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 Post subject: Science vs. Religion and Magic (Abiogenesis for Ceeboo)
PostPosted: Wed Dec 05, 2012 3:42 pm 
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Ceeboo,

On your Darwinian Evolution thread, you expressed the belief that claiming "God did it" (as religionists are wont to do) is no more an appeal to magic than is the claim by scientists that non-life eventually became life in the primordial world through wholly natural processes. Such statements by thoughtful folks deserve a thoughtful response and (as promised) here is mine.

Before starting I trust that you will forgive me if I refer to Science and Nature rather than to the Bible and the Book of Mormon in stating the case for abiogenesis, and if I ask you to imagine a world that is totally unlike the one you live in today.

The approximate abiotic origins of life have been dated to a time window from between about 3.9 and 3.5 billion years ago when the atmospheric pressure on Earth ranged from ca. 100 bar to ca. 10 bar. At these pressures chemical reactions proceed at a greater rate and in a greater variety than they do at the present atmospheric pressure on the Earth of approximately 1 bar. Also, the atmosphere during this era was comprised mainly of water vapor with varying concentrations of carbon monoxide, carbon dioxide, hydrogen sulfide, hydrogen cyanide, ammonia, methane and free hydrogen. It would have been instantly lethal to us modern day oxygen breathers. I will refer to this era as "primordial Earth".

As in many fields of science, there are completing models for abiogenesis. (I use the term model instead of theory because there are many here who have demonstrated a real lack of understanding as to what is meant by a scientific theory).

Possible chemical routes from non-life to life during this era abound and can be roughly classified according to the class of molecules or molecular reactions that are believed to have arisen first in the process. These models have been given names such as RNA World, Protein World, Lipid World and many others. These models can be roughly further separated into "genes first" and or "metabolism first" narratives or versions.

In order to evaluate these models, one must realize that there are a number of steps or functional gradations between non-life and life. The willingness to confer "living" status upon a chemical system depends on one's definition of life.

I am not trying to be obtuse here. All would probably agree that simple single cell chemical systems such as archaea or bacteria represent life. Archaea are single cell organisms without a nucleus or any other organelles within the membrane, and include a large number of extremophiles that can survive under conditions of temperature, salinity or pH that would be lethal to most bacteria or eukaryotes. (Extremophiles are mentioned on purpose here).

What about viruses? They exhibit growth, self-replication, adaptation to their environment and evolution through mutation. Do they represent life?

What about prions? They can grow and reproduce in much the same way that certain viruses do, cause changes in their host cell, and they can evolve. Alive?

What about protocells? These are simple cells made entirely in the laboratory comprised of a lipid bilayer membrane and simple RNA monomers and polymers (which form catalytic ribozymes). Protocells can also grow, replicate, pass along genetic information, and even evolve.

So, the definition that one uses for life is important. From a science perspective, simplist archaea certainly represent life.

While such has not always been the case, science now considers viruses as non-living, although they have had (and continue to have) a profound effect on the evolution of more complex life forms, including humans.

Prions are not considered to be living - nor are protocells - yet. Prokaryotes, archea, viruses, protocells and prions are points along a continuum between non-life and life.

(Continued in the following post.)

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Last edited by DrW on Fri Dec 07, 2012 5:35 am, edited 7 times in total.

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 Post subject: Re: Science, Mormonism and Magic (for Ceeboo)
PostPosted: Wed Dec 05, 2012 3:44 pm 
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On the chemical journey from non-life to life there are several important milestones. Proponents of abiogenesis must show, at a minimum, that organic compounds such as amino acids, nucleic acids and fatty acids could form naturally under the conditions that existed on primordial Earth.

Furthermore, it must be demonstrated, again at a minimum, that these classes of compounds could undergo polymerization or (in the case of fatty acids), at least some form of self-organization, under the conditions believed to exist on the primordial Earth.

Any number of experiments using only compounds found on primordial Earth, and mainly in the atmosphere, such as water, methane, carbon dioxide, carbon monoxide, hydrogen cyanide, hydrogen sulfide, ammonia and hydrogen, with energy sources such as electrical discharge (lightening) ionizing radiation, or even UV, and catalytic substrates such as iron sulfides, and various clays, have shown that organic molecules, including amino acids, small fatty acids and even nucleic acids, are formed (mainly in aqueous solutions).

http://www.sciencedirect.com/science/article/pii/S0273117703010457

Another supportable hypothesis is that much of the organic material on the primordial Earth arrived from extraterrestrial bombardment of the Earth by carbonaceous chondrites (meteorites), dirty comets, etc. during "late bombardment" period.

Once here and formed, these compounds needed to somehow form polymers or self-organize to relatively stable and long-lived structures that could eventually replicate themselves, pass on genetic information and evolve.

The spontaneous formation of micelles (or even vesicles) by fatty acids in aqueous solution is well known and well understood. Fatty acid micelles will spontaneously grow in solution, and when large enough, become unstable and divide to form two smaller micelles that will continue the process so long as there are fatty acids that can be taken up from the surrounding solution. So we have a crude but workable protocell membrane.

http://www.elmhurst.edu/~chm/vchembook/558micelle.html

It has now been shown that RNA monomers and polymers can also from naturally under the conditions that were believed to exist, for example, in down slope water pools on or near volcanoes that would periodically undergo evaporation. This is an important finding of which creationists appear to be completely unaware, so here is a complete citation:

Quote:
Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions Matthew W. Powner, Beatrice Gerland & John D. Sutherland. Nature, Vol. 460, May 13, 2009.


These RNA polymers can be catalytic, and can thus be self-replicating. These catalytic polymers are called ribozymes, and strangely enough, can stitch together strands of RNA monomers to form longer polymers, which themselves can be good catalysts. Since some ribozymes are better catalysts than others, the basis for genetic competition is already in place. (Science. 323: 1229–1232, 2009).

Like the nucleic acids, amino acids can spontaneously form small oligomers (peptides) under the conditions that existed on the primordial Earth. (Science 117 pp. 528-529, 1953)

In an award winning essay in Science in 2006 (Science 314, pp1558-1559), Irene Chan describes wholly synthetic protocells comprised of fatty acids and RNA that can grow, replicate, and pass on genetic information. Not yet life - but well along the chemical road between non-life and life. Here s a link to a graphic from the essay in Science.

http://www.sciencemag.org/content/314/5 ... nsion.html

There is a lot more that could be brought up and discussed by way of explanation, but this would seem like a good place to stop for now. I have described the most basic types of organic compounds required for life, explained how these could have arisen on the primordial Earth, shown that they can form polymers under these same conditions, and provided an example of a simple protocell that exhibits many of the characteristics of simple archaea.

As I mentioned on another thread, I am expecting that we will be able to add respiration to the capabilities of artificial cells during my lifetime. This goal is being approached from top down and from bottom up. Synthetic protocells are a bottom up approach.

The top down approach is to selectively remove components from simple cells until they no longer function and then see what a really minimal living cell might look like. Not sure if you remember this, but scientists have already removed the genome from a living cell and replaced it with a totally artificial genome. The re-engineered cell kept chugging along, because after all, it is only chemistry.

The main thing I hope you realize, my friend, is that it is all chemistry - and only chemistry. No magic is involved.

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“But if you are told by your leader to do a thing, do it. None of your business whether it is right or wrong.”—Heber C Kimball, Journal of Discourses, Vol 6, Page 32


Last edited by DrW on Fri Dec 07, 2012 5:41 am, edited 5 times in total.

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 Post subject: Re: Science, Religion and Magic (Abiogenesis for Ceeboo)
PostPosted: Wed Dec 05, 2012 4:11 pm 
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Great post, DrW. There is always a temptation to say: why haven't scientists been able to do X yet?" We've only understood the basic structure of DNA for less than 60 years. Understanding an entire genome requires massive computing power that we haven't had until the last couple of decades. It also requires lots of lots of money. Figuring out what each piece of genetic code does is a painstaking process. I'd love to be around when scientists create the first artificial living cell, but I don't feel in a position to demand that it happen in my relatively short lifetime.

Suppose we could somehow replicate a model earth with everything present that is needed to produce life. How long would we need to run the experiment before we could expect life? How long to progress from stage to stage until the line is crossed from "not-alive" to "alive?" Given the length of the relevant time period on earth, we might need to keep the experiment running for hundreds of thousands of years. So, scientists work on what they can: working on the steps in the process a little bit at a time. I don't believe that the research has ever hit a point where we can conclude that it's impossible for life to originate from natural processes.

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 Post subject: Re: Science, Religion and Magic (Abiogenesis for Ceeboo)
PostPosted: Wed Dec 05, 2012 4:21 pm 
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Brad Hudson wrote:
Great post, DrW. There is always a temptation to say: why haven't scientists been able to do X yet?" We've only understood the basic structure of DNA for less than 60 years. Understanding an entire genome requires massive computing power that we haven't had until the last couple of decades. It also requires lots of lots of money. Figuring out what each piece of genetic code does is a painstaking process. I'd love to be around when scientists create the first artificial living cell, but I don't feel in a position to demand that it happen in my relatively short lifetime.

Suppose we could somehow replicate a model earth with everything present that is needed to produce life. How long would we need to run the experiment before we could expect life? How long to progress from stage to stage until the line is crossed from "not-alive" to "alive?" Given the length of the relevant time period on earth, we might need to keep the experiment running for hundreds of thousands of years. So, scientists work on what they can: working on the steps in the process a little bit at a time. I don't believe that the research has ever hit a point where we can conclude that it's impossible for life to originate from natural processes.


As to man-made living cells in my (our) remaining lifetime; estimates are now that we are 15 - 20 years away. I would consider either "top down" or "bottom up" synthesis as valid, although bottom up would be much easier for everyone to agree on.

You may be right, it may take a lot longer than 20 years. One thing we can be sure of is that the achievement will come, and it won't depend on magic.

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 Post subject: Re: Science, Religion and Magic (Abiogenesis for Ceeboo)
PostPosted: Wed Dec 05, 2012 4:47 pm 
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Thanks for that. It's fascinating to see just how far science has come in understand abiogenesis. Kind of makes me want to live to a ripe old age so I can see what else they'll find.

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 Post subject: Re: Science vs. Religion and Magic (Abiogenesis for Ceeboo)
PostPosted: Thu Dec 06, 2012 6:18 am 
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To continue on a bit with the "it is all chemistry - and only chemistry" theme of this thread for Ceeboo and "scientific creationists" everywhere, it is interesting to note the profound effect that early life had on the evolution of Earth and it's atmosphere.

Cyanobacteria appeared on Earth some 3.5 billion years ago. In an earlier thread on Young Earth Creationism in the LDS Church, I mentioned cyanobacteria colony fossils known as stomatolites in Oman that are some 555 million years ago. Such fossils date back as far as 3.5 billion years. These cyanobacteria contributed significantly to the increased levels of oxygen in Earth's atmosphere as it evolved.

What some refer to as the "great oxidation event" in the natural history of Earth was more like a process that took place at various rates over some three billion years, slowly preparing the environment on Earth to host the Cambrian Explosion, a period starting just over 550 million years ago when most major animal phyla were able to establish themselves on a warm, moist planet with an atmosphere rich in oxygen.

So, in many aspects, the processes that prepared the primordial hot, hellish, high pressure, Hadean Earth for habitation by humans were biogenic.

In fact, one could reasonably claim that a major "creator" of this Earth as we know it was among the most lowly of lifeforms - a primitive archeaen extremophile.

Those who believe in their own private blend of science and religious myth might want to ask themselves why an omnipotent and omniscient God, whose ultimate goal was creation of humankind, would start with planet that would require transformation by single cell animals for billions of years. Why not just build it right the first time?

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 Post subject: Re: Science vs. Religion and Magic (Abiogenesis for Ceeboo)
PostPosted: Thu Dec 06, 2012 6:35 am 
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DrW wrote:
slowly preparing the environment on Earth to host the Cambrian Explosion,


I think popular science writing would be better off without this kind of phrasing. It ascribes intentionality that doesn't exist. No preparing, no hosting.

The enviroment of the Earth slowing changed and the Cambrian Expolosion developed out of that change.

PS love, love, love your science postings.

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 Post subject: Re: Science vs. Religion and Magic (Abiogenesis for Ceeboo)
PostPosted: Thu Dec 06, 2012 9:02 am 
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lulu wrote:
DrW wrote:

PS love, love, love your science postings.[/color]


X2

Thanks Dr W

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 Post subject: Re: Science vs. Religion and Magic (Abiogenesis for Ceeboo)
PostPosted: Thu Dec 06, 2012 9:15 am 
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lulu wrote:
DrW wrote:
slowly preparing the environment on Earth to host the Cambrian Explosion,


I think popular science writing would be better off without this kind of phrasing. It ascribes intentionality that doesn't exist. No preparing, no hosting.

The enviroment of the Earth slowing changed and the Cambrian Expolosion developed out of that change.

PS love, love, love your science postings.

Agree with your comment about ascribing intent to inanimate systems.

In this case, the idea was to eventually compare the role of cyanobacteria in the "creation" of the Earth we live on to the role ascribed to God by Christians. (Blasphemous, I know - but a comparison worth noting.)

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 Post subject: Re: Science vs. Religion and Magic (Abiogenesis for Ceeboo)
PostPosted: Thu Dec 06, 2012 10:16 am 
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Can I just point out how amazing it is that the RNA article's author's last name is Powner?

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 Post subject: Re: Science vs. Religion and Magic (Abiogenesis for Ceeboo)
PostPosted: Thu Dec 06, 2012 11:21 am 
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CaliforniaKid wrote:
Can I just point out how amazing it is that the RNA article's author's last name is Powner?

A nod to gaming slang?
An Ivory Tower Academic who is is also a gamer?
Just doesn't seem right, somehow.

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 Post subject: Re: Science vs. Religion and Magic (Abiogenesis for Ceeboo)
PostPosted: Thu Dec 06, 2012 12:04 pm 
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CK has been pwning apologetic newbs since closed beta. He has a lvl 60 sin who crits for over 9000 with T4 gear and 600 AA points.

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 Post subject: Re: Science vs. Religion and Magic (Abiogenesis for Ceeboo)
PostPosted: Thu Dec 06, 2012 12:17 pm 
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Hello Dr.W

First, in regard to your OP, I want to extend a hearty and sincere thank you for the enormous effort and time given! I do indeed appreciate that a lot! :smile:

After reading the OP twice, I am certain that I still miss much of what your OP talks about (To be clear, this probably has very little to do with you and it most surely has to do with the reality that much what you contribute is simply way over my pay grade. Such is the result when a Dr. of any letter, including a "W", attempts to communicate with a Ceeboo) :smile:

Okay, here is where I am at this moment (I reserve the right to change or naturally evolve at any time though) :razz:

There are a few abiogenesis models that the science community is tossing around, yes?

These different models (no matter which particular one we are speaking of) have entirely no bearing or influence on the theory of Darwinian evolution. As abiogenesis is a completely and totally separate issue (the origin of life) than that of the evolving of life once it was here. Is this right?

Still thinking. Still reading....................And....Still believing in a Creator! :lol:

Very interesting stuff, IMO!

Thanks again, W. :smile:

Peace,
Ceeboo


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 Post subject: Re: Science vs. Religion and Magic (Abiogenesis for Ceeboo)
PostPosted: Thu Dec 06, 2012 12:29 pm 
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Off topic alert!

Is it just me or do others have an enormously difficult time wrapping the mind around billions of years?

Peace,
Ceeboo


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 Post subject: Re: Science vs. Religion and Magic (Abiogenesis for Ceeboo)
PostPosted: Thu Dec 06, 2012 12:36 pm 
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Ceeboo wrote:
Off topic alert!

Is it just me or do others have an enormously difficult time wrapping the mind around billions of years?

Peace,
Ceeboo


I think it's very on topic, Ceeboo. I have a hard time wrapping my mind around a billion of anything. It's so far beyond my normal day-to-day experience, I can't picture it. The closest I can get is to remember that a billion seconds is equal to around 32 years. Mind boggling.

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 Post subject: Re: Science vs. Religion and Magic (Abiogenesis for Ceeboo)
PostPosted: Thu Dec 06, 2012 1:20 pm 
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Hello DrW,

Could you elaborate on a couple questions?

First, regarding your statements, "because after all, it is only chemistry." - "The main thing I hope you realize, my friend, is that it is all chemistry - and only chemistry. No magic is involved."

This is so confusing, what does "only chemistry" mean? Chemistry alone can be magical in and of itself to an attitude full of wonder and mystery, or it can be "only chemistry" to a mind that believes this is not mysterious or fraught with wonder. This is why one can agree with every article you posted and the facts you rely on and yet come to a completely different position - a lot of attitude, psychology and philosophy is simply taken for granted in your post.

Second, no its not "only chemistry" - it includes information processing. Where that information came from or solving the chicken or the egg question of what came first the information or processing doesn't reduce to a cliché - it's just chemistry. The information is much greater than say crystal formation as well it includes specific functions that need to be carried out like computer code.

I can only confront "Science" as the culmination of a complex and rich and historical method. It is not a sole position. It’s a set of tools and way of inquiry. It is hard to read your post otherwise than you think it is an established position - that science is simply a defined philosophical standpoint that coincidentally matches your personal philosophical position.

my regards, mikwut

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Last edited by mikwut on Thu Dec 06, 2012 2:24 pm, edited 2 times in total.

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 Post subject: Re: Science vs. Religion and Magic (Abiogenesis for Ceeboo)
PostPosted: Thu Dec 06, 2012 1:37 pm 
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Also,

Quote:
Those who believe in their own private blend of science and religious myth might want to ask themselves why an omnipotent and omniscient God, whose ultimate goal was creation of humankind, would start with planet that would require transformation by single cell animals for billions of years. Why not just build it right the first time?


If the discussion is scientific in nature your contention is irrelevant, or I assume you would admit isn't a scientific objection but a personal one. No one would claim that the creator of the AMC Pacer is so lowly in comparison to the creator of the new Mercedes M-Class - therefore, the AMC Pacer must have spontaneously, naturally and "just mechanically" been produced. Do you believe theological objections you have are relevant to a scientific discussion and conclusion that you draw?

mikwut

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 Post subject: Re: Science vs. Religion and Magic (Abiogenesis for Ceeboo)
PostPosted: Thu Dec 06, 2012 1:42 pm 
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Quote:
First, regarding your statements, "because after all, it is only chemistry." - "The main thing I hope you realize, my friend, is that it is all chemistry - and only chemistry. No magic is involved."

This is so confusing, what does "only chemistry" mean? Chemistry alone can be magical in and of itself to an attitude full of wonder and mystery, or it can be "only chemistry" to a mind that believes this is not mysterious or frought with wonder. This is why one can agree with every article you posted and the facts you rely on and yet come to a completely different position - a lot of attitude, psychology and philosophy is simply taken for granted in your post.


Maybe it might be helpful if mikwut was to explain whether he has ever taken a chemistry course, and if so to what level? That way DrW could judge where he is coming from with a question like this, and what kind of answer might be comprehensible to him. It would also give others a basis for judging how much mikwut's opinions on chemistry might be worth.

DrW will no doubt speak for himself on the question of magic. But I suspect that what he means by saying 'No magic is involved' is that what happens in a chemical reaction depends on only factors such as the following:

1. What molecules are present, and in what concentrations.

2. What state the components present are in - solid, liquid or gas, and in what modes of contact.

3. What conditions of pressure, temperature and other purely physical factors (such as incident photon flux) subsist.

What is completely irrelevant in any direct way is the intention of the human being observing the situation, including any prayers, objurgations or incantations he or she may utter, any amulets or clothing he or she may be wearing that do not interact with the reagent molecules, or any mantic gestures they may make.

An example of magic actually entering into chemistry would be if, for instance, I could make common salt decompose into metallic sodium and gaseous chlorine by pointing a wand at it and exclaiming "Decomposeantius!" in a commanding tone of voice. Or maybe saying "By the authority of Jesus Christ and the Melchizedek Priesthood which I hold, I command you to decompose!" If either procedure worked, that would be magic. But they don't.

But perhaps by chemistry being 'magical' you just mean that you find it really impressive and beautiful to think about? In that case, no worry, but I am pretty sure that is not what DrW meant.

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 Post subject: Re: Science vs. Religion and Magic (Abiogenesis for Ceeboo)
PostPosted: Thu Dec 06, 2012 1:45 pm 
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Ceeboo wrote:
Off topic alert!

Is it just me or do others have an enormously difficult time wrapping the mind around billions of years?

Peace,
Ceeboo


Ten fingers, ten toes. After that, it's all a little fuzzy for me. It's very embarrassing when I'm at the store and have to take my shoes off to see if I can go into the '15 items or less' check stand.

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 Post subject: Re: Science vs. Religion and Magic (Abiogenesis for Ceeboo)
PostPosted: Thu Dec 06, 2012 1:56 pm 
Holy Ghost

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Hello Chap,

Quote:
Maybe it might be helpful if mikwut was to explain whether he has ever taken a chemistry course, and if so to what level? That way DrW could judge where he is coming from with a question like this, and what kind of answer might be comprehensible to him. It would also give others a basis for judging how much mikwut's opinions on chemistry might be worth.


Hmmmm. I remember a discussion I had in the past with you where I quoted philosophical positions in my posts, education that I have, and your response was an attitude of the message board is not conducive basically because anyone can state any educational position they want. Now you request certain education credentials of me that whatever I would provide would be open to either it can't be trusted or it doesn't qualify for discussion on this message board. So I just won't take your bait.

Quote:
DrW will no doubt speak for himself on the question of magic. But I suspect that what he means by saying 'No magic is involved'


So my objection to DrW's use of a charged, only defined in a subjective and fraught with personal emotion with obvious overtones of bias towards theism use of the word magic in general is defended by Chap with his subjective use of the same charged, only defined in a subjective and fraught with personal emotion with obvious overtones of bias towards theism in general surmising. Which also ignores the information factor in my post.

Quote:
What is completely irrelevant in any direct way is the intention of the human being observing the situation, including any prayers, objurgations or incantations he or she may utter, any amulets or clothing he or she may be wearing that do not interact with the reagent molecules, or any mantic gestures they may make.


None of this is found in my post - why are you talking this nonsense?

Quote:
An example of magic actually entering into chemistry would be if, for instance, I could make common salt decompose into metallic sodium and gaseous chlorine by pointing a wand at it and exclaiming "Decomposeantius!" in a commanding tone of voice. Or maybe saying "By the authority of Jesus Christ and the Melchizedek Priesthood which I hold, I command you to decompose!" If either procedure worked, that would be magic. But they don't.


Why more nonsense I didn't say or even imply in any way?

Quote:
But perhaps by chemistry being 'magical' you just mean that you find it really impressive and beautiful to think about? In that case, no worry, but I am pretty sure that is not what DrW meant.


Or the words that I actually used that have their own definitions like "mystery" and "wonder".

mikwut

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 Post subject: Re: Science vs. Religion and Magic (Abiogenesis for Ceeboo)
PostPosted: Thu Dec 06, 2012 2:03 pm 
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Joined: Mon Jun 11, 2007 3:23 am
Posts: 7137
Location: On the imaginary axis
I was trying to work out what you meant by this:

Quote:
Chemistry alone can be magical in and of itself to an attitude full of wonder and mystery, or it can be "only chemistry" to a mind that believes this is not mysterious or frought with wonder.


Which you posted in response to DrW saying:

Quote:
"The main thing I hope you realize, my friend, is that it is all chemistry - and only chemistry. No magic is involved."


So when you say "Chemistry ... can be magical", in response to DrW saying magic has nothing to do with chemistry, what do you mean exactly?

I am pretty sure that you mean something quite different by 'magic' from what DrW means. My examples illustrated what I thought he was talking about.

But what DO you mean by it?

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