gene trees to species tree. A species tree shows the evolutionary relationships between the fly species, while a gene tree shows the relationships between the Diptericin sequences. These trees are not always identical. A gene can be duplicated, lost or evolve at different rates. This nuance is why analyzing both trees is essential for researchers to uncover patterns.

In my paper, I concluded that it is likely that Diptericin B was the most widely conserved paralog and was likely the most similar to the ancestral form of Diptericin. Diptericin A and Diptericin C appeared in more scattered groups that showed duplication in certain lineages, suggesting that the gene evolved differently in different species. 

Analyzing phylogenetic trees made me realize that evolution is much more complicated than one branch from ancestor to modern species. A tree can show conservation, duplication and divergence, all at once. In the case of Diptericin, the trees helped reveal how a small protein changed across insects and how these changes reflected different evolutionary pressures.

Studying Diptericin

        My research focused on analyzing the evolutionary history of Diptericin, an antimicrobial peptide found in insects. I studied the relationships between Diptericin A, Diptericin B, and Diptericin C to better understand how these related peptides diversified over time. One of the most interesting parts of the analysis was learning how many different techniques can be used to study a single peptide. By combining sequence analysis, phylogenetic trees, and 3D modeling, I was able to examine Diptericin from both an evolutionary and structural perspective. 

The first step to my analysis was gathering the Diptericin amino acid sequences. There were three main paralogs: Diptericin A, Diptericin B, and Diptericin C. Once collected, the sequences were aligned using MAFFT and AliView. This was the first technique I used to help organize the amino acids and match them. After the sequences were aligned, the second piece of technology I used was a program called IQ-TREE. IQ-TREE creates phylogenetic trees by analyzing how the amino acids are lined up and any inconsistencies between diptericins. The trees showed how the Diptericin sequences were related to each other. Some copies from the same species were clustered together, suggesting recent duplication. Other copies were more spread out, suggesting older divergence. I used iTOL to view the trees as it made it easier to compare patterns more clearly.

Another important part of the research was AlphaFold modeling which predicted the 3D structure of proteins. This program was especially useful as I was not only interested in the full sequence, but also specific regions like the pore. Being able to differentiate structures in the protein was essential as each had a specific purpose, for example, the pore was used to disrupt bacterial membranes. By identifying the regions, I could build more focused trees based only on that functional part.

My favorite part about learning these techniques was seeing how closely biology and technology are connected. Sequence alignments showed changes in amino acids, phylogenetic trees revealed evolutionary relationships, and AlphaFold used artificial intelligence to predict protein structure. Together, these methods made it possible to study how Diptericin diversified across insects and how gene duplication may have shaped immune defense in flies. This research also showed me that tools like AlphaFold are not limited to insect evolution. Similar technologies can be used to study many areas of biology, including human evolutionary history. Overall, studying Diptericin helped me understand how modern technology is changing biological research by making questions about evolution, structure, and function easier to explore.