Can Science Explain Everything? The Limits of Scientific Knowledge

Years ago, I lived and worked in the Middle East. My roommate was also a colleague. We were both lab scientists, so we trusted numbers. 

Her mother was diabetic. Because of that, she had regular blood tests. Her routine workup always included liver function tests along with her blood sugar. And her ALT and AST kept coming back normal. 

Then came the diagnosis: Stage 4 liver cancer. The doctors gave her about two months. 

My friend could not believe it. She knew these tests better than most people. The numbers had looked fine. 

But the tests did not lie. They did exactly what they were designed to do. They measured specific things. They were never built to tell the whole story. 

When her mother passed away, it took my friend a long time to accept it. And her questions changed. They were no longer about enzymes. They were about why, and what now, and where hope could be found. By then, I had already shared the Gospel with her, and she had started reading her Bible. 

No lab value could answer those questions. 

Science has changed our world. It helps us diagnose disease, explore planets, and understand genetics. I am grateful for it. 

But success can tempt us to make a bigger claim. If science cannot investigate something, maybe it cannot be known. Maybe it doesn’t exist. 

That conclusion does not follow from the scientific method. 

So, the real question is not whether science is valuable. It is this: what kinds of questions is science equipped to answer? And are there meaningful questions it was never designed to answer? 

This is the third post in a short series. If you are new here, you may want to start with Science and Faith: Can They Truly Coexist in Harmony? and Is Materialism Actually Scientific? 

What Science Does Best

Let me say this first: I love science. I spent more than 15 years in a lab, and I’ve seen what it can do. 

Science works by observing, measuring, and testing, and its results have to be repeatable. It asks how a disease spreads, how stars form, and how a medicine works in the body.

Those questions can be tested. That’s why science gave us vaccines, medical imaging, and the very blood tests I ran every day. 

Running quality control became second nature to me. Before I touched a single patient sample, I made sure the method was working.

That habit says a lot about science. It doesn’t ask for blind trust. It keeps checking itself.

In my previous post, I explained that this approach is called methodological naturalism. It’s a rule for how to investigate. It isn’t a claim about everything that exists.

So, if science has a scope, what’s outside it?

“Science Can’t Explain It” Is Not the Same as “It Can’t Be Explained” 

Quick caution. This isn’t a “God of the gaps” argument.

That argument says, “Science can’t explain this yet, so God did it.” It’s a risky way to build faith. Many things once thought mysterious now have natural explanations. If our faith depends on gaps, it shrinks every time science advances. 

So that is not my point. 

My point is that some questions sit outside the method itself. Not because science has not caught up. But because they are different kinds of questions. 

Here’s an example. Science can study what happens in the brain when someone makes a moral choice. It can show which areas are active and which chemicals are involved. That’s an empirical question. 

But ask this: why is that action truly right or wrong? That’s a philosophical and moral question. Better equipment will not settle it; different tools will. 

That doesn’t mean these questions have no answers. They need other kinds of evidence, like philosophy, history, logic, and revelation.

Science Operates Within a Larger Framework

Here’s what I find fascinating. Science works with assumptions no experiment can prove.

• Reason is reliable. You cannot run an experiment to prove reason works without using reason.
• Our senses and instruments tell us something true. Science can improve instruments. But why our minds should be trusted at all is not a lab question.
• Nature follows consistent patterns. Science relies on the expectation that natural processes behave consistently enough for observations and experiments to help us understand them. It keeps testing that expectation against evidence rather than just taking it for granted. 
• Logic and mathematics hold. Science uses them constantly, but it does not discover them under a microscope.

I saw this in my own work. Some days I followed the method down to the last step, and my QC results were still out of range. I was frustrated. But I never assumed chemistry had changed that day. I went back and retraced my steps. Most of the time, the problem was the reagent. Sometimes it was the machine.

Either way, the answer was never “nature changed.” It was something in the process. I trusted that nature behaves consistently. I didn’t prove that trust that morning.

These are reasonable assumptions, and scientists rely on them for good reasons. But they’re brought to the lab. They are not found there. 

None of this shakes my trust in science. It just means science works inside a bigger frame.

As a Christian, I find it fitting. If an orderly God created an orderly universe and gave us minds to understand it, we would expect exactly this kind of world. That is not a proof. Other thinkers explain these foundations differently. But that’s why I find these assumptions at home in my faith. 

Morality, Consciousness, and Meaning 

Three big questions deserve a closer look.

Morality

Science can study where moral instincts come from, how cooperation helps groups, and how cultures differ. Fascinating work. But describing why we feel something is wrong is not the same as showing that it is wrong. Some thoughtful people believe morality can be grounded in nature alone. That’s a philosophical argument, though, not a lab result. And it still leaves a hard question: why ought I be good when being selfish would benefit me? 

Consciousness

Neuroscience tells us more about the brain every year. I would never say it cannot make progress. But describing neural activity is not necessarily the same as explaining why there is something it is like to feel grief, joy, or love. I looked at this more closely in my last article. 

Meaning

Science can describe what happens in the body when a person loves, or when a person dies. It cannot, by measurement alone, tell us whether love ultimately matters or what lies beyond death. 

Those were the questions my friend was asking. 

What About God? 

I’m not saying science proves God. And science can’t, by itself, establish that God doesn’t exist. 

God is not a physical object like a cell, a planet, or a particle inside the universe. Christianity teaches that He is the Creator of the universe. So, asking science to place Him under a microscope misunderstands the question. 

That doesn’t make belief in God irrational or immune to evidence. Christianity makes claims about history, about human nature, and about Jesus Christ, His death, and His resurrection. These can be examined through historical, textual, philosophical, and theological reasoning. 

They just can’t all be reduced to laboratory experiments. 

When a Method Becomes a Worldview

This may be the heart of the whole series. 

There’s nothing wrong with saying, “Science investigates natural causes.” That’s a methodological statement. 

The problem comes when it quietly becomes, “Only natural causes exist.” That’s a philosophical claim about reality. 

The deeper question is whether everything real must be directly observable or measurable. We can’t put logic, moral obligation, or mathematical truth on a laboratory scale. Yet we use them constantly in science and everyday reasoning. Their reality isn’t established by weighing them or looking at them under a microscope. 

This doesn’t mean rejecting science. It doesn’t mean believing whatever we like, either. It means not every question is scientific. Some truths are explored through philosophy, logic, history, morality, and, from a Christian perspective, God’s revelation.

I don’t think people who make this leap are necessarily trying to dismiss faith. Science has been remarkably successful at explaining the natural world, so it’s understandable that some people assume scientific knowledge is the only reliable kind of knowledge. 

But admitting science has limits is not an attack on it. It is part of thinking carefully about what science actually does.

Does This Mean Faith Is Opposed to Science?

No.

The Christian faith does not ask us to reject scientific investigation. Scripture presents a creation we can observe and appreciate.

“The heavens declare the glory of God, and the sky above proclaims his handiwork.” (Psalm 19:1)

“For his invisible attributes, namely, his eternal power and divine nature, have been clearly perceived, ever since the creation of the world, in the things that have been made.” (Romans 1:20)

We can celebrate every discovery about how God’s world works. But faith is not a substitute for scientific explanation. It speaks to different questions: God, creation, morality, human dignity, sin, purpose, redemption, and eternal life. 

Science can help us understand how the natural world operates. Other questions, like ultimate meaning, moral obligation, and God, need other kinds of reasoning. 

Conclusion: Science Has Limits, But Those Limits Do Not Make Science Weak

I still love the lab. I still see science as a gift.

But knowing how something works is not always the same as knowing why it exists, whether it is good, what it means, or what we ought to do with that knowledge. 

The limits of science do not diminish it. They remind us that science is a method of investigating the natural world, not a complete philosophy of reality. 

A Christian doesn’t need to fear scientific discovery. We can follow the evidence wherever it leads while remembering that not every truth can be placed under a microscope or measured in a laboratory. 

For my friend, those questions became deeply personal. When the numbers could no longer tell her what would happen next, she began asking where hope could be found. And that was a question her lab results could never answer. 

I cannot see her heart. Only God can. But I’ve watched her turn to Scripture again and again, and I keep praying that she finds in Christ what no test result could ever give her. 

Frequently Asked Questions

Can science explain everything?

Science cannot explain everything through its own methods. It is extraordinarily effective at investigating natural processes, but questions about morality, meaning, purpose, and God involve philosophical, historical, and theological reasoning as well. 

Is this a “God of the gaps” argument?

No. A gaps argument says God fills what science has not explained yet. This article makes a different point: some questions are outside the method of science altogether, no matter how much science advances. 

Does science rely on anything it cannot prove?

Yes. Science assumes that reason is reliable, that our senses give us real information, that nature behaves consistently, and that logic and mathematics hold. These are reasonable assumptions, but they are not established by laboratory experiments. 

Should Christians be afraid of science?

No. Science helps us understand God’s creation. Christians can welcome discovery while recognizing that scientific knowledge is not the whole of human knowledge. 

Recommended Resource

Want to go deeper?
If this post raised questions for you, John Lennox’s short book Can Science Explain Everything? is a good next step. Lennox is an Oxford mathematics professor and a Christian, and he writes with skeptics in mind. Yes, it shares a title with this post. But it’s a separate work, and a helpful one.