On the Necessity of Proving Things

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That’s the anthropological interpretation. The image of the snake represents an evil intelligence,not just a cultural context. And anyway,the temptation to sin occured before the fall of man and before Adam and Eve had descendants,so the author of Genesis could not have used the image of the snake to represent pagan fertility cults,which came about only after the fall of man.
You are completely neglecting chronology, i.e. when the story was written, and who the intended audience was. Hence, it does not follow from the actual chronology that the serpent image was not known to the original audience of the text.

Furthermore, I did not say that the author of Genesis 3 was actually using the image as a representation of the fertility cults. You have misread what I said.
The author may have used the image of snake of fertility cults,since the cults were in effect serving Satan,but it does not follow that the image is intended to represent the fertility cults themselves.
Again, I did not say the author was using the image in this manner.
Even if it is a figure or symbol (I believe it is),it still represents a real intelligence. I think that the author of Genesis did have more knowledge about the Fall,but left it out because he was writing for the people. There are other Hebrew books dealing with the Genesis story that go into greater detail.
Apocryphal writings are not necessarily a reliable source to what is known. Many O.T. apocrypha are very imaginative.
Satan is himself a snake,in the same sense that Jesus is the Lamb of God and bread from heaven. There’s no way to know if Satan did not appear as a snake.
The genus litterarium of the text gives the clue as to what is most likely.
 
You are completely neglecting chronology, i.e. when the story was written, and who the intended audience was. Hence, it does not follow from the actual chronology that the serpent image was not known to the original audience of the text.
I don’t doubt that the serpent image and its connection to fertility cults was not known to the Hebrews,but the point is that the biblical authors recognized Satan to be behind the fertility cults,and the symbol for Satan was the snake. The snake was not a symbol for the fertility cults themselves,it was an object of veneration for fertility cults.
Furthermore, I did not say that the author of Genesis 3 was actually using the image as a representation of the fertility cults. You have misread what I said.
If the author didn’t use it as a representation of the cults themselves,then it must have been a representation for the evil intelligence behind the cults,or perhaps the author thought that Satan took on the form of a snake.
 
To state matters indelicately, your position is absurd, regardless of how one views science.

One need not examine every snake in existence, past, present, and future, to know snakes cannot talk. We know what a snake is essentially, by definition. It is, among other things, a non-human animal that possesses only sense knowledge. This fact excludes it from the possibility of talking.
Actually, that is incorrect. We don’t know what a snake is philosophically speaking. We know what we think a snake is.

May I ask: Why don’t we need to examine every snake to determine its classification? That is to say, doesn’t that mean your just assuming (and not wrongfully) a number of things? Then isn’t there a possibility for error?
Language use involves rationality and the ability to think and know via abstract concepts. This is a higher order cognitive ability than what is possessed by non-rational animals, your snakes included.
You mean only in so far as we have figure out. You know, we know so little about many things and language is certainly one of them. What if a highly intelligent spirit filled the snake and it started talking? Who’s to say that it wouldn’t? My point is not to say that your wrong, but for you to admit, as I’ve tried to convince others, that what you’re stating is not necessarily fact, but a number of assumptions based on the limited knowledge gained from discoveries (and by the way, are discoveries are probably extremely small compared to what will be discovered in history).
Every noun has a universal designation, such as “tree” which refers to all trees, regardless of their genus, species, or variety. Animals possessed of sense knowledge only are limited to perceiving particular things in their phenomenal presence. They do not know “what” a thing is, they only perceive their presence and react instinctively and with added, but very limited learning.
You are right. Words such as “tree” do have a universal designation. But you are severely mistaken if you believe that words such as the aforementioned fully describe what they have been assigned to. Words, as convenient as they are, do not fully capture the things to which they are assigned. To use your example, the word “tree” does not express whether the tree is pine or broadleaf. And even in those distinctions there are numerous others. And even in those there are numerous others and so on and so forth. Don’t get me wrong, I do believe that words have an objective quality to them, but there is nothing absolute in them.

Yes, we do know what a snake is, but do we know everything a snake is? ABSOLUTELY not. And to claim otherwise, no matter how many scientific discoveries there are is absolutely foolish because there is always the potential for another one.
Thus, aside from animals not possessing the proper physiology required to articulate the sounds of a language, they do not know “meanings” and hence cannot use language proper, speaking or not speaking.
You limit language to proper physiology. I agree that it is part of it, but only in so far as we know science to show us. There might be other ways…and that is simply a reality. As a true man of science, you must be open to the possibility.
In sum, your argument has no support of anything in reality. It is based on pure fantasy and lack of understanding of what is involved in language use. Sorry, to be so blunt, but your position is prima facie absurd.
Yes you are right. My argument has no support of anything in reality, if that reality is something like your own. But I do believe in the spiritual and to dismiss it will not be based on any “reality”, but on personal belief.
Your argument is also a reductio ad absurdum, in that if a snake were to talk, then it would not be a snake at all, not by any stretch of the imagination. You can’t win.
I cannot deny my desire “to win”. But I must confess that I am far more interested in the truth. And the truth is that our definition of snake is not the same as it was some time in the past and it will not be the same in the future. If we found a snake that could talk, we could say it was not a snake or we could expand our definition of snake.

Interestingly, Pluto was considered a planet until just recently. I must ask you, even as Pluto is no longer a planet, has it ceased to be what it was? I would say not. Pluto is what it is. It is our perception of Pluto and our definition of a planet that changed. If the meaning of the word “planet” can change, why not that of “snake”? After all, these words do not fully describe the realities they are assigned to. And that is the “reality”. 😉
 
I’ve been reading this thread (I stumbled upon it 🙂 ) and would like to thank you for pointing out that faith is a gift. I don’t have much faith. I want to, but I don’t. I agree that it is a gift and one I have been praying to receive, and will continue to pray for.

It would be wonderful if we didn’t require proof for the existence of God, but took it on faith.

Please pray for me.

*Holy Mother, please keep
all unborn children safe today.

St. Francis, please pray for all unwanted and hurt animals.*
Your welcome. Everyone is lacking in faith in some manner. We must always increase in it.
 
Actually, that is incorrect. We don’t know what a snake is philosophically speaking. We know what we think a snake is.

May I ask: Why don’t we need to examine every snake to determine its classification? That is to say, doesn’t that mean your just assuming (and not wrongfully) a number of things? Then isn’t there a possibility for error?

You mean only in so far as we have figure out. You know, we know so little about many things and language is certainly one of them. What if a highly intelligent spirit filled the snake and it started talking? Who’s to say that it wouldn’t? My point is not to say that your wrong, but for you to admit, as I’ve tried to convince others, that what you’re stating is not necessarily fact, but a number of assumptions based on the limited knowledge gained from discoveries (and by the way, are discoveries are probably extremely small compared to what will be discovered in history).

You are right. Words such as “tree” do have a universal designation. But you are severely mistaken if you believe that words such as the aforementioned fully describe what they have been assigned to. Words, as convenient as they are, do not fully capture the things to which they are assigned. To use your example, the word “tree” does not express whether the tree is pine or broadleaf. And even in those distinctions there are numerous others. And even in those there are numerous others and so on and so forth. Don’t get me wrong, I do believe that words have an objective quality to them, but there is nothing absolute in them.

Yes, we do know what a snake is, but do we know everything a snake is? ABSOLUTELY not. And to claim otherwise, no matter how many scientific discoveries there are is absolutely foolish because there is always the potential for another one.

You limit language to proper physiology. I agree that it is part of it, but only in so far as we know science to show us. There might be other ways…and that is simply a reality. As a true man of science, you must be open to the possibility.

Yes you are right. My argument has no support of anything in reality, if that reality is something like your own. But I do believe in the spiritual and to dismiss it will not be based on any “reality”, but on personal belief.

I cannot deny my desire “to win”. But I must confess that I am far more interested in the truth. And the truth is that our definition of snake is not the same as it was some time in the past and it will not be the same in the future. If we found a snake that could talk, we could say it was not a snake or we could expand our definition of snake.

Interestingly, Pluto was considered a planet until just recently. I must ask you, even as Pluto is no longer a planet, has it ceased to be what it was? I would say not. Pluto is what it is. It is our perception of Pluto and our definition of a planet that changed. If the meaning of the word “planet” can change, why not that of “snake”? After all, these words do not fully describe the realities they are assigned to. And that is the “reality”. 😉
Philosophically, we do know what a snake is as far as its anima or psyche is concerned, which is sufficient to determine that issue at hand. Additional scientific facts than what we have to date, will not alter one iota the following reality:

The snake is a brute animal with the powers of the sensitive or aesthetic soul only. The sensitive soul contains also the lower powers of the nutritive or threptic soul. But as snake has no faculties or powers proper to the rational or dianoetic soul, which are required and necessary for true language use, snakes never have and never will speak using a syntactical language.

If you have any doubts about this, then read Aristotle’s De Anima, or I can refer you to the proper sections of the Summa Theologica of St. Thomas Aquinas, or to an online critique of modern animal language studies by a Catholic philosopher.
 
I don’t doubt that the serpent image and its connection to fertility cults was not known to the Hebrews,but the point is that the biblical authors recognized Satan to be behind the fertility cults,and the symbol for Satan was the snake. The snake was not a symbol for the fertility cults themselves,it was an object of veneration for fertility cults.

If the author didn’t use it as a representation of the cults themselves,then it must have been a representation for the evil intelligence behind the cults,or perhaps the author thought that Satan took on the form of a snake.
Well, we do agree that Satan truly tempted Adam and Eve. That is the undeniable fact behind the imagery, however one may interpret the author’s use of the image.
 
Philosophically, we do know what a snake is as far as its anima or psyche is concerned, which is sufficient to determine that issue at hand. Additional scientific facts than what we have to date, will not alter one iota the following reality:
I don’t know about you, but I don’t think we know enough about a snake’s brain activity and psychology to claim that “we do know what a snake is as far as its…psyche is concerned…” Since I don’t think that snakes have a rational soul, I don’t think that they can make abstractions, nor do I think that they contemplate their own existence. I think that this is a human thing alone. But I won’t go so far as to say that I know everything about snake psychology. Interestingly enough, we know very little about our own psychology. Oh, God’s wonder and mystery!

So yes, if we find out new things about snakes, it may not alter all that we know about snakes, but it might alter some of what we know. Think about quantum physics. Before it, everyone thought they were learning almost everything there was to physics. But then Einstein and Planck and the others came and overturned a lot of the previous physics on its head. That is not to say that Newtonian physics was absolutely wrong. But it was not totally right either. I would not be surprised if quantum physics happens to be overturned by new discoveries. I think that we are gaining true knowledge slowly and surely and it is all leading us to God.
The snake is a brute animal with the powers of the sensitive or aesthetic soul only. The sensitive soul contains also the lower powers of the nutritive or threptic soul. But as snake has no faculties or powers proper to the rational or dianoetic soul, which are required and necessary for true language use, snakes never have and never will speak using a syntactical language.
I actually agree with you that the snake is a brute animal with the sensitive or aesthetic soul only. I do not believe that the snake has rational powers. I believe it to be false for those who claim it to be true. But this is philosophical not scientific. Philosophy answers this for us, not entirely science.

If an intelligent rational spirit or soul did happen to possess a snake, I do think it would talk. You might misunderstand me, but I don’t think that we will find talking snakes as a species anyway. But certainly God and other spirits can interact in nature and contradict scientific laws.
If you have any doubts about this, then read Aristotle’s De Anima, or I can refer you to the proper sections of the Summa Theologica of St. Thomas Aquinas, or to an online critique of modern animal language studies by a Catholic philosopher.
I, myself am a Thomist. And I agree with you. But I disagree with you when you say snakes can’t talk. Jesus tells us that nothing is impossible for God. If God chooses to intervene in nature and cause a snake to talk temporarily or permit it, he can do so because he is omnipotent. Think about Balaam and the donkey that talked to him. I don’t know about you, but I think the donkey story is literal, unlike Genesis.

I was talking to the other people on a purely scientific bases. Based on science, there is no sign that all snakes can talk. But philosophically, though there is the knowledge. Philosophy is far more constant than science and therefore far more reliable. That was what I was talking. I don’t think we disagree all too much. 😛
 
Well, we do agree that Satan truly tempted Adam and Eve. That is the undeniable fact behind the imagery, however one may interpret the author’s use of the image.
I agree, but are you saying it is impossible for spirits to possess snakes and make them talk?

What then will you say about the swine that talked to Jesus because they were possessed? Was that merely imagery, too? I think not.

I do agree with you however that only man has a rational soul. But that is because I trust in the constancy of philosophy and not entirely in the inconsistencies in science. Note, I am not saying that science doesn’t teach any truth. But it is not as certain as that of philosophy.
 
I agree, but are you saying it is impossible for spirits to possess snakes and make them talk?

What then will you say about the swine that talked to Jesus because they were possessed? Was that merely imagery, too? I think not.

I do agree with you however that only man has a rational soul. But that is because I trust in the constancy of philosophy and not entirely in the inconsistencies in science. Note, I am not saying that science doesn’t teach any truth. But it is not as certain as that of philosophy.
If a spirit possessed a snake, it would be merely taking control of the animal’s body. If the snake was then heard to be speaking, it would be the demon communicating through the physical medium of nature, and not the snake itself, as a snake, that was talking.

Jesus said God could raise up children of Abraham from stones: “and do not presume to tell yourselves, “We have Abraham as our father,” because, I tell you, God can raise children for Abraham from these stones.” However, we do not say that stones can speak Hebrew, if God wanted them to talk.

A snake is not the only image used for the devil. Peter compares the devil to a lion: “Keep sober and alert, because your enemy the devil is on the prowl like a roaring lion, looking for someone to devour.” *

Satanas* or *diabolos *is also compared to a “prince”. He is the prince of this world. And he can also disguise himself as an angel of light. Satanas is a sower, one who sows cockle in the field of the Lord’s wheat; he is the great dragon of ancient mythology (Apoc. 12:9), as well as the serpent in Paradise; he has a house and a kingdom (Mt. 12:26; Lk 11:18); his power is the “power of darkness”; his throne was found in Pergamum; and his angel is “a thorn in the flesh.”

Many images are used for satanas in the Bible and in the apocrypha, so I do not get fixated on a talking snake, or whether a demonically possessed snake can talk, since it misses the point of the comparative imagery.
 
I don’t know about you, but I don’t think we know enough about a snake’s brain activity and psychology to claim that “we do know what a snake is as far as its…psyche is concerned…”
By an animal’s psyche or animus I meant the same as “soul”. It is part the word’s historical origin.
 
The demonic possession of swine who can then talk, almost non-stop, is a rather common phenomena these days: they are called “politicians”, and they have been known to inhabit the White House from 4 to 8 years at a time. 😛
 
Image of God,

In answer to your initial question,anything that is worthy of belief must have a rational foundation,as Pope Benedict has said. The problem is that the word rational is often used to imply a naturalistic world view,as if the supernatural were solely a matter of unfounded belief or blind faith,or that natural reason could not apprehend the supernatural,or that the supernatural does not interfere with the world. This naturalistic way of thinking goes back to the Renaissance and to 18th century philosophers. For example,Francis Bacon rejected Scholastic philosophy with its supernatural causation out of hand as superstitious and useless to the advance of natural science,and concerned himself with the discover of natural causes alone. Ever since that time,rational or reasonable explanations have increasing come to mean,in effect,naturalistic and mechanistic explanations.
 
If a spirit possessed a snake, it would be merely taking control of the animal’s body. If the snake was then heard to be speaking, it would be the demon communicating through the physical medium of nature, and not the snake itself, as a snake, that was talking.

Jesus said God could raise up children of Abraham from stones: “and do not presume to tell yourselves, “We have Abraham as our father,” because, I tell you, God can raise children for Abraham from these stones.” However, we do not say that stones can speak Hebrew, if God wanted them to talk.

A snake is not the only image used for the devil. Peter compares the devil to a lion: “Keep sober and alert, because your enemy the devil is on the prowl like a roaring lion, looking for someone to devour.” *

Satanas* or *diabolos *is also compared to a “prince”. He is the prince of this world. And he can also disguise himself as an angel of light. Satanas is a sower, one who sows cockle in the field of the Lord’s wheat; he is the great dragon of ancient mythology (Apoc. 12:9), as well as the serpent in Paradise; he has a house and a kingdom (Mt. 12:26; Lk 11:18); his power is the “power of darkness”; his throne was found in Pergamum; and his angel is “a thorn in the flesh.”

Many images are used for satanas in the Bible and in the apocrypha, so I do not get fixated on a talking snake, or whether a demonically possessed snake can talk, since it misses the point of the comparative imagery.
I accept that the talking snake was probably metaphorically. But you are missing what we were originally talking about. We were talking about the possibility of snakes talking, not whether the reference was literal or not.

Let us not get to caught up with words. If I said that the snake is talking it would be clearly understood to the man of true reason that a spirit is speaking through the snake if that were the case. While we could say otherwise, I prefer not to entertain an argument of semantics. 😛
 
Image of God,

In answer to your initial question,anything that is worthy of belief must have a rational foundation,as Pope Benedict has said. The problem is that the word rational is often used to imply a naturalistic world view,as if the supernatural were solely a matter of unfounded belief or blind faith,or that natural reason could not apprehend the supernatural,or that the supernatural does not interfere with the world. This naturalistic way of thinking goes back to the Renaissance and to 18th century philosophers. For example,Francis Bacon rejected Scholastic philosophy with its supernatural causation out of hand as superstitious and useless to the advance of natural science,and concerned himself with the discover of natural causes alone. Ever since that time,rational or reasonable explanations have increasing come to mean,in effect,naturalistic and mechanistic explanations.
Thank you. And I agree with you here that anything that is worthy of belief must have a rational foundation. I have repeatedly stressed that the reason why we believe many of the things that we do is because of our rational thinking. But this is the intuitive part that precedes the use of logical reason. Axioms are accepted because of the intuition (which is truly reasonable). Only from there do we begin rational thinking.
 
I don’t doubt that the serpent image and its connection to fertility cults was not known to the Hebrews,but the point is that the biblical authors recognized Satan to be behind the fertility cults,and the symbol for Satan was the snake. The snake was not a symbol for the fertility cults themselves,it was an object of veneration for fertility cults.

If the author didn’t use it as a representation of the cults themselves,then it must have been a representation for the evil intelligence behind the cults,or perhaps the author thought that Satan took on the form of a snake.
Correction: I meant to say that the serpent image and its connection to fertility cults was known to the Hebrews.
 
Thank you. And I agree with you here that anything that is worthy of belief must have a rational foundation. I have repeatedly stressed that the reason why we believe many of the things that we do is because of our rational thinking. But this is the intuitive part that precedes the use of logical reason. Axioms are accepted because of the intuition (which is truly reasonable). Only from there do we begin rational thinking.
Yes. Aristotle said in his Posterior Analytics that no science can prove its proper principles but they are postulated as self-evident. Logical thinking assumes that there is rational order to reality that can be traced out by our reason. When Saint Paul said in the letter to the Romans that the divine attributes of God are manifest and known through creation,he was speaking in terms of intuitive rationality.
It makes sense to believe that the physical world and its order and life are created by the omnipotent power of a supernatural being. It does not make sense to believe that nothingness created physical existence,that order is created by randomness,or that life is created by dead physical matter. But that is what the natural sciences,which take the naturalistic world view,would have us believe.
 
Yes. Aristotle said in his Posterior Analytics that no science can prove its proper principles but they are postulated as self-evident. Logical thinking assumes that there is rational order to reality that can be traced out by our reason. When Saint Paul said in the letter to the Romans that the divine attributes of God are manifest and known through creation,he was speaking in terms of intuitive rationality.
It makes sense to believe that the physical world and its order and life are created by the omnipotent power of a supernatural being. It does not make sense to believe that nothingness created physical existence,that order is created by randomness,or that life is created by dead physical matter. But that is what the natural sciences,which take the naturalistic world view,would have us believe.
The natural sciences in themselves do not take the view you are referring to. The natural sciences observe a methodological naturalism, which is wholly proper for the emperiological nature of natural science.

If a scientists asserts that nature is ultimately random and matter is all that exists he is not speaking as a “scientist”, but is proffering the views of “philosophical” naturalism. Many scientists do believe that methodological naturalism requires philosophical naturalism, but that is an egregious philosophical error. The data of the natural sciences neither supports nor requires philosophical naturalism.
 
The natural sciences in themselves do not take the view you are referring to. The natural sciences observe a methodological naturalism, which is wholly proper for the emperiological nature of natural science.
Methodological naturalism is not actually methodological,it is only a way of interpreting how nature works. If you explain the workings of cells in terms of natural causes alone,that is not a matter of method,it is a matter of how you view nature,and
If a scientists asserts that nature is ultimately random and matter is all that exists he is not speaking as a “scientist”, but is proffering the views of “philosophical” naturalism.
But that is,in effect,what chaos theory and other naturalistic theories would have us believe. If a theory explains existence,order,or life in terms of natural causes alone,then it proposes a naturalistic world view,even if it does not explicitly say that nature is all that exists. Theoretical explanations become,in effect,doctrines.
Many scientists do believe that methodological naturalism requires philosophical naturalism, but that is an egregious philosophical error. The data of the natural sciences neither supports nor requires philosophical naturalism.
Naturalism as such is not necessarily a philosophy,it is just the belief or world view that only natural causes are real,or that natural causes are adequate to explain the workings of nature. Methodological naturalism is simply the application of that view to the study of nature. Whether or not scientists believe in God outside the context of science,they all explain everything in terms of naturalism within the context of science,rendering the belief in the power of God in nature unnecessary and irrational. It may be considered the proper and professional thing to do,but the naturalistic view is unjustifiable and false,and it leads to theories filled with false causation.
 
Methodological naturalism is not actually methodological,it is only a way of interpreting how nature works. If you explain the workings of cells in terms of natural causes alone,that is not a matter of method,it is a matter of how you view nature,and

But that is,in effect,what chaos theory and other naturalistic theories would have us believe. If a theory explains existence,order,or life in terms of natural causes alone,then it proposes a naturalistic world view,even if it does not explicitly say that nature is all that exists. Theoretical explanations become,in effect,doctrines.
Not necessarily. A scientific explanation of natural phenomena is proper to the sciences. If a scientist goes beyond science in his explanation, then he has violated methodological naturalism. An example would be Hawking’s A Brief History of Time in which he tries to spin off a theory of the universe which would eliminate God or a Creator. Science cannot disprove God’s existence, so Hawking has gone beyond the proper limitations of science and engaged in philosophical cosmology as if it was strictly scientific speculation… As Fr. Jaki once said, A Brief History of Time was not brief enough.

So, it is actually by the terms of methodological naturalism that we can call Hawking on his theory as having illegitimately gone beyond the natural sciences when he pretends that science has disproved God’s existence. Also, my sources tell me that God was not very impressed with Hawking’s theory.
Naturalism as such is not necessarily a philosophy,it is just the belief or world view that only natural causes are real,or that natural causes are adequate to explain the workings of nature. Methodological naturalism is simply the application of that view to the study of nature. Whether or not scientists believe in God outside the context of science,they all explain everything in terms of naturalism within the context of science,rendering the belief in the power of God in nature unnecessary and irrational. It may be considered the proper and professional thing to do,but the naturalistic view is unjustifiable and false,and it leads to theories filled with false causation.
I would have to disagree. Methodological naturalism is by no means an application
of philosophical naturalism to the study of nature. They are very different. A philosophical naturalist, if he is a metaphysical materialist, will assume a position of atheism or agnosticism.

Methodological naturalism makes no assumptions in regards to matters that are above the competence and proper scope of the natural sciences. Suppose we drop the expression methodological naturalism and consider this: If an astronomer says that he believes in a Creator of the cosmos, he is not speaking “as an astronomer.” He is speaking “as a man” or “as a philosopher.”

He never saw God through his telescope. He did not chart God’s location in the galaxy, etc. What he did was to engage in philosophical reflection on nature and arrived at a “meta-scientific” conclusion: God exists. God’s existence, though, will not provide a scientific explanation for the 2.7k background radiation or the red shift. God wants us to figure that out on our own.

Newton tried to fill in what were to him at the time, inexplicable parts of his scientific theories, by saying God does such and such. Later scientists were able to fill in Newton’s gaps with the proper scientific explanations.

Does that mean these later scientists are saying God does not exist? By no means, though by invoking a “god of the gaps” explanation in scientific theories, as Newton was prone to doing, tends to contribute, as it actually has historically, to a disbelief in God; disbelief is tempting when a scientists properly explains the natural phenomena based on proximate causes that were previously explained by a “god of the gaps” argument.

Science can only deal with proximate causes. Whenever a scientist invokes ultimate causation he has stepped outside the competence and proper limitations of natural science. The proper limitations of science have been described by many terms. Methodological naturalism just happens to be the popular term. Thomists have had other terms for explaining the methodology and proper object of study for the natural sciences.
 
Not necessarily. A scientific explanation of natural phenomena is proper to the sciences. If a scientist goes beyond science in his explanation, then he has violated methodological naturalism. An example would be Hawking’s A Brief History of Time in which he tries to spin off a theory of the universe which would eliminate God or a Creator. Science cannot disprove God’s existence, so Hawking has gone beyond the proper limitations of science and engaged in philosophical cosmology as if it was strictly scientific speculation… As Fr. Jaki once said, A Brief History of Time was not brief enough.
But what is a scientific explanation? Science pre se is just experimental research. It does not require a naturalistic perspective to properly conduct an experiment. The naturalism of science comes in with the way in which phenomena are explained. But when it comes to explaining the coming into existence of matter,and natural order,and life,naturalism leads to bad logic.
I would have to disagree. Methodological naturalism is by no means an application of philosophical naturalism to the study of nature. They are very different. A philosophical naturalist, if he is a metaphysical materialist, will assume a position of atheism or agnosticism.
My point was that naturalism per se is not necessarily a philosophy,it can also just be a point of view.

Methodological naturalism makes no assumptions in regards to matters that are above the competence and proper scope of the natural sciences. Suppose we drop the expression methodological naturalism and consider this: If an astronomer says that he believes in a Creator of the cosmos, he is not speaking “as an astronomer.” He is speaking “as a man” or “as a philosopher.”

He never saw God through his telescope. He did not chart God’s location in the galaxy, etc. What he did was to engage in philosophical reflection on nature and arrived at a “meta-scientific” conclusion: God exists. God’s existence, though, will not provide a scientific explanation for the 2.7k background radiation or the red shift. God wants us to figure that out on our own.

Newton tried to fill in what were to him at the time, inexplicable parts of his scientific theories, by saying God does such and such. Later scientists were able to fill in Newton’s gaps with the proper scientific explanations.

Does that mean these later scientists are saying God does not exist? By no means, though by invoking a “god of the gaps” explanation in scientific theories, as Newton was prone to doing, tends to contribute, as it actually has historically, to a disbelief in God; disbelief is tempting when a scientists properly explains the natural phenomena based on proximate causes that were previously explained by a “god of the gaps” argument.

Science can only deal with proximate causes. Whenever a scientist invokes ultimate causation he has stepped outside the competence and proper limitations of natural science. The proper limitations of science have been described by many terms. Methodological naturalism just happens to be the popular term. Thomists have had other terms for explaining the methodology and proper object of study for the natural sciences.

 
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