BIOL368/S20:Class Journal Week 2

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Karina Vescio

  1. I learned that deciphering the genetic code was a group process comprising of many different people from different fields of study. Also, that all forms of life on this planet use the same language when it comes to genetic code. I also learned how DNA relates to computer code.
  2. I had a hard time understanding the Nirenberg article as he discussed that "poly(U)stimulated the binding of radioactive polyphenylalanine-tRNA to ribosomes". Other aspects of the article were difficult to follow. I had to re-read the concepts several times. It would have been beneficial if he had given more background information that can be understood by people who are not well-versed on the subject.
  3. DNA is a type of code, similar to computer code. The genes are surrounded by sections of DNA that are not transcribed, similar to lack of transcription in computer programs. For example, when someone leaves a comment, but it is not seen or is ignored. Another way in which DNA is related to computer code is the way a computer will copy a disk or drive. The computer copies certain parts of the information on the drive, and sends them to other parts of the computer. This is similar to how in the cell, some of the portions of DNA are selected and sent to other parts of the cell as mRNA.

Kvescio (talk) 14:37, 29 January 2020 (PST)

Christina Dominguez

1) The biggest discovery I made from these readings was in terms of the scientific method and the mentality of a scientist. Marshall Nirenberg goes into detail of his desire to be involved in the research of a problem that is important to the scientific community. He also speaks of the fear that he had of failing. I found this to be refreshing in an article that speaks to the scientific results while still still addressing a very personal side to the process of researching.

2) The parts of the readings I understood the least were the methods and results of Nirenberg's work. It was very descriptive and had many moving parts to it. In the Kaji reading, it was also difficult to understand the full results that were obtained. I found myself having to reread it a couple times in order to get a better understanding of what had happened.

3) The genetic code and computer code are very similar. The genetic code guides all life as it codes for specific proteins and functions that create a system that works. Just like the genetic code, computer code creates a set of rules that are to be exactly followed in order to produce specific functions that work in a greater system. These codes are both able to function due to the set of rules and commands that they stand for, which must be followed in order to work properly.

Cdominguez (talk) 12:30, 29 January 2020 (PST)

Madeleine King

  1. What is the biggest discovery that I made from these readings?
    • The biggest discovery I made from these reasons were a lot of the facts about discovering the genetic code. I didn't know that the genetic code varied in some organisms, for example Mycoplasma. However, I learned in my Microbiology class that they have a very small genome (<1000, so maybe that has something to do with it. I also did not know that tRNA was discovered before mRNA; I just assumed they were discovered in linear order. I also didn't notice that amino acids with similar genetic code have similar properties. For example, the hydrophilic amino acids have A as a second base, and the hydrophobic ones have U as their second base. It shows that the code isn't random whatsoever and has a certain pattern. This makes it helpful if a hydrophilic amino acid was mutated to another hydrophilic amino acid, since the change would be relatively small.
  2. What part of the readings did I understand the least?
    • I had a little bit of difficulty reading the Nirenberg article, just because it was hard trying to visualize the experiments in my head. However, he explained nicely what they were trying to do and how they ran the experiments.
  3. What is the relationship between the genetic code and a computer code?
    • In the Moody article, he compares the genetic code to computer code. He emphasizes that DNA does not store information physically (for example the gene for encoding a purple protein isn't purple), but through information it encodes it by combinations of 4 nucleotides. In this way it is similar to computer processing. The code for a computer program isn't physically in the computer, but the information it contains encodes it by coding. He also shows that technically any DNA code can be converted into computer code by assigning conversions. He also makes the analogy that ribosomes act like the processing unit in living organisms because they make proteins which carry out certain functions.

Mking44 (talk) 14:13, 29 January 2020 (PST)

Maya Paniagua

  • What was the biggest discovery that I made from these readings?

I learned from the Nirenburg article how he discovered that mRNA existed and was used to make proteins! He did so by running a "sensitive assay" that demonstrated RNA was in fact responsible for the addition of radioactive amino acids when making a protein.

  • What part of the readings did I understand the least?

When reading the History of Deciphering the Genetic Code: Setting the Record Straight by Akira Kaji and Hideko Kaji I did not understand the why behind their methods. More specifically why did they want an extract with ribosomes containing poly (U) and what is sucrose-gradient centrifugation?

  • What is the relationship between the genetic code and computer code?

Moody states in his article that DNA is a computer code. He states that DNA itself is the message. The cell functions because DNA tells the cell through its own language of nucleotides what to do. Similarly, computer code tells a computer how to function.

Mpaniag1 (talk) 15:22, 29 January 2020 (PST)

Annika Dinulos

What is the biggest discovery I made from these readings?

  • The biggest discovery I made was more of a surprise. When reading the Nirenberg article, I was interested to learn that it took around a year and a half for the first definitive demonstration in vitro of mRNA to be discovered, which came about after the previous experiment need a more sensitive assay. Nirenberg stated that the techniques that needed to be changed were trivial, and I was shocked to learn that a few small changes could greatly impact the outcome. In science, I find that people try to make big changes to make big discoveries, but while it took a long time, the evidence and solutions were closer than originally thought.

What part of the readings did I understand the least?

  • It was a little difficult to understand the importance of The Kaji article, and the importance of the ribosome-recycling factor. I think the authors were trying to make a correction to the Nirenberg article, but the information included in the correction was hard for me to understand. Kaji mentions that the way that RRF ribosomal binding is different than tRNA rinding, but that the structures are almost identical. I do not have a clear understanding of the importance of this specific distinction of the RRF, and what the corrections mean for the original article that Nirenberg wrote.

What is the relationship between the genetic code and a computer code?

  • The relationship between the genetic code and a computer code is being able to take the genetic code and functionally manipulate it with computer code to observe changes. Programs were developed to construct specific proteins, change their sequences. Scientists are now able to manipulate and analyze DNA to make new discoveries when paired with the functions of computer code. Computer code, similarly to genetic code, is a bunch of information that gives rise to a program or process. The genetic code works in the same way, the information of a genetic code is used to create pathways and systems that organisms use.

Adinulos (talk) 15:33, 29 January 2020 (PST)

Nathan On

What is the biggest discovery that I made from these readings?

  • The biggest discovery I made from these readings was the immense amount of work that Nirenberg as well as many other scientists had worked on to decipher the genetic code. When I had learned about Nirenberg in Genetics class, I did not realize how many different experiments and variations had to be done just to even think about solving the problem.

What part of the readings did I understand the least?

  • I did not understand the Kaji "correction" article made in response to the Nirenberg article, as I did not understand exactly what or why the record was being corrected.

What is the relationship between the genetic code and a computer code?

  • Both the genetic code and computer code can use the idea of binary to code for simple ideas. As a result, the transition between computer code and genetic code is relatively straightforward and allowed for the computational analysis of the genome.

Non (talk) 22:04, 29 January 2020 (PST)

Drew Cartmel

What is the biggest discovery that I made from these readings?

  • The biggest discovery that I made from these readings was that there is a very strong relationship between the concepts and functions of computer coding and DNA processing. Both processes are very intricate and are critical for the proper functioning of larger systems/organisms.

What part of the readings did I understand the least?

  • The part of the readings that I understood the least was the part of the Nirenberg reading that mentioned the concept of poly(U) and poly(A) helices not being able to function as mRNA, whereas single stranded poly(U) having the capability of functioning as mRNA. I am a little confused as to the reasoning behind why such interactions exist.

What is the relationship between the genetic code and a computer code?

  • A genetic code refers to DNA, which acts as a sort of blueprint or guideline on how the various cells/proteins of the body are made and how certain functions are to be carried out. A computer code is similar because it encodes for information or particular functions that are to be performed by computer systems. Both genetic codes and computer codes need to be read/processed in various ways in order for the information they encode to be utilized within the larger systems they are associated with.

Dcartmel (talk) 19:32, 29 January 2020 (PST)

Nicholas Yeo

What is the biggest discovery that I made from these readings?

  • I made two discoveries that were interesting to me. I never thought to relate computer code to that of the genetic code. We throw around the term “code” when mentioning these terms separately, but it never occurred to me to see how they were related. I thought that it was interesting that the code that is built into us can be similarly used to power technology that has the capacity to drive entire organizations, and more so, our entire species forward. The second discovery that I made was how research was back when scientists were trying to crack the genetic code in the Nirenberg article. I got a glimpse of the collaboration, dedication, and reasoning that it took to work in a lab of that caliber. It makes me appreciate the knowledge that is already accessible to us.

What part of the readings did I understand the least?

  • I personally had a significant amount of trouble reading the article by Marshall Nirenberg. Although interesting, his experiments were very confusing. I could not seem to visualize them and I did not know many terms that he was mentioning. The terms seemed to be mentioned with the assumption that the reader had previous knowledge about them, which most of the time, is not the case.

What is the relationship between the genetic code and a computer code?

  • The genetic code operates the way it does because it is made of four letters, or nucleotides, in different combinations that lay out the blueprint for the production of proteins, which then carry out all of the functions within the organism. Similarly, computers run on a binary code, and the sequence in which they are typed, or synthesized, tell the computer to carry out a specific function. The code that we use to run our major processing systems is run in an almost analogous way to the natural code that governs our bodies.

Nyeo2 (talk) 21:44, 29 January 2020 (PST)

Sahil Patel

  • What is the biggest discovery that I made from these readings?
    • My biggest discovery in these readings was in the Moody piece. I was fascinated to see that during Watson and Crick's discovery of DNA, the general conception was that DNA's essence was in its shape and physical characteristics rather than looking at the heredity and uniquely inquiring about the information encoded by 4 nucleotides.
  • What part of the readings did I understand the least?
    • I did not quite understand what the adapter hypothesis was in the Kaji reading but then I did some research and educated myself.
  • What is the relationship between the genetic code and a computer code?
    • Both use a simple language formed by basic characters to create limitless outcomes and possibilities.

Sahil Patel (talk) 22:18, 29 January 2020 (PST)

Jenny Chua

What is the biggest discovery that I made from these readings?

The biggest discovery I made while reading these articles is how collaborative big discoveries in science are. That may seem like a trivial and pretty obvious fact, but solving the genetic code was like solving a bigger puzzle to assemble all the steps needed in the first place (a meta-puzzle). For example, Nirenberg cites in his reflection that he was inspired by a report by Hershey et al. that showed a fraction of E. coli RNA is synthesized and degraded by bacteriophage and another paper by Volkin and Astrachan that showed a bacteriophage infection of E. coli resulted in the rapid turnover of new RNA; both of these papers, and much more research, led Nirenberg to decipher whether RNA or DNA stimulated protein synthesis and that RNA might function as a template for such. Though today, I might read Volkin and Astrachan's paper and not think much of it, I can appreciate it for the major contribution it gave to a fact discussed in almost every biology class - the central dogma, or model, of biology.

What part of the readings did I understand the least?

I did not understand the Kaji correction article very well mostly because I did not follow the incorrect interpretation Nirenberg had made of Kaji's work or why Kaji's piece was necessary as a disclaimer.

What is the relationship between the genetic code and a computer code?

DNA, Moody argues, is a type of code - just like a computer code. DNA does not carry information, as it is the information itself. This information will later be transcribed and translated into simpler or more complex "readings" that a cell will carry out to produce proteins, which have many vital functions in the body to keep an organism functioning. A computer code also is purely information; for example, I can place three apostrophes in the front of and in the back of a word that I am typing in a code and while this does not look like it now, that code will be read by my operating machine and translated into making the word bold as a final step. Thus, both the genetic code and a computer code are informative messages to be read by larger operating systems and translated into more complex or higher-level functions for an intended purpose(s).

Jennymchua (talk) 22:51, 29 January 2020 (PST)

Jack Menzagopian

  1. I did not know how much work was put into deciphering the genetic code until I read the Nirenberg piece. The level of detail he went into about what methods he used and who he worked with and for how long is something that is omitted in classroom discussions about the history of the genetic code, and although I can see why, it was nice to get a glimpse of the thought process of someone who made one of the most significant contributions to the field of genetics.
  2. I found the Kaji piece as a whole to be the most difficult to understand, and I think it is because it is so short. Even after reading it again a few times I do not quite understand what he is saying about the poly(U) sequence. His complete work that was cited by Nirenberg would probably provide the much needed context to make this piece more clear since he is responding to Nirenberg's use of that paper.
  3. Genetic code and computer code both use a few characters to code for a multitude of things. The genetic code is made up of the same four nucleotides but, depending on how they are arranged, they can code for many different proteins that perform different functions. Similarly, computers operate on a binary code that can code for many different functions depending on the sequence that 0 and 1 are arranged in.

Jmenzago (talk) 22:54, 29 January 2020 (PST)

Lizzy Urbina

  1. The biggest discovery for me was to realized the amount of hardwork it took to develop a system that looks simple and it is so used in today's science. Additionally, the way scientist came up with ideas and getting a sense of how they think and how big theories in science are formed was fascinating. Morever, to appreciate the tools we have today to do science and appreciate the work done of other scientist.
  2. I did not undertand Kaji's article, and the correction or clarification it was presented. I got lost in the different manes and function they represent.
  3. The relationship between genetic code and computer code is that both have encripted information. Both have organized systems to store this infomation, that later must be trancribed to generate a fucntion. Therefore, what might look like simple letters, number or characters that could not make sense by itself, when the proper process of transcribing them; information is revelaed and a function is perfomed.

Lurbinah (talk) 23:45, 29 January 2020 (PST)

Carolyn Egekeze

  1. The biggest discovery that I made from these readings is that understanding the genetic code was a very collaborative and competitive process for the scientists involved. I was surprised at how many researchers were willing to help Nirenberg as he and his team worked to understand how the genetic code works by developing new techniques, allowing him to come research in their lab, providing materials, and just being supportive overall.
  2. The part of the readings that made the least sense to me were the moments that Nirenberg explained the experiments he and his team carried out to attain all of the amino acids, the possible triplet codons that could code for amino acids, and figure out which codons lead to which amino acids. I think the experiments are very interesting, but I do wish I could understand them more.
  3. Both the genetic code and a computer code share the fact that they are largely simple but can be arranged in a way that allows them to convey a great amount of information. Computer code is binary, and the sequence/writing in the lines of code can determine how the program will work. The genetic code is comprised of four nucleic acids in DNA, which correspond to 4 nucleic acids in RNA (5 nucleic acids total between the two molecules). The acids can be arranged in a sequence that can produce different functional proteins depending on the sequence. Because both DNA and computer codes are information, they work to direct larger systems and processes in analogous ways and are more similar than they initially appear to be.

CarolynCarolyne (talk) 23:51, 29 January 2020 (PST)