The Powerful Way to take Notes as A PhD Student

hi my name is dr miles and i'm a former phd student in physics specifically nano physics and nano optics so the study of tiny stuff what i want to talk about today is my approach for taking notes during my phd and the software i use now in my work and how my process has evolved over time because honestly a phd is or anything academic it's hard enough as it is just because of the volume of data coming up with your own good note-taking system is absolutely essential if you want to get through it as easily as possible when i started my phd program i quickly realized that the note-taking systems i've been using all my way through undergrad were just simply not going to cut it they wouldn't be up to the task of a phd because there's just so much information to read through so many manuscripts to read through so much to remember and so much to slowly build up on in terms of your knowledge base over like a four year period what got me through my undergrad was just basically highlighting textbooks uh sometimes i'd write notes in a notebook but the problem was these approaches just are impossible to easily ever reference again most of the time i found myself never even bothering to open the textbook or the notebook and i just have a nice stack of them that proudly were filled out quite diligently but i basically just never look at ever again my hope was essentially just the uh i would remember the information when it came time to the exam uh because finding anything in particular just was going to be an absolute nightmare what i learned after about a year of the phd uh which i affectionately refer to as my my write-off year uh was that i needed a better way of managing knowledge what i needed was a knowledge management system i just didn't know that those terms existed or that there was one out there that i could easily use not something that was just a notebook not something that was a word document or a napkin but an actual holistic way of keeping track of really complicated ideas and keeping track of how those complicated ideas related to each other so all that is to say i found a method that works for me and i'm hoping that some parts of it will work for you i built my system ultimately back when i was doing my phd using teeny tiny scraps of code that i wrote originally in python that also helped me run this microscope that i was building so it was a bit of a bodge together system back then but it kind of worked for me what i've started to turn this into now is actually my own app that i'm developing called protolist but it doesn't matter if you use that or if you use obsidian or if you use rome or if you use notion or if you use a pen paper or slip boxes or whatever it is that you want to use it doesn't actually matter so don't be held back by trying to find the perfect piece of software build a system that works for you take the bits of other people's systems that you like and discard the bits that you don't like find something at the end of the day that meshes with how you like to work i think that's probably the most important takeaway piece the system that i started to develop is based on something called the zettelkassen method which is probably something that if you're interested in this space you've come across before it was originally developed back in the 1960s i think by a guy called nicholas luhmann as a way of managing his knowledge network and he had a really difficult task of not having access to a computer so he wrote on tiny little index cards and kept those index cards strategically aligned near other index cards sounds like a really difficult system we've got computers nowadays so hopefully that process is much easier but really like this is an exercise in adaptation something that works for you is our end goal there are essentially three core principles when you go out and try and replicate some element of the zettelkassen system you should number one take notes in your own words try to use when you do that full sentences because i find in particular that bullet points even if i try and use those they aren't really that helpful because when you go back a month six months later down the line and you try and look at a bullet point and understand exactly the context of what idea you were trying to jot down you very much find yourself looking at the kind of skeleton of the idea what you want to do is put a little bit of meat on the bones give it some context give it some understanding compile it as a kind of complete thought and that complete thought point number two should be what they refer to as irreducible as in its own simplest kind of concept try and capture an idea that is an idea in its simplest form i guess not a list of different factors not an essay a simple idea framed simply in your own words and number three that that idea that piece of knowledge must have some sort of connection to all of the other pieces of information within your knowledge system within your brain at the end of the day so find a way of tying those links between this new piece of knowledge back to all of your other pieces of knowledge that you've created before what that will do for you is allow you to actually go back and find that information six months a year four years down the line because it will be nested in a sensible place and you'll happily and serendipitously kind of stumble across it so those are the three core concepts of going out and building a zettelkassen method so how do i use that system in kind of my own approach i'll talk you through some of my kind of high level ideas and then i'll show you actually in the system that i've built how that works kind of mechanically step one is a reasonably simple one you want to find something that you want to take notes on usually for me that was a research paper and usually that research paper came in the form of a pdf occasionally i would print it out but i hated the idea of tomes and tomes of paper being on my desk because of the trees but equally because they would go everywhere and i would lose them and things like that so i prefer to read pdfs on a good old-fashioned computer or a kindle or something like that very occasionally i would read books or textbooks but most of the information that i was working on was sufficiently i guess at the cutting edge of what the field was doing that people really hadn't had time to write textbooks about it yet so most of the stuff i found myself reading was was manuscripts or research papers your goal once you have something that you want to take notes on is to capture what they refer to as fleeting notes which are things like quick ideas maybe little highlights or inspirations that kind of hit you as you read this is what you want to frame those ideas that are kind of irreducible concepts little novel ideas that are complete in and of their own right there are two parts of a really good fleeting note there is kind of the source the thing that caused that inspiration the the thing that made you say you have that kind of aha moment and then there is the digested version of what that aha moment actually means kind of in your own words in your own context it's really important here that rather than just highlighting something you find interesting that you actually put it in your own words and add context there's actually been a whole bunch of different studies that show that highlighting doesn't actually improve retention or understanding of material and in fact there's a couple of studies that say that highlighting actually hurts retention in the long run and i'll put a link in the description to one such paper that kind of talks about some of those points so it's not only important to kind of reframe that aha moment in your own ideas so that it kind of lodges in your in your brain but equally don't just write down that idea that you've had as it will be really hard to find the source of that idea which you might want to go back and reference or cite or check that your understanding of it or your nuance of your understanding of it uh may have changed at some point in the future you want to be able to go back to it really quickly really easily find it and say does that actually marry up to my new understanding about this field as a whole this topic as a whole so what i want to do now that we've kind of talked to a very high level about how to take really good fleeting notes is i've replicated some of my knowledge system into protolist the software platform that i use so let's head in and take a little bit of a live tour about how i take notes in the platform and what that actually looks like so welcome to protalist so this is a small part of my knowledge system it's all stored online because i found i ended up saving a copy of my notes anyway to google drive and at the time that i was doing my phd i was using about 10 different devices in all of the different labs that i was working in and i was moving between those labs and a lot of them were things like clean rooms which had a dedicated computer that you're allowed to use in it and you weren't allowed to download computer programs onto that computer so i ended up needing to use a web application anyway so for this this works nicely for me it means that i can kind of turn up at any computer across the whole world and i will have access to all of my notes on my note system uh automatically there without having to download any software hashtag it doesn't work on mobile just yet so on the left hand side you'll see that i've kind of broken the way i work into a few key kind of categories at the top and what we'll take a little bit of a look at first is what i refer to as my bibliography notes or my source notes i guess which is basically any interesting source that i want to take notes on so kind of the first step that i'll usually do is upload a pdf or a manuscript or something like that that i'm interested in reading into the system which you can do just as a simple kind of drag and drop wait for it to upload and let's just open up that pdf and see what that actually looks like so you'll see the pdf is on the left hand uh and on the right-hand side is well we'll get to it in a second but it's all the information that i'm going to try and collect from this source so this will be where all my fleeting notes kind of appear what i'm doing as i'm going through and reading a manuscript say is looking for ideas that strike me as particularly interesting or particularly novel things that i want to kind of retain access to um that i may want to reference in the future so there's one that i found earlier which is here which i'm interested in capturing and keeping in the future so to do that i will press capture and what they'll do is it'll open up a little prompt for me uh looks like it didn't realize there's a couple spacebars that it extra spaces that it needs in there which i'll just stick in there quickly um but what this does it opens up a prompt for you to put in or to reframe or to redigest that quote that you've just extracted from that text so the actual source material won't be affected if you type in this box you can happily delete absolutely everything if you choose to usually i don't usually i keep it kind of in the box uh but i will kind of reframe that idea in my own words directly above it so this is something that probably is only interesting to me to capture or maybe other optical physicists out there in the world if there are any of you listening uh but this is a quote that kind of describes organic molecules that stop fluorescing after a certain number of photocycles if that doesn't mean anything to you don't worry about it it's interesting to me and something that i want to capture i will put that in my own words so that it's more easy for me to find so i'd maybe turn that into uh organic fluorophores quench during studies making them difficult whoa optical labels to work with for long term studies cool might not mean anything to you means something kind of useful to me uh what you will see as we captured that is that it has appeared on the right hand side of some of your fleeting notes you can open it uh to see kind of all of the notes that you've captured but the thing that i like about that is that you can always go back and reference it and find the source that it came from so it's been tagged with this particular page that we're in so it's all well and good that we've gone out and highlighted and captured and reframed this information in our own words but at the moment it's kind of locked in this particular document we want to extract these ideas out of this document and bring them into our kind of higher knowledge base to do this we want to turn them into something called a permanent note or we want to connect them to an existing permanent note but we want to sift which ideas are really valuable to us and move them out of just being stuck in a document and into a repository of all the interesting ideas that we've got i keep all of my permanent notes contained in one place in this separate table here i've only collected a couple of them out of my kind of wider knowledge base but here's a kind of good representative group of them that we can use just for kind of talking through how the system actually works so if from my permanent notes i go back into my bibliography and go back into my fleeting note you can create a new permanent note directly from this atom so reading again what i've just written organic fluorophores quench during long-term studies making them not very good uh point probes essentially for optical research what does that mean to me i want to try and condense that idea down really at the end of the day what i'm kind of saying is that the choice of optical label in experiments is influenced by how long i'm going to run that experiment optical flora 4 might be good for a short experiment it's not good for a longer experiment i'm just going to say by duration that is a useful concept in and by itself i'm going to add that to my workspace and click on type in permanent notes and add that as a new page within my system so i can go find that permanent note the choice of lay of optical labels and experiments is influenced by duration uh my type my spelling is terrible uh or equally i can get back to it by finding it here and if i click on that tag it will take me into that page that page at the moment is empty and arguably not really that useful to me it's got my kind of fleeting note that i've tagged into it on the side so that's a good starting point but if i want to expand what this permanent note actually means i need to do a little bit more work to it to make it a bit more valuable what i typically do here is drag my fleeting note into the page just to give me a bit of a kind of starting point i guess because i find it a bit intimidating starting from a blank page i think it's nicer to have some words already there now that we've dragged that fleeting note into this page what you actually find is that the symbol next to the fleeting note has changed from nothing to cited so we know that we've actually used this idea in a particular page somewhere and we can kind of trace back through where it originated from because we can go back to the source at any point if we need to uh what i typically do here is kind of rewrite again these words in my own kind of thoughts um so i probably don't need that bit because that's already been condensed a little bit i may some say something like um for long term studies or their or there other more advantageous probes that offer better measurement capabilities and this to me has started maybe not a fully complete idea just yet but the start of something that will be potentially valuable maybe a new course of direction for me to kind of design some experiments around and a place and a source that i can always look back to as to why that idea even arose in my mind in the very first place at any point by control and clicking on that idea that nested idea that i've cited in my document i can reopen the fleeting note if i do kind of want to reference any of the bits that maybe i deleted if i feel like i deleted too much and i want to kind of reference actually what was the original context or by clicking on the source i can go back to the original document and find uh the actual original context as to where that idea first came from and again i can then follow it kind of back through as to where i've actually used it so in that way you always have a really short loop between where does this idea come from and how am i using it and am i using it actually in the right context there's one last thing which is really important to do when it comes to permanent notes and that's to link that new idea to the rest of your knowledge base so if i look at the rest of my permanent notes there's actually a couple of them that strongly relate to this new idea one here in particular the iscar enhancement of metallic nano nanoprobes don't worry if that doesn't mean anything let me go back into this uh page and what i'm interested in doing is linking that other note into this permanent note so i'm going to add a new link and i'm going to type in that i scout enhancement so now if i want to at any point i can jump quickly between these sorts of ideas i can go and read that note and get a bit of understanding or equally i can go back uh to the choice to the note that we just created what you'll notice is that similar to the permanent note that we just created this permanent note also has a couple of fleeting notes uh kind of related to it that ultimately informed me kind of having this idea in the first place so these little fleeting notes are still valuable and they're valuable not only in the context of this permanent note but in the context of maybe any other notes that this permanent note is related to so what i actually like to do to kind of help me clarify ideas is to start in my permanent note and to change the relationship of how these notes interact from just being linked and on kind of an equal level to actually being a kind of a hierarchy in nature so by setting this secondary note as a child where we want to inherit all of the fleeting notes from it i get all of the fleeting notes see these two just have popped up that were recorded here and i can read through them and work out do they relate to this knowledge that i'm trying to write about and when you know it turns out that the second one actually helps me kind of advance my idea that i'm thinking about it says that mechanic nanoparticles produce signal proportional to the amount of incident light that they are illuminated by which actually potentially is an answer to the question that i've asked in my permanent note so i might want to actually incorporate that into my permanent note and kind of change this note to reflect this new understood knowledge this new linked knowledge so i'm going to remove that question and in its place i'm going to say could metallic nanoparticles uh be better long duration optical probes uh and actually this was the process that clued me in basically these exact ideas that clued me in uh to what ultimately became my phd project and they said that sounds really simple uh but i guess like we hadn't thought of using this sort of system within our research before and that was one of our aha moments and it's really satisfying to me even now to be able to retrace that idea that kind of started me in the right direction of what my phd project actually became uh beyond that point typically i turn off the kind of relationship you'll notice that the fleeting note stays here because now i've cited it in this page just here so i can find it again if i ever want to i can go back and find the source or i can find the permanent note that it was originally cited in or i can find this permanent note that it's also been cited in and that's kind of how my system works i would say one final point i guess why i like having these in a table rather than just as a page is because i can add properties to all of these things so what is this in relation to this is relation to i guess some future experiments that i'm interested in performing and if i only want to see the notes that relate to future experimentation i can filter by those and i can read through them and try and understand better how they kind of connect to one another which ultimately gives me a little bit more kind of fine-tuned granularity in how i'm managing my knowledge one thing i also like to do within my bibliography notes kind of on a similar context is look at some of these ideas on a to-do list so uh usually when i add something new into my database i'll click it as inbox and then i can see if i ever shift to my to-do list which is just a simple kanban board that i've got a paper that i really should read sometime soon and i can kind of move it around into the rest of my system so that is broadly how i manage my knowledge like i said hopefully there are some useful elements that you can take from this and build into how you're thinking about building a knowledge management system uh by no means like i said before are you do i expect you to kind of replicate every single step do something that works for you it can't be too onerous otherwise you'll find that you don't actually do it um really what's most important i guess is consistency this is an activity this kind of knowledge creation and curation uh process that just takes time and you need to invest small amounts of time in it every day so that it builds to be something much bigger than the sum of all of its individual parts in the long run once you have a lot of these core kind of clarified ideas as permanent notes the same way we drag the fleeting note in those can really be the kind of the starting points of what might become a research paper or might become your thesis or an essay you're writing or something like that so yeah hopefully that was useful it was a little bit of an introduction into how i kind of manage my knowledge uh do stick around i'll try and put some more kind of videos on the channel that relate to some of these sorts of knowledge management systems but yeah until next time thank you very much for watching i'll see you around goodbye

Channel: Quantum Of Knowledge

Views: 62,173

Keywords:

Id: 7_6ELlCIl1w

Length: 23min 3sec (1383 seconds)

Published: Fri May 06 2022