- The Molecular Composition of Cells
Reading Assignment #1
Please read all 3 readings in the folder “Readings for Week 2”. Please answer the following 6 questions. Answers should range from 50 to 200 words. Students are to use their own words and not copy text from another source unless specifically asked to. Make sure your response answers the question asked. Some questions are opinion questions; there is no right or wrong answer, but I want you to make it clear you have thought about the question being asked.
1) Please read the document “How To Read a Scientific Paper” and “Scrutinizing science: Peer review”. In pages 3-6 of the first paper and all of the second, there is a discussion of how a scientific paper is submitted and reviewed. Both papers talk about why the process is in place. What is one concern of scientists that led to the creation of the peer review? How does peer review prevent this problem?
2) In both papers, it is explained that peer review often takes a long period of time. It is not surprising for a paper to take multiple years to be published after submission. If you make a groundbreaking discovery that will change the way we treat a specific disease, in your opinion, is it a good idea to go through such a lengthy process? Is it important to get out information quickly or to make sure that it is highly accurate?
3) The peer review process requires scientists submit their work to peers to evaluate whether that work is good or bad, how good that work is, and allows other some say in how the work must be improved. How does this compare to the evaluation of art? How is this evaluation different in the art community compared to the scientific community?
4) The Null Hypothesis is a very tricky concept to understand. Let say that I was considering buying two bicycles, a red bike or a blue bike. I decide to test which bike is the faster bike. I hypothesize that the red bike is faster than the blue bike. What is the null hypothesis in this situation? Propose an experiment that would provide evidence for my hypothesis. What are the possible outcomes of this experiment be?
5) Try reading the paper “Walking Like Dinosaurs: Chickens with Artificial Tails Provide Clues about Non-Avian Theropod Locomotion”. If it seems dense, just remember to try to understand the most basic concept of it and evaluate how much you trust what is reported. Provide a brief summary of the findings of the paper. Try not to simply restate the abstract.
6) Did you like this paper? Why do you feel that way? Give a possible explanation as to why this paper was assigned.
One of the best ways of proving you understand a concept is to explain it to someone else. In this case, I want you to take the following vocabulary and define the terms, words, or phrases for me. Definitions should not exceed 100 words each. Make sure you are using your own words in the definition; do not copy them from another source. Words to be defined are BOLD.
For the first week, we’re looking at how “science” is conducted. Definitions are derived from the readings assigned for the week. Please define the parts of a paper and important concepts:
• Statistically Significant
• Null Hypothesis
• Peer Review
Reading Assignment #2
Please read the 2 readings in the folder “Readings for Week 3.” One is in the folder and one is linked to in a word document. Also, please watch the linked video. Please answer the following 6 questions. Answers should range from 50 to 200 words. Students are to use their own words and not copy text from another source unless specifically asked to. Make sure your response answers the question asked. Some questions are opinion questions; there is no right or wrong answer, but I want you to make it clear you have thought about the question being asked.
1) Please read the 1952 paper written by Watson and Crick. This paper is very different from the paper on theropod locomotion, but was explaining a lot more momentous of a discovery. Which style do you appreciate more? Do you think that this paper could have used more evidence or do you think that it was properly succinct?
2) In the second to last paragraph of the first page, Watson and Crick state that if there are two duplicate copies of the code at all times, this has obvious implications in regards to DNA replication. Is that as obvious as they make it appear? What do you interpret that to mean? What does it say about scientists that they assume this has obvious implications?
3) There is a large amount of drama associated with Rosalind Franklin and Watson and Crick. Watson and Crick looked at data belonging to Franklin that they used to elucidate their structure of DNA without her full permission. She later used that data herself and proposed an incorrect structure. There has been debate since about how much credit Franklin deserves in discovering the structure of DNA. Watson and Crick mention her in their paper here. Do you think that they needed to do more to credit Franklin? Do Watson and Crick deserve the credit for taking the information available to them and figuring out the right structure independent of whether they collected the data?
4) Please watch the video linked to in the readings. Drew Berry begins by talking about the importance of drawings and visualization in the understanding of how things work. Science and art, in his words, are linked. But how useful are these visualizations? People have seen the double helix of DNA many times without understanding the meaning and implications of it. How important do you think visualizations are to understanding science? Is it essential that one be able to “see” a molecule in order to understand it?
Please read the article linked to in the readings.This paper is very dense, but something you can use as a reference going forward. You are not required to read the whole paper, but I want you to at least read the introduction, the section on Carbohydrates, and the section on Proteins.
5) One of the key concepts going forward in this class is the idea of polymerization. Two molecules of a similar structure bond together to make a chain. This chain can then extend as more molecules link to the original pair. How these molecules stitch together can effect their use and function. Using the starting molecule of glucose as an example, why is it beneficial to be able to build more complex structures from small parts? Are all compounds made from the same parts the same?
6) Take your time to really think about this one. Protein structure is talked about in 4 different ways. Primary structure is the sequence of amino acids, secondary structure is a small, localized feature, tertiary structure is the groupings of these smaller structures into a large scaffold, and quatranery structure is how these scaffolds fit together to form a purpose. Scientists still do not know how to elucidate the quatranery or tertiary structure from the primary structure without experimentation. If a protein were composed of 10 amino acids, how many different primary structures could the protein have (Hint: there are 20 amino acids)? How many secondary structures? How many tertiary structures? How many possible functions could this protein have?
One of the best ways of proving you understand a concept is to explain it to someone else. In this case, I want you to take the following vocabulary and define the terms, words, or phrases for me. Definitions should not exceed 100 words each. Make sure you are using your own words in the definition; do not copy them from another source. Words to be defined are BOLD and underlined.
For the second week, we’re looking at how the cell looks inside so that we can contextualize genes and genetics. Please define these terms from the readings. All of the words appear in the readings, but you are encouraged to look at other resources to help with your definitions:
Polar molecules Ion Carbohydrate Polymer Lipid Nucleic Acid Amino Acid Protein Angstrom X-Ray