Building a Second Brain for Your PhD: A Researcher's Guide to PKM

It was time for my weekly supervisor meeting and I was desperately searching for a data file that I knew existed somewhere in the digital mess of my PhD life. Multiple hard drives, cloud storage services, and random folders all stared back at me mockingly. Like an overgrown garden where seeds had been scattered randomly, my information was everywhere - ideas sprouted in paper margins, flourished on paper towels, took root on post-its, and wormed their way across at least three notebooks.

Sound familiar?

The frustration of that moment became my tipping point. I realized that my scattered files were just a digital reflection of how my ideas were organized in my mind. Though I was building connections between things I'd read or discussed, these connections were like seedlings without proper soil - they couldn't develop strong roots because they lacked wider context.

"I've read that before somewhere..." became my daily mantra - a phrase I thought would fade with experience but instead grew more frequent as my reading expanded. It was then I realized that if I didn't find a better way to manage information, my dream of becoming an academic researcher would remain as distant as my hopes of being organized.

The 'information tsunami' of modern academia

The volume of academic papers published grows exponentially each month. For early career researchers especially, trying to stay current feels like drinking from a fire hose. When I first started my PhD in plant-environment interactions, I thought my niche was small enough that it would be OK. But soon I discovered relevant research hiding in ecology journals, soil science publications, agricultural research, and even social sciences papers. And we knew an awful lot about plant and soil interactions 100 years ago!

This constant influx of information has real consequences. I found myself hesitant to develop new ideas, worried they must already exist somewhere in the literature. Writing became more stressful as I questioned whether I'd missed crucial references. Like many PhD students, I started experiencing imposter syndrome - how could I contribute anything meaningful when I couldn't even keep track of what I'd read?

To a certain extent this all still exists. A Second Brain doesn't solve everything, but it does release you first brain to think more clearly, articulate ideas better and have a tighter overview of the research landscape.

Finding a Better Way to Learn

It was during this period of overwhelm that I discovered Personal Knowledge Management (PKM). While the concept has existed since the early 2000s, it's gained significant traction since the pandemic as more researchers grapple with information overload.

The premise seemed deceptively simple: create one integrated system to collect, curate, connect and create knowledge. But this raised an important question - why wasn't this a standard part of research training? We learn complex statistical methods and laboratory techniques, but rarely discuss how to effectively process and connect information.

In my field, we study how plant roots interact with soil structure. These interactions create complex networks underground that help nutrients and information flow between plants. I've come to think of PKM in a similar way - it's about building robust connections between ideas that allow knowledge to flow and grow naturally. It's why I take 'an ecological approach' to building it.

How PKM Changed My Research Process

Unlike traditional note-taking focused on summarizing content, PKM emphasizes building connections between ideas. It's less about storing information and more about creating a living network of knowledge that grows alongside your understanding.

For example, when reading papers about soil structure, I now make explicit connections to related concepts in ecology, physics, and even social sciences. These connections often reveal surprising insights - like how theories about plant succession might inform how we approach knowledge management itself.

The system compounds over time. After eight months of consistent use, I'm starting to see real benefits:

• I can more quickly find relevant references and notes for writing
• My writing has more depth as I can easily spot patterns across papers
• I'm more confident developing new ideas because I can clearly see gaps in current research
• My writing has improved as I practice explaining concepts in different ways for different audiences

Making PKM Work in Practice

A personal knowledge management system doesn't need to be complicated. While there are many specialized tools available, what matters most is finding an approach that fits naturally into your research workflow.

For me, this meant starting with basic organization:

• Creating clear templates for reading notes
• Developing a consistent way to tag and categorize information
• Setting aside regular time to review and connect ideas
• Building the habit of capturing thoughts immediately, rather than trying to remember them later

Finding Your Tools

Don't get too caught up in finding the "perfect" tool right away; you will be chasing the Holy Grail in this respect. Like many researchers, I've been on quite a journey with note-taking applications - trying different ones, switching back and forth, and sometimes running multiple systems in parallel. While it might feel like wasted time, each change taught me something valuable about how I process information and what I really need from a PKM system.

You'll probably do things 'wrong' for the first year, and that's okay. In fact, if you read around, nobody does it 'right'. What matters is starting somewhere and being willing to adapt as you learn. Focus first on developing good habits around capturing and connecting ideas - the specific tools can evolve as your needs become clearer.

The critical shift wasn't in the tools I used, but in how I approached thinking. Instead of just summarizing papers, I started asking:

• How does this connect to what I have already come to understand about this topic?
• What questions does this raise?
• What have the authors not answered, or done?
• Where might this idea be useful outside its original context?
• What assumptions or gaps exist in this research?
• Are their conclusions valid based on the evidence they provided?

My only suggestion here is to start simple and don't strive for perfection.

Integrating AI Thoughtfully

While there are valid concerns about AI in academic research, I've found it can be a helpful addition to a PKM system when used thoughtfully. For instance, I use Claude.ai and AI-powered plugins within my note-taking system to:

• Detect connections between notes I might have missed
• Help organize and structure my literature review - I use Claude.ai for this
• Generate different perspectives on my ideas
• Find patterns in my research notes

The key is using AI to enhance rather than replace your thinking. It's most valuable when helping you see new connections in your existing knowledge rather than generating new content.

In fact I will reiterate this. AI is only as good as the information you feed it. When you write notes yourself, rather than copy and paste from other sources, this is invaluable training data for your own models. For example, I wrote this article about two years ago. Since then my writing has vastly improved and I've written around 40 blog posts. I have uploaded 12 of my best posts to Claude to train it in my writing style. I then uploaded the first draft of this post and Claude has supercharged it with structure, some analogies and suggestions to improve it. It's my writing for the most part, my ideas for the whole part, but it's a whole load quicker and better for having Claude give it the once over.

Advice for Getting Started

If I could go back to the beginning of my PhD, here's what I'd tell myself about managing information:

1. Try some different software out and use the one that feel 'most natural'. They all have advantages and disadvantages but aim to find one that is 'the least worst' rather than continually looking for 'the best'. People switch - myself included - because they are not doing the work to keep it organised and efficient often because it is too complicated, rather than because the tool doesn't do what they need. They are all the same under the hood. Work out your three or so 'must haves' and go from there.
2. Start simple but start now - don't wait until you're overwhelmed
   1. Have a clear line of input so everything goes to as few a places as possible
   2. In the same way you have an email inbox, have a notes inbox which you process regularly ideally daily.
3. Focus on creating notes that will be useful and findable to your future self
   1. Give them a useful title and keep the titles consistent.
   2. Use a structure that is logical to you to find stuff (see below)
4. Make connection-making a regular part of your research practice
5. Design your system around how you naturally think and work - be inspired, not influenced
6. Review and refine your approach regularly

Most importantly, remember that a PKM system is personal - what works for others might not work for you. Give yourself permission to experiment and adapt until you find an approach that feels natural.

A Foundation for Research Growth

Building a personal knowledge management system isn't a one-time task - it's more like tending a garden. Some ideas take root quickly, while others need time to develop. Some connections flourish unexpectedly, while others need careful nurturing. And some just never grow.

What matters isn't creating a perfect system, but developing one that helps you think more clearly and work more effectively. For me, this has meant:

• Less time spent searching for lost files and references
• More confidence in developing and exploring new ideas
• Deeper understanding of connections across my research area
• Better writing and clearer thinking

Whether you're just starting your research journey or well into your academic career, it's never too late to improve how you manage information. Start small, stay consistent, and let your system grow alongside your knowledge.

And maybe keep a notebook by your bed - because you never know when a great research idea will strike. Just make sure to add it into whatever system you choose.

Key Takeaways:

• Start building your PKM system early in your research journey
• Focus on making connections between ideas, not just collecting them
• Your ideas and interpretations are the most valuable
• Don't worry about finding the perfect tools - they don't exist
• Make regular review and refinement part of your process
• Let your system grow and evolve with your needs - start simple

I haven't got it all figured out, but working on and in my PKM, helps me do so!

Annette X