Data, Information, and all that....

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Can you guess where that information is stored?

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So you would agree the information is stored in atoms such as carbon, nitrogen, hygrogen, oxygen, and phosphorous that undergo the same reactions as any other chemical? Therefore the information found in one atom of carbon which gives consistent results (methane is the same everywhere such as human hemoglobin is similar everywhere) as does DNA. So what is special about DNA compared to any other chemical reactant? I have yet to see it. DNA compared to a carbon atom as far as information content I can see, DNA compared to a book with respect to information I can't see at all.

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So you would agree the information is stored in atoms such as carbon, nitrogen, hygrogen, oxygen, and phosphorous that undergo the same reactions as any other chemical?

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No. Genetic information is stored in the specific BASE SEQUENCES of DNA.Sure, the DNA is made of the atoms you listed, but the atoms themselves do not contain the genetic information. For example, scramble their order and you don't get hemoglobin or the other proteins, even though the same atoms are present in the same quantities.DNA encodes information as specific base sequences. Biologists, chemists, and physicists all recognize this obvious fact.

Ok... I've decided to begin to respond to you again. I hope we don't have another falling out like before. For now, however, I'm going to limit myself to one such post per day.

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Sure, the DNA is made of the atoms you listed, but the atoms themselves do not contain the genetic information. For example, scramble their order and you don't get hemoglobin or the other proteins, even though the same atoms are present in the same quantities.

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In short, your definition of DNA involves some sort of qualitative judgement. I.e., one possibility is a human-made decision that a certain thing produced by the DNA is better than another thing produced by the DNA. Another possibility is that, if it leads to survival to reproductive maturity and reproductive success, then it is "information", but if it doesn't, then it is "not information" - in short, "natural selection" is judging its information content. Is this correct? Did I miss any possibilities? If you're not requiring a qualitative judgement as part of your definition of information, please say so.**Why is whether a judgement is being made critical? Because it means that there is no sort of *inherent* information to it. If one person can look at a random sequence of ones and zeros and see their mother's maiden name, then it has information under that judgement. However, most people looking at DNA make decisions about it based on things that it produces that they view as relevant. They view these things to be relevant because they view life as relevant. In short, success at life itself - i.e., natural selection - is the judging what is information. It is keeping things that have more "information", and throwing away things that have less "information".It is just as if I had a computer program that modified random sequences of 1s and 0s and kept or discarded them based on how they ranked according to an algorithm which I declared to be an "information assessment": the end result would always be something that does well under the algorithm. Your "information" is actually how well it survives to reproduce; thus, it is really better described as fitness. Fitness *can* be produced through random changes.In short, if how successful it is at living is your criteria, then your definition of information is getting to be its judge as well.Of course DNA can hold information, by your definition - in the context of whatever is judging. For a biologist doing research on hemoglobin, there's information in the DNA about hemoglobin. But there's only information in the DNA because the biologist considers the gene for producing it to be something that is relevant, and the biologist chose this to be relevant because of a view that hemoglobin is relevant. The biologist views hemoglobin as relevant because the biologist view life as relevant. Life is selected for by natural selection, so life itself is really judging information quality by this definition, and throwing out what contains "less information", and keeping what has "more information".** - If no judgement is being made (merely the odds of a particular combination occuring out of all possible sets, as you initially portrayed it), then snowflakes are information rich; I don't think you want to go down that route.------------------
"Illuminant light,
illuminate me."

Here's part of something I wrote up some time ago: you might find it helpful.*************************Transcription
Transcription is the process by which segments of DNA are copied into complementary strands of mRNA, rRNA, or tRNA. Since the information’s language is not being changed — it begins as nucleotides and ends as nucleotides — the term transcription is appropriate (transcribing relates to the copying of information).A series of three consecutive DNA nucleotides is called a triplet, but once they have been transcribed into mRNA, that series of three consecutive mRNA nucleotides is then called a codon (because it will code for a particular amino acid during translation).Transcription can be divided into four stages: binding, initiation, elongation, and termination (these will not be described individually). As in DNA replication, the DNA double helix must be unwound and the strands separated in order for enzymes to gain access to the individual nucleotides. An RNA polymerase binds to a particular DNA nucleotide sequence, called a promoter region, that is usually located just upstream (i.e., before) the gene to be transcribed. Similar to DNA replication, a new complementary nucleotide strand is created using the existing DNA strand as a template. However, unlike DNA replication, uracil (instead of thymine) is incorporated into the newly-synthesized strand for all occurrences of adenine on the template. Also unlike DNA replication, which continues until the entirety of the cell’s genetic information has been processed, transcription ceases as soon as a termination sequence is encountered (conceptually, once a single gene has been transcribed, the polymerase enzyme — its job complete - falls off the template).Note that there were many, many topics related to transcription that were not addressed: such as gene regulation (which genes get expressed/transcribed and which are not), the various transcription factors (enzymes required for binding and initiation), introns (intervening, non-expressed nucleotide sequences), exons (expressed nucleotide sequences that must be ligated together once all of the introns have been excised), ribozymes (catalytic RNA molecules, such as those that can catalyze the excision of introns internal to their own sequence), RNA processing (addition of poly(A) tails and 5’ caps), and so on. The reader, if interested, is again referred to an introductory text on cell biology.Translation
Translation is the synthesis of proteins based upon the informational content of mRNA. So for those products of transcription that are mRNA, the next step is translation (the other RNA’s are also involved in translation — rRNA is a component of ribosomes, and tRNA brings the correct amino acid to the ribosome, but these two types of RNA are not themselves translated). Since the information’s language is actually being changed — it begins as nucleotides and ends as amino acids — the term translation is appropriate here (the term transcription is inappropriate as it does not express the change in languages).Before continuing, both codons and the genetic code should be briefly discussed. As previously mentioned, three consecutive nucleotides on a mRNA molecule, which code for a particular amino acid, are called a codon. The genetic code is the association between mRNA codons (nucleotide ‘triplets’ on mRNA) and the corresponding amino acids for which they code. To call this a code is quite appropriate since without the proper deciphering mechanism the information encoded in nucleotide sequences could not be discerned by either biologists or cells (biologists use a lookup table which shows the mappings between codons and amino acids; cells use the tRNA adaptor molecules to translate between the two code sets). As with any other code, a certain sequence of symbols in the encrypted message can be decrypted into the proper symbol(s) of the natural language once the code has been ‘broken’. In the genetic code, mRNA codons code for amino acids — for example, the mRNA codons GGU, GGC, GGA, and GGG all code for the single amino acid glycine, always. Note that in many instances the third nucleotide in a codon is not that important — for glycine, it can be U, C, A, or G, as long as the first two nucleotides are GG. This ability for the correct amino acid to be specified by codons with different nucleotides in the third position is termed wobble to indicate the codes looseness in the third position in such cases. There are 64 possible codons when taking three nucleotides at a time (4^3 = 64), and each of the 20 biological amino acids is specified by from 1 to 6 of these codons. In addition, codons also specify the two punctuation marks of the code: start and stop.In cells, the association between codons and amino acids is made by tRNA. Each tRNA molecule has one site (acceptor stem) that will bind only a certain amino acid — that is, the tRNA for methionine will bind the amino acid methionine only. In addition, each tRNA has on its opposite end a particular anticodon, which is a linear sequence of three nucleotides on a tRNA molecule that is complementary to a particular mRNA codon. Therefore, since a particular mRNA’s codon specifies and particular tRNA (through complementary base pairing between codon and anticodon) , and that particular tRNA specifies a particular amino acid, tRNA acts to translate languages from nucleotide triplets to single amino acids.A functional ribosome consists of two parts: an LSU (large subunit) and an SSU (small subunit). These two subunits are separate and do not join until initiation of translation occurs. A functional ribosome has two key sites: the P site (Peptidyl site — so called because throughout most of translation, the growing polypeptide chain is attached to the tRNA bound to that site) and the A site (Aminoacyl site — so called because throughout most of translation, this site is occupied by the tRNA that binds the next amino acid to be incorporated into the growing polypeptide) — note that there is also an E site (Exit site), but it is not terribly important to a general understanding of translation. The ribosome also contains the ribozyme peptidyl transferase, which forms the peptide bond between the amino acids attached to the tRNAs in the P and A sites, and then transfers the growing polypeptide chain from the tRNA in the P site to the tRNA in the A site (this positioning of the growing polypeptide chain, passing it on to the tRNA in the A site, is only temporary - translocation of the tRNA in the A site to the P site will occur quickly such that the P site again contains the tRNA that possesses the growing polypeptide).Translation consists of three stages: initiation, elongation, and termination. During initiation, mRNA and a particular tRNA join with the large and small subunits of the ribosome to form an initiation complex. The first mRNA codon is always the start codon, AUG, so its associated amino acid, methionine (or a modified form), is always the first amino acid in every polypeptide. However, this single translation-initiating methionine is often removed at some point after initiation — once it has served its purpose and is no longer needed.After the initiation stage, chain elongation begins. The second amino acid, which is coded for by the mRNA codon currently associated with the A site, is brought to the ribosome by the appropriate tRNA molecule. With one tRNA in the P site and one in the A site, both with an amino acid attached, the ribosomal enzyme peptidyl transferase creates a peptide bond between the two amino acids, detaches the amino acid from the tRNA in the P site, and transfers it to the amino acid associated with the tRNA docked in the A site. The tRNA in the P site, which is no longer charged, is released from the ribosome. The next phase of elongation is translocation. During translocation, the ribosome moves exactly three nucleotides along the mRNA it is reading, which causes the mRNA-bound tRNA in the A site - with the dipeptide attached - to be moved to the just-vacated P site, and simultaneously positions the next mRNA codon into position to be read by the ribosome (that is, the next codon in sequence becomes associated with the A site). Now the process repeats. The tRNA specified by the mRNA now associated with the A site carries the correct amino acid to the ribosome and docks into the A site; peptidyl transferase peptide bonds the growing polypeptide (at this point, just a didpeptide) attached to the tRNA in the P site to the newly-arrived tRNA’s amino acid and transfers the growing polypeptide chain from the P-site tRNA to the A-site tRNA; the tRNA in the P site is released; the ribosome moves exactly three nucleotides along the mRNA, moving the tRNA in the A site to the P site as well as bringing yet another mRNA codon into the A site to be read.The series of steps that comprises elongation is repeated continually until one of the three stop codons (none of which specifies an amino acid) is reached in the mRNA, leading to termination: which involves the release of the completed polypeptide chain and the mRNA from the ribosome, followed by the dissociation of the two ribosomal subunits.[This message has been edited by DNAunion, 12-16-2003]

Blimey,
Thankyou very much DNAUnion for going to all that trouble. I'll read it thoroughly tomorrow . That's a great effort there, thanks!!!I doubt I'll understand it all but I'll sure try!

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The information in this sequence is in my head

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Let’s try logic again. If, as you claim, the information of these sentences was not contained in the symbol sequences but instead resides in your head, then how do we all agree upon what is being said? Clearly there is information contained in these symbol sequences. Either that or we are all telepathic: hmmm, maybe that’s your position.

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[DNA] does not CODE for an organism in anything but an analogous sense.

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Nah. The simple fact is, the base sequences of DNA carry the information that specifies the structure and functioning of the molecular machines and cells that make up an organism. That is undeniable.Let's try logic again. If there is no information contained in DNA, then why are you a human instead of a cactus? While she was pregnant with you, did your mommy and daddy offer up mystical chants to the great birth spirits? Did they repeatedly recite the following incantation?

Oh powerful and noble spirits of birth,
who wonder mystically about this Earth,
the plead you receive from the two of us,
is please don’t let our child be a cactus.

Is that how it worked? Or perhaps there were some eyes of newt, and ears of bats boiled in a caldrun too?Oh, and if DNA doesn't contain information, then how do you propose cloning work? Do the scientists also offer up mystical chants to the great spirits?

Oh mystical spirits who never sleep,
a spell please cast upon this sheep,
and show the world not our folly,
but rather a clone that we'll call Dolly.

Is that how it worked?[This message has been edited by DNAunion, 12-16-2003]

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...if you want a particular protein to be produced then you must input the precise amino acid sequence. Otherwise the PAM randomly selects amino acids and assembles them - who knows what will come out! ....

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And there's the rub!What if, from the cells point of view, it doesn't care what
proteins are produced?If ANY group of amino acids can be 'plugged' together to
form a protein, and that protein may or may not cause reactions
that help to maintain the cell, then the information isn't in
the DNA sequence (that's raw data).If any DNA sequence can produce a protein ... or almost any
at least ... how is that information?How can you tell the difference between something designed
by an intelligence to do a job, and something that adapted to
do that job because it is fundamentally based upon a completely
generic, non-specific protein manufacturing capability?Doesn't the simple fact that amino acids can be 'plugged' together
in any order suggest a lack of specificity in the DNA->protein
system?And there's not even a 1:1 mapping between amino-acid sequence
and protein.The only way that information makes any sense biologically
(to me anyhow) is in the emergent properties that define
different cells. That is a function of the interaction of the
proteins, not a function of what proteins are manufactured
off DNA 'templates'.

I read that before and it doesn't answer the question
of what is the logic that tells us that DNA contains
information.The definition of information in use is more of the measurement
for human purposes type (like how many bits do I need to store
the same information).If I feed almost any sequence of instructions into a
computer, the computer will do something.If I don't care what it does, but select only the instructions
that generate outputs that I like was there information
in the instruction set or not?

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I read that before and it doesn't answer the question of what is the logic that tells us that DNA contains information.

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Which I have presented multiple times.1) Why are you a human instead of a cactus? When you have children, why will they be human instead of earthworms?

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In Part I of the text we discussed the presence of genes on chromosomes that control phenotypic traits and the way in which the chromosomes are transmitted through gametes to future offspring. Logically, some form of information must be contained in genes, which, when passed to a new generation, influences the form and characteristics of the offspring; this is called the genetic information. (emphasis added, Concepts of Genetics: Fifth Edition, William S Klug & Michael R Cummings, Prentice Hall, 1997, p262)

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2) Of all the trillions of trillions of possible amino acid sequences, why is hemoglobin made time after time, in cell after cell, in human after human, in generation after generation?

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[Information] quantifies the instructions that are needed to produce a certain organization. ... In general, then, we compute the information inherent in any given arrangement of matter (or energy) from the number of choices we must make to arrive at that particular arrangement among all equally possible ones." (The Touchstone of Life: Molecular Information, Cell Communication, and the Foundations of Life, Werner R Loewenstein, Oxford University Press, 1999, p6-7)

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Clearly DNA contains information, stored in its base sequences. The logic is crystal clear.[This message has been edited by DNAunion, 12-17-2003]

The post that you have made ASSERTS that there must
logically be information, it does not explain the logic
by which that conclusion has been reached.

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The post that you have made ASSERTS that there must logically be information, it does not explain the logic by which that conclusion has been reached.

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Actually, the one quote quite nicely explain why there must be some form of information in DNA.

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In Part I of the text we discussed the presence of genes on chromosomes that control phenotypic traits and the way in which the chromosomes are transmitted through gametes to future offspring. Logically, some form of information must be contained in genes, which, when passed to a new generation, influences the form and characteristics of the offspring; this is called the genetic information. (emphasis added, Concepts of Genetics: Fifth Edition, William S Klug & Michael R Cummings, Prentice Hall, 1997, p262)

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Anyone who knows anything about biology/genetics sees the clear connection: they can easily follow the logic that says there MUST be some form of information in DNA that controls phenotypic traits.If you are too ignorant of biology/genetics to follow something that simple, I suggest you go read a book.[This message has been edited by DNAunion, 12-17-2003]

DNA does not "control" phenotype. Phenotype is a consequence of a DNA sequence, there are no conscious decisions made from a DNA sequence. If the DNA sequence changes and it affects the phenotype, the organism is selected for through natural selection. I think this is an important distinction that we both keep dancing around. DNA can change (the information can change) but that change is not tied directly to survival. The continuation of the genotype IS tied to survival, however, through natural selection. The information in DNA does not have foresight.

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Anyone who knows anything about biology/genetics sees the clear connection: they can easily follow the logic that says there MUST be some form of information in DNA that controls phenotypic traits.

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DNA does not "control" phenotype.

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DNA does control phenotypic traits exactly as I, and the college text, meant when we stated it. If you are putting your own spin on the word, it would be nice if you made it perfectly clear that you've changed things.

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Phenotype is a consequence of a DNA sequence, there are no conscious decisions made from a DNA sequence.

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Which neither I, nor the college text I quoted, stated or implied.

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The information in DNA does not have foresight.

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Which neither I, nor the college text I quoted, stated or implied.[This message has been edited by DNAunion, 12-17-2003]

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If I feed almost any sequence of instructions into a computer, the computer will do something.

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And an instruction already contains information predesigned to instruct the computer to do something. Little wonder then that the computer will...do something.Here’s an exercise/thought experiment for you. Toss a coin 500 times writing down the individual results in order: 1 for heads, 0 for tails. Then, feed that sequence into a CPU as machine code. Do you think the computer will do something meaningful as it did when you fed it prewritten and pre-validated instructions?****************************
Oh, and this would be only an analogy to biology. Humans get to determine how sparse or dense the instruction set is: cells don't have that ability.[This message has been edited by DNAunion, 12-17-2003]

Ironically, I was just skimming Internet Infidels » a drop of reason in a pool of confusion and found this posted by someone:

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Information,
Merriam-Webster: Definition 2b
The attribute inherent in and communicated by one of two or more alternative sequences or arrangements of something (as nucleotides in DNA or binary digits in a computer program) that produce specific effects.

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Hmm, seems everywhere one looks DNA is said to contain information.[This message has been edited by DNAunion, 12-17-2003]