Bi-Monthly Journal
This is a bi-monthly updated blog tracking Chase's progress throughout the completion of his project.
Summary of workI spent the beginning of November writing a rough draft of my Standard of Practice for my in-lab research this winter. I first made an outline, that contained these sections:
After creating these sections for the outline, I began to fill in each section, talking about the various information for each. As of now, the document is still a work in progress- each day, I have been adding various chemicals to the list of materials, researching where I can buy them, and making sure the science is there to back the content. Moving forwardBy the end of November, I hope to have a completed SOP, that is backed by my own research and actual science. I want to present this SOP as a proposal presentation to Ms. Carsley, Mr. DeMarte, Mr. Witzel, and the Eney's, to ultimately apply for funding for all of the various chemicals. This completed SOP will be comprehensive and will include all of the necessary details about the in-lab portion of this fellows.
0 Comments
Summary of WorkI spent the second half of October writing various drafts of a scientific abstract for my SLR. After about 10 different drafts, I finally created my finalized, general abstract. The key to this abstract is that it merely serves as a generalized abstract. The information inside is definitely complex and encompassing of the SLR, but every journal I am currently planning to submit my SLR for publication in (including JEI, NHSJS, and IJHSR) has it own requirements about what needs to be in an abstract. So, this "general" abstract is really an all-encompassing abstract, that can be cut-down/modified/edited/supplemented to satisfy the requirements of any given journal I will encounter during this publication phase. This abstract is copied below. I also had to write numerous research supplements to multiple schools, including MIT, Caltech, and UChicago. These research supplements not only allowed me to submit my SLR to various universities, but also forced me to learn how to summarize my work in short essays simple enough for anyone to read, yet complex enough to convey the ideas of the SLR. It was good practice for later in the year, when I will present my project to the rest of the school. I would have attached these research supplement documents in this blogpost, but I believe I am not allowed to post any personal documents relating to college applications. Copy of AbstractBelow is a copy of the aforementioned abstract. Looking ForwardLooking Forward, I plan to get the SLR submitted to the various journals ASAP. I also want to research more journals that my SLR might qualify for, and look into their various requirements for publication. Finally, I hope to begin and finish my SOP by the end of November, so I may order materials for the in lab portion by December.
Summary of WorkThe first half of October was largely focused on ensuring that the SLR was completed, so that way I can move onto developing the SOP. After the grammatical changes I discussed in the last post, I took the time to research some potential journals. The first is the National High School Journal of Science, or NHSJS. Specifically, I would submit to their "report" category, which is for literature reviews such as mine. Second is the International Journal of High School Research, or IJHSR. I have begun to format my paper for these two journals. Journal RequirementsThe NHSJS requires that its papers maintain a maximum reference count of 40, and a limit of 4 figures or tables. Because of my numerous references, I will need to significantly cut down the number of references my SLR has, as well as pick and choose the most important ones to include. The IJHSR only takes 2-3 literature reviews per issue, and they publish 4 issues per year, so the selection process is highly competitive. However, they have a specific template that should be easy to adapt my SLR to, with some minor modifications. I have included a screenshot of the template below: Looking ForwardThe rest of October will be focused on formatting the SLR for these two Journals, as well as finding more journals my literature review would be eligible for. Once that is done, I will put full efforts into my SOP.
SummaryThe second half of September was focused on cleaning up the SLR as well as my website. I spent a few days reading through my SLR and editing it, cleaning up some of the grammar as well as making some minor organizational changes. Also, there is now somewhat of a cohesive look to the website, focusing on red backgrounds and bolded text to make it look professional yet interesting. I also created a logo! It is at the top of the website header. I may change the name in the future, but for now I've settled for Bacteria2Blood, since my project researches the biosynthesis of Hemoglobin using bacteria like E. coli. Overall, some minor changes made the website cleaner, easier to navigate, and more inviting. Screenshots of Website UpdateLooking ForwardAs previously mentioned in the end of summer presentation, a road map has been developed for my project that my mentors agree is the right path. This roadmap is pictured below. First, will finish up any last SLR edits, which at this point is completed. From there, I will begin to format it for various journals. That will take place in the background, while I begin to work on my Standard of Practice, or SOP, outlining my in-lab steps. The development of the SOP will last me until late fall. These phases and more can be seen in the roadmap below.
Summary of Progress Since the end of August, I have finalized my preliminary SLR as well as created my 40% summer work presentation/recap. Additionally, as of 9/15, I have completed both 40% meetings- one on 9/14 with Mr. Witzel and Mr. DeMarte, and one on 9/15 with Ms. Carsley. Because the SLR rough draft was finished before the end of August, I spent the past 15 days both polishing my SLR and making my summer 40% presentations. The SLR has a final word count of about 4000 words, and the most up to date version is attached to this post. The presentation was made in powerpoint format, however it was intended to be a discussion based presentation. In both my mentor presentation and my presentation to Ms. Carsley, I had the powerpoint up, but it was merely a resource to guide the conversation. All 3 presentees were given a folder I prepared with a paper copy of my SLR, as well as a copy of my extensive (3700 word) notes printed out, so they could visualize part of my process from the summer. Ultimately, the presentation covered the work I did over the summer, broken up into June, July, and August-present. Additionally, it highlighted some of the problems I had this summer and the ways I tackled them and compromised to get to where I am today. Then, the presentation dove into the content of the SLR itself, supplemented by the physical copies each mentor was given at the beginning. Finally, I discussed the plan moving forward via a roadmap. Each of these elements are showcased in the presentation below. Summer 40% Final Presentation
Viewable Files- Preliminary SLR & Summer NotesLooking ForwardAssuming I am admitted officially into the fellows program, the next step in the process is to finalize the SLR and begin developing the Standard of Practice (SOP) for the In-Lab research this winter. In the short term, I plan to edit/polish the SLR, choose journals for publication, and begin to edit the SLR to comply to their various formats.
Summary of ProgressThese past 15 days have contained my largest work towards my fellows project thus far. I finalized my notes for my SLR in a document that is 3232 words long. They are extremely comprehensive and were instrumental not only in my understanding but also my writing. As soon as I completed the amount of notes I thought was necessary, I began to write my SLR. After days of writing, the SLR rough draft is essentially complete. It contains 6 distinct sections, each containing various subsections, and the total word count thus far is 2900 words- concise but comprehensive. I plan to finish the final two sections of the SLR purposely kept for the end of writing, the abstract and the conclusion, in the coming days. Gallery- Notes & SLR Rough DraftBelow are three picture galleries. The first is of my finalized notes sheet that has compiled data from all of the papers read thus far. The second gallery is of my SLR Rough Draft in its current state. Picture- CommunicationsBelow is a screenshot of an example communication I have had with my mentors during the past 15 days. Looking forwardLooking forward I hope to complete a few things. First, I am planning to reach out to my mentors this week about scheduling a meeting for my summer 40% review presentation. I have already had an informal discussion with Mr. DeMarte and we agreed later next week would be a good time, however I will formalize that and put it on the calendar soon. Second, I am planning to finish the Conclusion and Abstract sections of my SLR rough draft. These are the two sections of an SLR typically reserved for the finishing phase of writing because of their summative nature. Finally, I plan to clean up my website and begin preparing my presentation for my summer 40% meeting.
More long term, the goals are still the same for the coming months. Assuming I am accepted into the fellows program for the year, the first step is editing my SLR and making a final draft. This editing not only includes traditional essay editing, but also picking a journal and conforming my writing to their requirements (every journal has a different format and set of requirements to follow). After the SLR is edited and final drafts for each chosen journal are finalized, I will begin the publishing process by submitting them for review. After the SLR is submitted, I will begin to develop my SOP as mentioned in previous blog posts. The goal is to have a reasonable SOP with established financials, a very clear and actionable plan, and a solid materials list for lab set up. This detailed plan will be what I need to begin in-lab research either before winter break or after. Summary- Fellows Project ProgressThe first half of August was jam packed with fellows work for me, since it was the first part of the summer that I was 100% home and able to consistently work on my project. I made 2 major types of progress for my project, as well as 2 management-side developments. The first main category of project-specific progress was my extensive note taking on more articles, which included the note taking itself as well as answering the initial questions I wrote to myself while reading the articles. The second project specific part of my progress was my outlining of the SLR. With the goal of the summer being that I have some sort of preliminary rough draft of my SLR drafted by the start of school, making an outline was a very important step in this process. Outside of project-specific developments, I also had some general management tasks that I took care of. The first and most straight forward was continuing communication with my project mentors. I had a period of silence with my mentors when I was focused on grinding out research and did not contact them much, so I made a conscious effort to send more emails in this phase of the project. I also worked on the website more, trying my best to beautify some of the pages and picking a theme I will implement across all of the pages as time goes on. (more on this below) As mentioned above, the first major stride in project work for this update was the increase in note taking on research articles. I have amassed a list of well over 20 separate research articles that have been focuses in my research the past couple of months. They range from larger, more general articles such as the first few that I found back in early July, to specific research papers focused on synthesizing one type of hemoglobin or one specific step in the chemical pathway to synthesizing important molecules such as Heme (which is the small, organic compound that containes the iron making hemoglobin into a metaloprotein). I have been taking notes on these articles, and while I have read to some degree every paper I have found, I have taken notes on the first ~10 give or take. Part of the process is making connections between articles, so often times I will read a paper, find something really interesting or important in it, and then find another seperate paper that helps me to explore interesting thing x in greater detail. I end up taking notes on interesting thing x and note it as being from the first article, but some of the notes I take on interesting thing x are supplemented from my newfound knowledge developed in that second article. I have pictures of some of the notes I have taken thus far below, to better display my method. The second major development that is project focused in my work has been my work on making an outline for the preliminary SLR. At this point, I have created a pretty decent outline of what I want the SLR to look like. A lot of the formatting will change when I decide on a journal or journals(s) to submit the SLR to later this fall. However, the general structure of how I want to introduce ideas will stay the same. There is a screenshot of my outline below, but the general format will be a 4 stage paper:
Summary- Actual Scientific UnderstandingWhile I do not want to take up an entire blog post writing paragraphs upon paragraphs of my newfound understanding of scientific concepts, I did want to write a short summary on some of the things I have been learning related to the research in my project. I have found that overwhelmingly, the majority research on Hemoglobin synthesis has been done using microbial synthesis. In other words, microorganisms produce Hemoglobin. This is fascinating to me because it opens the door for an increased consideration on sustainability, a focus I have wanted to incorporate since the beginning. I actually did some in lab practice with these sorts of methods this past spring when I did some expiriments using CRISPR, the gene editing tool that has been making headlines recently. I am thinking, based on my understanding of the current research surrounding Hemoglobin synthesis, that this might be the way to go: levying the recent advances in microbial synthesis to essentially force bacteria to overproduce hemoglobin, which I can then harvest. This is super exciting and will help me make a SOP (Standard of Practice) for this winters in-lab research. Pictures- Notes from Articles & PapersBelow are some examples of notes I have taken on research papers. Notes in orange are small notes to self, whether it be a reminder to look up a concept, a note that the thing above is important, or any other kind of important note I want to find later. Picture- SLR OutlineBelow is a picture of my current outline for my SLR. I will continue to work on this, as well as use it as a guide for writing my preliminary SLR in the coming days. Picture- Various CommunicationsBelow are some screenshots of some communications between me and my mentors. These are here just to show my typical email communications. Picture- ResourcesOne of the resources I have been using recently to help in my research is RCSB.org, a nonprofit website dedicated to categorizing and cataloguing every protein out there. I was turned onto the website years ago by MIT's head of the MIT.NANO electron microscope department after I visited during MIT.NANO's grand opening in Boston. They have a wonderful database of proteins, including tons of information (way more than I even need!) and 3D models of the molecules I am researching. The website has been instrumental in my understanding of the 3D structure of Hemoglobin, including its 4 subunits and the differences/similarities between the 4, so I figured I would include a screenshot of the UI. (see below) Picture- Updated Website + Future PlansI have begun in my free time working on my website. I spent a while on my "About Us" page filing in some information like my summary, as well as making a nice looking scheme. While I don't love using typical pictures as a background, I like how the background I have chosen for the "About Us" page contrasts with the white text nicely. I will continue to implement this theme across the whole website as it grows. I also plan to reach out to Mr. DeMarte, Mr. Witzel, Dr. O'Donnell, and Ms. Carsley and request that they each write a very brief summary of themselves and their role in my project, so I can add it to the "Who Are We? page. Reflecting on Difficulties Regarding TravelWhile I have been keeping up with my fellows work, this summer has been very unstable for me because I have been constantly traveling. Training with the USNA sailing coach this summer, every week I was traveling to a different state across the country. I traveled to Newport, Rochester, New Jersey, and everywhere in-between, so I was always on the road at a different hotel. WIFI has not always been stable or even available, and this was especially the case in St. Croix during the end of July. While I originally made an entirely separate post for the middle to end of July, I tried to post it at the small camp on the south end of St. Croix where we were staying, which is very underdeveloped. The WIFI was spotty to say the least, and ultimately the post never went through. While this blog posts encompasses all of my work from late July as well as the significant strides I have made in the past few weeks, I learned an important lesson to always double check the work I submit. Researching a complicated topic while constantly traveling has not always been easy this summer, but it has been extremely rewarding. Not only for the actual work I am getting done, but also for the experience. Looking ForwardLooking forward, the main deliverable to complete is the preliminary SLR. At this point, I have done enough research that I can begin to write the SLR. My summer Fellows deliverable was to create essentially a rough draft of my SLR, and I will be getting into the nitty gritty of writing said SLR in the coming days.
As soon as I have a rough draft of the SLR completed, and have done editing myself, I will turn to my mentors for help. I am planning to reach out to them as soon as I have a rough draft, so hopefully the first few weeks of school I will be editing my SLR with them and by the end of September I want to have a decent draft of my SLR finalized. From there, it is a matter of formatting it for various journals and adding/subtracting information in order to conform to their requirements. I hope to submit my SLR for publication this fall. After completing the SLR, I will move it and all of the various small tasks I have to do during the publication process to the back burner while I focus on developing an SOP, or Standard of Practice, for my "In-Lab Research." I want to have my SOP done by the end of November, so I can begin getting resources for my experiments throughout December. I hope to start the actual in lab research before or if not, soon after the mid year fellows review in early January. SummaryOver the past ~15 days since the last update, I have focused on finding papers related to the topic I am researching, Hemoglobin synthesis. This has been harder than I expected, because it is difficult to find research from reputable researchers that is general enough for me to understand and use as preliminary documents (as I slowly wade into the very complicated research ahead of me) yet also as comprehensive and focused as necessary. While I knew that my topic was pretty specific and that there would potentially be limited amounts of research on hemoglobin synthesis, I didn't expect it to take as long as it has to find good papers to use. As a note for the future, I really have to make sure to be efficient with my time and use the tools of the various databases (such as google scholar's advanced search/filtering system) at my disposal to only find relevant articles. I ended up finding 5 papers that I can use as a starting point to dive into. These papers are all related to different topics within the realm of hemoglobin synthesis. While I was expecting to find more than 5 suitable papers in this timeframe, I am happy that I found any (which was a goal from my last update's "looking forward") and I now have the skills to find more papers in a shorter amount of time. Of the 5 papers, there are 2 that I have started to read. The first is called "Recent Advances in the Microbial Synthesis of Hemoglobin." This paper, published in March 2021, in the "Trends in Biotechnology, CellPress" journal, focuses on recent developments in hemeglobin synthesis, specifically organic synthesis. This is related to a potential route I was thinking of for my research later this year to synthesize hemoglobin. After completing my CRISPR research project & experiments with Mr. DeMarte and Mr, Witzel earlier this year, I thought of the ways that colonies of bacteria and other organisms could be genetically engineered to produce the hemoglobin protein as opposed to inorganically chemically synthesizing the heme group inside hemoglobin. This would be a potentially more efficient and even more costs effective way of producing hemoglobin, which would contribute to the sustainability aspect of the processes I want to research later this year. While I am not fully done digesting all this paper has to offer, it is a very good paper to explore the possibilities of taking an organic synthesis route. It also is made in a sort of SLR format, so it is very easy to approach without sacrificing any of the technicalities important to my genuine scientific understanding of the chemical processes. The second paper I am currently looking into is titled "Chlorophyll and hemoglobin—Two natural pyrrole pigments" and was written by Emma M. Dietz. Similar to the first paper, this research paper focuses on Hemoglobin. However, this paper was focused less on the synthesis of hemoglobin but more on the unique relationship between Chlorophyll-A and Heme, the compound in hemoglobin that hold oxygen and gives blood its distinct red color. This is a unique topic because most of the papers I have seen don't take the time to research relationships such as this one, which is actually a focus of my research and of the SLR. My original inspiration for this project came from my discovery of the similarities in chemical structure of Heme and Chlorophyll, so this article was great in connecting that original observation with the new knowledge I have been developing. Pictures of Research PapersBelow are screenshots of the 2 research papers I have begun to dig into. Picture of Zotero InterfaceBelow is a screenshot of the note taking/biblography software I am using, ZOTERO, in action. At the time of this screenshot's taking, I had already begun to fill in some information for the first of the 5 papers, as you can see below. Looking Forward Looking forward, I first want to continue to work on the website. I have worked to fill in some of the empty areas such as the "About Us" tab to create a more complete looking website. However, I have been very busy recently with travel sailing, and with daily practices and big regattas such as C420 North Americans, I have had very little down time to dedicate towards making my website look the best it can. I am hoping to continue to chip away at it every day little by little as much as I can, so eventually I will have a fully fledged website complete with everything I need.
Outside of the website, I hope to really dive into the first few research papers I have chosen. As mentioned above, I have begun to read them, however I want to make sure I can understand them and get as much out of them as possible. Given that they are the largest part of the SLR besides the writing of the SLR itself, it is important that I take good notes on each article going forward (which I will make sure to include pictures of). A roadblock I am beginning to find that both Mr. DeMarte and Dr. O'Donnell said could exist is the paywall that many of these articles are locked behind. Something I want to do in the near future is figure out who I need to talk to (Ms. Carsley, if you have any thoughts on this issue that would definitely be appreciated in the comments below!) in order to potentially unlock these articles. Earlier this summer Mr. DeMarte thought Severn's librarians might be able to help me get access to certain papers or journals, however I need to double check the actual logistics of making that happen. In addition to the actual research, I hope to continue to meet with my mentors. It has been a little while since I have been in contact with them, so I am planning to set up a zoom with all 3 mentors as soon as I get home from my next regatta, C420 National Championships. It would be good to touch base with them and describe what I am finding in the research papers, and see what their thoughts are in terms of beginning to organize/potentially outline the SLR itself. SummaryThe second half of June largely focused on finishing up all of the back-end planning for the project, as well as the set up for the SLR. First, I discussed the project in detail with Dr. O'Donnell and my Severn Mentors. We decided on moving forward with the SLR as outlined in my original constructed plan, as it seemed feasible for the scale of this project. Additionally, based on Dr. O'Donnell's past experience with similar summative papers, my order of events seemed like the correct progression in constructing an SLR. Dr. O'Donnell, Mr. DeMarte, Mr. Witzel, and myself all began to brainstorm on different journals I could write for. The main question was whether or not I should write for certain journals or rather just write a typically structured SLR and then adapt it from there. We came to the conclusion that I should write the SLR in a general format, with inspiration from real journals. Based on the quality of my end product, I will tailor my SLR to be formatted and later published in the appropriate journals. In terms of resources to find research papers, we came up with a number of different potential sources. The first is simply to use google scholars to find published papers on the specific topics I am looking for. Mr. DeMarte suggested that if there are any papers locked behind a pay wall or other restriction, that I could reach out to the Severn Librarians and ask for their & Severn's assistance in gaining access to said journals. Additionally, Dr. O'Donnell offered to reach out to the librarians at Sienna College and request that they make an account for me to use during the span of the fellows project. This would give me access to the SciFinder Scholar database as well as a ton of scientific research journals, which would be extremely helpful in finding resources for my SLR. I also set up a note taking and organizing system to keep track of the many papers I will have to read for this SLR. For now, I will be using Zotero, a free application for Mac that allows its users to organize research papers into groups and keep track of research. It will be immensely helpful in keeping all of the versos papers in order and organized by subject, focuses, etc. In the future, however, I am planning to rely on the new Safari UI coming with Mac OS Monterey in the fall of this year to organize my research. This system will be directly linked with safari since it is being developed my Apple for their next major MacBook update, and it will be extremely easy to use because of how integrated it will be with my research experience. essentially, it will allow me to organize all of my tabs and research papers into groups that will make writing my SLR and the other papers much easier. Until this update comes out, however, I am planning to use Zotero as my main organization system. Looking ForwardLooking forward, my main focuses are to meet with Dr. O'Donnell again over zoom to discuss some of the papers I am beginning to read, as well as choosing, organizing, and reading more research papers. The goal by mid July is to have chosen a number of papers to begin to look into and summarize, and hopefully have begun that process as well. I also plan to work on the website and fill in all of the remaining empty spots to make it easy to navigate, which should be complete as soon as I get home from sailing training in the coming week.
Project Planning + MentorsThis update contains all of the work done on the fellows project thus far, including the first half of June as well as before June Much of this initial period of the Fellows project has been largely focused on planning. Planning what the project consists of, who my mentors will be and when I can meet with them, and other nuts and bolts behind this project that need to be established prior to attacking the actual heart of the project itself. The first step in my process after receiving the go-ahead from the fellows committee was establishing my fellows mentors. I reached out to Mr. Nick DeMarte and Mr. Eric Witzel (my AP Chemistry and AP Biology teachers, respectively) and they both agreed to assist throughout the fellows project. Additionally, I reached out to Dr. Jodi O'Donnell from Sienna college to assist with the project. In addition to establishing my fellows mentors, I also spent a few days finalizing a preliminary project timeline and project plan. Using some free websites and Microsoft work, I outlined the phases of my project as well as the general time frame for each phase. Redefined Project Phases
In order to polish this outline into the final format it is above, I met with my Severn-based mentors, Mr. DeMarte and Mr. Witzel, over Zoom to help boil down my application and larger ideas into an executable list of deliverables. We also discussed the 40% summer work requirement for the fellows program, required for entrance into the program as a true fellow rather than a provisional fellow. The original plan was to finish some amount of the Scientific Literature Review (SLR), the first main deliverable outlined in Phase 1. However, after meeting with my Severn mentors, we decided the best course of action would be to create a preliminary SLR by the end of summer. This would essentially be a rough draft of the SLR, which includes all of the huge amounts of research necessary to review prior to actually writing the SLR itself. Brainstorming & Program Expectations- Leadership labAfter my 40% summer work bar was established and my preliminary project outline finalized, I felt ready to take on the Severn Fellows Leadership lab. Here, I met with the other 2021-2022 Severn Fellows to discuss each of our projects, work on brief elevator pitches (as a way of practicing discussing the projects in simple, engaging ways), and establishing the expectations of the Severn Fellows Program. Additionally, I set up this website as a means of recording and presenting the project, and fellows program director Ms. Mary E. Carsley discussed with the provisional fellows how to request funds and find success overall in the fellows program. This leadership lab overall was extremely helpful in establishing the rules and expectations as well as kickstarting any fellows projects not already started. Looking ForwardThe goals for the coming weeks are to finally meet Dr. O'Donnell over Zoom to discuss my project (currently in the works), begin to specify which journals I should write for, and find the best resources for research papers relevant to the SLR. From there, I will hopefully begin the very beginnings of choosing and organizing research papers to read, and potentially begin reading them for content. I will also hopefully set up an advanced note taking system to organize all of the many papers I will end of reading, as well as the key ideas from each integral to the SLR. Finally, I hope to polish the website so it is more visually pleasing and easy to navigate.
|