Data, Information, and all that....

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Precisely my point! Tell me, WHAT performs the 'interpretation'? DNA encodes the information for the assembly of proteins (via base sequences) and something has to interpret those base sequences as meaning exactly what the code intends it to mean. But that interpretative act is conducted by a system that is ALSO encoded within the DNA. The mother of all chicken-n-egg?

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I think the word "interpret" with respect to DNA transcription and translation is a bit of a misnomer. It is a chemical reaction, not a decision making process. It is very deterministic, as soon as a few requirements are met a sequence of DNA is transcribed, not read for content like a newspaper. There is no conscious decision at any point in this process.As to the origin of the system, current interdependency does not refute a possibly independent history. Societies dependence on electricity, for example, does not mean that society always had electricity.

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Adding or removing a base changes the data, it may or may not changed the information.

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That is an unsubstantiated assumption. In fact, while the contents in your brain are able to help you retain the information in 'To be, or not be to', changing a base will likely yield an interpretation producing B instead of A. The quantity of information may have remained the same but it is the quality of information that determines life.

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Differences in cytochrome C proteins among organisms seems to indicate that base and amino acid substitutions may not always affect activity or specificity. Human cytC works in E coli just as well as the native protein.Taking this one step further, can random proteins through mutation and selection become intergral parts of a genome? As it turns out, the answer is yes.
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Can an arbitrary sequence evolve towards acquiring a biological function?Hayashi Y, Sakata H, Makino Y, Urabe I, Yomo T.Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, 565-0871, Suita City, Osaka, Japan.To explore the possibility that an arbitrary sequence can evolve towards acquiring functional role when fused with other pre-existing protein modules, we replaced the D2 domain of the fd-tet phage genome with the soluble random polypeptide RP3-42. The replacement yielded an fd-RP defective phage that is six-order magnitude lower infectivity than the wild-type fd-tet phage. The evolvability of RP3-42 was investigated through iterative mutation and selection. Each generation consists of a maximum of ten arbitrarily chosen clones, whereby the clone with highest infectivity was selected to be the parent clone of the generation that followed. The experimental evolution attested that, from an initial single random sequence, there will be selectable variation in a property of interest and that the property in question was able to improve over several generations. fd-7, the clone with highest infectivity at the end of the experimental evolution, showed a 240-fold increase in infectivity as compared to its origin, fd-RP. Analysis by phage ELISA using anti-M13 antibody and anti-T7 antibody revealed that about 37-fold increase in the infectivity of fd-7 was attributed to the changes in the molecular property of the single polypeptide that replaced the D2 domain of the g3p protein. This study therefore exemplifies the process of a random polypeptide generating a functional role in rejuvenating the infectivity of a defective bacteriophage when fused to some preexisting protein modules, indicating that an arbitrary sequence can evolve toward acquiring a functional role. Overall, this study could herald the conception of new perspective regarding primordial polypeptides in the field of molecular evolution.PMID: 12574862 [PubMed - indexed for MEDLINE]
------------------------Improved infectivity through mutation of a random sequence. This would seem to show that evolution can create meaningful "information" and increase "quality" over time from an increase in "quantity".

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Again, the quantity of information may have remained the same but it is the quality (i.e., the specificity) of information that determines many aspects connected with life.

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I don't think that anyone here will argue that protein specificity is not important. What you are missing is that specificity can arise through naturalistic processes. I think the pubmed citation above attests to that. Another pubmed citation that shows an increase in specificity due a mutation in DNA polymerase:
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Variants of DNA polymerase Beta extend mispaired DNA due to increased affinity for nucleotide substrate.Shah AM, Maitra M, Sweasy JB.Yale University School of Medicine, Departments of Therapeutic Radiology and Genetics, New Haven, Connecticut 06520, USA.DNA polymerase beta offers an attractive system to study the biochemical mechanism of polymerase-dependent mutagenesis. Variants of DNA polymerase beta, Y265F and Y265W, were analyzed for misincorporation efficiency and mispair extension ability, relative to wild-type DNA polymerase beta. Our data show that the fidelity of the mutant polymerases is similar to wild-type enzyme on a one-nucleotide gapped DNA substrate. In contrast, with a six-nucleotide gapped DNA, the mutant proteins are slightly more accurate than the wild-type enzyme. The mutagenic potential of Y265F and Y265W is more pronounced when encountering a mispaired DNA substrate. Here, both variants can extend a G:G mispair quite efficiently, and Y265F can also extend a T:G mispair. The kinetic basis of the increased mispair extension efficiency is due to an improved ability to bind to the incoming nucleotide. Y265W extends the G:G mispair even with an incorrect nucleotide substrate. Overall, our results demonstrate that the Y265 hinge residue is important for stabilizing the architecture of the nucleotide binding pocket of DNA polymerase beta, and that alterations of this residue can have significant impacts upon the fidelity of DNA synthesis.
{emphasis mine}
---------------------So, specificity can be a hallmark of mutation. It would seem that specificity is not a hallmark of ID alone, but can come from mutation. So, why are we to believe that DNA arose from an intelligence when it's properties and plasticity in sequence seem to be natural?

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Not at all. The same thing applies to languages as does to organisms, namely, no one (certainly not I) disputes that 'evolution' occurs. 'Evolution' as in 'change'. But evolutionists want to promote that 'because things change, this supports the notion that Earth's entire flora and fauna had a common, single-celled ancestor'.

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Science does not contend that change alone supports the ToE, but rather the relationships between things that have changed. The fact (according to current methodology) that species fall into nested hierarchies with respect to morphology and genetics speaks to the explanatory power of the theory. Simply citing change ignores a great volume of evidence right from the start.

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Such a statement has exceeded the realm of science and has entered into the domain of metaphysics. That has been, and continues to be, my position in the matter.

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What I contend, and continue to contend, is that not all metaphysical positions are equal with respect to explaining objective truth. Humankind will never be able to rid themselves of bias (at least in my opinion) but what we can do is limit it's effects. Naturalistic methodology seems to be the best system we have right now both in its explanatory power and its predictive power due to its ability to limit personal bias. The very fact you can say that DNA has semantic rules relies upon naturalistic methodologies and assumptions. No one has ever been an eyewitness to a polymerase reaction, if you can understand this statement then you are one step closer to joining the naturalist parade.

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But the origin of language is as difficult a problem today as is the origin of life. 'Difficult', that is, to the Naturalist.

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Origin of life and the evolution of life are two separate theories. The best analogy I can think of is this:Does the manner in which a runner arrives at the starting line affect their position at the finish line?Abiogenesis is how life got to the starting line, evolution is the action after that. Abiogenesis is still a very young field, and in my opinion the word "theory" is used very loosely (hypothesis is more cogent, IMO).However, evolution has been tested to such a point, especially after genetic information became available, that it is a very very strong theory. Evolution is falsifiable by many fields and methodologies, but it still stands as the best explanation we have for species diversity. Creation has no explanatory power, no predictive power, and little to no evidence. So, which metaphysical position is strongest? I think it is the current Theory of Evolution.This is not a demand, but I was wondering if you have a response to the two pubmed citations above (msg 17). Arguments about information in DNA actually interest me more than arguments over metaphysical positions for some strange reason.Added in Edit: Crash, I swear I started typing before your message was posted, and I totally agree with what you wrote. Quetzal and I did the same thing earlier today, I'm starting to feel like someone put a hex on me.[This message has been edited by Loudmouth, 12-09-2003]

DNAunion,Information and Information from an Intelligent Source are probably what we are arguing. An organism doesn't read its own DNA like we read a book, searching for the protein it needs and making a conscious decision on whether to use that DNA sequence or not. The same goes for mutations. An organism does not change its DNA specifically to fit a certain environment. Rather, the environment chooses who dies and who lives determined by the proteins they express. Although humans can derive information from the DNA and ascribe information, it is not information to the organism who holds it. It is not something that they can consciously change or pre-determinstically control. These are two properties that intelligent information has that DNA information lacks.

I did not say it didn't carry information. I said that the information is not accessible to the organism who holds the DNA. If you disagree with this, ask yourself how much information you are getting from your DNA at this very moment. I can't derive any information, in situ, from my DNA. It is only through analysis and reduction that we can derive information from DNA in any useful. There is information in tree rings for example, but that information is useless to the tree.

There is information in everything, with this I would agree. Perhaps to get to the point that a few people are trying to make, how much information is there in Carbon. For example, if hydrogen is bound to each valence, you get methane. If a hydroxyl group is bound to one of those valences and hydrogen to the rest, you get methanol. It would make sense that there is information in the valences of carbon in order to have all of these possible states.What I think we are all leary of is the "information only comes from intelligence" that we are all tired of hearing, only because the logic behind this statement is lacking. This is why we need a better definition of the TYPE of information that is being alluded to here. Is it information in the Gitt sense, in the derived sense, so forth.Not to DNAunion in particular, but can everyone agree on an answer for the following questions:1) Is it possible for new information to arise in the genome? If not, what would new information look like in the genome?2) Is the information in a genome due to random mutation + natural selection? If not, why?3) Can an artificial sequence inserted into the genome become information through mutation and selection?4) Can the information in a genome increase with specific mutation selected artificially?

We read it the first time. Would you like to comment on the bits of information contained in one carbon atom? Since it has four possible valences it should contain information, just like there are four possible nucleotides. Do the R groups attached to carbon give it information? By your definitions, it does contain information. If it didn't contain information, then mass, density, and reactivity would not occur. Attachment of R groups give the carbon atom specificty.

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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.

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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And a ribosome does TRANSLATE base sequences into polypeptides.

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Not to get into a bigger debate about the definition of "translate" but I see the process of going from mRNA to protein as a transcription, not translation. I look at translation as a decision making process that requires foresight and understanding of the message as a whole while transcription is a tit-for-tat non-decision making process. tRNA's bind to DNA code triplets as guided by the ribosomes and protein elongation then commences. The ribosome does not look at the rest of the mRNA and decide if this is the correct amino acid to use or not, it is a straight transfer, or transcription. On top of this, no decision is made by the ribosome, tRNA, mRNA, or the transcribed DNA, that is everything that happens from one step to the next is guided by which reaction is the most energetically favorable as proscribed by the enzymes involved. I think this ties well with Peter's argument of each base not predicting the next and why "protein translation" is somewhat colloquial where "protein transcription" is closer to accurate.

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Look up translate in the dictionary and see if you don't find at least one definition that fits biological translation (I did).

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If you are using the definition below, I will agree.
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1 a : to bear, remove, or change from one place, state, form, or appearance to another
--------But I am not sure as you then state this:

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The information encoded in one "language" (nucleotides) is operated on by a function to produce specific information in a different "language" (amino acids). That's translation.

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Which is total poppycock. Chemistry is not language, sorry. You keep ascribing attributes to DNA that just do not exist. Control and encoded information denote forsight and striving towards a goal, both of which can not be observed in DNA. DNA no more controls the cell than oxygen controls the burning of a match. Either the DNA sequence works or the cell dies.DNA and proteins react in concert to RESULT in a cell. I could just as easily talk about the information in a protein, since it is the proteins that create DNA, and translate new proteins from the DNA that it creates. Why aren't we talking about the information in a protein molecule? Why should DNA be favored over proteins for information content?

No, you are the one lacking. You seem to put the chemistry involved in the cell outside of the normal realm of non-organic chemistry. This can be seen in this statement:

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And who’s talking about mere chemistry alone? Molecular cell biology exists at a higher level than mere chemistry. For example, a ribosome is not considered a mere chemical like NaOH, H2O, or CH4 are; a ribosome is an aggregate of several macromolecules that work together as a single unit to perform a specific, high-level function: translation. And translation involves coded symbol sequences, as in the mRNA base sequences that specify the order in which amino acids should be stitched together to form functional proteins. Is chemistry involved? Sure, so is the even lower-level physics. But molecular cell biology — of which translation is a part — is above both.

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This throws the doors wide open on your lack of understanding. Show me one instance where a protein, DNA molecule, or any organic molecule can break rules that non-organic chemistry must follow. The answer is none. The cell is chemistry and physics, nothing else. You might as well argue that complex storm systems are above fluid dynamics, or complex electrical circuits are above Ohm's law. You want to play the intellectual superior, but it just doesn't play out and the above quote shows why. I do understand the workings of the cell and work with it on a daily basis. As complex as cells are, they still obey the same rules that NaOH and NaCl have to follow, as does a buring match. DNA has AS MUCH control over the workings of the cell as oxygen does on a burning match. Notice I say AS MUCH. Show me how this is incorrect.

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And I haven’t said there is one. Do you not understand the concept of higher levels?

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Originally, you said the cell was "above" simple chemistry. I took this to mean something like "above the law," an ability to ignore rules and act outside of the rules. Higher leves? That I can understand and agree with. However, enzyme action and binding is rooted very heavily in activation energies and electro-static force, which are staples of simple chemistry as well. I guess the question becomes when are things put at a higher level, at which point are reactions complex enough to make the jump from simple chemistry and biomolecular reactions?

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In the burning match scenario, oxygen has NO control over what occurs. YOU can control the amount of oxygen present, thereby attempting to control the rate of combustion, but oxygen can do nothing to direct the process. And what does oxygen code for here? Nothing.

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If a gene is turned on, it has no control over what happens, much like with a match. It is a deterministic process under which no control is available once it is initiated. In this scenario, oxygen codes for the propagation of a flame which wouldn't be predictable and repeatable without the information in oxygen. The information is stored in the valence electrons, and by which all flames are made the same and propagate in the same fashion. It is the deterministic fashion of both DNA transcription/translation and oxygen in combustion that bear resemblence, as well as the predictable and repeatable attributes that both have.

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In simplified terms, if a cell has the DNA turned on to make the proteins required for a skeletal muscle, the cell will become a skeletal muscle; if the cell has the DNA turned on to make the proteins required for a neuron, the cell will become a neuron; if the cell has the DNA "turned on" to make the proteins required for a photorecptor, the cell will become a photorecptor; and so on.

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Here you make a very fair distinction between combustion and DNA products. Combustion has one outcome while DNA has numerous outcomes. However, both processes need initiation, be it a spark or binding of a promotion factor upstream of a gene. Once it is initiated it is deterministic, no control.

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Surely then the DNA is playing a role in controlling what type of cell is produced. Furthermore, a single celled zygote is what we all started off as. But here we are — humans, with brains, muscles, hearts, skeletons, intestines, and so on. Did all of these tissues, organs, and organ systems arise by an uncontrolled process like mere combustion? Nope.

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Uncontrolled processes like combustion? No. Uncontrolled processes like random mutation and selection? Yes. Systems that increased the fitness of the DNA preserved useful DNA. Therefore, the ultimate control of organ development is evolution, not DNA. DNA does not decide if the organism needs a brain or not, either you have the active coding regions or you don't. When these are turned on by appropriate cell to cell interactions, neurons form. Being able to differentiate cells into tissues was something that was selected for and has evolved over time, it was not a process that DNA controlled but rather something that was controlled through DNA, just like a match is controlled through oxygen.

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The process of cell differentiation and embryological development are far more complex and exist at a higher level than the mere chemistry involved in a burning match. And, this complex process is controlled, ultimately, by the DNA in the cells. For example, if we were to randomize the base sequences of the DNA, still leaving the same "chemicals" in the same quantities, then cellular control would be lost.

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Rearranging the DNA sequence IS altering its chemical properties since it changes binding to other chemicals. It is the same as rearranging the carbon/hydrogen and carbon/oxygen bonds in a match, but keeping the same ratios of carbon, hydrogen, and oxygen all the same. Suddenly the match is all acetic acid, but I have kept the ratios all the same. Now the information is not there to initiate and propagate a flame via control through oxygen.Although my analogy may fail in the long run, it still gets to the root of assigning certain types of information to DNA. Cellular systems are decidedly deterministic, there is no decision making process involved, as with oxygen in a combustion model. Codon to amino acid sequence translation is controlled by activation energies that allow the one amino acid over the rest to bind to the elongating peptide. That specific activation energy is created by the interaction of a ribosome, mRNA, and tRNA. Also, in a bacterial protein expression system, you can throw in any DNA sequence you want and it will be expressed (between a start and stop codon). All you need is a promoter system upstream of the DNA. The DNA doesn't care if it is toxic or not, it will be produced. This is the same for every gene. The ultimate control is that of selection on DNA, in that DNA sequences will be kept in a population or weeded out.

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If you weren't being such a die-hard reductionist you might be able to grasp all of this.

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You can't see the forest for the trees.

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Maybe I am, but I still remember that trees make up the forest and know what affects those trees. I grasp your argument, do you grasp mine?

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How do cells maintain their high degree of order and complexity? This is a VERY SPECIFIC, YET HIGHLY IMPROBABLE state - one that is very much thermodynamically unfavorable.

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Very specific? Yes, assuming a qualitative and subjective view of complexity. Highly improbable? No, if certain conditions are first met, ie starting from one fertilized human zygote the formation of a multi-cellular human is very probable. The cell overcomes thermodynamic unfavorable reactions by incorporating energy into the reaction (eg ATP), just like the unfavorable conditions of having fresh water and brine water separated here on Earth.

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If you will reread some of the recent quotes I posted, you will see the answer. It requires BOTH sufficient energy AND sufficient information.

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Like I have said before, I agree that there is information in DNA, but the way you characterize it seems to deviate from the definition that most geneticists use. It is the same information that allows oxygen and hydrogen to form water when supplied enough energy/catalyst.

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If take all of a cell's constituents and "jumble them up", you can supply all the undirected energy you want to those "chemicals": put them out in the sun, cook 'em up on the stove, smash them with a hammer, expose them to radiation, ... whatever. You won't get life, even though you've supplied sufficient energy. Mere energy and chemistry alone are not sufficient to make one of our cells...it takes control too, which is where the information comes in.

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Again, if you "jumble-up" the chemistry in any reaction, organic or inorganic, the resultants will be different. The cell is no different in this respect than acetic acid vs. ethanol. The information in the cells (DNA) is susceptible to the same thing, information is changed if the chemistry is changed. Changing the DNA sequence is changing it's chemical attributes.

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Can't "perfect" this because I've got to get to work. No doubt someone will complain about the word control. Maybe they should consider the context it was used in.

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We have gone back and forth on this one and I will stick by my earlier posts. One more example. Alcohol dehydrogenase takes a hydrogen off of ethanol and transfers it to NAD. The resultants are acetaldehyde and NADH. The reaction can be controlled by adding tetrasodium pyrophosphate and semicarbazide which bind to the acetaldehyde and cause the reaction to speed up by removing one of the resultants, ie control the reaction. Therefore, inorganic molecules can control molecular reactions in a cell. Therefore, inorganic molecules must have information, according to your criteria.

First you state:

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How do cells maintain their high degree of order and complexity? This is a VERY SPECIFIC, YET HIGHLY IMPROBABLE state - one that is very much thermodynamically unfavorable.
  —DNAUnion

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So, it was about maintainence of the complexity, not order from non-order, and I rebutted with:

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Very specific? Yes, assuming a qualitative and subjective view of complexity. Highly improbable? No, if certain conditions are first met, ie starting from one fertilized human zygote the formation of a multi-cellular human is very probable.
  —Loudmouth

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So, what do you do? You move from maintainence of complexity to origination of complexity:

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No, highly specificperiod.

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Theoretically, how many different ways could the atoms in your body be arranged.? 10^bajillion-gazillion? How many of those ways would make a human. Only an astronomically miniscule fraction. A human is an incredibly specific arrangement of matter. Even the simplest bacterium is in an incredibly specific state: as Richard Dawkins himself has famously said, There are far more ways to be not alive than there are to be alive (paraphrasing).

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Though this gets off the subject a bit, it makes the current point very strongly. Why haven’t OOL researchers been able to obtain a single, self-replicating RNA molecule? They make the RNA themselves, and they make trillions and trillions of different base sequences of RNA. Gee, could it be because even something as simple as a self-replicating RNA molecule is a very specific arrangement of matter? Yep. And that’s just an RNA molecule: that doesn’t count the proteins, mitochnodria, lysosomes, cells, tissues, organs, and organ systems of a human.
  —DNAUnion

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I would argue that the maintainence of complexity is a different issue than the origination of complexity. Do you disagree?

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Are you really that dense?

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The point is how improbable the arrangement of matter in a human isperiod. Nothing about starting with the DNA, proteins, ribosomes, etc of a zygote.

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Your argument is kind of like saying that a Pentium 4 3GHz CPU isn't an improbable state of matter. Why? Well, given a chip manufacturing plant, humans/robotics to run the machinery, instructions for making the chip, and so on, it's pretty much certain to occur.

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Here, let me explain it to you. If you took the individual X number of carbon atoms, Y number of oxygen atoms, Z number of hydrogen atoms, and so on, that make up a human, put them into a container of some sort and supplied undirected energy, how probable is it that the matter would end up being arranged as a living human being? Surely you realize that the probability of that occurring approaches 0.

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Is this just DNAunion saying that humans (or for that matter, any living thing) are a highly improbable arrangement of matter? No.
.... [numerous quotes from literature, see original post]
  —DNAUnion

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If you look at the first sentence in the above quote you will understand why Crashfrog thinks you are acting like an asshole. Just food for thought.Anyway, again you slip from the maintainence of complexity to the origination of complexity. Evolutionaryily, organisms that do not mantain complexity do not get past the single cell phase, and for unicellular life, they do not multiply by fission. Simply, systems that mantain complexity multiply.So, in what units is complexity measured in? How can you show that a 50-mer of human DNA is any more complex than an arbitrary 50-mer, what units can you use to differentiate? Do the same for a 50-mer amino acid peptide. Which is more complex, an actual small protein in a bacterium or a 50-mer with an arbitrary sequence? This is why I qualified complexity with "qualitative and subjective." Complexity can not be measured but can have explanatory power. Just to make you feel better, yes the human is complex and humans are highly improbable if they were birthed from a cake on St. Patty's Day, but not improbable within biology in that we understand the mechanisms of internal fertilization and the role of gametes.

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How then does it occur? Just as I said (and one of the above quotes alluded to also)...sufficient energy AND sufficient information. [edited out supporting references, see original post]

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I have never seen life occur by giving DNA suffecient energy. Therefore, the information in DNA is not sufficient for life. Where is the remaining information?

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Now how silly do you feel.

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No. I did drink a few Bloody Mary's the other night and got a little goofy though. Are you old enough to drink Bloody Mary's? Great Sunday morning quaff, I must say.