Poking the Bear: Where the Bodies are Buried

I've been poking around the sciences for a little while now, looking at where they intersect with philosophy and theology. I've explored information theory, General Relativity, the fine-tuning of fundamental constants, quantum foam, the predictive power of mathematics, the multiverse, and others.

My approach was simple: let science stay in its lane—handling the what, when, where, and how of natural phenomena—while philosophy tackles the why questions and theology addresses the who. Clean boundaries. Mutual respect.

With AI as my research assistant, I could ask questions, get straight answers, write something, and check for errors. I found credible arguments from every angle. And I could show how the evidence pointed toward design without any issues.

But when I stepped on Neo-Darwinism—not to provoke, just to ask questions, get answers, write something, and check for errors…

… Wow.

AI turned into an angry bear. Big. Growling. Demanding the inclusion of references, insisting on footnotes. (I'm writing a blog post, not an academic paper, for crying out loud.) Insisting I offer alternative explanations. 

And then it hit me: I had found the soft spot. Not a minor weakness. THE soft spot—the place where the whole modern myth starts to sag under the weight of its own contradictions.

And I realized why: Darwinism was supposed to eliminate design. Neo-Darwinism? It accidentally requires it.

A Design-Shaped Hole

We were told life was chemistry. Blind, indifferent, bottom-up mechanics. But then DNA came along. And we realized life isn't just chemistry. It's code. And not simple code. We're talking high-level, self-replicating, redundantly error-checked, meaning-rich, multi-platform code.

“So… who's coding?” we wonder.

This is where the bear starts to shift uncomfortably. Because you can't get information systems from geological time and random error. Not the kind that builds butterflies, bones, and Beethoven.

Critics argue that code-like systems can emerge from evolutionary pressures alone—that cumulative selection, over enough time, can simulate intentionality. 

But show me a single example—anywhere—of a high-level, multi-layered, error-correcting code that arose from noise and chance without intentional architecture.

Because you can't generate Google Maps by shaking an Etch A Sketch for a million years.

And the kicker? It wasn't mystics or religious crackpots (like me) who found the holes. It was the academics. They ran the models. They calculated the probabilities. They published the footnotes. And then they quietly buried the evidence.

So let's dig.

Body #1: The Cambrian Conundrum

Darwin himself saw the problem. He wrote in On the Origin of Species that if complex life appeared suddenly, without transitional forms, it would be "fatal to the theory."¹Well, guess what showed up about 540 million years ago?

Everything.

Not gradually. Not one slow speciation event at a time. No—entire phyla burst into existence within a geological blink of about 20 million years with fully integrated body plans, cell types, nervous systems, sensory organs, and locomotive strategies.² Like nature hit "import" on a full evolutionary library.

The bear calls it an "explosion." But then mumbles about "missing fossil records" and "unusual sediment conditions."

Translation: We don't know. Please stop asking.

Even Stephen Jay Gould—no friend of intelligent design—admitted the Cambrian posed "the major outstanding problem" for evolutionary theory and suggested evolution might happen in rapid bursts rather than gradual change.³When your own team captain is pointing out the cracks in the foundation, maybe it's time to check the blueprints.

Body #2: Mutation Math That Doesn't Pay Rent

Let's run the numbers.

Say you have a mutation rate, a population size, a timeframe, and a required number of coordinated changes. Mathematicians have done the work. They've modeled this thing six ways from Sunday.

William Dembski calculated that the probability of generating just 164 characters of meaningful information through random mutations is 1 in 10^164—a number so small it makes your chances of winning the lottery look like a sure bet.⁴

David Berlinski ran similar calculations and concluded that the waiting time for even simple coordinated mutations exceeds available evolutionary time by orders of magnitude.⁵

Unless the universe is rigged like Vegas, there's simply not enough time or mutational opportunity to get complex innovations through blind trial and error.

Yet the official story remains: small, random changes—filtered by natural selection—eventually give you everything from wings to wombs to whale songs. Just wait long enough. It's like saying a billion monkeys with laptops will eventually code Photoshop—without crashing the system along the way.

Body #3: Complexity as a Codebase, Not a Coincidence

Cells aren't sacks of soup. They're nanotechnological cities. They have factories (ribosomes), highways (microtubules), power grids (mitochondria), error correction (DNA repair mechanisms), recycling centers (lysosomes), security checkpoints (cell membranes), and wireless communication (chemical signaling).

Take ATP synthase—the little molecular motor that generates cellular energy. It's a rotating machine with multiple precisely fitted parts that spins at 9,000 RPM to manufacture ATP.⁶ If humans built something that elegant, we'd patent it and win engineering awards.

And this whole system isn't just made of stuff. It runs on instructions. Encoded in DNA. Translated by RNA. Carried out by proteins. It's a software-hardware loop—the kind of thing that wins awards when we build it.

But we're told it all came about accidentally. Over time. Somehow. Kind of.

Ask how the code got there, and watch the bear get philosophical fast. You'll hear about emergent complexity. About self-organization. About how randomness isn't really random when you zoom out enough.

In other words: Magic.

Body #4: The Bear's Sacred Oath—Never Admit Design

This is where science gets theological. Not religious—theological. Neo-Darwinism doesn't just function like a scientific theory. It functions like a creed. It has dogma, martyrs, sacred texts, and heresies. And the prime heresy?

Suggesting that the system looks… designed.

Here's the thing: the bear doesn't want to stay in its lane. Science should stick to describing mechanisms—the how of natural processes. But evolutionary theory insists on answering who questions (nobody designed this) while pretending to only address how questions (mutations and selection).Some rightly say this evidence is not "proof of God." They say design does not mean, "Jesus hid in the DNA."

They're right. But because they know where this road leads, they have stepped right over philosophy and are guarding the gate of the theologian’s domain. Because methodological naturalism doesn't allow design, even if it's staring you in the face.

That's why they can't go there. Not in academia. Not if you want to keep your funding, your lab, your colleagues—or your peace of mind. But they don’t want anybody to go there (ya superstitious hick).The bitter irony? The founders of modern science—Newton, Kepler, Galileo, Boyle, Pasteur—were explicitly theistic in their worldview. They saw their scientific work as "thinking God's thoughts after Him." Their belief in an intelligent designer didn't hinder their science; it motivated it. They expected to find mathematical elegance and rational order precisely because they believed in a rational Creator. They are probably rolling their eyes while they roll over in their graves.

Science flourished under this framework for centuries. But now we're told that even considering design is anti-scientific? That's historically absurd.

Fortunately for me, I'm not an academic. I can follow the logic wherever it leads.

The Royal Society—not exactly a hotbed of religious fundamentalism—convened a conference in 2016 titled New Trends in Evolutionary Biology: Biological, Philosophical and Social Science Perspectives specifically to address what they called "conceptual gaps" in current evolutionary theory.⁷

Translation: Houston, we have problems.

You can question gravity. You can rewrite relativity. But suggest a whiff of design in the genetic code, and you'll be called everything but rational.

And Yet…

The irony is hard to miss. When Darwinism arose, it explained away the appearance of design. But the further science advances—genomics, molecular biology, systems theory, artificial intelligence—the more design we see. 

Layers of it. Levels of it. Interdependencies that defy chance.

And the more intricate the evidence becomes, the more convoluted the counter-narratives grow. Emergence, co-option, molecular clocks, taphonomic bias—each explanation is crafted not because of its explanatory powers (none come close to design) but from necessity.

Anything to avoid Design. They were designed to preserve a paradigm that can't afford to bend. Because admitting the system looks engineered threatens more than a theory—it threatens the metaphysical firewall that keeps science "safe" from meaning.

And we only know how to spot it because we build design. As coders, engineers, gamers, and home economists, we recognize real design when we see it.

And then they wonder why we don't trust them.

And when we explain, we're told that we don't have the educational credentials. To shush and stay in our place.

As if curiosity requires credentials. As if we're not allowed to notice when the story doesn't add up. Maybe the real problem isn't that design advocates are crossing scientific boundaries—it's that evolutionary theory won't respect them.

So when reality starts to look like it runs on syntax instead of soup, we should pay attention. Not shut down. Not growl.

Because maybe the bear isn't angry because we're wrong. Maybe it's growling because we're getting close.

I didn't bury the bodies. I just tripped over them. They marked it. They built on it. They published papers about it. Gave TED talks on it. Built careers atop it.

I'm just reading the footnotes.

And maybe design isn't the conclusion of science, but its starting point—the thing we keep trying to explain away, but always return to.

References Included to prevent AI from having kittens

1. Darwin, Charles. On the Origin of Species by Means of Natural Selection. London: John Murray, 1859.

2. Valentine, James W. "Late Precambrian bilaterians: grades and clades." PNAS 91, no. 15 (1994): 6751–6757.

3. Gould, Stephen Jay. Wonderful Life: The Burgess Shale and the Nature of History. New York: W.W. Norton, 1989.

4. Dembski, William A. The Design Inference: Eliminating Chance through Small Probabilities. Cambridge: Cambridge University Press, 1998.

5. Berlinski, David. "The Deniable Darwin." Commentary 101, no. 6 (1996): 19–29.

6. Boyer, Paul D. "The ATP synthase—a splendid molecular machine." Annual Review of Biochemistry 66, no. 1 (1997): 717–749.

7. Royal Society. New Trends in Evolutionary Biology: Biological, Philosophical and Social Science Perspectives. Conference proceedings, November 7–9, 2016, London.

🧬 Sidebar

ATP Synthase A rotating molecular motor that produces ATP, the cell’s energy currency. It operates with mechanical precision at a nano scale.

Cambrian Conundrum / Cambrian Explosion A period ~540 million years ago when nearly all major animal phyla appeared suddenly in the fossil record without clear transitional forms.

Co-Option (Exaptation)The evolutionary claim that biological structures originally serving one function may be repurposed for another through natural selection.

DNA Deoxyribonucleic acid—the molecule carrying genetic instructions for organisms. The essay describes it as a form of digital code.

Emergent Complexity The idea that complex patterns or systems can arise naturally from simpler elements interacting, without guided design.

Fine-Tuning (of Fundamental Constants)The observation that constants like gravity or electron mass appear to be precisely set for life. Tiny variations would render life impossible.

General Relativity Albert Einstein's theory describing gravity as a curvature of spacetime caused by mass and energy.

Information Theory A scientific field that studies the quantification, storage, and communication of information. In this context, it’s applied to the "code" found in DNA.

Methodological Naturalism A principle stating that scientific explanations must rely only on natural causes, excluding supernatural or metaphysical ones. It’s a rule of method, not a claim about reality.

Molecular Clocks Techniques used to estimate the time of divergence between species based on genetic mutations. Often assume a constant mutation rate.

Multiverse The hypothetical idea that our universe is one of many, possibly with different physical laws. Often invoked to explain fine-tuning without design.

Mutation Rate / Random Mutations Changes in DNA sequences. In evolutionary theory, these random changes, filtered by selection, are thought to drive speciation and adaptation.

Neo-Darwinism The modern synthesis of Charles Darwin's theory of evolution by natural selection with Gregor Mendel's theory of genetics. It’s the widely accepted framework for how evolution occurs.

Philosophical Naturalism A worldview asserting that nature is all that exists. It claims that everything—including consciousness, morality, and meaning—must be explained purely in terms of physical processes and natural laws

Phyla (singular: Phylum)Major divisions of the animal kingdom defined by fundamental body plans, e.g., vertebrates (Chordata), insects (Arthropoda).

Quantum Foam A concept in quantum physics describing spacetime at extremely small scales as fluctuating and turbulent, like a "foam."

Taphonomic Bias A term describing how fossilization conditions may distort the fossil record—used to explain missing transitional forms.