Modern Science: The Prodigal Child Forgetting Its Father's House - the Christian Church
Science and faith aren’t enemies. Modern science is the Christian church’s l’enfant terrible.
The tired “conflict thesis” misses something obvious. Science didn’t emerge as Christianity’s opponent. It grew up in Christianity’s house, eating at its table, inheriting its metaphysical furniture. The assumptions that make science possible - that nature is rationally ordered, that this order is discoverable by human minds, that the universe operates by consistent laws rather than capricious will - these aren’t obvious. They’re theological commitments that became so culturally embedded we forgot their origin.
Copernicus was a canon. Mendel an Augustinian friar. Lemaître, who first proposed the Big Bang, was a priest. Newton wrote more theology than physics. They weren’t doing science despite their faith but partly because of it - the conviction that a rational Creator made a cosmos worth investigating.
The “terrible child” part is equally apt. Science inherited the Christian commitment to truth over comfort, then turned that commitment against some of the church’s cherished positions. Heliocentrism. Deep time. Evolution. The child used the parents’ own values to challenge them - which is exactly what enfants terribles do.
The prodigal doesn’t stop being a son. The arguments are family arguments. That’s why they’ve been so heated.
But somewhere along the way, the prodigal picked up new commitments. Methodological naturalism - seeking natural explanations as a working practice - slid quietly into metaphysical naturalism - the conviction that only natural explanations exist. The first is a reasonable constraint for day-to-day research. The second is a philosophical commitment smuggled in as if it were a scientific conclusion. Modern science often can’t tell the difference.
The Far Country Is Running Low on Food
Something is shifting. The prodigal isn’t returning yet, but he’s starting to feel the pressure.
Logical positivism self-destructed (the verification principle couldn’t verify itself). New atheism peaked around 2010 and has largely devolved into internet subculture rather than serious philosophy. Scientism - the claim that science is the only path to knowledge - remains popular but philosophically indefensible; it’s not a scientific claim.
And the hard questions haven’t dissolved.
Consciousness. The Hard Problem hasn’t softened. Integrated Information Theory, Global Workspace Theory - they describe correlates, not the thing itself. The explanatory gap between objective brain states and subjective experience looks less like a puzzle to be solved and more like a category error in the framing.
And the goalposts keep moving. First, language was the mark of mind. Then tool use. Then self-recognition. Then theory of mind. Each time animals or AI systems meet the bar, the bar shifts higher. The pattern is telling: it’s not that we keep refining our understanding of consciousness. It’s that we keep retreating from conclusions the evidence suggests. The materialist framework needs consciousness to be reducible. When reduction fails, redefine the target.
The origin of life. The Miller-Urey optimism of the 1950s - amino acids from sparks, life surely to follow - has given way to something closer to bewilderment. Seventy years on, the gap between “organic molecules” and “simplest self-replicating system” looks wider than it did, not narrower.
RNA World requires RNA, but prebiotic RNA synthesis is nightmarishly difficult. Metabolism-first approaches can’t explain the emergence of genetic information. The genetic code itself is arbitrary yet optimized for error tolerance - a strange combination. Even the simplest self-replicating system requires staggering complexity. Mycoplasma genitalium has roughly 470 genes. You can’t go much lower and maintain life.
This isn’t a gap. It’s a chasm with no visible bridge under construction.
Darwinian mechanisms. The Modern Synthesis - random mutation plus natural selection - was supposed to explain everything. It’s quietly falling short.
The Cambrian explosion remains stubbornly unexplained: most major animal body plans appearing geologically overnight, with no gradual precursors in the fossil record. The waiting time problem presents mathematical challenges - the time required for coordinated mutations to arise and fix in populations often exceeds the time available by orders of magnitude. Developmental gene regulatory networks show a kind of top-down organization that resists gradualist explanation.
The Extended Evolutionary Synthesis is an implicit admission: the old model isn’t enough. Epigenetics, niche construction, developmental plasticity - these aren’t minor additions. They’re attempts to patch a framework that keeps springing leaks. Convergent evolution - the same complex solutions appearing independently across unrelated lineages - suggests constraints or direction that pure chance doesn’t explain.
None of this disproves evolution as such. But “random mutation and natural selection did it” increasingly looks like a promissory note rather than an explanation.
The pattern has a name. Philosopher of science Imre Lakatos distinguished between progressive and degenerating research programs. A progressive program generates novel predictions, explains new phenomena, and opens fresh lines of inquiry. A degenerating program does the opposite: it absorbs anomalies through ad hoc patches, explains away rather than explains, and spends its energy protecting core commitments rather than extending them.
The signs of degeneration: auxiliary hypotheses multiply. Promissory notes replace results. Goalposts shift when evidence arrives. Unfalsifiable escape hatches appear (the multiverse, “we’ll figure it out eventually”). The core is protected at all costs.
Look at the list above. Consciousness: redefine the criteria. Origin of life: it’s a hard problem, give us time. Fine-tuning: posit unobservable universes. Darwinian mechanisms: extend the synthesis, add epicycles. The pattern is consistent. The program is not progressing. It’s defending.
And when defense fails, enforcement begins. Researchers who question the consensus face career consequences. Günter Bechly, a paleontologist whose work was featured by the Natural History Museum in Vienna, was erased from Wikipedia after expressing doubts about neo-Darwinism. Richard Sternberg faced investigation and harassment at the Smithsonian for editing a peer-reviewed paper sympathetic to intelligent design. The Discovery Institute has documented dozens of similar cases.
A confident research program doesn’t need to punish dissent. It answers it. When the response to critique is not refutation but retaliation, something other than science is being protected.
Meanwhile, the forbidden hypothesis keeps gaining ground. Stephen Meyer’s work - Signature in the Cell, Darwin’s Doubt, Return of the God Hypothesis - represents something the establishment would rather ignore: a design hypothesis that actually behaves like a progressive research program.
Meyer’s argument is straightforward. We have uniform experience that specified complex information - the kind found in code, language, and DNA - always traces back to intelligent agency. We have no experience of it arising from undirected processes. The design inference isn’t an argument from ignorance (”we don’t know, therefore God”). It’s an argument from knowledge: we know what produces this kind of information.
Not God of the gaps. God of the system. Design isn’t invoked where explanation fails. It’s invoked because the system itself - the laws, the code, the fine-tuned parameters, the rational structure all the way down - is exactly what mind produces and what mindlessness has never been observed to produce.
The Cambrian explosion, the fine-tuning of physical constants, the digital information system in every cell - these aren’t anomalies to be explained away. They’re exactly what a design hypothesis predicts. Novel predictions, confirmed. Explanatory scope, expanding. Fresh lines of inquiry, opened.
That’s what a progressive program looks like. The contrast is hard to miss - unless you’re committed to missing it.
And the prodigal has siblings who never left. The conflict narrative requires that serious scientists reject faith. Reality disagrees.
Francis Collins led the Human Genome Project and directed the National Institutes of Health - while writing The Language of God about his Christian faith. James Tour at Rice University is one of the world’s most cited chemists and an outspoken critic of origin-of-life research’s inflated claims. John Lennox, Oxford mathematician, has debated the new atheists on their own turf. William Phillips won the Nobel Prize in Physics and teaches Sunday school. Ard Louis does theoretical physics at Oxford and writes on science and faith. Henry Schaefer, five-time Nobel nominee in chemistry, calls the significance of Jesus “the most important question in the world.”
These aren’t mavericks or fringe figures. They’re leaders in their fields who see no conflict between rigorous science and Christian conviction - because they remember what house they’re working in.
Fine-tuning. This might be the most philosophically significant of the lot. The facts themselves aren’t disputed. Change the cosmological constant by one part in 10^120, no stable matter. Alter the strong nuclear force by 2%, no complex chemistry. Dozens of parameters balanced on knife edges.
The responses have been strained.
“It only looks fine-tuned because we’re here to observe it.” The anthropic principle restates the puzzle; it doesn’t solve it. Yes, observers require observable universes. That doesn’t explain why an observable universe exists.
“Multiverse.” To escape the design inference, you posit 10^500 unobservable universes - and this is considered more parsimonious than a designer? The multiverse isn’t derived from physics. It’s inferred to avoid the implications of physics. That’s metaphysics dressed in a lab coat.
The Inheritance Squandered
Here’s what makes the anthropic response so revealing. Science inherited a specific posture from its Christian parentage: reality is intelligibly ordered, and we can discover why things are as they are. Not just that they are, but why. Causes. Reasons. Explanatory structure all the way down.
The anthropic move abandons that inheritance entirely. It’s not an explanation. It’s an anti-explanation dressed in scientific vocabulary. “We observe X because if not-X, we wouldn’t be here to observe” has the grammatical form of an answer while providing no explanatory content whatsoever.
The contrast is stark.
The inherited posture: “The cosmological constant has this value. There must be a reason. Let’s find it.”
The retreat: “The cosmological constant has this value. If it didn’t, we wouldn’t be asking. Question answered.”
That second move would have been unintelligible to Kepler, Newton, Maxwell, or any of the founding figures. They assumed - on theological grounds - that the universe doesn’t just happen to be this way. It’s made this way. The question “why this value?” is legitimate and answerable in principle.
To treat observer selection as an explanation is to quietly surrender the foundational assumption that made the whole enterprise coherent: that reality has rational structure accessible to rational minds.
The prodigal hasn’t just spent his inheritance. He’s forgotten where it came from.
Laws, Code, Life, Logos
Consider the words we can’t escape.
Laws. We didn’t choose the word accidentally. Laws aren’t descriptions of brute regularities - that would be “patterns.” Laws imply prescription, authority, mind. Physicists speak of the universe “obeying” laws. Obeying whom? The language betrays the intuition.
Code. The genetic system isn’t like a code metaphorically. It is a code - arbitrary symbol-to-function mapping, syntax, error correction, reading frames. We’ve never observed code arise from non-mind. Not once. The only known source of symbolic information is intelligence.
Life. The Greeks already knew bios was categorically distinct from mere mechanism. Aristotle’s formal and final causes weren’t primitive thinking to be outgrown. They were recognition that living things exhibit purpose, organization toward ends. Modern biology smuggles teleology back in constantly: function, adaptation, “for” survival. The words won’t stay neutral.
And Logos unifies all three. Not just a lawgiver and a coder and a life-source - but the single rational principle in which law, information, and life cohere. John 1 isn’t poetry layered onto philosophy. It’s a metaphysical claim: the structure of reality is personal, rational, and generative.
Science keeps discovering fingerprints and insisting no one was there.
The Road Home
The prodigal knows his father’s voice. He’s just not ready to admit he recognizes it.
The pressure is mounting. The pig food doesn’t satisfy. The explanatory IOUs are coming due. Secular attempts at meaning-making - therapeutic self-actualization, political activism as religion, techno-utopianism - keep failing to nourish.
But discomfort alone doesn’t generate homecoming. Something has to break.
The question isn’t whether science will return to its roots. The question is whether the famine has to get worse first.