The “God of the Gaps” Paradox

Whenever you’re having a discussion about God and science, someone will say, “There’s no possible way that X could have happened all by itself, therefore there is a creator.”

Invariably you hear this retort:

“Aw, that’s just a god-of-the-gaps argument.”

For many, that’s the end of the discussion.

The retort usually comes with a sneer: “Don’t be stupid. People used to think that weather came from God. Now we know it comes from heat, cold, moisture and chaos. People used to think God hung the stars on a sphere in the sky. Now we know about gravity and orbits. People used to think God created man. Now we know man came from primates.”

You know the drill.

It’s not always obvious that this retort is a tacit admission that the person making the god-of-gaps argument did score a point. Some god-of-gaps arguments are quite persuasive.

I’ve been making a god-of-gaps argument right here on this website since 2005, in the form of a syllogism:

1. The pattern in DNA is a code.
2. All codes we know the origin of are designed.
3. Therefore we have 100% inference that DNA is designed and 0% inference that it is not.

Regardless of what position you take in the debate, I have some things to say about this which might surprise you. I hope you’ll stick with me for a few minutes because this goes to the very roots of how we practice science, and what science is capable of in the first place.

Let’s start with my syllogism. It doesn’t say “designed by who.” The genetic code could have been designed by aliens. It could have been designed by some entity or process we have no knowledge of. However it doesn’t take a genius to connect the metaphysical dots.

So far in 8 years nobody’s punched a hole in this argument. As god-of-gaps arguments go, it’s pretty sturdy. It’s rooted in the fact that codes require specific choices to be made which you cannot derive from the laws of physics. It is different than most god-of-gaps arguments because it’s an ontological argument: Coded information is not even known to exist without an act of intelligence.

When I presented this to my skeptical brother Bryan, he immediately disliked it. He said to me, What do you expect scientists to do, Perry… throw up their hands and say ‘Gee, I guess God did do that. Time to go home, there’s nothing else for us to investigate!’?

If you don’t have a strong scientific orientation, if you’re a fairly religious person, you might say “Yes, I think scientists should rein in their bloated egos and give God some credit for the amazing world He made.”

But if you do have a strong scientific orientation, you know the scientist would be abdicating his responsibility. “God did it” takes a scientist’s job away. If there’s any possibility that a naturalistic explanation might be found, the scientist’s job is to find it.

I shouldn’t have to explain the benefits of sticking to these rules. Almost all scientific discoveries have practical applications. Sooner or later we get better medicine, smarter doctors, better computers, better cars, and a better life, because we understand the laws of nature better with each passing year.

Modern science has no earthly idea where life came from and anyone who suggests otherwise is either deluded or picking your pocket. But these rules still apply even with utterly daunting questions like the Origin of Life.

Personally I think the evidence we have points to the Origin of Life being a “second singularity,” an event as unique and miraculous as the Big Bang itself. In fact I’ve never seen any evidence to the contrary.

Nevertheless I must respect any scientist who endeavors to bridge the gap between life and non-life. That gap, after all, may someday get filled. If and when it is, countless valuable insights and new technologies will ride along as a bonus.

Someone may overturn my syllogism. In the spirit of science I will celebrate when they do. Why? Because the universe once again turns out to be even more impressive than we’d previously thought.

OK, then what about God?

To answer this question we have to go back to the roots of “methodological naturalism” itself. Methodological naturalism is the scientific practice of always assuming the laws of nature are consistent. It assumes they’re sufficient to explain the normal and customary operation of the world.

To my knowledge, the earliest statement of naturalistic thought in ancient times comes from Wisdom of Solomon 11:21, which was written 2,500+ years ago, says, “Thou hast ordered all things in weight and number and measure.” This is found in the apocrypha, i.e. the books of the Catholic Bible.

This came from Jewish theologians who believed that God made a world that was self-sufficient. It didn’t require His constant tinkering in order to operate.

This was not seen to conflict with the assertion that God is also present in the world and does miracles. On the contrary, naturalism itself is defined in terms of miracles. Naturalism is the regular and customary order of things. Miracles are when God shows up and does something that is not the regular and customary order of things.

I’ve witnessed many miracles up-close and in-person. I document a half dozen here, with links to peer reviewed papers that report healing of blind and deaf people in controlled studies. I see no conflict between the job of a scientist and the active exercise of the supernatural by real human beings in past and the present.

What if a scientist does witness a miracle? If he’s working in his professional capacity, he’ll start by searching for a naturalistic explanation. On the other hand as a whole human being he is also free to say, “I conclude that it was a miracle.” If he believes a miracle has happened, then by definition he can’t reduce what happened to scientific process.

Prehistoric vs. Modern Miracles

If every species of plant and animal was the result of a miraculous act of God thousands or millions of years ago, then we cannot investigate how antelopes evolved into giraffes.

However, if life evolved from a single cell, and if the process of evolution was not guided by God, then there is an evolutionary algorithm at the heart of living things that is truly astounding. However antelopes evolve into giraffes, we ought to get busy and find out how it works.

I’ve shown in other parts of this blog that evolution cannot possibly be the result of random accidents. Evolution is engineered. Therefore I cannot think of any field of study ripe with more promising discoveries than evolution itself.

I believe God wants to use science to teach us as much about Himself as possible. Most theologians would agree. And I believe the way we make those discoveries is through naturalistic investigation via the scientific method.

It’s deeply ironic that many modern evangelical Christians believe that plenty o’ miracles happened 2000+ years ago and 6000+ years ago, but they don’t believe miracles happen today. (They sure didn’t get that from the Bible.)

What if you flip that around? The way you prove miracles exist is by doing what Jesus said: Laying hands on people and healing them. (Most American evangelical churches do not do this.) I think miracles began in earnest with the ancient prophets, and in the meanwhile, God had granted life its own amazing natural engineering capabilities long before.

After all, which is harder?

1) Building a zebra and beaming it onto the savannah, Star-Trek style,


2) Designing a cell that builds an ecosystem for a zebra to live in – then builds the zebra too?

or even

3) Designing a universe that gives birth to a cell that builds an ecosystem for a zebra to live in – then builds the zebra too?

An accurate understanding of evolution – one that acknowledges the engineering capabilities of cells, the ability for organisms to adapt to their environment – offers a far more impressive view of God than anything the Young Earth Creationists ever envisioned.

Many religious people have taken the bait from the atheists who claim evolution got rid of God. Now they’re forever selling from their heels.

What a con. Every organism that has the ability to self-replicate and evolve exceeds anything humans know how to engineer. The real question is: Why is it even possible for a universe to even give rise to such things? Why is the universe so incredibly orderly? Why does it obey mathematical laws? Why is it logical?

There’s a huge difference between proximal explanations and ultimate explanations. Science is incapable of disproving or eliminating God, because science cannot even explain itself. In science we have to take on faith the assumption that the universe is logical and consistent. Surely it must be that way for a reason.

So I’ve come to these conclusions:

1. Any theory that takes a job away from a scientist is probably wrong.
2. Any theory that attempts to eliminate God as an ultimate explanation is probably wrong.

These two statements stand forever in tension with each other. The solution to the God of the Gaps problem is for us to always assume ultimate intentionality and order. Yet at the same time we can never announce we’ve reached the end of the scientific rabbit hole. There’s always another layer of order to discover.

Robert Boyle, the world’s first modern chemist, said this around 1675: “… the universe being once framed by God, and the laws of motion settled, and all upheld by his perpetual concourse, and general providence; the same philosophy teaches, that the phenomena of the world, are physically produced by the mechanical properties of the parts of matter; and, that they operate upon one another according to mechanical laws.”

In closing, I want to point out that there is one time-honored assumption in science that is currently failing:


Materialism insists that the fixed laws of physics explain everything. In Darwinism, it is assumed that blind physical processes combined with natural selection explain the diversity of life.

What we know from bioinformatics and the last 50 years of genetics is, every cell in the world is purposeful, teleological, and has built-in DNA self-programming and adaptive features. Non-living things are not teleological; living things are. Evolutionary processes are. We see purposeful direction and natural engineering in living things.

The prevailing scientific paradigm has no room for this. The old guard resists new research because materialists had been assured for 150 years that Darwin got rid of God. Darwin accomplished no such thing. Darwin uncovered an even bigger mystery that is only beginning to come to light now. Darwin thought cells were blobs of goo; he had no idea they’re tiny supercomputers armed with sensors and equipped with digital signal processing.

“There are more things in heaven and earth, Horatio, Than are dreamt of in your philosophy.” -Hamlet

I vehemently disagree with Neo-Darwinists who insist evolution is a simple process of random mutation + natural selection + time. Their theory of randomness is anti-scientific.

As an electrical engineer, I sympathize with the Intelligent Design movement in its insistence that design is detectable and that design is a proper scientific discipline. Every university in the world has multiple departments that teach design, after all.

But I disagree with the ID movement’s tendency to ascribe everything we don’t understand to direct divine agency. Like many other areas of theology, we have no choice but to live in the tension between the natural and the divine.

Einstein said, “There are only two ways to live your life. One is as though nothing is a miracle. The other is as though everything is a miracle.” I submit to you, dear reader, that even the regularities and natural systems of science are, themselves, enduring miracles.

Perry Marshall

P.S.: The worst way to counter a god-of-gaps argument is with dodges and shell games. Example: Richard Dawkins, on radio station WBUR in Boston, glibly proclaimed that life was a “happy chemical accident.” This statement, and many theories that are much more substantive than that, still engage in wholesale avoidance of the question. When there’s a gap, the honest thing to do is admit it.

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2 Responses

  1. God Chaser says:

    Regarding DNA code, The problem I have with science is that we know 100% that all codes that we know the origins of, come from a mind, and we know of 0% of codes that come from only physics and chemistry, yet they devote 100% of their time to researching only material causes and have nothing but contempt for any scientist who even entertain this line of research!

  2. Kevin says:

    I think you’ll enjoy this:

    Of Metaphysics and Polynesian Navigation

    James Barr

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