Your Startup Methodology is What’s Failing: How the First Principles Approach Beats Lean, Agile, and Waterfall

Your Brain Is More Agile Than Your Project Plan

If there’s one thing founders can count on, it’s that nothing ever goes according to plan. Timelines slip, stakeholders pivot, technology evolves, and sometimes (typically), the whole thing implodes spectacularly. But what if the way we approach project management itself is fundamentally flawed—not because of poor execution but because of how we think about ventures in the first place?

I’ve been studying neuroplasticity, so if you’ll give me a moment, I’ll put on my psychologist hat and pretend to be an expert. This is the brain’s ability to rewire itself in response to new experiences. What if we applied the same principle to how we manage projects? Instead of rigid methodologies, bureaucratic Gantt charts, and process-heavy frameworks, could we rewire startup methodologies to be adaptive at its core? The answer lies in First Principles Thinking—a concept that, when combined with neuroplasticity, can redefine how we approach complex problem-solving in projects.

Why this matters and likely matters to you? If you’ve been a subscriber of mine for long you know that I’m a stickler for the definition of the word entrepreneur, an amateur professional when it comes to personality types, and an advocate for removing waste from startup ecosystems. How that relates, is that we know (definitively), that certain types of people just can’t or don’t think in a manner conducive to organizing, managing, and directing, tasks through to completion. Notably, the people least likely capable of this are also more likely startup founders (entrepreneurs). The fact that we have so many project management methodologies, books, platforms, and articles/podcasts, oriented to founders, isn’t because there is a right one, it’s because such people are seeking solutions to why their way of thinking doesn’t work well. As I’ve talked about in why there are so many platforms for startups, these startup models usually aren’t actually solutions to why founders are failing, they’re solutions proposed because founders are failing.

So, maybe we’re asking the wrong questions. Project execution frameworks, often treated as dogmatic methodologies, are rarely understood well enough to be adaptive problem-solving approaches. While you’re seeking a methodology to apply to your startup, you’re neglecting the fact that neither you, nor startups, adhere to the iterations of a process.

The Brain’s Secret to Success

Neuroplasticity refers to the brain’s ability to change and adapt by forming new neural connections. It’s how you learn a new language, recover from an injury, or pick up an entirely new skill in your 40s. And what do we need to do as founders? Test, learn, and pivot; neuroplasticity is the ability of the brain to form and reorganize synaptic connections, especially in response to learning or experience or following injury. The key takeaway? Your brain isn’t fixed, and neither should your project management approach be.

Traditionally, project management is built around best practices, precedent, and process-driven thinking — essentially, doing what has worked before. But that approach is fragile. In dynamic environments, sticking to conventional methods is like using a road map from the 1800s to navigate a self-driving car. Neuroplasticity, on the other hand, suggests that success comes from continuous adaptation, not static plans.

First Principles Thinking: Breaking Projects Down to Their Core

First Principles Thinking, popularized by Aristotle, forces you to break problems down to their fundamental truths and reason up from there, rather than relying on analogy or precedent. It’s the difference between saying, “We manage projects using Agile because that’s the industry standard,” versus asking, “What is a project at its core, and how can we optimize its execution?”

In project management, First Principles Thinking means:

1. Questioning assumptions – Why do we assume that project timelines should be fixed? Should budgets always be pre-determined? Why is failure seen as a setback rather than an input?
2. Breaking things down – Instead of assuming a project must follow a waterfall or agile approach, break it into its most essential components: people, resources, constraints, goals, and iterations.
3. Rebuilding from the ground up – What would project management look like if we built it from scratch today, without legacy thinking?

What struck me in considering First Principles though, wasn’t the reasoning up from there, it was the clearer establishment of fundamental truths. As a startup founder, we often lose sight of the fact that Mission and Values are more important than Vision or Pitch; we’re told to focus on our vision and work on our pitch but the fundamental fact of the matter is that we must be set about an established (certain) problem for which a solution is valued (truths), and we can only align our team and maintain commitments and focus to the mission, when everyone is on the same page that we are doing this, no matter what it takes.

Startups don’t fail because your methodology is wrong any more than startups fail because you can’t get sufficient cash flow. They fail because founders aren’t working with established, fundamental truths, and teams fracture because they’re littered with people who actually don’t agree, don’t care, or have other priorities (particularly when things get difficult). It’s the difference between saying, “We are developing a CRM that accounts for all of your contacts and scores their value to you as an individual,” versus asking, “CRMs fail most companies because they are oriented to customers and leads, drawn from emails and site visits.” The second statement, a valid Problem Statement that should be familiar in format to you if you’re a founder, is not a fundamental truth – it’s not First Principles thinking.

By applying neuroplasticity + First Principles, project management stops being about enforcing rigid methodologies and becomes about continuously rebuilding the system based on current reality.

What Neuroplasticity + First Principles Means for Startups

1. Adaptability Beats Rigid Frameworks

Most project management frameworks (Agile, Waterfall, Scrum, Six Sigma) are structured as fixed approaches. They work — until they don’t. A neuroplastic approach treats methodologies as flexible, allowing teams to switch between them as needed rather than being locked into one.

Example: Instead of forcing your startups into Scrum sprints (particularly, worse, if only because that’s the methodology you’re used to using), a neuroplastic team would recognize when Scrum is slowing things down and fluidly shift to a hybrid model that integrates Kanban, Lean, or even something entirely new.

2. Fail Fast? No — Learn Fast

“Fail fast” has been a startup mantra for years, but failure alone is useless without adaptation. Neuroplastic project teams don’t just fail fast; they reconfigure rapidly based on the failure.

Example: If a project sprint reveals that a core assumption was wrong, instead of adjusting the sprint slightly, a neuroplastic approach would rework the entire project scope in real time based on new information.

3. Prioritize Learning Over Process

A neuroplastic approach treats every project like an experiment—where the goal isn’t just delivery but continuous learning that informs better decision-making.

Example: Instead of post-mortem reviews at the end of a project (when it’s too late), teams could integrate real-time neural feedback loops—regularly questioning, “What assumptions have changed?” and “What must we rethink from First Principles?”

4. The Role of AI and Automation in Neuroplastic PM

AI is making it easier than ever to adjust projects dynamically. Predictive analytics can recognize when a project is going off-track before humans even notice. A neuroplastic approach would leverage AI not just for automation but for adaptive learning, using AI insights to reshape strategy mid-project.

Example: AI-powered tools like ClickUp, Asana, and Jira should do more than track tasks — they should actively suggest entirely new workflows based on evolving project conditions. And there, like my CRM scenario previously, we have an example of how and why startups fail: there are many founders trying to create better project management platforms, oriented to the notion (*ahem*) that lists, tasks, and tracking are what we need, but are failing us. This is the Problem Statement orientation that then has founders set about building a better mousetrap, when what they should be establishing as fundamental truth, is that how we’re going about it now is wrong and we’re going to build the right way.

Of course, founders can still be wrong! No one is suggesting that First Principles is infallible, but after decades of startup methodology thinking, we haven’t meaningful changed the rate at which startups fail (overwhelmingly) because we’re failing to definitively establish that startups don’t work like businesses, founders aren’t likely managers, and innovation can’t be structured because it’s inherently new and unknown.

---

This is a good point for me to remind myself that it gets pointed out to me that I ramble on so coming up, I’m going to compare this idea to the primary project management methodologies. Please, continue with me. If you’re good, and you found this meaningful, do me a favor and share this or subscribe to keep me inspired to write for everyone.

Hit me up on our Substack here

Lean, Agile, and Waterfall project management methodologies are not inherently aligned with First Principles Thinking, though aspects of them can be adapted to fit it. The key issue is that these methodologies, while once innovative, often become dogmatic frameworks rather than adaptable mental models. First Principles Thinking isn’t a methodology — it’s a way of thinking that questions foundational assumptions and builds from the ground up – frankly, it’s a way of thinking that rather defines and distinguishes entrepreneurs’ brains from others (and why methodologies fail us).

How Do These Methodologies Compare to First Principles Thinking?

Waterfall: The Opposite of First Principles

Waterfall project management is a sequential, phase-based approach where each stage (requirements, design, implementation, testing, deployment) must be completed before moving to the next. It assumes that projects can be planned comprehensively upfront with minimal need for adaptation.

• Fails First Principles Thinking because it’s built on the assumption that planning and prediction can eliminate uncertainty. In reality, startups face unpredictable variables—shifting requirements, market conditions, or technological disruptions. Waterfall lacks adaptability.
• Why It Fails: It assumes linearity in a non-linear world. By the time a startup reaches a testing phase, the original assumptions may no longer be valid, leading to wasted time and resources.
• Where It Could Be Useful: If the problem is well-defined, requirements are stable, and risks are low (e.g., manufacturing, construction… i.e. not startups). But even then, First Principles Thinking suggests breaking down the process into modular, adaptable units.

Agile: Closer to First Principles, But Not Quite There

Agile is designed to be adaptive—it breaks projects into smaller, iterative cycles (sprints) to incorporate feedback and continuously refine the product (which sounds appropriate, doesn’t it?). Agile challenges some traditional assumptions (e.g., that all requirements must be known upfront) but still has structural rigidity.

• Fails First Principles Thinking because it assumes incremental improvement within existing structures rather than questioning the entire structure itself. Agile optimizes iteration but doesn’t always challenge whether the entire project direction is even correct.
• Why It Fails: Many companies practice “Agile in name only” — they run sprints but still rely on hierarchical decision-making and rigid processes. Agile often becomes another rote framework rather than an actual adaptive mindset.
• Where It Could Be Useful: Agile works well in software development where customer feedback is continuous and rapid iterations are needed, which explains why this is popular in startups. But it struggles in high-uncertainty environments (which is what startups are) where even Agile assumptions (like needing a backlog or user stories) may not hold.

Lean: More Compatible With First Principles, But Still Has Limits

Lean Startup aims to eliminate waste, improve efficiency, and focus on delivering maximum value with minimal effort. It is closer to First Principles Thinking because it questions assumptions around resources, workflows, and customer value.

• More Aligned With First Principles because it encourages continuous learning and rethinking waste, but it still operates within a fixed system.
• Why It Fails: Lean focuses on efficiency, but First Principles Thinking asks whether the entire system should exist at all. Most startups I witness failing, are failing because of competition, market trends, or misunderstanding the problem – that is, whether or not the startup should even exist at all. Lean assumes optimization of an existing process, while First Principles asks if the process itself should be fundamentally different.
• Where It Could Be Useful: Lean works well in manufacturing, supply chains, or perhaps startups (but only where it is certain the company should exist and will create value – which is, frankly, never). Challenging that, Lean can become too efficiency-driven, sometimes at the cost of true innovation.

Why These Methodologies Fail in a First Principles Context

1. They Are Built on Assumptions Rather Than Core Truths
   • Waterfall assumes predictability in projects.
   • Agile assumes incremental iteration is always the best approach.
   • Lean assumes efficiency is the primary goal.
   First Principles Thinking says: Break the problem down to its fundamental truths first. Maybe the best way forward isn’t Agile, Lean, or Waterfall—it could be something entirely new.
2. They Often Become Rigid Frameworks
   • Agile was meant to be flexible but is often implemented rigidly.
   • Lean can lead to over-optimization, making it hard to pivot.
   • Waterfall forces teams to follow a linear approach, even in chaotic environments.
   First Principles Thinking says: Adaptability is more important than following a fixed system. Don’t just follow a methodology—build a dynamic approach that shifts with reality.
3. They Focus on Process Over Discovery
   • Agile is focused on incremental delivery, but what if the entire direction is wrong?
   • Lean prioritizes reducing waste, but sometimes breakthrough innovations require inefficiency.
   • Waterfall assumes a fixed plan, but First Principles Thinking values continuous questioning.
   First Principles Thinking says: The goal isn’t to follow a process—it’s to discover the best way forward.

I’m reminded of my work with the Department of Defense or through friends and founders with a history of military service. Therein, I’ve learned of the Commander’s Intent and Mission Command; the military leadership principle of “Take That Hill.” These concepts emphasize clear objectives while allowing flexibility in execution. Instead of micromanaging, leaders define the goal (“take the hill”) but empower subordinates to adapt tactics as needed.

What’s lacking there, and why startups and national security projects tend to struggle to work well together, is that First Principles (again, the entrepreneurial mindset) actually even asks “Do we even need to take this hill?”, challenging assumptions before execution. A First Principles approach ensures the mission itself is valid and optimal before committing resources—whereas traditional methodologies often focus on execution without questioning the premise.

Where I’ve witnessed firsthand veterans pivot to being successful founders, is with the addition of the notion of servant leadership:

1. Traditional “Take That Hill” (Directive Leadership) – A top-down, objective-first approach where orders are followed without question. Works well in high-stakes, immediate-action scenarios but can stifle adaptability.
2. Servant Leadership (Support-First Leadership) – Instead of just ordering “Take That Hill,” a servant leader asks, “What do you need to take that hill successfully?” This ensures soldiers (or employees) have the right tools, strategy, and autonomy to execute.
3. Mission Command (Blending the Two) – The military now emphasizes Commander’s Intent, where leaders set the objective but trust their teams to figure out the best way to achieve it. This aligns with First Principles Thinking, allowing subordinates to challenge assumptions and adjust tactics as needed.

THIS is an effective startup founder.

What a First Principles Approach to Startups Looks Like

Instead of blindly applying Agile, Lean, or Waterfall, a First Principles approach would start with fundamental questions:

1. What is the real goal? What is our mission and values? Not, the problem but rather why the problem exists. When advising, I challenge founders by asking them to explain the problem within the problem.
2. What assumptions are we making about how this should be done? Are we assuming Agile is the right approach because it’s popular? Similarly, I hear founders decide to focus on iOS, Facebook advertising, or coding in React, merely because it’s what they know. Stop!
3. If we had to start from scratch, how would we approach this problem? What if Agile, Lean, or Waterfall didn’t exist?
4. What is the simplest, most effective way deliver a sustainable startup? Not a Minimum Viable Product but the best path, based on first principles, to what it ultimately needs to be.

Example: A Startup Building a New Product

• A typical Agile team would create a backlog, prioritize features, and iterate.
• A Lean team would cut unnecessary features and focus on an MVP.
• A Waterfall team would define everything upfront and then execute in phases.
• A First Principles team would say: “What is the core problem we are solving? How can we deliver that in the fastest, most effective way — whether that’s code, a manual process, or something else?”

This might mean starting with a no-code prototype, testing with a single user manually, or rethinking the entire product before a line of code is written.