Class Journal Week 3

Hailey Ivanson

Reflection Questions

• Pull out a quote from the first two sections of “What is Code?” that you find particularly interesting. Explain why this quote is particularly resonant for you.

I found this quote: “I can talk to someone who used to work at Amazon.com or Microsoft about his or her work without feeling a burning shame,” to be hilariously relatable. I am tech savvy, and I find computers easy and relatively intuitive to use, but when the real tech people walk in, everything kind of falls apart. One reason I took this class was so I could try to hold up in conversations with my computer science friends when they say things that would usually go straight up and over my head. I think surrounding myself with more computer science knowledge will help with that, as it did with the author of this article, Paul Ford.

• What is something from the first two sections that you need further explanation of or that you want to know more about?

“‘Algorithm’ is a word writers invoke to sound smart about technology. Journalists tend to talk about ‘Facebook’s algorithm’ or a ‘Google algorithm,’ which is usually inaccurate. They mean ‘software.’” I’m curious about the implications of our changing language to fit what laypeople agree is an algorithm versus what was originally defined as an algorithm. I was just talking about “fitness” in an evolutionary context in my ethics and justice class, and how as biologists we define fitness as merely the ability to pass genetic information down to the next generation, but that term was morphed into a moral judgment by the non-biologist majority of English-speakers. Words, as we know, change their meaning with use. Perhaps in ten years, the scope of what is technically considered algorithms will have changed drastically due to the buzz about social media “algorithms.”

• Also, out of the four databases you accessed for this assignment (SGD itself, NCBI Gene Database, Ensembl, UniProt), which did you like the best, and why? Which did you like the least, and why? (Refer back to the question about differences in content or presentation that you noted on your gene's wiki page.)

I loved UniProt. UniProt was incredibly easy to navigate, intuitive to browse, and had attractive graphics and almost all of the information that could be found in the other databases. I also liked SGD, but found UniProt to be smoother in a sense. I liked the way the information was organized on UniProt. Ensembl on the other hand seemed to lack navigability and attractiveness. It was sparse and did not have as much information as SGD or UniProt and had very few graphics.

Hivanson (talk) 23:32, 31 January 2024 (PST)

Katie Miller

Reflection Questions

1. Pull out a quote from the first two sections of “What is Code?” that you find particularly interesting. Explain why this quote is particularly resonant for you. A quote that I found particularly interesting was, "The hardest work in programming is getting around things that aren’t computable, in finding ways to break impossible tasks into small, possible components, and then creating the impression that the computer is doing something it actually isn’t, like having a human conversation." I have always been curious how computers are able to replicate a real person and respond almost instantly to a seemingly random question. I didn't know that this is the work of many algorithms which are combined and applied to simulate conversation. I think it's also very interesting to consider how these algorithms were first developed and what there intended function was.
2. What is something from the first two sections that you need further explanation of or that you want to know more about? I want to know more about how software engineers are able to make websites more efficient. When talking about big companies like Google, Facebook, and Twitter, Ford said "Thus it’s absolutely worth their time to find excellent computer scientists, many with doctorates, who know where all the efficiencies are buried." I don't understand how a computer scientist could manipulate code or an algorithm so that it runs faster, because it seems like this would require removing steps so that less things would need to happen for some specific function.
3. Also, out of the four databases you accessed for this assignment (SGD itself, NCBI Gene Database, Ensembl, UniProt), which did you like the best, and why? Which did you like the least, and why? (Refer back to the question about differences in content or presentation that you noted on your gene's wiki page.)I preferred UniProt because it was the easiest to read and navigate, as well as having visual examples that helped to explain things. UniProt also had a more detailed summary of our gene's function than the other databases, which gave me more information on both how and where the gene operates. I found it helpful that you could click on terms in the aspects of cellular components, molecular functions, or biological processes and it would take you to another page that had more detail on the chosen term. For example, one of the molecular functions was sequence-specific DNA binding, and I was able to click a link that took me to a page with the general definition.

References

Ford, Paul. (2015). What is Code? Business Week, https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/

Kmill104 (talk) 17:09, 31 January 2024 (PST)

Natalija Stojanovic

Reflection Questions

1. A quote that really stood out to me was “Samsung makes computers that look like TVs, and Tesla makes computers with wheels and engines. Some things that aren’t yet computers–dental floss, flashlights–will fall eventually”. This quote stood out to me because it reminded me how much we have developed as a society in both positive and negative ways. The quote talks about how there are very few’ things that aren’t yet computers’, I feel like we have replaced so much with technology and it is upsetting to see because we have started to overuse and misuse it. It has completely taken over our lives, wherever you turn around there is some sort of computer. However, it has also greatly benefited us, people are able to do things so much more quickly and efficiently. Our daily lives have never been easier because of the help of computers, what used to take days and hours could be done in a matter of minutes or seconds.
2. I didn’t understand what the author meant when he said “If you can sell the software, if you can light up the screen, you’re selling infinitely reproducible nothing. The margins on nothing are great–until other people start selling even cheaper nothings or giving them away”. When I first read this, I thought that the author was talking about the prices of softwares and how there is always someone that can make the software for cheaper or for free. I’m particularly confused as to why he calls them ‘nothings’.
3. I liked the UniProt database the most because it was the easiest to use. All of the information was there and the page setup was extremely easy to navigate which was beneficial for someone like me that firstly knows nothing about the gene and secondly never used a database like that. I liked the large subheadings and informative subheadings. They described complex things in easy ways that I could comprehend and use in my research of the gene. My least favorite was Ensemble. It was so hard to navigate and understand what I was looking at. I felt as if there was nothing useful and half of the time I didn’t even understand what information they were providing me. It wasn't as user friendly and I probably would not use it again.

Nstojan1 (talk) 20:16, 31 January 2024 (PST)

Andrew Sandler

To User Page: User: Asandle1

To Assignment Page: Week 3

1)Pull out a quote from the first two sections of “What is Code?” that you find particularly interesting. Explain why this quote is particularly resonant for you.

I actually pulled this quote out of the reading before I read the assignment page. (I started reading the article and couldn't stop because it was interesting) Anyways, the quote I pulled was, "For your entire working memory, some Internet thing has come along every two years and suddenly hundreds of thousands of dollars (inevitably millions) must be poured into amorphous projects with variable deadlines".

This quote spoke to me because of how this concept is going to change in the future. We are on the exponential part of an exponential curve in our technology and research, but evolution has not changed pace. I just find it funny because every 2 years will become every year and then it will become during development, and then who knows what will happen next. I wonder how we will deal with this.

2) What is something from the first two sections that you need further explanation of or that you want to know more about?

I actually know about Euclid’s Algorithm, it’s a comp sci basic. But there are lots of other algorithms that do cool things. I need to learn more about how some newer algorithms, including one written by a guy named Tero Karras from the company Nvidia. It has huge implications in speeding up the process of AI image generation.

3) Also, out of the four databases you accessed for this assignment which did you like the best, and why? Which did you like the least, and why? (Refer back to the question about differences in *content* or *presentation* that you noted on your gene's wiki page.)

My favorite database was Ensembl by a gigantic margin! I liked the organizational structure on the sidebar and I just felt it was the easiest to understand and navigate. All the tools had question marks you could hover over for explanations as well.

Andrew Sandler's References

Acknowledgements

- Used the first week's template with Dean to base this week's template on.

- All work is my own except where acknowledged otherwise Asandle1 (talk) 21:24, 31 January 2024 (PST)

- I worked on this for about 40 minutes from 9 to 9:39pm

- Took the bibliography item for the reading from the Katie's journal and added my one additional source.

Bibliography

• Ford, Paul. (2015). What is Code? Business Week, https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/

• Karras, T., Laine, S., Aittala, M., Hellsten, J., Lehtinen, J., & Aila, T. (n.d.). Analyzing and improving the image quality of stylegan. https://openaccess.thecvf.com/content_CVPR_2020/papers/Karras_Analyzing_and_Improving_the_Image_Quality_of_StyleGAN_CVPR_2020_paper.pdf

Asandle1 (talk) 21:24, 31 January 2024 (PST)

Charlotte Kaplan

• Pull out a quote from the first two sections of “What is Code?” that you find particularly interesting. Explain why this quote is particularly resonant for you.

The quote "Code is inert. How do you make it ert? You run software that transforms it into machine language. The word 'language' is a little ambitious here, given that you can make a computing device with wood and marbles. Your goal is to turn your code into an explicit list of instructions that can be carried out by interconnected logic gates, thus turning your code into something that can be executed—software." is particularly resonant for me. The quote explains how code is essentially instructions, which was easier to understand than it being explained as functional software through a process involving logic gates and interconnected instructions. It emphasizes that despite its complexity, programming boils down to transforming ideas into working software. This helped me understand the essence of programming which is converting concepts into practical solutions using code.

• What is something from the first two sections that you need further explanation of or that you want to know more about?

I'm curious about "lexical analysis," which is mentioned when code is compiled into lower-level instructions. While I barely understand the basics of how programming languages work, I'd like to know more about how lexical analysis fits into the process of turning code into something a computer can understand. I'm also wondering why they used "Business Operating Language United System" as an example language for explaining compilation. It makes me wonder why certain languages are chosen to explain programming concepts and what makes them suitable for such explanations.

• Also, out of the four databases you accessed for this assignment (SGD itself, NCBI Gene Database, Ensembl, UniProt), which did you like the best, and why? Which did you like the least, and why? (Refer back to the question about differences in content or presentation that you noted on your gene's wiki page.)

SGD's organization into categories made it easier to navigate and find specific information about our gene, Sir2. The database neatly sorted details about the gene's function, expression patterns, associated research studies, and related publications into distinct categories. This clear organization allowed me to quickly locate the relevant sections I needed to understand Sir2's role in yeast biology. Whether I was looking for information about its function, expression patterns, or research studies, SGD's organized layout made the search process efficient and straightforward.

References

Ford, Paul. “What is Code?” Business Week, June 11, 2015. https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/

LMU BioDb 2024. (2024). Week 3. Retrieved January 31, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_3

Except for what is noted above, this individual journal entry was completed by me and not copied from another source. Ckapla12 (talk) 21:46, 31 January 2024 (PST)

Dean Symonds

1. A quote that I found very interesting is “An algorithm can be translated into a function, and that function can be called (run) when software is executed. I found this quote particularly interesting because the context of it explains why entire softwares or websites are not algorithms, for they are made up of several algorithms, and they run these individual algorithms. I think the quote also explains that algorithms by themselves do not need to be complex, and many of them are not, for they are just an individual function. However, when many algorithms are put together, they make something far greater that does a variety of tasks, for they are made of a variety of smaller functions.
2. A quote from the article that I need further explanation for is “we haven’t even considered how to store it, or what happens to the letters to the left and the right when you insert an “a” in the middle of a sentence. Or what “lines and circles” mean when reduced to binary data”. This quote needs further explanation to me because this section attempts to capture the complexity of doing such a simple task on a computer. I am not familiar with binary data, or how computers store information, or how computers are able to contain all of this information. It is all very foreign to me and seems like a world that I know nothing about. It feels like these computers are machines that speak a different language that attempt to display information in a way that we understand.
3. My favorite of all the databases was Uniprot, because it contained the most detailed summary for the function of the gene, as well as mentioning other genes and proteins that the gene interacts with to regulate transcription. It also contained a picture of the protein structure, which I consider to be a valuable piece of information. My least favorite was ensembl, for it was very difficult to even find the page with the gene on it, it required my homework partner to email my professor to find the page with the gene. Some sections of the page with the gene also contained limited information. Such as the phenotypes tab, in which most of the sections says “none found”.

Except for what is noted above, this individual journal entry was completed by me and not copied from another source. Msymond1 (talk) 22:49, 31 January 2024 (PST)