Class Journal Week 2

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Mary Balducci's Respones

  1. The biggest discovery that I made while doing these readings was that there was so much similarity between the genetic code and computer code. I've taken biology courses before, so I knew that DNA worked using four letters that coded for proteins. However, I've never taken a computer science course so I never really understood how computer coding worked. It was interesting to read the connections made in the Digital Code of Life between the two. I think this has also given me a better understanding of computer coding, since I can relate it to something I already know about.
  2. The thing I understood least from these readings was at the end of the Ode to the Code article. Hayes talks about the fact that there are 64 codons, but only 20 amino acids. One of the proposals for the organization of these is the 2x2x2x2x2x2 hypercube. I am confused about what this would look like, and how does it get across information differently than the 4x4x4 cube currently in use?
  3. The genetic code and computer code are similar because they both code digitally. By doing this, there are less mistakes made between the information and the copy of the information. Both types of codes work by having letters or numbers that convey a meaning that the computer or cell carries out.

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Page DesiignerMbalducc (talk) 18:15, 6 September 2017 (PDT)

Katie Wright's Responses

  1. My biggest discovery from the reading was that even brilliant scientists can make mistakes and need to be corrected. I thought the communication by Kanji and Kanji about "setting the record straight" was interesting because, had I not seen it, I would have read the autobiographical paper by Nirenberg without questioning it. I suppose it is a reminder that we should question and be critical of all science, regardless of who it is presented by.
  2. I understood the readings pretty well for the most part, although I did skim through some of the biology that Nirenberg describes in his autobiographical story. I tried to focus more on the narrative than the science, since I know the basics already from my previous classes.
  3. The genetic code is incredibly similar to computer code. As Glyn Moody demonstrates in his book, the genetic code can easily be converted to binary, which is one of the most important types of computer code. Since the genetic code can be easily digitized, we can use a wide array of computer programs to study the genetic code that would not be available in non-digital systems.
    Kwrigh35 (talk) 21:00, 9 September 2017 (PDT)


Zachary Van Ysseldyk's Responses

  1. The biggest discovery I made from these readings was from the Digital Code of Life reading. Specifically, when they compared DNA’s ATCG pairings with the computer’s 0 and 1 binary code. What I found interesting was that both ATCG and binary are representations of something rather than the actual property themselves. I also realized how much computers helped with mapping out DNA considering how large the human genome is. Furthermore, I discovered that both biology and coding have a very systematic approach. I always thought biology was arbitrarily observing living cells and seeing if they can find a connection. With the introduction of bioinformatics, a clear systematic approach becomes clear when it comes to biology.
  2. The deciphering of the genetic code was probably the most academic and confusing paper I have ever read in my life. I have never had to look up so many words in a sentence. The phrase: “in the presence of a high concentration of methanol, pancreatic RNase A catalyzes the synthesis of trinucleotides and higher homologues from oligoribonucleotide primers and pyrimidine 2’-3’-cyclic phosphates” was probably the most confusing sentence I have read. The last time I took biology was freshman year of high school so I really felt like I dove in head first here.
  3. Similar to my answer to question 1, I think that the biggest relationship between genetic and computer code is how the actual coding is a mere representation of what the data actually is. Also, both codes must be very exact and precise. If there is an error, then the entire code will spew out something other than what was intended.

Zvanysse

BIOL/CMSI 367-01: Biological Databases Fall 2017

Assignments

Week 1 | Week 2 | Week 3 | Week 4 | Week 5 | Week 6 | Week 7 | Week 8 | Week 9 | Week 10 | Week 11 | Week 12 | Week 14

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Zvanysse Week 1 | Zvanysse Week 2 | Zvanysse Week 3 | Zvanysse Week 4 | Zvanysse Week 5 | Zvanysse Week 6 | Zvanysse Week 7 | Zvanysse Week 8 | Zvanysse Week 9 | Zvanysse Week 10 | Zvanysse Week 11 | Zvanysse Week 12 | Zvanysse Week 14 | Zvanysse Week 15

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Zvanysse Week 1 Journal | Zvanysse Week 2 Journal | Zvanysse Week 3 Journal | Zvanysse Week 4 Journal | Zvanysse Week 5 Journal | Zvanysse Week 6 Journal | Zvanysse Week 7 Journal | Zvanysse Week 8 Journal | Zvanysse Week 9 Journal | Zvanysse Week 10 Journal | Zvanysse Week 11 Journal | Zvanysse Week 12 Journal | Zvanysse Week 14 JournalZvanysse (talk) 21:21, 9 September 2017 (PDT)


Simon Wroblewski's Response

  1. The biggest discovery I made while reading these works were about how recent the discovery of the genetic code was and still is. It's inspiring to think about how just a few decades ago, we discovered something so fundamental and crucial to the understanding of life. I also never knew what the proteome was which I found interesting because I had no idea how much of the cell proteins actually make up.
  2. Nirenberg's Deciphering the genetic code - a personal account I found to be the most difficult to understand due to the high level concepts being discussed. I'm not sure I retained much of the information due to the complicated systems and vocabulary.
  3. I think the closest relationship between computer code and genetic code is the algorithmic processes each one undergoes to achieve their goal. It is very fitting to include the word code in each of these phrases due to this similarity.


Emma Tyrnauer's Responses

  1. The biggest discovery I made from these readings is just how important computer coding has been in deciphering DNA. Moody points out in the Digital Code of Life that while understanding the genetic code is simple in terms of pairing rules, we would not have the knowledge we do today about genomics without computer coding. This is merely because of the immense scale of genomes. I found that deciphering the DNA strand given in the individual assignment (only 60 base pairs long) was very tedious and time consuming. I also found myself making a lot of simple mistakes.
  2. The part of the readings I understood the least was the paper, The history of deciphering the genetic code: setting the record straight. I don't really follow the experimental procedure of how Akira and Hideko Kaji were able to prove that the binding of tRNA to programmed ribosomes was very specific (in contrast to what was proven by others in earlier experiments).
  3. The relationship between the genetic code and computer code is that genetic code gives the instructions and guidelines for how processes are carried out in the body, similar to the way computer code defines how programs are run. Moody describes in the Digital Code of Life that like DNA, some parts of computer code are ignored when a program is run. Furthermore, "a computer copies parts of a program held on a disc and sends them down wires to other components of the system," just like a cell copies DNA and sends it as information stored a mRNA.

Emmatyrnauer (talk) 18:34, 11 September 2017 (PDT)

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Nicole Kalcic's Responses

  1. The biggest discovery I made from these readings was the very first sentence of Hayes' article. The Genetic Code was cracked 40 years ago?! Because of my age, I feel like the things I learn about in school are nowhere near my own timeline. But, 40 years is a shorter time span than that of my parents/our university/etc. This just reinforces the idea that there are still so many things we are bound to discover, and so many things we think we know that we are wrong about.
  2. I understood Akira Kaji and Hideko Kaji's procedure the least. I understood the result but had a hard time following the language.
  3. The genetic code and a computer code are so similar, in fact, that I am now really grasping the concept of this class. They are both so precise, one error causing an entirely different makeup. We often use a computer code to understand the genetic code and because the translation of information is done in the same alphabetical/numerical way.

Nicolekalcic (talk) 20:42, 11 September 2017 (PDT)

Corinne Wong's Responses

  1. I think it’s really cool that the mitochondria have special mRNA. Not only does it go against the rules of genetic decoding, but it also makes organisms that much more unique. It’s really interesting that there are different deviations in mitochondrial RNA in different organisms, and I would be interested in learning more about why that is and about the different types of deviations.
  2. I found it difficult to understand the article about how the genetic code was deciphered. Even as a science major, the frequent use of scientific jargon is a bit overwhelming, and I have to rely on my memory of the meanings of the terms that I actually know, which makes it a bit challenging to fully comprehend.
  3. The genetic code and a computer code are pretty similar. Both of them contain an input that is read and translated to create an output, which involves the use of signals and keys. That output is then further used and built upon to create a greater working system.

Cwong34 (talk) 22:41, 11 September 2017 (PDT)

cwong34

BIOL/CMSI 367-01: Biological Databases Fall 2017

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John Lopez's Responses

  1. The biggest discovery I made from these readings came from "Ode to the Code", where I learned how error-proof the genetic code could be, other than having common mutations. The fact that the genetic code is so well structured, using the term "one in a million", I believe is extremely fascinating to emerge out of nature.
  2. Most of the "Deciphering the Genetic Code-a Personal Account" was difficult for me to understand due to my lack of a biology background and the technical terms within the text. As I read I had to perform a Google search on several of the terms
  3. The first chapter of "Digital Code of Life" draws several similarities between genetic code and computer code to conclude that they function the same. Some examples of this include the comparison between binary code and the quaternary abbreviations of nucleotide bases, chromosomes as memory, and mutations as bugs. Furthermore, he mentions that treating genetic code like computer code and using computers to understand it is essential for genomics.

Johnllopez616 (talk) 21:43, 11 September 2017 (PDT)

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Blair Hamilton's Responses

  1. What is the biggest discovery that I made from these readings?
    1. The biggest discovery I made from the readings is the idea of the genetic code being "universal" according to the Nirenberg article. As a math major, I often realize while doing proofs that sometimes my understanding of the problem can be completely different from another's. Therefore, when describing and "proving" theorems it is important that anyone can read your work and immediately know what you are trying to do. In the case of Nirenberg, it is amazing to think someone can decipher and study for years about genetic code, and then something as simple as, "can someone understand this and/or read this?" is a necessary and important step.
  2. What part of the readings did I understand the least?
    1. The Akira Kaji and Hideko Kaji article as well as the Marshall Nirenberg article were the most technical and hardest to read. My most recent experience with scientific articles was in high school where the high level language was less frequently used. Primarily language and previous biological background knowledge seemed necessary to gain a better understanding of these experiments.
  3. What is the relationship between the genetic code and a computer code?
    1. Much like computer code, genetic code relies on being precise. If you go through genetic code too quickly, important codons and amino acids can be mixed up and changed. Computer code also needs to be methodical. When writing code if you have forgotten a semicolon or a bracket the entire code can be jeopardized. Additionally, genetic and computer code are used to continue a process, i.e. for genetic code a protein is used for some part of the body, while a computer code can be used to make a calculation or simplify a task.


Bhamilton18 (talk) 21:55, 11 September 2017 (PDT)

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Quinn Lanners' Responses

  1. The biggest discovery I made from these readings was the number of factors that contribute to large scientific discoveries. Focusing mainly on the Marshall Nirenberg article “Historical review: Deciphering the genetic code – a personal account” it was incredibly to read about all the factors that went into the discovery of the process of going from DNA to protein. I was amazed that at the time Nirenberg was researching the concept of RNA (specifically mRNA) as the intermediary between DNA and protein, there were very few people working on similar projects. In fact, he stated that he was the only scientist at the NIH “studying cell-free protein synthesis” (Nirenberg, 2004). It was also interesting to read how Nirenberg was taking a big risk by exploring such a risky topic so early in his career. Finally, I was surprised by the level of collaboration that Nirenberg noted in his research. In each step of the process he reached out to one of his colleagues for assistance. This goes to show that through collaboration with several experts we can accomplish much more in our academic pursuits. However, it was also a bit interesting, especially given the amount of collaboration he had with other scientists, how Nirenberg never did collaborate with Ochoa, who was working on the same topic. Nirenberg cited the competition between the laboratories as being a driving factor in his research, an interesting thought as the idea of competition in academics is often not talked about.
  2. I was very confused by the section in the article “Ode to the Code” that talked about finding a relation between the numbers 64 (number of distinct codons) and 20 (number of distinct amino acids). This section says that in “at least two schemes, the 64 codons could specify exactly 20 amino acids” (Hayes, 2004) and goes on to explain how mathematicians worked through different proposals to prove this. However, the article did not seem to go very in depth on this topic, and I was very confused as to what exactly they found and how they found a relationship suggesting that 64 codons could specify exactly 20 amino acids.
  3. The relationship between the two types of codes is that both can be stored as simple combinations of either binary or quaternary data. Furthermore, both data combinations code for the processes that are carried out within its respective host (the computer for computer code and the cell for the genetic code).

Qlanners (talk) 22:10, 11 September 2017 (PDT)

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Arash Lari's Responses

  1. The biggest discovery for me was how recently and exponentially the knowledge of the genetic code has been discovered. Most of the stuff we’ve discovered about the human genome has been in the past 50 years. The other surprising discovery is how much genes self-correct according to Hayes’ “Ode to the Code” and how much the genes being “perfect” matters.
  2. The Akira and Hideko Kaji procedure was pretty technical and I’m not very well versed in biology so that was difficult for me.
  3. What surprised me is how logical and understandable our genetic make up is. DNA is remarkably similar to binary code in that way.

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Arash Lari

BIOL/CMSI 367-01: Biological Databases Fall 2017

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Hayden Hinsch's Responses

  1. The biggest discovery I made from these readings is the idea that along with computer programs, people can potentially simulate all sorts of possibilities in order to calculate probability of mutations in genes along with other potential calculations. In Moody's article, he speaks of the idea that once scientists understand the code of the cell, they can potentially identify problems and treat them. This caused me to think about the extreme potential of using a computer's power to identify threats and problems to DNA almost immediately with the help of computer programs.
  2. The Kajis' article was definitely one of the most difficult for me to understand. There were a lot of phrases such as "the reaction mixture was subjected to sucrose-gradient centrifugation, and the sedimentation of the ribosomes was examined," (Kaji 293) which I hardly understood. Regardless of the lack of understanding, it was nice to broaden my vocabulary.
  3. I really enjoy the strong connections that can be drawn between genetic code and computer code. They both are incredibly precise, relying on certain sequences in order to run properly. For example, if a genetic code contains a mutation, it will be expressed(or fail to be expressed) in the way the proteins are synthesized. This is alike a computer in the sense that if a single bit of code is missing, the output of the program will have a sort of "mutation" and not function properly. Moody also mentioned that it was even possibly to express the quaternary code of DNA in terms of Binary code and notice the similarities of the codes although they are expressed differently.

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Hayden Hinsch Hhinsch (talk) 23:45, 11 September 2017 (PDT)

Dina Bashoura's Responses

  1. What is the biggest discovery that I made from these readings?
    1. The biggest discovery I made was from the book "The Digital Code of Life", where the author explains the translation of DNA and what the process was like in obtaining that translation. I had always been taught about the works of Watson and Crick, but I had the opportunity to read about it in depth and appreciate the process that they went through. I especially appreciated the unique and creative thinking that they needed to have in order to accomplish such a great task.
  2. What part of the readings did I understand the least?
    1. The most confusing reading was the Transcriptomes and Proteomes. Although very interesting, I found this difficult to understand because transcriptomes were never explained fully and I was not sure how this article tied in with the rest of the articles.
  3. What is the relationship between the genetic code and a computer code?
    1. In the book "The Digital Code of Life", the author correlates the DNA genetic code to a computer code, explaining how both are deciphered and translated in order to reveal its meaning. Both use symbols to represent something. The genetic code was thought of as something that needed to be "cracked" just like a computer code, and this genetic code was inside every cell, serving as the basis for how the cell is to be run, just how there is a code within every computer determining how it is to be run.

Dina Bashoura

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Antonio Porras' Responses

  1. What is the biggest discovery that I made from these readings?The biggest discover I made was how translatable biological information can be into computer code. Just as interestingly enough, as a biology major, it surprised me when discussing the natural code in which amino acids are associated with certain letter codons and how there are endless other codes which provide superior substitutions. In simpler terms, there are endless other ways for the natural code to be designed which would be more efficient than it is presently functioning. It captures the beauty of biology and also how DNA is a living, changing, document by which mutations are constantly occurring over millions of years to repetitively improve or adapt organisms to a constantly changing environment. DNA is dynamic and imperfect in it's nature.
  2. What part of the readings did I understand the least?Even as a biology major, some of the procedures explained in Akira Kaji and Hideko Kaji's paper were difficult to understand and I can only imagine what someone who doesn't have a background in biology would absorb through reading the paper. It took myself several times to read it over to fully understand how scientists came up with the mechanism (tRNAs) by which amino acids are translated from mRNA.
  3. What is the relationship between the genetic code and a computer code?Firstly, both genetic code and computer code store a significant amount of information. Secondly, we now have the technology to have a better understanding of the complexities and vastness of genetic and computer code. Lastly, from the reading, both are susceptible to errors or in biology terms, mutations. In these ways, they are extremely similar and their relevence to each other cannot be underestimated.

Antonio Porras Aporras1 (talk) 23:43, 11 September 2017 (PDT)

Edward Bachoura's Responses

  1. Reading about how all of these scientist used computer code as a way to better understand the genetic code was news to me. I haven't really truly realized that there was even the slightest of a connection between these two very seemingly different things.
  2. I didn't really understand the approach from J. Tze-Fei Wong in American Scientist. It says that he identified the best substitution for each amino acid and compared it to the computer generated codes, but I didn't really understand how he compared them to deduce that the code has not evolved to maximum error tolerance.
  3. In the Digital Code of Life, Niremberg talks about how, in order to learn more about how an unknown computer system or program is working, it is often helpful not only to measure the signals passing through the circuits naturally, but also to send carefully crafted signals and observe the response. Niremberg did the same thing with the cell and by constructing artificial mRNA he was able to observe which amino acids were output by the cell's machinery for a given output. He was able to use computer code as a metaphor to better understand the genetic code.

Ebachour (talk) 23:50, 11 September 2017 (PDT)

Eddie Azinge's Responses

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

I had a sort of intuition for this prior to the readings, but the ease of the translatability of biological information into a quantifiable binary code surprised me. I used this knowledge to code up the solution to our Week 2 assignment, taking note of the correlation between how I would process binary code to how I was processing the genetic code, and the same logic applied. The code can be found here, and outlines an interesting method of handling the genetic code from a programmer's point of view.

What part of the readings did I understand the least?

The part of the reading that I understood the least was the article on the link between the transcriptome and the proteome. I understood the more general concepts of the section, namely being that different beings have different genomic code maps, but the level of the technical writing in the article required me to reread it several times in order to get a reasonable grasp on the topics being discussed. Specifically, I still don't really understand the process of splicing, and alpha/beta-sheets still confuse me.

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

The genetic code compresses, stores, and translates information in order to create reproducible outcomes at some later time, much like a computer program.

Cazinge (talk) 00:00, 12 September 2017 (PDT)

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