Introduction to Information

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I gave you the tools to do that yourself.

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You may have given people tools, but nothing to work with. Where is the substance?You will notice when forced to use those tools yourself, you had to start by ASSUMING. What's worse is you then ASSUMED in a way that supports the very conclusion you were driving for.I can agree that there are more possibilities in the first statement than in the next, but there was no accurate quantification of the difference. You even say "ball park" figures. What good are estimated ballpark figures when one has no real concept of the ballpark (which is what we are facing with cosmological or evolutionary or biochemical systems)?We know you and I, and we know dog, and we know what dogs can do. Can you tell me anything we do know on that order about complex systems we are trying to model.I can almost buy into your system of evaluating (quantifying) information content in relative numerics based on halves. The problem is you first need an objective way to MEASURE initial numeric values of info content of some kind. We must move beyond assumption, or the whole argument you make is circular.This also does nothing to suggest that information is more than manmade, there is no intrinsic information content gained or lost in a molecule that must bind in a certain way to another under STP conditions.------------------
holmes

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The person asked me a question for which accurate numbers cannot be assigned. Then, when I assumed certain values to demonstrate the method you "gripe" that I had to make assumptions, implying that therefore the methodology is flawed.

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Where to begin...1) The "question" asked was the first example YOU supplied for your methodology. Why did you bring it up if it was a bad example for using your methodology?2) When replying to that "question" you never said it was a bad example because it forced you to assume numbers, and your methodology should only be applied when accurate numbers can be applied. Frankly, if you had said this rather than attempting to show how right your methodology was I wouldn't have said anything.3) Probability theory (especially with regard to asteroids) has little to do with information theory. We understand that probabilities are made based on estimates from human experience (which may not be accurate). Information theory (or its firm adherents) tend to inflate "information" into a real entity... like energy or something.

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I made no argument that could be considered circular. You've read more into my statements than were there, then attacked your own interpretation.

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If you were not attempting to prove the validity of your information theory in addressing the "question" (which once again I must point out was YOUR opening example of increasing information, not his) then I apologize.It really read as if you were suggesting your opening intro was a valid example of increasing info in a sentence, and that you were showing how it could be measured, even in a ballpark sort of way.If you were trying to do that then your argument was circular in its defense in that you front loaded estimates of information content, to show how your methods would show its information increasing (by possibilities decreasing).I don't believe your ballpark estimates were correct either, but that is a whole other subject.

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Sure there is, but until I can get you to see that the method I used to calculate information is valid, there's no point going off on other tangents that rely upon this foundation.

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I can see that if information is broken into "bits", which grows as whatever that content is is doubled (ex... a two layer cake has 2 bits of cake info compared to a 1 layer cake) then your methodology is sound.The point I am making is that methodology and accuracy with regard to info is only for human consumption. It is modelling and to view "information" as some inherent property of an entity being modelled, rather than a clever device for human understanding, is incorrect.I noticed within the link you gave in a later post that this very thing is mentioned...http://www.lecb.ncifcrf.gov/...alls.html#consensus_sequencesHeck, I came to really like that author's work as he skewered Dembski at just about every turn.Information theory gives humans wonderful models to help understand and predict. It does nothing to measure an actual property which exerts change inside or on another entity.------------------
holmes

Thanks peter for restating the point I was trying to make in much much clearer wording.------------------
holmes

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I think you need to explain exactly how that link shows this very thing, as opposed to it being a case of your interpreting the statements the way you want.

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The page that opens is a link of improper uses or mistakes made by those who like to conflate information theory. In specific the link brings you to the issue of..."Confusing a model with reality"It uses a sequence as an example, but the point is the same one I was talking about. I think it is up to you to explain how that link does not show what I was saying, and if it isn't exactly what is the author saying?I will note that if you continue reading the page it also addresses some other mistakes you have been making.

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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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Exactly who is reading these instructions? Cells? They read some "code" and then know what to do?These are simply chemicals. Molecules. Cells are collections of chemicals that interact in a specific way with each other. The way they interact promotes their continual interaction and organization in that same way.When chemicals don't do everything that is beneficial to a cell (but what chemicals normally do... react), what are they doing? Misreading instructions? Is it shoddy workmanship on their part?Do molecular enzymes pass instructions for the other chemicals to speed up?Do not confuse models with reality. We call it information for convenience. They are just chemicals which react as they do. Nothing more, nothing less.------------------
holmes

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It shows quite clearly the link between a reduction in uncertainty and an increase in information; it does exactly what it was intended to do — introduce the main ideas in a very simple way. Then, as the MAIN example, I dealt with cards and probability, which involved more math and thus was less suited for use as an opening example.

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Well what the first example shows is more clear statements, but nothing quantifiable. To say look at this example, then look over here for another example, makes it appear you are saying the first is also usable by the method you outline.

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the person who asked the question chose the wrong example of two to ask about in terms of calculating information

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Okay. And then as peter suggests everything where all probabilities and interactions are not known with certainty are equally "wrong" examples to ask regarding calculations of information.

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Second, it works even when accurate numbers cannot be assigned: it just doesn’t work quantitatively.

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By which you are suggesting it works qualitatively? How exactly does that work if one cannot assign accurate numbers?

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Wrong, information theory relies upon probability theory.

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You'll have to explain how determining the probability of floods or asteroids based on experienced frequencies has anything to do with "information".You may be right that information theory relies upon probability, but the reverse is not true, specifically when it is a conflated modelling information theory.

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When you know nothing, your uncertainty is maximum and your information is minimum. When I reduce the number of possibilities by giving you information — telling you that it relates specifically to my dog — I have reduced your uncertainty.

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Heheh...1) "Guess what happened?" ... that is maximum uncertainty? That actually rules out a huge ballpark (though undetermined quantity) of uncertainty. We know that it has something to do with something he could have done or heard of which is exclusive of anything we know he could have done or heard of (past and present).2) "My dog"... how much has this really reduced uncertainty? Half of all those things we know he could not have done or heard of? It also depends on us knowing how many dogs he has, or what a dog is (not so important for this particular example but very relevant for biology).3) "shook hands"... with who? with which paw? what does it mean to shake hands (again very relevant for biology)?Information theory methodology is helpless in measuring anything with unknowns.The number of examples that are "appropriate" are very limited in reality, and almost nonexistent in nature except on very very very small scales of modelling.------------------
holmes

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You still haven't explained, and in fact, you seem confused.

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You have got to be kidding me. I gave you a link which includes more links that hekp define what is meant.I am unsure what is unclear, especially starting with the title of that section which is confusing models with reality. One is not supposed to confuse a model with an existing reality in nature.Is this not what this section is talking about? Do I really need to cut and paste text in here?If I am confused, why don't YOU tell me what IT really says? It was taken from your link. Other than simply asserting that I am confused about what it says, why don't you explain how it proves your point?------------------
holmes

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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

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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

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

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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Sorry, but that does NOTHING to indicate that DNA doesn't contain information in its base sequences.

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Yes. I promise you that no matter how hard you look, and with any amount of instruments, you will not find "information" in its base sequences.These chemicals are merely situated in a position that they react to produce other chemicals which will ultimately self-replicate and preserve the intial chemicals and their environment.

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Nope. Let me ask you something. Do your red blood cells contain hemoglobin or not?

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Yes. Please explain the process by which hemoglobin is produced. Tell me where "information" is that it can be detected or measured in this process, and how it supercedes chemical properties which appear to regulate its production?And I don't mean modelling style quantification. I mean show how information is the driving and regulatory force of the reaction. Can I add info to drive the reaction in one direction or the other?Also, please answer the question in my post regarding the additional info content biomolecules contain to allow their detection.------------------
holmes