Introduction to Information

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Where does the section you linked to state that information is not an inherent property of DNA,

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He uses a different example than DNA. I stated this in my post and it is also stated in the link.He is not specifically stating that information is not an inherent property of anything. What he is saying is that models which are based in information theory should not be confused with representations of what is actually existent in nature.That has the definite implication that while you can certainly model molecular dynamics using terminology with analogies to information content and information exchange, this is not a physical reality.If I am wrong about this, please explain to me where I am wrong. You keep accusing me of avoiding logical debate but have not given me anything more than ad hominem and reassertion of your points in exchange. I have asked for you to explain what he is saying if I am so wrong... please explain.------------------
holmes

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your 'holmes' ID would refer perhaps to a certain John????

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Oh if only. And I'd have a much better career in that I don't use drugs, so I wouldn't have probs keeping my "role" up.Let me congratulate you again on your second post which once again did a much more concise job of saying what I wanted to say.I wish DNA'd at least attempt to answer you. Then maybe I'd get some real answers.------------------
holmes

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Information doesn’t require consciousness to exist, as I have made clear in numerous of my preceding posts.

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Whoaaaaa, back off. I have not seen these posts. This thread's title was "Introduction to Information" and I was assuming you had advanced all points in the first post.I have not seen anything which redefines "information" as something that is separate from consciousness (which is what is suggested when you used the term "read").If you are suggesting information handled by mechanical processes, then perhaps "process" would have been a better term. That entails input... process... output.But this still leaves information as a very vague term. It becomes "possible number of inputs which may or may not be handled by the process under discussion".

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Do enzymes select out of a myriad of molecules they encounter just the one(s) they interact with? Yes.

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Wrong. Enzymes will react with any other molecules they come in contact with, where current conditions allow for their interaction. It is based on the 3d configuration, and that may be created by DNA, but the reason is not choice by DNA but that DNA that had processed enzymes which did not have positive outcomes (reactions) would not survive.I notice that you used the word "select". I don't understand how you can be telling me I am putting a conscious spin on what I am saying when you also use anthropomorphic terminology?

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You seem to be confusing the use of a model with a belief that only the model is real: that that which is being modeled does not exist. Do you believe that atoms exist? Maybe you don’t: after all, scientists use models to explain them.

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Well you have my position half right. I worked at modelling molecular dynamics so I have some pretty healthy scepticism regarding how much one trusts a "model" as being an accurate reflection of reality. Unfortunately many people do this.Atoms... Sure "atoms" are real. They have mass which is detectable and made up of separate "particles" that can be detected in different ways. Now does that mean I believe the convenient model we use to depict an atom is real? No way.The atomic model has changed several times in the last century, and it is likely to change in the future. In fact, there is no real description of electron activity and position in atoms... but we have the models of electrons spinning in "orbits" or in "shells" of potential existence (and based on energy storage).We can determine mass and its influences, and energy based on its influences. Those are inherent properties that influence other particles and fields in measurable ways. It is my understanding (but maybe I am wrong) that you are suggesting information is a real property such as these. If it is, how? If it is not, what is it?If it is just calculations of probability of reaction in specific environments, then it is a model of convenience used to understand but not reflect reality.------------------
holmes

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Carbon contains information (as does every atom) that allows it to bind to other chemicals in a very specific nature. Methane, methanol, formic acid, etc are all molecules that involve one or two carbon atoms. The information stored in the valences of atoms allow predictable outcomes that could not exist if this information was not available.

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I would like this explained better. From all of my education there is potential energy and there is actual energy and that is all which explains (when combined with environment) how carbon atoms can and will combine.There was no mention of molecules or electrons storing information to determine how they can react... and we did just fine in making predictions/running experiments.How is information different from energy at the atomic level, and if not, why are we using that instead?I guess I am asking is what is it and what is the value added in considering it something separate?------------------
holmes

The same can be said for DNA. Transcribed, translated, and replicated DNA follows the same rules as carbon reactions. There is not a conscious decision by a "reader" in interpreting results. Therefore, if there is information in DNA then there is information in a carbon atom. Without atomic forces and relationships (the information so to speak) there would be no rules, or semantics. What I am trying to show is that the information stored in DNA is no different than the information stored in a carbon molecule. In fact, they may be directly comparable.Just as an example for semantics in carbon molecules, take the example of methane and methanol which differ by a hydrogen vs. hydroxyl group. One is a gas with a constant density (at room temp) and characteristics while methanol is a liquid (at room temp) with certain density and characteristics. As DNAunion pointed out, information in DNA allows the same hemoglobin to be expressed cell to cell, organism to organism, but the information in atoms allows the same characteristics for the molecule from reaction to reaction. DNA and carbon seem to hold the same type of information, ie chemical characterstics. I have yet to see how DNA is any different than any other chemical system, and the information content seems to be of the same type.

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Therefore, if there is information in DNA then there is information in a carbon atom. Without atomic forces and relationships (the information so to speak) there would be no rules, or semantics.

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Yeah, I understand and agree with this. It just seemed that you were going further and saying you believed it was a real property as DNAunion does. Or were you simply saying you agreed "information" (which is just a modelling term) can be handled by nonconscious systems?If you believe information is a real property, rather than one ascribed for convenience, I am interested in a better explanation of what that property is.------------------
holmes

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He is not specifically stating that information is not an inherent property of anything. What he is saying is that models which are based in information theory should not be confused with representations of what is actually existent in nature.

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No, that is not waht he is saying.What he appears to be saying in the section you linked to is that people shouldn't confuse a CONSENSUS SEQUENCE - which is an abstraction (model) - with actual BINDING SITES - which are actual sequences.In simple terms, if 100 organisms' sequences for a given binding site are aligned and compared, the consensus sequence is the "average" sequence. That is, each site in the consensus sequence has the nucleotide that occurs most frequently at that site in the 100 samples. But it may be that not one of the 100 organisms actually has that sequence for that binding site. So a consensus sequence is an abstraction - a model.Note that the author does NOT use consensus sequences when calculating the information found in DNA binding sites - he uses actual sequences.I don't see any statement - explicit or implicit - by the author in that section you linked to that indicates information in DNA is only for us humans and doesn't actually exist.[This message has been edited by DNAunion, 12-16-2003]

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Information doesn’t require consciousness to exist, as I have made clear in numerous of my preceding posts.

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Whoaaaaa, back off. I have not seen these posts. This thread's title was "Introduction to Information" and I was assuming you had advanced all points in the first post.

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I have not seen anything which redefines "information" as something that is separate from consciousness (which is what is suggested when you used the term "read").

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You haven’t? What about this, which I said in post #16 of this thread.

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Getting off track a bit, but...an organism’s DNA does contain information, stored in the sequence of bases (analogous to the way that these sentences store information in the sequence of characters). This cellular information is encoded instructions used by the cells to direct the synthesis of their constituents and to maintain themselves. That information, stored in the DNA of countless organisms. is there regardless whether or not humans exist or read it. If it weren’t there, living cells and organisms could not exist.

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And, though not found in this specific thread, on 12/13/2003 I said the following in post #32 of the other thread on information that has cross-posters (http://EvC Forum: Data, Information, and all that.... -->EvC Forum: Data, Information, and all that.... ).

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An organism's DNA is information even without us around. If it weren't, then a mouse could be born from a chicken, or a whale from a cactus, or a human from a moth. Why doesn't that occur? Because the genetic information is there, in the cell, directing the processes involved in life: it is encoded information - a list of instructions. And it is these things whether humans are around or not. In fact, it was happening billions of years before we were even here.

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And in that same thread (post 38), I said the following on 12/14/2003:

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SomeoneElse: The only reason that you and other intelligent design creationists want to get carried away with the information analogy is so you can use it to prove your point that design requires a designer.

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DNAunion: Wrong again. I didn't state that a designer was required to put information into DNA. What I stated — and was 100% correct to state — was that DNA contains information. The rest is just YOUR imagination running wild.

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[This message has been edited by DNAunion, 12-16-2003]

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Do molecular enzymes pass instructions for the other chemicals to speed up?

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DNAunion: Do enzymes select out of a myriad of molecules they encounter just the one(s) they interact with? Yes. And how do they do that? By their specific three-dimensional conformation. And what determines their conformation? Ultimately, the DNA (genes) that encodes them: they supply the information needed for the cell to synthesize those specific enzymes.

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Wrong. Enzymes will react with any other molecules they come in contact with, where current conditions allow for their interaction.

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Wrong. Enzymes interact only with specific substrates — the concept is called specificity...

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A consequence of the structure of the active site is that enzymes display a high degree of substrate specificity, evidenced by an ability to discriminate between very similar molecules. Specificity is probably one of the most characteristics of living systems, and enzymes are especially dramatic examples of biological specificity. (The World of the Cell: Third Edition, Becker, Reece, & Poenie, Benjamin/Cummings Publishing Co., 1996, p143)

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It is based on the 3d configuration,

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Just as I said...first.

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I notice that you used the word "select". I don't understand how you can be telling me I am putting a conscious spin on what I am saying when you also use anthropomorphic terminology?

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Simple...you’re doing it again. You are intentionally interpreting the non-conscious-requiring term SELECT as a conscious act.Here, look at what the following author states.

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The molecular operation that the ribosome must perform is to select the after sphere that represents its binding sites and to avoid all the other after spheres that represent different patterns. (http://www.lecb.ncifcrf.gov/.../paper/nano2/latex/index.html)

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Will you claim that this author considers ribosomes conscious because they select certain things?That is the sense in which I used the term SELECT. No conscious act stated or implied.In fact, I stated specifically that the selection was based on three-dimensional conformation: nothing about consciouness.In addition, look at the word the first quote I provided used: DISCRIMINATE. Do you claim that the authors think enzymes are conscious because the enzymes discriminate?You are playing games: tricks instead of logic.[This message has been edited by DNAunion, 12-16-2003]

Thank you. This was the kind of clarification I was looking for.

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No, that is not waht he is saying.

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While your detailed analysis of what is given as an example is correct, it is ONE example of what that kind of mistake is.I think I see what the problem is here.According to my point of view this can be extrapolated to all modelling in general, which information theory is a part of. (ie there is an implication)According to your point of view (if I am right about what you just said) you think I am conflating his criticism beyond what he meant. (ie there is no implication, I am making an incorrect inference).I guess the only way to answer whether this is what he meant or not, is to ask him directly so I guess I will.We can pretend I am wrong for the time being on this specific subject. I'd like to see you respond to Peter's posts as they more clearly state what I was trying to say.And that way you don't have to worry about my slipshod way of discussing the issue (which was easily seen when he made his posts). In this subject clarity is a virtue.------------------
holmes[This message has been edited by holmes, 12-16-2003]

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You are playing games: tricks instead of logic.

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No, you seem to be missing the point of what I am saying. I am unsure if it is because you took an emotionally charged reaction to what I said, or because my writing was simply not clear enough.I will try to clear up my wording, please stop reading into what I am saying.

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Wrong. Enzymes interact only with specific substrates — the concept is called specificity...

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Are you suggesting that enzymes do not interact chemically with chemicals other than the specific substrates which result in cellular processes?My point is that they certainly do. If there is "information" in one case (cellular), why is there not "information" in the second case (random interactions). They are all the same thing to the enzyme except when inside a certain self-sustaining environment.It is my argument that we call one "information" because it is part of a model that does something specific we are modelling. If for some reason something came in and was breaking down a cell and interacting with the enzyme (let's say at death), just not the ones we'd be interested in (the cellular life processes) and so "uninformative". Or at the very least has information content unmeasurable or untranslatable to the life cycle "information" content.Thus information content is context driven, which makes it a nonreal property. Energy and mass are not context driven.

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Simple...you’re doing it again. You are intentionally interpreting the non-conscious-requiring term SELECT as a conscious act.

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This was supposed to be my pointing out to you that every time I used an anthropomorphic term you jumped down my throat as having some ulterior motive. Yet you use them as well.Your use of anthropomorphic terms allows for subtle equivocations and misunderstandings.For example when you stated DNA "code" is around even if humans are not there to read it. My reply was supposed (and obviously failed, my fault) to make the point that there is never going to be anything to read it in nature except humans.It is not a "code". There is really nothing to read. For our own convenience we have created a way of understanding the chemicals there as "coded" sequences, based on how groups interact. Thus we read what we have created as a model "code".And the chemicals involved (like any other chemical) are not machines reading bits of information, they are simple reacting in an environment. If the environment is altered, then the code itself... while we might "read" it as one thing... may be expressed quite differently.Does this make what I said earlier make more sense?Whether you mean them as conscious or nonconscious entities, the idea that anything contains real "information" which is processed by another so it will produce an end product is not real.Or at least it becomes almost meaningless as indistinguishable from energy and mass, when it finally must take into account all possible interactions available to it.------------------
holmes

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Wrong. Enzymes interact only with specific substrates — the concept is called specificity...

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Are you suggesting that enzymes do not interact chemically with chemicals other than the specific substrates which result in cellular processes?

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Yes, I am, and what I said is considered correct when one uses the word interact as I originally did. You, however, are interpreting the word interact as you see fit, changing its meaning for that which was clear from the context of my original statements.

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It is my argument that we call one "information" because it is part of a model that does something specific we are modelling.

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And your position is wrong. Cells use genetic information without us having to build any models of it. They’ve been doing it for billions of years; billions of years before humans, or models, even existed.

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Simple...you’re doing it again. You are intentionally interpreting the non-conscious-requiring term SELECT as a conscious act.

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This was supposed to be my pointing out to you that every time I used an anthropomorphic term you jumped down my throat as having some ulterior motive. Yet you use them as well.

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No, I don’t. Selecting is exactly what enzymes do, and they do it based on three-dimensional conformation, not by conscious acts...just as I originally stated, quite clearly.Your terminology, on the other hand, is anthropomorphic. For example, you used WHO. An enzyme is most definitely not a WHO, it is a WHAT.

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Your use of anthropomorphic terms allows for subtle equivocations and misunderstandings.

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Grow up.

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For example when you stated DNA "code" is around even if humans are not there to read it. My reply was supposed (and obviously failed, my fault) to make the point that there is never going to be anything to read it in nature except humans.

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It is not a "code".

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Of course it is a code. In simple, BIO101 terms, a DNA triplet, through an mRNA codon, codes for an amino acid. A linear array of DNA triplets in a particular sequence — a gene — codes for a specific protein. Information is stored in one language, and then translated into a second functional language using a specific, consistent, and precise mapping from the elements of the first language to those of the second. Cells have been utilizing this code for billions of years.

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For our own convenience we have created a way of understanding the chemicals there as "coded" sequences, based on how groups interact. Thus we read what we have created as a model "code".

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Yes, we have a table that shows this coding system, and it is just a model we humans use. But we use it to decipher for ourselves the very real code that has been used by cells for billions of years. Don’t confuse the use of a model with nonexistence of that which is being modeled. Atoms exist, even though scientists use models of them in their work.

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And the chemicals involved (like any other chemical) are not machines reading bits of information, they are simple reacting in an environment.

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There are molecular machines in the cell that use the information stored in DNA. Why do you think all ribosomes always make a particular protein, such as hemoglobin, when fed a particular sequence of nucleotides? If there’s no information in that symbol sequence, then why the consistent selection of just one amino acid sequence out of the trillions of trillions possible? Obviously, there IS information in those nucleotide sequences, and obviously, cells do use it, and obviously, they do so whether or not we humans make models of them doing so.[This message has been edited by DNAunion, 12-16-2003]

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You define information as 'reduction in uncertainty', that has
nothing to do with 'selecting' or a 'template' understanding
of information.

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Apparently, you haven't bothered to read the pages I have provided links to.And don't you think the main example I used, dealing with cards, involves selection? The idea was to be able to select, out of all the possiblities, the one card the original person did. And it took information to do that, and uncertainty decreased with each increase in information.***********************************Came back to post this. It should explain a lot.

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A ribosome is a collection of proteins and RNAs which reads messenger RNA and uses that information to construct proteins. This translation process starts in a region called the ribosome binding site [Gold et al., 1981,Stormo et al., 1982b]. One problem facing ribosomes is to locate the binding sites.

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The bacterium Escherichia coli has approximately 2600 genes [Schneider et al., 1986], each of which starts with a ribosome binding site. These have to be located from about 4.7 million bases of RNA which the cell can produce [Kohara et al., 1987]. So the problem is to locate 2600 things from a set of 4.7 x 10^6 possibilities, and not make any mistakes. How many choices must be made?

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The solution to this question, log2(4.7 x 10^6/2600) bits, is ``obvious'' to those of us versed in information theory, but the reasoning behind how this works in a biological system is subtle and not obvious, so let's consider a simpler example

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How much information do we need to describe the patterns here? To say that position +1 always has a U requires telling you 2 bits of information since that is a selection of one thing (U) from four things (A, C, G, U). If a position has half A and half G, then that is a selection of 2 from 4, or only 1 bit. In the case of the ribosome we again apply the idea of before and after states. Before binding, the ribosome's ``fingers'' see 4 possibilities and don't distinguish amongst them. We say that each finger is ``uncertain'' by log2(4) = 2 bits. After binding, the uncertainty at each finger is lower. If there is 1 base, then the uncertainty is log2(1) = 0 bits. The decrease in uncertainty is a measure of the sequence conservation or information at the binding site. With 1 base this is log2(4) — log2(1) = 2 bits. If a finger accepts 2 bases after then the uncertainty remaining is log2(2) = 1 bit and the information is log2(4) - log2(2) = 1 bit. When a ``finger'' accepts all 4 bases, it really doesn't do anything and the information it demands in sequence conservation is log2(4) — log2(4) = 0 bits. (http://www.lecb.ncifcrf.gov/.../paper/nano2/latex/index.html)

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[This message has been edited by DNAunion, 12-16-2003]

Chemicals react based on chemical properties.Due to their active nature we can use anthropomorphic language. This is okay, but liable to equivocation and misunderstanding, especially when talking about details of specific theories.In biomolecules, which are part of replicating cellular systems, it is often common to use terms such as information, and understanding the set of chemical properties preserved in the biomolecules as stored information.Furthermore, long strands or sections of biomolecules can be broken into the active "sites" and term them as "codes" for the particular chemical reactions they will go through in order to produce specific chemical compounds. In reality the chemicals are bound together and work in conjunction when inside specific chemical/physical environments.None of this use of anthropomorphic terminology is wrong, but prone to error if the use is not clear.If you are with me on this:When interacting, chemicals are doing what they will do based on their chemical properties under the correct conditions and with the proper compounds...then there is no problem.My question is why do we need to consider "information" as a real property, when its level of content is dependent on what is being modelled, and chemical properties are enough to define and model what will actually happen?If you are not with me on the above statement, then I am not understanding how you view chemical reactions. I am trained as a chemist and even when doing modelling work never needed to use more than chemical/physical properties to do so.Concepts of "information" and "codes" are wonderful for understanding the complexity of biomolecules, and how they work, but I have not seen or worked with any biomolecule that is not merely a batch of chemicals that react according to purely chemical/physical properties.While working in analytical chemistry I was focused on detecting biomolecules and it is the fact that they do react to other chemicals (nonbiomolecules) in predictable ways which made analytical work much easier.Now here is where the idea of information gets complicated. It is possible to think of the latent chemical reactions a biochemical (I was trying to detect) was possible of, as "information". It must react in a specific way to produce other chemicals, which is what I could then detect. It is thus "coded" to do so.Does this make the information content for its cellular functions as something separate from the information is contains for detection functions? Does the fact that it has additional "information" affect its total information content? How do we know the number of possible chemical reactions it can go through which can be conceived of (or in some future state will be conceived of as) information?It is this specificity of "information" to particular function which makes information seem less a real property, and more a convenient conception (particularly for biomolecules) of preserved chemical properties which are necessary for self-replication. And the fact that it is self-replicating, is the reason we see it sticking around.------------------
holmes

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And don't you think the main example I used, dealing with cards, involves selection? The idea was to be able to select, out of all the possiblities, the one card the original person did. And it took information to do that, and uncertainty decreased with each increase in information.

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The problem with this as an analogy to DNA is that
the 'selection' you are referring to happens at the
cell/organism level not at the protein manufacturing level.DNA is more like a game of poker ... any five (or seven) cards
constitute a valid hand, but some are 'better' than others
with respect to the environment.[This message has been edited by Peter, 12-17-2003]