Extremophiles Discussion Practice

Discussion 1: Extremophiles 1 NAME: Wesley Beals PART 1: Analyzing the Papers Directions: • • This should be done before coming to class. • • Read both articles BEFORE answering the questions. • • Each question will refer to one or both articles as sources. • • This assignment should be a “deep dive” into the material. It will take time to do. You SHOULD NOT use AI for this part. You need to think and analyze the paper. 1. Coker 2019: How does the introduction set up the paper? Give examples. The introduction allows the focus of the paper to be clear: review the adaptations of organisms that live in extreme conditions and then what scientists have learned from the research on these organisms. It also gets the audience caught up on the topic matter and even subvert some common ideas such as, most of the Earth is habitable. It build interest in what each of these organisms do to not only survive but thrive in each of these circumstances. 2. Coker 2019: How are the headers used? (Include sub headers.) The different headers and sub headers are used to clearly display what the following section is about and further shows that breakdowns of each of the conditions that might be considered extreme and what they are called scientifically. It allows that paper to flow and have organization that is easier to follow. • 3. Both articles: Pick one of the major extremophile groups and discuss the following: a. How is it defined (what makes it an extremophile) The extremophile that I picked is the radiophiles which can survive in conditions of high levels of gamma or ionizing radiation and/ or UV radiation. • b. Environmental challenges With ionizing radiation, the challenge comes of dealing the damage that comes to DNA, proteins, and lipids. This causes DNA to not replicate properly and turns proteins and lipids into non- functioning variants. With UV radiation, the damage is different in that it is more subtle. With UV radiation, the normal nucleotides turn into their non-functioning dimers leading to parts of the DNA not functioning as needed. • c. Key adaptations With Ionizing radiation, the organism has adapted the ability for adaptive DNA repair mechanisms, Antioxidant and protective enzymes, and smaller nucleoid. For UV radiation, the adaptations include genes activated by light that increase DNA repair, Photoprotections, and a more condensed genome. • d. Any questions that still need to be addressed/ areas of future research. There is a lot of research on the applications of radiophiles for use against radioactive isotopes and many other things that harm the enviroments • • • 4. Both articles: Pick any three words you do not know and do the following for EACH of the three words: a. Define the word. Extremophile: A microorganism, especially an archaeon, that lives in conditions of extreme temperature, acidity, alkalinity, or chemical concentration Desiccation: The removal of moisture from something Efflux: The flowing out of a particular substance or particle • b. Briefly describe the context of how the word is being used. Extremophile is the main subject matter of the articles and is used in the context of being a blanket term for a subset of organisms that can survive in by human standards very extreme conditions. Desiccation was used in the context of describing the adaptations of Xerophiles in very dry and hot conditions. They maintain a high concentration in the cell to prevent them from drying out and dying. Efflux was used to describe the way that organisms survive in very acidic environments and they do that through pumping out the excess hydrogen ions in a way to make sure the internal pH stays stable. • • 5. Both articles: List three things that we talked about in class that are mentioned in these articles. Briefly describe the connection between the material in class and what you read. One thing is talked about in both class and the articles is that fact that studying extreme organisms has allowed us to see if we can find life on other planets and helped us better understand the extents to which life can exist and thrive. Another thing is that these organisms evolved in a way that allows for survival in such conditions that it is a great study in the process of natural selection. Lastly I think about how we discussed that as we better understand these organisms, the more we can then turn and apply the things that we find like PCR. • 6. Both articles: Compare and contrast the way information is presented in each article. Describe the advantages and disadvantages of each style of presenting information. Both the articles have a similar way of describing that allows it to feel very scientifically founded and allows for the reader to easily pick out the information. Coker’s article focuses heavily on a strict linear style that allows it to be straight forward and easy to follow. The lack of things such as pictures or diagrams can make it not as interesting to read or see the data being presented by Coker. Schmid uses pictures and diagrams that make it easier to read and understand each of the things presented in the article. This visuals can make it seem a little less professional but overall a quicker more interesting read with short points that feel quick and leave out fluff. • 7. Coker 2019: What is the advantage of having a model organism when studying biology? Model organisms allow for quick and easy production as well as a way to only focus on a few genes at a time and not many all at once. It allows for comparison when other organisms are studied providing a base line as well as understanding on how certain families of organisms function. • 8. Coker 2019: Pick one application of extremophiles and briefly expand on how they are being used. One of the most famous applications of extremophiles is through their DNA Polymerase the creation of PCR reactions that has allowed for the replication of small amounts of DNA and amplification of DNA fingerprints left behind. • 9. Coker 2019: What are the basic requirements for life on other worlds? Chemical building blocks, Energy source, and a liquid solvent. • 10. Both articles: Discuss the style or writing. a. How do the styles of writing in each article compare to things you normally read? I am not one that likes to read scientific journal articles and the two articles are different than what I normally read. I usually like to read things that can be straightforward and I appreciate the focused nature of the articles because it makes them more enjoyable and easier reads. • b. How frequently were citations used? Citations were use almost every sentence which show a strong foundation in research of others and not just one’s interpretation of the research as compared to your average news article or English paper. • c. Did the structure of the articles help you understand the material? Why or why not? I feel like the structures of both articles help me better understand the material because the focus is something that helps make the information clear even if there is bits and pieces that can be mired in microbiological terminology. Each section being separated allowed for each sections information to be clear and I know what to expect in each section. • • 11. Schmid et al 2020: Refer to the figure in the first page. a. List all the information presented in the image. (This is to help you “deep dive”) It showed the spread of species that are extremophiles across the globe and they are really sparse. It shows some of the molecular adaptations that have allowed them to survive in various conditions such as in cold climates the lipids are unsaturated that allows the cell membranes to be fluid despite the cold or how in areas of high pH there is a pumping of protons out of the cell. There are many of these adaptations available and shown which is really cool. There are also information of all the limits and record holder on the extremes of life in each kingdom and it is amazing. • b. How does the figure help you learn the material as compared to the text of each article? It helps one visualize the environments, structures, and spread of these organisms that books would not be able to convey. The illustrations help make the information seem more interesting and memorable then the articles words sometimes do leading to increased understanding and retention of information. • • 12. Both articles: Do you feel more knowledgeable extremophiles after reading the articles? Why or why not? I feel like I have learned much about these special organisms through the articles. Previously I was a aware of the only one of the possible extreme conditions that was high temperatures. The articles opened my eyes that life can survive in many more surrounding that we sometimes realize and give credit to. The articles were very straightforward and a lot easier to read compared to most scientific journal articles that can be mired in meandering information. I have a better understanding of all the adaptations that life has allowed to appear and it is great and amazing. • 13. Both articles: Both articles list funding sources, if any, and list acknowledgements and/or “no competing interests” for the authors and reviewers. a. What is the point of these statements? It is to show who funded the research and to put at the forefront the potential biases that may be in the data and also show who took part in the research. This is to lay out and be transparent. • b. Do these affect your reading of the material? Why or why not? These acknowledgements don’t really affect my reading of the material because of the fact that I don’t know any of the researchers who did the research for these articles. I do not have the expertise to know if these researchers know what they are talking about or if I should be suspicious of their information. 2 PART 2: Exploring with AI Directions: • • This part you can work on before class or wait and do with a group in class. • The purpose of this part is to explore and apply a topics you learned using an AI program. I want you to get familiar with using AI. Explore the benefits and limits of the program. o I used Chat GPT but you can use other programs as well if you like. DON’T pay for anything! Use the free stuff! • Talk with your group members about the experience. Include these answers when you upload your discussion guide. 1. List the AI program(s) that you used during this part. I used ChatGTP • 2. General questions: a. What is astrobiology? I would say that astrobiology is the study of life out in the star and finding out if there is potential for life out there in outer space • b. How are extremophiles related to astrobiology? They allow us to better understand the limitations of life and help broaden our search for life on other planets and help us better understand where we can find life and some of the bare essentials for life to exist on other planets • c. What is an exoplanet? They are planets that orbit a star outside the solar system. 一 d. Pick two questions from part 1. Ask the AI program to answer the questions. i. What questions did you ask? I asked “what is Astrobiology?” and “How are extremophiles related to Astrobiology?’ 一 ii. What answer did the AI program give you? For “what is Astrobiology?” ChatGTP said this: Astrobiology is a multidisciplinary field of science that seeks to understand the origin, evolution, distribution, and potential for life in the universe. It combines principles and methods from various scientific disciplines, including biology, chemistry, physics, astronomy, and geology, to study the possibility of life beyond Earth. Key areas of interest in astrobiology include: 1. **Origin of Life**: Astrobiology explores how life might have originated on Earth and whether similar processes could occur on other celestial bodies. 2. **Extremophiles**: The study of extremophiles, organisms that thrive in extreme environments on Earth, helps astrobiologists understand the potential for life to exist in extreme conditions on other planets or moons. 3. **Exoplanets**: Astrobiologists study exoplanets (planets outside our solar system) to identify potentially habitable ones by looking for conditions that could support life, such as the presence of water and suitable atmospheres. 4. **Mars Exploration**: Mars is a focal point of astrobiology research due to its proximity and potential for past or present life. Missions like the Mars rovers and the search for signs of water or organic molecules are part of this research. 5. **Outer Solar System Moons**: Moons of outer solar system planets like Europa (around Jupiter) and Enceladus (around Saturn) are of interest because they have subsurface oceans that might harbor microbial life. 6. **SETI (Search for Extraterrestrial Intelligence)**: While not directly part of astrobiology, SETI is closely related as it searches for signs of intelligent extraterrestrial life through radio signals or other communication methods. 7. **Planetary Habitability**: Astrobiologists study the conditions necessary for life to thrive, such as the right temperature range, availability of liquid water, and the presence of organic molecules. 8. **Astrochemistry**: Understanding the chemistry of space and how it might contribute to the formation of the building blocks of life is crucial in astrobiology. 9. **Astroecology**: This emerging subfield focuses on the interactions between living organisms and their environments in space, studying the potential for ecosystems beyond Earth. Astrobiology is a rapidly evolving field, and its findings have implications not only for our understanding of the potential for life elsewhere in the universe but also for our perspective on life on Earth and the broader scientific and philosophical questions about the nature of life itself. Then for “How are extremophiles related to astrobiology?” it said this: Extremophiles are microorganisms (bacteria and archaea) that thrive in extreme and often harsh environments on Earth. These environments can include extreme temperatures, high levels of radiation, acidic or alkaline conditions, high pressure, and more. Extremophiles are related to astrobiology in several important ways: 1. **Understanding Extreme Conditions**: Astrobiologists study extremophiles to better understand how life can adapt and survive in extreme conditions. This knowledge helps scientists speculate about the potential for life to exist in similar extreme environments on other celestial bodies in the universe. 2. **Analog Environments**: Some of Earth's extreme environments, such as hydrothermal vents on the ocean floor or acidic hot springs, serve as analogs for conditions on other planets or moons. By studying extremophiles in these locations, scientists gain insights into the types of organisms that might survive on other worlds. 3. **Origins of Life**: Extremophiles provide insights into the possible conditions for the origin of life on Earth. Some scientists hypothesize that life may have originated in extreme environments, and studying extremophiles helps test these hypotheses. 4. **Planetary Exploration**: When exploring other celestial bodies, such as Mars or Jupiter's moon Europa, astrobiologists consider the possibility of extremophiles living in subsurface environments. The search for extremophiles on Earth helps inform the design of missions and instruments used to search for life on these other worlds. 5. **Biosignatures**: Extremophiles challenge traditional notions of what constitutes a habitable environment and what signs of life (biosignatures) to look for. Astrobiologists must be open to the possibility that life on other planets may exist in conditions very different from Earth's, and extremophiles provide examples of alternative life forms and metabolic pathways. 6. **Limits of Life**: By studying extremophiles, scientists gain insights into the limits of life's adaptability and the range of conditions under which life can thrive. This knowledge informs our understanding of the potential for life beyond Earth. In summary, extremophiles are relevant to astrobiology because they expand our understanding of the diverse conditions under which life can exist and provide valuable insights into the search for life on other celestial bodies. They serve as models for how life might adapt and survive in extreme environments beyond Earth, making them a crucial part of astrobiological research. 一 一 iii. How did the answers compare to your answers? Explain. The answers given were way more specific and full of way more detail about the topic than I had ever known about the subject. This information discrepancy comes from the fact that people who have not studied these subjects extensively would not know as much as a computer which has access to the entire internet and can process it in to a digestible form. I will say it is hyper-specific as well because it is a computer. 一 iv. What is the tone/writing level of the AI’s response? Can you get it to change the response? Explain how. The style and tone seems to be very robotic and vey unnatural in how it phrases certain things that make it a give away that we are dealing with AI. The tone and writing level when you ask the questions initially are simple for the average layman to understand but still conveys the sophistication of the fields and the answers to those questions. It is really interesting. The answer is the same if I retype the question but if I want a different response I can either ask it to regenerate the response and the sometimes gives a different response or ask it to explain the response in a different level such as a five year old or a teenager. It is very interesting that the style can stay the same but can be explained differently when requested. 一 一 3. Digging deeper: a. Ask the program to do the following: (If the program cannot answer that question, explain why the program cannot answer that question.) i. Identify an exoplanet that might be able to have life. Before giving me an answer, ChatGTP had said that the last time it had a knowledge update in September 2021 and gave the disclaimer that it was not up to date. The answer it gave was the famous Kepler- 186f 一 ii. What conditions make this planet likely to have life? The three conditions it lists are Location in the Habitable zone, Similar size and composition to Earth, and Potential for a stable climate. The latter two conditions stemming from the fact that Kepler- 186f is the right distance away from its star leading to the possibility of liquid water on the surface. Then it lists multiple unknown factor s that make it hard for scientists to say definitively that the planet can sustain life 一 iii. How would life have to adapt to live on this planet? Before listing the possible adaptations, it gave the disclaimer that there is not a lot of information on the planet’s conditions and then proceed to explain many of the speculated adaptations needed to survive such as the organisms ability to regulate temperature and ability to work in less sunlight, the ability to obtain and conserve water, obtaining energy through possible other means, Radiation protection, obtaining minerals and vitamins, and different biosignatures. It would have many more but it was a start of the possible needs of adaptations. 一 iv. How would the chemistry of organisms be different on this planet compared to Earth? After reasserting that there are a lot of factors we don’t know about the planet, ChatGTP listed many ways that the chemistry might be different with changes such as with solvents not being water, biochemistry based on silicon or sulfur leading to different biological molecules different from earth. Other things that the AI lists were cellular respiration would be different if the planet’s atmosphere didn’t have oxygen or didn’t have adequate sunlight to preform photosynthesis. Other miscellaneous things it mentions are, temperature adaptations, radiation protections, reproductive strategies, and lastly biosignatures. 一 v. What extremophiles could be used as model organisms for life on this planet? Explain why. When I put that question into the AI program and asked it that question, it proceed to list all the extremophile already touched on in the articles and rehashed a lot of the same points brought up in the articles. The one extremophile that had lots of specificity to Kepler-186f was thermophiles with the capacity to survive in more extreme temperatures than was Earth’s average temperature. 一 一 b. Research: Is the information provided by the AI accurate? i. Find real sources (not the AI program) that backs up the information provided by the AI. From the research that I did from NASA and The James Web Discovery, I found that the things that the AI had said was mostly accurate in terms of reasons for suspected habitability of the planets I found the that scientists think that Kepler-186f is able to have life because of the fact that it is in the habitable zone, has size similar to Earth’s as well as the possibility of a stable climate. However this is where a lot of the similarities end, the articles I found didn’t speculate about the possible adaptations, chemical changes, or extremophiles. The articles talk heavily about a lot of unknowns that Kepler-186f has and that it is really hard to study the planet because of the fact that it is 500 light years away from Earth. ChatGTP is a little bit more willing to speculate about the possibility of conditions and adaptations than human scientists. 一 ii. If you cannot find sources to back up the information, what information is available. 一 一 • 4. Evaluation: a. Describe the experience using the AI program. Give specific examples of what worked didn’t work, the accuracy of the information, the depth of knowledge about the topic, etc. My experience was quite fascinating because of the fact that the it was my first time that I used AI to get answers to questions. Many of my opinions from AI are reinforced through this exercise because there were helpful things and definite limitations. The good of the use of AI comes from the fact that it can give very detailed and specific responses to questions such as what is astrobiology and things about how the two topics relate to one another. While the writing can seem a little unnatural and highly sterile, it does provide a good basis to understand things. The bas comes from the fact that it doesn’t really differentiate between fact and speculation which require some cross-referencing to assure what it says. There are also some holes in its knowledge so there are limits on what can be asked and possibly answered. Overall, this experience was a good start to knowing how AI works and how it can become a useful tool in the future. • b. How could AI technology be responsibly used in education? Give specific examples from your experience. It can be used responsibly in a couple different ways. AI can take very complex concepts and can explain them really simply as requested allowing people to better understand the simplicity of more complex concepts before jumping into the next steps of learning. In addition, AI can be used like Wikipedia is used in that both can be used to get a general knowledge on a subject before one gets started on their specific research for a paper or project. It can be used responsibly to elevate educational pursuits but at the same time it can be used to exploit the system and cheat and that is where I have mostly seen people use AI for. With some regulation and education about AI, it can become something that can help us become more knowledgeable and educated. • c. How could AI technology be responsibly used in research or industry? Give specific examples from your experience. As I said previously, AI can be used to quickly and efficiently get a surface level understanding on a topic or concept. This allows for a jumping off point for further specific inquiry. It can also be used to speculate possibilities and help determine a best course of research, experimentation, or interpretation. I haven’t had experience with AI outside of an educational setting, but I’m sure it can automate a lot of the monotonous tasks that human do in the current work market.