Comments for ASA PSCF Discussion http://www.asa3online.org/PSCF A members' forum for discussion of PSCF articles Wed, 21 Dec 2011 03:06:01 -0700 http://wordpress.org/?v=2.8.6 hourly 1 Comment on Biological Information, Molecular Structure, and the Origins Debate by Randy Isaac http://www.asa3online.org/PSCF/2011/11/18/biological-information-molecular-structure-and-the-origins-debate/comment-page-1/#comment-148 Randy Isaac Wed, 21 Dec 2011 03:06:01 +0000 http://www.asa3online.org/PSCF/?p=349#comment-148 <p>P.S. And perhaps I should add that in the thermodynamic sense, information and entropy scale in the same way, so that when the entropy increases, the total information content increases as well. That seems counterintuitive. After all, entropy is a measure of disorder and uncertainty while information is a measure of order and a reduction of uncertainty. So how can the both increase at the same time? One way to look at it is to consider that as entropy increases, uncertainty increases. Then, any given state of information will reduce a greater amount of uncertainty. Hence, information is greater in the system when entropy is higher. Simple example: suppose you have one marble and two holes in which you can put the marble. You have one bit of information. Then suppose you increase the entropy by adding two more holes. You still have only one marble in one hole, but you now have two bits of information. Both entropy and information have increased.</p> P.S. And perhaps I should add that in the thermodynamic sense, information and entropy scale in the same way, so that when the entropy increases, the total information content increases as well. That seems counterintuitive. After all, entropy is a measure of disorder and uncertainty while information is a measure of order and a reduction of uncertainty. So how can the both increase at the same time? One way to look at it is to consider that as entropy increases, uncertainty increases. Then, any given state of information will reduce a greater amount of uncertainty. Hence, information is greater in the system when entropy is higher.
Simple example: suppose you have one marble and two holes in which you can put the marble. You have one bit of information. Then suppose you increase the entropy by adding two more holes. You still have only one marble in one hole, but you now have two bits of information. Both entropy and information have increased.

]]> Comment on Biological Information, Molecular Structure, and the Origins Debate by Randy Isaac http://www.asa3online.org/PSCF/2011/11/18/biological-information-molecular-structure-and-the-origins-debate/comment-page-1/#comment-147 Randy Isaac Wed, 21 Dec 2011 02:45:13 +0000 http://www.asa3online.org/PSCF/?p=349#comment-147 <p>Perhaps it's appropriate for both of you to review thermodynamics a bit. David, you said "Thus, evolution violates the second law, as all PhDs in biology know." and Jonathan, you said "The second law, as you mentioned, applies to only a closed system." Neither statement is correct. The second law governs all processes and, as far as we know, is never violated. The entire second law can be succinctly stated as "The Gibbs Free Energy is always minimized." No conditions or constraints. Every process will reduce the Gibbs Free Energy, which includes terms like G = U - TS +PV, etc., where G is the Gibbs Free Energy, U is the total internal energy, T is the temperature, S is the entropy, P is the pressure, and V is the volume. Other terms cover stress, strain, magnetic moment, etc. What most people remember as being the Second Law is "Entropy tends to increase in a closed system." That follows from the definition above, with the constraint that U is constant in a closed system. If G decreases, then S must increase if U and the other terms are constant. But this is only a special case. In the general case, all parameters can vary. As energy enters the system from the environment, U and T and other parameters can change and S can decrease dramatically while G also decreases. In other words, the second law applies everywhere, not just to closed systems. And, perhaps biologists don't know it, but physicists know that the second law is not violated by any biological process or by evolution in any sense.</p> Perhaps it’s appropriate for both of you to review thermodynamics a bit. David, you said “Thus, evolution violates the second law, as all PhDs in biology know.” and Jonathan, you said “The second law, as you mentioned, applies to only a closed system.” Neither statement is correct. The second law governs all processes and, as far as we know, is never violated. The entire second law can be succinctly stated as “The Gibbs Free Energy is always minimized.” No conditions or constraints. Every process will reduce the Gibbs Free Energy, which includes terms like G = U – TS +PV, etc., where G is the Gibbs Free Energy, U is the total internal energy, T is the temperature, S is the entropy, P is the pressure, and V is the volume. Other terms cover stress, strain, magnetic moment, etc.
What most people remember as being the Second Law is “Entropy tends to increase in a closed system.” That follows from the definition above, with the constraint that U is constant in a closed system. If G decreases, then S must increase if U and the other terms are constant. But this is only a special case. In the general case, all parameters can vary. As energy enters the system from the environment, U and T and other parameters can change and S can decrease dramatically while G also decreases.
In other words, the second law applies everywhere, not just to closed systems. And, perhaps biologists don’t know it, but physicists know that the second law is not violated by any biological process or by evolution in any sense.

]]> Comment on Biological Information, Molecular Structure, and the Origins Debate by Jonathan Watts http://www.asa3online.org/PSCF/2011/11/18/biological-information-molecular-structure-and-the-origins-debate/comment-page-1/#comment-146 Jonathan Watts Wed, 21 Dec 2011 00:41:30 +0000 http://www.asa3online.org/PSCF/?p=349#comment-146 Hi David - Thanks for your comment.  I'll respond to a couple of points. First of all, entropy is a thermodynamic parameter that doesn't always correspond to our intuitive ideas of "randomness."   As an example, proteins fold in complex ways, and this is a process that intuitively increases their degree of "orderliness."  Yet the driving force for the folding of some proteins is actually an increase in entropy (in the example I'm thinking of, there is a complex structure of water molecules around the polypeptide chain, and when the protein folds, the water molecules are released into a more random arrangement in solution... this causes a net increase in entropy in spite of the reduction in the degrees of freedom of protein conformation upon folding.) The second law, as you mentioned, applies to only a closed system.  Thus we see a seed growing into a tree, I can clean my desk (although I do it far too rarely), a SELEX experiment can isolate a functional sequence from a random pool, and so on.  In all of these cases, the entropy of the universe increased overall even though the "orderliness" of a particular place and time has also increased.  All of these processes required energy input.  As you said, the growing plant absorbs energy from the sun allowing it to give order to biomolecules and cells.  Since evolution occurred on earth, which is not a closed system and absorbs energy from the sun, it doesn't work to disprove evolution with the second law.  Can you help me understand why you find this a convincing rebuttal to evolution? Hi David – Thanks for your comment.  I’ll respond to a couple of points.

First of all, entropy is a thermodynamic parameter that doesn’t always correspond to our intuitive ideas of “randomness.”   As an example, proteins fold in complex ways, and this is a process that intuitively increases their degree of “orderliness.”  Yet the driving force for the folding of some proteins is actually an increase in entropy (in the example I’m thinking of, there is a complex structure of water molecules around the polypeptide chain, and when the protein folds, the water molecules are released into a more random arrangement in solution… this causes a net increase in entropy in spite of the reduction in the degrees of freedom of protein conformation upon folding.)

The second law, as you mentioned, applies to only a closed system.  Thus we see a seed growing into a tree, I can clean my desk (although I do it far too rarely), a SELEX experiment can isolate a functional sequence from a random pool, and so on.  In all of these cases, the entropy of the universe increased overall even though the “orderliness” of a particular place and time has also increased.  All of these processes required energy input.  As you said, the growing plant absorbs energy from the sun allowing it to give order to biomolecules and cells.  Since evolution occurred on earth, which is not a closed system and absorbs energy from the sun, it doesn’t work to disprove evolution with the second law.  Can you help me understand why you find this a convincing rebuttal to evolution?

]]> Comment on Information, Intelligence, and the Origins of Life by Randy Isaac http://www.asa3online.org/PSCF/2011/11/18/information-intelligence-and-the-origins-of-life/comment-page-1/#comment-145 Randy Isaac Tue, 20 Dec 2011 16:08:11 +0000 http://www.asa3online.org/PSCF/?p=351#comment-145 <p>Very good summary, Bill. I would only quibble with your statement that "As result you and others introduce quantifiable measures..." No, Shannon and subsequent information theorists are the ones who really began to talk about quantifying information and figuring out how to measure it and understand it, long before ID came around. Leslie Orgel in the '70's and then Dembski in '97 tried to extend it to "complex specified" information, leaving the rigor of information theory and moving to semantics. As you point out, it doesn't work. I agree with you that talking about information in the context of origin of life is not very helpful. The ID community has won widespread applause from the Christian community by claiming that "DNA information can only be generated by an intelligent source." My main point is No! My article tries to clarify that there are many different uses of the term information and most discussions of information confuse various uses. As for "increasing" information, there is a valid qualitative perception that there is more useful information in a set of functional configurations than in a set of non-functional configurations, even if in a rigorous engineering sense, the quantitative measure of information indicate there may be less information. The point is the relevance of the information. That's really what ID folks are trying to get at with CSI. So "new" information doesn't need to be a measurable increase in bits, just a sequence that works. Rearranging the "wooden blocks" as you put it, is indeed interesting when it makes the difference between something that survives and works and something that doesn't. That concept is indeed very valuable in understanding how evolution proceeds. I think everything in my paper is not new, just an attempt at summarizing what has been known in the information theory world for a long time. Perhaps the only aspect that is slightly new, is the idea that the mark of intelligence in information is the connection of abstract relationships. I contend that none of the ID advocates has offered a connection between intelligence and information, relying solely on something like "in our experience, information is habitually associated with intelligence." But why should this be true? I suggest that the ability to carry out abstract reasoning has long been a hallmark of intelligence. It follows, therefore, that information that is characterized by abstract symbolism would also be necessarily related to intelligence. This is not a unique relationship since information not connected to abstract concepts can also be related to intelligence, but if you are looking for a mark of intelligence, abstraction is one possibility. Such abstraction is not evident as a signature in the cell. Randy</p> Very good summary, Bill. I would only quibble with your statement that “As result you and others introduce quantifiable measures…” No, Shannon and subsequent information theorists are the ones who really began to talk about quantifying information and figuring out how to measure it and understand it, long before ID came around. Leslie Orgel in the ’70’s and then Dembski in ‘97 tried to extend it to “complex specified” information, leaving the rigor of information theory and moving to semantics. As you point out, it doesn’t work.
I agree with you that talking about information in the context of origin of life is not very helpful. The ID community has won widespread applause from the Christian community by claiming that “DNA information can only be generated by an intelligent source.” My main point is No! My article tries to clarify that there are many different uses of the term information and most discussions of information confuse various uses.
As for “increasing” information, there is a valid qualitative perception that there is more useful information in a set of functional configurations than in a set of non-functional configurations, even if in a rigorous engineering sense, the quantitative measure of information indicate there may be less information. The point is the relevance of the information. That’s really what ID folks are trying to get at with CSI. So “new” information doesn’t need to be a measurable increase in bits, just a sequence that works. Rearranging the “wooden blocks” as you put it, is indeed interesting when it makes the difference between something that survives and works and something that doesn’t. That concept is indeed very valuable in understanding how evolution proceeds.
I think everything in my paper is not new, just an attempt at summarizing what has been known in the information theory world for a long time. Perhaps the only aspect that is slightly new, is the idea that the mark of intelligence in information is the connection of abstract relationships. I contend that none of the ID advocates has offered a connection between intelligence and information, relying solely on something like “in our experience, information is habitually associated with intelligence.” But why should this be true? I suggest that the ability to carry out abstract reasoning has long been a hallmark of intelligence. It follows, therefore, that information that is characterized by abstract symbolism would also be necessarily related to intelligence. This is not a unique relationship since information not connected to abstract concepts can also be related to intelligence, but if you are looking for a mark of intelligence, abstraction is one possibility. Such abstraction is not evident as a signature in the cell.
Randy

]]> Comment on Information, Intelligence, and the Origins of Life by William Powers http://www.asa3online.org/PSCF/2011/11/18/information-intelligence-and-the-origins-of-life/comment-page-1/#comment-144 William Powers Tue, 20 Dec 2011 06:29:51 +0000 http://www.asa3online.org/PSCF/?p=351#comment-144 Randy: I'm not the one focusing on information increase.  It's what everyone else wants to talk about.  It's behind Dembksi's claim that it can't increase by "natural" methods.  Story mentions it, as does Watts, and I think Freeland.  I would think that "new" information entails and increase in information.  It not, then why care that it's new?  If all that's happening is that we are rearranging by "natural" means wooden blocks on a table, I don't think it would be very interesting.  The idea appears to be that natural forces unintelligently and randomly move "components" around.  Then it runs through the survivability  filter or some "goodness of fit" criteria.  Intelligent search strategies do the same.  I have no immediate problem with this picture.  The problem I have, and have always had, is I don't see how talking about information is helpful.  What Dembski and many others want to get at is the probability, given "natural" processes, for some biological state to be achieved.  In order to answer this question not only must you list the available processes, but you must also have a handle on the density of states that survive.  If the distance between survivable states is large, the density decreases and the probability of moving from survivable state to another drops significantly.  This approach is at least in principle straightforward.  The information approach appears hopelessly confused.  What ID is after is a mark of intelligence.  I think that they roughly have this right.  Unfortunately, it seems, their understanding of the problem cannot be sufficiently quantified.  As result you and others introduce quantifiable measures, but, as far as I can tell, they are poor measures of what, at least Dembski is after.  As a result, ID folks and the folks in this issue of PSCF are not talking the same language.  Freeland attempts to describe very crudely a natural method for how life might arise.  He suggests that we began with a simpler alphabet, and that the relationship between symbol and meaning are not as physically arbitrary as they are in human languages.  He doesn't really answer any of the detailed questions required, but at least he's talking about the right subject.  Well, I better stop.  Thanks for putting up with my questions. Randy: I’m not the one focusing on information increase.  It’s what everyone else wants to talk about.  It’s behind Dembksi’s claim that it can’t increase by “natural” methods.  Story mentions it, as does Watts, and I think Freeland.  I would think that “new” information entails and increase in information.  It not, then why care that it’s new?  If all that’s happening is that we are rearranging by “natural” means wooden blocks on a table, I don’t think it would be very interesting.  The idea appears to be that natural forces unintelligently and randomly move “components” around.  Then it runs through the survivability  filter or some “goodness of fit” criteria.  Intelligent search strategies do the same.  I have no immediate problem with this picture.  The problem I have, and have always had, is I don’t see how talking about information is helpful.  What Dembski and many others want to get at is the probability, given “natural” processes, for some biological state to be achieved.  In order to answer this question not only must you list the available processes, but you must also have a handle on the density of states that survive.  If the distance between survivable states is large, the density decreases and the probability of moving from survivable state to another drops significantly.  This approach is at least in principle straightforward.  The information approach appears hopelessly confused.  What ID is after is a mark of intelligence.  I think that they roughly have this right.  Unfortunately, it seems, their understanding of the problem cannot be sufficiently quantified.  As result you and others introduce quantifiable measures, but, as far as I can tell, they are poor measures of what, at least Dembski is after.  As a result, ID folks and the folks in this issue of PSCF are not talking the same language.  Freeland attempts to describe very crudely a natural method for how life might arise.  He suggests that we began with a simpler alphabet, and that the relationship between symbol and meaning are not as physically arbitrary as they are in human languages.  He doesn’t really answer any of the detailed questions required, but at least he’s talking about the right subject.  Well, I better stop.  Thanks for putting up with my questions.

]]> Comment on Information, Intelligence, and the Origins of Life by Randy Isaac http://www.asa3online.org/PSCF/2011/11/18/information-intelligence-and-the-origins-of-life/comment-page-1/#comment-143 Randy Isaac Tue, 20 Dec 2011 03:06:32 +0000 http://www.asa3online.org/PSCF/?p=351#comment-143 <p>Bill, you're letting common sense get the better of you! Yes, information theory, like quantum theory, has a lot of features that are counterintuitive. As you correctly point out, there is a peculiar aspect of information in the syntax category when one consider Kolmogorov-Chaitin, or algorithmic complexity. The highest information content, in that usage, is the most random sequence. The most orderly sequence has much lower information. But when it comes to usefulness, neither the most random (highest amount of information) nor the most orderly (lowest amount of information) is the most useful. Some theorists have tried to introduce other measures to indicate usefulness. Charles Bennett has proposed a concept of logical depth, for example, but it isn't particularly easy or useful! In DNA, there are many repetitive sequences that aren't particularly useful and also many nearly random sequences that aren't so useful. Maximum usefulness is somewhere in between, and that's where a lot of DNA is, like the coding regions. You seem to be focused on an "increase" in information. That differs widely depending on what definition of information and in what category you are talking. From a capacity point of view, DNA information increases when the length of the DNA increases. That's fairly simple. From a syntactical point of view, there's no particular value in talking about an "increase" in information. Generally, a change in syntax generates "new" information, not in the sense of increasing the number of bits of information but in changing the sequence to a new sequence. Some sequences turn out to be useful and some don't. That's where natural selection comes in. And that's where the higher levels of organization get established and form the basis for the next step. Another way to think about it is that through the reproduction with variation process, organisms are search in DNA information space to find useful regions of survivial. That process can lead to an increase or decrease or a constant number of bits of information, but much more importantly, it can find new sequences that are more useful. That is "new" information, even though it might not be a technical "increase" in information in the engineering sense. In the antibody generation process, the number of nucleotides is generally constant. What is varying is the sequence. The system uses random variation to search for the information states that are the most useful in identifying and attaching to antigens. Finding the right one is what ID folks call "specificity." Complexity just means that the sequence isn't trivial or repetitive. It is an increase in the right sequences, not an increase in the number of bits. Keep asking. These are not easy concepts to grasp. Randy</p> Bill, you’re letting common sense get the better of you! Yes, information theory, like quantum theory, has a lot of features that are counterintuitive. As you correctly point out, there is a peculiar aspect of information in the syntax category when one consider Kolmogorov-Chaitin, or algorithmic complexity. The highest information content, in that usage, is the most random sequence. The most orderly sequence has much lower information. But when it comes to usefulness, neither the most random (highest amount of information) nor the most orderly (lowest amount of information) is the most useful. Some theorists have tried to introduce other measures to indicate usefulness. Charles Bennett has proposed a concept of logical depth, for example, but it isn’t particularly easy or useful!
In DNA, there are many repetitive sequences that aren’t particularly useful and also many nearly random sequences that aren’t so useful. Maximum usefulness is somewhere in between, and that’s where a lot of DNA is, like the coding regions.
You seem to be focused on an “increase” in information. That differs widely depending on what definition of information and in what category you are talking. From a capacity point of view, DNA information increases when the length of the DNA increases. That’s fairly simple. From a syntactical point of view, there’s no particular value in talking about an “increase” in information. Generally, a change in syntax generates “new” information, not in the sense of increasing the number of bits of information but in changing the sequence to a new sequence. Some sequences turn out to be useful and some don’t. That’s where natural selection comes in. And that’s where the higher levels of organization get established and form the basis for the next step.
Another way to think about it is that through the reproduction with variation process, organisms are search in DNA information space to find useful regions of survivial. That process can lead to an increase or decrease or a constant number of bits of information, but much more importantly, it can find new sequences that are more useful. That is “new” information, even though it might not be a technical “increase” in information in the engineering sense.
In the antibody generation process, the number of nucleotides is generally constant. What is varying is the sequence. The system uses random variation to search for the information states that are the most useful in identifying and attaching to antigens. Finding the right one is what ID folks call “specificity.” Complexity just means that the sequence isn’t trivial or repetitive. It is an increase in the right sequences, not an increase in the number of bits.
Keep asking. These are not easy concepts to grasp.
Randy

]]> Comment on Information, Intelligence, and the Origins of Life by William Powers http://www.asa3online.org/PSCF/2011/11/18/information-intelligence-and-the-origins-of-life/comment-page-1/#comment-142 William Powers Mon, 19 Dec 2011 15:52:59 +0000 http://www.asa3online.org/PSCF/?p=351#comment-142 Randy: It seems to me that your definition of physical syntactical information is problematic.  Unless I have this wrong, the greater the coherence of the information, the smaller the physical syntactic information.  Hence, when you take a random collection of rocks and make it into a Rolls Royce you have decreased the syntactical information since it now requires few bits to describe the state of the system.  To increase syntactical information you must increase the randomness of the system.  This is very counter intuitive.  What this entails is that specificity, the very aspect that Dembski associates most with intelligence, according to your definition is the mark of low information content, and, metaphorically stupidity.  It seems that according this understanding of syntactical information, CSI are not complex, but simple. Dembski is clearly more correct in this regard.  If syntactical information is the wrong measure, it must be a measure that finds order in complexity.  What must be distinguished here is what is called disorganized complexity and organized complexity.  In order to distinguish the two you must take into account more than the number of possible states available to the system.  I don't see how algorithmic complexity (Komolgorov) helps in this regard.  I can easily see two systems with the same algorithmic complexity having vastly different organized complexities.  It is organized complexity that is related to information.  It doesn't seem that by simply randomly varying some genetic material, as in antibody generation, that we are taking a given complexity and organizing it to a greater extent.  The antibody generation system as a whole is "brilliant," but the antibodies generated have no more organization than was already extant in their creation.  According to this view, new species, or new antibody generating systems indicate increasing information.  According to this view, the generation of a living organism, since it represents the  greater coordination of complex states, increases information.  It is not clear to me that according to physical syntactical information, as you've defined it, the inception of living organisms would increase information.  I must be getting this all wrong because I can't believe that your approach could be getting it this wrong.  So I'll stop and let you show me where I've gone astray. Randy: It seems to me that your definition of physical syntactical information is problematic.  Unless I have this wrong, the greater the coherence of the information, the smaller the physical syntactic information.  Hence, when you take a random collection of rocks and make it into a Rolls Royce you have decreased the syntactical information since it now requires few bits to describe the state of the system.  To increase syntactical information you must increase the randomness of the system.  This is very counter intuitive.  What this entails is that specificity, the very aspect that Dembski associates most with intelligence, according to your definition is the mark of low information content, and, metaphorically stupidity.  It seems that according this understanding of syntactical information, CSI are not complex, but simple. Dembski is clearly more correct in this regard.  If syntactical information is the wrong measure, it must be a measure that finds order in complexity.  What must be distinguished here is what is called disorganized complexity and organized complexity.  In order to distinguish the two you must take into account more than the number of possible states available to the system.  I don’t see how algorithmic complexity (Komolgorov) helps in this regard.  I can easily see two systems with the same algorithmic complexity having vastly different organized complexities.  It is organized complexity that is related to information.  It doesn’t seem that by simply randomly varying some genetic material, as in antibody generation, that we are taking a given complexity and organizing it to a greater extent.  The antibody generation system as a whole is “brilliant,” but the antibodies generated have no more organization than was already extant in their creation.  According to this view, new species, or new antibody generating systems indicate increasing information.  According to this view, the generation of a living organism, since it represents the  greater coordination of complex states, increases information.  It is not clear to me that according to physical syntactical information, as you’ve defined it, the inception of living organisms would increase information.  I must be getting this all wrong because I can’t believe that your approach could be getting it this wrong.  So I’ll stop and let you show me where I’ve gone astray.

]]> Comment on Information, Intelligence, and the Origins of Life by Randy Isaac http://www.asa3online.org/PSCF/2011/11/18/information-intelligence-and-the-origins-of-life/comment-page-1/#comment-141 Randy Isaac Sun, 18 Dec 2011 19:27:57 +0000 http://www.asa3online.org/PSCF/?p=351#comment-141 <p>P.S. I should add a word about physical vs abstract symbolism. The distinction is not to be found in whether or not there is a physical translator between the code and the message nor in the source of the resources for such a translator. Rather, it has to do with the criterion for the specificity or significance of the information. For example, in your example of the Morse code, a triple dot, "...", could be mechanically translated into an "S" or someone could mechanically translate it into an "R". How would one distinguish which is "correct?" In the case of Morse code, it is a correspondence to an abstract coding table. It isn't physical symbolism even though there is a physical translator. In the case of DNA, codons are translated into biomolecules. Let's assume they get translated to two different biomolecules. Which is "correct?" The criterion is a physical one--which ever enables the cell or organism to survive and reproduce. That is physical symbolism, not abstract. Does that help? Randy</p> P.S. I should add a word about physical vs abstract symbolism. The distinction is not to be found in whether or not there is a physical translator between the code and the message nor in the source of the resources for such a translator. Rather, it has to do with the criterion for the specificity or significance of the information. For example, in your example of the Morse code, a triple dot, “…”, could be mechanically translated into an “S” or someone could mechanically translate it into an “R”. How would one distinguish which is “correct?” In the case of Morse code, it is a correspondence to an abstract coding table. It isn’t physical symbolism even though there is a physical translator.
In the case of DNA, codons are translated into biomolecules. Let’s assume they get translated to two different biomolecules. Which is “correct?” The criterion is a physical one–which ever enables the cell or organism to survive and reproduce. That is physical symbolism, not abstract.
Does that help?
Randy

]]> Comment on Seeking a Signature by Randy Isaac http://www.asa3online.org/PSCF/2011/05/24/seeking-a-signature/comment-page-1/#comment-132 Randy Isaac Sun, 18 Dec 2011 03:41:14 +0000 http://www.asa3online.org/PSCF/?p=311#comment-132 <p>Bill, it's not clear to me that "non-information" is a valid concept. The only context in which I have heard people advocate that information can be generated in a thermodynamic sense is the idea of quantum fluctuations in vacuum that can be resolved in a way that generates new information. Otherwise no one I know is talking of generating information from non-information, whatever that might be. In their replies, Meyer and Venema left much confusion, in my opinion. Here is my perspective. Meyer and the ID community has tended to convey the idea that complex specified information is habitually associated with intelligent agents. Note that claims of universality are carefully avoided by using terms like "habitually" or "in our experience" etc. Venema wondered in his review why Meyer hadn't addressed common ancestry, presumably because that shows the generation of new biological information (read that as both capacity and syntax, which has new semantic interpretation) without intelligent agents. Meyer's response that Venema set up a straw man is interesting. Private conversations with him, as well as selected quotes in his book,  reveal that he and ID leaders acknowledge that in biological systems, CSI is generated without intelligent agents. It is just in non-biological systems that information cannot be generated. My personal view is that once it is acknowledged that biological systems can generate CSi without intelligence, the game is over for ID. There is no longer any basis for claiming the origin of life could not occur without an intelligent agent. Non-biological systems certainly increase information everywhere around us. It's just that these systems are not very complex. But if complex biological systems generate CSI, then complexity isn't the differentiator. There is no more argument for claiming that non-biological systems cannot give rise to DNA information, at least from an information perspective. Randy</p> Bill, it’s not clear to me that “non-information” is a valid concept. The only context in which I have heard people advocate that information can be generated in a thermodynamic sense is the idea of quantum fluctuations in vacuum that can be resolved in a way that generates new information. Otherwise no one I know is talking of generating information from non-information, whatever that might be.

In their replies, Meyer and Venema left much confusion, in my opinion. Here is my perspective. Meyer and the ID community has tended to convey the idea that complex specified information is habitually associated with intelligent agents. Note that claims of universality are carefully avoided by using terms like “habitually” or “in our experience” etc. Venema wondered in his review why Meyer hadn’t addressed common ancestry, presumably because that shows the generation of new biological information (read that as both capacity and syntax, which has new semantic interpretation) without intelligent agents. Meyer’s response that Venema set up a straw man is interesting. Private conversations with him, as well as selected quotes in his book,  reveal that he and ID leaders acknowledge that in biological systems, CSI is generated without intelligent agents. It is just in non-biological systems that information cannot be generated.
My personal view is that once it is acknowledged that biological systems can generate CSi without intelligence, the game is over for ID. There is no longer any basis for claiming the origin of life could not occur without an intelligent agent. Non-biological systems certainly increase information everywhere around us. It’s just that these systems are not very complex. But if complex biological systems generate CSI, then complexity isn’t the differentiator. There is no more argument for claiming that non-biological systems cannot give rise to DNA information, at least from an information perspective.

Randy

]]> Comment on Information, Intelligence, and the Origins of Life by Randy Isaac http://www.asa3online.org/PSCF/2011/11/18/information-intelligence-and-the-origins-of-life/comment-page-1/#comment-131 Randy Isaac Sun, 18 Dec 2011 03:15:24 +0000 http://www.asa3online.org/PSCF/?p=351#comment-131 <p>Bill, it's good to hear from you again. I always enjoy your dialog. In response, let me share a few observations to see if they might help: Semantic information is not part of information theory (see the quote in my article from Shannon) and is not quantifiable with any precision. Thermodynamic, capacity, and syntax information are measured in bits and are real physical parameters. The closest one might get is to quantify the subset of syntax information that has a relevant semantic significance. For example, we could enumerate all the words of the English language that have a meaning. One can't be very precise about the number of words in English dictionary, but conceptually there is a subset of all possible combinations of the alphabet which constitute an entry in a dictionary. But the meaning itself is not quantified. As for Craig Story's article on antibodies, it should be clarified that the new information is a new sequence of DNA, and therefore new in the syntax category of information, not in the number of bits. That new information (sequence) did not exist in any previous form and was constituted by a random process. Through the B cell production process, the information in the DNA sequence was not merely duplicated but duplicated with variation to produce a new information state, which was then selected for optimum binding to an antigen. The net result is new information. In some of your sentences, you seem to conflate various categories of information. If you call into question the Second Law of Thermodynamics, then you must indeed consider the thermodynamic category and include all possible microstates. However, that's not what we usually talk about in bioinformation or the information we use in any practical context. All cells and organisms use energy from the environment in the reproduction process and the Second Law is not violated in any way whether information or entropy of that cell  is increased or decreased. And then we come back to your favorite topic, physical symbolism. I'm glad you think we're making progress. I agree, it is a hard one to articulate and I appreciate your helping me refine that attempt. I thought you gave an extraordinarily clear explanation of it. thank you! But then I started to get lost. I'm not sure what you meant by "types." If by "types" you mean abstract categories into which humans place phenomena in order to discuss and understand them, then, yes, these constitute semantic information and are examples of abstract symbolism. An electron that is produced in a decay process doesn't care about types. It just appears. Whether any of this is an "increase in information" is not particularly relevant. Let's talk a little more about what it means to "increase" or "decrease" information. Thermodynamically, we can expect information to scale in the same way as energy or entropy. There are interesting papers in the literature debating how information and energy and entropy are related. Generally, a deterministic closed system will not have a net change in information, energy, or entropy. But typically we talk about information as capacity and syntax. In this context, information can be added like entropy and information can be erased which really means it is transferred to the environment into a non-usable form. A new syntax is really new information even without changing the number of bits. But why the focus on whether or not information increases? It really isn't an issue outside the unsupported claim that information cannot be generated without an intelligent source. Finally, you said "It seems to me that until and unless you and others can present a clear notion of what information is, all talk of it increasing or decreasing is nonsense." I was hoping I had presented at least a clearer notion of what information is. For thermodynamic, capacity, and syntax categories, there are clear ways of quantifying information. Information theorists build on Shannon's seminal work in this area. The difficulty comes when we try to extend that to semantic information, as is done with the concept of complex specified information. Alas, that is not quantifiable in the same way and I agree that all talk of it increasing or decreasing or being conserved is nonsense. Hope this helps, Randy</p> Bill, it’s good to hear from you again. I always enjoy your dialog. In response, let me share a few observations to see if they might help:
Semantic information is not part of information theory (see the quote in my article from Shannon) and is not quantifiable with any precision. Thermodynamic, capacity, and syntax information are measured in bits and are real physical parameters. The closest one might get is to quantify the subset of syntax information that has a relevant semantic significance. For example, we could enumerate all the words of the English language that have a meaning. One can’t be very precise about the number of words in English dictionary, but conceptually there is a subset of all possible combinations of the alphabet which constitute an entry in a dictionary. But the meaning itself is not quantified.

As for Craig Story’s article on antibodies, it should be clarified that the new information is a new sequence of DNA, and therefore new in the syntax category of information, not in the number of bits. That new information (sequence) did not exist in any previous form and was constituted by a random process. Through the B cell production process, the information in the DNA sequence was not merely duplicated but duplicated with variation to produce a new information state, which was then selected for optimum binding to an antigen. The net result is new information.

In some of your sentences, you seem to conflate various categories of information. If you call into question the Second Law of Thermodynamics, then you must indeed consider the thermodynamic category and include all possible microstates. However, that’s not what we usually talk about in bioinformation or the information we use in any practical context. All cells and organisms use energy from the environment in the reproduction process and the Second Law is not violated in any way whether information or entropy of that cell  is increased or decreased.

And then we come back to your favorite topic, physical symbolism. I’m glad you think we’re making progress. I agree, it is a hard one to articulate and I appreciate your helping me refine that attempt. I thought you gave an extraordinarily clear explanation of it. thank you! But then I started to get lost. I’m not sure what you meant by “types.” If by “types” you mean abstract categories into which humans place phenomena in order to discuss and understand them, then, yes, these constitute semantic information and are examples of abstract symbolism. An electron that is produced in a decay process doesn’t care about types. It just appears. Whether any of this is an “increase in information” is not particularly relevant.

Let’s talk a little more about what it means to “increase” or “decrease” information. Thermodynamically, we can expect information to scale in the same way as energy or entropy. There are interesting papers in the literature debating how information and energy and entropy are related. Generally, a deterministic closed system will not have a net change in information, energy, or entropy.

But typically we talk about information as capacity and syntax. In this context, information can be added like entropy and information can be erased which really means it is transferred to the environment into a non-usable form. A new syntax is really new information even without changing the number of bits. But why the focus on whether or not information increases? It really isn’t an issue outside the unsupported claim that information cannot be generated without an intelligent source.

Finally, you said “It seems to me that until and unless you and others can present a clear notion of what information is, all talk of it increasing or decreasing is nonsense.” I was hoping I had presented at least a clearer notion of what information is. For thermodynamic, capacity, and syntax categories, there are clear ways of quantifying information. Information theorists build on Shannon’s seminal work in this area. The difficulty comes when we try to extend that to semantic information, as is done with the concept of complex specified information. Alas, that is not quantifiable in the same way and I agree that all talk of it increasing or decreasing or being conserved is nonsense.

Hope this helps,
Randy

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