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The Dover Trial and "Nova" special

stevevw

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I did find this about that issue:

In the 16 December issue of New Scientist, there was an editorial (“It’s still about Religion”, subscription required) and an article “The God Lab” (free access), which investigated the Biologic Institute, an institute that was set up with money from the Discovery Institute supposedly to do laboratory work into Intelligent Design. Not surprisingly, the Biologic Institute does not come out well. On the 13th of January, Douglas Axe, Brendan Dixon and Ann Gauger wrote a letter (subscription required) addressing the editorial, saying they are convinced that Intelligent Design will lead to good science, but they won’t talk until their research is finished. I wrote a letter myself in response, but it didn’t make it into either the print or web letters. For the record, here is my unpublished letter.


Douglas Axe, and fellow members of the Biologic Institute claim that they are doing science (Letters 13 January Pg 18), and that they insist on completing their research projects before talking about them. However, this has not stopped their sponsors, the Discovery Institute from funding and distributing glossy DVD’s on Intelligent Design to schools, promoting Intelligent Design in various political fora, nor from funding expensive (and ultimately disastrous) legal forays to support teaching of Intelligent Design in High Schools. Indeed, their admission that only now, 16 years after the beginning of the Intelligent Design movement, are they beginning to get around to doing any research at all is a damning indictment of the movement.


In contrast, Stanley Prusiner, who came up with the truly heretical idea that the scrapie agent was a self-replicating protein (prions), had published over 250 papers alone, and won a Noble Prize in less than 16 years. Hundreds of more papers were produced by others in the same time frame, in a fruitful research program. And yet the concept of prions was a truly radical and unpopular one, striking at some of our central notions of how cells work. That the Intelligent Design movement has failed to do any scientific research themselves yet, let alone inspire other to do research, shows the intellectual and scientific vacuity of intelligent design.


Disclaimer, Ian Musgrave is a chapter contributor to Why Intelligent Design Fails (reviewed New Scientist 17 July 2004, p 47)


Now there is not much you can go into with a letter to the editor. I was pretty gobsmacked by this statement from Axe and co.


If that [the ability of nature to produce complex systems without intelligent input] is wrong - and we think it is - whole new fields open up, waiting to be explored. Perhaps neurobiologists would learn something from computer designers and network whizzes. Maybe systems biologists would start hanging out with systems engineers.


Where have these people been? Engineers, computer scientists and biologists have been hanging out together for as long as the respective disciplines have existed.

(Barbarian comments: I'm a biologist, but I have an MS in Systems. Ironic, um?)


At just one local university, people are studying visual systems of insects to improve robotic vision and motion sensors. To quote from one of the researchers here:


How has the brain evolved to optimally extract the features from scenes that are most relevant to the behavior adopted?…….We adopt a wide variety of techniques drawn from biology, computer science and engineering to augment our basic neurophysiological approach to studying this system.


And there are hundreds, if not thousands of collaborations like this around the world. In many cases, evolutionary biology has informed engineering, just like the evolutionary algorithms that are used to design aircraft wings and antenna. Computer designers have been working with neurobiologists for decades (what about brain cells on a chip).


If Douglas Axe and his co-signers are so badly misinformed about something as basic and well known as the relations between engineers, computer designers and biologists, can we trust their judgment on any research that comes out of this Institute?
My letter to New Scientist

By the time I had my Masters degree (1978), my Alma Mater had a functioning Biomedical engineering department, collaborating with engineers, biologists,and biochemists. At least I don't feel singled out when I couldn't get a look at the Biologic Institute lab. No one else can, either.
I have not got into the history of DI that much. I am not sure which year you are talking about with the letter Doug Axe wrote as the link does not work. But to say that they have only just started their work on ID 16 years after they initially declared they were doing lab work has to be wrong as Axe has papers dating back to 2004 which are the main ones on ID that people like Panda's dispute.

There has been contention about his work but there has also been support. I have found those who mostly criticize him are from more pro-active evolution sites like Panda's. But he always will reply to any criticism and can account for his work. Here is a video where he talks about some of his work which seems pretty straight forward. By the way this video also has a superimposed pic which has been green screened so it must be a something they use often.
http://www.youtube.com/watch?v=8ZiLsXO-dYo
 
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The Barbarian

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There has been contention about his work but there has also been support. I have found those who mostly criticize him are from more pro-active evolution sites like Panda's. But he always will reply to any criticism and can account for his work. Here is a video where he talks about some of his work which seems pretty straight forward. By the way this video also has a superimposed pic which has been green screened so it must be a something they use often.

What did you find to be the most significant new finding first discovered by this person?
 
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The Barbarian

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Yes but contingency would be expected if God designed life.

"Designed" no. But it would be expected if God created the rules by which all things unfolded after an initial creation. In His universe, there's something quite interesting; if a theory is ugly (complex and odd-looking), it's almost always wrong. So far, God seems to be very parsimonous in His creation, using just a few basic rules (or maybe, just one rule) on which every other thing depends.

There would be inherent mechanisms that helped living things in different environments to be able to adapt rather than be subjected to chance situations.

You're running the tape too far forward. Those mechanisms depend on the physics of particles that form the substance of living things. As you may have heard, the fundamental molecules of life do form spontaneously in many environments. God knew what He was doing, from the start. No designing necessary.

IE living things can get genetic info from other living things in the same environment.

Early living things seem to have had no barrier between them; even today, prokaryotes like bacteria can sexually conjugate and swap genes even between very different species.

They have a certain amount of plasticity in their phenotype to change in order to fit into environments due to environmental influences on them.

Which was already inherent in the chemistry of this universe.

These changes are often well suited and integrated.

If we look downstream a bit. For example, humans have evolved protection against malaria. Hemoglobin-S, if you are a heterozygote (just one copy of the mutated gene) gives excellent protection. But homozygotes almost always die before reproducing. If you look at the numbers, heterozygotes have a considerable advantage in leaving offspring, compared to normal Hb individuals.
But that's a pretty rough adaptation. Useful, but at a huge reproductive cost. "Better than nothing."

But now, there's been another mutation, HbC, which gives the same protection, but doesn't disable and kill people who happen to get two copies of the gene. It's not perfect; homozygotes for HbC still have some health problems. But it's clearly better than then earlier mutations.

The human hand is an example. Chimpanzees are very dexterous, but not nearly as much as humans are. The thumb has been moved up and strengthened relative to the other digits and muscles have been repositioned to allow a relatively more powerful grip, and at the same time, two other grips (3-point chuck and pinch) which permit much more precise movement.

But it's not optimum. The repositioning puts greater forces on the carpal tunnel, through which the tendons run,and under certain conditions of frequency, force, and deviation of the wrist, a disabling inflammation results. Each step tends to be better, but perfection rarely occurs on the first iteration.

All these mechanisms allow living things to be active and connected when evolving. This is opposed to Neo Darwinism that makes living creatures passive actors

No. There's a very large body of literature in evolution about the way organisms change environments to suit their needs. A simple example is forests. If there's enough water to allow trees to grow well, they change the soil. Leaves falling down to the forest floor, contain acids that go into the soil, and dissolve minerals, carrying them down into the subsoil. This makes it harder for small plants to live there, leaving more nutrients to the trees. It's a very useful adaptation. Not perfect though, since it make it harder for young trees, or for reforestation of areas that lose trees by fire, or cutting. This is why there's a sequence of reforestation, eventually leading to a mature population.

subject to environments and chance occurrences through random mutations that may or may not produce beneficial changes and blind natural selection that cannot know what is needed ahead of time

Right. Luria and Delbruck demonstrated that mutations are random, not in response to need. Natural selection primarily acts in the present, but it also determines the future by limiting the alleles that will be passed on to succeeding generations.
 
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stevevw

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"Designed" no. But it would be expected if God created the rules by which all things unfolded after an initial creation. In His universe, there's something quite interesting; if a theory is ugly (complex and odd-looking), it's almost always wrong. So far, God seems to be very parsimonous in His creation, using just a few basic rules (or maybe, just one rule) on which every other thing depends.



You're running the tape too far forward. Those mechanisms depend on the physics of particles that form the substance of living things. As you may have heard, the fundamental molecules of life do form spontaneously in many environments. God knew what He was doing, from the start. No designing necessary.



Early living things seem to have had no barrier between them; even today, prokaryotes like bacteria can sexually conjugate and swap genes even between very different species.



Which was already inherent in the chemistry of this universe.



If we look downstream a bit. For example, humans have evolved protection against malaria. Hemoglobin-S, if you are a heterozygote (just one copy of the mutated gene) gives excellent protection. But homozygotes almost always die before reproducing. If you look at the numbers, heterozygotes have a considerable advantage in leaving offspring, compared to normal Hb individuals.
But that's a pretty rough adaptation. Useful, but at a huge reproductive cost. "Better than nothing."

But now, there's been another mutation, HbC, which gives the same protection, but doesn't disable and kill people who happen to get two copies of the gene. It's not perfect; homozygotes for HbC still have some health problems. But it's clearly better than then earlier mutations.

The human hand is an example. Chimpanzees are very dexterous, but not nearly as much as humans are. The thumb has been moved up and strengthened relative to the other digits and muscles have been repositioned to allow a relatively more powerful grip, and at the same time, two other grips (3-point chuck and pinch) which permit much more precise movement.

But it's not optimum. The repositioning puts greater forces on the carpal tunnel, through which the tendons run,and under certain conditions of frequency, force, and deviation of the wrist, a disabling inflammation results. Each step tends to be better, but perfection rarely occurs on the first iteration.



No. There's a very large body of literature in evolution about the way organisms change environments to suit their needs. A simple example is forests. If there's enough water to allow trees to grow well, they change the soil. Leaves falling down to the forest floor, contain acids that go into the soil, and dissolve minerals, carrying them down into the subsoil. This makes it harder for small plants to live there, leaving more nutrients to the trees. It's a very useful adaptation. Not perfect though, since it make it harder for young trees, or for reforestation of areas that lose trees by fire, or cutting. This is why there's a sequence of reforestation, eventually leading to a mature population.



Right. Luria and Delbruck demonstrated that mutations are random, not in response to need. Natural selection primarily acts in the present, but it also determines the future by limiting the alleles that will be passed on to succeeding generations.
 
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The Barbarian

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Science is getting closer and closer to the very core of existence. The closer they get the more they will see that there had to be a creator.

That would be a good thing. But so far, no such result. It would be very unexpected, since the methodology of science limits it to the physical universe.

And anyone open to that fact, will have already seen it in the universe:
Romans 1:20 For the invisible things of him, from the creation of the world, are clearly seen, being understood by the things that are made; his eternal power also, and divinity: so that they are inexcusable.
 
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The Barbarian

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Not sure if its a new finding but still significant is the rarity of functional protein folds.

No, it's pretty obvious. The paper, IIRC found that the odds of such folds being established randomly were very, very small.

Darwin's discovery was that such things aren't randomly selected. That "finding" is like seeing an arrow stuck in a tree, and drawing a bulls-eye around it.
 
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stevevw

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That would be a good thing. But so far, no such result. It would be very unexpected, since the methodology of science limits it to the physical universe.

And anyone open to that fact, will have already seen it in the universe:
Romans 1:20 For the invisible things of him, from the creation of the world, are clearly seen, being understood by the things that are made; his eternal power also, and divinity: so that they are inexcusable.
Yes but as we get better at understanding how things work such as DNA and the universe the more we will see that there is order and design in things. Often you hear of astronauts or astronomers coming to God because they have had the chance to take a closer look at the universe and have realized that it could not have happened by chance. Romans 1:20 is testament to that. We are without excuse. When we look at nature we see that there had to be a creator behind it.

But some will deny this and try to find substitute ideas to account for this. Richard Dawkins says that nature gives the appearance of design but it is not really designed because of evolution. But that appearance may be a reflection of what really is designed and how we can see it in nature. So those who are able to look deeper into nature are able to see Gods work in even greater detail and realize that there has to be some creator behind things. Yes sooner or later science will not be able to account for what we see as with quantum physics and maybe things breakdown to something non-physical such as some say with consciousness. But that is exactly what we would expect with Gods creation.

Science will be able to reveal Gods creation to a point and then things break down. The problem is materialists will continue to try and find a naturalistic explanation. We are beginning to see this with ideas like multiverses and string theory which step beyond verifiable science. So it seems they can appeal to ideas that will never be verified but when we turn to God it is immediately rejected because it is not scientifically verifiable.
 
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stevevw

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No, it's pretty obvious. The paper, IIRC found that the odds of such folds being established randomly were very, very small.

Darwin's discovery was that such things aren't randomly selected. That "finding" is like seeing an arrow stuck in a tree, and drawing a bulls-eye around it.
So if a new functional change in a protein needs a few mutations to occur each of those mutations are going to be random. They are not going to know what nucleotide sequence will need to be mutated to continue to build towards that specific function. Or when multiple mutations are needed all at once. In that sense it is random and the odds of lining everything up is unlikely.

Whereas if the genome has the ability to mutate certain combinations that go together then this makes more sense. This relates to what I was posting about how living things have all the genetic info needed to evolve through HGT and within their own genomes. God has installed this in life to allow them to adapt to environments.
 
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The Barbarian

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Yes but as we get better at understanding how things work such as DNA and the universe the more we will see that there is order and design in things. Often you hear of astronauts or astronomers coming to God because they have had the chance to take a closer look at the universe and have realized that it could not have happened by chance. Romans 1:20 is testament to that. We are without excuse. When we look at nature we see that there had to be a creator behind it.

They didn't have to go to space for that. I merely have to cross the road into the parkland and sit down by the pond for a bit. You're right; Romans 1:20 does correctly say that the world shows God's creation. That's why the great majority of people in the world have always been theists.

Science can't apprehend the supernatural, but scientists can.
 
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stevevw

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They didn't have to go to space for that. I merely have to cross the road into the parkland and sit down by the pond for a bit. You're right; Romans 1:20 does correctly say that the world shows God's creation. That's why the great majority of people in the world have always been theists.
Studies show that we are all born believers and lose this as we grow and are indoctrinated by materialistic worldviews. Many seen to think its the other way around. There are many bible verses that speak about Gods creation reflecting Gods creative qualities.
Psalm 19:1
1 The heavens declare the glory of God; the skies proclaim the work of his hands.

You have to ask your self why are people natural theists. Is it because they recognize that what they see cannot be a result of chance and that there is some creative mind behind things. This must play some part as we humans intuitively recognize something in nature that points to something beyond mere chemicals and particles that involved in the mix of nature. Perhaps the God particle and not the Higgs boson lol. Something that is beyond the physical world.
Science can't apprehend the supernatural, but scientists can.
Yes sorry I mean t to say scientists. The human aspect of the equation. The problem is sometimes this can get mixed without people realizing. A persons worldview can bias how they interpret what they see. An atheist scientists will always look for material answers. This is best seen with consciousness where there is a debate about whether consciousness is something that comes from physical brains or something else beyond.

This can be applied to many areas. Dark matter is another. When a theory goes wrong or is contradicted the go to solution is always a material one even if the idea seems counter intuitive to physics. They come up with something that cannot be seen or tested yet can have a major effect on the universe. Using the science method is really a philosophical position anyway. To assume that everything can be explained with materialism.

If we take space and gravity for example we may have a great theory for this with relativity but this does not tell us why or the how in the greater scheme of things. Especially now we are finding it hard to unite this with the quantum world which is so counter intuitive to classical physics and is potentially more like the supernatural. But for all we know some strange force that allows massive heavy objects to be suspended in space and keeps everything together like some big orchestrated clock seems beyond the natural to me.

Just because someone puts a materialistic explanation on things does not mean it is not something that is supernatural in its origin. If we encountered something supernatural scientists would attempt to explain it materially even if it was truly supernatural. So how do we really know what is going on.
 
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The Barbarian

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Studies show that we are all born believers and lose this as we grow and are indoctrinated by materialistic worldviews. Many seen to think its the other way around. There are many bible verses that speak about Gods creation reflecting Gods creative qualities.
Psalm 19:1
1 The heavens declare the glory of God; the skies proclaim the work of his hands.

You have to ask your self why are people natural theists. Is it because they recognize that what they see cannot be a result of chance and that there is some creative mind behind things. This must play some part as we humans intuitively recognize something in nature that points to something beyond mere chemicals and particles that involved in the mix of nature. Perhaps the God particle and not the Higgs boson lol. Something that is beyond the physical world.

Well said, but iIt's not that complicated. As Paul writes, His hand is obvious in nature, to those who are willing to see. You have to be trained not to see.

But science can't do that for you. We're wired to see it, even if the methodology of science can't demonstrate it.

Yes sorry I mean t to say scientists. The human aspect of the equation. The problem is sometimes this can get mixed without people realizing. A persons worldview can bias how they interpret what they see. An atheist scientists will always look for material answers. This is best seen with consciousness where there is a debate about whether consciousness is something that comes from physical brains or something else beyond.

Yes. As one wise Christian observed, the soul is not merely an epiphenomenon of the brain. That might be one of the things it is, but the nature and relationship of body and soul is beyond our understanding, no less then the nature of three persons in one God.
 
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stevevw

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Well said, but iIt's not that complicated. As Paul writes, His hand is obvious in nature, to those who are willing to see. You have to be trained not to see.

But science can't do that for you. We're wired to see it, even if the methodology of science can't demonstrate it.
Ok, perhaps I am not explaining things correctly. From what I have read that some scientists who may have been skeptical of God but were awakened to His creative ability when they seen the inner workings of DNA for example that they were unable to deny there had to be some mind behind it. The average person does not get this opportunity so in that way science which enabled the scientists to take a deeper look has opened the door to a greater insight to Gods creation.

The more we peer into the inner workings of life the greater it reflects Gods creation. A hand gives a certain degree of Gods creative ability though great but the inner workings down to the molecular level show an even greater orchestration of Gods ability because it is not just a mishmash of stuff going on but something so great that it had to have required some orchestration beyond chance or something coming from nothing without a creator. This was the same for some astronauts who see the greater picture of the universe.

So in that sense science and technology has opened the door for some to see a deeper level of Gods creation. But I agree that the science itself cannot make a person realize Gods creation. A person has to be open to seeing this in the first place.

Yes. As one wise Christian observed, the soul is not merely an epiphenomenon of the brain. That might be one of the things it is, but the nature and relationship of body and soul is beyond our understanding, no less then the nature of three persons in one God.
And maybe no less than understanding how the universe and life came to be which is something scientists try to explain through a material worldview such as the "nothing is really something" argument.
 
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The Barbarian

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Ok, perhaps I am not explaining things correctly. From what I have read that some scientists who may have been skeptical of God but were awakened to His creative ability when they seen the inner workings of DNA for example that they were unable to deny there had to be some mind behind it. The average person does not get this opportunity so in that way science which enabled the scientists to take a deeper look has opened the door to a greater insight to Gods creation.

Happens to me a lot. But unfortunately, those "invisible things clearly seen" are obvious only if we are willing to see them. God does not make Himself unambiguously there. I think it has to do with giving us the freedom to chose Him or not. If He moved the stars around one night to read "This is God, letting you know that I'm watching." Who would not believe?

So in that sense science and technology has opened the door for some to see a deeper level of Gods creation. But I agree that the science itself cannot make a person realize Gods creation. A person has to be open to seeing this in the first place.

Right.

And maybe no less than understanding how the universe and life came to be which is something scientists try to explain through a material worldview such as the "nothing is really something" argument.

The very fabric of the universe is such that virtual particles and their corresponding antiparticles spontaneously form out of nothing. That's not just a hypothesis; it's observed. Might be part of the reason that black holes are so bright.

But to get any data on the question of "something rather than nothing" you'd need to look outside the system. And I don't think science will ever be able to do that. But as I said, scientists can.
 
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stevevw

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Happens to me a lot. But unfortunately, those "invisible things clearly seen" are obvious only if we are willing to see them. God does not make Himself unambiguously there. I think it has to do with giving us the freedom to chose Him or not. If He moved the stars around one night to read "This is God, letting you know that I'm watching." Who would not believe?
Yet if I understand Romans 1:20 properly everyone regardless of faith or lack of it can see Gods creative ability in what they see in nature and as the verse says "they are without excuse" for not knowing. It is like this is something built into us that we know intuitively that there is more to it than just what we see. There is something mindful and organised going on. I think it is that some choose to block this out and find substitutes for it. Science is just one way of accounting for what we see and this is very powerful for some to become materialism.

The very fabric of the universe is such that virtual particles and their corresponding antiparticles spontaneously form out of nothing. That's not just a hypothesis; it's observed. Might be part of the reason that black holes are so bright.

But to get any data on the question of "something rather than nothing" you'd need to look outside the system. And I don't think science will ever be able to do that. But as I said, scientists can.
But the nothing you talk about needs to have certain qualities to create virtual particles. They don't form from absolutely nothing in the true sense. ie

There must be special requirements for this “nothing.” These include:
  • empty space
  • a law of quantum gravity
  • some sort of “laws of nature”
  • a variable of time so that the equations of quantum mechanics can be meaningful
  • a “false vacuum” and
  • a multiverse from which our universe can expand from some other empty space containing zero energy and mass.
A Simple Refutation of the "Universe from Nothing" | Evolution News

Whereas the state of things that the bible talks about in John 1 is something that transcends time, space and matter.

In the beginning was the Word, and the Word was with God, and the Word was God. He was with God in the beginning. Through him all things were made; without him nothing was made that has been made.
 
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The Barbarian

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But the nothing you talk about needs to have certain qualities to create virtual particles. They don't form from absolutely nothing in the true sense. ie

Correct. And this is perhaps the key to understanding all of it. He didn't go about creation like so many myths have it, building this and that and the other thing. He created it with a few simple rules (or maybe just one;we're still not sure) and then it worked as He intended it to. Even stochastic processes serve His purposes, and counter-intuitively, chaotic systems in this universe have an underlying order.

As St. Tom wrote, divine providence can be done by contingency or by necessity, as He wills it to be.

And yes, I think it takes indoctrination for a person to miss the fact of divine providence in nature. Humans might not be aware of exactly who the creator is, but history has shown that almost all humans can perceive that there is one.
 
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stevevw

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Correct. And this is perhaps the key to understanding all of it. He didn't go about creation like so many myths have it, building this and that and the other thing. He created it with a few simple rules (or maybe just one;we're still not sure) and then it worked as He intended it to. Even stochastic processes serve His purposes, and counter-intuitively, chaotic systems in this universe have an underlying order.

As St. Tom wrote, divine providence can be done by contingency or by necessity, as He wills it to be.

And yes, I think it takes indoctrination for a person to miss the fact of divine providence in nature. Humans might not be aware of exactly who the creator is, but history has shown that almost all humans can perceive that there is one.
I find it fascinating that just as we are discovering there is more to reality than we can see so to with Gods creation as whatever we find whether in the macro or micro world it is part of Gods creation. He has created those laws and those laws were there before there was reality. IMO this is why we will always find it hard to unite quantum physics with classical physics as I believe quantum physics touches on that immaterial aspect of God that we can never fully comprehend. Still this is only a glimpse of God and what is beyond our physical world.
 
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I find it fascinating that just as we are discovering there is more to reality than we can see so to with Gods creation as whatever we find whether in the macro or micro world it is part of Gods creation. He has created those laws and those laws were there before there was reality. IMO this is why we will always find it hard to unite quantum physics with classical physics as I believe quantum physics touches on that immaterial aspect of God that we can never fully comprehend. Still this is only a glimpse of God and what is beyond our physical world.

Maybe so, it's why they talk about the "God particle." Personally, I find the deepest mystery to be consciousness. We seem entirely unable to understand how that works, or even determine what has consciousness.

Which suggests that Pope John Paul was correct:
‘Theories of evolution which, in accordance with the philosophies inspiring them, consider the mind as emerging from the forces of living matter, or as a mere epiphenomenon of this matter, are incompatible with the truth about man. Nor are they able to ground the dignity of the person.’
Communion and Stewardship: Human Persons Created in the Image of God

While the mind may be an epiphenomenon of the brain, that is not all that it is, and the mystery therein may never be solved, perhaps because the solution is beyond the reach of science.
 
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stevevw

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Maybe so, it's why they talk about the "God particle." Personally, I find the deepest mystery to be consciousness. We seem entirely unable to understand how that works, or even determine what has consciousness.

Which suggests that Pope John Paul was correct:
‘Theories of evolution which, in accordance with the philosophies inspiring them, consider the mind as emerging from the forces of living matter, or as a mere epiphenomenon of this matter, are incompatible with the truth about man. Nor are they able to ground the dignity of the person.’
Communion and Stewardship: Human Persons Created in the Image of God

While the mind may be an epiphenomenon of the brain, that is not all that it is, and the mystery therein may never be solved, perhaps because the solution is beyond the reach of science.
The Pope is a very wise man
 
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