Difference between revisions of "Class Journal Week 2"

Revision as of 05:33, 15 September 2015

Mahrad Saeedi

1. What is the biggest discovery that I made from these readings?
   • The biggest discovery I made from the readings was that prior to the deciphering of the genetic code scientists proposed very advanced, complex codes of their own. They expected the code to be so intricate, and it actually turned out that the real code was actually simpler than they initially thought, which is quite ironic. I found it funny how it said they were disappointed when they discovered the actual code.
2. What part of the readings did I understand the least?
   • I had a very hard time following the 'History of the genetic code: setting the record straight.' I don't really understand what this article is discussing and the problem it is addressing. I don't even quite understand the procedure they are discussing; was their experiment a continuation of Nirenbirg's or did it simply happen to further delve into the topics Nirenbirg researched?
3. What is the relationship between the genetic code and a computer code?
   • The genetic code can be seen as a specific sequence of programming which is necessary in order to produce the functions they encode and to also carry them out. It's the understanding of how a cell uses this DNA code to produce certain affects just as recognizing a specific computer code in order to understand its programming affects.

Msaeedi23 (talk) 20:45, 14 September 2015 (PDT)

Nicole Anguiano

1. What is the biggest discovery that I made from these readings?
   • The biggest discovery that I made from these readings was the existence of selenocysteine. Coded by UGA (typically only a termination codon in the majority of organisms), it is only differentiated from the typical termination codon by a hairpin loop in the mRNA. The fact that such a tiny difference in the structure of the codon makes such a dramatic difference was incredible to me, especially considering the fact that in the organisms with the selenocysteine, UGA also codes for a termination codon when it does not have the loop (Brown, pg 14).
2. What part of the readings did I understand the least?
   • Many of the details of Nirenbirg's experiments were very confusing to me. While I understood the overall purpose of the experiments and the results found from them, the exact details of the methods of the experiments were difficult for me to understand.
3. What is the relationship between the genetic code and a computer code?
   • The genetic code can be represented in binary, the language of computers. Each nucleotide can be mapped to a binary sequence (for example, A - 00, C - 01, G - 10, T - 11). With this mapping, the genetic code can be represented equivalently in binary. DNA can be considered like a large computer program that serves not only the purpose of storing data, but also running the functions that determine the actions that a particular cell will take, the proteins that will be created and relatively how much of them should be, and also regulates itself to determine which functions need to be run at any given time (Moody, pg 3).
   • Considering DNA as a program, it can be thought that the DNA is a program written in a higher level language. The RNA is what is created when the program is run - it is the assembly or machine code that is then processed by the computer. The proteins then are the results of the program, for example, an output on the screen or a change in a GUI (Moody, pg 4-5).

Nanguiano (talk) 11:29, 9 September 2015 (PDT)

Emily Simso

1. What was the biggest discovery that I made from these readings?
   • The biggest discovery for me was from the article "Ode to the Code" by Brian Hayes, specifically that the genetic code is so resilient to substitutions. I thought it was interesting that the experimenters arranged the amino acids according to their polar arrangement to judge whether the code dealt with permutations. It seemed incredible that the genetic code could do better than a million other random codes, showing nature's role in creating the code.
2. What part of the readings did I understand the least?
   • There were sections of the Nirenberg reading that were hard to follow, such as when he described the techniques he used to find mRNA "in vitro." While I feel that I understood the general points he made, the details were a little too complex, such as the relationship between C-labeled valine and mRNA. The graphs were somewhat helpful, but I feel like I don't have a full grasp on the experiments.
3. What is the relationship between the genetic code and a computer code?
   • I thought the Moody reading was helpful for this question. He states that genetic code and computer code are "completely equivalent," since a binary can be assigned to the four bases (4). Genetic code and computer code are also similar since they both allow for "programs" to run, which are dependent upon the exact order of the individual units (5). Both types of code allow for a variety of functions as well, but when a mistake occurs in the order of the code, the function either changes or does not run correctly.

Emilysimso (talk) 10:29, 11 September 2015 (PDT)

Kristin Zebrowski

1. What was the biggest discovery that I made from these readings?
   • The biggest discovery I made from these readings was the notion that the antisense strand might have a more significant purpose than just being a placeholder, which was addressed in "Ode to the Code" by Brian Hayes. I found it interesting that the antisense strand creates an antigene that is opposite of the normal gene--I didn't know that before. It also opens up the door for a lot of opportunities for studying the genetic code by showing that it might code for more than just protein synthesis, which is something I hadn't thought of before, although it makes sense now.
2. What part of these readings did I understand the least?
   • While at first I understood Nirenberg's methodology, it was eventually very difficult to follow the techniques he and his colleagues were using to decipher DNA, such as Heppel's synthesis of "trinucleotides and higher homologues" and the significance that the many different experiments had. This made it more difficult to understand the implications of Akira Haji and Hideko Haji's corrections in response to Nirenberg. It was interesting to read about the collaborative effort involved but I feel as though the details of the many trial-and-error experiments conducted in the process made me lose sight of the big picture until the final paragraphs.
3. What is the relationship between the genetic code and the computer code?
   • The genetic code stores information and instructions just like a computer code does and it can be translated into a binary code, despite DNA being encoded by a 4-nucleotide sequence. DNA is a program that runs a cell like a computer code runs a computer and it is capable of being copied. Like all software, DNA can have "bugs" or errors in the form of mutations.

Kzebrows (talk) 21:03, 13 September 2015 (PDT)

Brandon Litvak

1. What is the biggest discovery that I made from these readings?
   • One of the things that really surprised me in the readings was the fact that the genetic code is neither universal nor applicable to all proteins. Section 3.3.2. from Genomes mentions that context-dependent codon reassignment is widespread and applies to a variety of organisms; it was fascinating to learn about the factors (hairpin structures, protein interactions along the mRNA) that further complicate the genetic code. I would say, however, that my biggest discovery was learning that the natural genetic code is the best (or very close to the best) possible code for error minimization. The evolution of this “optimum” genetic code, through the course of billions of years, is really remarkable.
2. What part of the readings did I understand the least?
   • The readings exposed me to a lot of new technical language relating to protein synthesis and its underlying biochemistry and, while it was interesting, it made some of the articles relatively difficult to understand. The article by Marshall Nirenberg employed a lot of unfamiliar terms, which made some of his methods and strategies a bit unclear for me. I don’t feel like I have a good understanding of his cell-free synthesis system (and how exactly he manipulated it). Nirenberg’s descriptions of the experiments/methods of his contemporaries also seemed confusing. Overall, the core message of each article was fairly clear, despite the new language.
3. What is the relationship between the genetic code and a computer code?
   • DNA, essentially, is biological computer code. Like computer code, the genetic code can be executed to perform many (and a variety of) operations. Cells contain ribosomes that are much like the processing units found in computers; the DNA code acts on the ribosomes to cause certain actions that lead to a certain physical output (protein). Like code, DNA can be used, in certain situations, for very specialized purposes (maintaining the “form and properties” of specialized cells) and stay unexecuted in other situations. Being “digital”, DNA can come to have errors or “bugs” which can prove disastrous/harmless.
   • Powerful computers, computer code, and programs, interestingly enough, are the perfect tools for DNA analysis. Computers, via the field of bioinformatics, are being employed to store, search, and compare massive sequences of DNA. Computer code achieves what people cannot: it is able to work with the vast amount of information that is DNA.

Blitvak (talk) 00:45, 14 September 2015 (PDT)

Jake Woodlee

1. What is the biggest discovery that I made from these readings?
   • The biggest discovery that I made was that the genetic code chart that was handed out to us isn't a universal chart. There are exceptions to the rule, even in the human body one codon may generally code for one amino acid but in some cells that particular codon codes for something else entirely.
2. What part of the readings did I understand the least?
   • I had difficulty understanding the biological jargon that many of the biologists threw around in their research papers. This includes methods they use to do their research and at times it was difficult to follow because in order to understand the next part of the paper we needed to understand the preliminary parts. Specifically phrases like sucrose-gradient centrifugation, ribosome sedimentation, polysomes, deacylated tRNA, etc. Usually esoteric phrases can be figured out with a quick google search but it just took too long to look everything up. The article in question really just is "The history of deciphering the genetic code:setting the record straight", but there were other concepts in other papers that weren't completely absorbed.
3. What is the relationship between the genetic code and a computer code?
   • There are several similarities drawn between genetic code and computer code in the reading. DNA stores information with 4 characters while computers only store information with 2 characters, but representing DNA in binary is a simple task: 10 00 11 01. To further highlight similarities, DNA between genes is compared to comments, and DNA sequences are compared to programs as they are sent around the cell/computer. Also, DNA can have mutations which act much like bugs in computer programs and can have disastrous results. Also, computers allow for relatively easy handling of massive amounts of genetic data, without them biologist's jobs would be much more difficult.

Jwoodlee (talk) 09:01, 14 September 2015 (PDT)

Kevin Wyllie

1. What is the biggest discovery that I made from these readings?
   • This might be more of a small detail than a profound, grandiose discovery, but I was previously unaware of "context-dependent codon reassignment." Even after the molecular biology unit in biochemistry, which went a lot more in-depth on molecular bio than I had ever gone before, I have never heard of this. Not only is it interesting to see flexibility in the genetic code within an organism, but the example provided (a codon yielding selenocysteine) was particularly fascinating because the codon in question is usually a stop codon. It sounds like the bioinformatic implications of this would be a nightmare. Hopefully I can avoid Mycoplasma in any future bioinformatic projects that I may be involved in!
2. What part of the readings did I understand the least?
   • The Nirenberg article was very confusing, both in terms of the explanations of the experimental methods, and the figures themselves (Figures 2 and 7 were particularly difficult to interpret). On top of that, Nirenberg mentions "DNA/RNA from ribosomes" multiple times, which I'm entirely clueless on, as neither nucleic acids comes "from" ribosomes (excluding rRNA, which I'm fairly certain he isn't referring to). To my knowledge, ribosomes don't even interact with DNA.
3. What is the relationship between the genetic code and a computer code?
   • Moody's first comparison between the two involves their characters. Although computers are binary (so a computer code, on the most fundamental level, consists of 1's and 0's) and the DNA code is not (with four characters), the DNA code can easily be mimicked in binary by thinking of one piece of information as two digits instead of one (00, 01, 10 and 11 can each correspond to a nucleotide base). Another similarity between the two is that they store information "digitally" which allows for copying in mass quantities without introducing any decrease in quality. Moody also draws an analogy - albeit, briefly - between non-coding DNA sequences and comments in computer code which aren't apparent when actually running the program. Also, he points out the parallel between mRNA and wires, in that they both are mediums for converting a digital code to an analog signal. Continuing the analogy, he points out that the entire genome can be thought of as an operating system, which does employ some programs all of the time, but has others which only need to be run to accomplish a particular task (like how cells in the muscles need to contract, but others may not). However, one difference between the two that Moody implicitly points out is the accessibility of the information. (In eukaryotes) DNA is wound up extremely tightly into chromosomes which are ligated to other proteins, and this can make acquiring the code much more difficult than in computers.

Kwyllie (talk) 21:53, 14 September 2015 (PDT)

Josh Kuroda

1. What is the biggest discovery that I made from these readings?
   • The most significant discovery I made from these readings was that Marshall Nirenberg employed a "hacking" technique to discover the codons that produced each amino acid. It's interesting that he was able to come up with this method in the early 1960s, before computer programming and hacking was widely studied. I was also intrigued by the fact that Nirenberg decided to move on and study neurobiology after this discovery.
2. What part of the readings did I understand the least?
   • The reading by Marshall Nirenberg was relatively confusing, mostly because I am unfamiliar with many of the terms and phrasing used. It was interesting to read about the process by which he made the ground-breaking discovery, but I struggled at times with certain parts as well as some of the graphs. In contrast, the reading by Moody was the easiest to understand, because I am more familiar with computer programming, so I was able to relate to what the author was saying about the similarities between genetic and computer code.
3. What is the relationship between the genetic code and a computer code?
   • According to the Moody reading, there is a clear relationship between quaternary genetic code (A, T, G, C) and binary computer code (00, 11, 10, 01). Moody goes on to call DNA a digital program of instructions, which simply describes programs that are created with computer code. In addition, sections of DNA that are not transcribed are conceptually similar to comments that are in most computer program code. Moody also compares the CPU of a computer to the ribosome, since both seem to process the "code" inputted to them. Finally, there are sometimes small errors or mutations within DNA codes that can have disastrous results for a human, while logical or syntactic bugs in computer code can cause a program to crash or fail to finish.

Jkuroda (talk) 16:51, 14 September 2015 (PDT)

Anu Varshneya

1. What is the biggest discovery that I made from these readings?
   • The ideas that Brian Hayes mentioned in his article about primordial genetic code potentially using both strands of DNA in order to determine each amino acid was new and incredibly interesting to me. I thought it was incredibly interesting to learn that in some cases, while the sense strand produced a hydrophilic amino acid, the antisense strand would produce a hydrophobic amino acid, acting almost as an "antigene" as the article described.
2. What part of the readings did I understand the least?
   • Though the Nirenberg article was incredibly dense, and I found myself having to reread certain portions in order to fully understand the different steps of the research that he was participating in, the most difficult of the four articles to comprehend was ironically the shortest article by Akira Kaji and Hideko Kaji. This was mostly due to lack of knowledge regarding several of the terms in the paper including "sedimentation of the ribosomes," and "tRNAphe".
3. What is the relationship between the genetic code and a computer code?
   • The relationship between the genetic code and computer code was nicely summarized in the article by Moody. In his article, Moody explained the digital features of DNA in that it is copied almost perfectly consistently, with almost no loss of quality or effectiveness. He compared this to digital copies of music as opposed to analogue copies of music, which lose quality with each copy of the music. Furthermore, he compared each of the bases in DNA to binary, effectively explaining that they are just placeholders and are used in several combinations in order to produce other sorts of information. Another comparison between DNA and code made in this article was that they both act as messages, and no secret can be "uncoded" from them. Beyond the similarities between genetic code and computer code, they are important to each other in that genetic code is so vast that without computer programs, the feats in genomics in the last 30 years would be impossible. The interconnectedness of computers and DNA in bioinformatics is what makes it possible for modern day scientists to be able to determine all of the defects/mutations that could exist in DNA, their repercussions, and ultimately ways to undo or repress their potentially detrimental effects.

Anuvarsh (talk) 19:24, 14 September 2015 (PDT)

Lena Olufson

1. What is the biggest discovery that I made from these readings?
   • The biggest discovery that I made from these readings is how much effort and work has been put into the genetic code. It amazes me that humans have taken so many steps and solved so many puzzles to arrive at the conclusion of the genetic code as it exists today. The continuous trial and error performed by the numerous deciphers of the code goes to show how science is constantly evolving and new discoveries and advances are occurring everyday. With the hard work and eagerness of multiple scientists, it is possible to make valuable discoveries that are beneficial to humans as a species.
2. What part of the readings did I understand the least?
   • I had a difficult time understanding the paper by the Kajis when they expressed the materials and methods they used in their soluble RNA experiment. I was unsure about some of the language that was used in the description and therefore had a hard time piecing together what exactly occurred to produce the results found.
3. What is the relationship between the genetic code and a computer code?
   • The genetic code and the computer code are similar in many ways with a few key differences. The genetic code acts by storing information as well as instruction in a similar fashion to computer codes. The genetic code can be translated into a binary code even though the DNA is encoded with a four nucleotide base sequence. DNA is responsible for the operation and functions of a cell just as a computer code is in charge of operating a computer and running programs. Both computers and DNA can have malfunctions that result from a virus/bug or a mutation respectively.

Lenaolufson

Veronica Pacheco

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

• The biggest discovery I made during these readings were about transcriptomes, in particular the fact that transcriptomes play a role in cancers. I had taken a class a while back on how cancer is operates in the body. It barely scratched the surface but reading tapped into some depth. I found in really interesting to see that transcriptomes were used in research to help distinguish between the different types of lymphomas. The B-cell lymphoma can divide into two types. This also hits home for me because a dear friend in high school was diagnosed with Hodgkins lymphoma.

What part of the readings did I understand the least?

• I really enjoyed how the historical review was written by Nirenberg because the narrative makes it more inviting. However I could really follow the graphs for Figure 7. I understand the figure 7 explains that the experiment led to the results that the genetic code is a triplet code. I couldn't comprehend the experiment. I point out the graph because normally I am able to get a better grasp of the experiment by looking at the graph but in this case the graph let me more confused.

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

• The genetic code and the computer code are connected through their function. They both are specialized codes. Each function has their own code.

Ron Legaspi

1. What is the biggest discovery that I made from these readings?
2. What part of the readings did I understand the least?
3. What is the relationship between the genetic code and a computer code?