Information and Genetics

Wrong. The appeal to authority is always a fallacy, no matter who the authority in question is.If I were to say that spacetime is curved in the presence of mass and you would ask "how so?" and I would answer "because Einstein said so", I would be commiting the fallacy of appeal to authority. Although experimental evidence supports the assertion, it is a fallacy to say it is true just because Einstein said so, even if Einstein can be said to be a real authority on the subject and even if it can be proven that the assertion is indeed true.Whatever anyone says can never be used as proof for anything.------------------
"In the beginning the Universe was created. This has made a lot of people very angry and been widely regarded as a bad move." - Douglas N. Adams

This seems to be connected with the common confusion between citing a specific original piece of research and making an appeal to authority, many people don't seem to be able to tell the difference.

Zhimbo,I think you hit the nail on the head. Intelligent Design Creationists are eager to make their case on the strength of the following deduction:All codes are the result of intelligence.
DNA is a code.
Therefore, DNA is the result of intelligence.I have already pointed out that calling DNA a code only satisfies the minor premise, but the major premise surely remains in debate. We hear IDC proponents declare all the time that non-teleological processes never create codes. However, I think it would be more relevant if they addressed the fact that we have never seen a teleological process create anything in nature: a tree, a child, a bacterial flagellum, or a biochemical replicator.------------------
I would not let the chickens cross the antidote road because I was already hospitlized for trying to say this!-Brad McFall

RNA editing is indeed very interesting, but as a programmed sequence it in no way changes the fact that DNA codons have specific amino acid associated with them. The RNA editing occurs after DNA transcription and from what I understand there are specific, targeted sequences that may be edited to produce a distinct but different target amino acid than originally transcribed by the DNA. It is quite an elaborate programming system!If I get a chance I’ll try to run down the article you suggested, as I would be interested to see how the authors try to explain how such a complex system arose via naturalistic processes. It appears from the abstract that they can’t attribute the editing RNA to common ancestry, which seems they are going to instead rely on the oft-used grab bag answer of convergence. For those who don’t know what convergence is, by its very definition it is an anti-evolutionary term. It means that similar traits evolved down independent pathways since common decent cannot be used to explain the trait’s. An example is the eyes of octopus’s and humans, both are remarkably similar but according to evolutionists must have evolved down independent paths since we are too far apart on the evo tree to share a recent common ancestor with the octopus. The hoops you guys must jump through! PS. Mammuthus, would you mind confirming for me wheter or not the authors rely on convergence to explain RNA editing? Thanks.

I disagree. See appeal to authority - logical fallacies - The Skeptic's Dictionary - Skepdic.comA snippet:

The appeal to authority is a fallacy of irrelevance when the authority being cited is not really an authority...

I think the last paragraph relates to the application used in this thread:

Finally, it should be noted that it is not irrelevant to cite an authority to support a claim one is not competent to judge. However, in such cases the authority must be speaking in his or her own field of expertise and the claim should be one that other experts in the field do not generally consider to be controversial. In a field such as physics, it is reasonable to believe a claim about something in physics made by a physicist that most other physicists consider to be true. Presumably, they believe it because there is strong evidence in support of it. Such beliefs could turn out to be false, of course, but it should be obvious that no belief becomes true on the basis of who believes it.

None of the stuff in your list is 'encoded'. There is no syntax, or semantics. Ie a tree ring does not always equal 1 yr.As I mentioned earlier, all codes can produce a blueprint to build something, such as your computer. Can you describe a 'code' in the tree rings (manipulated it if you like) such that it can produce a blueprint of your computer?BTW, that avatar of yours looks pretty nasty. What the heck is it?

The original use in this thread referred to an insistence that expert opinion was the only acceptable evidence on the point in question. When apparently neither side knew what the expert opinion might be.Pointing out that it may be valid to rely on an appropriate authority when that authority's opinions is available is not relevant to that particular issue - since no such authority has been cited on either side.

Then clearly morse code encodes nothing either by that definition.

I don't know if this has been covered recently or not, but what information does DNA really convey?I am involved in microbiology and molecular biology and know from experience that it is very difficult to know what a gene does without studying the protein it codes for. It is difficult to look at the DNA sequence and to calculate substrate specificity, enzymatic effeciency, pH optimums, oxygen lability, temperature optimum, oligimerisation (sp?), and so forth. As far as I can see, the only real information a DNA sequence conveys is in the activity of the protein it codes for. In general, mutations in the DNA sequence may or may not affect protein effeciency or specificity. You can theorize if site specific mutations will cause an effect, but working with the protein is the only way to test the theory. Also, wouldn't different DNA sequences "mean" the same thing if they produce proteins that do the same thing?In practice, genetic sequences are often given hypothetical designations due to their genetic homology to other gene sequences. For instance, you can look at a sequence and say with high probability that it codes for a polymerase because it has 98% homology to another polymerase. However, the activities of the homolog were only discovered by observing the protein. Protein motifs (helix-helix turns and so forth) are treated in the same way. Amino acid sequences (motifs) are compared to known activies/structures derived from observing the protein.As a thought experiment, if you were to randomly assemble a 4 kb DNA sequence without internal stops (i.e., an open reading frame with a promoter) could you deduce the activity of the protein produced, if it is active at all? And if you don't know what the protein does, what information does the DNA sequence convey?Sorry if this is going over heavily trodden territory, but these thoughts just kept coming to me when reading this thread. Those, and how TATTA boxes always make gene jockeys snicker like school boys.

Easy, given a large enough tree. You'd could just make wide dark rings 1, and narrow dark rings 0. Then you could encode anything you like. Of course, then you're adding an abstraction layer...

Would these rings always include '666'?

There have been several replies to my posts. So many that I will not bother to reply to them all. Many of them bring up the same points. Some of you do not want me to make analogies to other information systems that have resulted by intelligence, but rather give independent evidence that the DNA was intelligently designed. This is impossible-since no one was present to see life begin. If you held the same standard for evolultionary theories you would be forced to admit that there is no evidence for evolution either. I am merely trying to use logic and inference to prove my point.In relation to the representational function of the DNA, my argument is simply that the nucleotides represent amino acids that may not be constructed until a later time. This is very different from tree rings. The DNA depends upon these amino acids, and because of the fantastic coordination of the DNA these amino acids are actually processed, understood, and incorporated into proteins to perform a certain function for the organism. The 'meaning' in tree rings is irrelevant to the tree and is not incorporated as a major factor in its' growth, reproduction, etc.. Gaining information from tree rings would be like gaining information about my handwriting style if I wrote the statement, "Evolution is untrue." You may determine how I hold my pencil, however this information is not encoded or meant to be encoded in my message. The only way that the rings actually have meaning is if there is an intelligence to interpret the meaning (since the tree does not interpret the meaning of the rings, whereas the DNA does interpret how to incorporate and use the sequence of nucleotides to manufacture amino acids). However once the 'information' gained from tree rings is thus from directly observing reality, and the abstract representational function is absent. It is also not a code in the Gitt sense because that the rings pattern is determined from physics and chemistry (and only physics and chemistry). Its' information also doesn't fill the apobetic and pragmatic requirements. Gitt defines pragmatics as, "Every transfer of information is, however, performed with the intention of producing a particular result in the receiver. To achieve the intended result, the transmitter considers how the receiver can be made to satisfy his planned objective. This intentional aspect is expressed by the term pragmatics. In language, sentences are not simply strung together; rather, they represent a formulation of requests, complaints, questions, inquiries, instructions, exhortations, threats and commands, which are intended to trigger a specific action in the receiver." He defines apobetics as, "The final and highest level of information is purpose. The concept of apobetics has been introduced for this reason by linguistic analogy with the previous definitions. The result at the receiving end is based at the transmitting end on the purpose, the objective, the plan, or the design. The apobetic aspect of information is the most important one, because it inquires into the objective pursued by the transmitter. The following question can be asked with regard to all items of information: Why is the transmitter transmitting this information at all? What result does he/she/it wish to achieve in the receiver?" It is obvious that the pragmatics in the DNA is translation, the construction of the organism, and the realisation of all biological functions. The apobetics are the existence of life. What is the purpose, or apobetics, for the tree in creating a semantic value in tree rings? Indeed this information is not understood, while the meaning of amino acids is. If this information is not understood, then it has no purpose. In fact, the tree does not even try to interpret it, so the pragmatic function is absent. Trying to say that tree rings are a code because they tell about the climate of the area at a certain time is like saying that moss growing on a tree is an information system because we can gain information about the direction it grows (north). No information scientist would classify moss and tree rings as a code.The stop codons that Mr. Williams refers to may indeed be another representational function. He is referring to how it is understood in its' natural state by the DNA.There have been claims that the RNA world hypothesis may solve the problem for the origin of life. However, this position may be implausible for several reasons. One being the short 'life spans' of chemicals like cytosine and uracil. Check these links out: Missing Link | Answers in Genesis Geoscience Research Institute | I think we need more research on that...http://www.arn.org/docs/odesign/od171/rnaworld171.htmThere have also been claims that RNA's readily form from random sequence pools. However, these experiments have the fingerprints of design on them, and the conditions never reflect reality. See:http://www.arn.org/docs/odesign/od171/ribo171.htmAt The RNA World and other origin-of-life theories. by Brig Klyce the author states, "But these and other similar findings arrived at in highly orchestrated experiments that start with biologically produced RNA are very far from proving that the RNA world is the pathway between nonlife and life. In nature, far from the sterilized laboratory, uncontaminated RNA strands of any size would be unlikely to form in the first place. '... The direct synthesis of ... nucleotides from prebiotic precursors in reasonable yield and unaccompanied by larger amounts of unrelated molecules could not be achieved by presently known chemical reactions' (Joyce, Gerald F. and Leslie E. Orgel. "Prospects for Understanding the Origin of the RNA World" p 1-25. The RNA World, R.F. Gesteland and J.F. Atkins, eds. Cold Spring Harbor Laboratory Press, 1993.)"By the way, PaulK what makes you think that Gitt thinks that an intelligence has to be present every time information is transmitted? He states in his book that information only comes from information, and that its' ultimate origin is a mental source. He says in his article,"Theorem 10: Each item of information needs, if it is traced back to the beginning of the transmission chain, a mental source (transmitter)."That means that if you trace back every DNA transcprition and translation all the way back to the beginning of life you would find that it is the result of intelligence.

Glad you are interested. I was addressing your point of 100% ability to determine the protein sequence from the codons when RNA editing shows that the RNA may not be co-linear with DNA.In any case, some more references....if you decide this is an interesting enough topic in itself let me know and I will start a new thread..reading some of the other posts I already see it does not fit here particularly well.J Mol Evol. 2001 Oct-Nov;53(4-5):327-32. Related Articles, LinksComparative analysis of RNA editing sites in higher plant chloroplasts.Tsudzuki T, Wakasugi T, Sugiura M.Computer Center, Aichi-Gakuin University, Araike 12, Iwasaki, Nisshin 470-0795, Japan.Transcripts of land plant chloroplast genomes undergo C-to-U RNA editing. Systematic search disclosed 31 editing sites in tobacco, 27 in maize, and 21 in rice. Based on these identified sites, potential editing sites have been predicted in the transcripts from four angiosperm chloroplast genomes which have been completely sequenced. Most RNA editing events occur in internal codons, which result in amino-acid substitutions. The initiation codon AUG was found to be created from ACG by RNA editing in the transcripts from rpl2, psbL, and ndhD genes. Comparison of editing patterns raises a possibility that many editing sites were acquired in the evolution of angiosperms.RNA. 2000 Oct;6(10):1339-46. Related Articles, LinksEvolution of four types of RNA editing in myxomycetes.Horton TL, Landweber LF.Department of Molecular Biology, Princeton University, New Jersey 08544, USA.The myxomycete Physarum polycephalum requires extensive RNA editing to create functional mitochondrial transcripts. The cytochrome c oxidase subunit 1 (col) transcript exhibits a combination of editing forms not found together in any other eukaryotic RNA: 66 insertions of ribonucleotides (59 Cs, a single U, and three mixed dinucleotides) as well as base conversion of four Cs to Us (Gott et al., J Biol Chem, 1993, 268:25483-25486). Through a phylogenetic survey of col DNA genes and RNA transcripts in representative myxomycetes, we have decoupled the four types of editing in this lineage. Some myxomycetes share insertional editing with P. polycephalum, yet lack C--> U conversion, consistent with previous reports of separation of insertional and base conversion editing in P. polycephalum extracts (Visomirski-Robic & Gott, RNA, 1995, 3:821-837). Most remarkably, we detect unique evolutionary histories of the three different types of insertional editing, though these have been indistinguishable in vitro. For example, Clastoderma debaryanum exhibits insertions of Us, but not Cs or dinucleotides.Proc Natl Acad Sci U S A. 2000 Jun 20;97(13):6986-93. Related Articles, LinksEvolution of RNA editing in trypanosome mitochondria.Simpson L, Thiemann OH, Savill NJ, Alfonzo JD, Maslov DA.Howard Hughes Medical Institute and Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA. Simpson@hhmi.ucla.eduTwo different RNA editing systems have been described in the kinetoplast-mitochondrion of trypanosomatid protists. The first involves the precise insertion and deletion of U residues mostly within the coding regions of maxicircle-encoded mRNAs to produce open reading frames. This editing is mediated by short overlapping complementary guide RNAs encoded in both the maxicircle and the minicircle molecules and involves a series of enzymatic cleavage-ligation steps. The second editing system is a C(34) to U(34) modification in the anticodon of the imported tRNA(Trp), thereby permitting the decoding of the UGA stop codon as tryptophan. U-insertion editing probably originated in an ancestor of the kinetoplastid lineage and appears to have evolved in some cases by the replacement of the original pan-edited cryptogene with a partially edited cDNA. The driving force for the evolutionary fixation of these retroposition events was postulated to be the stochastic loss of entire minicircle sequence classes and their encoded guide RNAs upon segregation of the single kinetoplast DNA network into daughter cells at cell division. A large plasticity in the relative abundance of minicircle sequence classes has been observed during cell culture in the laboratory. Computer simulations provide theoretical evidence for this plasticity if a random distribution and segregation model of minicircles is assumed. The possible evolutionary relationship of the C to U and U-insertion editing systems is discussed.There are more but most RNA editing is found in the mitochondrial genome.

Yes, but if you're looking at DNA, and you see information or a message, isn't it possible that the mental source of that information is your own mind, not God's?I mean, I've seen clouds that appeared to have information, like the shape of a rabbit or Abraham Lincoln. But nobody designed the cloud to look like that. The data came from my mind, not anyone else's.

Can you explain to me why, instead of answering the point I did make (that according to Gitt semantic information cannot be mechanically translated - as DNA is) in favour of answering a point I never made (that intelligence must be present every time information is copied) ?
That these are different points can be clearly seen by considering that in the reproductive process DNA is not simply copied - the information is extracted and used to produce a new individual. And this is the only information in DNA that we know of. The reproductive systems (in a wide sense, including eggs) *are* the receivers, so there seems to be no intelligent receiver either. Surely these facts are a major obstacle to the conclusion that DNA contaims Gitt information and I would appreciate it if they were answered instead of my points being misrepresented.And even when you have answered those you face the problem that the identification of prgamatics and apobetics requires showing that there is an intent. To claim that DNA has either without evidence of intent begs the question. Any argument which tries to conclude that life has an intelligent source based on the idea that DNA contains Gitt information cannot make much use of these levels since any argument that DNA does contain them would work just as well to support the conclusion that DNA has an intelligent source without the concept of Gitt information at all.