Evaluating Evolution and Design in Science

This page does not evaluate theories of evolution and design.
Instead, it looks at the logical process of evaluation.

7A. The many meanings of evolution — how can we evaluate?

What is the scientific support for evolution? This is a "trick question" that cannot be properly answered, because it is imprecise. Instead, we should ask about four evolutions: astronomical, geological, chemical, and biological. Most scientists think the scientific support is very strong for astronomical evolution (in an old universe) and geological evolution (on an old earth), but is much weaker for chemical evolution (of the first life). For biological evolution the support varies when we ask four sub-questions, as explained below. EVALUATION OF EVOLUTIONS

Logical Comparisons
Is a theory proposing that "John is an Olympic Weightlifter" supported if we observe that John can lift a hat and place it on his head? No, because a plausible alternative theory — "John has average strength" — also correctly predicts the result. To justify a response of "Wow!" instead of "So what?", the evidence must be relevant for helping us compare the theories, like seeing John lift a heavy weight that's close to the world record. To distinguish between competitive theories, we must focus on their differences (they disagree about John's ability to lift the near-record weight), not their similarities (they both agree that John can lift the hat).
This principle of logic is often ignored when evolution is evaluated, when scientists and educators claim support for evolution because "it can lift hats" instead of asking questions that are more useful for evaluation.

The Many Meanings of Evolution
We must define "evolution" before we can evaluate it.
In general, evolution is any process of gradual change. In biology, evolution (E) is a change in the gene pool of a population. But "evolution" can also refer to fossil-E progressions (in the geological record), common descent (with all species related by shared ancestors), micro-E within a species, macro-E to produce new species (with minor or major changes), neo-Darwinian subtheories proposing that E occurs by specific mechanisms (including genetic variation, natural selection, and more), or a Total Macro-E claim that all biocomplexity and biodiversity was produced by the cumulative effects of macro-E. A nonscientific meaning of E is a claim — made by some atheists (Richard Dawkins,...) and some Christians — that "evolution is inerently atheistic" so theistic evolution is impossible.

Logical Comparisons of Theories
This table shows whether each of four "evolutions" is accepted in four views of creation: evolutionary creation (by natural evolution), old-earth progressive creation (by modification of already-existing genes), old-earth progressive creation (by independent creation of new species "from scratch"), and young-earth creation.

theories of creation: For each E, does a creation theory say yes or no?	creation by natural evolution	progressive creations by modification	progressive independent creations	young-earth independent creation
micro-E and minor macro-E	YES	YES	YES	YES
old earth with basic fossil-E	YES	YES	YES	no
full common descent	YES	YES	no	no
natural Total Macro-E	YES	no	no	no

Using four definitions of E (by describing four related aspects of E) — which is more precise than just calling it "evolution" — allows logical comparisons:
All theories agree (YES YES YES YES) about "micro-E and minor macro-E" so these are irrelevant for helping us compare neo-Darwinian evolution (in "creation by natural evolution") with the other three creation theories.
Evidence for an old earth (with evolutionary fossil progressions) is not evidence against the two theories of old-earth progressive creation, which say "YES YES".
Similarly, evidence for common descent — such as homologous adaptations of previously existing structures, vestigial structures, "molecular clock" analyses, and a sharing of genetic code, Hox genes, and pseudogenes — counts against one old-earth theory (with independent creations) but not another (with creations by genetic modification).
To distinguish between any two theories, we must compare them to see where they agree and disagree. Then we should focus on evidence about disputed components (where one theory says YES and the other says NO), not shared components (where both say YES or both say NO). For example, the table shows that much of the common "evidence for evolution" — for minor macro-E, old-earth fossil progressions, and common descent — is not evidence for natural Total Macro-E when it is compared with progressive creations by genetic modification.

Shifts of Meaning
When using a word with many meanings, we should not mix the meanings by shifting from one meaning to another, in either of the two ways below.
evolution-shifting: Often, scientific evidence for a strongly supported meaning of evolution (micro-E, minor macro-E, fossil-E,...) is shifted to a less strongly supported meaning (Total Macro-E) without carefully analyzing the causal and evidential relationships between different aspects.
creation-shifting: Often, scientific evidence against young-earth creation is shifted onto old-earth creation. Also, the important scientific differences between two old-earth theories, proposing independent creation and genetic modification, are usually ignored. { What are the similarities and differences between young-earth creation and intelligent design? }
In each type of shifting, the shift is not logically justified. Unfortunately, sloppy logic allows sloppy claims, as in declaring that "evolution is a fact" without defining the meaning of evolution.
For example, common descent is often defined as the essence of evolution, but even though Michael Behe accepts common descent he is often attacked as a "creationist" because he challenges Total Macro-E with his claims about irreducible complexity.

7B. Can we use scientific methods to detect design?

Common Ways to Detect Design
FAQ-6 describes four types of design and explains that "design-action by a natural agent... is accepted by everyone... and is obvious in everyday life when we wake up in a house, listen to a radio, read a newspaper, or drive a car." In these situations and others, we're confident that we are detecting the results of design-directed action when we decide that observed "signs of design" could not be produced by undirected natural process.
Would you propose "design" if you receive a radio signal — 2, 3, 5, 7, 11, 13, 17,... — that you recognize as a long string of prime numbers?
William Dembski, a prominent design theorist, uses the concept of complex specified information to describe signs of design. A short string of prime numbers (like "2 3") is not complex, so it could easily occur by chance. A long string of random numbers is complex, but is not specified because it has no pattern or function. But a long string of prime numbers is complex and (due to its conceptual functionality) is specified.
Other types of specification due to functionality occur when you read a paragraph and understand the meaning, or when a combination of metal is a "bicycle" you can pedal to the store.

Historical Science & Common Design, and Controversial Design
Many arguments against design are also arguments against some areas of conventional science, in areas that study history (is historical science reliable?) or propose unobservable causes or agency action.
In all examples above (house,... bicycle) we infer "design-directed action" when we observe "signs of design" even if the agent and action were not observed. This logical principle is common in science, and scientists often infer an unobservable cause — an electron (in chemistry), a thought (in psychology), a volcano acting in the past (in geology), an agent acting in the past (in archaeology),... — from the observable effects it produces, in studies of current events or historical events.
In many historical situations only undirected natural process was involved, so an explanatory theory with only mechanistic action is adequate. But scientists agree that in some situations, as when trying to explain ancient cave drawings, a theory must include agency action as part of a plausible explanation. The actions of an agent (natural or supernatural) can be unpredictable, but a historical scientist only has to determine what did occur, not predict what will occur.
The examples above (house,... drawings) are uncontroversial, and theories of design are common in everyday life and in science. But questions arise when the design-action seems unfamiliar (so it might be supernatural) and we're looking at design in biology. In these situations the main concerns are religious, and a common criticism is that a design theory is a creation theory. But critics also have methodological questions:
What are the similarities and differences between design inferences in a common context and controversial context? Is an "argument by analogy" justifiable, in a claim that because scientists commonly infer design in one context (for a house, radio signal, or cave painting, when the agent and design-action seem to be natural) they should accept the possibility of infering design in another context (when we ask if design-action was required to produce biological functionality in the first living cell, or in the DNA specifying a functional protein, biochemical system, or whole organism, and when the agent and design-action might be supernatural)?

Scientific Questions about Evolutions — Biological and Chemical
• For each step in a total macro-evolutionary scenario — and for the whole scenario — how many mutations and how much selection would be required, how long would this take, and how probable is it?
• Do systems exist that are irreducibly complex because all parts are required for the system's function? if yes, could these systems be produced by a process of step-by-step evolution, if there would be no function to "select for" until all parts are present? { To understand irreducible complexity, think about a mousetrap with five interacting parts: a base, hammer, spring, catch, and holding bar. Each part is necessary, and there is no function unless all parts are present. A trap with only four parts doesn't just catch mice poorly, it doesn't catch them at all. / This illustrative analogy is from Darwin's Black Box: The Biochemical Challenge to Evolution (1996) by Michael Behe. }
• Could a nonliving system naturally achieve the minimal complexity required to replicate itself and thus become capable of changing, in successive generations, through natural selection in neo-Darwinian evolution? { Most scientists think this would require hundreds of biomolecular parts, not just the five parts in a simple mousetrap. }
These questions, and others, are examined in EVALUATIONS OF EVOLUTIONS.

Scientific Knowledge about Evolution
Most scientists think neo-Darwinian evolution could have produced all biological complexity. Loren Haarsma & Terry Gray explain why: "We know several evolutionary mechanisms that increase the size of a cell's genome (e.g., gene duplication, horizontal transfer, polyploidy, endosymbiont capture). Combined with natural selection, this allows information transfer from the environment to the cell's genome. In addition, the genomes of living organisms display redundancy and multitasking, allowing for the evolution of novelty and interlocking complexity. (from Perspectives on an Evolving Creation)"
And they recognize the limits of current knowledge: Until the past few years, we knew very little about the genomes of humans and other species. But even when we "map the genetic sequences of many species,... we will have only begun the work of understanding the capabilities and limits of evolution. In order to know whether or not some complex piece of biological machinery could have evolved, we must know each species' genetic sequences, but also understand in great detail how gene products interact with each other in living cells." They think that currently "the jury is still out" on design questions, but "it seems most promising — both scientifically and theologically — to study biological complexity expecting to find more evidence that God designed into it the ability to self-organize." {more from their chapter}

Can design be proved?
A particular feature (a star, bacteria, whale, biochemical system,...) was produced either by detectable design-action or by what appears to be undirected natural process. These two possibilities, which I'll call design and non-design, are mutually exclusive, so if non-design is highly improbable, design is highly probable. And vice versa. The evaluative status of non-design (and thus design) can be decreased or increased by empirical observations, so a theory of design is empirically responsive and is testable. Based on a logical evaluation of evidence, we can conclude that a design theory is probably true (if all non-design theories seem highly implausible) or is probably false (if any non-design theory seems highly plausible).
A design theory does not claim that non-design is impossible and design is certain, it only claims that design seems more probable. But proof is always impossible in science. Instead, scientists try to develop a logically justified confidence in the truth or falsity of a theory, and a high level of confidence (not proof) is the goal. Therefore, it seems unreasonable for critics of design to demand — along with radical postmodern skeptics who challenge the credibility of all science — that if design proponents cannot claim the certainty of proof, they can claim nothing.

Should scientists consider all possibilities?
All current theories for a natural chemical evolution from nonlife to life seem implausible, because what is necessary (for life) seems greater than what is possible (by undirected natural process). Is it rational for scientists to consider the possibility that carbon-based life on earth did not originate by undirected natural process, but was the result of design-directed action? The certainty of "proof" is impossible because we can never propose and test all possibilities for non-design. But could we develop a logically justified confidence that our search has been thorough yet futile, and no promising possibilities remain unexplored?
What are the possibilities? Perhaps a feature, such as the first life, was produced by undirected natural process that: • did occur even though it was extremely improbable (so we should reject it as a scientifically plausible explanation), or • would be improbable in a universe but was highly probable because we live in a multiverse; or did occur and was reasonably probable and can be described in a naturalistic theory that • is currently known (even if this theory currently seems inadequate) or • will be known in the future, or • will never be known because the natural process was too complex or unfamiliar for us to propose. Or maybe the feature was produced by design-directed action, by: • natural design and construction, or • supernatural design and creation. Should scientists ignore the last two possibilities?

False Negatives and False Positives?
When evaluating a claim that a particular feature was designed, a false negative — by concluding "no design" when there was design — occurs when we are unable to detect design-action. Sometimes this occurs when an agent wants design-action to be undetectable, as in the actions of an illusionist, criminal, plastic surgeon, or a movie-maker's "special effects," or a divine guiding of natural process.
A false positive — by concluding "design" when there was no design — could be caused by a wrong conclusion about current science (saying "undirected natural process could not produce the feature" when in reality it could and did) or by wrong predictions about future science (saying "it will never find a naturalistic explanation" when in reality it can and will), or in other ways.

What might happen in the future of science?
A major challenge in evaluating design is uncertainty about the adequacy of our current science. Advocates of non-design imply that future science, when it becomes more adequate, will support their claims. But the change in support could go either up or down. Will non-design seem more plausible because we have discovered how a feature could have been produced by natural process? Or will non-design seem less plausible — as with chemical evolution since 1953 when the Miller-Urey experiments were "hot news" that inspired naturalistic optimism — because we have learned more about the limits of natural process?
What will happen? We can try to predict improvements in current theories and inventions of new theories, by using current knowledge (*) plus creative thinking (to imagine what could be) and critical thinking (to predict what is probable in reality, not just possible in our imaginations) so we can avoid the extremes of insisting that "nothing new will happen" or "anything could happen." / * For example, we can "critically imagine" how future knowledge might change our views about each obstacle to a natural origin of life: the unfavorable chemical equilibria in reactions for synthesis of biomolecules, the biocomplexity required for life,...

Scientific Evaluation and Philosophical Perspectives
Typically, scientific theories are evaluated based on scientific evidence-and-logic combined with philosophical perspectives that include deciding what to conclude when the evidence is not conclusive. For every question about design, scientists currently give non-design (the reigning paradigm) the "benefit of doubt" and put the "burden of proof" on design (as the challenger). But if the evidence-and-logic is not conclusive, maybe saying "no conclusion" is the best conclusion. Instead of thinking it's necessary to "declare a winner," can we just say "we're not sure at this time" and continue searching, with a humble open-minded attitude, in our efforts to learn more?

Should we ask the question?
Imagine a "super science" constructed by trillions of super-intelligent space aliens who have studied biochemistry for billions of years, have explored the universe searching for life and environments for producing it, but have not yet constructed a plausible theory for a natural origin of life. Even in this situation a denial of design would be possible, but would it be rational?
Compared with this imaginary super-science, in the near future the actual state of human knowledge will remain much less advanced. For awhile, scientists will continue to disagree about the plausibility of design, but this is healthy for science when it stimulates thinking and discussions between advocates for different points of view. Proof is impossible in science, and it can be difficult to confidently answer the question, "Was design-action involved in producing this feature?" Although it should be easier to decide, "Should we ask the question?", there are also vigorous arguments about this, as you'll see in Sections 7C and 7D.

Appendix to Section 7B:

Usually, non-design and design are mutually exclusive. But sometimes — although not for the usual questions being debated — there is a "gray area" when defining design, so we may have to define types of design (or degrees of design) based on a multi-dimensional system of criteria that include intelligence and intention:
intelligence: The Hoover Dam is a result of design-action, but what about a beaver dam? or a bird nest or ant hill? There is action, but is it "intelligent" or just the undirected natural process of creatures doing "by instinct" what they naturally do? How much intelligence is necessary for intelligent design?
intention: If a company accidentally releases untreated waste-chemicals into a river and changes its ecosystem, is this change a result of design-action? Should we say "yes" if the results (in the river) cannot be explained without considering the "extra chemicals" that were the result of human decisions? Would our confidence in a conclusion of "design-directed action" be different if the pollution was an unintended surprise, or if it was predictable and (because the chemicals were dumped anyway) the pollution was intentional?

And what about other factors that might be relevant when we're deciding whether to say YES or NO to questions about design-action?

goals and abilities: Elliott Sober claims that a basic design theory (which simply claims "design did occur") can be plausible only if it is "supplemented with further assumptions [supported by independent evidence] about what the designer's goals and abilities would be if he existed. (source)"
But sometimes a "logical inference to the best explanation of observations" automatically includes inferences about goals and abilities. For example, the mere fact that we are observing a radio signal with prime numbers will justify a conclusion that a "signal designer" must have the cognitive ability to understand prime numbers, and the technological capability and motivation to encode these numbers into a radio signal.

competence and compassion: Do biological imperfections show that the designer is incompetent? And does suffering in nature — due to predators, viruses,... — show that the designer lacks compassion and morality?
These anti-design arguments are much weaker if, instead of designing every feature of every creature, God used a combination of natural evolution plus design-directed action, as in progressive creation by genetic modification. And theological humility is often ignored, as in Stephen Jay Gould's claim that "God surely would not have used a collection of parts generally fashioned for other purposes," as if he knew what God would have done. But in the Bible, God's actions are not always obvious or easy to understand.
And when we ask, "Why does God allow bad things to happen?", one part of a satisfactory answer is the incarnation of Jesus, when God lived among us, sharing our joys and sorrows, pleasures and suffering.

7C. Is methodological naturalism useful in science?
Should intelligent design be allowed in science?

Currently, most scientists use methodological naturalism by including only natural cause-and-effect in their scientific theories, when studying the current operation of nature or the formative history of nature. Therefore, the inevitable conclusion for every question about the history of nature — no matter what is being studied, or what is the evidence — must be that "it happened by natural process." But these forced conclusions might lead to some wrong conclusions. If we want science to be more effective in our search for truth, one option is to replace rigid-MN with testable-MN in which a scientific investigation begins by assuming "it happened by natural process" but considers this an assumption that can be tested, not a conclusion that must be accepted.

Should scientists search everywhere?
Perhaps with rigid-MN a scientific search for truth is occasionally futile, like trying to explain how the faces on Mount Rushmore were produced by natural processes of erosion. If scientists are restricted by an assumption that is wrong — that does not match historical reality — their finest creativity and logic will fail to find the true origin of the faces.
Or think about a man who is looking for missing keys in the kitchen when the keys are on the front porch. No matter how hard he searches the kitchen, he won't find the keys because they aren't there! They can be found only by someone who is open-minded and is willing to search the porch. When we're not sure where the keys are, instead of demanding an either-or choice (by restricting the search to either kitchen or porch) it seems more rational to search everywhere, in both kitchen and porch.
In science — when we're using evidence-and-logic to search for truth about nature — is rigid methodological naturalism a useful strategy? MN will probably be useful IF its assumption about history (that it included only natural events) matches the reality of history, since rigid-MN will help scientists avoid being distracted by false theories about non-natural events. But IF non-natural events really did occur in history, so the premise of MN is false, rigid-MN will force scientists to reach some false conclusions, and this doesn't seem useful.
Since we don't know whether MN matches the reality of history, what is our best scientific strategy? Should we search with a humble attitude by refusing to assume that we already know — with certainty, beyond any doubt — what kind of world we live in? Should we assume answers, or investigate questions?

Is methodological naturalism required by The Rules?
In natural science, do we have to explain natural phenomena and natural history by natural causes? No, this claim is just circular logic that's camouflaged with verbal ambiguity by using natural to mean both "pertaining to nature" (three times) and "normal appearing" (once).
A principle of methodological naturalism cannot be derived from science (so it is non-scientific) but is compatible with science (so it is not un-scientific).
But if we define science as "whatever scientists do," and most scientists currently use methodological naturalism (MN), doesn't this make it scientific? If those with power to make decisions (about publishing, funding, and hiring) decide that MN is a "rule of science" that is unwritten yet is enforced, does this settle the issue?
Is science a game with rules? This is an interesting sociological perspective, useful for thinking about interpersonal dynamics and institutional structures. But overall it seems more useful to think about science as an activity with goals rather than a game with rules.
Let's compare "cheating" in sports, business, and science. In a Strong Man Contest, if other contestants carry a refrigerator on their backs, one man should not be allowed to move it using a two-wheel cart because this is not useful for achieving the goal of the game, for deciding who is the strongest man. But if the goal of a business is to deliver refrigerators quickly, many times throughout the day, a two-wheeler is useful.
Although it isn't the only goal, for most scientists the main goal of science is finding truth about nature. But rigid-MN might lead to unavoidable false conclusions. When some scientists recognize this and question the usefulness of rigid-MN, is it cheating or wisdom?

design and MN: A basic design theory (which only claims "design did occur" *) does not explicitly propose supernatural action, but — since design-action can be either natural (as in genetic engineering) or supernatural (as in miraculous biblical healings) — it implicitly acknowledges the possibility of divine action, so design isn't limited by methodological naturalism. {* it does not try to explain the details of who, how, and why }

Can science investigate the supernatural?
Can the logical methods of science be used to study non-natural events? In some ways, no. But in other ways, yes.
As explained in Section 7B: scientists can infer an unobservable cause (electrons, ideas, historical events, actions of an unseen agent,...) if it produces observable effects; sometimes agency action must be part of a plausible explanation, and historical scientists just describe what did happen, they don't predict what will happen; design inferences are common in science, but there are differences (and similarities) between this common design and the controversial design that makes claims about biological systems; design and non-design are mutually exclusive, so scientists can evaluate design (which could be natural or non-natural) by evaluating non-design using conventional scientific methods; when the evidence-and-logic is not conclusive, instead of rigidly defending the status quo (of non-design) against the challenger (design), maybe the best conclusion is a non-conclusion, by simply saying "at this time we're not sure."

Is design a science-stopper? Is MN-Science more effective?
If scientists think "a designer did it," won't this stop scientific progress because there is nothing left to study?
No. This is unrealistic because when most scientists hear a claim that "maybe a non-design explanation doesn't exist" they will continue their non-design research, probably with renewed vigor because they are responding to a challenge. Yes, if the keys really are in the (naturalistic) kitchen, they probably will be found by someone who believes "the keys are in the kitchen" and is diligently searching there. Proponents of rigid-MN think that testable-MN would lead to decreased scientific effectiveness, because of decreased motivation (due to doubts about "where the keys are" and whether diligent searching will be productive) or decreased funding of research, or in other ways.
Currently, most biologists think non-design research is more productive for helping us understand the history of life. I agree, and I think non-design theories, especially the modern synthesis of neo-Darwinism, will continue to be more fruitful in stimulating productive research. But design can also be scientifically useful when the perspectives of design and non-design are combined, with creative-and-critical thinking (in non-design) supplemented by additional critical thinking (in design). And a design perspective could also promote creative thinking by its proponents and opponents.
We don't have to make an either-or choice. We all share the goal of finding truth, and proponents of design want non-design research to continue and prosper so we can learn more, so in future science we can better evaluate the merits of non-design and design. Design proponents want to supplement non-design research, not replace it. They want to stimulate productive action and critical thinking, with invigorating debates between critics of a theory and its loyal defenders. This has occurred due to Michael Behe's claims for irreducible complexity in 1996, even though the current scientific community does not want to acknowledge or encourage this scientific stimulation, as you can see in Mike Behe's Adventures with Science Journals.
What difference will design make? It will have little overall impact, because most areas of science are not affected by controversial claims for design. But for some questions about origins of the universe, first life, and complex life, maybe design deserves to be viewed as a potentially useful idea, worthy of serious consideration and further development.

Should science be logical?
Of course, everyone says YES. But if there is a conflict between logical and natural, which criterion should have higher priority? Should we let methodological naturalism force us to accept a "scientific" conclusion that is less logical, just because it is natural? Should we define science as a search for natural explanations, or a search for logical explanations?

Bypass the Process, Claim the Support
The Conclusion of MN-Science — that (no matter what is being studied, or what is the evidence *) "it happened by natural process" — is actually The Assumption of MN. The circular logic of MN is unavoidable, and no science is needed to guarantee a naturalistic conclusion. Of course, the irrelevance of evidence does not mean there is no evidence, or that MN is leading to the wrong conclusion. But it does illustrate a logical weakness of MN. Instead of acknowledging this logical weakness, however, usually MN-Humility is ignored and there is an implication that the naturalistic assumption is a conclusion of science, and is therefore true. Strange as it seems, methodological naturalism provides a way to bypass the process of science and then claim the support of science.
* For example, despite the weak scientific support for chemical evolution the prestigious National Academy of Sciences confidently asserts (in the second edition of Science and Creationism, 1999) that "the question is no longer whether life could have originated by chemical processes involving nonbiological components. The question instead has become which of many pathways might have been followed to produce the first cells. (source)" Is this confidence based on the process of science or an assumption of MN?

When is critical thinking unscientific?
Are scientists "unscientific" when they strongly criticize chemical evolution? What would make their critical thinking unscientific: describing the inadequacy of all current theories? claiming that future theories will also be inadequate? that a natural origin of life is extremely improbable, maybe impossible? a perception that this claim implies a non-natural cause? an explicit proposal for a non-natural cause? But if strong criticism is accompanied by a proposal for a new naturalistic theory, does this make it scientific?
Can scientists admit that "we are far from finding the answer" but not that "maybe there is no natural answer"? Consistent with rigid-MN, should we control the thinking of scientists by removing their freedom to propose that "maybe..."? Or should we let scientists use the entire process of science, including a logical evaluation of all competitive theories, when they are determining the conclusions of science?

7D. Methodological Naturalism: Can a Christian use it?

What is it?
Currently, most scientists use methodological naturalism by including only natural cause-and-effect in their scientific theories, when studying the current operation of nature or the formative history of nature. Therefore, the inevitable conclusion for every question about the history of nature — no matter what is being studied, or what is the evidence — must be that "it happened by natural process."

Can science coexist with miracles?
The Bible claims that God does miracles. If this is true and miracles do occur, is science possible? Yes. Effective science requires a world that is usually natural, but it doesn't have to be always natural. Science would be impossible in a world with constant "Alice in Wonderland" surprises and no reliable cause-effect relationships. But if, despite occasional miracles, our world usually operates with its normal/natural patterns, science will be possible and useful. In fact, the logic of science — which helps us recognize the usual patterns in nature — can help us recognize when results seem to differ from these patterns, when a miracle may have occurred.
Christians do not have to choose between science and miracles. We can believe that science is a reliable source of knowledge, and that miracles did occur in the Bible, do occur now, and might have occurred in the formative history of nature.

Is methodological naturalism theologically satisfactory?
A devout Christian who believes "miracles occurred in salvation history" can evaluate all available evidence and conclude that "formative history was all-natural with no miracles." But should an all-natural history be the only possibility that is considered during scientific evaluation? In my opinion, Christians can view methodological naturalism (MN) in two theologically satisfactory ways:
In one approach, proponents of an open search accept MN but consider MN-science to be only one aspect of a broader "open search for truth" that considers all possibilities, including miracles. Their scientific search, but not their open search, is restricted by MN. Although MN-science is respected as an expert witness, it is not allowed to be the judge and jury when we're defining rationality and searching for truth.
In another approach, proponents of open science claim that — if we think miracles do occur in salvation history and might have occurred in formative history — we should not assume, as demanded by MN, that "miracles never occurred" while doing historical science. They think science will be more effective, in our search for truth, if they replace rigid-MN with testable-MN in which a scientific investigation begins by assuming "it happened by natural process" but considers this an assumption that can be tested, not a conclusion that must be accepted.
In both approaches, a Christian believes that natural process was designed and created by God, is sustained by God, and can be guided by God, so "natural" does not mean "without God."

Can science avoid the possibility of unavoidable error?
Imagine two possible worlds: one has a history of nature with only natural process, while the other includes both natural-appearing and miraculous-appearing events. When we ask, "Which type of world do we live in?", we hope our science will help us, not hinder us, in our search for truth. But in one of the two possible worlds, a science with rigid-MN — which implies that we already know (with certainty, beyond any doubt) what kind of world we live in — must inevitably reach some wrong conclusions. By contrast, in either world a science with testable-MN — which allows both MN and non-MN modes of thinking, by starting with an MN-assumption but not demanding an MN-conclusion — will allow, although it cannot guarantee, correct conclusions.

Two Limits for Science
Scientists who decide to use methodological naturalism, which places a limit on what can claim to be science, will automatically place a limit on what science can claim to explain. Why? Because MN logically requires MN-Humility to acknowledge the possibility of unavoidable error: If the origin of a feature actually involved a non-natural cause, then any explanation of the feature's origin by MN-Science (in terms of only natural causes) will be incomplete or incorrect.

The Rarity and Futility of Humility
In principle, an open search that combines MN-Science with MN-Humility seems logically and theologically acceptable. In practice, a weakness is the rarity and futility of humility.
MN-Humility is rare. In the open phase of a search, Christian scholars rarely question the authority of closed MN-Science by suggesting that it can err (in general) or has erred (in a specific situation) by reaching a wrong conclusion. And non-Christian scholars are even less likely to be humble about the naturalistic conclusions of MN-Science.
MN-Humility is rarely effective (in producing a "level playing field" for comparative evaluation of naturalistic and non-naturalistic theories), even when it is acknowledged. Why? Think about what happens when a "scientific" theory and a "nonscientific" theory both claim to describe the same feature of history, such as the origin of life. The nonscientific theory is not respected because most people assume that, for a theory about nature, "not scientific" means "probably not true." Due to the cultural authority of science, the scientific theory is viewed as being more plausible, even if the scientific evidence does not support it, as in a natural origin of life.

Naturalism is not Naturism
Confusion is caused by the common use of "naturalism" with two meanings: in a narrow meaning, naturalism is a specific claim — which is compatible with Christian theism — of "only natural process" for a particular event, series of events, or period of history; in a broad meaning, NATURALISM (or naturism) is a general claim — which is not compatible with Christian theism — that "only nature exists" with matter/energy but with no God and thus no divine action.
But when we're thinking intuitively about "narrow" and "wide" we must be careful because a wide range of people (including theists and non-theists) affirm the narrow meaning, while a narrow range of people (only non-theists) affirm the broad meaning. { This distinction makes sense when you think about it, but you do have to think about it, to avoid thinking "narrow" means "accepted by a narrow range of people." }
A naturalistic explanation (in science) does not provide logical support for atheistic naturism (in philosophy), since theists believe that God designed, created, and sustains natural process, governs it and can guide it. Does "natural" mean "without God"?
Do you see the two differences between methodological naturalism and philosophical naturism?

Open Science is not Theistic Science
A theistic science is based on the principle that theists should use all they have reasons to believe (including their theology) when doing science, when constructing and evaluating theories. But theistic science is not a single way of thinking, because our differences — when interpreting the Bible (in theology) and nature (in science) and combining these interpretations — can lead to different ideas about God, scripture, divine actions, nature, and science, which can produce dogmatic rigidity (ranging from extremes of young-earth geocentrism to evolutionary deism) or open-minded flexibility.
But everyone, whether they are a theist or nontheist, has a worldview that influences their science and their willingness to "follow the evidence" to any conclusion.
An open science welcomes all perspectives — including atheism, agnosticism, pantheism, and theistic sciences with differing views about MN and about questions of age and evolution — but is not restricted by the dogmatism of any perspective, so it can maintain an open mind about a wider range of scientific conclusions.

Methodology can influence Worldview
In principle, methodology and worldview-philosophy can be independent, but in practice they are mutually interactive and each tends to influence the other.
In principle, an open search for truth (using MN-Humility) can prevent the naturalistic methodology of MN-science from influencing our philosophical worldviews of "the way the world is, what is and isn't real, what can and cannot happen."
In practice, methodology can influence our thinking because naturalistic assumptions automatically (*) become naturalistic conclusions about "the way the world is (regarding what can and cannot happen) according to science," and many people are influenced by science, as discussed in FAQ-1 (science and worldviews) and FAQ-2 (science and scientism). {* The circular logic of MN lets science bypass the process of science. }