Wednesday, July 23, 2014

Conceptual Development

Today in class we discussed how concepts are learned by children and how at certain ages, concepts are still not understood. Because I had a late night last night, I was very tired in class. To deal with this, I took very detailed notes of everything we were going over in class. I usually just take notes on the main ideas, but this helped me keep focused. 

Like many of the topics of developmental psychology, conceptual development allows for another debate between nativists and empiricists. Nativists believe that infants are born with specific learning systems for things like physical concepts, language, etc. Empiricists believe that what an infant learns is based off of their experience and the input that they are receiving. So for conceptual development the argument of a nativist argument could be that infants are born with a specific module to learn certain concepts. The empiricist argument could be that babies learn these concepts because they experience them repeatedly, and learn them this way. 

When kids are much younger, their thinking is very egocentric, and they do not understand the concept that other people think through a different perspective. A way to show this is called the Smarties test. In this test, kids are shown a box labeled smarties. When asked what they think will be in the box, they of course answer smarties, but then when the box is opened they find that the box actually contains pencils. Then the administrator of the test asks the kid what a peer who hasn't seen the contents of the box will think is in the closed box. Younger kids seem to only be able to think from their own perspective, so they answer that the peer will think the box contains pencils. At some point in children's conceptual development, there is a change, whether it is gradual or sudden, and then children understand thinking from the perspective of others. 

She let us go to lunch about half an hour early, so we had some extra time to converse. After lunch, we got into our research groups to work on the method section part of our final paper. We also got our introduction and literature review with comments on it so we could correct it. It was basically just time to work on any assignments we needed to complete before the experiment and that we needed to catch up on. That is how we spent class time until about 3:30. Then she dismissed us.

As soon as I got back to campus, I got ready to go to the gym with Victoria. We spent about an hour their before heading back to dinner to eat with the whole cohort. After dinner we worked on homework in the lounges.

DNA Sequencing

I woke up today at 8:00 AM, got ready, and went to breakfast. Soon after I went to class and walked with Katherine and Alexa. Then they went to class and I kept walking my way and caught up with Dani and Kaitlyn because our classes are in the same building. When I got to class we did an hour lecture and then to the lab until lunch. In the lecture Dr. Fineschi talked about the different RNAs there are and what they do. They are mRNA (messenger), rRNA (ribosomal), tRNA (transfer). The mRNA is transported in the cytoplasm and tRNA has a complementary way with the mRNA codon. She also talked about ribosomes. They keep the mRNA in place, they allow mRNA and tRNA alignment, catalyze the formation of bonds between successive amino acids that are carried by tRNA.

I learned that Fredrick Sanger won two noble prizes, noble in chemistry 1958 for the structure of insulin and noble in chemistry 1975 for DNA sequencing. He also invented DNA sequencing. She told us that large scale DNA sequencing uses the dideoxy method with some improvements for increased efficiency and speed. Before we left to go to the lab we sequenced DNA off of DNA sequence paper from a while back. It was fun because we were all confused at the beginning but then got used to it. But it didn't work because Dr. Fineschi gave us the wrong sequence. But I learned that scientists sequence 200 genes at a time because there are a lot of genes to sequence.

 When we went  to the lab and extracted DNA from our mutant in the environmental plates and used PCR to amplify the rpoB gene. Next we mixed the 3 different colonies in 3 different tubes with lysis in it. After that we put the sample tubes into the thermocycler because the lysis solution needs to be heated up in order to be activated. As we waited, we put 40 mL of water into 3 separate tubes labeled for red, blue, and environmental. After we put the water in, we put the diluted samples into the tube that matched the label. Then we used a pipette and inserted 2.5 mL of the lysed dilution into the tac bead tube. Next, we added 17.5 mL of primer and then 5.0 mL of water. Next, we put it into the centrifuge for the short cycle and then put it in the thermocycler.

Dawn, the TA, Helping my Partner Sofi
Then I went to lunch and had meatloaf and fruit. After I came from lunch our class went to the lab first and before class Dani brought me a milkshake. I thought that was nice of her to bring me one since I didn't get to go with her and Kaitlyn during lunch. For the next part of the lab we got three more tubes and put 4.0 mL of loading dye and 1.0 mL of PCR in each one. We labeled the tubes red, blue, and environmental. Then we loaded the solution into the gel. The purpose of this lab was to verify if there was data from our samples. Our plans for tomorrow is to go to a sequencing facility to see how it actually works.

At dinner we all ate in the main dining hall. I ate fruit, rice, chicken nuggets, and for desert I had one scoop of cotton candy ice cream in a cone. At dinner we made a lot of jokes and laughed almost the whole time we were there. I ate with Alexa, Jimmy, Oyin, Dani, and Kaitlyn. Then we left and I went to my room for a while until I went to go play soccer with Jimmy and some more people from the program. I had fun and we stayed until 8:45 PM. Sadly my team lost but it's okay because I still had fun playing with them. But ending the night with my Chicago Family is the best thing every night.

Sustainability Field Trip #2

We went on a field trip in my class today. We first visited AIA Chicago which is the Chicago Chapter of the American Institute of Architecture. When we first got into the office, we were approached by a friend of my professor's Zurich. He gave us an overview of what the AIA was and our speaker for the day, Bill came in. Bill spoke to us about the Committee on the Environment (COTE)which serves the community on behalf of the AIA regarding sustainable buildings. He shared some of his past with us and he then went into how the sustainable buildings are built. The process is very extraneous and involves many different factors that needed to be considered like how much sunlight can they get in the building and if they can go underground to cool down a building. I wasn't aware that a lot of the sustainable building practices that he mentioned and the one that interested me the most is the living wall. It is basically a wall of plants and it's put in buildings to purify the air and it also looks decorative. 

After our visit at AIA, we went to the Environmental Law and Policy Center. The ELPC is the Midwest’s leading public interest environmental legal advocacy and eco-business innovation organization. They develop and lead successful strategic advocacy campaigns to improve environmental quality and protect our natural resources.  Seth Johnson works for the ELPC as a policy advocate and organizer, an example of this that he gave us was the work he did then the Englewood neighborhood here in Chicago. A railroad company made a deal with the city to start building around the neighborhood. Englewood has a high number of people who suffer from asthma and a railroad company moving close to them wouldn't help fix that problem. The deal was already sealed and it looked like it would be a grim future for Englewood. The community members decided to team up with the ELPC to advocate for a better deal. After a lot of work, it was agreed that both sides would sit down and come up with a solution that would benefit everyone. The ELPC's public advocacy links environmental progress and economic development together while improving the quality of life for those who they help.

We had the afternoon portion of class at the University of Chicago Business School in the city. It isn't near the main campus and it was really close to the two companies that we visited today so my professor figured that we would have class there. We got to choose from a list of conventions and treaties and we had to give a presentation on them today. I had the World Conservation Strategy and it was a lot of fun researching it because I really had no idea what it was and I was surprised at how much it related to the triple bottom line that we learned earlier in class. When it was my turn, I was kind of nervous but mostly because I was afraid that I would forget all of the facts that I was going to use to make my presentation good. I feel like I wasn't as nervous as I was the first time that I presented and I can feel myself getting better at public speaking.

We ran really late in class today so we had to cut our schedule for today short and tomorrow, we are going on another field trip to visit Interface. We have to take the train to get there and my plan is to follow someone who knows where they are going so I don't get lost. Tomorrow we are visiting Interface which is a company that produces carpet tiles. This invention is really ingenious to me and I'm really excited to learn everything that goes on in the making of it.

The Calm Before the Storm

Sadly, today was Dr. Bhasin’s last full day with our class! It’s disappointing—we’ve already gotten attached to her. I’ll miss her challenging, in-depth lectures and how she was always willing to help us learn as much as possible (her lectures have been exceedingly easier to understand).

However, we will have Dr. Schonbaum acting as our new lecturer. Though we’ve had limited interaction with him this past week, he seems as friendly as Dr. Bhasin is.

Today’s lecture was about proteins in biotechnology. Dr. Bhasin went over the many applications of proteins in industry—proteins have resulted in the creation of medical applications, food processing, textiles and leather goods, detergents, adhesives, and more. We talked about protein structure, protein purification methods (like size exclusion chromatography, ion exchange chromatography, and affinity chromatography), and postpurification analysis methods like protein sequencing and x-ray crystallography.
The frog Dr. Bhasin took us to see

After the lecture, we went to the lab to set up the gels we’d use for gel electrophoresis. After pipetting our DNA into the small gel wells (it was my first time using a vertical gel, so it took me some time to get the thin pipette tip into the well), we ran our gels and went out to lunch.

Dollar Milkshake Day! Ice cream every day and milkshakes every Wednesday makes for a very happy—though very unhealthy—student.

After Kaitlyn, April, Peace, and I grabbed milkshakes at Einstein Bagels, we went back to the building and talked to the rest of our classmates. I stand by my theory on how labs, tests, and quizzes always bring a class together. Our class is no exception to the rule.

"Gelyonce", our gel
Once in lab, we analyzed our DNA for the D1S80 locus, which has VNTRs (variable number of tandem repeats) that are analyzed and used for human identification. Based on the number of bands I had (1), I found out that I’m homozygous in the D1S80 locus. Having hands-on experience with gels as well as analyzing the bands will prove highly helpful if I decide research is the career path for me. We also said our goodbyes to Dr. Bhasin (she hugged me!). I’ll miss her.

I went to my dorm after lab, read some of the Stem Cells and Cloning reading material I’ll use for my book report, took a twenty minute nap, and went to the Dining Commons at around 6:15 PM.

Today was a relaxed day. I know these next few days will be the calm before the storm… The storm of book reports, oral presentations, research papers, news article presentations, and exams. I’m preparing for it all by doing my readings, planning my paper and presentation with April, and studying with the cohort. I wonder what new adventure is in store for me tomorrow!
Taking a quick study break

The Love of the Game

Evan getting ready to work on our story.
I woke up late today, at 8:40 AM. I missed breakfast because I didn't have enough time to eat. I was in a hurry and I had eight minutes to get to class. Fortunately, I got to class on dot at 9 AM. We started doing our journal from 9 AM to 10 AM. Achy told us to stop and started talking about the elements. She told the class that in our road story we are missing the point of the elements. One story would have the desire, but it won’t describe the obstacle and how they are going to overcome it. 
The view on fifth floor.
Another story would have the obstacle and the plan, but there will be no consequences or failures. Achy told the class that we need to take control of the POV character, that they are the one driving the story. She also said that the obstacle is divided in two, either fear of what would happen if the plan fails or a promise of what would happen if the plan is successful. Then, she let us go, and we needed to revise our story with our group. Before Achy let the class go, she change one of our team member and we needed to work with “fresh new blood”. 
Dining Hall
Achy changed Lisa out of our team and our new team member was Wendy. At first, I was like what is she doing this is not going to work, but then I realized that it was a great idea. Wendy was able to tell us what was wrong with our story and things we should add. We needed to finish revising before 2 PM, and send it to Achy email. I took a break to go eat lunch, and then went back to the fifth floor Wendt lounge. My team and I end up finish revising at 1:55 PM, and we needed to hurry up because class was about to start. We got to class and Achy asked us what we changed in the story. My group and I added that the teddy bear, Mister, could move just like a Toys Story movie. We made Mister to be more control of his actions. Then, Achy let us out because we need to work on our personal story. 

On my way to my room, I was walking with Evan and Robert; we are the only guys in the class. They asked me if I have started on my story and I told them no. Robert gave me a good advice; he told me that I should write something I really love. When he said that the first thing that pop in my head was soccer because that’s something I really love and enjoy playing. Robert also told me that if you write something you love, I would have more fun writing about it and it would be easier. I already have the title of my story, “The Love of the Game”.  I was brainstorming, but I didn't get a lot of stuff down and it was time for me to go with Pamela.

International House
I walked to the International House that is ten minutes away from the dorms. The first thing that Pamela asked me was if I did my homework yesterday night. It was a quiz about knowing what kind of learner I am; if I am a visual, audio or a physical.  Physical learners do: move around the room to revise, revise while jogging, swimming, or cycling, add actions to key points, when testing myself – if I make a mistake, do a push up, sit up or some other light form of exercise for a few seconds, and make sure to get plenty of exercise between revision periods to reduce stress. Then we brainstorm for ten minutes and she timed me. It was a fun exercise because I needed to remember my whole life from childhood to present. I needed to do this because I’m going to talk about how I started loving soccer. I like the exercise because it showed me that I am really good at saying stuff out loud and not on paper. Pamela also gave me a website called OWL, to work on my fragment and run-ons sentences. She gave me an assignment to do on the website and tomorrow we going to go over it. 

Later on, I went to play soccer with some of my peers that goes in the midway where there’s grass. I was enjoying playing with them, but then, my legs started hurting and I could of barely walk. My leg was hurting a lot that if I bend it would give me a big pain that I couldn't handle. I stopped playing and started stretching my leg. I decided to be goal keeper instead because I wasn't able to run. It was getting dark and I stopped playing because I have homework to do.
I went back to my room and started working on the assignment that Pamela left me. When I finished the assignment, I received a text from Alexa, telling me that she was in Keller lounge with the rest of the girls. I came down to meet them and started working on my homework and having conversation with them. That’s how I ended my night. 
Chicago Family

Getting Ready for Experiments

This morning I woke up on time (luckily), and went down to breakfast, where I met up with Esin and Sheila. Esin is taking Green Business and sustainability with Oyin, and Sheila is taking the Physics of Stars. We know each other because we have the same RA. After a quick breakfast, I went to class. 

Today in class we discussed more about language and Cassie asked us some basic questions about languages that were surprisingly difficult to answer simply. These were questions like, "Who has language?", and "When does someone have a language?” 

Before we could start answering these questions, she told us to put everything on our desks away because we were about to start our first pop quiz. This is the first of three that we have been promised. I did not think the test was too hard, but we will get the results tomorrow. It was quick, about fifteen questions in ten minutes about for everybody to finish. Some were multiple choice, and others were short answer, but all of the questions were on subjects that we had definitely learned in class. Some of the harder questions for me were putting a name to an experiment because that is more memorization than anything. Hopefully I did well, and I will find out tomorrow.

Alex the African Grey Parrot
 We discussed much more about language today, and what constitutes language. A lot of the first half of the day was spent speculating about special cases where animals seem to be able to speak (in the case on an African Grey Parrot), or sign (in the case of an orangutan). These animals were able to answer simple questions and communicate to some extent with humans, which was just amazing to me. Later though, we discussed if what these animals were doing could be considered language. In the end, one of the stronger arguments I came up with for why it should not be considered language is because while these animals can use it to communicate with humans, they do not use sign, or human language to communicate with their own kind. They already have their own species-specific form of communication that we do not consider language. They have no need to communicate with each other with what humans consider language if they already have their own system. Some of the things we use to define language are syntax and grammar. 

Chantek the signing orangutan

 After this language discussion, we broke for lunch. Instead of going to the dining hall like usual, Eugenia, Catherine and I went to a cafe in the quad. I bought pad Thai and tea, and we ate on the grass. Back in class again, we spent the rest of our time in our research groups, finalizing our scripts, questionnaires, consent forms, etc., for the experiments. We were told that we would probably have about six participants to work with for our study. Since we are all very knew to this experience in our group, less kids is probably better and more controlled. I feel nervous to start the experiment, but also excited because it allows us as students to become much more involved in what we are learning. We are also writing a research paper on our study, so it is like a mini version of an actual study with a research paper that gets published. 

We were allowed to leave at around four, and I walked back to the dorms to Dani's room where the four girls in the cohort worked on homework together. Soon, it was six o'clock and time to head into the city to get some deep dish pizza with Alie for dinner. We ate at a restaurant called Gio's Pizza, and we ordered Veggie pizza, which I ate, and a pizza with meat in it. It was really good and very filling, but with the six of us, we nearly finished both pizzas.

 After our dinner, we headed back to campus to work on our homework and to blog. Tomorrow is the last day of class before we start our experiments with the kids.

A Possible Field for my Future--Forensics!

Dr. Bhasin’s lecture today was on forensic sciences. She told us about the abilities and limitations of two types of forensic DNA testing. RFLPs (restriction fragment length polymorphism) require larger amounts of DNA that can’t be degraded, while PCR (polymerase chain reaction) requires less DNA that can be partly degraded, though it’s sensitive to contaminating DNA.

We discussed DNA fingerprinting, the extraction of DNA (can be done chemically or mechanically [the French press method—apply pressure with your hands!]), and well-known case studies that have used forensics to solve criminal cases.

One of the cases was the Narborough Village murders. Two girls in the UK were murdered, resulting in the analysis and comparison of 5,500 samples from suspects in the area. However, none of the DNA profiles matched the DNA found at the crime scene. Police later found out that the real perpetrator (Colin Pitchfork) had his friend donate DNA in his place. When the police tested his DNA, it was a complete match.

Another application we discussed was identifying remains of 9/11 victims. Dr. Bhasin told us how forensic scientists set up booths around the city that would receive cheek swabs and personal items from families so they could identify their relative’s body.

I love forensics. I really do. I found out I was interested in criminal justice after taking a Criminal Law class last semester, and consider it one possible area I’ll study in college. This Biotechnology class has shown me how much I enjoy working in a lab as well. Shows like Bones and CSI: Miami have always made a part of me enjoy the thought of being a forensic scientist, but until taking this Biotech class, I never really thought it feasible. Forensics will definitely be one of the top three majors I’ll consider in college.

After taking our lab protocol quiz, my classmates and I extracted our cheek cells and set up a PCR reaction to amplify the D1S80 locus. Tomorrow, we’ll set up our gels, run them through gel electrophoresis, and analyze our DNA. I can’t wait for tomorrow’s lab; being able to analyze my own DNA was one of the reasons I chose the class in the first place.

Lunch was delicious, as usual. If I attend UChicago in the future, the birthday cake ice cream will be a problem (Freshman 15, anyone?).

The afternoon portion of class consisted of a How to Write a Scientific Paper presentation by Ciara and a discussion on our latest reading material, New Life for Ancient DNA. The paper talked about the ancient mammoths cells and how two groups of scientists have collaborated to piece genes from ancient remnant DNA, insert the genes into living cells, and coax the cells to re-create the proteins. We talked about the relevance (we learn more about these ancient proteins which we may someday need! We can use this technique not to necessarily bring back extinct species (which I think, though extremely interesting, would slightly be a waste of money and resources when we can study proteins instead) and ethics of actually “bringing a mammoth back up from the dead” (what about the mammoth? How will we care for it? How will it sustain itself? Isn’t the mammoth gone for a reason? Bringing an extinct species back would require a lot of work. Anyway, finding accurate and complete enough genes to bring mammoths “back from the dead” would be extremely rare).

Besides talking about the hemoglobin found in cold-adapted mammoths (three amino acid mutations allow the hemoglobin to release more oxygen, which allowed mammoths to keep their extremities warm without having to use as many calories) and the blonde hair they had (the blonde hair scattered radiation to their skin, which is absorbed as heat), we got sidetracked and talked about Mars and setting up cold-adapted cows in Mars (random, I know. I'm just glad our class is becoming friendlier to each other).

Finally, I went home (home! I think of South Campus as home now!) and relaxed before getting some pizza with the cohort at Gino’s East. It was so fun! The deep dish pizzas took about 45 minutes to cook, but it felt like no time at all with the cohort and Alie. I love how I've found a sense of community, a possible field of study, and new friends at UChicago (and it's only the second week!).
"It takes a long time... Relax!" 
So delicious (though I think I might like Giordano's better..)!
Studying in the Halperin Lounge