Class Journal Week 2
Contents
- 1 David Ramirez's Response
- 2 Naomi Tesfaiohannes's Response
- 3 John Nimmers-Minor's Response
- 4 Emma Young's Response
- 5 Michael Armas' Response
- 6 Mihir Samdarshi's Response
- 7 Kaitlyn Nguyen's Response
- 8 Iliana Crespin's Response
- 9 Christina Dominguez's Response
- 10 DeLisa Madere's Response
- 11 Marcus Avila's Response
- 12 Ivy Macaraeg's Response
- 13 Aby Mesfin's Response
- 14 Jonar Cowan's Response
David Ramirez's Response
User:Dramir36 template:Dramir36 Skinny Genes
- Week 1
- Week 2
- Week 3
- Week 4
- Week 5
- Week 6
- Week 7
- Week 8
- Week 9
- Week 10
- Week 11
- Week 12/13
- Week 14
- Week 15
1. What is the biggest discovery that I made from these readings?
The fact that the genetic code was barely cracked 40 years ago as stated in the "Ode to the Code" article. The process that was taken to crack the code is really eye opening of how it took five years to crack the code. That's five years of trial and error, as well as so much deep thinking by professional scientists. There is so much more of the genetic code that we do not know of, but have made so much progress in understanding that there is a translation from the language of nucleotide bases in DNA and RNA and converting that to the language of amino acids for proteins. I thought previous, that the genetic code was cracked at least two generations ago, but in actuality, was discovered during my parents' time.
2. What part of the readings did I understand the least?
The article that I understood the least was the "Historical review: Deciphering the genetic code - a personal account." Much of the article spoke about the specific descriptions of how the genetic code was cracked. I have no idea what Marshall Nirenberg conducted at the National Institutes of Health because the methods were very complex and the scientific vocabulary were advanced. Many of the experiments that were mentioned contained terms like T2 bacteriophage, which I have never encountered that organism before.
3. What is the relationship between the genetic code and a computer code?
According to "The Digital Code of Life" reading, DNA is another type of code - computer code. DNA is the message itself, where the lines of programming that need to be run for the operations they encode are to be carried out. Just as a computer program may contain comments that are ignored when the program is run, there are sections of DNA text that are not transcribed. Just as the computer copies parts of a program held on a disc and sends them down wires to other components of the system, so the cell, it seems, could copy selected portions of DNA and send them down virtual wires as mRNA. Nirenberg was able to construct artificial mRNA and was able to observe which amino acids were output by the cell's machinery for a given output. This relates to computer code in a way that if a person wants to learn more about how an unknown computer system or program is working, it is helpful to measure the signals passing through the circuits naturally, but also to send carefully crafted signals and observe the response.
Dramir36 (talk) 22:07, 11 September 2019 (PDT)
Naomi Tesfaiohannes's Response
1. What is the biggest discovery that I made from these readings?
The Brown, T.A. (2002) reading explained transcriptome and Proteome. Transcriptome is a collection of RNA molecules from protein-coding genes. These molecules are in charge of the synthesis of the product of genome expression. The proteome specifies the biochemical reactions a cell is able to produce. Both transcriptome and Proteome are a part of the what makes gene expression.
The Nirenburg, M. (2004) reading explained the steps that led to the breaking of the genetic code and how it was understood. This was done in a 5 year span (1961-1966). First the base composition was deciphered by directing cell-free protein. Second, nucleotide sequences of RNA codons were deciphered.
The Kaji, A (2004) reading explained how their work helped decipher the genetic code by providing a method (binding of tRNA to programmed ribosomes). It touched on how other researchers examined amino acid contributions to polypeptides while using heteropolymers but that the results from these studies were not consistent.
The Moody, G (2004) reading explained the "Digital Code of Life" and said how DNA is a computer code. To understand the DNA message we must also understand how the cell interprets the DNA. What purpose does DNA have? It also touched on Gregor Mendel and his discovery of heredity. He stated that traits come from parents. However, instead of mixing there was one dominant factor over the other (one from each parents). With these understandings, scientists are most equipped with understanding DNA.
The Hayes, B (2004) reading explained how although the genetic code was discovered, it is not fully understood. It also explained how a change in nucleotides, such as a single nucleotide change, will not make the same amino acid but can produce a similar one. The triplet genetic code "the diamond code" was discovered in 1955. The discovery of genetic code was made with the help of multiple researchers adding to the recognition of the genetic code.
Overall, all the reading had to do with genetic coding and how it has been discovered, but is still not completely understood today. The components of how it was discovered was touched on by each author listed above, however some being more in detail. Being that these articles are relatively recent, the latest being 17 years ago, the information presented was constructed based on previous research and discoveries, such as the breaking of the genetic code in 1961-1966 (Nirenburg, M 2004).
2. What part of the readings did I understand the least?
In the Hayes, B. (2004) reading ribosome- recycling factors (RRF) were discovered to bind to the ribosome and share tRNA-binding sites. Even with its near-perfect structure to tRNA and its ability to bind to tRNA sites why is it that it has a different function? Can it replace tRNA in any way or mimic its function?
3. What is the relationship between the genetic code and a computer code?
This was briefly addressed in the Moody, G. (2004) article. DNA was described as being a digital code by Watson & Crick. Similar to a computer code, DNA holds a large amount of information that is deciphered by the cell. The use of mRNA is essential, and although it is closely related to DNA it comes as a single strand. It too had a coding that is to be transcribed from the DNA sequence. Similar to a computer code, the genetic code has information that opens and processes more information. Without it, mRNA does not have the information it needs to transcribe. The ribosomes get the message carried by mRNA and use it to make protein. It takes the computer-like information and makes it into a product, protein. Similar to how a computer can take data points for example and make a table. Both genetic codes and computer codes work to bring about a certain product, that is only capable of being done by instilling proper function of its key parts.
John Nimmers-Minor's Response
Biological Databases
Jnimmers
Assignment Table
What is the biggest discovery that I made from these readings?
- A. I think that the biggest discovery of my reading came from learning of the history of transcriptome study's in medicine. Specifically, the study of the transcriptome in order to differentiate between acute lymphoblasts and acute myloid cells in order to create different types of treatments for each of the type of B-cell cancers as well as non-Hodgkin lymphoma. This part stood out to me because I have had a family member who was diagnosed with B-cell lymphoma, and so to hear that his treatment was a direct product of the studying of the transcription was a very significant discovery for me.
What part of the readings did I understand the least?
- A. The hardest part of the reading to understand was the Nirenberg reading on deciphering genetic code. The steps that he took to the deciphering of the code were difficult to follow giving the complex wording that he used along with the fact that this was told from a narrative point of view that was very unexpected given the nature of the rest of the readings assigned. The connects between the human information system and computer science/coding systems presented by Moody also seemed far-fetched at times, but I understand what he's conveying.
'What is the relationship between the genetic code and a computer code?
- A. Genetic code and computer code are both the transferring of information through two entirely different languages (codons, hormones, nucleotides vs. binary and coding languages). Besides this, both systems create sub units of larger processes that carry out functions. While genetic coding may create proteins for a certain function that may work with other proteins in the body to complete a great task, genetic code uses words and binary to build upon one another and create meaning and purpose for a word/input. Both are incredibly complex systems that work efficiently in the right conditions and work to build larger "bodies" using small subunits (Genetic "body"=Functioning organism using proteins and DNA for the sub units, Computer coding "body"=A website or program using programming lines and processing systems).
Jnimmers (talk) 23:43, 11 September 2019 (PDT)
Emma Young's Response
- What is the biggest discovery that I made from these readings?
- The biggest Discovery I made from these readings is really about how in such a short amount of time we have made such rapid progress in understanding how a cell functions, in relation to DNA, RNA and protiens. This really Hit me because you had Nirenberg in the 1960's just figuring out what exactly RNA was. It is crazy to think about how now just 60 years later we can decode an entire genome rather quickly, when they spent huge chunks of time on small pieces of RNA and Proteins.
- What part of the readings did I understand the least?
- The conversion of gene sequences to code is a little bit abstract to me still, most likely because for me coding is still a very abstract concept in my mind.
- What is the relationship between the genetic code and a computer code?
- Genetic Code and Computer code are both in a way a set of directions for operation. They are both of corse a form of code that for us to understand they need to be translated. Both of these codes are a simple way to carry complex data and allow a system to preform complex multifaceted functions.
Eyoung20 (talk) 23:53, 11 September 2019 (PDT)
Michael Armas' Response
What is the biggest discovery that I made from these readings?
- Chapter 1: Most of this reading was review, as I have plenty of biology and biochemistry experience. However, I found it very interesting that the human genome project is limited by current technology, making what is still considered as a scientific frontier even though it has be studied since the 70s.
- Chapter 3: Once, again, the chapter is mostly review, but I was refreshed on the function of the transcriptome and proteome. I forgot about these collections of biological structures that make up these different "-omes". Intuitively, these are similar to the genome in such that they are a collection of RNA and proteins for the transcriptome and proteome, respectively.
- Nirenberg 2004: This paper was somewhat complex to understand the exact steps taken to deduce the genetic code. I feel as if this is the greatest discovery I made. Of course, I assumed that breaking the genetic code would be no easy matter, but reading through the steps that these scientists took to achieve one of the most important biochemical marvels and the progression of difficulty is fascinating.
- Kaji 2004: In this letter, I discovered the inconsistencies of the Nirenburg paper with that Kaji and Kaji actually discovered. While reading the Nirenberg paper, this section regarding the 'poly(U) binding of the polyphenylalanine was somewhat confusing. However, this letter describes how the findings described by Kaji and Kaji do not support "that 'poly(U) stimulated the binding of radioactive polyphenylalanine-tRNA to ribosomes."
- Moody 2004: In this reading, I discovered the early stages of the digital age and its relation to genetics (what is now considered bioinformatics). On page 6, Moody introduces the skepticism of the viability of computing power in relation to a genome. Today, the world of bioinformatics has expanded so much that so many discoveries were made only with the power of computing and computer science.
- Hayes 2004: A discovery that I found very intriguing was the effiency of the amino acid codons. Specifically, Hayes talks about the codons of similar amino acids are similar enough that, in some mutative cases, a mutation in the codon will still result in the same amino acid. He states how the table of amino acids is not just random, and that its similarities are organized and represent the viability of how multiple codons can code for one amino acid.
What part of the readings did I understand the least?
In the Nirenberg (2004) paper, I was very confused about the steps taken to finally break the genetic code. The deductions made through advanced experimentation were difficult to comprehend. It is interesting to me that all of this highly advanced research resulted in making the simple codon table we all know today.
What is the relationship between the genetic code and a computer code?
Moody regards genetic code and computer code very similar in the single character code. He relates the binary language of computers to the quaternary language of the genome. Binary consists of the characters 1 and 0, while the genetic code consists of the characters A, C, T, and G. To get literal, one can think of transcription factors as a computer that is used to run DNA as code. Once the "code" has been "run," the result (protein) is given. Another literal sense would be how bugs are often present in computer programs; if they are in the code, the code won't run, or the code may run but not in the intended way. Similarly, mutations in the genome may cause an organism to be born normally, as its genetic code may be mutated in such a way that results in loss of function.
Marmas (talk) 21:05, 11 September 2019 (PDT)
Mihir Samdarshi's Response
What is the biggest discovery that I made from these readings?
I did not know that the genetic code wasn't universal. I always thought that the codons that encode the different amino acids were universal. However, I learned from the Transcriptomes and Proteomes readings that there are certain organisms that do not follow the standard genetic code. Although this makes sense because of the vast number of organisms that exist, I did not draw the conclusion that mutations could lend variability in the genetic code. Additionally, reading Nirenberg's account of his discovery of mRNA was fascinating, as I never realized the specifics of the experiments that lead to the discovery of that particular molecule. I also thought that it was interesting that his goal was not to discover mRNA but in fact to achieve cell-free synthesis of penicillinase.
What part of the readings did I understand the least?
The part of the readings that I understood the least was the response by Kaji and Kaji to Nirenberg. I did not understand the purpose of the author's response to Nirenberg. It seemed that Nirenberg had interpreted the paper a certain way, or at least used it as an inspiration in order to develop a hypothesis about mRNA. I did not think that the response was necessary, although I can see why Kaji and Kaji would not want to scientists to erroneously attribute the discovery to them because the contents of the paper had not been described correctly by Nirenberg. Additionally, I did not understand why Nirenberg did the antisense RNA polymer experiments. From what I understood, it simply demonstrated that the RNA was able to be synthesized off of a DNA template.
What is the relationship between the genetic code and a computer code?
Moody showed that the genetic code and computer code are in fact very similar. Similar to how computer code instructs a computer to do a certain task, the genetic code instructs a cell to carry out certain tasks. Furthermore, Moody uses the "analog" vs "digital" analogy to describe the role that genetic code plays. The four base pairs in sequence are relatively immutable, similar to how binary bits in a computer are relatively immutable. Additionally, just how computer code is translated into machine code for a computer to execute, genetic code is translated to mRNA in order to direct the cell to actually create a protein.
Msamdars (talk) 21:23, 11 September 2019 (PDT)
Kaitlyn Nguyen's Response
Reflection
- What is the biggest discovery that I made from these readings?
- After reading all the listed readings, the biggest discovery I made was of the RRF (Ribosome Recycling Factor). While I thought of this binding factor similar to that of tRNA used in translation (protein synthesis), it is different. Not only the mode of binding is different, but the RFF itself is used after the completion of protein synthesis to release the ribosome from the mRNA. After looking it up and reading a little bit more, I realized that both Ribosome Recycling Factor and Ribosome Release Factor are the same.
- What part of the readings did I understand the least?
- In regards to readings Ch.1 Genome 2 and Ch.2 Genome 2, most of the studies on the human genome I have previously studied in Genetics; such as, transcription, reverse transcription, Watson and Crick's experiments, etc. What I understood the least were pseudogenes. I have learned that mutations would have an effect on gene expression, whether it be minor or major, but my question is if a gene is no longer useful, would it be considered a pseudogene and degrade or be inactive, or is it expressed and cause similar effects as those born with extra/fewer chromosomes?
- What is the relationship between the genetic code and a computer code?
- Similar to the genetic code, the computer code functions to decipher specific systems (ie. softwares) and/or organisms (ie. synthesizing and characterizing amino acids in proteins). In both, scientists are able to observe cause and effect and trends that the data of the code presents.
Knguye66 (talk) 21:14, 11 September 2019 (PDT)
Iliana Crespin's Response
- What is the biggest discovery that I made from these readings?
- After looking over all the assigned readings, the biggest discovery was about the autobiographical description regarding genetic code. It was fascinating to know that there were two stages involved in this process and how such information known today was a very tricky thing to discover. In General Biology, many students are being taught about genetic code in a broad aspect. There are discussions about RNA and codons, but there isn't much discussion on how the whole process came to be. Going over different readings, there are different viewpoints and narratives on this. It kind of shows every person's take on the information. It is pretty amazing how each person interprets this topic.
- What part of the readings did I understand the least?
- The part of the readings that was understood the least was from Marshall Nirenberg (2004) regarding the article, "Historical review: Deciphering the genetic code - a personal account". It was very confusing how this article is placed in a first person point-of-view and discussing on how they discuss genetic code. It kind of diverges to a whole other thing about the life of an author and not what genetic code actually is about.
- What is the relationship between the genetic code and a computer code?
- The relationship between the genetic code and a computer code is that they both play a key role in the functioning aspect of a system/organism. The genetic code defines the organism. The computer code defines a system (a computer). They both consist of their own "rules" to transfer information or translate it. Without these codes, there wouldn't be anything telling an organism or system how to function properly.
Icrespin (talk) 15:19, 11 September 2019 (PDT)
Christina Dominguez's Response
What is the biggest discovery that I made from these readings?
The biggest discovery I made is switching from emphasizing the part of DNA that is physical/chemical to the information that it stores. It can almost be seen more simplistic by seeing it as a type of computer code. I was able to see many more connections between computer science and DNA in Moody’s Digital Code of Life- such as DNA components as computer software.
What part of the readings did I understand the least?
In Nirenberg’s Deciphering the Genetic Code, it was difficult to follow what exactly he was doing in his experimentation and research. I also found Kaji’s explanation of further and more detailed experimentation to be confusing. It became more clear when it was explained in simpler terms in Moody’s Digital Code of Life.
What is the relationship between the genetic code and a computer code?
The genetic code devises a type of language that can be applied to every living thing as stated by Nirenberg: “These results had a profound philosophical impact on me because they indicate that all forms of life on this planet use essentially the same language” (53). I like to think of computer code as a type of language as well. This language can be used universally to give a certain output. It follows a logical set of information that apply and will give the same outcome or command. In this way, the genetic code and computer code are similar in their set of code or language that are able to dictate a certain outcome that is universal.
Cdomin12 (talk) 00:06, 11 September 2019 (PDT)
DeLisa Madere's Response
- What is the biggest discovery that I made from these readings?
- The biggest discovery that I made from these readings was learning about how the genetic code was deciphered. The genetic code is what makes up all the physical characteristics of a person's body and functions. What is interesting about this is that this code is the foundation to making proteins and understanding the human body. There are only 4-5 letters that make up the code and yet these combinations are what code for protein synthesis. It is a very difficult process to decipher yet these brave scientists dedicated their lives to understanding it better and making the discovery.
- What part of the readings did I understand the least?
- The part of the readings that I did not understand very well was the actual description of the process of deciphering the code itself. Since there were so many different theories to breaking the code, there were many different processes for each discoverer. These process were a bit confusing since all the experiments got really complicated.
- What is the relationship between the genetic code and a computer code?
- The biggest relationship between the genetic code and a compute code is the fact that you have to "crack it". In order to understand either topics, you have to do a range of research to be able to interpret and tell others. For each, there is a lot of trial and error that is put with it until you finally get it figured out. I never really thought of the genetic code as similar as a computer code, so to really compare the two is really interesting since they are so similar. Each also have a series of letters or in the case of computer coding, numbers and symbols, that are all put together to mean something else and can generate something else.
Dmadere (talk) 23:43, 11 September 2019 (PDT)
Marcus Avila's Response
What is the biggest discovery that I made from these readings?
The biggest discovery that I made from these readings was that the genetic code can be compared to computer binary code. This is interesting because it makes me think of the difficulty in creating artificial intelligence based on binary code and various if then statements.
What part of the readings did I understand the least?
I did not understand how binary was able to give identical information as the DNA nucleotides.
What is the relationship between the genetic code and a computer code?
Both genetic code and computer code give information based on the arrangement of symbols. Genetic code uses nucleotides abbreviated to A T/U G C, while computer code uses numerical binary of 1 and 0. The arrangement of each coding stands for information that is used to carry out actions.
Ivy Macaraeg's Response
- What is the biggest discovery that I made from these readings?
- The biggest discovery I made was how the genetic code was figured out by binding tRNA bound to complexes of polyalanine-ribosomes instead of polyphenylalanine-ribosomes. I think this is also interesting because it reminds us of how little changes in what we already know as biologists are still happening, and the field is always evolving to know more.
- What part of the readings did I understand the least?
- The part of the readings that I understood the least was Nirenberg's article. I thought the jargon was very specialized. Also, to read this kind of biology paper told in a narrative, historical way was unusual, and not something that I was practiced in reading.
- What is the relationship between the genetic code and a computer code?
- The genetic and computer codes are very similar. They each use digitalized language (in DNA, it is letters A,G,C,T, and in computers, it is binary code 01) to convey a certain message in order to enact a certain function. The codes for both are usually complex and expansive, while being contained in such a small space.
Imacarae (talk) 17:17, 11 September 2019 (PDT)
Aby Mesfin's Response
What is the biggest discovery that I made from these readings?
I was most surprised by variety of genetic codes that exist in nature, as suggested by the reading Genomes 2, Ch. 3.3.2. As a student, understanding the genetic code has been an essential part of my academic career, especially given that I have learned about gene expression almost every semester of my college career. However, I think that because of how frequently it is taught, it was somewhat easy for me to think of the genetic code as a universal language through which DNA was expressed. That isn't the case, however. DNA exists beyond the nucleus and resided also in the mitochondria, and while that fact was not unbeknownst to me, I never considered that the genetic code for mitochondrial DNA could even have been different from that of nucleic DNA.
What part of the readings did I understand the least?
While I was surprised to learn that mitochondria contained their own genetic code, I was still unclear as to the necessity of a different code, evolutionarily speaking. How does the mitochondrial genetic code confer advantages over a cell that is limited to the nuclear genetic code? I understand that maybe this could be further evidence to the endosymbiotic origins of the mitochondria, but was looking for more information regarding why different genetic codes were even necessary.
What is the relationship between a genetic code and a computer code?
Upon first glance, the relationship between a genetic and computer code isn't very apparent, but given that the two carry information, the nucleotide sequence of the DNA within a cell can be thought of as a digital code as well. In the same way that computer codes construct specific outputs, a genetic code creates proteins that build upon one another to eventually create an organism.
Ymesfin (talk) 20:59, 11 September 2019 (PDT)
Jonar Cowan's Response
What is the biggest discovery that I made from these readings?
- One of the biggest discoveries I made is how the genetic makeup of the human body is based on nucleotides that are arranged in certain patterns that decide our genetic makeup. In a sense, we have all the tools in our body to express the same physical appearances another person has. The defining factor is that the transcriptomes switch on and off the expression of certain genes. It is very fascinating to understand that down to the smallest parts we are the same and if we had the ability to alter our own genetics then we have a possibility to completely change our appearance.
What part of the readings did I understand the least?
- Due to my lack of upper-division biology knowledge, I had a difficult time understanding the concept of transcriptomes. From what I have come to understand is that the transcriptomes are responsible for the expression of genes because of its ability to switch on and off. I believe that the transcriptomes do not have any expression.
What is the relationship between the genetic code and a computer code?
- The human body is similar to a computer because our genetic makeup could be broken down into simple bases that create amino acids, which is synonymous with the way coding a computer works. Functions are defined by amino acids that grouped in a certain order to express a certain feature and like in coding language certain words are used to create a certain function to do/express certain features in software. In many ways, genetic code can be used to build a human by describing features and physical appearance and similarly in a computer code software is built on the use of functions working together to make a complex program.
