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Author Topic:   coded information in DNA
WordBeLogos
Member (Idle past 5422 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 160 of 334 (511032)
06-05-2009 8:10 PM
Reply to: Message 143 by bluegenes
06-04-2009 10:42 AM


Hi bluegenes,
bluegenes writes:
That's one you probably won't make, because we know a lot about the formation of stars. You won't make the caveman one, because we now understand a lot about lightning and volcanoes. But we don't know much about chemical evolution and the formation of the genetic code, so you do make that one.
But this is today. The laws of nature are well understood. We know they can account for fire and nuclear power. The physics and chemistry of DNA are also very well understood. This *IS* the problem. And yet again...
Yockey: The reason that there are principles of biology that *CANNOT* be derived from the laws of physics and chemistry lies simply in the fact that the genetic information content of the genome for constructing even the simplest organisms is *MUCH LARGER* than the information content of *THESE LAWS*. The existence of a genome and the genetic code divides living organisms from nonliving matter. There is nothing in the physico-chemical world that remotely resembles reactions being determined by a sequence and codes between sequences.
Emphasis mine.
That's pretty clear. Can't sqweeze water out of a dry towel.
-Word
Edited by WordBeLogos, : No reason given.

John 1:1 In the beginning was the Word, and the Word was with God, and the Word was God.

This message is a reply to:
 Message 143 by bluegenes, posted 06-04-2009 10:42 AM bluegenes has not replied

WordBeLogos
Member (Idle past 5422 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 161 of 334 (511033)
06-05-2009 8:18 PM
Reply to: Message 144 by Taq
06-04-2009 4:22 PM


Hi Tag,
Tag writes:
But you are taking it one step further. You are saying that no such mechanism exists. Surely you can see the difference, no? If you want to claim that no natural mechanism exists by which coded information can be produced then you need to show this. I don't envy the task.
As of yet, we observe none exists. Just as of yet, we observe that neither energy nor matter can be destroyed. Neither are proven impossible, there is just simply no evidence to the contrary.
-Word
Edited by WordBeLogos, : No reason given.

John 1:1 In the beginning was the Word, and the Word was with God, and the Word was God.

This message is a reply to:
 Message 144 by Taq, posted 06-04-2009 4:22 PM Taq has not replied

WordBeLogos
Member (Idle past 5422 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 162 of 334 (511034)
06-05-2009 8:25 PM
Reply to: Message 145 by Taq
06-04-2009 4:25 PM


Tag,
Tag writes:
But what happens when that code is duplicated and changed? Could new variation in the code give rise to new information? That is what happens in DNA, the code evolves without the intervention of intelligence.
All communication systems are subject to mutations, according to the laws of probability. Thats why Ethernet and IP/TCP have error correction / redundancy features. Yes, DNA has error correction / redundancy features also. Good point.
-Word

John 1:1 In the beginning was the Word, and the Word was with God, and the Word was God.

This message is a reply to:
 Message 145 by Taq, posted 06-04-2009 4:25 PM Taq has not replied

WordBeLogos
Member (Idle past 5422 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 163 of 334 (511035)
06-05-2009 8:34 PM
Reply to: Message 150 by lyx2no
06-04-2009 10:46 PM


Re: Burden of Proof
Hello lyx2no,
The code is not at all amazing: square pegs fit in square holes.
And what accounts for the square holes being arranged in the precise order which spells out the complete assemblage instructions to build a space shuttle? Chance?
-Word

John 1:1 In the beginning was the Word, and the Word was with God, and the Word was God.

This message is a reply to:
 Message 150 by lyx2no, posted 06-04-2009 10:46 PM lyx2no has replied

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WordBeLogos
Member (Idle past 5422 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 165 of 334 (511038)
06-05-2009 8:40 PM
Reply to: Message 151 by Dr Adequate
06-05-2009 12:20 AM


Re: Burden of Proof
Dr,
Dr writes:
Word writes:
The question of where the molecule came from and how it operates is an important one but not relevant to the discussion at hand.
But they're the same question. The origin of the code, and the origin of the molecules that instantiate the code, are the same thing. If the DNA and the mechanisms of transcription and translation didn't exist, then we would not be having this discussion.
Hardware does not give rise to software Dr.
-Word

John 1:1 In the beginning was the Word, and the Word was with God, and the Word was God.

This message is a reply to:
 Message 151 by Dr Adequate, posted 06-05-2009 12:20 AM Dr Adequate has not replied

Replies to this message:
 Message 166 by Rahvin, posted 06-05-2009 8:52 PM WordBeLogos has replied

WordBeLogos
Member (Idle past 5422 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 167 of 334 (511040)
06-05-2009 8:53 PM
Reply to: Message 152 by bluegenes
06-05-2009 4:33 AM


bluegenes,
A parody:
1 - All known intelligent creatures require the genetic code.
2 - The genetic code must be a prerequisite for intelligence.
3 - The genetic code, therefore, cannot be designed.
Precisley.
3 - The genetic code, therefore, cannot be designed. ( by creatures derived from DNA )
Which is why the only available explnantion left, is, an uncaused cause of all that has been caused.
If you can provide an example of an intelligent being who does not depend on the genetic code you can prove this false. All you need is one.
It's inferred. The only current option left, an Uncaused cause.
pmarshall writes:
I have already addressed this question — re-quoting an earlier post: Everything we currently know about nature rules out an infinite regress of causes. In absence of a material explanation, the only alternative for the origin of code is an uncaused coder. Which is why a human designer (re: HRG's question earlier) is not a plausible explanation. Thus the only available explanation that remains is an uncaused, conscious, metaphysical designer. (This is also the limit of my syllogism's ability to identify God.) Those who dislike this option always do, of course, have the option of waiting for a naturalistic cause to be discovered. But one cannot say one has empirical evidence until such evidence is produced.
-Word

John 1:1 In the beginning was the Word, and the Word was with God, and the Word was God.

This message is a reply to:
 Message 152 by bluegenes, posted 06-05-2009 4:33 AM bluegenes has replied

Replies to this message:
 Message 170 by onifre, posted 06-05-2009 9:08 PM WordBeLogos has replied
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WordBeLogos
Member (Idle past 5422 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 168 of 334 (511041)
06-05-2009 8:57 PM
Reply to: Message 154 by Blue Jay
06-05-2009 2:53 PM


Bluejay,
To be specific, Son means the "reply" button at the bottom of each post, not the "gen reply" button at the bottom of the page: this links your post to the post you're replying to and helps us know who you're talking to.
Thanks.
Gotcha, thanks buddy. It's much easier since I'm dealing with so many questions to do them all together, but I'll do them seperately if it helps.
-Word
Edited by WordBeLogos, : No reason given.

This message is a reply to:
 Message 154 by Blue Jay, posted 06-05-2009 2:53 PM Blue Jay has not replied

WordBeLogos
Member (Idle past 5422 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 169 of 334 (511042)
06-05-2009 9:01 PM
Reply to: Message 157 by Taq
06-05-2009 4:03 PM


Tag,
Tag writes:
Word writes:
When we see an arrangement of pebbles that say "It is appointed unto man once to die, then after this the judgment," is this just the inherent physical properties of pebbles lining up according to "laws of nature?"
According to your argument, as soon as we observe humans arranging pebbles then we must assume that all unknown arrangement of pebbles are also intelligently guided.
You don't have to, no. Would you think, if you observed "Every knee will bow, and every toungue confess that Jesus Christ is Lord," written out in pebbles was a natural occurence?
-Word

John 1:1 In the beginning was the Word, and the Word was with God, and the Word was God.

This message is a reply to:
 Message 157 by Taq, posted 06-05-2009 4:03 PM Taq has not replied

WordBeLogos
Member (Idle past 5422 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 172 of 334 (511045)
06-05-2009 9:16 PM
Reply to: Message 166 by Rahvin
06-05-2009 8:52 PM


Re: Burden of Proof
Hello Rahvin,
Rahvin writes:
Biological systems are not analogous to computer systems, Logos. In particular, the analogy that DNA is similar to software betrays an utter ignorance of both software and DNA.
Actually they are almost identical...
"The book Information Theory, Evolution and the Origin of Life is written by Hubert Yockey, the foremost living specialist in bioinformatics. The publisher is Cambridge University press. Yockey rigorously demonstrates that the coding process in DNA is identical to the coding process and mathematical definitions used in Electrical Engineering. This is not subjective, it is not debatable or even controversial. It is a brute fact:
Information, transcription, translation, code, redundancy, synonymous, messenger, editing, and proofreading are all appropriate terms in biology. They take their meaning from information theory (Shannon, 1948) and are not synonyms, metaphors, or analogies. (Hubert P. Yockey, Information Theory, Evolution, and the Origin of Life, Cambridge University Press, 2005)"
-Word

John 1:1 In the beginning was the Word, and the Word was with God, and the Word was God.

This message is a reply to:
 Message 166 by Rahvin, posted 06-05-2009 8:52 PM Rahvin has replied

Replies to this message:
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WordBeLogos
Member (Idle past 5422 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 173 of 334 (511046)
06-05-2009 9:19 PM


Hey welcome back onifre!
Hey gotta run guys, peace.
-Word

Replies to this message:
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WordBeLogos
Member (Idle past 5422 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 178 of 334 (511103)
06-06-2009 6:26 AM
Reply to: Message 158 by Percy
06-05-2009 4:53 PM


Mornin Percy,
Percy writes:
You don't really mean to say that they didn't "originate from the laws of nature."
Notice what "they" refers to here, the new conded information. Which did not have it's origin in the laws of nature, but someones mind. Yes the construction certainly does obey the laws of nature (working through someones hands physically arranging them etc.)
Percy writes:
We do know that information arises naturally all the time. Nothing happens anywhere that doesn't create new information.
Show me one example of a information comunication system that does not arise from mind. Besides that of DNA. Just one.
The only kind of properties and processes we've ever observed in the universe are all natural,...
Correct, of which none are known to produce coded information systems. That's precisely the problem. Observing DNA operate does not explain the origin of the coded information in the same way that "observing" a computer operate does not explain the sofware running it.
and so we explain DNA in terms of those properties and processes.
Yes, we can know computers obey the laws of physics. Which says nothing about the code running it.
You postulate that there are properties and processes of which we're yet unaware, and perhaps that is so, but again, you need evidence.
The coded information, that we never observe originating from the laws of physics and chemistry.
There's another bigger problem that rarely gets addressed in ID discussions, and that's where the designer came from. If DNA requires a designer, and if the designer was an advanced alien, then the alien's DNA would have required a designer. And that alien's DNA would also have required a designer. And so on back to the beginning of time, and at some point you just have to call a halt and say God did it.
Exactly, that's why the Designer must be uncaused Himself. There must ultimately be some uncaused first cause. An eternal original cause. If not we run into a infinite regress of causes. That's why humans ans aliens etc., cannot be an option.
So why not just admit that ID requires God and is religion.
God is the only available option at this time, simply by reason alone.
-Word

John 1:1 In the beginning was the Word, and the Word was with God, and the Word was God.

This message is a reply to:
 Message 158 by Percy, posted 06-05-2009 4:53 PM Percy has replied

Replies to this message:
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WordBeLogos
Member (Idle past 5422 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 183 of 334 (511282)
06-08-2009 9:14 PM


Gentlemen,
Ok, it looks like we are getting of track again.
Lets start from the beginning.
Even if we somehow had all the necessary molecules which are required to produce life, it still wouldn't solve the problem of assembling these materials into functioning proteins and DNA.
We now know functioning proteins require a lenghty and specific sequential arrangment of amino acids. Just as any meaningful English sentense, paragraph or book requires a specific sequencial arrangment of letters.
Obviously this creates a real problem for any kind of chemical evolution. Amino acids on their own do not make proteins any more than letters on their own make sentenses, paragraphs or books. We know that English letters are directed by human intelligence to produce meaningful text. Likewise, amino acids are specifically sequenced as dictated by information encoded inside the DNA molecule.
This finding, raises the question of the ultimate origin of this encoded information. Many now concider this information problem the "Holy Grail" of the origins of life. As Bernd Olaf Kuppers said..."the problem of the orgin of life is clearly basically equivalent to the problem of biological information."
Theres basically three naturalistic explanations for the origin of information. Chance, prebiotic natural selection and chemical necessity.
Chance was once thought to give account for biological information, but not many hold to this view now. Especially since we have now come to appreciate the sequential specificity of proteins and nucleic acids. As A. Graham Cairns-Smith says:
"Blind chance is very limited. Blind chance can produce low levels of cooperation, exceedingly easily, the equivalent of letters and small words, but it becomes very quickly incompetent as the amount of organization increases. Very soon indeed long waiting periods and massive material resources become irrelevant."
If you stil hold out for a "happy frozen accident" as Mr. Dawkins puts it, then that's your choice. A miracle is a miracle.
The natural selection scenario suffers the same problems. Begging the question, in order for natural selection to take place self replication must already be assumed. But this is the very thing that needs explained. Natural selection only selects from what chance has already produced.
Some suppose chemicals having certain affinities for other chemicals might be able to account for information. That maybe the laws of nature plus chemical attraction could account for information in DNA. Chemicals having self-ordering properties such as salt. So to maybe amino acids with special affinities for each other might order themselves to form proteins etc. But ironically Dean Kenyon who wrote the book himself, Biochemical Predestination, now says such theories are incompatible with empircal findings.
The problem can be seen just by examining the DNA molecule itself. DNA depends on several chemical bonds. Theres the bond between the sugar and phosphate molecules which forms the two twisting backbones. Then you have the bond that bonds the base pairs to the sugar-phosphate backbones itself. But there is no bond between the base pairs running along the spine of the double helix from one end to the other. Left or right, there is no bond one base to the next. But this is precisely where the coded message resides.
The base pairs can bond to any site along the sugar-phosphate backbone. Just like magnet letters on a metal surface. They bond to the metal surface itself (the sugar-phosphate backbone), but they can be placed in any order. No one spot is preferred over anyother by chemical attraction. All four bases can bond to any site. So sequential bonding affinities don't account for the order of the base pairs.
Right where the specific sequencing is observed, which creates the coded information, is right where there is no speacial affinity one for the other.
The information contained in DNA is both specified and complex in the same way as a meaningful english sentense is. Just as lines of code in computer software is. But the information of these do not originate from the chemistry of ink or the physics of magnetism, but from a source completely outside / independent of either.
Likewise, in the same manner, the information in DNA is also independent of the properties of the medium which hold it. Becuase the chemical bonds do not determine for the arrangment of the base pairs.
So if the properties of the medium itself don't account for the origin of information, then what does? All of human observation tells us that information systems, languages and codes, always come from an intelligent source.
As of now, observing that all naturalistic explanations have failed to explain the origin of biological information, intelligence stands alone as the *ONLY* known process to produce such information intense systems.
We can observe the past actions of intelligence even if we can't observe direct intervention of said intelligence. Here in Ohio we can see a flower arrangment saying "Welcome to Ohio." We know intelligence was involved even if we never saw them planted and arranged thus.
There are many branches of science which look for these signs of intelligence and make inferences based on such today. Archeologist rightly infer intelligence when observing inscriptions on the Rosetta Stone. SETI searches for signals containing information out in space. But as of yet we have found no information bearing signals from space. But at the same time, right under our noses, we have discovered information in DNA. Thus we are justified to infer intelligence.
But you guys will say it's simply a God-of-the-gaps fallacy since science can't explain it yet. But heres the catch, I'm not infering design simply because there is no naturalistic explanation. But *BECAUSE* DNA infact *DOES* manifest the very thing that intelligently designed information systems have, coded information and language!
Intelligence has powers that nature does not. When we observe effects that we know by empirical observation are only the effects of intelligence, we are justified to infer intelligence even if we were not there to see it. Since DNA contains that which we know by 100% of human observation, is *ALWAYS* the product of intelligence, then intelligence, as of now, stands as the best explanation for what we observe in DNA.
-Word
Edited by WordBeLogos, : No reason given.

John 1:1 In the beginning was the Word, and the Word was with God, and the Word was God.

Replies to this message:
 Message 184 by Percy, posted 06-08-2009 9:42 PM WordBeLogos has not replied
 Message 185 by Blue Jay, posted 06-08-2009 11:24 PM WordBeLogos has replied
 Message 189 by Dr Adequate, posted 06-09-2009 1:02 PM WordBeLogos has replied

WordBeLogos
Member (Idle past 5422 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 186 of 334 (511314)
06-09-2009 9:17 AM
Reply to: Message 158 by Percy
06-05-2009 4:53 PM


Hello there Percy,
I earlier gave you example of Alphabits cereal. If you arrange three letters to spell "yes", that is information. But if you jostle the box and three letters fall out to spell "yes", that is also information.
Yes, it mimics real intended coded information. This falls within the probabilty of chance, especially given the fact there are already intelligently designed letters to begin with. The initial conditions which allow three English letters to fall out spelling the word "yes," in the first place, are themselves the product of design. A box full of English letters in the form of cereal does not arise naturally.
In fact, any arrangement of letters is information. That some arrangements happen to correspond to words to which we attach meaning (which as Shannon tells us is independent of information) is irrelevant to the information itself. Speaking digitally, information is just bits, it doesn't matter what meaning people might attach to the arrangement of bits.
Until you can make the distinction between information and coded information systems you will never understand what is being argued here Percy. Yes anything that happens gives off "information" just by it's very state. It tells us something about itself, or possibly something about what it may have encounted. But there is no code intended to be sent and decoded. No intended information.
All the examples you continue to offer are only information about themselves or other things they have come in contact with in some fashion. There is no decoder that this information is intended for. This information means nothing until we assign meaning to it. In DNA, there is real coded information, a real signal which is intended to be successfully decoded and implemented. And this language and communication takes place if we are there or not, all on it's own.
Just like the garage door example here... Message 108
We do know that information arises naturally all the time. Nothing happens anywhere that doesn't create new information. Your fundamental argument is actually that the origin of DNA could not have been a natural event, in that it would have required intelligence to create it and the processes that surround it. You have so far produced no evidence to support your position.
DNA being a coded information system is the evidence Percy. Just as matter and energy are never observed to be destroyed or created, coded information systems are NEVER observed to be the product of processes absent of intelligence. NEVER. Unless you have an example?
The only kind of properties and processes we've ever observed in the universe are all natural, and so we explain DNA in terms of those properties and processes.
And again, it is those very properties and processes which are the problem Percy. Again from Yockey...
Yockey writes:
The reason that there are principles of biology that cannot be derived from the laws of physics and chemistry lies simply in the fact that the genetic information content of the genome for constructing even the simplest organisms is much larger than the information content of these laws."
I'm sorry Percy, but what part of that don't you understand? You are saying blood can come from a turnip. He's saying but turnips don't contain blood. You are saying, but they must, because look, there is blood. You are again begging the question. "All that we observe is natural, since we observe DNA, it has a natural origin." This is the QUESTION we are trying to determine. If we knew this, there would be no need for this very forum.
Neptune was discovered in part because the orbit of Uranus deviated from its calculated path, so it was presumed that there must be another planetary body out there perturbing its orbit. You need the equivalent of something that deviates from known physical laws in ways we can't currently explain in order to claim that there must be something more going on than we're currently aware. Just stating over and over and over again that DNA could not have arisen naturally won't get you anywhere.
The coded information system contained in biological life ought to tell you, "hey this doesn't jive!"
So why not just admit that ID requires God and is religion.
Reason alone using the scientific method of induction, points to an original uncaused Encoder as the only available exlplanation, at this time. Of course one is free to wait for some other explanation. Religion / theology, has nothing to do with this argument.
-Word
Edited by WordBeLogos, : No reason given.
Edited by WordBeLogos, : No reason given.

John 1:1 In the beginning was the Word, and the Word was with God, and the Word was God.

This message is a reply to:
 Message 158 by Percy, posted 06-05-2009 4:53 PM Percy has replied

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WordBeLogos
Member (Idle past 5422 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 194 of 334 (511379)
06-09-2009 2:47 PM
Reply to: Message 164 by onifre
06-05-2009 8:37 PM


Hey onifre,
onifre writes:
Word writes:
The same thing is true with coded information systems such as DNA, but with one exception, we observe that minds do produce coded information systems. Natural processes do not.
How do you know that natural processes do not? - because we don't see it occuring today?
How do we know that matter and energy can neither be created nor destroyed? Because we don't see it occuring today?
DNA exists, there was a point in time when it did not, so some kind of process happened, right? - So you think something supernatural had to construct this?
The question that we can’t answer, is where the code came from in the first place. The question of where the molecule came from and how it operates is an important one but not relevant to this discussion. The distinction has to be made between the physical molecule and the imaterial information. People keep trying to explain how the paper and the ink may have come together thus producing the book. But this is not the question..the question is where did the story line come from??
What "organized" the complexity of this supernatural "thing" that was able to construct natural things? - And why don't we see this process today? Or, was it's only objective to simply organize a few chemicals then vanish, forever?
This argument cannot identify the personal characteristics of God. It simply leaves God as the only logical possibility, because no natural causes are known, and a infinite regress of finite intelligent causes is not rational. So the only available explanation left, is an uncaused, conscious, metaphysical designer. Which ironically fits the description of the biblical God.
Why do natural, chemical processes construct whole organisms now, each one different from the next? Wouldn't that require that the "original" information in the first DNA structure changed through time, causing the information to change also? Wouldn't a new set of information be required to change the DNA for every single species every time there's an enviromental change?
I have no problem with codes that can change *ONCE* there is one to start with. I believe evolution is an engineered process. I believe the beneficial mutations are by design. Protozoa can splice its own DNA into over 100,000 pieces and rearrange them, this is not some random or haphazard process, this is a highly engineered process.
pmarshall writes:
I do not have a problem with evolution. What I have a problem with is the notion that it’s purely random. Successful evolution can only proceed if mutations are in some degree ordered by a pre-programmed mechanism, just as we see in all the genetic programs like Avida. It’s intentional engineered mutation filtered by not only natural selection, but maybe even some mechanism that knows that permutations have already been tried unsuccessfully. It’s not a random walk. It’s more like the intentional competition that we see in technology, business and culture.
James A. Shapiro has some great papers on this, especially this one:
01/07/30 - ICBP 2000
-Word

John 1:1 In the beginning was the Word, and the Word was with God, and the Word was God.

This message is a reply to:
 Message 164 by onifre, posted 06-05-2009 8:37 PM onifre has not replied

Replies to this message:
 Message 195 by Son, posted 06-09-2009 3:13 PM WordBeLogos has replied
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WordBeLogos
Member (Idle past 5422 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 196 of 334 (511383)
06-09-2009 3:18 PM
Reply to: Message 170 by onifre
06-05-2009 9:08 PM


Onifre,
Fuzzy wuzzy was a what...? "An uncaused cause of all that is caused" - What does that even mean...?
All finite things have a cause. The only logical conclusion is, that there must ultimately be some original Uncaused (eternal) cause of all finite things which themselves have been caused. If not, you run into an irrational infinite regress of finite causes and effects.
So, let me beg the question, 'cause I'm in the mood, why can't DNA fit the bill of "an uncaused cause of all organisms that are caused"?
Because DNA is finite. As you have rightly said, there was a time it didn't exist. Therefore, it can't be the uncaused cause.
-Word

John 1:1 In the beginning was the Word, and the Word was with God, and the Word was God.

This message is a reply to:
 Message 170 by onifre, posted 06-05-2009 9:08 PM onifre has replied

Replies to this message:
 Message 208 by onifre, posted 06-09-2009 5:57 PM WordBeLogos has replied

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