Assembly Theory and the Third Transition in Science

Before I describe Life as No One Knows It, I need to point out that Sara Imari Walker has achieved something extraordinarily difficult. Despite being a highly credentialed scientist with first class collaborators (including Lee Cronin, Paul Davies and her team at ASU), the task she’s undertaken is a scientific and cultural slalom run.

What she’s attempting in this book is almost impossible. But she does it anyway.

-Cultural and Institutional Resistance
Walker challenges a deeply entrenched narrative that “life is just physics and chemistry.” Media and journals endlessly repeat oversimplified origin-of-life theories. The topic is battle-scarred from debates over religion, philosophy, and meaning.

-Intellectual and Disciplinary Complexity
Physics, biology, information theory, and philosophy each have their own assumptions and gatekeepers. She has no safe camp — too philosophical for hard scientists, too scientific for philosophers.

-Scientific Isolation and Risk
There’s no consensus around life as an informational process. She’s building the plane while flying it. Aligning with any faction (like various evolution groups, ID or strong-AI) risks being pigeonholed or dismissed. In science, speculation outside accepted models risks being labeled fringe — yet explaining life without speculation is impossible.

-Narrative and Communication Challenges
Assembly Theory is mathematical. Everyone in publishing knows each math equation cuts readership by half. Media and science journals endlessly repeat comically oversimplified origin-of-life theories. The topic is battle scarred from debates over religion, philosophy, and purpose.

So for me, this is a 5-star book right out the starting blocks. The fact that Walker has expanded this conversation into major podcasts and social media channels (Joe Rogan, Lex Fridman) is cause for major celebration – whether or not you agree with all her scientific conclusions.

Assembly Theory says biological systems can be quantified by the minimum number of steps needed to assemble a structure from basic building blocks. These steps are instructions, meaning they are abstract computations (information) and not reducible to standard physical or chemical laws.

So for example there is no physical or chemical law governing the genetic code that says the letters GGG in a DNA should make Glycine. In theory they could just as well make any other pattern, but a specific set of assembly instructions is in place that dictates the structure of a ribosome, making this mapping what it is.

There is no good theory as to why this is so, and most biology books gloss over the question.

Assembly Theory shares common ground with James Shapiro’s Natural Genetic Engineering, the Extended Evolutionary Synthesis, Behe’s Irreducible Complexity, William Dembsky‘s design argument from Complex Specified Information, Denis Noble’s “Third Way of Evolution.”

Add to that list Michael Levin’s Agential Materials, Bill Miller’s Cognition Based Evolution, and the Origin of Information problem the Evolution 2.0 Prize seeks to solve. She defines Origin of Information as “The Hard Problem of Life” placing it alongside David Chalmers’ “Hard Problem of Consciousness.” I believe these two problems are one and the same.

Walker observes that any instructions for biological structures beyond 15 steps is a sure signature of life and has never been seen outside the living world. This undermines the longtime presumption that life is an inevitable consequence of chemistry, chance and selection. It’s related to the design argument that chance events cannot create more than about 500 bits of code during the span of known history.

It also leads to a brilliant, under-rated paper by Lee Cronin and Sara Walker in Nature asserting that life creates unique and identifiable light spectra due to its assembled complexity. They say this can be used to detect alien life from far away.

In building this idea, the book touches many philosophical and epistemological issues long debated in science.

I enjoyed her quirky choice to call all the hoary revered scientists by their first names. She reminds you that they’re all human. They’re not demigods after all. 

She points out that some objects are outright impossible without design. Barbara McClintock figured out in the 1940s that corn plants redesign their own DNA and engineer their genetic future. Michael Levin has more recently shown that embryo development is not an “algorithm” but a unique live engineering problem solved in real time, every time.

No theory in biology or medicine can achieve its potential without acknowledging that all biological systems communicate, measure and assess; and actively pursue future goals and objectives. Evolution is not random events; it’s active response to random events. That is design. A more formal term is autopoiesis.

You’ll never cure cancer (or any other complex disease) as long as you think it’s caused by mere “chemical reactions”. Complex diseases can only be understood in terms of the agency and goals for both organism and pathogen. This is why very few medications actually cure any disease.

I am puzzled that some in the intelligent design community criticize Assembly Theory so harshely. Once theological claims are set aside, the theory creates ample space for discussing information, construction, algorithmic processes, even agency — all within a scientifically grounded framework. Assembly Theory doesn’t invoke a designer, but it does shift focus toward causation that includes memory, structure, and goal-oriented behavior. That shift alone should interest anyone concerned with information in life.

I applaud her for including Lee Cronin’s “Origin of Life Scam” accusation. 80% of OOL literature is stuck in the 1970s. The field is due for a reckoning. The tone of this book is a peaceful changing of the guard rather than a wrecking ball.

There are a few areas where I thought the book might have been stronger. The biggest is its treatment of the term “selection.” In almost all scientific literature, the word “selection” is almost indistinguishable from “how things turned out.” For a century, selection has been defined using circular logic (survival explains fitness and fitness explains survival) and I never felt this was squarely addressed. Natural selection is an outcome not an explanation. 

When she says “Function is notoriously tricky to define, but a good working definition is in terms of the relationships between objects that arise due to selection.” That’s a post-hoc definition. No object arises due to natural selection alone. Selection takes place after objects which are already assembled compete for resources in an ecological niche. So this doesn’t escape the tautology.

She mentions this when she discusses Stuart Kauffman’s assertion that the space of affordances (possible functions & relationships between objects) is not mathematically computable; rather, evolution is open ended.

I am convinced Stu is right about this (because he is not merely making an assertion; his papers all include mathematical proofs), and what this means is that neither life nor biology can ever be successfully described or defined by equations.

This does not invalidate Assembly Theory in the slightest, because it proposes that objects can be described by the minimal number of steps required to construct them from basic building blocks.

However it does push science into new territory which Kauffman calls “The Third Transition” – the realization (based on Godel’s Incompleteness Theorems and Turing Mathematics) that a purely mathematical ‘clockwork’ universe is not merely difficult but impossible.

Mathematicians swallowed that pill a few decades ago, but science is still stuck in a Newtonian paradigm.

This implies that Assembly Theory can detect agency and measure information, but will never be able to fully model or define life. It also suggests that the essence of “function” cannot be captured by mathematical formalisms alone.

I favor Assembly Theory because it provides a mathematical framework for what chance events and fixed physical laws can produce without agency. It puts information and consciousness on equal footing with more traditional material causes, and I believe that without this change in the profession, MANY branches of science and medicine will continue to remain stuck for decades. Assembly Theory raises the bar by a large margin.

For example, medical treatments (reaching beyond today’s narrow notion of a “drug”) could one day be defined not just chemically, but as constructive pathways — sequences of functional changes to molecules, tissues, or even systems. This echoes Michael Levin’s prediction that future medicine will look like “physiological psychiatry” — where healing arises from dialogue with the body’s own goals and intelligences. Assembly Theory is a step toward that future.

I celebrate her cordial, open-handed tone. The conversation is long-overdue.

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