Here’s a concise summary of my view
Scientific methods are fully capable of answering scientific questions. But not all questions are scientific.
Methodological naturalism can adequately provide deterministic answers to certain scientific questions. For example, when will sunrise occur on October 17, 2019 in Marty’s back yard? Newtonian mechanics are completely sufficient to answer this question. I don’t need to make references to God’s providence or miracles.
Methodological naturalism can adequately provide probabilistic answers to other scientific questions. For example, what will be the low and high temperatures in Marty’s neighborhood on October 17, 2019? I could use statistical methods to calculate the normal distribution of high/low temperatures over the past 100 years at that location, then provide a confidence level for temperature ranges (i.e., a 64% chance the high temperature will be between 61o F. and 69o F.; a 95% chance the high temperature will be between 57o F. and 73o F.; etc.) Again, this probabilistic analysis requires no reference to providence or miracles.
We can even extend predictions backward in time. When was the supernova that created the Crab Nebula? In 1928, Hubble looked at the data about its rate of expansion and determined that the supernova had flared in the mid-11th century. And it just so happens that Arab and Chinese astronomers left records of a supernova at that location in 1054. Given these observations, astronomers are 100% certain that the supernova observed in 1054 and the Crab Nebula today are the same object observed at different times, in spite of the changes that have occurred in its structure, size, and apparent magnitude. And once again, astronomers do not need to refer to divine intervention as an explanatory mechanism.
Biologists, like astronomers, can look backwards in time to make predictions. Just as Hubble looked at the expansion rate of the Crab Nebula, biologists can use observations about existing processes (mutation rates, genomic sequences, measures of selection pressure, speciation) to build reliable nested hierarchies of life across the kingdoms. Just as today’s astronomers were able to anchor their prediction using the records left by Chinese and Arab astronomers, today’s biologists anchor their backwards predictions using the fossil record. Also like astronomers, they do not need to refer to divine intervention when they make predictions.
There are some important differences, of course. The processes of life are far messier and stochastic than the processes described by general relativity, so the biology predictions are in some ways more like predicting the weather than like predicting sunrise.
A final note about the sufficiency of the scientific method: both in physics and in biology, many questions remain unanswered. A physicist cannot tell you anything but informed speculations about the 93% of the universe that is dark matter and dark energy. A biologist cannot tell you anything but informed speculations about how the first cellular life came to exist. These limitations need not lead us to conclude that dark matter and dark energy are explained by angels and demons–although that is one possibility. These limitations need not lead us to conclude that the first cellular life was a pure miracle that could not in any way be described by methodological naturalism–although that, too, is a possibility. I see no value in speculating what scientists and/or theologians will discover about those questions in the coming decades. What will be discovered is what will be discovered.
I’m seven paragraphs in, but I’m just getting started! Please hang with me a bit longer.
There are other questions that science cannot answer: What are the purposes of sunrises and weather changes and the evolution of life? How does God interact with these processes? Science can say nothing, but good theology can give us at least partial answers. The features and processes of the universe give us a place where we humans, who are created in God’s image, can discover His creativity and goodness and even interact with Him. And there is no process, whether it be gravity, quantum mechanics, or evolution, which is not somehow sustained in every moment by God’s providence. Science is sufficient to give reliable answers to scientific questions, but it cannot tell us for what or for Whom we are made, and how all of creation hangs together.
Does that make sense?