Writing in Biology

• Install R and Rcmdr.
• Refer to R Commander Installation Notes for details: http://socserv.socsci.mcmaster.ca/jfox/Misc/Rcmdr/installation-notes.html
• Import the data:
  • In Rcmdr. under “Data” menu “Import data” from “text file”
  • Set the “Field Separator” to “Commas”.
  • Navigate to the CSV file and select it.
  • Click the “Edit data set” button to open the data set in a window.
  • Make a note of all outliers (to put in the legend of the figure).
  • Click on the number of each row with an outlier, then right-click and “Delete current row”.
  • Click OK to save edited data set.
• Under “Graphs” choose “Scatterplot matrix...”
  • Select all three variables.
  • Click “Plot by groups”, select Gender, and click OK.
  • Click “Options” and select the checkbox for Least-squares line and click OK.
  • Check for outliers and repeat as necessary.
• Each student independently choose one pair of variables to report in a scatter plot
  • Choose independent and dependent variables
  • Click “Plot by groups”, select Sex, and click OK.
  • Click “Options” and select the checkbox for Least-squares line and click OK.
  • Save as PDF (use this for posters)
  • Convert to PNG (use this to post at website)
  • Post as Image: write legend that includes title, description, and reports outliers.
  • (If time available, report relevant statistics, e.g. means, linear regression, or one-way ANOVA)

GIYF and here is a book for additional assistance: https://stellmack.dl.umn.edu/sites/g/files/pua2461/f/media/_the_rcmdr_gu...

In classifying birds, Thomas Huxley had the idea of arranging the bones of the avian bony plate, a skeletal partition between the nasal cavities and the mouth to assemble a grouping. Since Huxley set a foundation, scientists started adding more detailed characteristics such as muscles, vocalization, and toes to the group of birds but in more specific details. After the characteristics are grouped properly, birds can be present in different orders. Orders can be branch out from common ancestors with unique characters that are easy to distinguish from the rest. Songbirds, member of Passeriformes have unique morphological traits. The more complex traits are, there is a better chance that the species won’t be related. As years go by, technology makes it clearer and easier to find similarities and differences among species because not only the physical anatomy and morphologies but also DNA sequencing plays a big role in birds classification.

With the Methods Project of the Writing in Biology Spring 2019 class, I found that when writing a procedure, everything has to be written down. A procedure needs to be written step-by-step as the experiment is conducted so others can get as close to the original results as possible. The interaction I focused on for this project was an interaction between koi fish and the plants around their pond at the Durfree Conservatory on the UMass campus.

Factors in my methods were:

Time of day

Point of entry into the conservatory

The fish as they are moving and living creatures

Temperature

Differences in my original figure (Figure 1) and the replica made by Max Scheller include:

Scale of the fish and plant subject

Color of subject

Figure border size

Arrow type

Photo glare and watermarks

The Methods Project for Writing in Biology is a tool to show how important it is for the scientific community to conduct research with procedures that allow for an experiment to be replicated and achieve the same results. For the methods project, I had to make a figure showing an interaction between two species around the University of Massachusetts campus.

I choose to use Durfree Conservatory as a space to find one. Inside, there is a pond there with koi fish and plants surrounding it. I noticed that the fish sometimes nibble on the plants that either grow in the pond or those that happen to fall in.

Seeing as the building was an enclosed, temperature controlled environment where the plants and the pond are maintains without much outside influence, I thought it would be a perfect area. The subjects of the study were not affected by the outside winter temperature and snow. Also, both the fish and plants are stuck in one easily accessible area. As the conservatory has a glass ceiling, the time of day matters in order to get a photo with sufficient light and the conservatory is only open from 10 am to 4 pm on weekdays. By going late morning, the sun is overhead and gives enough light for the photos to be taken.

Please download this directory, unzip it, and work in your group to analyze the data: https://bcrc.bio.umass.edu/data_practice/data_practice_files.tar.gz

One thing I remember from Statistics was two different tests for determining if the error in our data was significantly different of if the difference was due to random chance. The two tests I remembered where the z test and Chi squared the latter of which I have  seen used in many of my classes this semester. I also remember that  tested for statistical significance for the hypothesis of the experiment was the main goal, not necessarily to say this is 100% true. In General as a rule of thumb the number usually used for if we could confirm our hypothesis was statistically confirmed was 95%. For most of our tests we were looking for a P value of less than 5% to confirm that our data was significant. Some terms  I remember from this this class was H0 was used for the null hypothesis, Mu was used for the mean population, and Ha was used for an alternative hypothesis.

    In Japanese culture, there is a famous saying that (when translate) states, “do your best not to bother the people around you”. This causes a huge culture of respect to emerge from this mindset, where the people do their best to keep anything public as clean as possible. This means public bathrooms are always very clean, the streets are kept clean from garbage, and even at the train stations, the people will line up in order to enter the train, and will always wait until everyone leaves the car before entering. The trains and public transport are also all very quiet. If someone were to talk on the phone in the front of the bus, that person could be whispering the conversation and they would still be loud enough that someone in the back can tell someone is saying something at the front. I feel as though America could do it’s part in trying to adopt this mindset, compared to the cultural mindset that we currently have which is more similar to “do whatever’s best for you”. This means littering occurs a lot more often, public bathrooms are not treated with respect, and there’s constantly people running into each other as people are trying to get off public transit. It’s unfortunate people live in such a “greedy” mindset, but that is what occurs when we all are trying to live in a way that is focused on just ourselves.

Another possible experiment our class could perform is a study on when different species flower. April is the month that flowers begin to sprout and flower again, and we can measure the difference between different species at this time. Individuals could find random plants and record the species, color, size, shape, and location of the flower over time. In this way, we can track the level and speed of development of various species. We could also study plants that we grow ourselves. Everyone in the class could grow different flowers, or we could choose a few select species to divide amongst the class. We would subject these plants to varying conditions while growing them, including differences in lighting, temperature, watering, soil, and density of flowers grown in an area. This study could reveal information on the best conditions for flower growth and development and at what point the conditions are not enough to sustain correct flowering. 

Organisms in hot environments use multiple different methods to try and stay cool and keep their body temperature regulated. Panting, which is commonly seen in dogs, helps cool the organism by passing air over their moist tongue. Not only does this keep their mouth cool, but it also helps keep the brain cool which is crucial to an organism’s life. The difference between breathing and panting is the frequency at which it happens. Normal breathing is about 30-40 respirations per minute whereas panting is somewhere between 300-400 respirations per minute. Panting occurs at fast paces for short periods alongside normal slow frequency periods. Panting is not only seen in dogs however. Birds, reptiles, and many other organisms use panting to maintain a cool body temperature.