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Author Topic:   coded information in DNA
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 226 of 334 (511547)
06-10-2009 11:33 AM
Reply to: Message 218 by WordBeLogos
06-09-2009 8:46 PM


*Operating* through, and *originating* from, are two different things.
Quite so. And I am talking about the origins of codes.
This is why I used the phrase "come from", rather than "operate through" when I said:
All of human observation tells us that information systems, languages and codes, always come from sources that do not break the laws of nature.
A supernatural explanation is inferred.
Wrongly.
Natural processes do not stand alone as the *ONLY* known process, they have never been observed to produce information intense systems.
This is absolutely, 100%, incorrect.
We have never, ever observed any code being produced in a way that violates the laws of nature.
We have never, ever observed anything whatsoever being produced in a way that violates the laws of nature.

This message is a reply to:
 Message 218 by WordBeLogos, posted 06-09-2009 8:46 PM WordBeLogos has replied

Replies to this message:
 Message 256 by WordBeLogos, posted 06-14-2009 12:00 AM Dr Adequate has replied

Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 227 of 334 (511548)
06-10-2009 11:34 AM
Reply to: Message 220 by WordBeLogos
06-09-2009 8:58 PM


Re: Let's Make It Easier ...
The universe.
Did you just claim to have observed the origin of the Universe?
I guess you must be God.
I'd always thought of him as being smarter.
The laws of nature did not exist prior to their creation in this universe.
Assertion is not evidence.
The creation of the universe was a supernatural event.
Assertion is not evidence.
The existence of the supernatural is a fact.
Assertion is not evidence.
Edited by Dr Adequate, : No reason given.

This message is a reply to:
 Message 220 by WordBeLogos, posted 06-09-2009 8:58 PM WordBeLogos has not replied

Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 228 of 334 (511552)
06-10-2009 11:53 AM
Reply to: Message 225 by Admin
06-10-2009 8:39 AM


Re: Topic Reminder
This topic is about coded information in DNA. Please take discussion about evidence for the supernatural to another thread, or propose a new thread over at Proposed New Topics.
I think it has a certain relevance.
If WordBeLogos started a thread entitled: "Disappearance Of Socks", in which he proposed the hypothesis that his missing socks were being eaten by dragons, thus proving the existence of dragons ... and if I pointed out that no-one had ever seen a dragon ... then it would make little sense for you to complain that the topic was missing socks, and that the evidence, or lack thereof, of dragons belonged in a different thread. For the fact that there is no evidence for dragons is highly germane to the question of whether their alleged sockivorous habits can account for WordBeLogos's missing socks.

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 Message 225 by Admin, posted 06-10-2009 8:39 AM Admin has not replied

New Cat's Eye
Inactive Member


Message 229 of 334 (511597)
06-10-2009 2:59 PM
Reply to: Message 205 by WordBeLogos
06-09-2009 5:16 PM


But here is the problem. The word "yes," can be accounted for statistically through the laws of probability. Not to mention the very favorable conditions of having a box full of intelligently designed letters to begin with.
How about a complete sentense of 30 or so words? How about a complete paragraph of a few hundred words? This is why many scientists no longer hold to the chance or "happy frozen accident" hypothesis.
So you're changing the argument to DNA being too complex to have arrisen naturally...
You might want to catch up with the science behind this so your Argument from Incredulity doesn't look so ignorant. Here ya go:
quote:
Some theorists suggest that the atmosphere of the early Earth may have been chemically reducing in nature, composed primary of methane (CH4), ammonia (NH3), water (H2O), hydrogen sulfide (H2S), carbon dioxide (CO2) or carbon monoxide (CO), and phosphate (PO43-), with molecular oxygen (O2) and ozone (O3) either rare or absent.
In such a reducing atmosphere, electrical activity can catalyze the creation of certain basic small molecules (monomers) of life, such as amino acids. This was demonstrated in the Miller-Urey experiment by Stanley L. Miller and Harold C. Urey in 1953.
Phospholipids (of an appropriate length) can spontaneously form lipid bilayers, a basic component of the cell membrane.
A fundamental question is about the nature of the first self-replicating molecule. Since replication is accomplished in modern cells through the cooperative action of proteins and nucleic acids, the major schools of thought about how the process originated can be broadly classified as "proteins first" and "nucleic acids first".
The principal thrust of the "nucleic acids first" argument is as follows:
The polymerization of nucleotides into random RNA molecules might have resulted in self-replicating ribozymes (RNA world hypothesis)
Selection pressures for catalytic efficiency and diversity might have resulted in ribozymes which catalyse peptidyl transfer (hence formation of small proteins), since oligopeptides complex with RNA to form better catalysts. The first ribosome might have been created by such a process, resulting in more prevalent protein synthesis.
Synthesized proteins might then outcompete ribozymes in catalytic ability, and therefore become the dominant biopolymer, relegating nucleic acids to their modern use, predominantly as a carrier of genomic information.
source
Not so.
Yes it is!
wow, what a fun game
CS, in order for you to be an informed particpant in this discussion I suggest that you read the entire thread. Or at least all mine.
I have read it. All you've done is repeat refuted assertions. You've failed miserably and the thread now sucks.
When the sperm reaches the egg and a new cell with it's DNA are formed following the rules of genetics we have encoding. When the cell devides and forms limbs and organs we have decoding.
But that's just chemistry. Are you just as enthralled by salt dissolving in water?
ZOMG!1! Its so amazing! It proves god exists! Hooray!
Dumbass.

This message is a reply to:
 Message 205 by WordBeLogos, posted 06-09-2009 5:16 PM WordBeLogos has not replied

Parasomnium
Member
Posts: 2224
Joined: 07-15-2003


Message 230 of 334 (511618)
06-10-2009 4:56 PM
Reply to: Message 213 by WordBeLogos
06-09-2009 7:57 PM


Re: Faulty premises
WordBeLogos writes:
If we are simply going to reduce this down to "mights," then it might actually be what it looks like.
Indeed, to some it looks like a code, and to some it looks like a complex Rube Goldberg machine. (A naturally occurring one at that, not to get you started on the origin of Rube Goldberg machines.) And to some, including myself, it looks like both. I think it started as an increasingly complex chain of causes and effects; I think the code-like character is an emergent property of the process, which I think came about as a result of feedback loops.
So, to set something straight, I was not suggesting that DNA is not a code, I was merely pointing out that there are more ways to look at things.
Your "DNA is a consciously designed code" argument is just another incarnation of the intelligent design argument, and the rebuttal is as easy as it was before: what looks like design by a conscious mind is in fact design by evolution.
Can you show me evidence to the contrary that coded information systems only come from a mind? All you need is one.
No, I'm afraid one is not enough, because the one that has been staring you in the face all along apparently can't convince you. Besides, if we came up with something else, you'd probably dismiss that out of hand as well, because you have defined the concept of a code to be of intelligent origin by necessity. What can we do?
But it can be demonstrated not all mammals can fly. Can you demonstrate not all coded information systems come from minds?
No, because it's an impossible task. And I don't mean it's impossible because there are no such codes (there are, DNA is the prime example, but you won't accept that, we've been there), but because there are no codes that a mind could not think of. Any code we encounter and are able to identify as such, like we have done with DNA, we could also have invented, had it not existed, and so could any intelligence. There are no characteristics of a code that tell us that this code could not have been designed by intelligence.
I'm reminded of Christopher Hitchens' famous challenge to religious people to "name one moral statement or action made by a theist, that couldn't have been made by a non-believer". I'd paraphrase it thus: name one natural code that couldn't have been thought of by an intelligence. To date, Hithens hasn't had any takers, and I have no high hopes for myself either.

"Ignorance more frequently begets confidence than does knowledge: it is those who know little, not those who know much, who so positively assert that this or that problem will never be solved by science." - Charles Darwin.
Did you know that most of the time your computer is doing nothing? What if you could make it do something really useful? Like helping scientists understand diseases? Your computer could even be instrumental in finding a cure for HIV/AIDS. Wouldn't that be something? If you agree, then join World Community Grid now and download a simple, free tool that lets you and your computer do your share in helping humanity. After all, you are part of it, so why not take part in it?

This message is a reply to:
 Message 213 by WordBeLogos, posted 06-09-2009 7:57 PM WordBeLogos has replied

Replies to this message:
 Message 231 by Phage0070, posted 06-10-2009 5:52 PM Parasomnium has replied
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Phage0070
Inactive Member


Message 231 of 334 (511631)
06-10-2009 5:52 PM
Reply to: Message 230 by Parasomnium
06-10-2009 4:56 PM


Re: Faulty premises
Parasomnium writes:
..."name one moral statement or action made by a theist, that couldn't have been made by a non-believer".
"You don't believe my dreams are real, therefore I must now kill you!"
What is my reward?

This message is a reply to:
 Message 230 by Parasomnium, posted 06-10-2009 4:56 PM Parasomnium has replied

Replies to this message:
 Message 232 by Parasomnium, posted 06-11-2009 4:15 AM Phage0070 has not replied

Parasomnium
Member
Posts: 2224
Joined: 07-15-2003


Message 232 of 334 (511669)
06-11-2009 4:15 AM
Reply to: Message 231 by Phage0070
06-10-2009 5:52 PM


Off-topic
Phage0070 writes:
What is my reward?
Don't know, you'd have to ask Hitchens. However, you forfeit any reward for going off-topic.

This message is a reply to:
 Message 231 by Phage0070, posted 06-10-2009 5:52 PM Phage0070 has not replied

LucyTheApe
Inactive Member


Message 233 of 334 (511839)
06-12-2009 8:40 AM
Reply to: Message 1 by WordBeLogos
05-25-2009 7:13 PM


WordBeLogos writes:
Hi guys, I couldn't find a thread on this specific question which I'm sure has been mentioned somewhere, please forgive me. But how do we account for the coded symbolic information in DNA through the laws of physics and chemistry?
Thats a good question WordBeLogos but the answer is obvious, we can't.
We can try using voodoo science and create black holes, dark matter, dark energy and junk DNA, chance and Billions of years. But that brings us no closer to answering your question.
We can insert a purpose and design and that will answer your question. We can look forever outward and make things more complicated or we can look inside ourselves and see the reality.
Edited by LucyTheApe, : No reason given.

There no doubt exist natural laws, but once this fine reason of ours was corrupted, it corrupted everything.
blz paskal

This message is a reply to:
 Message 1 by WordBeLogos, posted 05-25-2009 7:13 PM WordBeLogos has not replied

Replies to this message:
 Message 234 by Vacate, posted 06-12-2009 9:55 AM LucyTheApe has not replied

Vacate
Member (Idle past 4600 days)
Posts: 565
Joined: 10-01-2006


Message 234 of 334 (511846)
06-12-2009 9:55 AM
Reply to: Message 233 by LucyTheApe
06-12-2009 8:40 AM


LucyTheApe writes:
We can look forever outward and make things more complicated or we can look inside ourselves and see the reality.
Typical. Now that we already know there is DNA you are quite comfortable with "looking inside ourselves" for the answer. How much success did that have in discovering DNA in the first place? Or all the discoveries that where necessary to enable DNA to be discovered? How nice it must be to accept only what you are comfortable with and deny the rest calling it "voodoo science".
We can try using voodoo science and create computers, light bulbs, electricity for the microwave, and cars to drive my lazy ass to work, Blue Ray players and still have thankless jerks to insult our progress.
Slight rewording from your original statement but that is still accurate to your way of thinking correct?

This message is a reply to:
 Message 233 by LucyTheApe, posted 06-12-2009 8:40 AM LucyTheApe has not replied

WordBeLogos
Member (Idle past 5392 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 235 of 334 (512036)
06-13-2009 5:31 PM


Gentlemen, real quick..
And I showed you what that symbolic code was. For neon it is 1s^2 2s^2 2p^6. For the W Boson it is Charge -1, Spin 1, Mass 80.4.
To catch up...
An information system contains the following: an encoder, a code, and a decoder.
Information / code, is comunication between an encoder and a decoder using agreed upon symbols.
The ultimate test for all these things is, can you take these molecules and show that there is an encoder, a code / message, being transmitted through a channel and a decoder. And draw a table of agreed upon symbols? In the same manner as we can take the sender and reciever of a morse code and show that the morse code table and what is being communicated is crystal clear? The electron orbital does not specify a structure in advance, it is completely dependent on what is brought into contact with it.
Upon offering further examples of codes / comunication systems etc., first see if it fits into Shannons model.
Now we know you’re insisting that the information from the sun is not *encoded information*, but it is. For example, the elements in the sun’s outer atmosphere are encoded in the sun’s absorption spectrum. Every black line in the spectrum represents an energy change in the electron shells of the isotope of a specific element. Now explain to us how this correspondence between black lines at a frequency (symbols, since you’re so insistent about them) and elements is not a code.
Sun light traveling to the earth is not a code / language / comunication system etc. There is no set of agreed upon symbols, there is no encoding or decoding. It's just light being produced and absorbed. Nothing is assigning meaning to it, it is just energy.
When we look into the sky and interpret what we see, our own intelligence is required for the information to exist.
Not the case in DNA. DNA both encodes and decodes all on it's own in the absence of any observers. The ribosomes decode the mRNA, and assign meaning in producing a protein. DNA is completely different from purely material objects, this does not take place in sand, pebbles, gravity or sunlight.
Manmade codes are used to impart information from one mind to another, and as such the medium is largely irrelevant. I could send this post to you over the internet, via ink and paper, through a messenger who had memorized it and would repeat it back to you, etc.
That is NOT the case for DNA. DNA works via direct, physical, molecular interaction. Period. You can’t slip a (microscopic) ink-and-paper representation of a DNA sequence into a cell and have it do anything. It *has* to be a molecular of sequence of exactly the right type, because *all* of the interactions in a cell, including the transcription/translation of a DNA sequence is done by the *physical* interaction of molecules literally bumping into each other and affecting each other (or not) due to their molecular shapes and atomic properties. It’s how they physically fit together (or not) that determines where a DNA sequence is going to cause certain kinds of changes in other molecules around it and throughout the cell’s interior. The medium and the message are *intimately* intertwined. The medium *is* the message and vice versa. This is very, very different from human codes.
Just like a CD player reading a CD. This system is also constrained in the same manner DNA is. Only one way for the player to read a CD. The fact that we have more ways of inputs and can code information in more ways is irrelevant to the problem, it just adds more codes.
Modern life’s system of DNA -> RNA -> ribosome-mediated production of proteins may seem too baroque, too code-based to have arisen naturally through variation and selection, but thanks to the molecular medium-is-the-message nature of the cell’s molecular machinery, there are numerous conceivable pathways by which it could have arisen from simpler beginnings in a series of evolutionary refinements.
We can provide all sorts of plausible abiogenesis scenarios, but the fact is, none of these experiments are successful, and none explain the origin of the genetic code itself.
Does it code for whether an alligator egg produces a male or female? Oh, wait, no it doesn’t Care to try again?
Genetics is not nearly so simplistic as you falsely presume.
Comunication systems need only code for one thing to qualify as code.
The laws of mendelian genetics are themselves a higher level code.
No. My knowledge that no code of known origins came into existence in a way that violated the laws of nature keeps me from having blind faith that some other code came into existence in a way that did violate the laws of nature.
All other codes are ultimately derivatives of DNA. All codes that you know the origin of come from biological code makers, humans (or animals, insects etc). So all of human observation, 100% of it, tells us codes ONLY come from intelligence. But, codes proceed ALL biological life. So did humans, insects or animals create the coded information DNA carries? No. But by empirical observation, codes ONLY come by intelligence. So, as it stands now, intelligence is the *ONLY* way we *KNOW* codes are made. And we *KNOW* humans, animals nor insects produced the coded information in DNA.
In my post 87 I described (in very outline) how an E. coli bacterium regulates the production of the proteins required to metabolism lactose to only be expressed when lactose is present. This mechanism only works because certain proteins coded for by the DNA can attach themselves to the chemical structure of the DNA molecule.
So the message (protein) actually works because the medium by which it is communicated is the DNA molecule. This is not equivalent to say, the message of a music CD. You could take that message and transmit it any way you like (MP3, AM radio, FM radio, vinyl, etc.) and you’d get the same music out the end.
The proteins (and other bits) produced by DNA require DNA to be the medium in which they are encoded in order to function - that is, in order to produce a working cell, plant or animal.
Does that clarify my meaning for you?
Information is interchangable. We can take the specific sequence of bases in a given DNA and represent it in any way we chose as long as the same sequence is used in building some other DNA molecule and the result will be the same. It doesnt matter how the sequence got carried before it got there.
When we say "I can send you this message through email or a phone call, or write it on a piece of paper," the point is that when it finally gets to your brain it has meaning no matter how many different ways it was transformed before it arrived. The same with DNA, if we store the sequence of bases on a hard drive. Information has this property, and the information still has to arrive in the proper form.
Another fact worth mentioning is DNA tertiary structure as it relates to DNA binding. A good example is the Arabinose operon. In this example two proteins bind to the DNA creating a loop in the DNA. This tertiary shape blocks access to the promoter.
What happens when you fold a page of code? Nothing.
Not all coding systems will share every characteristic with DNA. This is irrelevant to the fact that the sequence in DNA is code.
While genomics has an encoder, a decoder and a message, thus making it compatible with a grouping based on these characteristics, it is different from other things that you have grouped it with in other ways.
For example, computers, radios and human languages are not inextricably tied to their substrates. You can download information onto a computer, adjust the reception of a radio and interpret several different languages, all without changing the chemical composition of your computer, radio or eardrum.
However, you cannot change the information content of DNA without changing the chemical composition of the DNA. This suggests that the information content of DNA is just a chemical property of the molecule, and not an externally-enforced message.
Radios and computers *ARE* confined to their substrates. You cant change the information on a CD without changing its composition either, but the CD and player are still a coding system.
-Word

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

Replies to this message:
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 Message 240 by lyx2no, posted 06-13-2009 7:05 PM WordBeLogos has replied
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lyx2no
Member (Idle past 4716 days)
Posts: 1277
From: A vast, undifferentiated plane.
Joined: 02-28-2008


Message 236 of 334 (512038)
06-13-2009 6:10 PM
Reply to: Message 235 by WordBeLogos
06-13-2009 5:31 PM


Oh! Now I See
Your post
Why didn't you just say that from the begging? Oh! That's right you did. Then you said it in your second post. Then in your third post. Then I think you might have hinted at it in your fourth post; nope! you said it specifically. Then in your fifth post you said that too. Let me see; what did you say in your sixth post, hummm, that.
It's not that we didn't understand. We disagree. You've added nothing new in 235 posts even though you've been supplied with 117 new arguments against what someone you keep repeating says.
I hope this catches you up.
Edited by lyx2no, : Missed a verb.

Ridicule is the only weapon which can be used against unintelligible propositions. Ideas must be distinct before reason can act upon them.
Thomas Jefferson

This message is a reply to:
 Message 235 by WordBeLogos, posted 06-13-2009 5:31 PM WordBeLogos has not replied

WordBeLogos
Member (Idle past 5392 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 237 of 334 (512041)
06-13-2009 6:46 PM
Reply to: Message 195 by Son
06-09-2009 3:13 PM


Son,
Son writes:
The only conclusion you can reach with: "no natural causes are known" is that we don't know and we must keep looking for it.
Appreciate your candor Son. Glad to see someone is forthright enough to acknowledge that scientific naturalism currently provides no explanation for the existence of an ingredient that’s essential for life- coded information.
Theres only three possibilities.
1) DNA occured spontaneously. As in Dawkins words.." a happy accident" (an unscientific statment because it is non-testable)
2) DNA resulted from some yet undiscovered principle of physics that can produce codes. (also an unscientific statment for the same reason above)
3) DNA was designed.
Of these, *ONLY* one, #3, is supported by the scientific method of induction.
-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 195 by Son, posted 06-09-2009 3:13 PM Son has not replied

Replies to this message:
 Message 239 by Dr Adequate, posted 06-13-2009 7:01 PM WordBeLogos has replied

WordBeLogos
Member (Idle past 5392 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 238 of 334 (512042)
06-13-2009 6:54 PM
Reply to: Message 200 by New Cat's Eye
06-09-2009 4:24 PM


CS,
CS writes:
Who decodes it and what does it say?
When the cell divides and forms limbs and organs - that's decoding.
-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 200 by New Cat's Eye, posted 06-09-2009 4:24 PM New Cat's Eye has not replied

Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 239 of 334 (512043)
06-13-2009 7:01 PM
Reply to: Message 237 by WordBeLogos
06-13-2009 6:46 PM


There's only two possibilities:
1) DNA was produced by the sort of supernatural processes that we never, ever, ever see occurring, unlike any other code the origin of which is known to us.
2) DNA was produced in accordance with the natural laws that we see operating around us all the time and that we have never, ever, ever seen broken, like every other code the origin of which is known to us.
Of these, *ONLY* one, #2, is supported by the scientific method of induction.
Edited by Dr Adequate, : No reason given.

This message is a reply to:
 Message 237 by WordBeLogos, posted 06-13-2009 6:46 PM WordBeLogos has replied

Replies to this message:
 Message 258 by WordBeLogos, posted 06-14-2009 12:56 AM Dr Adequate has not replied

lyx2no
Member (Idle past 4716 days)
Posts: 1277
From: A vast, undifferentiated plane.
Joined: 02-28-2008


Message 240 of 334 (512044)
06-13-2009 7:05 PM
Reply to: Message 235 by WordBeLogos
06-13-2009 5:31 PM


I'm Having a Ball
Slope:  Hi, I'm a plain that is not perpendicular to my local gravity field.

Ball:   Hello, Slope, I'm within a few percent of a sphere.

Slope:  Well, that's something. Tell me a bit more about yourself;
        could be together we can induce a conversion of some of your
        potential energy into kinetic energy.

Ball:   I have mass and radius, my density is several hundred times
        greater then air; been working out; and I'm rather proud of
        this little fact: a modicum of surface texture and cohesion.

Slope:  Yes, surface texture, I adore surface texture. Mine's about
        twice yours. That kinetic energy I mentioned earlier, we can
        fritter some of it away as heat. I've always liked doing
        that. You?

Ball:   Nothing better. I've got to ask, just a round-about, how steep
        is your grade  five, ten percent. It's just that I used that
        information to determine how fast I'm going to roll.

Sphere: Don't you also have to take your mass distribution into
        account as well. I read something about angular momentum, but
        as a plain I've little practical experience.  I'd bet you're
        just the man to ask. I'll enjoy seeing it in practice.

Ball:   Here we go then.
And the ball roles down hill. Seems we have encoders/decoders and an agreed upon code for an action. Must be evidence of God.
Edited by Admin, : Reduce message width.

Ridicule is the only weapon which can be used against unintelligible propositions. Ideas must be distinct before reason can act upon them.
Thomas Jefferson

This message is a reply to:
 Message 235 by WordBeLogos, posted 06-13-2009 5:31 PM WordBeLogos has replied

Replies to this message:
 Message 259 by WordBeLogos, posted 06-14-2009 1:01 AM lyx2no has replied

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