There is NO evidence for God!

I hear the "There is no evidence for God" line all the time from atheists and other critics, but I think that it's untrue; there IS evidence for God.

An analogy: The Big Bang Theory is widely accepted, but that doesn't mean that there is no evidence for the Steady State universe or a cyclical universe. It just means that the Big Bang Theory explains more of the data/evidence better than those other two. The same data/evidence is used by all three.

Similarly, Christians, atheists, and other critics all see the same data/evidence, however Christians offer an explanation but atheists, and other critics usually do not.

The data/evidence

1) Reason is the basis for all knowledge - thus one cannot default to scientific explanations.

2) Philosophical Naturalism is logically incoherent, thus 1) one cannot default to physical explanations; 2) we now have at least one reason to see non-physical explanations as reasonable.

3) Our thoughts are not just brain activity, rather they are the result of an immaterial mind thus, we now have a second reason to see non-physical explanations as reasonable

4) A metaphysically necessary, efficient cause solves the problem of an infinite regress of causes

5) the origin of DNA is more likely on design than chance.

6) The fine-tuning of the universe is more likely on design than chance or necessity - thus, given all the above, a transcendent metaphysically necessary God is the best explanation for life as we know it.

7) Jesus was a historical person, see also Bart Erhman, NT Scholar agnostic/atheist where he says ["no question Jesus existed"] since there are many, early, independent sources.

8) Jesus' resurrection was historical rather than a myth

Conclusion: Sans the presumption of philosophical naturalism, 1–8 above, and the explanation offered for each, offer a critical thinker good reasons to conclude that the Christian God is the best explanation for the world as we know it.

If atheists and other critics with "I don't know" or "I'm not convinced" then they are admitting that they do not have any explanations and tacitly conceding that the Christian has the better explanation.

If one has no better explanation(s), why reject the Christian's?

Objection A - This is a God of the gaps fallacy

Reply: I’m not citing a gap in our knowledge and saying "God did it". This is a series of arguments; first showing that reason is the basis for knowledge not science; second, that must be a non-physical aspect to reality; third that design is a better explanation for our existence and life; fourth that God is the best explanation for whom that designer is.

Objection B - The theory of the existence of a mind makes no predictions, thus there can be no evidence for it. 

Reply: It doesn't need to. You seem assuming that it must meet the criteria for a scientific theory, but this is a logical argument. See point 1 Reason is the basis for all knowledge - thus one cannot default to scientific explanations.

Objection C - this is just a list of assertions based on your own ignorance, incredulity, and gullibility; that's not evidence for God. This is just "apologist goulash"  

Reply:  You are just sticking your head in the sand, refusing to engage in a discussion of the evidence/data/arguments. 

Objection D - You might want to post this on a Reddit sub where you debate atheists, not Christians. I'm sure the Christians here could offer some constructive feedback, though.

Reply:  In my experience: 1) there are enough atheists in Christian subs to get feedback/debate, 2) what I mostly get on when I used to post atheist Subreddits is derision and downvotes, no intelligent discussion. Look at the current comments on Reddit. Additionally, Christians can be edified, educated, and enriched with this.

Objection E - Your points/arguments are incredibly inaccurate

Reply: Which ones specifically and where exactly are the errors for each? 

Objection F - Is the universe really so perfect? It’s extreme and harsh. Completely inhospitable for life, with vast excesses of empty space. Is that the mark of design?

Reply: When scientists speak of fine-tuned universes, they are referring to universes that are life-permitting. By life-permitting, they do not mean that life can exist wherever, or whenever, or that it's a paradise, or that there is no suffering/death; they do not even guarantee that life will exist. It’s a much more modest claim. It only holds that the fine-tuning will permit the existence of life. That’s it.

Objection G - You misunderstand what constitutes evidence.

Reply: Evidence is an item or information proffered to make the existence of a fact more or less probable. Evidence can take the form of testimony, documents, archaeological finds, DNA, etc

DNA is evidence. The findings of neuroscience for an an immaterial mind is evidence. Fine-Tuned Constants is evidence. Philosophical Naturalism is logically incoherent is evidence

Objection H -  Where you see design, others see chaos.

Reply: What better explains the Fine-Tuned Constants of the universe? Design, or chaos? Why?

What better explains the multitude of DNA-based micromachines like the ATP Synthase? Design, or chaos? Why?

SETI looks for design [or artificiality - i.e. not generated by natural processes], an arson investigator can tell if a fire came about naturally or was started by a human, the police can determine if a death was natural or at the hands of a human, an archeologist can say whether it’s a just rock or an arrowhead, etc. An appeal to a designer is accepted in every field of inquiry, including biology - we can determine whether a virus, like Covid-19 was designed of was natural.

An a priori non-design stance seems to be an a priori ideological conclusion, rather one that is driven by the facts

Objection I -  The problem with this is sooner or later we hit a brute fact. I say that the fact is there are natural laws that describe how reality functions.  You say, because a magic guy made it that way.  We can show the laws, testable, repeatable, and consistent.

Reply: First, you cite "reality"; so what is reality, and how do you know? 

It can't be Philosophical Naturalism since it's logically incoherent and since Reason is the basis for all knowledge this seems to be how we should evaluate arguments

And the "magic guy" is better understood as A metaphysically necessary, efficient cause 

Additional info

Atheist Engineer Explains How Reason Led Him To GOD (Part 1) [Video]

Scientific Evidence for an Immaterial Mind - aka the Soul

Yes, we do have some evidence that the mind is separate from the brain.

1) cerebral localization

It's been known since the 19th century that for motor and sensory function there are very specific locations in the brain that seem to mediate those functions. Hand movements are controlled by a specific part of the opposite cerebral hemisphere. Vision is controlled by a very discrete area in the occipital lobes.

However, Higher intellectual functions, such as abstract thought, mathematics, ethics, are not localized like that. There is no calculus center of my brain. There's no ethics center in my brain.

The brain seems to be necessary for doing calculus and doing addition and thinking about concepts like justice and mercy, and so on, but it's not localizable. The belief that higher abstract thought was going to be localizable was held by materialism in the 19th century, and they developed the theory of phrenology from that. He has the idea that all of these individual higher intellectual Functions have a spot in the brain that controlled them. Phrenology has been discredited. It's been shown to be wrong.

Because only certain things in the brain seem to be mediated by the brain other aspects of the mind, don't have a spot in the brain. The implication there is that they're not really material, but they're an immaterial power of being able to reason and use logic. And frankly, that's a very old dualist idea. It was an idea proposed by Aristotle. So for thousands of years duelists have predicted that and modern neuroscience, for now, confirms that.

2) split brain operations

Back in the 1960s, Roger Sperry, a prominent neuroscientist did a series of studies on patients, who had split brain operations due to severe epilepsy. An epileptic focus would begin in one hemisphere of the brain and travel through the corpus colosum, which is a bundle of fibers connecting the two hemispheres, and cause a generalized seizure.

It was recognized by surgeons in the mid-20th century that if you cut the fiber bundle that connected, the two hemispheres of the brain that you could prevent the seizures from becoming generalized, and you could greatly improve the quality of the patient's life. So a number of patients had this operation called corpus callosotomy. The patient's seizures would get better. But they really weren't much different, that is that their brains were essentially cut in half, but they still seem to be a unitary person. They still seem to be fairly normal. Sperry was a neuroscientist who studied these people in detail, and he did find that there were some subtle abnormalities as a result of cutting the brain in half, but the abnormalities were very subtle; so subtle that the experiments he won him the Nobel Prize.

And what that implies is that the human mind is not purely generated by the matter of the brain, otherwise cutting the brain in half would have profound effects on the human mind. It might make two people. Certainly, it should create a profound difference in a person's state of consciousness, but it doesn't. You've cut the brain in half and the person can't tell the difference, except that he has fewer seizures.

3) epilepsy neurosurgery

Dr. Penfield was the first neurosurgeon to systematically operate on the human brain when people were awake; he would work on the brain while they were awake in an effort to identify the focus of their seizures and to remove the focus from the brain. So their seizures would stop, and he operated on upwards of a thousand patients like this and very carefully recorded his results. He believed that all the mind originated from activity of the brain., but by the end of his career, he was a passionate dualist.

He repeatedly observed that there were aspects of the patient's mind that no matter what he did to the brain he couldn't affect. He could elicit memories, make a muscle move, or make a patient have a sensation. But he couldn't change their consciousness, he couldn't change their intellect, he couldn't change their sense of self. There was a fundamental core, that no matter what he did to the brain, remain the same. So, he said there was something he couldn't reach.

He asked the question, why are there no intellectual seizures? When people have epilepsy, commonly a person will have jerking of a muscle. Sometimes so many muscles jerk that they actually go unconscious. Sometimes they have a tingling on their skin, or sometimes they'll have a funny smell, or sometimes they can even have a little behavioral tick.

But they never start doing calculus. They never contemplate, justice or mercy. They never think about Shakespeare. So Penfield says, why aren't there intellectual seizures? If the mind comes from the brain entirely, the mind is material in some sense, then you ought to have seizures that make you do addition. Or think about politics. But you don't. What that implies is that the intellect is not the brain.

4) vegetative state brain function

Neuroscientist Adrian Owen looked at brain function in people who were in persistent vegetative state, Persistent vegetative, where a person has such severe brain damage that they show no sign of consciousness. And sometimes their caretakers will say something like, *I get the sense that the person is there that they understand things*, but there's no clinical evidence for it. Doctors would examine them, but there's no sign of any reaction at all and scan their brains are shrunken and obviously severely damage.

So Owen did a fascinating experiment. He used the technique called functional MRI imaging, which is mRI machine that images changes in blood flow in the brain that seems to correlate with brain function. So if you're moving your arm, the part of your brain that involves moving your arm lights up on the functional MRI. If you're thinking about stuff, your frontal lobe, slide up, things like that. So what Owen did is that he took a woman who had been diagnosed for several years and persistent vegetative state from a car accident, who showed no sign at all of any awareness, deep common, put her in the MRI machine and ask your questions. He said, pretend that you are playing tennis. Or imagine that you're walking across the room. He asked her to imagine all these things, and her brain kind of lit up in places.

But you could say that the brain lighting up, doesn't mean she was understanding anything. Maybe the sound coming into her ears, was causing a reflex or something. So, he took 15 normal people. And he did the same thing with them. Stuck them in a machine, put an asked the same questions. And then he asked, neurobiologists to look at the functional MRI images of this woman and the 15 normal people, And see if you can tell a difference between the two and they couldn't. Her pattern of reaction was identical to the normal people. That seemed to imply that she could understand what he was asking.

But perhaps the lighting up of areas in her brain and the lighting up of the area is a normal people's brains was just because of the reception of the sound, and didn't really understand. So what he then did is he took the same words that he had asked her before, but he took away the semantics. And just left some syntax. And her brain stop stopped reacting. As did the normal controls. Her brain only reacted when what he said to her made sense. It didn't react from just sound.

And this has been repeated by a number of different investigators that show the same thing that he found. That even when your brain is so massively destroyed and there's no clinical evidence for any mental activity at all, functional MRI can find that these patients are capable of thinking. Some patients who can do mathematics, ask "what's six plus six" and then give them different answers and when you hit the right answer of the brain lights up. So, very clearly, there are aspects of the mind that cannot be destroyed by severe brain damage. That's what Owen's work is showing us. It's showing us our aspects of the mind that aren't connected tightly to the brain, our minds are immaterial.

Conclusion

So not only is this a blow to a naturalistic understanding of the world it is also evidence for the existence of the soul, since in religion and philosophy, the soul is often considered to be synonymous with the mind or the self.

And while this doesn't show how an immaterial mind could interact with the physical brain in A Scientific Case for the Soul Robin Collins offers some idea how the immaterial mind can interact with the material brain - see sections 4 & 5.

This added with the argument that Philosophical Naturalism is logically self-refuting is additional evidence that a physical only view of the world is not sufficient to explain it; i.e. there must be some supernatural, nonphysical, element at play in the world

The Inference to the Best Explanation

Offering an inference to the best explanation occurs when we conclude that the best available explanation of the current data is probably true because it’s the best addresses all or most of the data or observations. A little more formally:

S is a state of affairs; a collection of data, facts, observations, givens.
H hypothesis, would, if true, explain S.
No other hypothesis [A, B, C] can explain S as well as H does.
Therefore, it is probable that H is true.

Inferences to the best explanation are common in all fields of inquiry, including scientific, and everyday life. For a more thorough exploration:

Inference to the Best Explanation - Peter Lipton

Inference to the Best Explanation - An Overview

Pushbacks

We may be choosing the best of a bad lot, and that we have no way of knowing whether the truth is contained in our set to begin with.

Reply: Scientists don't claim to have completely certainty on any scientific fact, no fact from any field of inquiry does. We've gone from Newtonian physics to special and general relativity, and guess what? Einstein's work is likely to only be partially correct. Qualms with IBE on this account are off base. Abductive inferences [IBE] are used in every field of inquiry, including science, history, linguistics, and everyday life,

Explanations help us to understand why something happened, not simply convince us that something happened. However, there is a common kind of inductive argument that takes the best explanation of why x occurred as an argument for the claim that x occurred. For example, suppose that your car window is broken and your iPod (which you left visible in the front seat) is missing. 

The immediate inference you would probably make is that someone broke the window of your car and stole your iPod. What makes this a reasonable inference? What makes it a reasonable inference is that this explanation explains all the relevant facts (broken window, missing iPod) and does so better than any other competing explanation. In this case, it is perhaps possible that a stray baseball broke your window, but since (let us suppose) there is no baseball diamond close by, and people normally don’t play catch in the parking garage you are parked in, this seems unlikely. 

Moreover, the baseball scenario doesn’t explain why the iPod is gone. Of course, it could be that some inanimate object broke your window and then someone saw the iPod and took it. Or perhaps a dog jumped into the window that was broken by a stray baseball and took your iPod. These are all possibilities, but they are remote and thus much less likely explanations of the facts at hand. The much better explanation is that a thief both broke the window and took the iPod. 

This explanation explains all the relevant facts in a simple way (i.e., it was the thief responsible for both things) and this kind of thing is (unfortunately) not uncommon—it happens to other people at other times and places. The baseball-dog scenario is not as plausible because it doesn’t happen in contexts like this one (i.e., in a parking garage) nearly as often, and it is not as simple (i.e., we need to posit two different events that are unconnected to each other—stray baseball, stray dog—rather than just one—the thief). Inference to the best explanation is a form of inductive argument whose premises are a set of observed facts, a hypothesis that explains those observed facts, and a comparison of competing explanations, and whose conclusion is that the hypothesis is true. The example we’ve just been discussing is an inference to the best explanation. 

Explanation: The hypothesis that a thief broke the window and stole your iPod provides a reasonable explanation of the observed facts.

Comparison: No other hypothesis provides as reasonable an explanation.

Conclusion: Therefore, a thief broke your car window and stole your iPod.

Notice that this is an inductive argument because the premises could all be true and yet the conclusion false. Just because something is reasonable, doesn’t mean it is true. After all, sometimes things happen in the world that defy our reason. So perhaps the baseball-dog hypothesis was actually true. In that case, the premises of the argument would still be true (after all, the thief hypothesis is still more reasonable than the baseball-dog hypothesis) and yet the conclusion would be false. 

But the fact that the argument is not a deductive argument isn’t a defect of the argument, because inference to the best explanation arguments are not intended to be deductive arguments, but inductive arguments.  That isn’t a defect of an inductive argument, it is simply a definition of what an inductive argument is! As we’ve seen, in order to make a strong inference to the best explanation, the favored explanation must be the best - i.e. the most reasonable. 

But what makes an explanation reasonable? There are certain conditions that any good explanation must meet. The more of these conditions are met, the better the explanation. The first, and perhaps most obvious condition, is that the hypothesis proposed must actually explain all the observed facts. 

Commonly acknowledged criteria for inference to the best explanation

1. Explanatory scope. The best hypothesis will explain a wider range of data than will rival hypotheses. An explanation has explanatory scope if it

• makes fewer assumptions
• accounts for more facts or observations
• more details of causal relations are provided
• depends less on authorities and more on observations
• is more falsifiable (more testable by observation or experiment
• offers greater predictive power (if it offers more details about what should be expected to be seen and not seen);

2. Explanatory power. The best hypothesis will make the observable data more epistemically probable than rival hypotheses; an epistemic possibility is a statement that may be true given the current state of knowledge about the world. For example, "Given what we know about the weather, it might rain tomorrow" is an epistemic possibility

3. Plausibility. The best hypothesis will be implied by a greater variety of accepted truths, and its negation implied by fewer accepted truths than rival hypotheses.

4. Less ad hoc. The best hypothesis will involve fewer new suppositions not already implied by existing knowledge than rival hypotheses.

5. Accord with accepted beliefs. The best hypothesis, when conjoined with accepted truths, will imply fewer falsehoods than rival hypotheses.

6. Consistency: Is the hypothesis consistent with other established facts or theories?

7. Comparative superiority: The best hypothesis will so exceed its rivals in meeting conditions (1) through (6) that there is little chance of a rival hypothesis’s exceeding it in fulfilling those conditions.

It’s Turtles All the Way Down - the Infinite Regress Problem

An Infinite Regress entails the inconceivable; an actual infinity. This quantity, in different contexts, yields different answers; many of which are in contradiction.

For instance, consider 2 + 3 =5. Thus, 5 - 3 = 2

So,

Infinity + Infinity = Infinity. 

Therefore; Infinity - Infinity = Infinity

However

Infinity + 0 = infinity. Therefore, infinity - Infinity = 0; but that's different to the answer above.

There are two major forms that the infinite regress problem takes.

Epistemic Regress: Knowledge is a true, justified belief. In every chain of logical reasoning, each step depends on the previous one (its justification) for its existence. For the sake of understanding, let’s take a step T1 in a logical argument. T1 relies on T2 for its justification, and similarly, T2 relies on T3, which again would require a justification in the form of T4. T1 will never be supported adequately, because the needed series of support would be infinite, and we would never have any justified knowledge. Thus, it has been proposed that reason is the basis for knowledge.  

 
Metaphysical Impossibility: This can be explained by taking an ontological example. Things in the external world are taken to exist because of the parts that they are composed of. These things (parts) must also depend on their own parts for existence. This chain continues till infinity, which many thinkers claim to be impossible.

Everything in the world has an origin. Something cannot come from nothing. Yet, something must have come from nothing if we want to be logically coherent . The idea of an origin-less universe seems absurd. Especially in light of the scientific evidence for it.

Those who propose an infinite/infinite universe, what do you do about the problem of an infinite regress of causes?

In other words, a series of things that are each ontologically dependent on the next; in this case, the singularity, the singularity -1, the singularity -2, the singularity -3....

How do we reach the singularity if there is an infinite/endless series of causes?

For example, if a giraffe had an infinitely long neck, he would die of starvation - even if he had eaten for an infinite amount of time - since the food would always have another inch to travel before it reached the stomach. So this string of infinite causes would always have another casual step to take before the singularity happened.

To say that "that there is no first moment, because every moment is preceded by earlier moments" is to be logically and philosophically hanging in midair.

Christians would say that God is a metaphysically necessary [efficient] cause for the material universe, thus avoiding regress problems.

Infinite regress can be a problem because it can lead to answers that never terminate. When people ask for justification for something, they want an answer that is compelling. However, answers that result in an infinite regress aren't rationally compelling

It’s more logical to believe in an uncreated Creator or First cause than an infinite universe. Why? Because If God had a creator [or a cause had a cause] who brought Him into existence, then we could ask “who created that God?” 

Ockam’s Razor - the philosophical principle used in science that suggests you shouldn’t multiply causes to explain something beyond what’s necessary - would suggest that we not have a regression of creators at all. The one who brought our universe into being is the uncreated one.

This isn’t special pleading for God. This is what the atheist has typically said about the universe; that the universe is uncreated and eternal in its existence. No atheist was asking “Who created the universe”? They thought the universe was “Just there,” that it was a brute fact. Although that conclusion is now invalidated by powerful scientific evidence and philosophical arguments. 

Objection - There is no problem whatsoever traversing an infinite chain of events. Every event on that chain can logically be reached. The only thing you cannot do with an infinite chain of events is reach the beginning or the end because those don't exist. Every event is logically reachable. The only way you could not reach your destination on an infinite chain is if you set your destination to the end, but that's because by definition there is no end and no beginning. Every other destination is not only possible but guaranteed.

Reply This makes no sense.

Let's say that the Big Bang is 0 and our present time is 14.  Yes, we can count from -99 to 0 and then to 14.  But first you have to get to -99, and then you have to get to -100, then you have to get to -101, then you have to get to -102, ad infinitum. It's absurd to think because we can count to 100 that the problem of the infinite regress has been solved. 

Theists are TERRIFIED of this CRUCIAL argument - Rationality Rules - A response

[Here's the vid]

The argument is that a perfectly Loving God who has created this perfect world would not create worms that eat children's eyes. Thus, a perfectly Loving God doesn't exist. 

Where do you get the idea that this world is what God intended? It's not, it's a fallen world. This atheist's error is presuming that we live in a perfect world. 

So this "argument", is based on a strawman fallacy - distortion of someone else's argument or view by exaggerating, misrepresenting, or just completely fabricating someone's position, it's much easier to attack their view and present your own position as being reasonable; but this kind of dishonesty serves to undermine honest rational debate. 

The fact is, that God created various forms of life according to their kinds, with the ability to reproduce and fill the earth (Genesis 1:21– 22, 24–28). This view includes the concepts that God had purpose in what He created and that it originally was very good (Genesis 1:31; Isaiah 45:18). Disease-causing bacteria, viruses, and "bad bugs" like the worms referenced are descendants of that which was non-harmful. We now live in a fallen world, and all creation “groans” under the consequences of our sin (Romans 8:22). 

Why would a loving God "create" a worm that destroys children's eyes? This is what is known as a loaded question - a complex question that contains an assumption or accusation that the person being questioned is likely to disagree with, or a question that has a presumption built into it so that it couldn't be answered without appearing guilty. 

The most famous example is: Have you stopped beating your wife?  Answer yes, and at best, you are a former wife-beater. But this is the tactic used; the question assumes that God created the worm in question. But, He didn't.

Furthermore, the question posed by those in the vid is valid; if one thinks that only the physical exists [i.e. Philosophical Naturalism] - and thus every event/action in the world must be the result of the interaction of particles in antecedent physical states, in accordance to the physical laws - how can they say that anything is bad or evil?  All actions/events are just the result of unguided, unintentional, unintelligent, purposeless, goalless process. 

So in their worldview, how can anything be said to be bad or good? 

A further problem is, how can they say that they are reasoning or thinking critically - defined as "careful thinking directed to a goal" [per the Stanford Encyclopedia of Philosophy] if they have no dominion of their thoughts? They cannot make any molecule act in a manner inconsistent with the physical laws; i.e. their thoughts must come via interaction of particles in antecedent physical states in accordance to the physical laws.  Again, all actions/events [including human thought] are just the result of unguided, unintentional, unintelligent, purposeless, goalless process. 

Thus, Philosophical Naturalism is logically self-refuting as a physical-only model of the world cannot account for human reasoning - i.e. goal-directed thinking. 

Rationality Rules seems to assume Philosophical Naturalism, which leads to used two self-refuting statements; the existence of morality and the existence of reason are not grounded in Philosophical Naturalism. Rationality Rules used that plus two logical fallacies to try to refute Christianity.   So, FOUR fatal errors in one short vid - an interesting strategy by a You-tuber by the name of "Rationality" Rules. 

[this assumes that Rationality Rules is a Philosophical Naturalist - but given his vids with regard to miracles, it's likely true]

Philosophical Naturalism is logically self-refuting

Definition: 

Determinism, a theory or doctrine that acts of the will, occurrences in nature, or social or psychological phenomena are causally determined by preceding events or natural laws

A self-refuting idea or self-defeating idea is an idea or statement whose falsehood is a logical consequence of the act or situation of holding them to be true.

Examples: 

1) Truth cannot be known (If so, then how does one know this truth claim?)

2) Language cannot carry meaning  (If language cannot carry meaning, then what about this claim? Is it meaningful?)

3) Science is the only way to determine truth, or I only trust things I can determine through a scientific process  (Can science determine if that statement [about science] is true or what scientific experiment provided that conclusion for you?)

The problem:

Justification [the action of showing something to be right or reasonable] requires some kind of "cognitive freedom" - you need to have control over your deliberations, over what you do [or don't accept] on the basis of evidence, reason, However, determinism [the belief that all actions and events result from other actions [i.e not you - so people cannot in fact choose what to do] makes this freedom impossible. 

Therefore, the person who argues for determinism, or is tempted to accept it, is in a weird position: their conclusion apparently undermines the very reasoning process they're using to justify it.

The Argument:

Philosophical Naturalism is the belief that nature is all that exists, and that all things supernatural (including gods, spirits, souls and non-natural values) therefore do not exist. It is sometimes called Metaphysical Naturalism or Ontological Naturalism to distinguish it from Methodological Naturalism. Philosophical Naturalism entails physical determinism

Methodological Naturalism is the assumption of philosophical naturalism when working with the scientific method. Methodological naturalists limit their scientific research to the study of natural/physical causes for all events and phenomenon. From Rationalwiki - An online rationalist skeptical resource with is decidedly anti-religious, anti-theistic bent.

Michael Ruse an atheist and Philosopher of science in The Oxford Handbook of Atheism writes "It is usual to distinguish between "methodological naturalism" and "metaphysical naturalism" whereby the latter we need a complex denial of the supernatural - including atheism as understood in the context of this publication - and by the former a conscious decision to act in inquiry and understanding, especially scientific inquiry and understanding as if metaphysical naturalism were true. The intention is not to assume that metaphysical naturalism is true, but to act as if it were.  [p383]

That's methodological naturalism - assuming naturalism is true, or acting as if it were, in one's methodology.

Philosophical Naturalism holds that any mental properties that exist are causally derived from, and ontologically dependent on, systems of non-mental properties, powers or things (i.e. all minds, and all the contents and powers and effects of minds, are entirely constructed from or caused by natural phenomena). 

Philosophical Naturalism entails physical determinism - all events are physically determined, including human thoughts. 

To do science one must only presume that the universe is orderly, i.e. disposed in some order or pattern, or governed by law.

1) Reason is the basis for all knowledge, since all epistemological theories or methods must employ it.

2) Every truth claim requires the laws of logic. It is impossible to deny the laws of logic without using them. Thus, logic reason, and critical thinking are an aspect of reality. In fact, everyone is using logic in this discussion, so it seems evident that all believe that logic is an aspect of reality.

3) All debates presuppose a reality that exists. Each debater is trying to show that their claims are closer to that reality or are best explained by that reality.

4) Critical thinking's definition is contested, but the competing definitions can be understood as differing conceptions of the same basic concept: careful thinking directed to a goal. [source] Critical thinking is purposeful, reasoned, and goal-directed; an intellectually disciplined process of actively and skillfully conceptualizing, applying, analyzing, synthesizing, and/or evaluating information gathered from, or generated by, observation, experience, reflection, reasoning, or communication, as a guide to belief and action.

5) Under Philosophical Naturalism all actions, including human thoughts, words and deeds, are the result of matter which must act in accordance with antecedent physical conditions and the physical laws without exceptions.

6) 4 above is incoherent under Philosophical Naturalism; logic, reason, and critical thinking are an aspect of reality that cannot be explained via Philosophical Naturalism, since no one has dominion over their thoughts - i.e. no one makes any molecule act in a manner inconsistent with the physical laws, as they must act only in accordance to the physical laws Note: Just saw this vid where William Lane Craig agrees with this point

7) The best explanation for the existence of logic is that there is an aspect of reality that is free from the constraints of the physical; i.e. not being caused to do something by causes other than oneself. It is up to me how I choose, and nothing determines my choice. One's decisions are differentiated from natural events by being done by the agent himself for reasons the agent has in mind.

J. P. Moreland in his book, “Scaling the Secular City: A Defense of Christianity" offers a perfect summary: “Physicalism cannot be offered as a rational theory because physicalism does away with the necessary preconditions for there to be such a thing as rationality.” If a naturalist wants to argue that rationality does not exist, they will be making two grave errors: 1- They would be claiming to be non-rational, and 2- they would be making a rational argument that rationality does not exist. It seems the rational decision one ought to come to is that naturalism is irrational, and therefore, false.

In Daniel O. Dhalstrom's Heidegger's concept of truth the author writes: There is, for example, a metaphysical sense of naturalism that Husserl deems self-refuting: the theoretical pretense that everything - including, preeminently, ideas and consciousness - is part of "nature", conceived as the ensemble of empirical facts governed by laws uncovered by natural science....The claim is self-refuting and a pretense because it cannot justify itself; 

Conclusion: Philosophical Naturalism is not simply less likely to be correct, it is logically self-refuting and is necessarily false since it cannot account for reason - careful, purposeful, intellectually disciplined, goal directed thinking as a guide to belief and action. Under PN every thought action is physically determined. Thus, the existence of logic is best explained in a reality where more than the physical exists - something that is not bound by physical restraints - which allows one the freedom of not being caused to do something by causes other than oneself.

As Haldane once said, “It seems to me immensely unlikely that mind is a mere by-product of matter. For if my mental processes are determined wholly by the motions of atoms in my brain I have no reason to suppose that my beliefs are true. They may be sound chemically, but that does not make them sound logically. And hence I have no reason for supposing my brain to be composed of atoms.”

Either “reason” is merely an illusion of physics—in which case there is no justification for relying on it to produce truthful beliefs—or “reason” is something more than physical—in which case naturalism is false. If human reason is driven by mindless particle interactions, it does not necessarily correspond to truth. If we believe reason corresponds to truth, we cannot also believe reason is determined purely by physical means.

No belief is rationally inferred if it can be fully explained in terms of non-rational causes.

Objection A: We live in a natural world. There is no supernatural. Deal with it

Reply: Yes, we live in a natural world, that's not the question. Which is, is reality encompassed by just the natural world?  Given the above argument, that's not likely. 

Objection B: Naturalism is not a presumption. Its induction. If you have only ever seen white swans, and you have to guess what color the next swan you see will be, the best guess is white.

Reply: How does this show that only the physical exists? 

Objection C: this argument does not sufficiently demonstrate that philosophical naturalism is self refuting. So it still stands.

Reply: This is an assertion. It can be, and should be, lopped off with Hitchens's razor: what can be asserted without evidence can also be dismissed without evidence. If you have an argument, please provide it. 

Objection D: Quantum Mechanics shows that the world/universe that is just physical isn't necessarily deterministic

Reply: While that is true, it hardly solves the problem of grounding rational, logical, goal-oriented thoughts in a physical world where there are only determined thoughts or random thoughts. 

Scientific prayer studies are fatally flawed

Why Scientific prayer studies are fatally flawed

Scientific prayer studies are fatally flawed for the following reasons:

1) Science assumes naturalism in its methodology - only the physical exists and therefore only natural explanations suffice.  source

Ask yourself a question, how many scientific studies seriously consider a supernatural causes to any phenomenon? Go to JSTOR or Google Scholar and look at 100 random scientific studies and see how many seriously consider anything but natural causes.

Michael Ruse an atheist and Philosopher of science writes in The Oxford Handbook of Atheism writes "It is usual to distinguish between "methodological naturalism" and "metaphysical naturalism" whereby the latter we need a complex denial of the supernatural - including atheism as understood in the context of this publication - and by the former a conscious decision to act in inquiry and understanding, especially scientific inquiry and understanding as if metaphysical naturalism were true. The intention is not to assume that metaphysical naturalism is true, but to act as if it were.

What I think Ruse means here is that a scientist can be a theist at home, but is the course of their work they must employ metaphysical naturalism. I'd ask what is the difference between assuming that metaphysical naturalism is true vs acting as if it were in the context of my essay here? I'd say None. My point above stands, even if I have to reword it to say that "Science assumes act as if naturalism in its methodology"

{As an aside, Philosophical naturalism - a physical only model of the world - is logically self-refuting}

2) Science works because the natural world is consistent; i.e. matter **must** act in accordance with the physical laws.

3) Prayer isn't a natural thing; God does **not** have to act in accordance with the physical laws. God is a person, not something bound by the laws of physics. 

Example: Water heated to 100 degrees Celsius for X amount of time will boil [at sea level] Given the above, water will boil **every** single time since matter **must** act in accordance with the physical laws. 

4) God's actions may take longer

5) God may say no, as God's purpose may not be what one expects.

6) Studies do not take all the Scriptural texts on prayer into account - they usually just consider the ones that say something along the lines of Matthew 7:7 - "Ask, and it will be given to you; seek, and you will find; knock, and it will be opened to you. Or cite no Scriptures at all.

The following are usually ignored:

A) Pray to the Heavenly Father (see Matthew 6:9). This condition to prayer might seem obvious, but it’s important. We don’t pray to false gods, to ourselves, to angels, to Buddha, or to the Virgin Mary. We pray to the God of the Bible, who revealed Himself in Jesus Christ and whose Spirit indwells us. Coming to Him as our “Father” implies that we are first His children—made so by faith in Christ (see John 1:12). 

B) Pray for good things (see Matthew 7:11). We don’t always understand or recognize what is good, but God knows, and He is eager to give His children what is best for them. Paul prayed three times to be healed of an affliction, and each time God said, “No.” Why would a loving God refuse to heal Paul? Because God had something better for him, namely, a life lived by grace. Paul stopped praying for healing and began to rejoice in his weakness (2 Corinthians 12:7–10). Is this accounted for in any of the studies? 

C) Pray for needful things (see Philippians 4:19). Placing a priority on God’s kingdom is one of the conditions to prayer (Matthew 6:33). The promise is that God will supply all our needs, not all our wants. There is a difference.

D) Pray from a righteous heart (see James 5:16). The Bible speaks of having a clean conscience as a condition to answered prayer (Hebrews 10:22). It is important that we keep our sins confessed to the Lord. “*If I regard wickedness in my heart, The Lord will not hear*” (Psalm 66:18, NAS).

E) Pray from a grateful heart (see Philippians 4:6). Part of prayer is an attitude of thanksgiving.

F) Pray according to the will of God (see 1 John 5:14). An important condition to prayer is that it is prayed within the will of God. Jesus prayed this way all the time, even in Gethsemane: “*Not my will, but yours be done*” (Luke 22:42). We can pray all we want, with great sincerity and faith, for XYZ, but, if God’s will is ABC, we pray wrongly.

G) Pray in the authority of Jesus Christ (see John 16:24). Jesus is the reason we are able to approach the throne of grace (Hebrews 10:19–22), and He is our mediator (1 Timothy 2:5). A condition to prayer is that we pray in His name.

H) Pray persistently (see Luke 18:1). 

I) Pray unselfishly (see James 4:3). Our motives are important.'

J) Pray in faith (see James 1:6). Without faith, it is impossible to please God (Hebrews 11:6), who alone can do the impossible (Luke 1:37). Without faith, why pray?

Even scientists agree that some prayer studies are seriously flawed, but please note that even the ones that they think are good, there is no way to verify that conditions A-J were followed; and if they were not then they are  flawed.

Conclusion: Given the parameters set forth in the Scriptures, and the methodology used, scientific prayer studies are 

1) arbitrarily attempting to apply a certain set of parameters to a Person to whom they do not apply and 

2) incorrectly using verses which seem to imply that God always answers prayers 

3) failing to use all of what God has said concerning prayer. 

This makes scientific prayer studies fatally flawed. The errors are both systematic and theoretical in nature.

Note:

Systematic Error in science - These errors in science are caused by the way in which the experiment is conducted; they are caused by the design of the system. Systematic errors can not be eliminated by averaging. In principle, they can always be eliminated by changing the way in which the experiment was done. In actual fact, though, you may not even know that the error exists.

Theoretical Error in science: When experimental procedures, a model system or equations for instance, create inaccurate results. How does one obtain the accurate equation for God answering prayers? Where is the proof that this equation is correct?

Objection A  - Science does not assume philosophical naturalism.

The response: You misread my argument, I said Science assumes naturalism in its methodology. - i.e. methodological naturalism; or as Michael Ruse puts it, science needs "to act as if  methodological naturalism were true.