Class Journal Week 2 - Revision history

Nstojan1: edited syntax

2024-01-26T04:39:49Z

edited syntax

Nstojan1: /* Natalija Stojanovic */ edited joural

2024-01-26T04:38:54Z

‎Natalija Stojanovic: edited joural

Nstojan1: added level

2024-01-26T03:58:18Z

added level

Msymond1: deleted my references

2024-01-25T22:07:20Z

deleted my references

Hivanson: /* References */ removed references from week 2 journal page

2024-01-25T22:05:29Z

‎References: removed references from week 2 journal page

Asandle1: /* Acknowledgements */ added signature that all work is mine except where acknowledged

2024-01-25T07:01:24Z

‎Acknowledgements: added signature that all work is mine except where acknowledged

Asandle1: /* Bibliography */ added signature

2024-01-25T07:00:57Z

‎Bibliography: added signature

Hivanson: /* Hailey Ivanson */ added references to journal

2024-01-25T07:00:43Z

‎Hailey Ivanson: added references to journal

Asandle1: /* Bibliography */ added khan academy

2024-01-25T07:00:39Z

‎Bibliography: added khan academy

Asandle1: Added Andrew Sandler's Section

2024-01-25T06:59:55Z

Added Andrew Sandler's Section

← Older revision		Revision as of 04:39, 26 January 2024
Line 160:		Line 160:
	#I think that the relationship between computer code and genetic code is similar in the way that they both encode information. For example, genetic code tells a cell how to make a protein and a computer code can create a set of instructions which will tell the computer what it can and cannot do. They are similar in the way they function and can detect errors, however they also have their limitations. It is a lot harder to manipulate a genetic code than it is a computer code because genetic code evolves throughout generations.		#I think that the relationship between computer code and genetic code is similar in the way that they both encode information. For example, genetic code tells a cell how to make a protein and a computer code can create a set of instructions which will tell the computer what it can and cannot do. They are similar in the way they function and can detect errors, however they also have their limitations. It is a lot harder to manipulate a genetic code than it is a computer code because genetic code evolves throughout generations.

−	[[User:Nstojan1\|Nstojan1]] ([[User talk:Nstojan1\|talk]]) 20:38, 25 January 2024 (PST)n	+	[[User:Nstojan1\|Nstojan1]] ([[User talk:Nstojan1\|talk]]) 20:38, 25 January 2024 (PST)

← Older revision		Revision as of 04:38, 26 January 2024
Line 155:		Line 155:

	==Natalija Stojanovic==		==Natalija Stojanovic==
		+
		+	#The biggest discovery I made during this reading was how similar our DNA and computer code really is and how much technology, specifically computers, have impacted our study of genomes. Thinking about how our DNA codes for everything in our bodies makes me realize how one little error in the code can change the entire function which can be life threatening. Thankfully, due to bioinformatics, scientists are able to analyze all kinds of DNA and do things such as identifying cancer types.
		+	#I didn’t really understand the ‘antievolutionist’ part in “Ode to the Code” by Brian Hayes. Specifically the part that talks about how when traits are evolving, you would expect to see some variation, especially in organisms that live in extreme environments, however even though they have unusual proteins and nucleic acids they still have the standard genetic code. I didn’t quite understand this because if they have unusual proteins and nucleic acids, how could they still have the standard genetic code.
		+	#I think that the relationship between computer code and genetic code is similar in the way that they both encode information. For example, genetic code tells a cell how to make a protein and a computer code can create a set of instructions which will tell the computer what it can and cannot do. They are similar in the way they function and can detect errors, however they also have their limitations. It is a lot harder to manipulate a genetic code than it is a computer code because genetic code evolves throughout generations.
		+
		+	[[User:Nstojan1\|Nstojan1]] ([[User talk:Nstojan1\|talk]]) 20:38, 25 January 2024 (PST)n

← Older revision		Revision as of 03:58, 26 January 2024
Line 152:		Line 152:
	#What I understood the least about the readings was the article by Marshall Nirenberg, in which he discusses how he was able to decipher the genetic code, and in which he conducted an experiment to determine if protein synthesis was caused by DNA or RNA. I do not understand well what he means when he says he conducted the experiment via cell free synthesis of proteins, and much of the recollection of the experiment also used jargon which was difficult for me to understand.		#What I understood the least about the readings was the article by Marshall Nirenberg, in which he discusses how he was able to decipher the genetic code, and in which he conducted an experiment to determine if protein synthesis was caused by DNA or RNA. I do not understand well what he means when he says he conducted the experiment via cell free synthesis of proteins, and much of the recollection of the experiment also used jargon which was difficult for me to understand.
	#The reading titled digital code of life describes how to represent the genetic code with the computer code known as binary. Because binary is, as the name suggests, a binary code, and DNA is a quaternary code, it requires two units of binary code to represent any nucleotide. The sections of an RNA sequence called introns can also be compared to the segments of code in a program that a computer does not run.		#The reading titled digital code of life describes how to represent the genetic code with the computer code known as binary. Because binary is, as the name suggests, a binary code, and DNA is a quaternary code, it requires two units of binary code to represent any nucleotide. The sections of an RNA sequence called introns can also be compared to the segments of code in a program that a computer does not run.
		+
		+
		+	==Natalija Stojanovic==

← Older revision		Revision as of 22:07, 25 January 2024
Line 152:		Line 152:
	#What I understood the least about the readings was the article by Marshall Nirenberg, in which he discusses how he was able to decipher the genetic code, and in which he conducted an experiment to determine if protein synthesis was caused by DNA or RNA. I do not understand well what he means when he says he conducted the experiment via cell free synthesis of proteins, and much of the recollection of the experiment also used jargon which was difficult for me to understand.		#What I understood the least about the readings was the article by Marshall Nirenberg, in which he discusses how he was able to decipher the genetic code, and in which he conducted an experiment to determine if protein synthesis was caused by DNA or RNA. I do not understand well what he means when he says he conducted the experiment via cell free synthesis of proteins, and much of the recollection of the experiment also used jargon which was difficult for me to understand.
	#The reading titled digital code of life describes how to represent the genetic code with the computer code known as binary. Because binary is, as the name suggests, a binary code, and DNA is a quaternary code, it requires two units of binary code to represent any nucleotide. The sections of an RNA sequence called introns can also be compared to the segments of code in a program that a computer does not run.		#The reading titled digital code of life describes how to represent the genetic code with the computer code known as binary. Because binary is, as the name suggests, a binary code, and DNA is a quaternary code, it requires two units of binary code to represent any nucleotide. The sections of an RNA sequence called introns can also be compared to the segments of code in a program that a computer does not run.
−	~~===References===~~
−	~~Brown, T.A. (2002) Genomes 2, Ch. 3.3.2: The link between the transcriptome and the proteome (freely available on NCBI Bookshelf)~~
−
−	~~Nirenberg, M. (2004) Deciphering the Genetic Code—a Personal Account.~~
−	~~Trends in Biochemical Sciences 29: 46-54. DOI: 10.1016/j.tibs.2003.11.009 (also on Brightspace)~~
−
−	~~Kaji, A., Kaji, H. (2004) The history of deciphering the genetic code: setting the record straight.~~
−
−	~~Trends in Biochemical Sciences 29: 293. DOI: 10.1016/j.tibs.2004.04.005 (also on Brightspace)~~
−
−	~~Moody, G. (2004) Digital Code of Life, Chapter 1, Hoboken, New Jersey: John Wiley & Sons, pp. 1-9. (on Brightspace)~~
−
−	~~Hayes, B. (2004) Ode to the Code, American Scientist 92: 494-498. (on Brightspace)~~

@@ Line 68: / Line 68: @@
 Moody states that the genetic code, DNA, is itself computer code. Moody draws parallels between DNA and a code-containing software suite, transcribing mRNA running a computer program, ribosomes and wires, mutations and bugs, and other direct genetics:computer parallels. The bottom line is that both DNA and computer code tell a functioning unit what to do. The genetic code for its organism and computer code for its computer.
-===References===
 [[User:Hivanson|Hivanson]] ([[User talk:Hivanson|talk]]) 22:29, 24 January 2024 (PST)

@@ Line 36: / Line 36: @@
 - I would have had so much trouble understanding a lot of this if Dr. Dahlquist hadn't given up her time to graciously help explain both the textbook reading assigned and the questions I had on the other readings, especially the reading ''American Scientist'' where she helped me understand the 20 amino acids and the way they are coded for. I hope I correctly explained that in my answer to question 1.
-- All work is my own except where acknowledged otherwise [[User:Asandle1|Asandle1]] ([[User talk:Asandle1|talk]]) 21:32, 24 January 2024 (PST)
+- All work is my own except where acknowledged otherwise [[User:Asandle1|Asandle1]] ([[User talk:Asandle1|talk]]) 23:01, 24 January 2024 (PST)
 - I don't have an exact time estimate for when I worked on this, but most of the work on the journal was done at home the night before class from around 9pm. I plan on working until the midnight deadline and really hope to have this done on time.

@@ Line 54: / Line 54: @@
 *Khan Academy Videos on AP Biology
-[[User:Asandle1|Asandle1]] ([[User talk:Asandle1|talk]]) 21:40, 24 January 2024 (PST)
+[[User:Asandle1|Asandle1]] ([[User talk:Asandle1|talk]]) 23:00, 24 January 2024 (PST)
 ==[[User:Hivanson|Hailey Ivanson]]==

← Older revision		Revision as of 06:59, 25 January 2024
Line 1:		Line 1:
		+	==Andrew Sandler==
		+
		+	To User Page: [[User: Asandle1]]
		+
		+	To Assignment Page: [[Week 2]]
		+
		+	[[Category:Shared]]
		+
		+	'''1) What is the biggest discovery I made from these readings?'''
		+
		+	It is tough to select a biggest discovery I made from the readings. Coming from a high school science background, everything in the reading was stuff I had heard really abstract versions of. Getting to know more really helped me appreciate everything, especially learning the really hard work over numerous years by different scientists that went into everything. If I had to select one single thing I learned, I would say it has to do with the "redundancy" of the genetic code in its coding for proteins. I knew that when you have SNP's or other mutations they could cause major problems and diseases or even death. What I didn't understand was something that comes up in Figure 1 in the article ''American Scientist''.
		+
		+	Figure 1 says: "Consequences of mutations and other errors in transmitting genetic information are ameliorated by the structure of the genetic code." The article goes on to explain how the changes to a single codon can be less drastic than they otherwise would be because of the way the triplets are used to code proteins exist. You can get an SNP in still have the same amino acid produced. Even if you have an error in a spot that doesn't produce the same amino acid, the way it is set up, you still are likely to get either a hydrophilic or hydrophobic resulting compound based on whichever type the original intended molecule was. I think that is so cool! And then going further with what was proposed by "Pierre Béland and T. F. H. Allen of the St. Lawrence National Institute of Ecotoxicology in Montreal" that DNA might have originally been palindromic (read both ways) and the way the math worked out for them on that proposition is so exciting! Basically they found that if DNA was palindromic you could only have it work with the 20 -> 64 scheme that DNA actually uses. (I don't know how RNA fits in since they didn't mention it specifically reference so I added looking into that to my weekend to-do list.)
		+
		+	I also want to mention as a further piece of info to keep in mind that even though this is a very cool idea about the way DNA works and in my opinion (not fact) seems quite likely, not everyone agrees that DNA evolved actively to work this way. This is mentioned in the article as well.
		+
		+
		+	'''2) What part of the readings did I understand the least?'''
		+
		+
		+	To be frank, there was a whole lot I couldn't even read at first. It was like reading spanish. I know some spanish but there are also a lot of words I don't know. It ended up being a process of reading a paragraph. Looking up some words, watching some AP BIO on Khan Academy and reading again. It was super motivating when I didn't understand something and would then have to research and was able to come back and read it again and understand at least somewhat. It's also really motivating to see yourself learning. I think I probably repeated that process for most of the reading, except for the letter by Akira Kaji and Hideko Kaji. That article, even though I couldn't decipher the exact meaning of all of the stuff they were talking about, the overall point was apparent. I do need to mention I still need to read the Historical Review by Marshall Nirenberg because I took almost nothing from it the first time because of all the new terms. I plan doing a more comprehensive read through tomorrow evening after studying for some other courses.
		+
		+
		+	'''3) What is the relationship between computer and genetic code?'''
		+
		+	After reading the article ''Digital Code of Life'' I would answer like this. There is not a direct relationship between computer code and genetic code. By this I mean they are completely different things. I think it is important to be careful how we talk about this topic. The comparison between computer code and genetic code is definitely a good framework to help people perceive these ideas. That being said one is based off of XAND XOR and other such switches and circuits, while the other has a molecular and atomic underpinning. You could argue both do, but I would argue that so does everything else in existence. I think the reason we compare the two information carrying processes is just because they both have a "digital" aspect to them, and have the ability to read the stored "digital" information. If we wrote information or paper or a rock for example they both store the information but don't have a retrieval process. I think the underlying Idea I am trying to get across is that they are similar really only in the fact that we don't have any other "digital" informational processes that we can really compare them with that have a similar storage capacity. (Even your hard drive and the information on your computer is just physical information written by lasers on a disk, and analog tapes are just another form of the same thing. DNA and RNA are currently in a league of their own, and this is exemplified by the massive push we see by people to figure out how to store computer information on DNA or by using DNA like processes. DNA is just the best way we currently have of storing information. And from my limited knowledge it seems it copies much faster than a computer disk.
		+
		+
		+	====Andrew Sandler's References====
		+
		+	=====Acknowledgements=====
		+
		+
		+	- Used the first week's template with Dean to base this week's template on.
		+
		+	- I would have had so much trouble understanding a lot of this if Dr. Dahlquist hadn't given up her time to graciously help explain both the textbook reading assigned and the questions I had on the other readings, especially the reading ''American Scientist'' where she helped me understand the 20 amino acids and the way they are coded for. I hope I correctly explained that in my answer to question 1.
		+
		+	- All work is my own except where acknowledged otherwise [[User:Asandle1\|Asandle1]] ([[User talk:Asandle1\|talk]]) 21:32, 24 January 2024 (PST)
		+
		+	- I don't have an exact time estimate for when I worked on this, but most of the work on the journal was done at home the night before class from around 9pm. I plan on working until the midnight deadline and really hope to have this done on time.
		+
		+	- Texted with Hailey to discuss the journal entries
		+
		+	- Took the bibliography section directly from the Read section on the Shared Journal Assignment page made by Dr. Dahlquist to save time with making the bibliography.
		+
		+	===== Bibliography =====
		+
		+	* [http://www.ncbi.nlm.nih.gov/books/NBK21121/#A5818 Brown, T.A. (2002) ''Genomes 2'', Ch. 3.3.2: The link between the transcriptome and the proteome]
		+	* [https://www.sciencedirect.com/science/article/pii/S0968000403003025 Nirenberg, M. (2004) Deciphering the Genetic Code—a Personal Account. ''Trends in Biochemical Sciences'' 29: 46-54. DOI: 10.1016/j.tibs.2003.11.009] (also on [https://brightspace.lmu.edu Brightspace])
		+	* [https://www.cell.com/trends/biochemical-sciences/fulltext/S0968-0004(04)00083-0 Kaji, A., Kaji, H. (2004) The history of deciphering the genetic code: setting the record straight. ''Trends in Biochemical Sciences'' 29: 293. DOI: 10.1016/j.tibs.2004.04.005] (also on [https://brightspace.lmu.edu Brightspace])
		+	* Moody, G. (2004) ''Digital Code of Life'', Chapter 1, Hoboken, New Jersey: John Wiley & Sons, pp. 1-9. (on [https://brightspace.lmu.edu Brightspace])
		+	* Hayes, B. (2004) Ode to the Code, ''American Scientist'' 92: 494-498. (on [https://brightspace.lmu.edu Brightspace])
		+
		+
		+
		+	[[User:Asandle1\|Asandle1]] ([[User talk:Asandle1\|talk]]) 21:40, 24 January 2024 (PST)
		+
		+
	==[[User:Hivanson\|Hailey Ivanson]]==		==[[User:Hivanson\|Hailey Ivanson]]==
	===Reflection Questions===		===Reflection Questions===