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An Open Intelligent Design Challenge

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Posted on Jul 25, 2012, 3:16:31 AM PDT
Last edited by the author on Jul 25, 2012, 3:36:08 AM PDT
So let me restate my initial claim a little more clearly:
Uh. Yes. The codes in DNA do use the symbols G, A, T and C. The code in DNA makes no use of chemistry. Chemistry is not responsible for the sequencing of DNA, any more than it is responsible for why ink sticks to paper. The laws of physics and chemistry are redundant. The code in DNA uses four symbols to convey meaningful messages: G, A, T, and C, just as English uses 26 symbols to convey meaningful messages: A, B....X, Y, Z.
The codes that give DNA meaning transcend simple, redundant chemistry.

So now challenge me with facts and theory, instead of meaningless links to things I have been studying since the '90s.
And don't call me names either. It just makes you look stupid.

In reply to an earlier post on Jul 25, 2012, 4:34:07 AM PDT
David Félix says:
"G may always mean guanine, but what does G mean in the sequence GCATCAGTAA compared to CGATCATGAA?"

In the context of DNA sequences, G may always mean guanine, no matter what sequence it is inserted in.

"G itself contains no information. The sequence does."

Not according to you. Guanine can be represented by it's IUPAC name 2-amino-1H-purin-6(9H)-one, which provides information on it's compostition. It can also be represented by it's empirical formula C5H8N5O, which provides simple information on the number of which atoms in the molecule. It can also be represented by it's molecular model, which provides more specific information on the tridimensional structure of the molecule and the types of bonds present.

So to beat up your example, a C itself contains no information (also controversial). The sequence C5H8N5O does.

In reply to an earlier post on Jul 25, 2012, 4:48:35 AM PDT
David Félix says:
"DNA sequences are NOT redundant. Is that better?"

Of course they are! Here, let's do an exercise:

Which sequence of A, T, G and/or C produces the following amino acid sequence?
(Nterm) - Met-Arg-Ser-Gly-Ala-Thr - (Cterm)

Should be simple, no? Good luck!

Posted on Jul 25, 2012, 4:57:17 AM PDT
Last edited by the author on Jul 25, 2012, 4:58:35 AM PDT
David Félix says:
"In the same way, chemistry will tell you why the nucleotides will adhere to the backbone, but chemistry will never tell you what the code means."

Hmmm, I'm having some trouble with your use of the word "means". We know with increasingly amazing details the chemical steps that go into producing your "letters" A, G, T and C, that go on to concentrate them into polymers. We know how transcription and translation work (hint: it's all chemistry) and we have a surprisingly strong theory for how DNA sequences change and get fixed, both in the context of molecular localized effects (i.e., tridimensional structure, how it comes about and how it influences itself) and in the context of expressed phenotypes (proteins, physical traits).

If "chemistry will never tell you what the code means", what does tell you and what does it mean?

EDIT: duplication :P

In reply to an earlier post on Jul 25, 2012, 4:59:55 AM PDT
Your argument: All codes are created by a conscious mind; DNA is a code; therefore DNA was created by a conscious mind. I.e., statement A, statement B, therefore statement C.

Statement A is unproven, therefore statement C is unproven.

In reply to an earlier post on Jul 25, 2012, 5:01:14 AM PDT
Study of patterns "best described" as being caused by intelligence.

Please define "best described".

That has been the central failing of ID.

In reply to an earlier post on Jul 25, 2012, 5:02:55 AM PDT
Specific facts:

1. It is unproven to say that a code requires a conscious mind to produce it.
2. It is unproven to say that there is a way to define how ID "best describes" a pattern in nature.

In reply to an earlier post on Jul 25, 2012, 5:06:49 AM PDT
The code in DNA is in fact redundant. Several different sequences of 3 nucleotide bases (codons) can code for the same thing. Of the amino acids, only tryptophan is represented by a single codon. The others are represented by as many as 4 different codons.

See Wikipedia article "DNA codon table".

In reply to an earlier post on Jul 25, 2012, 5:18:55 AM PDT
David Félix says:
Hey aspard,

Even then you have codon usage bias (i.e., the same sequence of DNA produces slightly different sequences of amino acids in different, unrelated, organisms), and the probabilistic (not deterministic) nature of codon translation - translational "errors" are common, sometimes the wrong amino-acid is incorporated, a stop codon is ignored, etc.

In reply to an earlier post on Jul 25, 2012, 5:23:35 AM PDT
Agree.

In reply to an earlier post on Jul 25, 2012, 6:01:55 AM PDT
Brian Curtis says:
I'm not dealing with him, Robert. I have Haynes on ignore too; I simply post the same reminder of his cowardice and dishonesty every time he pollutes a Science thread with his nonsense.

In reply to an earlier post on Jul 25, 2012, 6:02:07 AM PDT
Brian Curtis says:
Still running and hiding from the question you're scared to answer, eh Haynes? Too bad it's not going to work. Here it is again:

"So basically, every sighting of a UFO, dragon, ghost, Superman, sharks with lasers, or any other outrageous claim made by someone actually DID happen because, after all, they observed it happening, right?"

In reply to an earlier post on Jul 25, 2012, 8:56:54 AM PDT
Last edited by the author on Jul 25, 2012, 9:08:12 AM PDT
Mr. Saunders, Physics Geek, et al.,

This notion that DNA is a code is one I've seen staunchly defended, even to the point of citations for writers who declare that the concept is not metaphor, claim that DNA is a literal code.

I understand that most specialists use the term "code" as a metaphor. I have seen the same metaphor used by astrophysicists who describe starlight as a code (from which humans can "read" the chemical composition of stars and dust in interstellar space as well as relative velocities). Obviously, the sense is that any phenomenon from which human ingenuity can extract meaningful information may be described as a "code."

Anti-science types, especially religious believers (who tend on average to use System 1 thinking, i.e., intuition, imagination, "commonsense," etc.) seem to have difficulty with metaphor, reading literally where a "1:1 correspondence" isn't necessary or helpful. It figures, however, since some research shows that such folk tend to be rigid in thinking, relying on authority and tradition while also not being open to new experiences. Obviously, these folks have difficulty conceiving that information found in a natural system was not planted there by some intelligent source. Well, if that's the case, then what message are we supposed to read from the "code" of the geological column? Or the "code" of climatic patterns? If these "codes" aren't telling us what scientists have found, what is the "real" message?

In reply to an earlier post on Jul 25, 2012, 9:37:39 AM PDT
Re David Felix, 7-25 1:50 AM: "DNA does not use symbols." Correct. The symbology related to DNA is an artifact of the biochemists who use it as a convenient shortcut. This relates to the kerfuffle over whether DNA is a "code"; since a code is simply a mapping from one set of symbols to another, DNA is, in this sense, indeed a code. The ID'ers often make the mistake of supposing that this code implies an intelligence of some sort, since it encodes information -- which of course it does not; the information derives from natural selection.

In reply to an earlier post on Jul 25, 2012, 9:41:35 AM PDT
Re MadFat, 7-25 2:38 AM: "digital code in DNA, by definition, is not redundant. For if it was, it could not be a code." This is simply wrong. Many codes, such as the UPC on your cereal box, are intentionally redundant for the sake of error checking. As Felix pointed out, DNA is redundant in that given either of the double strands, the other can be constructed.

In reply to an earlier post on Jul 25, 2012, 9:58:04 AM PDT
Re Felix, 7-25 4:48 AM: The redundancy of your example here (a many-to-one mapping) isn't the same thing as the redundancy involved with two complementary DNA strands. (In your example, there are 1 x 2 x 2 x 4 X 4 x 4 = 256 possible DNA sequences which could make that amino acid sequence.)

In reply to an earlier post on Jul 25, 2012, 10:04:23 AM PDT
Re fazakas, 7-25 5:06 AM: It appears that methionine is also a single-codon protein (AUG) [1].

1. Handbook of Chemistry and Physics, 86th ed., p. 7-6.

In reply to an earlier post on Jul 25, 2012, 10:08:13 AM PDT
Re Felix, 7-25 5:18 AM: "the same sequence of DNA produces slightly different sequences of amino acids in different, unrelated, organisms" I question this. Can you elaborate or provide references? (If this is true, then the DNA code is not quite as universal as I had supposed.)

In reply to an earlier post on Jul 25, 2012, 10:32:01 AM PDT
Last edited by the author on Jul 25, 2012, 10:32:52 AM PDT
KS says:
There are some very minor differences between some taxa. Bacteria and archaeans have extra start codons, for example. There is also some variation in mDNA. The "code" is almost universal, but not quite.

http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi/

In reply to an earlier post on Jul 25, 2012, 10:33:55 AM PDT
The Weasel says:
Kevin L. Williams says:
I'm not an ID'er but when Dawkins says that a watchmaker lays out his cogs and gears with foreknowledge whereas there is no such thing in nature, I like to remind people that the atoms were thusly laid out in such a manner so as to interconnect as sophisticated building blocks. The odds of such an 'accidental' occurrence seem quite unlikely to me...
***
Uhhhh, and the concept of a hidden designer doesn't?

Posted on Jul 25, 2012, 10:50:18 AM PDT
David Félix says:
Robert, check out PSW's excellent link above.
The not-quite-so-universal nature of the genetic code has been a problem the biotechnology industry has had to deal with often.
However, I made a mistake when I referred to the exceptions to the genetic code as codon bias, which is indeed a different, albeit also interesting, phenomenon (to wit, the preference, in some generally fast-growing organisms, for particular codons, supposedly for optimal transcription efficiency).

In reply to an earlier post on Jul 25, 2012, 11:14:46 AM PDT
The Weasel, Mr. Williams, et al.,

I have seen the estimate that the Universe, as a whole, is some 10^40,000 times the size of our visible universe. That's an awful lot of opportunity for an array of events restricted to the interactions of the known subatomic particles. (For context: IDers get it wrong when they insist on completely random combinations which, by definition, would include things like "atoms" composed of two protons in mutual orbitals, rather like a binary star system.) Granted there are particles and kinds of matter we don't know about yet ("dark matter?") but I think we can justifiably restrict our comments to the kind of matter we know about.

In reply to an earlier post on Jul 25, 2012, 11:15:32 AM PDT
KS says:
Your posts are confusing to me. I don't get this:

"DNA sequences are NOT redundant. Is that better?"

What about STRs? There is a lot of redundancy in the non-coding regions. I'm late to the party so perhaps I'm missing something, but much of what you are saying doesn't make much sense to me.

Your focus seems to deal with coding regions. What about the non-coding regions? How do those fit into the "meaning" of the code as you see it? They seem to be surprisingly important in producing certain phenotypes.

In reply to an earlier post on Jul 25, 2012, 11:16:30 AM PDT
The Weasel says:
Agreed

In reply to an earlier post on Jul 25, 2012, 11:19:36 AM PDT
MadFatChickKiller: Intelligent design is the study of patterns in nature that are best described as being caused by intelligence.

Rachel: It's quite the leap between seeing patterns in nature and assuming that those patterns are caused by an intelligence. Google "apophenia" and "pareidolia."
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